An analog of Hölder's inequality for the spectral radius of Hadamard products

KAUST Repository

Li, Muxingzi

2017-12-03

We prove new inequalities related to the spectral radius ρ of Hadamard products (denoted by ◦ ) of complex matrices. Let p, q ∈ [1 , ∞ ] satisfy 1/p + 1/q = 1, we show an analog of Hölder’s inequality on the space of n × n complex matrices ρ ( A ◦ B ) ≤ ρ ( | A |^( ◦ p) ) ^(1/p) ρ ( | B |^( ◦ q) ) ^(1/q)  for all A, B ∈ C n × n , where |·| denotes entry-wise absolute values, and ( · ) ^ (◦ p) represents the entry-wise Hadamard power. We derive a sharper inequality for the special case p = q = 2. Given A, B ∈ C ^(n × n) , for some β ∈ (0 , 1] depending on A and B , ρ ( A ◦ B ) ≤ βρ ( | A ◦ A | ) ^(1/2) ρ ( | B ◦ B | )^ (1/2) . Analysis for another special case p = 1 and q = ∞ is also included.

Hadamard upper bound on optimum joint decoding capacity of Wyner Gaussian cellular MAC

KAUST Repository

Shakir, Muhammad

2011-09-01

This article presents an original analytical expression for an upper bound on the optimum joint decoding capacity of Wyner circular Gaussian cellular multiple access channel (C-GCMAC) for uniformly distributed mobile terminals (MTs). This upper bound is referred to as Hadamard upper bound (HUB) and is a novel application of the Hadamard inequality established by exploiting the Hadamard operation between the channel fading matrix G and the channel path gain matrix Ω. This article demonstrates that the actual capacity converges to the theoretical upper bound under the constraints like low signal-to-noise ratios and limiting channel path gain among the MTs and the respective base station of interest. In order to determine the usefulness of the HUB, the behavior of the theoretical upper bound is critically observed specially when the inter-cell and the intra-cell time sharing schemes are employed. In this context, we derive an analytical form of HUB by employing an approximation approach based on the estimation of probability density function of trace of Hadamard product of two matrices, i.e., G and Ω. A closed form of expression has been derived to capture the effect of the MT distribution on the optimum joint decoding capacity of C-GCMAC. This article demonstrates that the analytical HUB based on the proposed approximation approach converges to the theoretical upper bound results in the medium to high signal to noise ratio regime and shows a reasonably tighter bound on optimum joint decoding capacity of Wyner GCMAC.

Robust Hadamard gate for optical and ion trap holonomic quantum computers

OpenAIRE

Kuvshinov, V. I.; Kuzmin, A. V.

2005-01-01

We consider one possible implementation of Hadamard gate for optical and ion trap holonomic quantum computers. The expression for its fidelity determining the gate stability with respect to the errors in the single-mode squeezing parameter control is analytically derived. We demonstrate by means of this expression the cancellation of the squeezing control errors up to the fourth order on their magnitude.

A Workshop on Algebraic Design Theory and Hadamard Matrices

CERN Document Server

2015-01-01

This volume develops the depth and breadth of the mathematics underlying the construction and analysis of Hadamard matrices and their use in the construction of combinatorial designs. At the same time, it pursues current research in their numerous applications in security and cryptography, quantum information, and communications. Bridges among diverse mathematical threads and extensive applications make this an invaluable source for understanding both the current state of the art and future directions. The existence of Hadamard matrices remains one of the most challenging open questions in combinatorics. Substantial progress on their existence has resulted from advances in algebraic design theory using deep connections with linear algebra, abstract algebra, finite geometry, number theory, and combinatorics. Hadamard matrices arise in a very diverse set of applications. Starting with applications in experimental design theory and the theory of error-correcting codes, they have found unexpected and important ap...

Some Hermite–Hadamard Type Inequalities for Geometrically Quasi ...

Indian Academy of Sciences (India)

Abstract. In the paper, we introduce a new concept 'geometrically quasi-convex function' and establish some Hermite–Hadamard type inequalities for functions whose derivatives are of geometric quasi-convexity.

Analytical upper bound on optimum joint decoding capacity of Wyner GCMAC using hadamard inequality

KAUST Repository

Shakir, Muhammad

2011-11-01

This paper presents an original analytical expression for an upper bound on the optimum joint decoding capacity of Wyner circular Gaussian cellular multiple access channel (C-GCMAC) for uniformly distributed mobile terminals (MTs) across the cells. This upper bound is referred to as Hadamard upper bound (HUB) and is a novel application of the Hadamard inequality established by exploiting the Hadamard operation between the channel fading and channel path gain matrices. In this context, we employ an approximation approach based on the estimation of probability density function (PDF) of Hadamard product of two matrices. A closed-form expression has been derived to capture the effect of variable user density in adjacent cells on optimal joint decoding capacity. The results of this paper demonstrate that the analytical HUB based on the proposed approximation approach converges to the theoretical results for medium range of signal to noise ratios and shows a comparable tighter bound on optimum joint decoding capacity. © 2011 IEEE.

Optimized Fast Walsh–Hadamard Transform on GPUs for non-binary LDPC decoding

OpenAIRE

Andrade, Joao; Falcao, Gabriel; Silva, Vitor

2014-01-01

The Fourier Transform Sum-Product Algorithm (FT-SPA) used in non-binary Low-Density Parity-Check (LDPC) decoding makes extensive use of the Walsh–Hadamard Transform (WHT). We have developed a massively parallel Fast Walsh–Hadamard Transform (FWHT) which exploits the Graphics Processing Unit (GPU) pipeline and memory hierarchy, thereby minimizing the level of memory bank conflicts and maximizing the number of returned instructions per clock cycle for different generations of graphics processor...

High-resolution 1H NMR spectroscopy of fish muscle, eggs and small whole fish via Hadamard-encoded intermolecular multiple-quantum coherence.

Directory of Open Access Journals (Sweden)

Honghao Cai

Full Text Available BACKGROUND AND PURPOSE: Nuclear magnetic resonance (NMR spectroscopy has become an important technique for tissue studies. Since tissues are in semisolid-state, their high-resolution (HR spectra cannot be obtained by conventional NMR spectroscopy. Because of this restriction, extraction and high-resolution magic angle spinning (HR MAS are widely applied for HR NMR spectra of tissues. However, both of the methods are subject to limitations. In this study, the feasibility of HR (1H NMR spectroscopy based on intermolecular multiple-quantum coherence (iMQC technique is explored using fish muscle, fish eggs, and a whole fish as examples. MATERIALS AND METHODS: Intact salmon muscle tissues, intact eggs from shishamo smelt and a whole fish (Siamese algae eater are studied by using conventional 1D one-pulse sequence, Hadamard-encoded iMQC sequence, and HR MAS. RESULTS: When we use the conventional 1D one-pulse sequence, hardly any useful spectral information can be obtained due to the severe field inhomogeneity. By contrast, HR NMR spectra can be obtained in a short period of time by using the Hadamard-encoded iMQC method without shimming. Most signals from fatty acids and small metabolites can be observed. Compared to HR MAS, the iMQC method is non-invasive, but the resolution and the sensitivity of resulting spectra are not as high as those of HR MAS spectra. CONCLUSION: Due to the immunity to field inhomogeneity, the iMQC technique can be a proper supplement to HR MAS, and it provides an alternative for the investigation in cases with field distortions and with samples unsuitable for spinning. The acquisition time of the proposed method is greatly reduced by introduction of the Hadamard-encoded technique, in comparison with that of conventional iMQC method.

Applications of Hadamard transform-gas chromatography/mass spectrometry to the detection of acetone in healthy human and diabetes mellitus patient breath.

Science.gov (United States)

Fan, Gang-Ting; Yang, Chien-Lin; Lin, Cheng-Huang; Chen, Chien-Chung; Shih, Chung-Hung

2014-03-01

The Hadamard transform-gas chromatography/mass spectrometry (HT-GC/MS) technique was successfully employed to detect acetone, a biomarker for diabetes mellitus (DM) prediction, in human breath. Samples of exhaled breath were collected from four DM patients (one type-I and three type-II) and eight volunteers (nondiabetic healthy subjects), respectively. The gas samples, without any pretreatment, were simultaneously injected into a GC column through a Hadamard-injector based on Hadamard codes. Under optimized conditions, when cyclic S-matrix orders of 255, 1023 and 2047 were used, the S/N ratios of the acetone signals were substantially improved by 8.0-, 16.0- and 22.6-fold, respectively; these improvements are in good agreement with theoretically calculated values. We found that the breath acetone concentration levels in the four DM patients and the eight volunteers ranged from 1 to 10 ppmv and 0.1 to 1 ppmv, respectively. Copyright © 2014 Elsevier B.V. All rights reserved.

Hadamard Kernel SVM with applications for breast cancer outcome predictions.

Science.gov (United States)

Jiang, Hao; Ching, Wai-Ki; Cheung, Wai-Shun; Hou, Wenpin; Yin, Hong

2017-12-21

Breast cancer is one of the leading causes of deaths for women. It is of great necessity to develop effective methods for breast cancer detection and diagnosis. Recent studies have focused on gene-based signatures for outcome predictions. Kernel SVM for its discriminative power in dealing with small sample pattern recognition problems has attracted a lot attention. But how to select or construct an appropriate kernel for a specified problem still needs further investigation. Here we propose a novel kernel (Hadamard Kernel) in conjunction with Support Vector Machines (SVMs) to address the problem of breast cancer outcome prediction using gene expression data. Hadamard Kernel outperform the classical kernels and correlation kernel in terms of Area under the ROC Curve (AUC) values where a number of real-world data sets are adopted to test the performance of different methods. Hadamard Kernel SVM is effective for breast cancer predictions, either in terms of prognosis or diagnosis. It may benefit patients by guiding therapeutic options. Apart from that, it would be a valuable addition to the current SVM kernel families. We hope it will contribute to the wider biology and related communities.

Performance enhancement of successive interference cancellation scheme based on spectral amplitude coding for optical code-division multiple-access systems using Hadamard codes

Science.gov (United States)

Eltaif, Tawfig; Shalaby, Hossam M. H.; Shaari, Sahbudin; Hamarsheh, Mohammad M. N.

2009-04-01

A successive interference cancellation scheme is applied to optical code-division multiple-access (OCDMA) systems with spectral amplitude coding (SAC). A detailed analysis of this system, with Hadamard codes used as signature sequences, is presented. The system can easily remove the effect of the strongest signal at each stage of the cancellation process. In addition, simulation of the prose system is performed in order to validate the theoretical results. The system shows a small bit error rate at a large number of active users compared to the SAC OCDMA system. Our results reveal that the proposed system is efficient in eliminating the effect of the multiple-user interference and in the enhancement of the overall performance.

On the hadamard products of Schlicht functions and applications

Directory of Open Access Journals (Sweden)

H. S. Al-Amiri

1985-01-01

and strongly starlike with respect to symmetric points is invariant under the Hadamard product with the class of convex functions. The influence of certain operators over these classes is also investigated.

Non-moving Hadamard matrix diffusers for speckle reduction in laser pico-projectors

Science.gov (United States)

Thomas, Weston; Middlebrook, Christopher

2014-12-01

Personal electronic devices such as cell phones and tablets continue to decrease in size while the number of features and add-ons keep increasing. One particular feature of great interest is an integrated projector system. Laser pico-projectors have been considered, but the technology has not been developed enough to warrant integration. With new advancements in diode technology and MEMS devices, laser-based projection is currently being advanced for pico-projectors. A primary problem encountered when using a pico-projector is coherent interference known as speckle. Laser speckle can lead to eye irritation and headaches after prolonged viewing. Diffractive optical elements known as diffusers have been examined as a means to lower speckle contrast. This paper presents a binary diffuser known as a Hadamard matrix diffuser. Using two static in-line Hadamard diffusers eliminates the need for rotation or vibration of the diffuser for temporal averaging. Two Hadamard diffusers were fabricated and contrast values measured showing good agreement with theory and simulated values.

On Hadamard-Type Inequalities Involving Several Kinds of Convexity

Directory of Open Access Journals (Sweden)

Dragomir SeverS

2010-01-01

Full Text Available We do not only give the extensions of the results given by Gill et al. (1997 for log-convex functions but also obtain some new Hadamard-type inequalities for log-convex -convex, and -convex functions.

Finding a Hadamard matrix by simulated annealing of spin vectors

Science.gov (United States)

Bayu Suksmono, Andriyan

2017-05-01

Reformulation of a combinatorial problem into optimization of a statistical-mechanics system enables finding a better solution using heuristics derived from a physical process, such as by the simulated annealing (SA). In this paper, we present a Hadamard matrix (H-matrix) searching method based on the SA on an Ising model. By equivalence, an H-matrix can be converted into a seminormalized Hadamard (SH) matrix, whose first column is unit vector and the rest ones are vectors with equal number of -1 and +1 called SH-vectors. We define SH spin vectors as representation of the SH vectors, which play a similar role as the spins on Ising model. The topology of the lattice is generalized into a graph, whose edges represent orthogonality relationship among the SH spin vectors. Starting from a randomly generated quasi H-matrix Q, which is a matrix similar to the SH-matrix without imposing orthogonality, we perform the SA. The transitions of Q are conducted by random exchange of {+, -} spin-pair within the SH-spin vectors that follow the Metropolis update rule. Upon transition toward zeroth energy, the Q-matrix is evolved following a Markov chain toward an orthogonal matrix, at which the H-matrix is said to be found. We demonstrate the capability of the proposed method to find some low-order H-matrices, including the ones that cannot trivially be constructed by the Sylvester method.

Some Hermite–Hadamard type inequalities for geometrically quasi ...

Indian Academy of Sciences (India)

Hermite–Hadamard's integral inequality; geometrically quasi-convex function. 2010 Mathematics Subject Classification. Primary: 26A51, 26D15; Secondary: ... If f : I ⊆ R → R is a convex function on [a,b] and a,b ∈ I with a

High-SNR spectrum measurement based on Hadamard encoding and sparse reconstruction

Science.gov (United States)

Wang, Zhaoxin; Yue, Jiang; Han, Jing; Li, Long; Jin, Yong; Gao, Yuan; Li, Baoming

2017-12-01

The denoising capabilities of the H-matrix and cyclic S-matrix based on the sparse reconstruction, employed in the Pixel of Focal Plane Coded Visible Spectrometer for spectrum measurement are investigated, where the spectrum is sparse in a known basis. In the measurement process, the digital micromirror device plays an important role, which implements the Hadamard coding. In contrast with Hadamard transform spectrometry, based on the shift invariability, this spectrometer may have the advantage of a high efficiency. Simulations and experiments show that the nonlinear solution with a sparse reconstruction has a better signal-to-noise ratio than the linear solution and the H-matrix outperforms the cyclic S-matrix whether the reconstruction method is nonlinear or linear.

Existence and Hadamard well-posedness of a system of simultaneous generalized vector quasi-equilibrium problems

Directory of Open Access Journals (Sweden)

Wenyan Zhang

2017-03-01

Full Text Available Abstract An existence result for the solution set of a system of simultaneous generalized vector quasi-equilibrium problems (for short, (SSGVQEP is obtained, which improves Theorem 3.1 of the work of Ansari et al. (J. Optim. Theory Appl. 127:27-44, 2005. Moreover, a definition of Hadamard-type well-posedness for (SSGVQEP is introduced and sufficient conditions for Hadamard well-posedness of (SSGVQEP are established.

Sequence complexity and work extraction

International Nuclear Information System (INIS)

Merhav, Neri

2015-01-01

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

ALGEBRAIC EQUATIONS WITH LINEAR SHIFT OPERATORS ON SEQUENCES

Directory of Open Access Journals (Sweden)

SEVER ANGEL POPESCU

2016-04-01

Full Text Available In this note we recall (see also [8] the structure of all recurrent sequences which satisfy a fixed recurrence relation, with entries in a perfect field. As a consequence of these considerations we give a reasonable proof for the known result that the Hadamard product of two recurrent sequences is also a recurrent sequence.

Probabilistic implementation of Hadamard and unitary gates

International Nuclear Information System (INIS)

Song Wei; Yang Ming; Cao Zhuoliang

2004-01-01

We show that the Hadamard and unitary gates could be implemented by a unitary evolution together with a measurement for any unknown state chosen from a set A={ vertical bar Ψi>, vertical bar Ψ-bar i>} (i=1,2) if and only if vertical bar Ψ1>, vertical bar Ψ2>, vertical bar Ψ-bar 1>, vertical bar Ψ-bar 2> are linearly independent. We also derive the best transformation efficiencies

Hermite-Hadamard type inequalities for GA-s-convex functions

Directory of Open Access Journals (Sweden)

İmdat İşcan

2014-10-01

Full Text Available In this paper, The author introduces the concepts of the GA-s-convex functions in the first sense and second sense and establishes some integral inequalities of Hermite-Hadamard type related to the GA-s-convex functions. Some applications to special means of real numbers are also given.

Discrete Hadamard transformation algorithm's parallelism analysis and achievement

Science.gov (United States)

Hu, Hui

2009-07-01

With respect to Discrete Hadamard Transformation (DHT) wide application in real-time signal processing while limitation in operation speed of DSP. The article makes DHT parallel research and its parallel performance analysis. Based on multiprocessor platform-TMS320C80 programming structure, the research is carried out to achieve two kinds of parallel DHT algorithms. Several experiments demonstrated the effectiveness of the proposed algorithms.

The fermionic projector in a time-dependent external potential: Mass oscillation property and Hadamard states

Science.gov (United States)

Finster, Felix; Murro, Simone; Röken, Christian

2016-07-01

We give a non-perturbative construction of the fermionic projector in Minkowski space coupled to a time-dependent external potential which is smooth and decays faster than quadratically for large times. The weak and strong mass oscillation properties are proven. We show that the integral kernel of the fermionic projector is of the Hadamard form, provided that the time integral of the spatial sup-norm of the potential satisfies a suitable bound. This gives rise to an algebraic quantum field theory of Dirac fields in an external potential with a distinguished pure quasi-free Hadamard state.

The fermionic projector in a time-dependent external potential: Mass oscillation property and Hadamard states

International Nuclear Information System (INIS)

Finster, Felix; Murro, Simone; Röken, Christian

2016-01-01

We give a non-perturbative construction of the fermionic projector in Minkowski space coupled to a time-dependent external potential which is smooth and decays faster than quadratically for large times. The weak and strong mass oscillation properties are proven. We show that the integral kernel of the fermionic projector is of the Hadamard form, provided that the time integral of the spatial sup-norm of the potential satisfies a suitable bound. This gives rise to an algebraic quantum field theory of Dirac fields in an external potential with a distinguished pure quasi-free Hadamard state.

The fermionic projector in a time-dependent external potential: Mass oscillation property and Hadamard states

Energy Technology Data Exchange (ETDEWEB)

Finster, Felix, E-mail: finster@ur.de, E-mail: simone.murro@ur.de, E-mail: Christian.Roeken@mathematik.ur.de; Murro, Simone, E-mail: finster@ur.de, E-mail: simone.murro@ur.de, E-mail: Christian.Roeken@mathematik.ur.de; Röken, Christian, E-mail: finster@ur.de, E-mail: simone.murro@ur.de, E-mail: Christian.Roeken@mathematik.ur.de [Fakultät für Mathematik, Universität Regensburg, D-93040 Regensburg (Germany)

2016-07-15

We give a non-perturbative construction of the fermionic projector in Minkowski space coupled to a time-dependent external potential which is smooth and decays faster than quadratically for large times. The weak and strong mass oscillation properties are proven. We show that the integral kernel of the fermionic projector is of the Hadamard form, provided that the time integral of the spatial sup-norm of the potential satisfies a suitable bound. This gives rise to an algebraic quantum field theory of Dirac fields in an external potential with a distinguished pure quasi-free Hadamard state.

Trade-off capacities of the quantum Hadamard channels

International Nuclear Information System (INIS)

Bradler, Kamil; Hayden, Patrick; Touchette, Dave; Wilde, Mark M.

2010-01-01

Coding theorems in quantum Shannon theory express the ultimate rates at which a sender can transmit information over a noisy quantum channel. More often than not, the known formulas expressing these transmission rates are intractable, requiring an optimization over an infinite number of uses of the channel. Researchers have rarely found quantum channels with a tractable classical or quantum capacity, but when such a finding occurs, it demonstrates a complete understanding of that channel's capabilities for transmitting classical or quantum information. Here we show that the three-dimensional capacity region for entanglement-assisted transmission of classical and quantum information is tractable for the Hadamard class of channels. Examples of Hadamard channels include generalized dephasing channels, cloning channels, and the Unruh channel. The generalized dephasing channels and the cloning channels are natural processes that occur in quantum systems through the loss of quantum coherence or stimulated emission, respectively. The Unruh channel is a noisy process that occurs in relativistic quantum information theory as a result of the Unruh effect and bears a strong relationship to the cloning channels. We give exact formulas for the entanglement-assisted classical and quantum communication capacity regions of these channels. The coding strategy for each of these examples is superior to a naieve time-sharing strategy, and we introduce a measure to determine this improvement.

On the optimum joint decoding capacity of wyner circular GCMAC by exploiting hadamard inequality

KAUST Repository

Shakir, Muhammad

2010-09-01

This paper presents an original expression of the theoretical upper bound for the optimum joint decoding capacity of Wyner Circular Gaussian Cellular Multiple Access Channel (C-GCMAC). This upper bound is a novel application of the Hadamard inequality established by exploiting the Hadamard operation between the channel fading (G) and channel slow gain (Ω) matrices. This paper demonstrates that the theoretical upper bound converges to the actual capacity for negligible channel slow gain among the mobile terminals and the base stations for the entire range of Signal to Noise Ratios (SNRs). The behaviour of the theoretical bound is critically observed when the intercell and the intra-cell time sharing schemes are employed. © 2010 IEEE.

Hermite-Hadamard type inequality for φ{sub h}-convex stochastic processes

Energy Technology Data Exchange (ETDEWEB)

Sarıkaya, Mehmet Zeki, E-mail: sarikayamz@gmail.com [Department of Mathematics, Faculty of Science and Arts, Düzce University, Düzce (Turkey); Kiriş, Mehmet Eyüp, E-mail: kiris@aku.edu.tr [Department of Mathematics, Institute of Science and Arts, Afyon Kocatepe University, Afyonkarahisar (Turkey); Çelik, Nuri, E-mail: ncelik@bartin.edu.tr [Department of Statistics, Faculty of Science, Bartın University, Bartın-Turkey (Turkey)

2016-04-18

The main aim of the present paper is to introduce φ{sub h}-convex stochastic processes and we investigate main properties of these mappings. Moreover, we prove the Hadamard-type inequalities for φ{sub h}-convex stochastic processes. We also give some new general inequalities for φ{sub h}-convex stochastic processes.

A Calibration Method for Nonlinear Mismatches in M-Channel Time-Interleaved Analog-to-Digital Converters Based on Hadamard Sequences

Directory of Open Access Journals (Sweden)

Husheng Liu

2016-11-01

Full Text Available The time-interleaved analog-to-digital converter (TIADC is an architecture used to achieve a high sampling rate and high dynamic performance. However, estimation and compensation methods are required to maintain the dynamic performance of the constituent analog-to-digital converters (ADCs due to channel mismatches. This paper proposes a blind adaptive method to calibrate the nonlinear mismatches in M-channel TIADCs (M-TIADCs. The nonlinearity-induced error signal is reconstructed by the proposed multiplier Hadamard transform (MHT structure, and the nonlinear parameters are estimated by the filtered-X least-mean square (FxLMS algorithm. The performance of cascade calibration is also analyzed. The numerical simulation results show that the proposed method consumes much less hardware resources while maintaining the calibration performance.

Hadamard States for the Klein-Gordon Equation on Lorentzian Manifolds of Bounded Geometry

Science.gov (United States)

Gérard, Christian; Oulghazi, Omar; Wrochna, Michał

2017-06-01

We consider the Klein-Gordon equation on a class of Lorentzian manifolds with Cauchy surface of bounded geometry, which is shown to include examples such as exterior Kerr, Kerr-de Sitter spacetime and the maximal globally hyperbolic extension of the Kerr outer region. In this setup, we give an approximate diagonalization and a microlocal decomposition of the Cauchy evolution using a time-dependent version of the pseudodifferential calculus on Riemannian manifolds of bounded geometry. We apply this result to construct all pure regular Hadamard states (and associated Feynman inverses), where regular refers to the state's two-point function having Cauchy data given by pseudodifferential operators. This allows us to conclude that there is a one-parameter family of elliptic pseudodifferential operators that encodes both the choice of (pure, regular) Hadamard state and the underlying spacetime metric.

A note on "The Cartan-Hadamard conjecture and the Little Prince"

OpenAIRE

Michalakis, Spyridon

2017-01-01

We provide elementary proofs of Lemmas 7.1 and 7.4 appearing in "The Cartan-Hadamard conjecture and the Little Prince", by B. Kloeckner and G. Kuperberg. The Lemmas play an important role in the derivation of novel isoperimetric inequalities. The original proofs relied on Sage, a symbolic algebra package, to factor certain algebraic varieties into irreducible components.

Fast Estimation Method of Space-Time Two-Dimensional Positioning Parameters Based on Hadamard Product

Directory of Open Access Journals (Sweden)

Haiwen Li

2018-01-01

Full Text Available The estimation speed of positioning parameters determines the effectiveness of the positioning system. The time of arrival (TOA and direction of arrival (DOA parameters can be estimated by the space-time two-dimensional multiple signal classification (2D-MUSIC algorithm for array antenna. However, this algorithm needs much time to complete the two-dimensional pseudo spectral peak search, which makes it difficult to apply in practice. Aiming at solving this problem, a fast estimation method of space-time two-dimensional positioning parameters based on Hadamard product is proposed in orthogonal frequency division multiplexing (OFDM system, and the Cramer-Rao bound (CRB is also presented. Firstly, according to the channel frequency domain response vector of each array, the channel frequency domain estimation vector is constructed using the Hadamard product form containing location information. Then, the autocorrelation matrix of the channel response vector for the extended array element in frequency domain and the noise subspace are calculated successively. Finally, by combining the closed-form solution and parameter pairing, the fast joint estimation for time delay and arrival direction is accomplished. The theoretical analysis and simulation results show that the proposed algorithm can significantly reduce the computational complexity and guarantee that the estimation accuracy is not only better than estimating signal parameters via rotational invariance techniques (ESPRIT algorithm and 2D matrix pencil (MP algorithm but also close to 2D-MUSIC algorithm. Moreover, the proposed algorithm also has certain adaptability to multipath environment and effectively improves the ability of fast acquisition of location parameters.

On the optimum joint decoding capacity of wyner circular GCMAC by exploiting hadamard inequality

KAUST Repository

Shakir, Muhammad; Durrani, Tariq Salim; Alouini, Mohamed-Slim

2010-01-01

inequality established by exploiting the Hadamard operation between the channel fading (G) and channel slow gain (Ω) matrices. This paper demonstrates that the theoretical upper bound converges to the actual capacity for negligible channel slow gain among

Analytical upper bound on optimum joint decoding capacity of Wyner GCMAC using hadamard inequality

KAUST Repository

Shakir, Muhammad; Durrani, Tariq Salim; Alouini, Mohamed-Slim

2011-01-01

an approximation approach based on the estimation of probability density function (PDF) of Hadamard product of two matrices. A closed-form expression has been derived to capture the effect of variable user density in adjacent cells on optimal joint decoding

First-order and higher order sequence learning in specific language impairment.

Science.gov (United States)

Clark, Gillian M; Lum, Jarrad A G

2017-02-01

A core claim of the procedural deficit hypothesis of specific language impairment (SLI) is that the disorder is associated with poor implicit sequence learning. This study investigated whether implicit sequence learning problems in SLI are present for first-order conditional (FOC) and higher order conditional (HOC) sequences. Twenty-five children with SLI and 27 age-matched, nonlanguage-impaired children completed 2 serial reaction time tasks. On 1 version, the sequence to be implicitly learnt comprised a FOC sequence and on the other a HOC sequence. Results showed that the SLI group learned the HOC sequence (η p ² = .285, p = .005) but not the FOC sequence (η p ² = .099, p = .118). The control group learned both sequences (FOC η p ² = .497, HOC η p 2= .465, ps < .001). The SLI group's difficulty learning the FOC sequence is consistent with the procedural deficit hypothesis. However, the study provides new evidence that multiple mechanisms may underpin the learning of FOC and HOC sequences. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Discrete canonical transforms that are Hadamard matrices

International Nuclear Information System (INIS)

Healy, John J; Wolf, Kurt Bernardo

2011-01-01

The group Sp(2,R) of symplectic linear canonical transformations has an integral kernel which has quadratic and linear phases, and which is realized by the geometric paraxial optical model. The discrete counterpart of this model is a finite Hamiltonian system that acts on N-point signals through N x N matrices whose elements also have a constant absolute value, although they do not form a representation of that group. Those matrices that are also unitary are Hadamard matrices. We investigate the manifolds of these N x N matrices under the Sp(2,R) equivalence imposed by the model, and find them to be on two-sided cosets. By means of an algorithm we determine representatives that lead to collections of mutually unbiased bases.

Experimental demonstration of a Hadamard gate for coherent state qubits

DEFF Research Database (Denmark)

Tipsmark, Anders; Dong, Ruifang; Laghaout, Amine

2011-01-01

We discuss and make an experimental test of a probabilistic Hadamard gate for coherent state qubits. The scheme is based on linear optical components, nonclassical resources, and the joint projective action of a photon counter and a homodyne detector. We experimentally characterize the gate for t...... for the coherent states of the computational basis by full tomographic reconstruction of the transformed output states. Based on the parameters of the experiment, we simulate the fidelity for all coherent state qubits on the Bloch sphere....

Experimental demonstration of a Hadamard gate for coherent state qubits

Energy Technology Data Exchange (ETDEWEB)

Tipsmark, Anders; Laghaout, Amine; Andersen, Ulrik L. [Department of Physics, Technical University of Denmark, Fysikvej, DK-2800 Kgs. Lyngby (Denmark); Dong, Ruifang [Quantum Frequency Standards Division, National Time Service Center (NTSC), Chinese Academy of Sciences, 710600 Lintong, Shaanxi (China); Department of Physics, Technical University of Denmark, Fysikvej, DK-2800 Kgs. Lyngby (Denmark); Marek, Petr [Department of Optics, Palacky University, 17. listopadu 12, CZ-77146 Olomouc (Czech Republic); Jezek, Miroslav [Department of Optics, Palacky University, 17. listopadu 12, CZ-77146 Olomouc (Czech Republic); Department of Physics, Technical University of Denmark, Fysikvej, DK-2800 Kgs. Lyngby (Denmark)

2011-11-15

We discuss and make an experimental test of a probabilistic Hadamard gate for coherent state qubits. The scheme is based on linear optical components, nonclassical resources, and the joint projective action of a photon counter and a homodyne detector. We experimentally characterize the gate for the coherent states of the computational basis by full tomographic reconstruction of the transformed output states. Based on the parameters of the experiment, we simulate the fidelity for all coherent state qubits on the Bloch sphere.

On the stress–energy tensor of quantum fields in curved spacetimes—comparison of different regularization schemes and symmetry of the Hadamard/Seeley–DeWitt coefficients

International Nuclear Information System (INIS)

Hack, Thomas-Paul; Moretti, Valter

2012-01-01

We review a few rigorous and partly unpublished results on the regularization of the stress–energy in quantum field theory on curved spacetimes: (1) the symmetry of the Hadamard/Seeley–DeWitt coefficients in smooth Riemannian and Lorentzian spacetimes, (2) the equivalence of the local ζ-function and the Hadamard-point-splitting procedure in smooth static spacetimes and (3) the equivalence of the DeWitt–Schwinger- and the Hadamard-point-splitting procedure in smooth Riemannian and Lorentzian spacetimes. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical in honour of Stuart Dowker’s 75th birthday devoted to ‘Applications of zeta functions and other spectral functions in mathematics and physics’. (paper)

The Hadamard construction of Green's functions on a curved space-time: physics and explicit rigorous results

International Nuclear Information System (INIS)

John, R.W.

1987-01-01

First, in connection with their construction due to Hadamard, the mathematical and physical meaning of covariant Green's functions in relativistic gravitational fields - according to Einstein: on curved space-time - is discussed. Then, in the case of a general static spherically symmetric space-time the construction equations for a scalar Green's function are cast into symmetry-adapted form providing a convenient starting point for an explicit calculation of the Hadamard building elements. In applying the obtained basic scheme to a special one-parameter family of model metrics one succeeds in advancing to the explicit exact calculation of tail-term coefficients of a massless Green's function which are simultaneously coefficients in the Schwinger-De Witt expansion of the Feynman propagator for the corresponding massive Klein-Gordon equation on curved space-time. (author)

Hadamard states from light-like hypersurfaces

CERN Document Server

Dappiaggi, Claudio; Pinamonti, Nicola

2017-01-01

This book provides a rather self-contained survey of the construction of Hadamard states for scalar field theories in a large class of notable spacetimes, possessing a (conformal) light-like boundary. The first two sections focus on explaining a few introductory aspects of this topic and on providing the relevant geometric background material. The notions of asymptotically flat spacetimes and of expanding universes with a cosmological horizon are analysed in detail, devoting special attention to the characterization of asymptotic symmetries. In the central part of the book,  the quantization of a real scalar field theory on such class of backgrounds is discussed within the framework of algebraic quantum field theory.  Subsequently it is explained how it is possible to encode the information of the observables of the theory in a second, ancillary counterpart, which is built directly on the conformal (null) boundary.  This procedure, dubbed bulk-to-boundary correspondence, has the net advantage of allowing t...

Compressed sensing with cyclic-S Hadamard matrix for terahertz imaging applications

Science.gov (United States)

Ermeydan, Esra Şengün; ćankaya, Ilyas

2018-01-01

Compressed Sensing (CS) with Cyclic-S Hadamard matrix is proposed for single pixel imaging applications in this study. In single pixel imaging scheme, N = r . c samples should be taken for r×c pixel image where . denotes multiplication. CS is a popular technique claiming that the sparse signals can be reconstructed with samples under Nyquist rate. Therefore to solve the slow data acquisition problem in Terahertz (THz) single pixel imaging, CS is a good candidate. However, changing mask for each measurement is a challenging problem since there is no commercial Spatial Light Modulators (SLM) for THz band yet, therefore circular masks are suggested so that for each measurement one or two column shifting will be enough to change the mask. The CS masks are designed using cyclic-S matrices based on Hadamard transform for 9 × 7 and 15 × 17 pixel images within the framework of this study. The %50 compressed images are reconstructed using total variation based TVAL3 algorithm. Matlab simulations demonstrates that cyclic-S matrices can be used for single pixel imaging based on CS. The circular masks have the advantage to reduce the mechanical SLMs to a single sliding strip, whereas the CS helps to reduce acquisition time and energy since it allows to reconstruct the image from fewer samples.

Generalization of the fejer-hadamard type inequalities for p-convex functions via k-fractional integrals

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Ghulam Farid

2017-10-01

Full Text Available The aim of this paper is to obtain some more general fractional integral inequalities of Fejer Hadamard type for p-convex functions via Riemann-Liouville k-fractional integrals. Also in particular fractional inequalities for p-convex functions via Riemann-Liouville fractional integrals have been deduced.

Abstract generalized vector quasi-equilibrium problems in noncompact Hadamard manifolds

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Haishu Lu

2017-05-01

Full Text Available Abstract This paper deals with the abstract generalized vector quasi-equilibrium problem in noncompact Hadamard manifolds. We prove the existence of solutions to the abstract generalized vector quasi-equilibrium problem under suitable conditions and provide applications to an abstract vector quasi-equilibrium problem, a generalized scalar equilibrium problem, a scalar equilibrium problem, and a perturbed saddle point problem. Finally, as an application of the existence of solutions to the generalized scalar equilibrium problem, we obtain a weakly mixed variational inequality and two mixed variational inequalities. The results presented in this paper unify and generalize many known results in the literature.

Attempt to generalize fractional-order electric elements to complex-order ones

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Si, Gangquan; Diao, Lijie; Zhu, Jianwei; Lei, Yuhang; Zhang, Yanbin

2017-06-01

The complex derivative {D}α +/- {{j}β }, with α, β \\in R+ is a generalization of the concept of integer derivative, where α=1, β=0. Fractional-order electric elements and circuits are becoming more and more attractive. In this paper, the complex-order electric elements concept is proposed for the first time, and the complex-order elements are modeled and analyzed. Some interesting phenomena are found that the real part of the order affects the phase of output signal, and the imaginary part affects the amplitude for both the complex-order capacitor and complex-order memristor. More interesting is that the complex-order capacitor can do well at the time of fitting electrochemistry impedance spectra. The complex-order memristor is also analyzed. The area inside the hysteresis loops increases with the increasing of the imaginary part of the order and decreases with the increasing of the real part. Some complex case of complex-order memristors hysteresis loops are analyzed at last, whose loop has touching points beyond the origin of the coordinate system.

Single-pixel imaging by Hadamard transform and its application for hyperspectral imaging

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Mizutani, Yasuhiro; Shibuya, Kyuki; Taguchi, Hiroki; Iwata, Tetsuo; Takaya, Yasuhiro; Yasui, Takeshi

2016-10-01

In this paper, we report on comparisons of single-pixel imagings using Hadamard Transform (HT) and the ghost imaging (GI) in the view point of the visibility under weak light conditions. For comparing the two methods, we have discussed about qualities of images based on experimental results and numerical analysis. To detect images by the TH method, we have illuminated the Hadamard-pattern mask and calculated by orthogonal transform. On the other hand, the GH method can detect images by illuminating random patterns and a correlation measurement. For comparing two methods under weak light intensity, we have controlled illuminated intensities of a DMD projector about 0.1 in signal-to-noise ratio. Though a process speed of the HT image was faster then an image via the GI, the GI method has an advantage of detection under weak light condition. An essential difference between the HT and the GI method is discussed about reconstruction process. Finally, we also show a typical application of the single-pixel imaging such as hyperspectral images by using dual-optical frequency combs. An optical setup consists of two fiber lasers, spatial light modulated for generating patten illumination, and a single pixel detector. We are successful to detect hyperspectrul images in a range from 1545 to 1555 nm at 0.01nm resolution.

f ( λ , μ $f_{(\\lambda,\\mu}$ -statistical convergence of order α̃ for double sequences

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Mahmut Işik

2017-10-01

Full Text Available Abstract New concepts of f λ , μ $f_{\\lambda,\\mu }$ -statistical convergence for double sequences of order α̃ and strong f λ , μ $f_{\\lambda,\\mu }$ -Cesàro summability for double sequences of order α̃ are introduced for sequences of (complex or real numbers. Furthermore, we give the relationship between the spaces w α ˜ , 0 2 ( f , λ , μ $w_{\\tilde{\\alpha },0}^{2} ( f,\\lambda,\\mu $ , w α ˜ 2 ( f , λ , μ $w_{\\tilde{\\alpha }}^{2} ( f,\\lambda,\\mu $ and w α ˜ , ∞ 2 ( f , λ , μ $w_{\\tilde{\\alpha},\\infty }^{2} ( f,\\lambda,\\mu $ . Then we express the properties of strong f λ , μ $f_{\\lambda,\\mu }$ -Cesàro summability of order β̃ which is related to strong f λ , μ $f_{\\lambda,\\mu }$ -Cesàro summability of order α̃. Also, some relations between f λ , μ $f_{\\lambda,\\mu }$ -statistical convergence of order α̃ and strong f λ , μ $f_{\\lambda,\\mu }$ -Cesàro summability of order α̃ are given.

Computational complexity of algorithms for sequence comparison, short-read assembly and genome alignment.

Science.gov (United States)

Baichoo, Shakuntala; Ouzounis, Christos A

A multitude of algorithms for sequence comparison, short-read assembly and whole-genome alignment have been developed in the general context of molecular biology, to support technology development for high-throughput sequencing, numerous applications in genome biology and fundamental research on comparative genomics. The computational complexity of these algorithms has been previously reported in original research papers, yet this often neglected property has not been reviewed previously in a systematic manner and for a wider audience. We provide a review of space and time complexity of key sequence analysis algorithms and highlight their properties in a comprehensive manner, in order to identify potential opportunities for further research in algorithm or data structure optimization. The complexity aspect is poised to become pivotal as we will be facing challenges related to the continuous increase of genomic data on unprecedented scales and complexity in the foreseeable future, when robust biological simulation at the cell level and above becomes a reality. Copyright © 2017 Elsevier B.V. All rights reserved.

Generalized Combination Complex Synchronization for Fractional-Order Chaotic Complex Systems

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Cuimei Jiang

2015-07-01

Full Text Available Based on two fractional-order chaotic complex drive systems and one fractional-order chaotic complex response system with different dimensions, we propose generalized combination complex synchronization. In this new synchronization scheme, there are two complex scaling matrices that are non-square matrices. On the basis of the stability theory of fractional-order linear systems, we design a general controller via active control. Additionally, by virtue of two complex scaling matrices, generalized combination complex synchronization between fractional-order chaotic complex systems and real systems is investigated. Finally, three typical examples are given to demonstrate the effectiveness and feasibility of the schemes.

TOUR CONSTRUCTION HEURISTICS FOR AN ORDER SEQUENCING PROBLEM

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De Villiers, A. P.

2012-11-01

Full Text Available An order picking system that requires pickers to move in a clockwise direction around a picking line with fixed locations is considered. The problem is divided into three tiers. The tier in which orders must be sequenced is addressed. Eight tour construction heuristics are developed and implemented for an order picking system operating in unidirectional picking lines. Two classes of tour construction heuristics the tour construction starting position ( and the tour construction ending position ( are developed to sequence orders in a picking line. All algorithms are tested and compared using real life data sets. The best solution quality was obtained by a heuristic with adaptations.

Performance analysis of stationary Hadamard matrix diffusers in free-space optical communication links

Science.gov (United States)

Burrell, Derek J.; Middlebrook, Christopher T.

2017-08-01

Wireless communication systems that employ free-space optical links in place of radio/microwave technologies carry substantial benefits in terms of data throughput, network security and design efficiency. Along with these advantages comes the challenge of counteracting signal degradation caused by atmospheric turbulence in free-space environments. A fully coherent laser source experiences random phase delays along its traversing path in turbulent conditions forming a speckle pattern and lowering the received signal-to-noise ratio upon detection. Preliminary research has shown that receiver-side speckle contrast may be significantly reduced and signal-to-noise ratio increased accordingly through the use of a partially coherent light source. While dynamic diffusers and adaptive optics solutions have been proven effective, they also add expense and complexity to a system that relies on accessibility and robustness for successful implementation. A custom Hadamard diffractive matrix design is used to statically induce partial coherence in a transmitted beam to increase signal-to-noise ratio for experimental turbulence scenarios. Atmospheric phase screens are generated using an open-source software package and subsequently loaded into a spatial light modulator using nematic liquid crystals to modulate the phase.

The Fermionic Signature Operator and Hadamard States in the Presence of a Plane Electromagnetic Wave

Science.gov (United States)

Finster, Felix; Reintjes, Moritz

2017-05-01

We give a non-perturbative construction of a distinguished state for the quantized Dirac field in Minkowski space in the presence of a time-dependent external field of the form of a plane electromagnetic wave. By explicit computation of the fermionic signature operator, it is shown that the Dirac operator has the strong mass oscillation property. We prove that the resulting fermionic projector state is a Hadamard state.

Convolution of second order linear recursive sequences II.

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Szakács Tamás

2017-12-01

Full Text Available We continue the investigation of convolutions of second order linear recursive sequences (see the first part in [1]. In this paper, we focus on the case when the characteristic polynomials of the sequences have common root.

Rotated Walsh-Hadamard Spreading with Robust Channel Estimation for a Coded MC-CDMA System

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Raulefs Ronald

2004-01-01

Full Text Available We investigate rotated Walsh-Hadamard spreading matrices for a broadband MC-CDMA system with robust channel estimation in the synchronous downlink. The similarities between rotated spreading and signal space diversity are outlined. In a multiuser MC-CDMA system, possible performance improvements are based on the chosen detector, the channel code, and its Hamming distance. By applying rotated spreading in comparison to a standard Walsh-Hadamard spreading code, a higher throughput can be achieved. As combining the channel code and the spreading code forms a concatenated code, the overall minimum Hamming distance of the concatenated code increases. This asymptotically results in an improvement of the bit error rate for high signal-to-noise ratio. Higher convolutional channel code rates are mostly generated by puncturing good low-rate channel codes. The overall Hamming distance decreases significantly for the punctured channel codes. Higher channel code rates are favorable for MC-CDMA, as MC-CDMA utilizes diversity more efficiently compared to pure OFDMA. The application of rotated spreading in an MC-CDMA system allows exploiting diversity even further. We demonstrate that the rotated spreading gain is still present for a robust pilot-aided channel estimator. In a well-designed system, rotated spreading extends the performance by using a maximum likelihood detector with robust channel estimation at the receiver by about 1 dB.

Instruction sequences and non-uniform complexity theory

NARCIS (Netherlands)

Bergstra, J.A.; Middelburg, C.A.

2008-01-01

We develop theory concerning non-uniform complexity in a setting in which the notion of single-pass instruction sequence considered in program algebra is the central notion. We define counterparts of the complexity classes P/poly and NP/poly and formulate a counterpart of the complexity theoretic

Operon Gene Order Is Optimized for Ordered Protein Complex Assembly

Science.gov (United States)

Wells, Jonathan N.; Bergendahl, L. Therese; Marsh, Joseph A.

2016-01-01

Summary The assembly of heteromeric protein complexes is an inherently stochastic process in which multiple genes are expressed separately into proteins, which must then somehow find each other within the cell. Here, we considered one of the ways by which prokaryotic organisms have attempted to maximize the efficiency of protein complex assembly: the organization of subunit-encoding genes into operons. Using structure-based assembly predictions, we show that operon gene order has been optimized to match the order in which protein subunits assemble. Exceptions to this are almost entirely highly expressed proteins for which assembly is less stochastic and for which precisely ordered translation offers less benefit. Overall, these results show that ordered protein complex assembly pathways are of significant biological importance and represent a major evolutionary constraint on operon gene organization. PMID:26804901

First order deformations of the Fourier matrix

Energy Technology Data Exchange (ETDEWEB)

Banica, Teodor, E-mail: teo.banica@gmail.com [Department of Mathematics, Cergy-Pontoise University, 95000 Cergy-Pontoise (France)

2014-01-15

The N × N complex Hadamard matrices form a real algebraic manifold C{sub N}. The singularity at a point H ∈ C{sub N} is described by a filtration of cones T{sub H}{sup ×}C{sub N}⊂T{sub H}{sup ∘}C{sub N}⊂T{sub H}C{sub N}⊂T{sup ~}{sub H}C{sub N}, coming from the trivial, affine, smooth, and first order deformations. We study here these cones in the case where H = F{sub N} is the Fourier matrix, (w{sup ij}) with w = e{sup 2πi/N}, our main result being a simple description of T{sup ~}{sub H}C{sub N}. As a consequence, the rationality conjecture dim{sub R}(T{sup ~}{sub H}C{sub N})=dim{sub Q}(T{sup ~}{sub H}C{sub N}∩M{sub N}(Q)) holds at H = F{sub N}.

Determination of residence times of ions in a resistive glass selected ion flow-drift tube using the Hadamard transformation.

Science.gov (United States)

Spesyvyi, Anatolii; Španěl, Patrik

2015-09-15

Selected ion flow tube mass spectrometry, SIFT-MS, used for trace gas analyses has certain fundamental limitations that could be alleviated by adding a facility that allows reaction times and ion interaction energies to be varied. Thus, a selected ion flow-drift tube, SIFDT, has been created to explore the influence of an embedded electric field on these parameters and on reaction processes. The new SIFTD instrument was constructed using a miniature resistive glass drift tube. Arrival times of ions, t, analysed by a downstream quadrupole mass spectrometer over the m/z range 10-100 were studied by modulating the injected ion current using a gate lens. Single pulse modulation was compared with pseudorandom time multiplexing exploiting the Hadamard transformation. A simple model involving analysis of ethanol and water vapour mixture in air was used to explore the advantages of the SIFDT concept to SIFT-MS analysis. It is shown that the resistive glass drift tube is suitable for SIFDT experiments. The Hadamard transformation can be used to routinely determine reagent ion residence time in the flow-drift tube and also to observe differences in arrival times for different product ions. Two-dimensional data combining arrival time and mass spectra can be obtained rapidly. The calculated ion drift velocities vary with the reduced field strength, E/N, and the calculated ion mobilities agree with theoretical and previous literature values. This study has provided evidence that the SIFDT-MS technique can be implemented in a miniature and low-cost instrument and two- or three-dimensional data can be obtained (product ion count rates as functions of m/z, t and E/N) using the Hadamard transformation thus providing exciting possibilities for further analytical additions and extensions of the SIFT-MS technique. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Instruction sequence based non-uniform complexity classes

NARCIS (Netherlands)

Bergstra, J.A.; Middelburg, C.A.

2013-01-01

We present an approach to non-uniform complexity in which single-pass instruction sequences play a key part, and answer various questions that arise from this approach. We introduce several kinds of non-uniform complexity classes. One kind includes a counterpart of the well-known non-uniform

Symbolic complexity for nucleotide sequences: a sign of the genome structure

International Nuclear Information System (INIS)

Salgado-García, R; Ugalde, E

2016-01-01

We introduce a method for estimating the complexity function (which counts the number of observable words of a given length) of a finite symbolic sequence, which we use to estimate the complexity function of coding DNA sequences for several species of the Hominidae family. In all cases, the obtained symbolic complexities show the same characteristic behavior: exponential growth for small word lengths, followed by linear growth for larger word lengths. The symbolic complexities of the species we consider exhibit a systematic trend in correspondence with the phylogenetic tree. Using our method, we estimate the complexity function of sequences obtained by some known evolution models, and in some cases we observe the characteristic exponential-linear growth of the Hominidae coding DNA complexity. Analysis of the symbolic complexity of sequences obtained from a specific evolution model points to the following conclusion: linear growth arises from the random duplication of large segments during the evolution of the genome, while the decrease in the overall complexity from one species to another is due to a difference in the speed of accumulation of point mutations. (paper)

Constructive Lower Bounds on Model Complexity of Shallow Perceptron Networks

Czech Academy of Sciences Publication Activity Database

Kůrková, Věra

2018-01-01

Roč. 29, č. 7 (2018), s. 305-315 ISSN 0941-0643 R&D Projects: GA ČR GA15-18108S Institutional support: RVO:67985807 Keywords : shallow and deep networks * model complexity and sparsity * signum perceptron networks * finite mappings * variational norms * Hadamard matrices Subject RIV: IN - Informatics, Computer Science Impact factor: 2.505, year: 2016

ClonEvol: clonal ordering and visualization in cancer sequencing.

Science.gov (United States)

Dang, H X; White, B S; Foltz, S M; Miller, C A; Luo, J; Fields, R C; Maher, C A

2017-12-01

Reconstruction of clonal evolution is critical for understanding tumor progression and implementing personalized therapies. This is often done by clustering somatic variants based on their cellular prevalence estimated via bulk tumor sequencing of multiple samples. The clusters, consisting of the clonal marker variants, are then ordered based on their estimated cellular prevalence to reconstruct clonal evolution trees, a process referred to as 'clonal ordering'. However, cellular prevalence estimate is confounded by statistical variability and errors in sequencing/data analysis, and therefore inhibits accurate reconstruction of the clonal evolution. This problem is further complicated by intra- and inter-tumor heterogeneity. Furthermore, the field lacks a comprehensive visualization tool to facilitate the interpretation of complex clonal relationships. To address these challenges we developed ClonEvol, a unified software tool for clonal ordering, visualization, and interpretation. ClonEvol uses a bootstrap resampling technique to estimate the cellular fraction of the clones and probabilistically models the clonal ordering constraints to account for statistical variability. The bootstrapping allows identification of the sample founding- and sub-clones, thus enabling interpretation of clonal seeding. ClonEvol automates the generation of multiple widely used visualizations for reconstructing and interpreting clonal evolution. ClonEvol outperformed three of the state of the art tools (LICHeE, Canopy and PhyloWGS) for clonal evolution inference, showing more robust error tolerance and producing more accurate trees in a simulation. Building upon multiple recent publications that utilized ClonEvol to study metastasis and drug resistance in solid cancers, here we show that ClonEvol rediscovered relapsed subclones in two published acute myeloid leukemia patients. Furthermore, we demonstrated that through noninvasive monitoring ClonEvol recapitulated the emerging subclones

Two-Stage orders sequencing system for mixed-model assembly

Science.gov (United States)

Zemczak, M.; Skolud, B.; Krenczyk, D.

2015-11-01

In the paper, the authors focus on the NP-hard problem of orders sequencing, formulated similarly to Car Sequencing Problem (CSP). The object of the research is the assembly line in an automotive industry company, on which few different models of products, each in a certain number of versions, are assembled on the shared resources, set in a line. Such production type is usually determined as a mixed-model production, and arose from the necessity of manufacturing customized products on the basis of very specific orders from single clients. The producers are nowadays obliged to provide each client the possibility to determine a huge amount of the features of the product they are willing to buy, as the competition in the automotive market is large. Due to the previously mentioned nature of the problem (NP-hard), in the given time period only satisfactory solutions are sought, as the optimal solution method has not yet been found. Most of the researchers that implemented inaccurate methods (e.g. evolutionary algorithms) to solving sequencing problems dropped the research after testing phase, as they were not able to obtain reproducible results, and met problems while determining the quality of the received solutions. Therefore a new approach to solving the problem, presented in this paper as a sequencing system is being developed. The sequencing system consists of a set of determined rules, implemented into computer environment. The system itself works in two stages. First of them is connected with the determination of a place in the storage buffer to which certain production orders should be sent. In the second stage of functioning, precise sets of sequences are determined and evaluated for certain parts of the storage buffer under certain criteria.

Particle tracking from image sequences of complex plasma crystals

International Nuclear Information System (INIS)

Hadziavdic, Vedad; Melandsoe, Frank; Hanssen, Alfred

2006-01-01

In order to gather information about the physics of the complex plasma crystals from the experimental data, particles have to be tracked through a sequence of images. An application of the Kalman filter for that purpose is presented, using a one-dimensional approximation of the particle dynamics as a model for the filter. It is shown that Kalman filter is capable of tracking dust particles even with high levels of measurement noise. An inherent part of the Kalman filter, the innovation process, can be used to estimate values of the physical system parameters from the experimental data. The method is shown to be able to estimate the characteristic oscillation frequency from noisy data

Generalized statistical convergence of order β for sequences of fuzzy numbers

Science.gov (United States)

Altınok, Hıfsı; Karakaş, Abdulkadir; Altın, Yavuz

2018-01-01

In the present paper, we introduce the concepts of Δm-statistical convergence of order β for sequences of fuzzy numbers and strongly Δm-summable of order β for sequences of fuzzy numbers by using a modulus function f and taking supremum on metric d for 0 < β ≤ 1 and give some inclusion relations between them.

Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways.

Science.gov (United States)

Mallik, Saurav; Kundu, Sudip

2017-07-01

Is the order in which biomolecular subunits self-assemble into functional macromolecular complexes imprinted in their sequence-space? Here, we demonstrate that the temporal order of macromolecular complex self-assembly can be efficiently captured using the landscape of residue-level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high-affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183-1189. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Metaheuristic approaches to order sequencing on a unidirectional picking line

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AP de Villiers

2013-06-01

Full Text Available In this paper the sequencing of orders on a unidirectional picking line is considered. The aim of the order sequencing is to minimise the number of cycles travelled by a picker within the picking line to complete all orders. A tabu search, simulated annealing, genetic algorithm, generalised extremal optimisation and a random local search are presented as possible solution approaches. Computational results based on real life data instances are presented for these metaheuristics and compared to the performance of a lower bound and the solutions used in practise. The random local search exhibits the best overall solution quality, however, the generalised extremal optimisation approach delivers comparable results in considerably shorter computational times.

Sufficient conditions for Hadamard well-posedness of a coupled thermo-chemo-poroelastic system

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Tetyana Malysheva

2016-01-01

Full Text Available This article addresses the well-posedness of a coupled parabolic-elliptic system modeling fully coupled thermal, chemical, hydraulic, and mechanical processes in porous formations that impact drilling and borehole stability. The underlying thermo-chemo-poroelastic model is a system of time-dependent parabolic equations describing thermal, solute, and fluid diffusions coupled with Navier-type elliptic equations that attempt to capture the elastic behavior of rock around a borehole. An existence and uniqueness theory for a corresponding initial-boundary value problem is an open problem in the field. We give sufficient conditions for the well-posedness in the sense of Hadamard of a weak solution to a fully coupled parabolic-elliptic initial-boundary value problem describing homogeneous and isotropic media.

Complementary Walsh-Hadamard coded optical CDMA coder/decoders structured over arrayed-waveguide grating routers

Science.gov (United States)

Huang, Jen-Fa; Yang, Chao-Chin; Tseng, Shin-Pin

2004-01-01

In this paper, an optical code-division multiple-access (OCDMA) system with complementary Walsh-Hadamard coded optical encoder/decoder configuration structured over arrayed-waveguide grating (AWG) routers is examined. In the proposed system, each network user requires only two AWG routers to accomplish spectral encoding and decoding for complementary keying, thus, resulting a simpler and low cost system. Performance of the proposed system is analyzed by taking the effect of phase-induced intensity noise into account. The result indicates that the established system not only preserves the capability of suppressing multiple-access interference (MAI), but also improves bit-error-rate performance as compared to the conventional coders employing simple on-off keying.

Complex Sequencing Problems and Local Search Heuristics

NARCIS (Netherlands)

Brucker, P.; Hurink, Johann L.; Osman, I.H.; Kelly, J.P.

1996-01-01

Many problems can be formulated as complex sequencing problems. We will present problems in flexible manufacturing that have such a formulation and apply local search methods like iterative improvement, simulated annealing and tabu search to solve these problems. Computational results are reported.

454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher

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Gustafsson Lars

2010-12-01

Full Text Available Abstract Background Because of their functional significance, the Major Histocompatibility Complex (MHC class I and II genes have been the subject of continuous interest in the fields of ecology, evolution and conservation. In some vertebrate groups MHC consists of multiple loci with similar alleles; therefore, the multiple loci must be genotyped simultaneously. In such complex systems, understanding of the evolutionary patterns and their causes has been limited due to challenges posed by genotyping. Results Here we used 454 amplicon sequencing to characterize MHC class IIB exon 2 variation in the collared flycatcher, an important organism in evolutionary and immuno-ecological studies. On the basis of over 152,000 sequencing reads we identified 194 putative alleles in 237 individuals. We found an extreme complexity of the MHC class IIB in the collared flycatchers, with our estimates pointing to the presence of at least nine expressed loci and a large, though difficult to estimate precisely, number of pseudogene loci. Many similar alleles occurred in the pseudogenes indicating either a series of recent duplications or extensive concerted evolution. The expressed alleles showed unambiguous signals of historical selection and the occurrence of apparent interlocus exchange of alleles. Placing the collared flycatcher's MHC sequences in the context of passerine diversity revealed transspecific MHC class II evolution within the Muscicapidae family. Conclusions 454 amplicon sequencing is an effective tool for advancing our understanding of the MHC class II structure and evolutionary patterns in Passeriformes. We found a highly dynamic pattern of evolution of MHC class IIB genes with strong signals of selection and pronounced sequence divergence in expressed genes, in contrast to the apparent sequence homogenization in pseudogenes. We show that next generation sequencing offers a universal, affordable method for the characterization and, in perspective

Computationally Efficient Robust Color Image Watermarking Using Fast Walsh Hadamard Transform

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Suja Kalarikkal Pullayikodi

2017-10-01

Full Text Available Watermark is the copy deterrence mechanism used in the multimedia signal that is to be protected from hacking and piracy such a way that it can later be extracted from the watermarked signal by the decoder. Watermarking can be used in various applications such as authentication, video indexing, copyright protection and access control. In this paper a new CDMA (Code Division Multiple Access based robust watermarking algorithm using customized 8 × 8 Walsh Hadamard Transform, is proposed for the color images and detailed performance and robustness analysis have been performed. The paper studies in detail the effect of spreading code length, number of spreading codes and type of spreading codes on the performance of the watermarking system. Compared to the existing techniques the proposed scheme is computationally more efficient and consumes much less time for execution. Furthermore, the proposed scheme is robust and survives most of the common signal processing and geometric attacks.

A Note on Starlike Functions of Order α Associated with a Fractional Calculus Operator Involving Caputo’s Fractional

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Jamal Salah

2011-01-01

Full Text Available In this article, we introduce a class of starlike functions of order α by using a fractional operator involving Caputo's fractional which was introduced recently by the authors. The coefficient inequalities and distortion theorems are determined. Further some subordination theorems are given. In addition, results involving Hadamard product are also discussed.

The convergence of the order sequence and the solution function sequence on fractional partial differential equation

Science.gov (United States)

Rusyaman, E.; Parmikanti, K.; Chaerani, D.; Asefan; Irianingsih, I.

2018-03-01

One of the application of fractional ordinary differential equation is related to the viscoelasticity, i.e., a correlation between the viscosity of fluids and the elasticity of solids. If the solution function develops into function with two or more variables, then its differential equation must be changed into fractional partial differential equation. As the preliminary study for two variables viscoelasticity problem, this paper discusses about convergence analysis of function sequence which is the solution of the homogenous fractional partial differential equation. The method used to solve the problem is Homotopy Analysis Method. The results show that if given two real number sequences (αn) and (βn) which converge to α and β respectively, then the solution function sequences of fractional partial differential equation with order (αn, βn) will also converge to the solution function of fractional partial differential equation with order (α, β).

Complex Modified Hybrid Projective Synchronization of Different Dimensional Fractional-Order Complex Chaos and Real Hyper-Chaos

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Jian Liu

2014-11-01

Full Text Available This paper introduces a type of modified hybrid projective synchronization with complex transformationmatrix (CMHPS for different dimensional fractional-order complex chaos and fractional-order real hyper-chaos. The transformationmatrix in this type of chaotic synchronization is a non-square matrix, and its elements are complex numbers. Based on the stability theory of fractional-order systems, by employing the feedback control technique, necessary and sufficient criteria on CMHPS are derived. Furthermore, CMHPS between fractional-order real hyper-chaotic Rössler system and other two different dimensional fractional-order complex Lorenz-like chaotic systems is provided as two examples to discuss reduced order and increased order synchronization, respectively.

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

International Nuclear Information System (INIS)

Xiao Fanghong

2004-01-01

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

A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome

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Scoté-Blachon Céline

2008-09-01

Full Text Available Abstract Background "Open" transcriptome analysis methods allow to study gene expression without a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression, LongSAGE and MPSS (Massively Parallel Signature Sequencing are the mostly used methods for "open" transcriptome analysis. Both LongSAGE and MPSS rely on the isolation of 21 pb tag sequences from each transcript. In contrast to LongSAGE, the high throughput sequencing method used in MPSS enables the rapid sequencing of very large libraries containing several millions of tags, allowing deep transcriptome analysis. However, a bias in the complexity of the transcriptome representation obtained by MPSS was recently uncovered. Results In order to make a deep analysis of mouse hypothalamus transcriptome avoiding the limitation introduced by MPSS, we combined LongSAGE with the Solexa sequencing technology and obtained a library of more than 11 millions of tags. We then compared it to a LongSAGE library of mouse hypothalamus sequenced with the Sanger method. Conclusion We found that Solexa sequencing technology combined with LongSAGE is perfectly suited for deep transcriptome analysis. In contrast to MPSS, it gives a complex representation of transcriptome as reliable as a LongSAGE library sequenced by the Sanger method.

An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes

Science.gov (United States)

Li, Huilin; Nguyen, Hong Hanh; Ogorzalek Loo, Rachel R.; Campuzano, Iain D. G.; Loo, Joseph A.

2018-02-01

Mass spectrometry (MS) has become a crucial technique for the analysis of protein complexes. Native MS has traditionally examined protein subunit arrangements, while proteomics MS has focused on sequence identification. These two techniques are usually performed separately without taking advantage of the synergies between them. Here we describe the development of an integrated native MS and top-down proteomics method using Fourier-transform ion cyclotron resonance (FTICR) to analyse macromolecular protein complexes in a single experiment. We address previous concerns of employing FTICR MS to measure large macromolecular complexes by demonstrating the detection of complexes up to 1.8 MDa, and we demonstrate the efficacy of this technique for direct acquirement of sequence to higher-order structural information with several large complexes. We then summarize the unique functionalities of different activation/dissociation techniques. The platform expands the ability of MS to integrate proteomics and structural biology to provide insights into protein structure, function and regulation.

THE ALGORITHM AND PROGRAM OF M-MATRICES SEARCH AND STUDY

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Y. N. Balonin

2013-05-01

Full Text Available The algorithm and software for search and study of orthogonal bases matrices – minimax matrices (M-matrix are considered. The algorithm scheme is shown, comments on calculation blocks are given, and interface of the MMatrix software system developed with participation of the authors is explained. The results of the universal algorithm work are presented as Hadamard matrices, Belevitch matrices (C-matrices, conference matrices and matrices of even and odd orders complementary and closely related to those ones by their properties, in particular, the matrix of the 22-th order for which there is no C-matrix. Examples of portraits for alternative matrices of the 255-th and the 257-th orders are given corresponding to the sequences of Mersenne and Fermat numbers. A new way to get Hadamard matrices is explained, different from the previously known procedures based on iterative processes and calculations of Lagrange symbols, with theoretical and practical meaning.

Optical image encryption using fresnel zone plate mask based on fast walsh hadamard transform

Science.gov (United States)

Khurana, Mehak; Singh, Hukum

2018-05-01

A new symmetric encryption technique using Fresnel Zone Plate (FZP) based on Fast Walsh Hadamard Transform (FWHT) is proposed for security enhancement. In this technique, bits of plain image is randomized by shuffling the bits randomly. The obtained scrambled image is then masked with FZP using symmetric encryption in FWHT domain to obtain final encrypted image. FWHT has been used in the cryptosystem so as to protect image data from the quantization error and for reconstructing the image perfectly. The FZP used in proposed scheme increases the key space and makes it robust to many traditional attacks. The effectiveness and robustness of the proposed cryptosystem has been analyzed on the basis of various parameters by simulating on MATLAB 8.1.0 (R2012b). The experimental results are provided to highlight suitability of the proposed cryptosystem and prove that the system is secure.

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

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

2018-01-01

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

SSFSE sequence functional MRI of the human cervical spinal cord with complex finger tapping

International Nuclear Information System (INIS)

Xie Chuhai; Kong Kangmei; Guan Jitian; Chen Yexi; He Jiankang; Qi Weili; Wang Xinjia; Shen Zhiwei; Wu Renhua

2009-01-01

Purpose: Functional MR imaging of the human cervical spinal cord was carried out on volunteers during alternated rest and a complex finger tapping task, in order to detect image intensity changes arising from neuronal activity. Methods: Functional MR imaging data using single-shot fast spin-echo sequence (SSFSE) with echo time 42.4 ms on a 1.5 T GE Clinical System were acquired in eight subjects performing a complex finger tapping task. Cervical spinal cord activation was measured both in the sagittal and transverse imaging planes. Postprocessing was performed by AFNI (Analysis of Functional Neuroimages) software system. Results: Intensity changes (5.5-7.6%) were correlated with the time course of stimulation and were consistently detected in both sagittal and transverse imaging planes of the cervical spinal cord. The activated regions localized to the ipsilateral side of the spinal cord in agreement with the neural anatomy. Conclusion: Functional MR imaging signals can be reliably detected with finger tapping activity in the human cervical spinal cord using a SSFSE sequence with 42.4 ms echo time. The anatomic location of neural activity correlates with the muscles used in the finger tapping task.

Complex programmable logic device based alarm sequencer for nuclear power plants

International Nuclear Information System (INIS)

Khedkar, Ravindra; Solomon, J. Selva; KrishnaKumar, B.

2001-01-01

Complex Programmable Logic Device based Alarm Sequencer is an instrument, which detects alarms, memorizes them and displays the sequences of occurrence of alarms. It caters to sixteen alarm signals and distinguishes the sequence among any two alarms with a time resolution of 1 ms. The system described has been designed for continuous operation in process plants, nuclear power plants etc. The system has been tested and found to be working satisfactorily. (author)

Complex proofs of real theorems

CERN Document Server

Lax, Peter D

2011-01-01

Complex Proofs of Real Theorems is an extended meditation on Hadamard's famous dictum, "The shortest and best way between two truths of the real domain often passes through the imaginary one." Directed at an audience acquainted with analysis at the first year graduate level, it aims at illustrating how complex variables can be used to provide quick and efficient proofs of a wide variety of important results in such areas of analysis as approximation theory, operator theory, harmonic analysis, and complex dynamics. Topics discussed include weighted approximation on the line, Müntz's theorem, Toeplitz operators, Beurling's theorem on the invariant spaces of the shift operator, prediction theory, the Riesz convexity theorem, the Paley-Wiener theorem, the Titchmarsh convolution theorem, the Gleason-Kahane-Żelazko theorem, and the Fatou-Julia-Baker theorem. The discussion begins with the world's shortest proof of the fundamental theorem of algebra and concludes with Newman's almost effortless proof of the prime ...

A New Fractional-Order Chaotic Complex System and Its Antisynchronization

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Cuimei Jiang

2014-01-01

with phase portraits, bifurcation diagrams, the histories, and the largest Lyapunov exponents. And we find that chaos exists in this system with orders less than 5 by numerical simulation. Additionally, antisynchronization of different fractional-order chaotic complex systems is considered based on the stability theory of fractional-order systems. This new system and the fractional-order complex Lorenz system can achieve antisynchronization. Corresponding numerical simulations show the effectiveness and feasibility of the scheme.

A hybrid metaheuristic method to optimize the order of the sequences in continuous-casting

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Achraf Touil

2016-06-01

Full Text Available In this paper, we propose a hybrid metaheuristic algorithm to maximize the production and to minimize the processing time in the steel-making and continuous casting (SCC by optimizing the order of the sequences where a sequence is a group of jobs with the same chemical characteristics. Based on the work Bellabdaoui and Teghem (2006 [Bellabdaoui, A., & Teghem, J. (2006. A mixed-integer linear programming model for the continuous casting planning. International Journal of Production Economics, 104(2, 260-270.], a mixed integer linear programming for scheduling steelmaking continuous casting production is presented to minimize the makespan. The order of the sequences in continuous casting is assumed to be fixed. The main contribution is to analyze an additional way to determine the optimal order of sequences. A hybrid method based on simulated annealing and genetic algorithm restricted by a tabu list (SA-GA-TL is addressed to obtain the optimal order. After parameter tuning of the proposed algorithm, it is tested on different instances using a.NET application and the commercial software solver Cplex v12.5. These results are compared with those obtained by SA-TL (simulated annealing restricted by tabu list.

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

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Yu-Chih Tsai

2016-02-01

Full Text Available Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation.

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

Science.gov (United States)

Tsai, Yu-Chih; Deming, Clayton; Segre, Julia A.; Kong, Heidi H.; Korlach, Jonas

2016-01-01

ABSTRACT Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation. PMID:26861018

Quantum Privacy Amplification for a Sequence of Single Qubits

International Nuclear Information System (INIS)

Deng Fuguo; Long Guilu

2006-01-01

We present a scheme for quantum privacy amplification (QPA) for a sequence of single qubits. The QPA procedure uses a unitary operation with two controlled-not gates and a Hadamard gate. Every two qubits are performed with the unitary gate operation, and a measurement is made on one photon and the other one is retained. The retained qubit carries the state information of the discarded one. In this way, the information leakage is reduced. The procedure can be performed repeatedly so that the information leakage is reduced to any arbitrarily low level. With this QPA scheme, the quantum secure direct communication with single qubits can be implemented with arbitrarily high security. We also exploit this scheme to do privacy amplification on the single qubits in quantum information sharing for long-distance communication with quantum repeaters.

A CU-Level Rate and Distortion Estimation Scheme for RDO of Hardware-Friendly HEVC Encoders Using Low-Complexity Integer DCTs.

Science.gov (United States)

Lee, Bumshik; Kim, Munchurl

2016-08-01

In this paper, a low complexity coding unit (CU)-level rate and distortion estimation scheme is proposed for High Efficiency Video Coding (HEVC) hardware-friendly implementation where a Walsh-Hadamard transform (WHT)-based low-complexity integer discrete cosine transform (DCT) is employed for distortion estimation. Since HEVC adopts quadtree structures of coding blocks with hierarchical coding depths, it becomes more difficult to estimate accurate rate and distortion values without actually performing transform, quantization, inverse transform, de-quantization, and entropy coding. Furthermore, DCT for rate-distortion optimization (RDO) is computationally high, because it requires a number of multiplication and addition operations for various transform block sizes of 4-, 8-, 16-, and 32-orders and requires recursive computations to decide the optimal depths of CU or transform unit. Therefore, full RDO-based encoding is highly complex, especially for low-power implementation of HEVC encoders. In this paper, a rate and distortion estimation scheme is proposed in CU levels based on a low-complexity integer DCT that can be computed in terms of WHT whose coefficients are produced in prediction stages. For rate and distortion estimation in CU levels, two orthogonal matrices of 4×4 and 8×8 , which are applied to WHT that are newly designed in a butterfly structure only with addition and shift operations. By applying the integer DCT based on the WHT and newly designed transforms in each CU block, the texture rate can precisely be estimated after quantization using the number of non-zero quantized coefficients and the distortion can also be precisely estimated in transform domain without de-quantization and inverse transform required. In addition, a non-texture rate estimation is proposed by using a pseudoentropy code to obtain accurate total rate estimates. The proposed rate and the distortion estimation scheme can effectively be used for HW-friendly implementation of

Markovian Model in High Order Sequence Prediction From Log-Motif Patterns in Agbada Paralic Section, Niger Delta, Nigeria

International Nuclear Information System (INIS)

Olabode, S. O.; Adekoya, J. A.

2002-01-01

Markovian model in the elucidation of high order sequence was applied to repetitive events of regressive and transgressive phases in the Agbada paralic section Niger Delta. The repetitive events are made up of delta front, delta topset and fluvio-deltaic sediments. The sediments consist of sands, sandstones, siltstones and shales in various proportions. Five wells: MN1, AA1, NP2, NP6 and NP8 were studied.Summary of biostratigraphic report and well log-motif patterns was used to delineate the third order depositional sequences in the wells.Various Markovian properties - observed transition frequency matrix, observed transition probability matrix, fixed probability vector, expected random matrix (randomised transition matrix) and difference matrix were determined for stacked high order sequence (high frequency cyclic events) nested within the third-order sequences using the log-motif patterns for the various sand bodies and shales. Flow diagrams were constructed for each of the depositional sequences to know the likely occurrence of number of cycles.Upward transition matrix between the log-motif patterns and flow diagram to elucidate cyclicity show that the overall regressive sequence of the Niger Delta has been modified by deltaic depositional elements and fluctuations in sea level. The predictions of higher order sequence within third order sequences from Markovian Properties provide good basis for correlation within the depositional sequences. The model has also been used to decipher the dominant depositional processes during the formation of the sequences. Discrete reservoir intervals and seal potentials within the sequences were also predicted from the flow diagrams constructed

Not All Order Memory Is Equal: Test Demands Reveal Dissociations in Memory for Sequence Information

Science.gov (United States)

Jonker, Tanya R.; MacLeod, Colin M.

2017-01-01

Remembering the order of a sequence of events is a fundamental feature of episodic memory. Indeed, a number of formal models represent temporal context as part of the memory system, and memory for order has been researched extensively. Yet, the nature of the code(s) underlying sequence memory is still relatively unknown. Across 4 experiments that…

FINGERPRINT VERIFICATION IN PERSONAL IDENTIFICATION BY APPLYING LOCAL WALSH HADAMARD TRANSFORM AND GABOR COEFFICIENTS

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K N Pushpalatha

2017-05-01

Full Text Available In an era of advanced computer technology world where innumerable services such as access to bank accounts, or access to secured data or entry to some national important organizations require authentication of genuine individual. Among all biometric personal identification systems, fingerprint recognition system is most accurate and economical technology. In this paper we have proposed fingerprint recognition system using Local Walsh Hadamard Transform (LWHT with Phase Magnitude Histograms (PMHs for feature extraction. Fingerprints display oriented texture-like patterns. Gabor filters have the property of capturing global and local texture information from blur or unclear images and filter bank provides the orientation features which are robust to image distortion and rotation. The LWHT algorithm is compared with other two approaches viz., Gabor Coefficients and Directional Features. The three methods are compared using FVC 2006 Finger print database images. It is found from the observation that the values of TSR, FAR and FRR have improved results compared to existing algorithm.

Quasi-projective synchronization of fractional-order complex-valued recurrent neural networks.

Science.gov (United States)

Yang, Shuai; Yu, Juan; Hu, Cheng; Jiang, Haijun

2018-08-01

In this paper, without separating the complex-valued neural networks into two real-valued systems, the quasi-projective synchronization of fractional-order complex-valued neural networks is investigated. First, two new fractional-order inequalities are established by using the theory of complex functions, Laplace transform and Mittag-Leffler functions, which generalize traditional inequalities with the first-order derivative in the real domain. Additionally, different from hybrid control schemes given in the previous work concerning the projective synchronization, a simple and linear control strategy is designed in this paper and several criteria are derived to ensure quasi-projective synchronization of the complex-valued neural networks with fractional-order based on the established fractional-order inequalities and the theory of complex functions. Moreover, the error bounds of quasi-projective synchronization are estimated. Especially, some conditions are also presented for the Mittag-Leffler synchronization of the addressed neural networks. Finally, some numerical examples with simulations are provided to show the effectiveness of the derived theoretical results. Copyright © 2018 Elsevier Ltd. All rights reserved.

Variances as order parameter and complexity measure for random Boolean networks

International Nuclear Information System (INIS)

Luque, Bartolo; Ballesteros, Fernando J; Fernandez, Manuel

2005-01-01

Several order parameters have been considered to predict and characterize the transition between ordered and disordered phases in random Boolean networks, such as the Hamming distance between replicas or the stable core, which have been successfully used. In this work, we propose a natural and clear new order parameter: the temporal variance. We compute its value analytically and compare it with the results of numerical experiments. Finally, we propose a complexity measure based on the compromise between temporal and spatial variances. This new order parameter and its related complexity measure can be easily applied to other complex systems

Variances as order parameter and complexity measure for random Boolean networks

Energy Technology Data Exchange (ETDEWEB)

Luque, Bartolo [Departamento de Matematica Aplicada y EstadIstica, Escuela Superior de Ingenieros Aeronauticos, Universidad Politecnica de Madrid, Plaza Cardenal Cisneros 3, Madrid 28040 (Spain); Ballesteros, Fernando J [Observatori Astronomic, Universitat de Valencia, Ed. Instituts d' Investigacio, Pol. La Coma s/n, E-46980 Paterna, Valencia (Spain); Fernandez, Manuel [Departamento de Matematica Aplicada y EstadIstica, Escuela Superior de Ingenieros Aeronauticos, Universidad Politecnica de Madrid, Plaza Cardenal Cisneros 3, Madrid 28040 (Spain)

2005-02-04

Several order parameters have been considered to predict and characterize the transition between ordered and disordered phases in random Boolean networks, such as the Hamming distance between replicas or the stable core, which have been successfully used. In this work, we propose a natural and clear new order parameter: the temporal variance. We compute its value analytically and compare it with the results of numerical experiments. Finally, we propose a complexity measure based on the compromise between temporal and spatial variances. This new order parameter and its related complexity measure can be easily applied to other complex systems.

Local causal structures, Hadamard states and the principle of local covariance in quantum field theory

Energy Technology Data Exchange (ETDEWEB)

Dappiaggi, Claudio [Erwin Schroedinger Institut fuer Mathematische Physik, Wien (Austria); Pinamonti, Nicola [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Porrmann, Martin [KwaZulu-Natal Univ. (South Africa). Quantum Research Group, School of Physics; National Institute for Theoretical Physics, Durban (South Africa)

2010-01-15

In the framework of the algebraic formulation, we discuss and analyse some new features of the local structure of a real scalar quantum field theory in a strongly causal spacetime. In particular we use the properties of the exponential map to set up a local version of a bulk-to-boundary correspondence. The bulk is a suitable subset of a geodesic neighbourhood of any but fixed point p of the underlying background, while the boundary is a part of the future light cone having p as its own tip. In this regime, we provide a novel notion for the extended *-algebra of Wick polynomials on the said cone and, on the one hand, we prove that it contains the information of the bulk counterpart via an injective *-homomorphism while, on the other hand, we associate to it a distinguished state whose pull-back in the bulk is of Hadamard form. The main advantage of this point of view arises if one uses the universal properties of the exponential map and of the light cone in order to show that, for any two given backgrounds M and M{sup '} and for any two subsets of geodesic neighbourhoods of two arbitrary points, it is possible to engineer the above procedure such that the boundary extended algebras are related via a restriction homomorphism. This allows for the pull-back of boundary states in both spacetimes and, thus, to set up a machinery which permits the comparison of expectation values of local field observables in M and M{sup '}. (orig.)

Local causal structures, Hadamard states and the principle of local covariance in quantum field theory

International Nuclear Information System (INIS)

Dappiaggi, Claudio; Pinamonti, Nicola

2010-01-01

In the framework of the algebraic formulation, we discuss and analyse some new features of the local structure of a real scalar quantum field theory in a strongly causal spacetime. In particular we use the properties of the exponential map to set up a local version of a bulk-to-boundary correspondence. The bulk is a suitable subset of a geodesic neighbourhood of any but fixed point p of the underlying background, while the boundary is a part of the future light cone having p as its own tip. In this regime, we provide a novel notion for the extended *-algebra of Wick polynomials on the said cone and, on the one hand, we prove that it contains the information of the bulk counterpart via an injective *-homomorphism while, on the other hand, we associate to it a distinguished state whose pull-back in the bulk is of Hadamard form. The main advantage of this point of view arises if one uses the universal properties of the exponential map and of the light cone in order to show that, for any two given backgrounds M and M ' and for any two subsets of geodesic neighbourhoods of two arbitrary points, it is possible to engineer the above procedure such that the boundary extended algebras are related via a restriction homomorphism. This allows for the pull-back of boundary states in both spacetimes and, thus, to set up a machinery which permits the comparison of expectation values of local field observables in M and M ' . (orig.)

Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS).

Science.gov (United States)

Lou, Tzu-Fang; Weidmann, Chase A; Killingsworth, Jordan; Tanaka Hall, Traci M; Goldstrohm, Aaron C; Campbell, Zachary T

2017-04-15

RNA-binding proteins (RBPs) collaborate to control virtually every aspect of RNA function. Tremendous progress has been made in the area of global assessment of RBP specificity using next-generation sequencing approaches both in vivo and in vitro. Understanding how protein-protein interactions enable precise combinatorial regulation of RNA remains a significant problem. Addressing this challenge requires tools that can quantitatively determine the specificities of both individual proteins and multimeric complexes in an unbiased and comprehensive way. One approach utilizes in vitro selection, high-throughput sequencing, and sequence-specificity landscapes (SEQRS). We outline a SEQRS experiment focused on obtaining the specificity of a multi-protein complex between Drosophila RBPs Pumilio (Pum) and Nanos (Nos). We discuss the necessary controls in this type of experiment and examine how the resulting data can be complemented with structural and cell-based reporter assays. Additionally, SEQRS data can be integrated with functional genomics data to uncover biological function. Finally, we propose extensions of the technique that will enhance our understanding of multi-protein regulatory complexes assembled onto RNA. Copyright © 2016 Elsevier Inc. All rights reserved.

A sequence-based survey of the complex structural organization of tumor genomes

Energy Technology Data Exchange (ETDEWEB)

Collins, Colin; Raphael, Benjamin J.; Volik, Stanislav; Yu, Peng; Wu, Chunxiao; Huang, Guiqing; Linardopoulou, Elena V.; Trask, Barbara J.; Waldman, Frederic; Costello, Joseph; Pienta, Kenneth J.; Mills, Gordon B.; Bajsarowicz, Krystyna; Kobayashi, Yasuko; Sridharan, Shivaranjani; Paris, Pamela; Tao, Quanzhou; Aerni, Sarah J.; Brown, Raymond P.; Bashir, Ali; Gray, Joe W.; Cheng, Jan-Fang; de Jong, Pieter; Nefedov, Mikhail; Ried, Thomas; Padilla-Nash, Hesed M.; Collins, Colin C.

2008-04-03

The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using End Sequencing Profiling (ESP), which relies on paired-end sequencing of cloned tumor genomes. In this study, brain, breast, ovary and prostate tumors along with three breast cancer cell lines were surveyed with ESP yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization (FISH) confirmed translocations and complex tumor genome structures that include coamplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison of the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms (SNPs) revealed candidate somatic mutations and an elevated rate of novel SNPs in an ovarian tumor. These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than previously appreciated and that genomic fusions including fusion transcripts and proteins may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.

'End of life' conversations, appreciation sequences, and the interaction order in cancer clinics.

Science.gov (United States)

Maynard, Douglas W; Cortez, Dagoberto; Campbell, Toby C

2016-01-01

To address the organization of conversations in oncology visits by taking an "interaction order" perspective and asking how these visits are intrinsically organized. Conversation analysis. Using audio recordings of talk in oncology visits involving patients with non-small cell lung cancer, we identify and analyze an "appreciation sequence" that is designed to elicit patients' understanding and positive assessment of treatments in terms of their prolongation of life. An "appreciation sequence," regularly initiated after the delivery of scan results and/or treatment recommendations, simultaneously reminds patients of their mortality while suggesting that the treatment received has prolonged their lives, and in some cases significantly beyond the median time of survival. We explore the functions of the appreciation sequence for cancer care and set the stage for considering where and when physicians have choices about the order and direction the talk can take and how to allocate time for end of life and quality of life conversations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Observing complex action sequences: The role of the fronto-parietal mirror neuron system.

Science.gov (United States)

Molnar-Szakacs, Istvan; Kaplan, Jonas; Greenfield, Patricia M; Iacoboni, Marco

2006-11-15

A fronto-parietal mirror neuron network in the human brain supports the ability to represent and understand observed actions allowing us to successfully interact with others and our environment. Using functional magnetic resonance imaging (fMRI), we wanted to investigate the response of this network in adults during observation of hierarchically organized action sequences of varying complexity that emerge at different developmental stages. We hypothesized that fronto-parietal systems may play a role in coding the hierarchical structure of object-directed actions. The observation of all action sequences recruited a common bilateral network including the fronto-parietal mirror neuron system and occipito-temporal visual motion areas. Activity in mirror neuron areas varied according to the motoric complexity of the observed actions, but not according to the developmental sequence of action structures, possibly due to the fact that our subjects were all adults. These results suggest that the mirror neuron system provides a fairly accurate simulation process of observed actions, mimicking internally the level of motoric complexity. We also discuss the results in terms of the links between mirror neurons, language development and evolution.

Distinguished quantum states in a class of cosmological spacetimes and their Hadamard property

Energy Technology Data Exchange (ETDEWEB)

Dappiaggi, Claudio; Pinamonti, Nicola [Hamburg Univ. (Germany). II. Inst. fuer Theoretische Physik; Moretti, Valter [Trento Univ. (Italy). Dipt. di Matematica; Ist. Nazionale di Alta Matematica, Unita locale di Trento (Italy); Ist. Nazionale di Fisica, Povo (Italy)

2008-12-15

In a recent paper, we proved that a large class of spacetimes, not necessarily homogeneous or isotropic and relevant at a cosmological level, possesses a preferred codimension one submanifold, i.e., the past cosmological horizon, on which it is possible to encode the information of a scalar field theory living in the bulk. Such bulk-to-boundary reconstruction procedure entails the identification of a preferred quasifree algebraic state for the bulk theory, enjoying remarkable properties concerning invariance under isometries (if any) of the bulk and energy positivity, and reducing to well-known vacua in standard situations. In this paper, specialising to open FRW models, we extend previously obtained results and we prove that the preferred state is of Hadamard form, hence the backreaction on the metric is finite and the state can be used as a starting point for renormalisation procedures. That state could play a distinguished role in the discussion of the evolution of scalar fluctuations of the metric, an analysis often performed in the development of any model describing the dynamic of an early Universe which undergoes an inflationary phase of rapid expansion in the past. (orig.)

Distinguished quantum states in a class of cosmological spacetimes and their Hadamard property

International Nuclear Information System (INIS)

Dappiaggi, Claudio; Pinamonti, Nicola

2008-12-01

In a recent paper, we proved that a large class of spacetimes, not necessarily homogeneous or isotropic and relevant at a cosmological level, possesses a preferred codimension one submanifold, i.e., the past cosmological horizon, on which it is possible to encode the information of a scalar field theory living in the bulk. Such bulk-to-boundary reconstruction procedure entails the identification of a preferred quasifree algebraic state for the bulk theory, enjoying remarkable properties concerning invariance under isometries (if any) of the bulk and energy positivity, and reducing to well-known vacua in standard situations. In this paper, specialising to open FRW models, we extend previously obtained results and we prove that the preferred state is of Hadamard form, hence the backreaction on the metric is finite and the state can be used as a starting point for renormalisation procedures. That state could play a distinguished role in the discussion of the evolution of scalar fluctuations of the metric, an analysis often performed in the development of any model describing the dynamic of an early Universe which undergoes an inflationary phase of rapid expansion in the past. (orig.)

Decay of Complex-Time Determinantal and Pfaffian Correlation Functionals in Lattices

Science.gov (United States)

Aza, N. J. B.; Bru, J.-B.; de Siqueira Pedra, W.

2018-06-01

We supplement the determinantal and Pfaffian bounds of Sims and Warzel (Commun Math Phys 347:903-931, 2016) for many-body localization of quasi-free fermions, by considering the high dimensional case and complex-time correlations. Our proof uses the analyticity of correlation functions via the Hadamard three-line theorem. We show that the dynamical localization for the one-particle system yields the dynamical localization for the many-point fermionic correlation functions, with respect to the Hausdorff distance in the determinantal case. In Sims and Warzel (2016), a stronger notion of decay for many-particle configurations was used but only at dimension one and for real times. Considering determinantal and Pfaffian correlation functionals for complex times is important in the study of weakly interacting fermions.

Decay of Complex-Time Determinantal and Pfaffian Correlation Functionals in Lattices

Science.gov (United States)

Aza, N. J. B.; Bru, J.-B.; de Siqueira Pedra, W.

2018-04-01

We supplement the determinantal and Pfaffian bounds of Sims and Warzel (Commun Math Phys 347:903-931, 2016) for many-body localization of quasi-free fermions, by considering the high dimensional case and complex-time correlations. Our proof uses the analyticity of correlation functions via the Hadamard three-line theorem. We show that the dynamical localization for the one-particle system yields the dynamical localization for the many-point fermionic correlation functions, with respect to the Hausdorff distance in the determinantal case. In Sims and Warzel (2016), a stronger notion of decay for many-particle configurations was used but only at dimension one and for real times. Considering determinantal and Pfaffian correlation functionals for complex times is important in the study of weakly interacting fermions.

Distinguishing cognitive state with multifractal complexity of hippocampal interspike interval sequences

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Dustin eFetterhoff

2015-09-01

Full Text Available Fractality, represented as self-similar repeating patterns, is ubiquitous in nature and the brain. Dynamic patterns of hippocampal spike trains are known to exhibit multifractal properties during working memory processing; however, it is unclear whether the multifractal properties inherent to hippocampal spike trains reflect active cognitive processing. To examine this possibility, hippocampal neuronal ensembles were recorded from rats before, during and after a spatial working memory task following administration of tetrahydrocannabinol (THC, a memory-impairing component of cannabis. Multifractal detrended fluctuation analysis was performed on hippocampal interspike interval sequences to determine characteristics of monofractal long-range temporal correlations (LRTCs, quantified by the Hurst exponent, and the degree/magnitude of multifractal complexity, quantified by the width of the singularity spectrum. Our results demonstrate that multifractal firing patterns of hippocampal spike trains are a marker of functional memory processing, as they are more complex during the working memory task and significantly reduced following administration of memory impairing THC doses. Conversely, LRTCs are largest during resting state recordings, therefore reflecting different information compared to multifractality. In order to deepen conceptual understanding of multifractal complexity and LRTCs, these measures were compared to classical methods using hippocampal frequency content and firing variability measures. These results showed that LRTCs, multifractality, and theta rhythm represent independent processes, while delta rhythm correlated with multifractality. Taken together, these results provide a novel perspective on memory function by demonstrating that the multifractal nature of spike trains reflects hippocampal microcircuit activity that can be used to detect and quantify cognitive, physiological and pathological states.

Complexity Analysis and DSP Implementation of the Fractional-Order Lorenz Hyperchaotic System

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Shaobo He

2015-12-01

Full Text Available The fractional-order hyperchaotic Lorenz system is solved as a discrete map by applying the Adomian decomposition method (ADM. Lyapunov Characteristic Exponents (LCEs of this system are calculated according to this deduced discrete map. Complexity of this system versus parameters are analyzed by LCEs, bifurcation diagrams, phase portraits, complexity algorithms. Results show that this system has rich dynamical behaviors. Chaos and hyperchaos can be generated by decreasing fractional order q in this system. It also shows that the system is more complex when q takes smaller values. SE and C 0 complexity algorithms provide a parameter choice criteria for practice applications of fractional-order chaotic systems. The fractional-order system is implemented by digital signal processor (DSP, and a pseudo-random bit generator is designed based on the implemented system, which passes the NIST test successfully.

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.

Science.gov (United States)

Liu, Bin; Liu, Fule; Fang, Longyun; Wang, Xiaolong; Chou, Kuo-Chen

2015-04-15

In order to develop powerful computational predictors for identifying the biological features or attributes of DNAs, one of the most challenging problems is to find a suitable approach to effectively represent the DNA sequences. To facilitate the studies of DNAs and nucleotides, we developed a Python package called representations of DNAs (repDNA) for generating the widely used features reflecting the physicochemical properties and sequence-order effects of DNAs and nucleotides. There are three feature groups composed of 15 features. The first group calculates three nucleic acid composition features describing the local sequence information by means of kmers; the second group calculates six autocorrelation features describing the level of correlation between two oligonucleotides along a DNA sequence in terms of their specific physicochemical properties; the third group calculates six pseudo nucleotide composition features, which can be used to represent a DNA sequence with a discrete model or vector yet still keep considerable sequence-order information via the physicochemical properties of its constituent oligonucleotides. In addition, these features can be easily calculated based on both the built-in and user-defined properties via using repDNA. The repDNA Python package is freely accessible to the public at http://bioinformatics.hitsz.edu.cn/repDNA/. bliu@insun.hit.edu.cn or kcchou@gordonlifescience.org Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences

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Charalambos Chrysostomou

2015-01-01

Full Text Available Complex informational spectrum analysis for protein sequences (CISAPS and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.

Outer synchronization between two different fractional-order general complex dynamical networks

International Nuclear Information System (INIS)

Xiang-Jun, Wu; Hong-Tao, Lu

2010-01-01

Outer synchronization between two different fractional-order general complex dynamical networks is investigated in this paper. Based on the stability theory of the fractional-order system, the sufficient criteria for outer synchronization are derived analytically by applying the nonlinear control and the bidirectional coupling methods. The proposed synchronization method is applicable to almost all kinds of coupled fractional-order general complex dynamical networks. Neither a symmetric nor irreducible coupling configuration matrix is required. In addition, no constraint is imposed on the inner-coupling matrix. Numerical examples are also provided to demonstrate the validity of the presented synchronization scheme. Numeric evidence shows that both the feedback strength k and the fractional order α can be chosen appropriately to adjust the synchronization effect effectively. (general)

The Pagoda Sequence: a Ramble through Linear Complexity, Number Walls, D0L Sequences, Finite State Automata, and Aperiodic Tilings

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Fred Lunnon

2009-06-01

Full Text Available We review the concept of the number wall as an alternative to the traditional linear complexity profile (LCP, and sketch the relationship to other topics such as linear feedback shift-register (LFSR and context-free Lindenmayer (D0L sequences. A remarkable ternary analogue of the Thue-Morse sequence is introduced having deficiency 2 modulo 3, and this property verified via the re-interpretation of the number wall as an aperiodic plane tiling.

The order of prenominal adjectives in natural language generation

NARCIS (Netherlands)

Malouf, R; et, al.

2000-01-01

The order of prenominal adjectival modifiers in English is governed by complex and difficult to describe constraints which straddle the boundary between competence and performance. This paper describes and compares a number of statistical and machine learning techniques for ordering sequences of

Characterization of Aftershock Sequences from Large Strike-Slip Earthquakes Along Geometrically Complex Faults

Science.gov (United States)

Sexton, E.; Thomas, A.; Delbridge, B. G.

2017-12-01

Large earthquakes often exhibit complex slip distributions and occur along non-planar fault geometries, resulting in variable stress changes throughout the region of the fault hosting aftershocks. To better discern the role of geometric discontinuities on aftershock sequences, we compare areas of enhanced and reduced Coulomb failure stress and mean stress for systematic differences in the time dependence and productivity of these aftershock sequences. In strike-slip faults, releasing structures, including stepovers and bends, experience an increase in both Coulomb failure stress and mean stress during an earthquake, promoting fluid diffusion into the region and further failure. Conversely, Coulomb failure stress and mean stress decrease in restraining bends and stepovers in strike-slip faults, and fluids diffuse away from these areas, discouraging failure. We examine spatial differences in seismicity patterns along structurally complex strike-slip faults which have hosted large earthquakes, such as the 1992 Mw 7.3 Landers, the 2010 Mw 7.2 El-Mayor Cucapah, the 2014 Mw 6.0 South Napa, and the 2016 Mw 7.0 Kumamoto events. We characterize the behavior of these aftershock sequences with the Epidemic Type Aftershock-Sequence Model (ETAS). In this statistical model, the total occurrence rate of aftershocks induced by an earthquake is λ(t) = λ_0 + \\sum_{i:t_i

Key Issues in Modeling of Complex 3D Structures from Video Sequences

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Shengyong Chen

2012-01-01

Full Text Available Construction of three-dimensional structures from video sequences has wide applications for intelligent video analysis. This paper summarizes the key issues of the theory and surveys the recent advances in the state of the art. Reconstruction of a scene object from video sequences often takes the basic principle of structure from motion with an uncalibrated camera. This paper lists the typical strategies and summarizes the typical solutions or algorithms for modeling of complex three-dimensional structures. Open difficult problems are also suggested for further study.

An accurate evaluation of the performance of asynchronous DS-CDMA systems with zero-correlation-zone coding in Rayleigh fading

Science.gov (United States)

Walker, Ernest; Chen, Xinjia; Cooper, Reginald L.

2010-04-01

An arbitrarily accurate approach is used to determine the bit-error rate (BER) performance for generalized asynchronous DS-CDMA systems, in Gaussian noise with Raleigh fading. In this paper, and the sequel, new theoretical work has been contributed which substantially enhances existing performance analysis formulations. Major contributions include: substantial computational complexity reduction, including a priori BER accuracy bounding; an analytical approach that facilitates performance evaluation for systems with arbitrary spectral spreading distributions, with non-uniform transmission delay distributions. Using prior results, augmented by these enhancements, a generalized DS-CDMA system model is constructed and used to evaluated the BER performance, in a variety of scenarios. In this paper, the generalized system modeling was used to evaluate the performance of both Walsh- Hadamard (WH) and Walsh-Hadamard-seeded zero-correlation-zone (WH-ZCZ) coding. The selection of these codes was informed by the observation that WH codes contain N spectral spreading values (0 to N - 1), one for each code sequence; while WH-ZCZ codes contain only two spectral spreading values (N/2 - 1,N/2); where N is the sequence length in chips. Since these codes span the spectral spreading range for DS-CDMA coding, by invoking an induction argument, the generalization of the system model is sufficiently supported. The results in this paper, and the sequel, support the claim that an arbitrary accurate performance analysis for DS-CDMA systems can be evaluated over the full range of binary coding, with minimal computational complexity.

Representation of the quantum Fourier transform on multilevel basic elements by a sequence of selective rotation operators

Science.gov (United States)

Ermilov, A. S.; Zobov, V. E.

2007-12-01

To experimentally realize quantum computations on d-level basic elements (qudits) at d > 2, it is necessary to develop schemes for the technical realization of elementary logical operators. We have found sequences of selective rotation operators that represent the operators of the quantum Fourier transform (Walsh-Hadamard matrices) for d = 3-10. For the prime numbers 3, 5, and 7, the well-known method of linear algebra is applied, whereas, for the factorable numbers 6, 9, and 10, the representation of virtual spins is used (which we previously applied for d = 4, 8). Selective rotations can be realized, for example, by means of pulses of an RF magnetic field for systems of quadrupole nuclei or laser pulses for atoms and ions in traps.

Protein scaffolds and higher-order complexes in synthetic biology

NARCIS (Netherlands)

den Hamer, A.; Rosier, B.J.H.M.; Brunsveld, L.; de Greef, T.F.A.; Ryadnov, M.; Brunsveld, L.; Suga, H.

2017-01-01

Interactions between proteins control molecular functions such as signalling or metabolic activity. Assembly of proteins via scaffold proteins or in higher-order complexes is a key regulatory mechanism. Understanding and functionally applying this concept requires the construction, study, and

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

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Martin Mascher

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

An Automated Approach to Very High Order Aeroacoustic Computations in Complex Geometries

Science.gov (United States)

Dyson, Rodger W.; Goodrich, John W.

2000-01-01

Computational aeroacoustics requires efficient, high-resolution simulation tools. And for smooth problems, this is best accomplished with very high order in space and time methods on small stencils. But the complexity of highly accurate numerical methods can inhibit their practical application, especially in irregular geometries. This complexity is reduced by using a special form of Hermite divided-difference spatial interpolation on Cartesian grids, and a Cauchy-Kowalewslci recursion procedure for time advancement. In addition, a stencil constraint tree reduces the complexity of interpolating grid points that are located near wall boundaries. These procedures are used to automatically develop and implement very high order methods (>15) for solving the linearized Euler equations that can achieve less than one grid point per wavelength resolution away from boundaries by including spatial derivatives of the primitive variables at each grid point. The accuracy of stable surface treatments is currently limited to 11th order for grid aligned boundaries and to 2nd order for irregular boundaries.

RNA assemblages orchestrate complex cellular processes

DEFF Research Database (Denmark)

Nielsen, Finn Cilius; Hansen, Heidi Theil; Christiansen, Jan

2016-01-01

Eukaryotic mRNAs are monocistronic, and therefore mechanisms exist that coordinate the synthesis of multiprotein complexes in order to obtain proper stoichiometry at the appropriate intracellular locations. RNA-binding proteins containing low-complexity sequences are prone to generate liquid drop...

A Comparison of Molecular Typing Methods Applied to Enterobacter cloacae complex: hsp60 Sequencing, Rep-PCR, and MLST

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Roberto Viau

2017-02-01

Full Text Available Molecular typing using repetitive sequenced-based PCR (rep-PCR and hsp60 sequencing were applied to a collection of diverse Enterobacter cloacae complex isolates. To determine the most practical method for reference laboratories, we analyzed 71 E. cloacae complex isolates from sporadic and outbreak occurrences originating from 4 geographic areas. While rep-PCR was more discriminating, hsp60 sequencing provided a broader and a more objective geographical tracking method similar to multilocus sequence typing (MLST. In addition, we suggest that MLST may have higher discriminative power compared to hsp60 sequencing, although rep-PCR remains the most discriminative method for local outbreak investigations. In addition, rep-PCR can be an effective and inexpensive method for local outbreak investigation.

Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition.

Science.gov (United States)

Penny, D; Hasegawa, M; Waddell, P J; Hendy, M D

1999-03-01

We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.

Pitch Sequence Complexity and Long-Term Pitcher Performance

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Joel R. Bock

2015-03-01

Full Text Available Winning one or two games during a Major League Baseball (MLB season is often the difference between a team advancing to post-season play, or “waiting until next year”. Technology advances have made it feasible to augment historical data with in-game contextual data to provide managers immediate insights regarding an opponent’s next move, thereby providing a competitive edge. We developed statistical models of pitcher behavior using pitch sequences thrown during three recent MLB seasons (2011–2013. The purpose of these models was to predict the next pitch type, for each pitcher, based on data available at the immediate moment, in each at-bat. Independent models were developed for each player’s most frequent four pitches. The overall predictability of next pitch type is 74:5%. Additional analyses on pitcher predictability within specific game situations are discussed. Finally, using linear regression analysis, we show that an index of pitch sequence predictability may be used to project player performance in terms of Earned Run Average (ERA and Fielding Independent Pitching (FIP over a longer term. On a restricted range of the independent variable, reducing complexity in selection of pitches is correlated with higher values of both FIP and ERA for the players represented in the sample. Both models were significant at the α = 0.05 level (ERA: p = 0.022; FIP: p = 0.0114. With further development, such models may reduce risk faced by management in evaluation of potential trades, or to scouts assessing unproven emerging talent. Pitchers themselves might benefit from awareness of their individual statistical tendencies, and adapt their behavior on the mound accordingly. To our knowledge, the predictive model relating pitch-wise complexity and long-term performance appears to be novel.

On Sequences of Numbers and Polynomials Defined by Linear Recurrence Relations of Order 2

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Tian-Xiao He

2009-01-01

Full Text Available Here we present a new method to construct the explicit formula of a sequence of numbers and polynomials generated by a linear recurrence relation of order 2. The applications of the method to the Fibonacci and Lucas numbers, Chebyshev polynomials, the generalized Gegenbauer-Humbert polynomials are also discussed. The derived idea provides a general method to construct identities of number or polynomial sequences defined by linear recurrence relations. The applications using the method to solve some algebraic and ordinary differential equations are presented.

Higher-Order Structure in Bacterial VapBC Toxin-Antitoxin Complexes

DEFF Research Database (Denmark)

Bendtsen, Kirstine L; Brodersen, Ditlev E

2017-01-01

Toxin-antitoxin systems are widespread in the bacterial kingdom, including in pathogenic species, where they allow rapid adaptation to changing environmental conditions through selective inhibition of key cellular processes, such as DNA replication or protein translation. Under normal growth...... that allow auto-regulation of transcription by direct binding to promoter DNA. In this chapter, we review our current understanding of the structural characteristics of type II toxin-antitoxin complexes in bacterial cells, with a special emphasis on the staggering variety of higher-order architecture...... conditions, type II toxins are inhibited through tight protein-protein interaction with a cognate antitoxin protein. This toxin-antitoxin complex associates into a higher-order macromolecular structure, typically heterotetrameric or heterooctameric, exposing two DNA binding domains on the antitoxin...

Anomalous diffusion measured by a twice-refocused spin echo pulse sequence: analysis using fractional order calculus.

Science.gov (United States)

Gao, Qing; Srinivasan, Girish; Magin, Richard L; Zhou, Xiaohong Joe

2011-05-01

To theoretically develop and experimentally validate a formulism based on a fractional order calculus (FC) diffusion model to characterize anomalous diffusion in brain tissues measured with a twice-refocused spin-echo (TRSE) pulse sequence. The FC diffusion model is the fractional order generalization of the Bloch-Torrey equation. Using this model, an analytical expression was derived to describe the diffusion-induced signal attenuation in a TRSE pulse sequence. To experimentally validate this expression, a set of diffusion-weighted (DW) images was acquired at 3 Tesla from healthy human brains using a TRSE sequence with twelve b-values ranging from 0 to 2600 s/mm(2). For comparison, DW images were also acquired using a Stejskal-Tanner diffusion gradient in a single-shot spin-echo echo planar sequence. For both datasets, a Levenberg-Marquardt fitting algorithm was used to extract three parameters: diffusion coefficient D, fractional order derivative in space β, and a spatial parameter μ (in units of μm). Using adjusted R-squared values and standard deviations, D, β, and μ values and the goodness-of-fit in three specific regions of interest (ROIs) in white matter, gray matter, and cerebrospinal fluid, respectively, were evaluated for each of the two datasets. In addition, spatially resolved parametric maps were assessed qualitatively. The analytical expression for the TRSE sequence, derived from the FC diffusion model, accurately characterized the diffusion-induced signal loss in brain tissues at high b-values. In the selected ROIs, the goodness-of-fit and standard deviations for the TRSE dataset were comparable with the results obtained from the Stejskal-Tanner dataset, demonstrating the robustness of the FC model across multiple data acquisition strategies. Qualitatively, the D, β, and μ maps from the TRSE dataset exhibited fewer artifacts, reflecting the improved immunity to eddy currents. The diffusion-induced signal attenuation in a TRSE pulse sequence

Idaho CERCLA Disposal Facility Complex Compliance Demonstration for DOE Order 435.1

Energy Technology Data Exchange (ETDEWEB)

Simonds, J.

2007-11-06

This compliance demonstration document provides an analysis of the Idaho CERCLA Disposal Facility (ICDF) Complex compliance with DOE Order 435.1. The ICDF Complex includes the disposal facility (landfill), evaporation pond, administration facility, weigh scale, and various staging/storage areas. These facilities were designed and constructed to be compliant with DOE Order 435.1, Resource Conservation and Recovery act Subtitle C, and Toxic Substances Control Act polychlorinated biphenyl design and construction standards. The ICDF Complex is designated as the Idaho National Laboratory (INL) facility for the receipt, staging/storage, treatment, and disposal of INL Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) waste streams.

Complex Quasi-Two-Dimensional Crystalline Order Embedded in VO2 and Other Crystals

Science.gov (United States)

Lovorn, Timothy; Sarker, Sanjoy K.

2017-07-01

Metal oxides such as VO2 undergo structural transitions to low-symmetry phases characterized by intricate crystalline order, accompanied by rich electronic behavior. We derive a minimal ionic Hamiltonian based on symmetry and local energetics which describes structural transitions involving all four observed phases, in the correct order. An exact analysis shows that complexity results from the symmetry-induced constraints of the parent phase, which forces ionic displacements to form multiple interpenetrating groups using low-dimensional pathways and distant neighbors. Displacements within each group exhibit independent, quasi-two-dimensional order, which is frustrated and fragile. This selective ordering mechanism is not restricted to VO2 : it applies to other oxides that show similar complex order.

The power of non-determinism in higher-order implicit complexity

DEFF Research Database (Denmark)

Kop, Cynthia Louisa Martina; Simonsen, Jakob Grue

2017-01-01

We investigate the power of non-determinism in purely functional programming languages with higher-order types. Specifically, we consider cons-free programs of varying data orders, equipped with explicit non-deterministic choice. Cons-freeness roughly means that data constructors cannot occur...... in function bodies and all manipulation of storage space thus has to happen indirectly using the call stack. While cons-free programs have previously been used by several authors to characterise complexity classes, the work on non-deterministic programs has almost exclusively considered programs of data order...... 0. Previous work has shown that adding explicit non-determinism to consfree programs taking data of order 0 does not increase expressivity; we prove that this—dramatically—is not the case for higher data orders: adding non-determinism to programs with data order at least 1 allows...

Using nanopore sequencing to get complete genomes from complex samples

DEFF Research Database (Denmark)

Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Nielsen, Per Halkjær

The advantages of “next generation sequencing” has come at the cost of genome finishing. The dominant sequencing technology provides short reads of 150-300 bp, which has made genome assembly very difficult as the reads do not span important repeat regions. Genomes have thus been added...... to the databases as fragmented assemblies and not as finished contigs that resemble the chromosomes in which the DNA is organised within the cells. This is especially troublesome for genomes derived from complex metagenome sequencing. Databases with incomplete genomes can lead to false conclusions about...... the absence of genes and functional predictions of the organisms. Furthermore, it is common that repetitive elements and marker genes such as the 16S rRNA gene are missing completely from these genome bins. Using nanopore long reads, we demonstrate that it is possible to span these regions and make complete...

Rigorous construction and Hadamard property of the Unruh state in Schwarzschild spacetime

International Nuclear Information System (INIS)

Dappiaggi, Claudio; Pinamonti, Nicola

2009-07-01

The discovery of the radiation properties of black holes prompted the search for a natural candidate quantum ground state for a massless scalar field theory on Schwarzschild spacetime, here considered in the Eddington-Finkelstein representation. Among the several available proposals in the literature, an important physical role is played by the so-called Unruh state which is supposed to be appropriate to capture the physics of a black hole formed by spherically symmetric collapsing matter. Within this respect, we shall consider a massless Klein-Gordon field and we shall rigorously and globally construct such state, that is on the algebra of Weyl observables localised in the union of the static external region, the future event horizon and the non-static black hole region. Eventually, out of a careful use of microlocal techniques, we prove that the built state fulfils, where defined, the so-called Hadamard condition; hence, it is perturbatively stable, in other words realizing the natural candidate with which one could study purely quantum phenomena such as the role of the back reaction of Hawking's radiation. From a geometrical point of view, we shall make a profitable use of a bulk-to-boundary reconstruction technique which carefully exploits the Killing horizon structure as well as the conformal asymptotic behaviour of the underlying background. From an analytical point of view, our tools will range from Hoermander's theorem on propagation of singularities, results on the role of passive states, and a detailed use of the recently discovered peeling behaviour of the solutions of the wave equation in Schwarzschild spacetime. (orig.)

Rigorous construction and Hadamard property of the Unruh state in Schwarzschild spacetime

Energy Technology Data Exchange (ETDEWEB)

Dappiaggi, Claudio; Pinamonti, Nicola [Hamburg Univ. (Germany). II. Inst. fuer Theoretische Physik; Moretti, Valter [Trento Univ., Povo (Italy). Dipt. di Matematica; Istituto Nazionale di Fisica Nucleare, Povo (Italy); Istituto Nazionale di Alta Matematica ' ' F. Severi' ' , GNFM, Sesto Fiorentino (Italy)

2009-07-15

The discovery of the radiation properties of black holes prompted the search for a natural candidate quantum ground state for a massless scalar field theory on Schwarzschild spacetime, here considered in the Eddington-Finkelstein representation. Among the several available proposals in the literature, an important physical role is played by the so-called Unruh state which is supposed to be appropriate to capture the physics of a black hole formed by spherically symmetric collapsing matter. Within this respect, we shall consider a massless Klein-Gordon field and we shall rigorously and globally construct such state, that is on the algebra of Weyl observables localised in the union of the static external region, the future event horizon and the non-static black hole region. Eventually, out of a careful use of microlocal techniques, we prove that the built state fulfils, where defined, the so-called Hadamard condition; hence, it is perturbatively stable, in other words realizing the natural candidate with which one could study purely quantum phenomena such as the role of the back reaction of Hawking's radiation. From a geometrical point of view, we shall make a profitable use of a bulk-to-boundary reconstruction technique which carefully exploits the Killing horizon structure as well as the conformal asymptotic behaviour of the underlying background. From an analytical point of view, our tools will range from Hoermander's theorem on propagation of singularities, results on the role of passive states, and a detailed use of the recently discovered peeling behaviour of the solutions of the wave equation in Schwarzschild spacetime. (orig.)

Adaptive Synchronization of Fractional Order Complex-Variable Dynamical Networks via Pinning Control

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Ding, Da-Wei; Yan, Jie; Wang, Nian; Liang, Dong

2017-09-01

In this paper, the synchronization of fractional order complex-variable dynamical networks is studied using an adaptive pinning control strategy based on close center degree. Some effective criteria for global synchronization of fractional order complex-variable dynamical networks are derived based on the Lyapunov stability theory. From the theoretical analysis, one concludes that under appropriate conditions, the complex-variable dynamical networks can realize the global synchronization by using the proper adaptive pinning control method. Meanwhile, we succeed in solving the problem about how much coupling strength should be applied to ensure the synchronization of the fractional order complex networks. Therefore, compared with the existing results, the synchronization method in this paper is more general and convenient. This result extends the synchronization condition of the real-variable dynamical networks to the complex-valued field, which makes our research more practical. Finally, two simulation examples show that the derived theoretical results are valid and the proposed adaptive pinning method is effective. Supported by National Natural Science Foundation of China under Grant No. 61201227, National Natural Science Foundation of China Guangdong Joint Fund under Grant No. U1201255, the Natural Science Foundation of Anhui Province under Grant No. 1208085MF93, 211 Innovation Team of Anhui University under Grant Nos. KJTD007A and KJTD001B, and also supported by Chinese Scholarship Council

Evidence for a Complex Mosaic Genome Pattern in a Full-length Hepatitis C Virus Sequence

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R.S. Ross

2008-01-01

Full Text Available The genome of the hepatitis C virus (HCV exhibits a high genetic variability. This remarkable heterogeneity is mainly attributed to the gradual accumulation of mutational changes, whereas the contribution of recombination events to the evolution of HCV remains controversial so far. While performing phylogenetic analyses including a large number of sequences deposited in the GenBank, we encountered a full-length HCV sequence (AY651061 that showed evidence for inter-subtype recombination and was, therefore, subjected to a detailed analysis of its molecular structure. The obtained results indicated that AY651061 does not represent a “simple” HCV 1c isolate, but a complex 1a/1c mosaic genome, showing five putative breakpoints in the core to NS3 regions. To our knowledge, this is the first report on a mosaic HCV full- length sequence with multiple breakpoints. The molecular structure of AY651061 is reminiscent of complex homologous recombinant variants occurring among other members of the flaviviridae family, e.g. GB virus C, dengue virus, and Japanese encephalitis virus. Our finding of a mosaic HCV sequence may have important implications for many fields of current HCV research which merit careful consideration.

Importance of the temporal structure of movement sequences on the ability of monkeys to use serial order information.

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Deffains, Marc; Legallet, Eric; Apicella, Paul

2011-10-01

The capacity to acquire motor skills through repeated practice of a sequence of movements underlies many everyday activities. Extensive research in humans has dealt with the importance of spatial and temporal factors on motor sequence learning, standing in contrast to the few studies available in animals, particularly in nonhuman primates. In the present experiments, we studied the effect of the serial order of stimuli and associated movements in macaque monkeys overtrained to make arm-reaching movements in response to spatially distinct visual targets. Under different conditions, the temporal structure of the motor sequence was varied by changing the duration of the interval between successive target stimuli or by adding a cue that reliably signaled the onset time of the forthcoming target stimulus. In each condition, the extent to which the monkeys are sensitive to the spatial regularities was assessed by comparing performance when stimulus locations follow a repeating sequence, as opposed to a random sequence. We observed no improvement in task performance on repeated sequence blocks, compared to random sequence blocks, when target stimuli are relatively distant from each other in time. On the other hand, the shortening of the time interval between successive target stimuli or, more efficiently, the addition of a temporal cue before the target stimulus yielded a performance advantage under repeated sequence, reflected in a decrease in the latency of arm and saccadic eye movements accompanied by an increased tendency for eye movements to occur in an anticipatory manner. Contrary to the effects on movement initiation, the serial order of stimuli and movements did not markedly affect the execution of movement. Moreover, the location of a given target in the random sequence influenced task performance based on the location of the preceding target, monkeys being faster in responding as a result of familiarity caused by extensive practice with some target transitions

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

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Scholz, Christian F P; Jensen, Anders

2017-01-01

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

Perbandingan Algoritma Simulated Annealing dan Harmony Search dalam Penerapan Picking Order Sequence

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Tanti Octavia

2017-12-01

Full Text Available Implementation of mobile rack warehouse is commonly used in manufacturing industry because it can minimize the warehouse area used. Applying picking orders in taking of Stock Keeping Unit (SKU on mobile rack warehouses could give fast loading order. This research aims to find out which algorithm is better in applying picking order sequence in mobile rack warehouse. The algorithm used is Simualted Annealing (SA and Harmony Search (HS algorithm. Both of these algorithms will be compared in terms of the gap with the shortest path method.The result shows that the HS algorithm produces a better solution than the SA algorithm with lower CPU time, but the convergence rate of HS is lower than that of SA.HS was able to produce a better solution than the shortest path method of 9 cases, while SA only 8 cases from 15 cases.

Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex

OpenAIRE

Hand, Melanie L.; Spangenberg, German C.; Forster, John W.; Cogan, Noel O. I.

2013-01-01

Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca...

Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T.

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Ronald M Weiner

2008-05-01

Full Text Available The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40 is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.

Idaho CERCLA Disposal Facility Complex Compliance Demonstration for DOE Order 435.1

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J. Simonds

2006-09-01

This compliance demonstration document provides an analysis of the Idaho CERCLA Disposal Facility (ICDF) Complex compliance with DOE Order 435.1. The ICDF Complex includes the disposal facility (landfill), evaporation pond, admin facility, weigh scale, decon building, treatment systems, and various staging/storage areas. These facilities were designed and are being constructed to be compliant with DOE Order 435.1, Resource Conservation and Recovery Act Subtitle C, and Toxic Substances Control Act polychlorinated biphenyl design and construction standards. The ICDF Complex is designated as the central Idaho National Laboratory (INL) facilityyy for the receipt, staging/storage, treatment, and disposal of INL Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) waste streams. This compliance demonstration document discusses the conceptual site model for the ICDF Complex area. Within this conceptual site model, the selection of the area for the ICDF Complex is discussed. Also, the subsurface stratigraphy in the ICDF Complex area is discussed along with the existing contamination beneath the ICDF Complex area. The designs for the various ICDF Complex facilities are also included in this compliance demonstration document. These design discussions are a summary of the design as presented in the Remedial Design/Construction Work Plans for the ICDF landfill and evaporation pond and the Staging, Storage, Sizing, and Treatment Facility. Each of the major facilities or systems is described including the design criteria.

Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome.

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Belova, Tatiana; Grønvold, Lars; Kumar, Ajay; Kianian, Shahryar; He, Xinyao; Lillemo, Morten; Springer, Nathan M; Lien, Sigbjørn; Olsen, Odd-Arne; Sandve, Simen R

2014-09-01

A total of 3,671 sequence contigs and scaffolds were mapped to deletion bins on wheat chromosome 7B providing a foundation for developing high-resolution integrated physical map for this chromosome. Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC) we are focused on assembling a reference sequence for chromosome 7B. The successful completion of the reference chromosome sequence is highly dependent on the integration of genetic and physical maps. To aid the integration of these two types of maps, we have constructed a high-density deletion bin map of chromosome 7B. Using the 270 K Nimblegen comparative genomic hybridization (CGH) array on a set of cv. Chinese spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8 % of chromosome 7B physical length) were mapped into nine deletion bins. Our method of genotyping deletions on chromosome 7B relied on a model-based clustering algorithm (Mclust) to accurately predict the presence or absence of a given genomic sequence in a deletion line. The bin mapping results were validated using three different approaches, viz. (a) PCR-based amplification of randomly selected bin mapped sequences (b) comparison with previously mapped ESTs and (c) comparison with a 7B genetic map developed in the present study. Validation of the bin mapping results suggested a high accuracy of the assignment of 7B sequence contigs and scaffolds to the 7B deletion bins.

Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

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Chao Shiaoman

2011-01-01

Full Text Available Abstract Background Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. Results Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM analysis. Of these, 52 (54% were polymorphic between parents of the Ogle1040 × TAM O-301 (OT mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry. Conclusions The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide

Basal ganglia and cortical networks for sequential ordering and rhythm of complex movements

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Jeffery G. Bednark

2015-07-01

Full Text Available Voluntary actions require the concurrent engagement and coordinated control of complex temporal (e.g. rhythm and ordinal motor processes. Using high-resolution functional magnetic resonance imaging (fMRI and multi-voxel pattern analysis (MVPA, we sought to determine the degree to which these complex motor processes are dissociable in basal ganglia and cortical networks. We employed three different finger-tapping tasks that differed in the demand on the sequential temporal rhythm or sequential ordering of submovements. Our results demonstrate that sequential rhythm and sequential order tasks were partially dissociable based on activation differences. The sequential rhythm task activated a widespread network centered around the SMA and basal-ganglia regions including the dorsomedial putamen and caudate nucleus, while the sequential order task preferentially activated a fronto-parietal network. There was also extensive overlap between sequential rhythm and sequential order tasks, with both tasks commonly activating bilateral premotor, supplementary motor, and superior/inferior parietal cortical regions, as well as regions of the caudate/putamen of the basal ganglia and the ventro-lateral thalamus. Importantly, within the cortical regions that were active for both complex movements, MVPA could accurately classify different patterns of activation for the sequential rhythm and sequential order tasks. In the basal ganglia, however, overlapping activation for the sequential rhythm and sequential order tasks, which was found in classic motor circuits of the putamen and ventro-lateral thalamus, could not be accurately differentiated by MVPA. Overall, our results highlight the convergent architecture of the motor system, where complex motor information that is spatially distributed in the cortex converges into a more compact representation in the basal ganglia.

Linear complexity for multidimensional arrays - a numerical invariant

DEFF Research Database (Denmark)

Gomez-Perez, Domingo; Høholdt, Tom; Moreno, Oscar

2015-01-01

Linear complexity is a measure of how complex a one dimensional sequence can be. In this paper we extend the concept of linear complexity to multiple dimensions and present a definition that is invariant under well-orderings of the arrays. As a result we find that our new definition for the proce...

The 2016-2017 Central Italy Seismic Sequence: Source Complexity Inferred from Rupture Models.

Science.gov (United States)

Scognamiglio, L.; Tinti, E.; Casarotti, E.; Pucci, S.; Villani, F.; Cocco, M.; Magnoni, F.; Michelini, A.

2017-12-01

The Apennines have been struck by several seismic sequences in recent years, showing evidence of the activation of multiple segments of normal fault systems in a variable and, relatively short, time span, as in the case of the 1980 Irpinia earthquake (three shocks in 40 s), the 1997 Umbria-Marche sequence (four main shocks in 18 days) and the 2009 L'Aquila earthquake having three segments activated within a few weeks. The 2016-2017 central Apennines seismic sequence begin on August 24th with a MW 6.0 earthquake, which strike the region between Amatrice and Accumoli causing 299 fatalities. This earthquake ruptures a nearly 20 km long normal fault and shows a quite heterogeneous slip distribution. On October 26th, another main shock (MW 5.9) occurs near Visso extending the activated seismogenic area toward the NW. It is a double event rupturing contiguous patches on the fault segment of the normal fault system. Four days after the second main shock, on October 30th, a third earthquake (MW 6.5) occurs near Norcia, roughly midway between Accumoli and Visso. In this work we have inverted strong motion waveforms and GPS data to retrieve the source model of the MW 6.5 event with the aim of interpreting the rupture process in the framework of this complex sequence of moderate magnitude earthquakes. We noted that some preliminary attempts to model the slip distribution of the October 30th main shock using a single fault plane oriented along the Apennines did not provide convincing fits to the observed waveforms. In addition, the deformation pattern inferred from satellite observations suggested the activation of a multi-fault structure, that is coherent to the complexity and the extension of the geological surface deformation. We investigated the role of multi-fault ruptures and we found that this event revealed an extraordinary complexity of the rupture geometry and evolution: the coseismic rupture propagated almost simultaneously on a normal fault and on a blind fault

Complete Chloroplast Genome Sequence of Aquilaria sinensis (Lour.) Gilg and Evolution Analysis within the Malvales Order.

Science.gov (United States)

Wang, Ying; Zhan, Di-Feng; Jia, Xian; Mei, Wen-Li; Dai, Hao-Fu; Chen, Xiong-Ting; Peng, Shi-Qing

2016-01-01

Aquilaria sinensis (Lour.) Gilg is an important medicinal woody plant producing agarwood, which is widely used in traditional Chinese medicine. High-throughput sequencing of chloroplast (cp) genomes enhanced the understanding about evolutionary relationships within plant families. In this study, we determined the complete cp genome sequences for A. sinensis. The size of the A. sinensis cp genome was 159,565 bp. This genome included a large single-copy region of 87,482 bp, a small single-copy region of 19,857 bp, and a pair of inverted repeats (IRa and IRb) of 26,113 bp each. The GC content of the genome was 37.11%. The A. sinensis cp genome encoded 113 functional genes, including 82 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. A total of 45 polymorphic simple-sequence repeat loci and 60 pairs of large repeats were identified. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited high A/T content. Moreover, 33 pairs of large repeat sequences were located in the protein-coding genes, whereas 27 pairs were located in the intergenic regions. Aquilaria sinensis cp genome bias ended with A/T on the basis of codon usage. The distribution of codon usage in A. sinensis cp genome was most similar to that in the Gonystylus bancanus cp genome. Comparative results of 82 protein-coding genes from 29 species of cp genomes demonstrated that A. sinensis was a sister species to G. bancanus within the Malvales order. Aquilaria sinensis cp genome presented the highest sequence similarity of >90% with the G. bancanus cp genome by using CGView Comparison Tool. This finding strongly supports the placement of A. sinensis as a sister to G. bancanus within the Malvales order. The complete A. sinensis cp genome information will be highly beneficial for further studies on this traditional medicinal

RNA motif search with data-driven element ordering.

Science.gov (United States)

Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa

2016-05-18

In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .

Facies-succession and architecture of the third-order sequences and their stratigraphic framework of the Devonian in Yunnan-Guizhou-Guangxi area, South China

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Mei Mingxiang

2013-01-01

Full Text Available The Caledonian orogeny at the end of the Silurian resulted in great changes in the palaeogeography in the Yunnan-Guizhou-Guangxi area of South China; the continental area of the Early Paleozoic evolved into the extensive Dian-Qian-Gui Sea in the Late Paleozoic. Early in the Devonian, as a result of a major transgression, seawater encroached gradually from the south to the north and clastic facies were deposited. Carbonate deposition was then established in the Yunnan-Guizhou-Guangxi area, with a palaeogeography marked by attached platforms, isolated platforms and narrow basins. As a result of the Ziyun movement towards the end of the Devonian, the Upper Devonian strata are regressive and thin out from the open-sea to the land areas. A study of the nature and distribution of sedimentary facies in space and time recognises 13 third-order sequences in the Devonian strata in Yunnan-Guizhou-Guangxi area, and these form two second-order sequences. The strata of the Lower Devonian comprise 5 third-order sequences (SQ1 to SQ5, which are dominated by transgressive clastics. 4 third-order sequences (SQ6 to SQ9 in the Middle Devonian are characterized by alternations of transgressive clastics and highstand carbonates. In the Upper Devonian, carbonates constitute 4 third-order sequences (SQ10 to SQ13, which are generally marked by the transgressive limestones and highstand dolomites. On the basis of earlier biostratigraphic studies, sea-level changes represented by the third-order sequences with their different facies successions are explored, and the sequence stratigraphic framework is established. Therefore, the Devonian strata in the study area provide an example for further understanding of depositional trends within the sequence-stratigraphic framework.

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

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Yuichi eYamashita

2011-04-01

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

Emergence of dynamical order synchronization phenomena in complex systems

CERN Document Server

Manrubia, Susanna C; Zanette, Damián H

2004-01-01

Synchronization processes bring about dynamical order and lead tospontaneous development of structural organization in complex systemsof various origins, from chemical oscillators and biological cells tohuman societies and the brain. This book provides a review and adetailed theoretical analysis of synchronization phenomena in complexsystems with different architectures, composed of elements withperiodic or chaotic individual dynamics. Special attention is paid tostatistical concepts, such as nonequilibrium phase transitions, orderparameters and dynamical glasses.

The Optimization of Magnetic Resonance Imaging Pulse Sequences in Order to Better Detection of Multiple Sclerosis Plaques.

Science.gov (United States)

Farshidfar, Z; Faeghi, F; Haghighatkhah, H R; Abdolmohammadi, J

2017-09-01

Magnetic resonance imaging (MRI) is the most sensitive technique to detect multiple sclerosis (MS) plaques in central nervous system. In some cases, the patients who were suspected to MS, Whereas MRI images are normal, but whether patients don't have MS plaques or MRI images are not enough optimized enough in order to show MS plaques? The aim of the current study is evaluating the efficiency of different MRI sequences in order to better detection of MS plaques. In this cross-sectional study which was performed at Shohada-E Tajrish in Tehran - Iran hospital between October, 2011 to April, 2012, included 20 patients who suspected to MS disease were selected by the method of random sampling and underwent routine brain Pulse sequences (Axial T2w, Axial T1w, Coronal T2w, Sagittal T1w, Axial FLAIR) by Siemens, Avanto, 1.5 Tesla system. If any lesion which is suspected to the MS disease was observed, additional sequences such as: Sagittal FLAIR Fat Sat, Sagittal PDw-fat Sat, Sagittal PDw-water sat was also performed. This study was performed in about 52 lesions and the results in more than 19 lesions showed that, for the Subcortical and Infratentorial areas, PDWw sequence with fat suppression is the best choice, And in nearly 33 plaques located in Periventricular area, FLAIR Fat Sat was the most effective sequence than both PDw fat and water suppression pulse sequences. Although large plaques may visible in all images, but important problem in patients with suspected MS is screening the tiny MS plaques. This study showed that for revealing the MS plaques located in the Subcortical and Infratentorial areas, PDw-fat sat is the most effective sequence, and for MS plaques in the periventricular area, FLAIR fat Sat is the best choice.

Use of cycle stacking patterns to define third-order depositional sequences: Middle to Late Cambrian Bonanza King Formation, southern Great basin

Energy Technology Data Exchange (ETDEWEB)

Montanez, I.P.; Droser, M.L. (Univ. of California, Riverside (United States))

1991-03-01

The Middle to Late Cambrian Bonanza King Formation (CA, NV) is characterized by superimposed scales of cyclicity. Small-scale cycles (0.5 to 10m) occur as shallowing-upward peritidal and subtidal cycles that repeat at high frequencies (10{sup 4} to 10{sup 5}). Systematic changes in stacking patterns of meter-scale cycles define several large-scale (50-250 m) third-order depositional sequences in the Bonanza King Formation. Third-order depositional sequences can be traced within ranges and correlated regionally across the platform. Peritidal cycles in the Bonanza King Formation are both subtidal- and tidal flat-dominated. Tidal flat-dominated cycles consist of muddy bases grading upward into thrombolites or columnar stromatolites all capped by planar stromatolites. Subtidal cycles in the Bonanza King Formation consist of grainstone bases that commonly fine upward and contain stacked hardgrounds. These are overlain by digitate-algal bioherms with grainstone channel fills and/or bioturbated ribbon carbonates with grainstone lenses. Transgressive depositional facies of third-order depositional sequences consist primarily of stacks of subtidal-dominated pertidial cycles and subtidal cycles, whereas regressive depositional facies are dominated by stacks of tidal flat-dominated peritidal cycles and regoliths developed over laminite cycle caps. The use of high frequency cycles in the Bonanza King Formation to delineate regionally developed third-order depositional sequences thus provides a link between cycle stratigraphy and sequence stratigraphy.

J.F. Schouten revisited : pitch of complex tones having many high-order harmonics

NARCIS (Netherlands)

Smurzynski, J.; Houtsma, A.J.M.

1988-01-01

Four experiments are reported which deal with pitch perception of harmonic complex tones containing many high-order, aurally unresolvable partials. Melodic-interval identilication performance ill the case of sounds with increasing harmonic order remains significantly above chalice level, even if the

Pleiotropy constrains the evolution of protein but not regulatory sequences in a transcription regulatory network influencing complex social behaviours

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Daria eMolodtsova

2014-12-01

Full Text Available It is increasingly apparent that genes and networks that influence complex behaviour are evolutionary conserved, which is paradoxical considering that behaviour is labile over evolutionary timescales. How does adaptive change in behaviour arise if behaviour is controlled by conserved, pleiotropic, and likely evolutionary constrained genes? Pleiotropy and connectedness are known to constrain the general rate of protein evolution, prompting some to suggest that the evolution of complex traits, including behaviour, is fuelled by regulatory sequence evolution. However, we seldom have data on the strength of selection on mutations in coding and regulatory sequences, and this hinders our ability to study how pleiotropy influences coding and regulatory sequence evolution. Here we use population genomics to estimate the strength of selection on coding and regulatory mutations for a transcriptional regulatory network that influences complex behaviour of honey bees. We found that replacement mutations in highly connected transcription factors and target genes experience significantly stronger negative selection relative to weakly connected transcription factors and targets. Adaptively evolving proteins were significantly more likely to reside at the periphery of the regulatory network, while proteins with signs of negative selection were near the core of the network. Interestingly, connectedness and network structure had minimal influence on the strength of selection on putative regulatory sequences for both transcription factors and their targets. Our study indicates that adaptive evolution of complex behaviour can arise because of positive selection on protein-coding mutations in peripheral genes, and on regulatory sequence mutations in both transcription factors and their targets throughout the network.

Visual artificial grammar learning by rhesus macaques (Macaca mulatta): exploring the role of grammar complexity and sequence length.

Science.gov (United States)

Heimbauer, Lisa A; Conway, Christopher M; Christiansen, Morten H; Beran, Michael J; Owren, Michael J

2018-03-01

Humans and nonhuman primates can learn about the organization of stimuli in the environment using implicit sequential pattern learning capabilities. However, most previous artificial grammar learning studies with nonhuman primates have involved relatively simple grammars and short input sequences. The goal in the current experiments was to assess the learning capabilities of monkeys on an artificial grammar-learning task that was more complex than most others previously used with nonhumans. Three experiments were conducted using a joystick-based, symmetrical-response serial reaction time task in which two monkeys were exposed to grammar-generated sequences at sequence lengths of four in Experiment 1, six in Experiment 2, and eight in Experiment 3. Over time, the monkeys came to respond faster to the sequences generated from the artificial grammar compared to random versions. In a subsequent generalization phase, subjects generalized their knowledge to novel sequences, responding significantly faster to novel instances of sequences produced using the familiar grammar compared to those constructed using an unfamiliar grammar. These results reveal that rhesus monkeys can learn and generalize the statistical structure inherent in an artificial grammar that is as complex as some used with humans, for sequences up to eight items long. These findings are discussed in relation to whether or not rhesus macaques and other primate species possess implicit sequence learning abilities that are similar to those that humans draw upon to learn natural language grammar.

Temperature-dependent vibrational spectroscopy to study order-disorder transitions in charge transfer complexes

Science.gov (United States)

Isaac, Rohan; Goetz, Katelyn P.; Roberts, Drew; Jurchescu, Oana D.; McNeil, L. E.

2018-02-01

Charge-transfer (CT) complexes are a promising class of materials for the semiconductor industry because of their versatile properties. This class of compounds shows a variety of phase transitions, which are of interest because of their potential impact on the electronic characteristics. Here temperature-dependent vibrational spectroscopy is used to study structural phase transitions in a set of organic CT complexes. Splitting and broadening of infrared-active phonons in the complex formed between pyrene and pyromellitic dianhydride (PMDA) confirm the structural transition is of the order-disorder type and complement previous x-ray diffraction (XRD) results. We show that this technique is a powerful tool to characterize transitions, and apply it to a range of binary CT complexes composed of polyaromatic hyrdocarbons (anthracene, perylene, phenanthrene, pyrene, and stilbene) and PMDA. We extend the understanding of transitions in perylene-PMDA and pyrene-PMDA, and show that there are no order-disorder transitions present in anthracene-PMDA, stilbene-PMDA and phenanthrene-PMDA in the temperature range investigated here.

Deficit in complex sequence processing after a virtual lesion of left BA45.

Directory of Open Access Journals (Sweden)

Emeline Clerget

Full Text Available Although the contribution of Broca's area to motor cognition is generally accepted, its exact role remains controversial. A previous functional imaging study has suggested that Broca's area implements hierarchically organised motor behaviours and, in particular, that its anterior (Brodmann area 45, BA45 and posterior (BA44 parts process, respectively, higher and lower-level hierarchical elements. This function of Broca's area could generalize to other cognitive functions, including language. However, because of the correlative nature of functional imaging data, the causal relationship between Broca's region activation and its behavioural significance cannot be ascertained. To circumvent this limitation, we used on-line repetitive transcranial magnetic stimulation to disrupt neuronal processing in left BA45, left BA44 or left dorsal premotor cortex, three areas that have been shown to exhibit a phasic activation when participants performed hierarchically organised motor behaviours. The experiment was conducted in healthy volunteers performing the same two key-press sequences as those used in a previous imaging study, and which differed in terms of hierarchical organisation. The performance of the lower-order hierarchical task (Experiment #1 was unaffected by magnetic stimulation. In contrast, in the higher-order hierarchical task (Experiment #2, "superordinate" task, we found that a virtual lesion of the anterior part of Broca's area (left BA45 delayed the processing of the cue initiating the sequence in an effector-independent way. Interestingly, in this task, the initiation cue only informed the subjects about the rules to be applied to produce the appropriate response but did not allow them to anticipate the entire motor sequence. A second important finding was a RT decrease following left PMd virtual lesions in the superordinate task, a result compatible with the view that PMd plays a critical role in impulse control. The present study

Correlation in chicken between the marker LEI0258 alleles and Major Histocompatibility Complex sequences

DEFF Research Database (Denmark)

Chazara, Olympe; Juul-Madsen, Helle Risdahl; Chang, Chi-Seng

Background The LEI0258 marker is located within the B region of the chicken Major Histocompatibility Complex (MHC), and is surprisingly well associated with serology. Therefore, the correlation between the LEI0258 alleles and the MHC class I and the class II alleles at the level of sequences is w...

Mapping sequences by parts

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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.

Order and correlations in genomic DNA sequences. The spectral approach

International Nuclear Information System (INIS)

Lobzin, Vasilii V; Chechetkin, Vladimir R

2000-01-01

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

Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes.

Science.gov (United States)

Kumar, Ajay; Seetan, Raed; Mergoum, Mohamed; Tiwari, Vijay K; Iqbal, Muhammad J; Wang, Yi; Al-Azzam, Omar; Šimková, Hana; Luo, Ming-Cheng; Dvorak, Jan; Gu, Yong Q; Denton, Anne; Kilian, Andrzej; Lazo, Gerard R; Kianian, Shahryar F

2015-10-16

The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average

A Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex

Energy Technology Data Exchange (ETDEWEB)

Aller, Pierre; Duclos, Stéphanie; Wallace, Susan S.; Doublié, Sylvie (Vermont)

2012-06-27

Thymine glycol (Tg) is the most common oxidation product of thymine and is known to be a strong block to replicative DNA polymerases. A previously solved structure of the bacteriophage RB69 DNA polymerase (RB69 gp43) in complex with Tg in the sequence context 5'-G-Tg-G shed light on how Tg blocks primer elongation: The protruding methyl group of the oxidized thymine displaces the adjacent 5'-G, which can no longer serve as a template for primer elongation [Aller, P., Rould, M. A., Hogg, M, Wallace, S. S. and Doublie S. (2007). A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol. Proc. Natl. Acad. Sci. USA, 104, 814-818.]. Several studies showed that in the sequence context 5'-C-Tg-purine, Tg is more likely to be bypassed by Klenow fragment, an A-family DNA polymerase. We set out to investigate the role of sequence context in Tg bypass in a B-family polymerase and to solve the crystal structures of the bacteriophage RB69 DNA polymerase in complex with Tg-containing DNA in the three remaining sequence contexts: 5'-A-Tg-G, 5'-T-Tg-G, and 5'-C-Tg-G. A combination of several factors - including the associated exonuclease activity, the nature of the 3' and 5' bases surrounding Tg, and the cis-trans interconversion of Tg - influences Tg bypass. We also visualized for the first time the structure of a well-ordered exonuclease complex, allowing us to identify and confirm the role of key residues (Phe123, Met256, and Tyr257) in strand separation and in the stabilization of the primer strand in the exonuclease site.

A Novel Entropy-Based Decoding Algorithm for a Generalized High-Order Discrete Hidden Markov Model

Directory of Open Access Journals (Sweden)

Jason Chin-Tiong Chan

2018-01-01

Full Text Available The optimal state sequence of a generalized High-Order Hidden Markov Model (HHMM is tracked from a given observational sequence using the classical Viterbi algorithm. This classical algorithm is based on maximum likelihood criterion. We introduce an entropy-based Viterbi algorithm for tracking the optimal state sequence of a HHMM. The entropy of a state sequence is a useful quantity, providing a measure of the uncertainty of a HHMM. There will be no uncertainty if there is only one possible optimal state sequence for HHMM. This entropy-based decoding algorithm can be formulated in an extended or a reduction approach. We extend the entropy-based algorithm for computing the optimal state sequence that was developed from a first-order to a generalized HHMM with a single observational sequence. This extended algorithm performs the computation exponentially with respect to the order of HMM. The computational complexity of this extended algorithm is due to the growth of the model parameters. We introduce an efficient entropy-based decoding algorithm that used reduction approach, namely, entropy-based order-transformation forward algorithm (EOTFA to compute the optimal state sequence of any generalized HHMM. This EOTFA algorithm involves a transformation of a generalized high-order HMM into an equivalent first-order HMM and an entropy-based decoding algorithm is developed based on the equivalent first-order HMM. This algorithm performs the computation based on the observational sequence and it requires OTN~2 calculations, where N~ is the number of states in an equivalent first-order model and T is the length of observational sequence.

Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex

Science.gov (United States)

Hand, Melanie L.; Spangenberg, German C.; Forster, John W.; Cogan, Noel O. I.

2013-01-01

Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL–psaI intergenic region, however, revealed a “hot-spot” of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses. PMID:23550121

Crystal structure of the Msx-1 homeodomain/DNA complex.

Science.gov (United States)

Hovde, S; Abate-Shen, C; Geiger, J H

2001-10-09

The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.

A novel color image encryption scheme using fractional-order hyperchaotic system and DNA sequence operations

International Nuclear Information System (INIS)

Zhang Li-Min; Sun Ke-Hui; Liu Wen-Hao; He Shao-Bo

2017-01-01

In this paper, Adomian decomposition method (ADM) with high accuracy and fast convergence is introduced to solve the fractional-order piecewise-linear (PWL) hyperchaotic system. Based on the obtained hyperchaotic sequences, a novel color image encryption algorithm is proposed by employing a hybrid model of bidirectional circular permutation and DNA masking. In this scheme, the pixel positions of image are scrambled by circular permutation, and the pixel values are substituted by DNA sequence operations. In the DNA sequence operations, addition and substraction operations are performed according to traditional addition and subtraction in the binary, and two rounds of addition rules are used to encrypt the pixel values. The simulation results and security analysis show that the hyperchaotic map is suitable for image encryption, and the proposed encryption algorithm has good encryption effect and strong key sensitivity. It can resist brute-force attack, statistical attack, differential attack, known-plaintext, and chosen-plaintext attacks. (paper)

Temperature-dependent vibrational spectroscopy to study order-disorder transitions in charge transfer complexes

Directory of Open Access Journals (Sweden)

Rohan Isaac

2018-02-01

Full Text Available Charge-transfer (CT complexes are a promising class of materials for the semiconductor industry because of their versatile properties. This class of compounds shows a variety of phase transitions, which are of interest because of their potential impact on the electronic characteristics. Here temperature-dependent vibrational spectroscopy is used to study structural phase transitions in a set of organic CT complexes. Splitting and broadening of infrared-active phonons in the complex formed between pyrene and pyromellitic dianhydride (PMDA confirm the structural transition is of the order-disorder type and complement previous x-ray diffraction (XRD results. We show that this technique is a powerful tool to characterize transitions, and apply it to a range of binary CT complexes composed of polyaromatic hyrdocarbons (anthracene, perylene, phenanthrene, pyrene, and stilbene and PMDA. We extend the understanding of transitions in perylene-PMDA and pyrene-PMDA, and show that there are no order-disorder transitions present in anthracene-PMDA, stilbene-PMDA and phenanthrene-PMDA in the temperature range investigated here.

Adaptative synchronization in multi-output fractional-order complex dynamical networks and secure communications

Science.gov (United States)

Mata-Machuca, Juan L.; Aguilar-López, Ricardo

2018-01-01

This work deals with the adaptative synchronization of complex dynamical networks with fractional-order nodes and its application in secure communications employing chaotic parameter modulation. The complex network is composed of multiple fractional-order systems with mismatch parameters and the coupling functions are given to realize the network synchronization. We introduce a fractional algebraic synchronizability condition (FASC) and a fractional algebraic identifiability condition (FAIC) which are used to know if the synchronization and parameters estimation problems can be solved. To overcome these problems, an adaptative synchronization methodology is designed; the strategy consists in proposing multiple receiver systems which tend to follow asymptotically the uncertain transmitters systems. The coupling functions and parameters of the receiver systems are adjusted continually according to a convenient sigmoid-like adaptative controller (SLAC), until the measurable output errors converge to zero, hence, synchronization between transmitter and receivers is achieved and message signals are recovered. Indeed, the stability analysis of the synchronization error is based on the fractional Lyapunov direct method. Finally, numerical results corroborate the satisfactory performance of the proposed scheme by means of the synchronization of a complex network consisting of several fractional-order unified chaotic systems.

Projective synchronization of a complex network with different fractional order chaos nodes

International Nuclear Information System (INIS)

Wang Ming-Jun; Wang Xing-Yuan; Niu Yu-Jun

2011-01-01

Based on the stability theory of the linear fractional order system, projective synchronization of a complex network is studied in the paper, and the coupling functions of the connected nodes are identified. With this method, the projective synchronization of the network with different fractional order chaos nodes can be achieved, besides, the number of the nodes does not affect the stability of the whole network. In the numerical simulations, the chaotic fractional order Lü system, Liu system and Coullet system are chosen as examples to show the effectiveness of the scheme. (general)

An Efficient Approach to Mining Maximal Contiguous Frequent Patterns from Large DNA Sequence Databases

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Md. Rezaul Karim

2012-03-01

Full Text Available Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. Biologists are interested in finding frequent orderly arrangements of motifs that are responsible for similar expression of a group of genes. In order to reduce mining time and complexity, however, most existing sequence mining algorithms either focus on finding short DNA sequences or require explicit specification of sequence lengths in advance. The challenge is to find longer sequences without specifying sequence lengths in advance. In this paper, we propose an efficient approach to mining maximal contiguous frequent patterns from large DNA sequence datasets. The experimental results show that our proposed approach is memory-efficient and mines maximal contiguous frequent patterns within a reasonable time.

Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding.

Science.gov (United States)

Bhat, Javaid A; Ali, Sajad; Salgotra, Romesh K; Mir, Zahoor A; Dutta, Sutapa; Jadon, Vasudha; Tyagi, Anshika; Mushtaq, Muntazir; Jain, Neelu; Singh, Pradeep K; Singh, Gyanendra P; Prabhu, K V

2016-01-01

Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.

Scanning mutagenesis of the amino acid sequences flanking phosphorylation site 1 of the mitochondrial pyruvate dehydrogenase complex

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Nagib eAhsan

2012-07-01

Full Text Available The mitochondrial pyruvate dehydrogenase complex is regulated by reversible seryl-phosphorylation of the E1α subunit by a dedicated, intrinsic kinase. The phospho-complex is reactivated when dephosphorylated by an intrinsic PP2C-type protein phosphatase. Both the position of the phosphorylated Ser-residue and the sequences of the flanking amino acids are highly conserved. We have used the synthetic peptide-based kinase client assay plus recombinant pyruvate dehydrogenase E1α and E1α-kinase to perform scanning mutagenesis of the residues flanking the site of phosphorylation. Consistent with the results from phylogenetic analysis of the flanking sequences, the direct peptide-based kinase assays tolerated very few changes. Even conservative changes such as Leu, Ile, or Val for Met, or Glu for Asp, gave very marked reductions in phosphorylation. Overall the results indicate that regulation of the mitochondrial pyruvate dehydrogenase complex by reversible phosphorylation is an extreme example of multiple, interdependent instances of co-evolution.

Adaptive generalized function matrix projective lag synchronization between fractional-order and integer-order complex networks with delayed coupling and different dimensions

International Nuclear Information System (INIS)

Dai, Hao; Si, Gangquan; Jia, Lixin; Zhang, Yanbin

2013-01-01

This paper investigates generalized function matrix projective lag synchronization between fractional-order and integer-order complex networks with delayed coupling, non-identical topological structures and different dimensions. Based on Lyapunov stability theory, generalized function matrix projective lag synchronization criteria are derived by using the adaptive control method. In addition, the three-dimensional fractional-order chaotic system and the four-dimensional integer-order hyperchaotic system as the nodes of the drive and the response networks, respectively, are analyzed in detail, and numerical simulation results are presented to illustrate the effectiveness of the theoretical results. (paper)

Neutron scattering studies on magnetic excitations in complex ordered manganites

International Nuclear Information System (INIS)

Senff, D.

2007-09-01

This thesis deals with magnetic excitations in three different Manganese oxides, single-layered LaSrMnO 4 , charge- and orbital-ordered La 1/2 Sr 3/2 MnO 4 , and multiferroic TbMnO 3 , which are studied by means of inelastic neutron scattering. The properties of the first system, LaSrMnO 4 , are governed by the complex interplay of orbital, spin, and lattice degrees of freedom typical for the physics of manganites. The magnetic low-temperature behavior is quite unusual, and the comprehensive analysis of the spin-wave spectrum of LaSrMnO 4 suggests a heterogenous ground state with ferromagnetic orbital polarons embedded in an antiferromagnetic background. The doped system La 1/2 Sr 3/2 MnO 4 exhibits a stable charge- and orbital-ordered state, which today is discussed very controversially, as it is of great relevance for the colossal increase of electric conductivity at the metal-insulator transition in perovskite manganites. Analyzing the spin-wave dispersion of the ordered state, we find an excellent agreement with classical predictions by Goodenough and reject a recent alternative proposal. The different strength of the ferromagnetic and antiferromagnetic exchange in the CE-type ordering leads to the conclusion that the magnetic state has to be considered as a weak AFM coupling of stable FM elements. This thesis is further supported by the thermal evolution of the ordered state, revealing anisotropic correlations and the close competition of FM and AFM correlations above the Neel transition, as well as by the doping dependence of the charge- and orbital-ordered state, which is interpreted on the basis of a different response of the magnetic system with respect to additional electrons or holes. In the orthorhombic perovskite TbMnO 3 the electric polarization is closely coupled to the magnetic degrees of freedom via a complex, non-collinear magnetic ordering. Precisely characterizing the different magnon excitations allows to identify all relevant modes of the

Recalling visual serial order for verbal sequences

NARCIS (Netherlands)

Logie, R.H.; Saito, S.; Morita, A.; Varma, S.; Norris, D.

2016-01-01

We report three experiments in which participants performed written serial recall of visually presented verbal sequences with items varying in visual similarity. In Experiments 1 and 2 native speakers of Japanese recalled visually presented Japanese Kanji characters. In Experiment 3, native speakers

Construction, classification and parametrization of complex Hadamard matrices

Science.gov (United States)

Szöllősi, Ferenc

To improve the design of nuclear systems, high-fidelity neutron fluxes are required. Leadership-class machines provide platforms on which very large problems can be solved. Computing such fluxes efficiently requires numerical methods with good convergence properties and algorithms that can scale to hundreds of thousands of cores. Many 3-D deterministic transport codes are decomposable in space and angle only, limiting them to tens of thousands of cores. Most codes rely on methods such as Gauss Seidel for fixed source problems and power iteration for eigenvalue problems, which can be slow to converge for challenging problems like those with highly scattering materials or high dominance ratios. Three methods have been added to the 3-D SN transport code Denovo that are designed to improve convergence and enable the full use of cutting-edge computers. The first is a multigroup Krylov solver that converges more quickly than Gauss Seidel and parallelizes the code in energy such that Denovo can use hundreds of thousand of cores effectively. The second is Rayleigh quotient iteration (RQI), an old method applied in a new context. This eigenvalue solver finds the dominant eigenvalue in a mathematically optimal way and should converge in fewer iterations than power iteration. RQI creates energy-block-dense equations that the new Krylov solver treats efficiently. However, RQI can have convergence problems because it creates poorly conditioned systems. This can be overcome with preconditioning. The third method is a multigrid-in-energy preconditioner. The preconditioner takes advantage of the new energy decomposition because the grids are in energy rather than space or angle. The preconditioner greatly reduces iteration count for many problem types and scales well in energy. It also allows RQI to be successful for problems it could not solve otherwise. The methods added to Denovo accomplish the goals of this work. They converge in fewer iterations than traditional methods and enable the use of hundreds of thousands of cores. Each method can be used individually, with the multigroup Krylov solver and multigrid-in-energy preconditioner being particularly successful on their own. The largest benefit, though, comes from using these methods in concert.

An AU-rich element in the 3{prime} untranslated region of the spinach chloroplast petD gene participates in sequence-specific RNA-protein complex formation

Energy Technology Data Exchange (ETDEWEB)

Chen, Qiuyun; Adams, C.C.; Usack, L. [Cornell Univ., Ithaca, NY (United States)] [and others

1995-04-01

In chloroplasts, the 3{prime} untranslated regions of most mRNAs contain a stem-loop-forming inverted repeat (IR) sequence that is required for mRNA stability and correct 3{prime}-end formation. The IR regions of several mRNAs are also known to bind chloroplast proteins, as judged from in vitro gel mobility shift and UV cross-linking assays, and these RNA-protein interactions may be involved in the regulation of chloroplast mRNA processing and/or stability. Here we describe in detail the RNA and protein components that are involved in 3{prime} IR-containing RNA (3{prime} IR-RNA)-protein complex formation for the spinach chloroplast petD gene, which encodes subunit IV of the cytochrome b{sub 6}/f complex. We show that the complex contains 55-, 41-, and 29-kDa RNA-binding proteins (ribonucleoproteins [RNPs]). These proteins together protect a 90-nucleotide segment of RNA from RNase T{sub 1} digestion; this RNA contains the IR and downstream flanking sequences. Competition experiments using 3{prime} IR-RNAs from the psbA or rbcL gene demonstrate that the RNPs have a strong specificity for the petD sequence. Site-directed mutagenesis was carried out to define the RNA sequence elements required for complex formation. These studies identified an 8-nucleotide AU-rich sequence downstream of the IR; mutations within this sequence had moderate to severe effects on RNA-protein complex formation. Although other similar sequences are present in the petD 3{prime} untranslated region, only a single copy, which we have termed box II, appears to be essential for in vivo protein binding. In addition, the IR itself is necessary for optimal complex formation. These two sequence elements together with an RNP complex may direct correct 3{prime}-end processing and/or influence the stability of petD mRNA in chloroplasts. 48 refs., 9 figs., 2 tabs.

Integrating a Genetic Algorithm Into a Knowledge-Based System for Ordering Complex Design Processes

Science.gov (United States)

Rogers, James L.; McCulley, Collin M.; Bloebaum, Christina L.

1996-01-01

The design cycle associated with large engineering systems requires an initial decomposition of the complex system into design processes which are coupled through the transference of output data. Some of these design processes may be grouped into iterative subcycles. In analyzing or optimizing such a coupled system, it is essential to be able to determine the best ordering of the processes within these subcycles to reduce design cycle time and cost. Many decomposition approaches assume the capability is available to determine what design processes and couplings exist and what order of execution will be imposed during the design cycle. Unfortunately, this is often a complex problem and beyond the capabilities of a human design manager. A new feature, a genetic algorithm, has been added to DeMAID (Design Manager's Aid for Intelligent Decomposition) to allow the design manager to rapidly examine many different combinations of ordering processes in an iterative subcycle and to optimize the ordering based on cost, time, and iteration requirements. Two sample test cases are presented to show the effects of optimizing the ordering with a genetic algorithm.

Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

DEFF Research Database (Denmark)

Nielsen, Jeppe Lund; Schramm, Andreas; Bernhard, Anne E.

2004-01-01

for Systems Biology,3 Seattle, Washington, and Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany2 A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting......  FLOW CYTOMETRY-ASSISTED CLONING OF SPECIFIC SEQUENCE MOTIFS FROM COMPLEX 16S RRNA GENE LIBRARIES Jeppe L. Nielsen,1 Andreas Schramm,1,2 Anne E. Bernhard,1 Gerrit J. van den Engh,3 and David A. Stahl1* Department of Civil and Environmental Engineering, University of Washington,1 and Institute......-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.  ...

Emergence of complex space-temporal order in nonlinear field theories

International Nuclear Information System (INIS)

Gleiser, Marcelo

2006-01-01

We investigate the emergence of time-dependent nonperturbative configurations during the evolution of nonlinear scalar field models with symmetric and asymmetric double-well potentials. Complex space-temporal behavior emerges as the system seeks to establish equipartition after a fast quench. We show that fast quenches may dramatically modify the decay rate of metastable states in first order phase transitions. We discuss possible applications in condensed matter systems and in inflationary cosmology. (author)

Complexity and Hopf Bifurcation Analysis on a Kind of Fractional-Order IS-LM Macroeconomic System

Science.gov (United States)

Ma, Junhai; Ren, Wenbo

On the basis of our previous research, we deepen and complete a kind of macroeconomics IS-LM model with fractional-order calculus theory, which is a good reflection on the memory characteristics of economic variables, we also focus on the influence of the variables on the real system, and improve the analysis capabilities of the traditional economic models to suit the actual macroeconomic environment. The conditions of Hopf bifurcation in fractional-order system models are briefly demonstrated, and the fractional order when Hopf bifurcation occurs is calculated, showing the inherent complex dynamic characteristics of the system. With numerical simulation, bifurcation, strange attractor, limit cycle, waveform and other complex dynamic characteristics are given; and the order condition is obtained with respect to time. We find that the system order has an important influence on the running state of the system. The system has a periodic motion when the order meets the conditions of Hopf bifurcation; the fractional-order system gradually stabilizes with the change of the order and parameters while the corresponding integer-order system diverges. This study has certain significance to policy-making about macroeconomic regulation and control.

Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales.

Directory of Open Access Journals (Sweden)

Sanae Sakai

Full Text Available We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS. Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-I(MRE50, which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-I(MRE50 CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-I(MRE50, further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens.

Neutron scattering studies on magnetic excitations in complex ordered manganites

Energy Technology Data Exchange (ETDEWEB)

Senff, D

2007-09-15

This thesis deals with magnetic excitations in three different Manganese oxides, single-layered LaSrMnO{sub 4}, charge- and orbital-ordered La{sub 1/2}Sr{sub 3/2}MnO{sub 4}, and multiferroic TbMnO{sub 3}, which are studied by means of inelastic neutron scattering. The properties of the first system, LaSrMnO{sub 4}, are governed by the complex interplay of orbital, spin, and lattice degrees of freedom typical for the physics of manganites. The magnetic low-temperature behavior is quite unusual, and the comprehensive analysis of the spin-wave spectrum of LaSrMnO{sub 4} suggests a heterogenous ground state with ferromagnetic orbital polarons embedded in an antiferromagnetic background. The doped system La{sub 1/2}Sr{sub 3/2}MnO{sub 4} exhibits a stable charge- and orbital-ordered state, which today is discussed very controversially, as it is of great relevance for the colossal increase of electric conductivity at the metal-insulator transition in perovskite manganites. Analyzing the spin-wave dispersion of the ordered state, we find an excellent agreement with classical predictions by Goodenough and reject a recent alternative proposal. The different strength of the ferromagnetic and antiferromagnetic exchange in the CE-type ordering leads to the conclusion that the magnetic state has to be considered as a weak AFM coupling of stable FM elements. This thesis is further supported by the thermal evolution of the ordered state, revealing anisotropic correlations and the close competition of FM and AFM correlations above the Neel transition, as well as by the doping dependence of the charge- and orbital-ordered state, which is interpreted on the basis of a different response of the magnetic system with respect to additional electrons or holes. In the orthorhombic perovskite TbMnO{sub 3} the electric polarization is closely coupled to the magnetic degrees of freedom via a complex, non-collinear magnetic ordering. Precisely characterizing the different magnon excitations

Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

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O'Brien Kimberly

2008-06-01

Full Text Available Abstract Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC clone library (87 Mb and sequencing of 22 potato BAC clones (2.9 Mb. The GC content of potato is very similar to Solanum lycopersicon (tomato and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that

High-frequency Total Focusing Method (TFM) imaging in strongly attenuating materials with the decomposition of the time reversal operator associated with orthogonal coded excitations

Science.gov (United States)

Villaverde, Eduardo Lopez; Robert, Sébastien; Prada, Claire

2017-02-01

In the present work, the Total Focusing Method (TFM) is used to image defects in a High Density Polyethylene (HDPE) pipe. The viscoelastic attenuation of this material corrupts the images with a high electronic noise. In order to improve the image quality, the Decomposition of the Time Reversal Operator (DORT) filtering is combined with spatial Walsh-Hadamard coded transmissions before calculating the images. Experiments on a complex HDPE joint demonstrate that this method improves the signal-to-noise ratio by more than 40 dB in comparison with the conventional TFM.

Auditory temporal-order processing of vowel sequences by young and elderly listeners.

Science.gov (United States)

Fogerty, Daniel; Humes, Larry E; Kewley-Port, Diane

2010-04-01

This project focused on the individual differences underlying observed variability in temporal processing among older listeners. Four measures of vowel temporal-order identification were completed by young (N=35; 18-31 years) and older (N=151; 60-88 years) listeners. Experiments used forced-choice, constant-stimuli methods to determine the smallest stimulus onset asynchrony (SOA) between brief (40 or 70 ms) vowels that enabled identification of a stimulus sequence. Four words (pit, pet, pot, and put) spoken by a male talker were processed to serve as vowel stimuli. All listeners identified the vowels in isolation with better than 90% accuracy. Vowel temporal-order tasks included the following: (1) monaural two-item identification, (2) monaural four-item identification, (3) dichotic two-item vowel identification, and (4) dichotic two-item ear identification. Results indicated that older listeners had more variability and performed poorer than young listeners on vowel-identification tasks, although a large overlap in distributions was observed. Both age groups performed similarly on the dichotic ear-identification task. For both groups, the monaural four-item and dichotic two-item tasks were significantly harder than the monaural two-item task. Older listeners' SOA thresholds improved with additional stimulus exposure and shorter dichotic stimulus durations. Individual differences of temporal-order performance among the older listeners demonstrated the influence of cognitive measures, but not audibility or age.

Operational Momentum During Ordering Operations for Size and Number in 4-Month-Old Infants

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Viola Macchi Cassia

2017-12-01

Full Text Available An Operational Momentum (OM effect is shown by 9-month-old infants during non-symbolic arithmetic, whereby they overestimate the outcomes to addition problems, and underestimate the outcomes to subtraction problems. Recent evidence has shown that this effect extends to ordering operations for size-based sequences in 12-month-olds. Here we provide evidence that OM occurs for ordering operations involving numerical sequences containing multiple quantity cues, but not size-based sequences, already at 4 months of age. Infants were tested in an ordinal task in which they detected and represented increasing or decreasing variations in physical and/or numerical size, and then responded to ordinal sequences that exhibited greater or lesser sizes/numerosities, thus following or violating the OM generated during habituation. Results showed that OM was absent during size ordering (Experiment 1, but was present when infants ordered arrays of discrete elements varying on numerical and non-numerical dimensions, if both number and continuous magnitudes were available cues to discriminate between with-OM and against-OM sequences during test trials (Experiments 2 vs. 3. The presence of momentum for ordering number only when provided with multiple cues of magnitude changes suggests that OM is a complex phenomenon that blends multiple representations of magnitude early in infancy.

Necessity and complexity of order picking routing optimisation based on pallet loading features

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Bódis Tamás

2017-12-01

Full Text Available Order picking is the most labour-intensive and costly activity of warehouses. The main challenges of its improvement are the synchronisation of warehouse layout, storage assignment policy, routing, zoning, and batching. Furthermore, the competitiveness of the warehouse depends on how it adapts to the unique customer demands and product parameters and the changes. The operators usually have to manage the picking sequence based on best practices taking into consideration the product stacking factors and minimising the lead time. It is usually necessary to support the operators by making e ective decisions. Researchers of the pallet loading problem, bin packing problem, and order picking optimisation provide a wide horizon of solutions but their results are rarely synchronised.

Second-Order Statistics for Wave Propagation through Complex Optical Systems

DEFF Research Database (Denmark)

Yura, H.T.; Hanson, Steen Grüner

1989-01-01

Closed-form expressions are derived for various statistical functions that arise in optical propagation through arbitrary optical systems that can be characterized by a complex ABCD matrix in the presence of distributed random inhomogeneities along the optical path. Specifically, within the second......-order Rytov approximation, explicit general expressions are presented for the mutual coherence function, the log-amplitude and phase correlation functions, and the mean-square irradiance that are obtained in propagation through an arbitrary paraxial ABCD optical system containing Gaussian-shaped limiting...

Unusual Gene Order and Organization of the Sea Urchin HoxCluster

Energy Technology Data Exchange (ETDEWEB)

Richardson, Paul M.; Lucas, Susan; Cameron, R. Andrew; Rowen,Lee; Nesbitt, Ryan; Bloom, Scott; Rast, Jonathan P.; Berney, Kevin; Arenas-Mena, Cesar; Martinez, Pedro; Davidson, Eric H.; Peterson, KevinJ.; Hood, Leroy

2005-05-10

The highly consistent gene order and axial colinear expression patterns found in vertebrate hox gene clusters are less well conserved across the rest of bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3' gene is Hox5. (The gene order is : 5'-Hox1,2, 3, 11/13c, 11/13b, '11/13a, 9/10, 8, 7, 6, 5 - 3)'. The finished sequence result is corroborated by restriction mapping evidence and BAC-end scaffold analyses. Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex.

Development of a serial order in speech constrained by articulatory coordination.

Science.gov (United States)

Oohashi, Hiroki; Watanabe, Hama; Taga, Gentaro

2013-01-01

Universal linguistic constraints seem to govern the organization of sound sequences in words. However, our understanding of the origin and development of these constraints is incomplete. One possibility is that the development of neuromuscular control of articulators acts as a constraint for the emergence of sequences in words. Repetitions of the same consonant observed in early infancy and an increase in variation of consonantal sequences over months of age have been interpreted as a consequence of the development of neuromuscular control. Yet, it is not clear how sequential coordination of articulators such as lips, tongue apex and tongue dorsum constrains sequences of labial, coronal and dorsal consonants in words over the course of development. We examined longitudinal development of consonant-vowel-consonant(-vowel) sequences produced by Japanese children between 7 and 60 months of age. The sequences were classified according to places of articulation for corresponding consonants. The analyses of individual and group data show that infants prefer repetitive and fronting articulations, as shown in previous studies. Furthermore, we reveal that serial order of different places of articulations within the same organ appears earlier and then gradually develops, whereas serial order of different articulatory organs appears later and then rapidly develops. In the same way, we also analyzed the sequences produced by English children and obtained similar developmental trends. These results suggest that the development of intra- and inter-articulator coordination constrains the acquisition of serial orders in speech with the complexity that characterizes adult language.

Complexity the emerging science at the edge of order and chaos

CERN Document Server

Waldrop, M Mitchell

1992-01-01

Why did the stock market crash more than 500 points on a single Monday in 1987? Why do ancient species often remain stable in the fossil record for millions of years and then suddenly disappear? In a world where nice guys often finish last, why do humans value trust and cooperation? At first glance these questions don't appear to have anything in common, but in fact every one of these statements refers to a complex system. The science of complexity studies how single elements, such as a species or a stock, spontaneously organize into complicated structures like ecosystems and economies; stars become galaxies, and snowflakes avalanches almost as if these systems were obeying a hidden yearning for order. Drawing from diverse fields, scientific luminaries such as Nobel Laureates Murray Gell-Mann and Kenneth Arrow are studying complexity at a think tank called The Santa Fe Institute. The revolutionary new discoveries researchers have made there could change the face of every science from biology to cosmology to ...

De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley

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Scholz Uwe

2009-11-01

Full Text Available Abstract Background De novo sequencing the entire genome of a large complex plant genome like the one of barley (Hordeum vulgare L. is a major challenge both in terms of experimental feasibility and costs. The emergence and breathtaking progress of next generation sequencing technologies has put this goal into focus and a clone based strategy combined with the 454/Roche technology is conceivable. Results To test the feasibility, we sequenced 91 barcoded, pooled, gene containing barley BACs using the GS FLX platform and assembled the sequences under iterative change of parameters. The BAC assemblies were characterized by N50 of ~50 kb (N80 ~31 kb, N90 ~21 kb and a Q40 of 94%. For ~80% of the clones, the best assemblies consisted of less than 10 contigs at 24-fold mean sequence coverage. Moreover we show that gene containing regions seem to assemble completely and uninterrupted thus making the approach suitable for detecting complete and positionally anchored genes. By comparing the assemblies of four clones to their complete reference sequences generated by the Sanger method, we evaluated the distribution, quality and representativeness of the 454 sequences as well as the consistency and reliability of the assemblies. Conclusion The described multiplex 454 sequencing of barcoded BACs leads to sequence consensi highly representative for the clones. Assemblies are correct for the majority of contigs. Though the resolution of complex repetitive structures requires additional experimental efforts, our approach paves the way for a clone based strategy of sequencing the barley genome.

Three perspectives on complexity: entropy, compression, subsymmetry

Science.gov (United States)

Nagaraj, Nithin; Balasubramanian, Karthi

2017-12-01

There is no single universally accepted definition of `Complexity'. There are several perspectives on complexity and what constitutes complex behaviour or complex systems, as opposed to regular, predictable behaviour and simple systems. In this paper, we explore the following perspectives on complexity: effort-to-describe (Shannon entropy H, Lempel-Ziv complexity LZ), effort-to-compress (ETC complexity) and degree-of-order (Subsymmetry or SubSym). While Shannon entropy and LZ are very popular and widely used, ETC is relatively a new complexity measure. In this paper, we also propose a novel normalized complexity measure SubSym based on the existing idea of counting the number of subsymmetries or palindromes within a sequence. We compare the performance of these complexity measures on the following tasks: (A) characterizing complexity of short binary sequences of lengths 4 to 16, (B) distinguishing periodic and chaotic time series from 1D logistic map and 2D Hénon map, (C) analyzing the complexity of stochastic time series generated from 2-state Markov chains, and (D) distinguishing between tonic and irregular spiking patterns generated from the `Adaptive exponential integrate-and-fire' neuron model. Our study reveals that each perspective has its own advantages and uniqueness while also having an overlap with each other.

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

Science.gov (United States)

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

2018-03-01

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

Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation

DEFF Research Database (Denmark)

Czaban, Adrian; Sharma, Sapna; Byrne, Stephen

2015-01-01

species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family...... clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity...... enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some...

Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

Science.gov (United States)

Simon, Joseph R.; Carroll, Nick J.; Rubinstein, Michael; Chilkoti, Ashutosh; López, Gabriel P.

2017-06-01

Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments. Using theoretical analyses, we interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a vast library of multicomponent protein-rich structures that ranges from uniform nano-, meso- and microscale puncta (distinct protein droplets) to multilayered orthogonally phase-separated granular structures. The ability to predict and program IDP-rich assemblies in this fashion offers new insights into (1) genetic-to-molecular-to-macroscale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in cell biology and (3) molecular-level engineering of self-assembled recombinant IDP-rich materials.

Binding of canonical Wnt ligands to their receptor complexes occurs in ordered plasma membrane environments.

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Sezgin, Erdinc; Azbazdar, Yagmur; Ng, Xue W; Teh, Cathleen; Simons, Kai; Weidinger, Gilbert; Wohland, Thorsten; Eggeling, Christian; Ozhan, Gunes

2017-08-01

While the cytosolic events of Wnt/β-catenin signaling (canonical Wnt signaling) pathway have been widely studied, only little is known about the molecular mechanisms involved in Wnt binding to its receptors at the plasma membrane. Here, we reveal the influence of the immediate plasma membrane environment on the canonical Wnt-receptor interaction. While the receptors are distributed both in ordered and disordered environments, Wnt binding to its receptors selectively occurs in more ordered membrane environments which appear to cointernalize with the Wnt-receptor complex. Moreover, Wnt/β-catenin signaling is significantly reduced when the membrane order is disturbed by specific inhibitors of certain lipids that prefer to localize at the ordered environments. Similarly, a reduction in Wnt signaling activity is observed in Niemann-Pick Type C disease cells where trafficking of ordered membrane lipid components to the plasma membrane is genetically impaired. We thus conclude that ordered plasma membrane environments are essential for binding of canonical Wnts to their receptor complexes and downstream signaling activity. © 2017 The Authors. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

Lagrange α-exponential stability and α-exponential convergence for fractional-order complex-valued neural networks.

Science.gov (United States)

Jian, Jigui; Wan, Peng

2017-07-01

This paper deals with the problem on Lagrange α-exponential stability and α-exponential convergence for a class of fractional-order complex-valued neural networks. To this end, some new fractional-order differential inequalities are established, which improve and generalize previously known criteria. By using the new inequalities and coupling with the Lyapunov method, some effective criteria are derived to guarantee Lagrange α-exponential stability and α-exponential convergence of the addressed network. Moreover, the framework of the α-exponential convergence ball is also given, where the convergence rate is related to the parameters and the order of differential of the system. These results here, which the existence and uniqueness of the equilibrium points need not to be considered, generalize and improve the earlier publications and can be applied to monostable and multistable fractional-order complex-valued neural networks. Finally, one example with numerical simulations is given to show the effectiveness of the obtained results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sedimentary dynamics and high-frequency sequence stratigraphy of the southwestern slope of Great Bahama Bank

Science.gov (United States)

Wunsch, Marco; Betzler, Christian; Eberli, Gregor P.; Lindhorst, Sebastian; Lüdmann, Thomas; Reijmer, John J. G.

2018-01-01

New geophysical data from the leeward slope of Great Bahama Bank show how contour currents shape the slope and induce re-sedimentation processes. Along slope segments with high current control, drift migration and current winnowing at the toe of slope form a deep moat. Here, the slope progradation is inhibited by large channel incisions and the accumulation of large mass transport complexes, triggered by current winnowing. In areas where the slope is bathed by weaker currents, the accumulation of mass transport complexes and channel incision is rather controlled by the position of the sea level. Large slope failures were triggered during the Mid-Pleistocene transition and Mid-Brunhes event, both periods characterized by changes in the cyclicity or the amplitude of sea-level fluctuations. Within the seismic stratigraphic framework of third order sequences, four sequences of higher order were identified in the succession of the upper Pleistocene. These higher order sequences also show clear differences in function of the slope exposure to contour currents. Two stochastic models emphasize the role of the contour currents and slope morphology in the facies distribution in the upper Pleistocene sequences. In areas of high current influence the interplay of erosional and depositional processes form a complex facies pattern with downslope and along strike facies alterations. In zones with lower current influence, major facies alternations occur predominately in downslope direction, and a layer-cake pattern characterizes the along strike direction. Therefore, this study highlights that contour currents are an underestimated driver for the sediment distribution and architecture of carbonate slopes.

Discovery of rare variants via sequencing: implications for the design of complex trait association studies.

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Bingshan Li

2009-05-01

Full Text Available There is strong evidence that rare variants are involved in complex disease etiology. The first step in implicating rare variants in disease etiology is their identification through sequencing in both randomly ascertained samples (e.g., the 1,000 Genomes Project and samples ascertained according to disease status. We investigated to what extent rare variants will be observed across the genome and in candidate genes in randomly ascertained samples, the magnitude of variant enrichment in diseased individuals, and biases that can occur due to how variants are discovered. Although sequencing cases can enrich for casual variants, when a gene or genes are not involved in disease etiology, limiting variant discovery to cases can lead to association studies with dramatically inflated false positive rates.

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

Science.gov (United States)

Staňková, Helena; Hastie, Alex R; Chan, Saki; Vrána, Jan; Tulpová, Zuzana; Kubaláková, Marie; Visendi, Paul; Hayashi, Satomi; Luo, Mingcheng; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

2016-07-01

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Time spans and spacers : Molecular phylogenetic explorations in the Cladophora complex (Chlorophyta) from the perspective of rDNA gene and spacer sequences

NARCIS (Netherlands)

Bakker, Frederik Theodoor

1995-01-01

In this study, phylogenetic relationships among genera, species and biogeographic representatives of single Cladophora species within the Cladophorales were analyzed using rDNA gene and spacer sequences. Based on phylogenetic analysis of 18S rRNA gene sequences, the Cladophora complex is shown to be

Novel Complexity Indicator of Manufacturing Process Chains and Its Relations to Indirect Complexity Indicators

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Vladimir Modrak

2017-01-01

Full Text Available Manufacturing systems can be considered as a network of machines/workstations, where parts are produced in flow shop or job shop environment, respectively. Such network of machines/workstations can be depicted as a graph, with machines as nodes and material flow between the nodes as links. The aim of this paper is to use sequences of operations and machine network to measure static complexity of manufacturing processes. In this order existing approaches to measure the static complexity of manufacturing systems are analyzed and subsequently compared. For this purpose, analyzed competitive complexity indicators were tested on two different manufacturing layout examples. A subsequent analysis showed relevant potential of the proposed method.

Maximum likelihood sequence estimation for optical complex direct modulation.

Science.gov (United States)

Che, Di; Yuan, Feng; Shieh, William

2017-04-17

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

Development of a serial order in speech constrained by articulatory coordination.

Directory of Open Access Journals (Sweden)

Hiroki Oohashi

Full Text Available Universal linguistic constraints seem to govern the organization of sound sequences in words. However, our understanding of the origin and development of these constraints is incomplete. One possibility is that the development of neuromuscular control of articulators acts as a constraint for the emergence of sequences in words. Repetitions of the same consonant observed in early infancy and an increase in variation of consonantal sequences over months of age have been interpreted as a consequence of the development of neuromuscular control. Yet, it is not clear how sequential coordination of articulators such as lips, tongue apex and tongue dorsum constrains sequences of labial, coronal and dorsal consonants in words over the course of development. We examined longitudinal development of consonant-vowel-consonant(-vowel sequences produced by Japanese children between 7 and 60 months of age. The sequences were classified according to places of articulation for corresponding consonants. The analyses of individual and group data show that infants prefer repetitive and fronting articulations, as shown in previous studies. Furthermore, we reveal that serial order of different places of articulations within the same organ appears earlier and then gradually develops, whereas serial order of different articulatory organs appears later and then rapidly develops. In the same way, we also analyzed the sequences produced by English children and obtained similar developmental trends. These results suggest that the development of intra- and inter-articulator coordination constrains the acquisition of serial orders in speech with the complexity that characterizes adult language.

On the Complexity of the Universal Order in Vico’s Establishing Principles

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Taha Al-Douri

2017-04-01

Full Text Available In his seminal work The Principles of a New Science of the Common Nature of Nations (Principii di una scienza nuova d’intorno alla natura delle nazioni, published in 1725 then again in 1730 and posthumously in 1744, Giambattista Vico (Born in 1668 wrote to qualify the scientific to include the humanities and their complexity beyond the popular Cartesian circumscription within the laws of physics—divinely instituted and set in motion—in describing its phenomena. The work is, for one, a manifesto of the essential complexity inherent in universal order, and against a reduction of scholarship to the pure sciences, in which elimination is key. Vico proposed a structure that afforded the organic integration of the humanities within the laws of physics as parts of “a tree of knowledge” whose trunk branched out into a progression toward certainty, drawn out of the most fluid humanities at the roots, in an order of premise and conclusion. The tree metaphor is the juncture of early moments of disparity and interdependence between complexity, on the one hand, and certainty on the other. Starting at the unknown, the immeasurably immense ultimate uncertainty, perception is shaped through fear, self-protection and subject to survival instincts. And so, crude metaphysics makes the trunk rooted in “poetic wisdom” with a natural mixture of limited sensuous cognition and unlimited imagination—or one striving beyond the fetters of immediate reality, logic, ethics, economics and politics which are all poetic sciences to Vico—branch out. On the other side of those branches, physics extends into chronology and geography—the most certain—in agreement that the faculties of the human mind, including imagination, may not be outside of physics: the trunk from whence all knowledge cometh, and by the laws of which life is governed. Past validating human uncertainty as a measure of complexity—not lack of knowledge—in scientific inquiry, key concepts

The mathematician's mind the psychology of invention in the mathematical field

CERN Document Server

Hadamard, Jacques

1996-01-01

Fifty years ago when Jacques Hadamard set out to explore how mathematicians invent new ideas, he considered the creative experiences of some of the greatest thinkers of his generation, such as George Polya, Claude Lévi-Strauss, and Albert Einstein. It appeared that inspiration could strike anytime, particularly after an individual had worked hard on a problem for days and then turned attention to another activity. In exploring this phenomenon, Hadamard produced one of the most famous and cogent cases for the existence of unconscious mental processes in mathematical invention and other forms of creativity. Written before the explosion of research in computers and cognitive science, his book, originally titled The Psychology of Invention in the Mathematical Field, remains an important tool for exploring the increasingly complex problem of mental life. The roots of creativity for Hadamard lie not in consciousness, but in the long unconscious work of incubation, and in the unconscious aesthetic selection of ide...

Third order nonlinear optical properties and optical limiting behavior of alkali metal complexes of p-nitrophenol

Science.gov (United States)

Thangaraj, M.; Vinitha, G.; Sabari Girisun, T. C.; Anandan, P.; Ravi, G.

2015-10-01

Optical nonlinearity of metal complexes of p-nitrophenolate (M=Li, Na and K) in ethanol is studied by using a continuous wave (cw) diode pumped Nd:YAG laser (532 nm, 50 mW). The predominant mechanism of observed nonlinearity is thermal in origin. The nonlinear refractive index and the nonlinear absorption coefficient of the samples were found to be in the order of 10-8 cm2/W and 10-3 cm/W respectively. Magnitude of third-order optical parameters varies according to the choice of alkali metal chosen for metal complex formation of p-nitrophenolate. The third-order nonlinear susceptibility was found to be in the order of 10-6 esu. The observed saturable absorption and the self-defocusing effect were used to demonstrate the optical limiting action at 532 nm by using the same cw laser beam.

D20S16 is a complex interspersed repeated sequence: Genetic and physical analysis of the locus

Energy Technology Data Exchange (ETDEWEB)

Bowden, D.W.; Krawchuk, M.D.; Howard, T.D. [Wake Forest Univ., Winston-Salem, NC (United States)] [and others

1995-01-20

The genomic structure of the D20S16 locus has been evaluated using genetic and physical methods. D20S16, originally detected with the probe CRI-L1214, is a highly informative, complex restriction fragment length polymorphism consisting of two separate allelic systems. The allelic systems have the characteristics of conventional VNTR polymorphisms and are separated by recombination ({theta} = 0.02, Z{sub max} = 74.82), as demonstrated in family studies. Most of these recombination events are meiotic crossovers and are maternal in origin, but two, including deletion of the locus in a cell line from a CEPH family member, occur without evidence for exchange of flanking markers. DNA sequence analysis suggests that the basis of the polymorphism is variable numbers of a 98-bp sequence tandemly repeated with 87 to 90% sequence similarity between repeats. The 98-bp repeat is a dimer of 49 bp sequence with 45 to 98% identity between the elements. In addition, nonpolymorphic genomic sequences adjacent to the polymorphic 98-bp repeat tracts are also repeated but are not polymorphic, i.e., show no individual to individual variation. Restriction enzyme mapping of cosmids containing the CRI-L1214 sequence suggests that there are multiple interspersed repeats of the CRI-L1214 sequence on chromosome 20. The results of dual-color fluorescence in situ hybridization experiments with interphase nuclei are also consistent with multiple repeats of an interspersed sequence on chromosome 20. 23 refs., 6 figs.

Estimation of isolation times of the island species in the Drosophila simulans complex from multilocus DNA sequence data.

Directory of Open Access Journals (Sweden)

Shannon R McDermott

2008-06-01

Full Text Available The Drosophila simulans species complex continues to serve as an important model system for the study of new species formation. The complex is comprised of the cosmopolitan species, D. simulans, and two island endemics, D. mauritiana and D. sechellia. A substantial amount of effort has gone into reconstructing the natural history of the complex, in part to infer the context in which functional divergence among the species has arisen. In this regard, a key parameter to be estimated is the initial isolation time (t of each island species. Loci in regions of low recombination have lower divergence within the complex than do other loci, yet divergence from D. melanogaster is similar for both classes. This might reflect gene flow of the low-recombination loci subsequent to initial isolation, but it might also reflect differential effects of changing population size on the two recombination classes of loci when the low-recombination loci are subject to genetic hitchhiking or pseudohitchhikingNew DNA sequence variation data for 17 loci corroborate the prior observation from 13 loci that DNA sequence divergence is reduced in genes of low recombination. Two models are presented to estimate t and other relevant parameters (substitution rate correction factors in lineages leading to the island species and, in the case of the 4-parameter model, the ratio of ancestral to extant effective population size from the multilocus DNA sequence data.In general, it appears that both island species were isolated at about the same time, here estimated at approximately 250,000 years ago. It also appears that the difference in divergence patterns of genes in regions of low and higher recombination can be reconciled by allowing a modestly larger effective population size for the ancestral population than for extant D. simulans.

C-terminal low-complexity sequence repeats of Mycobacterium smegmatis Ku modulate DNA binding.

Science.gov (United States)

Kushwaha, Ambuj K; Grove, Anne

2013-01-24

Ku protein is an integral component of the NHEJ (non-homologous end-joining) pathway of DSB (double-strand break) repair. Both eukaryotic and prokaryotic Ku homologues have been characterized and shown to bind DNA ends. A unique feature of Mycobacterium smegmatis Ku is its basic C-terminal tail that contains several lysine-rich low-complexity PAKKA repeats that are absent from homologues encoded by obligate parasitic mycobacteria. Such PAKKA repeats are also characteristic of mycobacterial Hlp (histone-like protein) for which they have been shown to confer the ability to appose DNA ends. Unexpectedly, removal of the lysine-rich extension enhances DNA-binding affinity, but an interaction between DNA and the PAKKA repeats is indicated by the observation that only full-length Ku forms multiple complexes with a short stem-loop-containing DNA previously designed to accommodate only one Ku dimer. The C-terminal extension promotes DNA end-joining by T4 DNA ligase, suggesting that the PAKKA repeats also contribute to efficient end-joining. We suggest that low-complexity lysine-rich sequences have evolved repeatedly to modulate the function of unrelated DNA-binding proteins.

Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

Directory of Open Access Journals (Sweden)

Caselle Michele

2007-09-01

Full Text Available Abstract Background Specific binding of proteins to DNA is one of the most common ways gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a simple recognition code, therefore the prediction of DNA target sequences is not straightforward. DNA-protein interactions can be studied using computational methods which can complement the current experimental methods and offer some advantages. In the present work we use physical effective potentials to evaluate the DNA-protein binding affinities for the λ repressor-DNA complex for which structural and thermodynamic experimental data are available. Results The binding free energy of two molecules can be expressed as the sum of an intermolecular energy (evaluated using a molecular mechanics forcefield, a solvation free energy term and an entropic term. Different solvation models are used including distance dependent dielectric constants, solvent accessible surface tension models and the Generalized Born model. The effect of conformational sampling by Molecular Dynamics simulations on the computed binding energy is assessed; results show that this effect is in general negative and the reproducibility of the experimental values decreases with the increase of simulation time considered. The free energy of binding for non-specific complexes, estimated using the best energetic model, agrees with earlier theoretical suggestions. As a results of these analyses, we propose a protocol for the prediction of DNA-binding target sequences. The possibility of searching regulatory elements within the bacteriophage λ genome using this protocol is explored. Our analysis shows good prediction capabilities, even in absence of any thermodynamic data and information on the naturally recognized sequence. Conclusion This study supports the conclusion that physics-based methods can offer a completely complementary

Phonological Processes in Complex and Compound Words

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Alieh Kord Zaferanlu Kambuziya

2016-02-01

Full Text Available Abstract This research at making a comparison between phonological processes in complex and compound Persian words. Data are gathered from a 40,000-word Persian dictionary. To catch some results, 4,034 complex words and 1,464 compound ones are chosen. To count the data, "excel" software is used. Some results of the research are: 1- "Insertion" is the usual phonological process in complex words. More than half of different insertions belongs to the consonant /g/. Then /y/ and // are in the second and the third order. The consonant /v/ has the least percentage of all. The most percentage of vowel insertion belongs to /e/. The vowels /a/ and /o/ are in the second and third order. Deletion in complex words can only be seen in consonant /t/ and vowel /e/. 2- The most frequent phonological processes in compounds is consonant deletion. In this process, seven different consonants including /t/, //, /m/, /r/, / ǰ/, /d, and /c/. The only deleted vowel is /e/. In both groups of complex and compound, /t/ deletion can be observed. A sequence of three consonants paves the way for the deletion of one of the consonants, if one of the sequences is a sonorant one like /n/, the deletion process rarely happens. 3- In complex words, consonant deletion causes a lighter syllable weight, whereas vowel deletion causes a heavier syllable weight. So, both of the processes lead to bi-moraic weight. 4- The production of bi-moraic syllable in Persian is preferable to Syllable Contact Law. So, Specific Rules have precedence to Universals. 5- Vowel insertion can be seen in both groups of complex and compound words. In complex words, /e/ insertion has the most fundamental part. The vowels /a/ and /o/ are in the second and third place. Whenever there are two sequences of ultra-heavy syllables. By vowel insertion, the first syllable is broken into two light syllables. The compounds that are influenced by vowel insertion, can be and are pronounced without any insertion

Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

KAUST Repository

Zhu, Yihan

2012-08-28

The determination of the atomic structure of a functional material is crucial to understanding its "structure-to-property" relationship (e.g., the active sites in a catalyst), which is however challenging if the structure possesses complex inhomogeneities. Here, we report an atomic structure study of an important MoVTeO complex metal oxide catalyst that is potentially useful for the industrially relevant propane-based BP/SOHIO process. We combined aberration-corrected scanning transmission electron microscopy with synchrotron powder X-ray crystallography to explore the structure at both nanoscopic and macroscopic scales. At the nanoscopic scale, this material exhibits structural and compositional order within nanosized "domains", while the domains show disordered distribution at the macroscopic scale. We proposed that the intradomain compositional ordering and the interdomain electric dipolar interaction synergistically induce the displacement of Te atoms in the Mo-V-O channels, which determines the geometry of the multifunctional metal oxo-active sites.

Prediction of Antimicrobial Peptides Based on Sequence Alignment and Support Vector Machine-Pairwise Algorithm Utilizing LZ-Complexity

Directory of Open Access Journals (Sweden)

Xin Yi Ng

2015-01-01

Full Text Available This study concerns an attempt to establish a new method for predicting antimicrobial peptides (AMPs which are important to the immune system. Recently, researchers are interested in designing alternative drugs based on AMPs because they have found that a large number of bacterial strains have become resistant to available antibiotics. However, researchers have encountered obstacles in the AMPs designing process as experiments to extract AMPs from protein sequences are costly and require a long set-up time. Therefore, a computational tool for AMPs prediction is needed to resolve this problem. In this study, an integrated algorithm is newly introduced to predict AMPs by integrating sequence alignment and support vector machine- (SVM- LZ complexity pairwise algorithm. It was observed that, when all sequences in the training set are used, the sensitivity of the proposed algorithm is 95.28% in jackknife test and 87.59% in independent test, while the sensitivity obtained for jackknife test and independent test is 88.74% and 78.70%, respectively, when only the sequences that has less than 70% similarity are used. Applying the proposed algorithm may allow researchers to effectively predict AMPs from unknown protein peptide sequences with higher sensitivity.

Simultaneous measurement of Aspartate, NAA, and NAAG using HERMES spectral editing at 3 Tesla.

Science.gov (United States)

Chan, Kimberly L; Saleh, Muhammad G; Oeltzschner, Georg; Barker, Peter B; Edden, Richard A E

2017-07-15

It has previously been shown that the HERMES method ('Hadamard Encoding and Reconstruction of MEGA-Edited Spectroscopy') can be used to simultaneously edit pairs of metabolites (such as N-acetyl-aspartate (NAA) and N-acetyl aspartyl glutamate (NAAG), or glutathione and GABA). In this study, HERMES is extended for the simultaneous editing of three overlapping signals, and illustrated for the example of NAA, NAAG and Aspartate (Asp). Density-matrix simulations were performed in order to optimize the HERMES sequence. The method was tested in NAA and Asp phantoms, and applied to the centrum semiovale of the nine healthy control subjects that were scanned at 3T. Both simulations and phantom experiments showed similar metabolite multiplet patterns with good segregation of all three metabolites. In vivo measurements show consistent relative signal intensities and multiplet patterns with concentrations in agreement with literature values. Simulations indicate co-editing of glutathione, glutamine, and glutamate, but their signals do not significantly overlap with the detected aspartyl resonances. This study demonstrates that a four-step Hadamard-encoded editing scheme can be used to simultaneously edit three otherwise overlapping metabolites, and can measure NAA, NAAG, and Asp in vivo in the brain at 3T with minimal crosstalk. Copyright © 2017 Elsevier Inc. All rights reserved.

Genome-wide identification and characterization of Notch transcription complex-binding sequence paired sites in leukemia cells

Science.gov (United States)

Severson, Eric; Arnett, Kelly L.; Wang, Hongfang; Zang, Chongzhi; Taing, Len; Liu, Hudan; Pear, Warren S.; Liu, X. Shirley; Blacklow, Stephen C.; Aster, Jon C.

2018-01-01

Notch transcription complexes (NTCs) drive target gene expression by binding to two distinct types of genomic response elements, NTC monomer-binding sites and sequence-paired sites (SPSs) that bind NTC dimers. SPSs are conserved and are linked to the Notch-responsiveness of a few genes, but their overall contribution to Notch-dependent gene regulation is unknown. To address this issue, we determined the DNA sequence requirements for NTC dimerization using a fluorescence resonance energy transfer (FRET) assay, and applied insights from these in vitro studies to Notch-“addicted” leukemia cells. We find that SPSs contribute to the regulation of approximately a third of direct Notch target genes. While originally described in promoters, SPSs are present mainly in long-range enhancers, including an enhancer containing a newly described SPS that regulates HES5. Our work provides a general method for identifying sequence-paired sites in genome-wide data sets and highlights the widespread role of NTC dimerization in Notch-transformed leukemia cells. PMID:28465412

Implicitly Defined Neural Networks for Sequence Labeling

Science.gov (United States)

2017-07-31

ularity has soared for the Long Short - Term Memory (LSTM) (Hochreiter and Schmidhuber, 1997) and vari- ants such as Gated Recurrent Unit (GRU) (Cho et...610. Sepp Hochreiter and Jürgen Schmidhuber. 1997. Long short - term memory . Neural computation 9(8):1735– 1780. Zhiheng Huang, Wei Xu, and Kai Yu. 2015...network are coupled together, in order to improve perfor- mance on complex, long -range dependencies in either direction of a sequence. We contrast our

Counterbalancing for serial order carryover effects in experimental condition orders

OpenAIRE

Brooks, Joseph L

2012-01-01

Reactions of neural, psychological, and social systems are rarely, if ever, independent of previous inputs and states. The potential for serial order carryover effects from one condition to the next in a sequence of experimental trials makes counterbalancing of condition order an essential part of experimental design. Here, a method is proposed for generating counterbalanced sequences for repeated-measures designs including those with multiple observations of each condition on one participant...

A shared representation of order between encoding and recognition in visual short-term memory.

Science.gov (United States)

Kalm, Kristjan; Norris, Dennis

2017-07-15

Many complex tasks require people to bind individual events into a sequence that can be held in short term memory (STM). For this purpose information about the order of the individual events in the sequence needs to be maintained in an active and accessible form in STM over a period of few seconds. Here we investigated how the temporal order information is shared between the presentation and response phases of an STM task. We trained a classification algorithm on the fMRI activity patterns from the presentation phase of the STM task to predict the order of the items during the subsequent recognition phase. While voxels in a number of brain regions represented positional information during either presentation and recognition phases, only voxels in the lateral prefrontal cortex (PFC) and the anterior temporal lobe (ATL) represented position consistently across task phases. A shared positional code in the ATL might reflect verbal recoding of visual sequences to facilitate the maintenance of order information over several seconds. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Data-assisted reduced-order modeling of extreme events in complex dynamical systems.

Science.gov (United States)

Wan, Zhong Yi; Vlachas, Pantelis; Koumoutsakos, Petros; Sapsis, Themistoklis

2018-01-01

The prediction of extreme events, from avalanches and droughts to tsunamis and epidemics, depends on the formulation and analysis of relevant, complex dynamical systems. Such dynamical systems are characterized by high intrinsic dimensionality with extreme events having the form of rare transitions that are several standard deviations away from the mean. Such systems are not amenable to classical order-reduction methods through projection of the governing equations due to the large intrinsic dimensionality of the underlying attractor as well as the complexity of the transient events. Alternatively, data-driven techniques aim to quantify the dynamics of specific, critical modes by utilizing data-streams and by expanding the dimensionality of the reduced-order model using delayed coordinates. In turn, these methods have major limitations in regions of the phase space with sparse data, which is the case for extreme events. In this work, we develop a novel hybrid framework that complements an imperfect reduced order model, with data-streams that are integrated though a recurrent neural network (RNN) architecture. The reduced order model has the form of projected equations into a low-dimensional subspace that still contains important dynamical information about the system and it is expanded by a long short-term memory (LSTM) regularization. The LSTM-RNN is trained by analyzing the mismatch between the imperfect model and the data-streams, projected to the reduced-order space. The data-driven model assists the imperfect model in regions where data is available, while for locations where data is sparse the imperfect model still provides a baseline for the prediction of the system state. We assess the developed framework on two challenging prototype systems exhibiting extreme events. We show that the blended approach has improved performance compared with methods that use either data streams or the imperfect model alone. Notably the improvement is more significant in

Data-assisted reduced-order modeling of extreme events in complex dynamical systems.

Directory of Open Access Journals (Sweden)

Zhong Yi Wan

Full Text Available The prediction of extreme events, from avalanches and droughts to tsunamis and epidemics, depends on the formulation and analysis of relevant, complex dynamical systems. Such dynamical systems are characterized by high intrinsic dimensionality with extreme events having the form of rare transitions that are several standard deviations away from the mean. Such systems are not amenable to classical order-reduction methods through projection of the governing equations due to the large intrinsic dimensionality of the underlying attractor as well as the complexity of the transient events. Alternatively, data-driven techniques aim to quantify the dynamics of specific, critical modes by utilizing data-streams and by expanding the dimensionality of the reduced-order model using delayed coordinates. In turn, these methods have major limitations in regions of the phase space with sparse data, which is the case for extreme events. In this work, we develop a novel hybrid framework that complements an imperfect reduced order model, with data-streams that are integrated though a recurrent neural network (RNN architecture. The reduced order model has the form of projected equations into a low-dimensional subspace that still contains important dynamical information about the system and it is expanded by a long short-term memory (LSTM regularization. The LSTM-RNN is trained by analyzing the mismatch between the imperfect model and the data-streams, projected to the reduced-order space. The data-driven model assists the imperfect model in regions where data is available, while for locations where data is sparse the imperfect model still provides a baseline for the prediction of the system state. We assess the developed framework on two challenging prototype systems exhibiting extreme events. We show that the blended approach has improved performance compared with methods that use either data streams or the imperfect model alone. Notably the improvement is more

Structure and Sequence Search on Aptamer-Protein Docking

Science.gov (United States)

Xiao, Jiajie; Bonin, Keith; Guthold, Martin; Salsbury, Freddie

2015-03-01

Interactions between proteins and deoxyribonucleic acid (DNA) play a significant role in the living systems, especially through gene regulation. However, short nucleic acids sequences (aptamers) with specific binding affinity to specific proteins exhibit clinical potential as therapeutics. Our capillary and gel electrophoresis selection experiments show that specific sequences of aptamers can be selected that bind specific proteins. Computationally, given the experimentally-determined structure and sequence of a thrombin-binding aptamer, we can successfully dock the aptamer onto thrombin in agreement with experimental structures of the complex. In order to further study the conformational flexibility of this thrombin-binding aptamer and to potentially develop a predictive computational model of aptamer-binding, we use GPU-enabled molecular dynamics simulations to both examine the conformational flexibility of the aptamer in the absence of binding to thrombin, and to determine our ability to fold an aptamer. This study should help further de-novo predictions of aptamer sequences by enabling the study of structural and sequence-dependent effects on aptamer-protein docking specificity.

Managing complexity of product mix and production flow in configure-to-order production systems

DEFF Research Database (Denmark)

Myrodia, Anna; Bonev, Martin; Hvam, Lars

2014-01-01

In designing configure-to-order production systems for a growing product variety, companies are challenged with an increased complexity for obtaining high productivity levels and cost-effectiveness. In academia several optimization methods and conceptual frameworks for substituting components, or...

Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity.

Science.gov (United States)

Mulligan, M E; Hawley, D K; Entriken, R; McClure, W R

1984-01-11

We describe a simple algorithm for computing a homology score for Escherichia coli promoters based on DNA sequence alone. The homology score was related to 31 values, measured in vitro, of RNA polymerase selectivity, which we define as the product KBk2, the apparent second order rate constant for open complex formation. We found that promoter strength could be predicted to within a factor of +/-4.1 in KBk2 over a range of 10(4) in the same parameter. The quantitative evaluation was linked to an automated (Apple II) procedure for searching and evaluating possible promoters in DNA sequence files.

Minimized state complexity of quantum-encoded cryptic processes

Science.gov (United States)

Riechers, Paul M.; Mahoney, John R.; Aghamohammadi, Cina; Crutchfield, James P.

2016-05-01

The predictive information required for proper trajectory sampling of a stochastic process can be more efficiently transmitted via a quantum channel than a classical one. This recent discovery allows quantum information processing to drastically reduce the memory necessary to simulate complex classical stochastic processes. It also points to a new perspective on the intrinsic complexity that nature must employ in generating the processes we observe. The quantum advantage increases with codeword length: the length of process sequences used in constructing the quantum communication scheme. In analogy with the classical complexity measure, statistical complexity, we use this reduced communication cost as an entropic measure of state complexity in the quantum representation. Previously difficult to compute, the quantum advantage is expressed here in closed form using spectral decomposition. This allows for efficient numerical computation of the quantum-reduced state complexity at all encoding lengths, including infinite. Additionally, it makes clear how finite-codeword reduction in state complexity is controlled by the classical process's cryptic order, and it allows asymptotic analysis of infinite-cryptic-order processes.

Probing Interactions in Complex Molecular Systems through Ordered Assembly

International Nuclear Information System (INIS)

De Yoreo, J.J.; Bartelt, M.C.; Orme, C.A.; Villacampa, A.; Weeks, B.L.; Miller, A.E.

2002-01-01

Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

Environmental Enrichment Expedites Acquisition and Improves Flexibility on a Temporal Sequencing Task in Mice

Directory of Open Access Journals (Sweden)

Darius Rountree-Harrison

2018-03-01

Full Text Available Environmental enrichment (EE via increased opportunities for voluntary exercise, sensory stimulation and social interaction, can enhance the function of and behaviours regulated by cognitive circuits. Little is known, however, as to how this intervention affects performance on complex tasks that engage multiple, definable learning and memory systems. Accordingly, we utilised the Olfactory Temporal Order Discrimination (OTOD task which requires animals to recall and report sequence information about a series of recently encountered olfactory stimuli. This approach allowed us to compare animals raised in either enriched or standard laboratory housing conditions on a number of measures, including the acquisition of a complex discrimination task, temporal sequence recall accuracy (i.e., the ability to accurately recall a sequences of events and acuity (i.e., the ability to resolve past events that occurred in close temporal proximity, as well as cognitive flexibility tested in the style of a rule reversal and an Intra-Dimensional Shift (IDS. We found that enrichment accelerated the acquisition of the temporal order discrimination task, although neither accuracy nor acuity was affected at asymptotic performance levels. Further, while a subtle enhancement of overall performance was detected for both rule reversal and IDS versions of the task, accelerated performance recovery could only be attributed to the shift-like contingency change. These findings suggest that EE can affect specific elements of complex, multi-faceted cognitive processes.

Ordered groups and infinite permutation groups

CERN Document Server

1996-01-01

The subjects of ordered groups and of infinite permutation groups have long en­ joyed a symbiotic relationship. Although the two subjects come from very different sources, they have in certain ways come together, and each has derived considerable benefit from the other. My own personal contact with this interaction began in 1961. I had done Ph. D. work on sequence convergence in totally ordered groups under the direction of Paul Conrad. In the process, I had encountered "pseudo-convergent" sequences in an ordered group G, which are like Cauchy sequences, except that the differences be­ tween terms of large index approach not 0 but a convex subgroup G of G. If G is normal, then such sequences are conveniently described as Cauchy sequences in the quotient ordered group GIG. If G is not normal, of course GIG has no group structure, though it is still a totally ordered set. The best that can be said is that the elements of G permute GIG in an order-preserving fashion. In independent investigations around that t...

ProteinSplit: splitting of multi-domain proteins using prediction of ordered and disordered regions in protein sequences for virtual structural genomics

International Nuclear Information System (INIS)

Wyrwicz, Lucjan S; Koczyk, Grzegorz; Rychlewski, Leszek; Plewczynski, Dariusz

2007-01-01

The annotation of protein folds within newly sequenced genomes is the main target for semi-automated protein structure prediction (virtual structural genomics). A large number of automated methods have been developed recently with very good results in the case of single-domain proteins. Unfortunately, most of these automated methods often fail to properly predict the distant homology between a given multi-domain protein query and structural templates. Therefore a multi-domain protein should be split into domains in order to overcome this limitation. ProteinSplit is designed to identify protein domain boundaries using a novel algorithm that predicts disordered regions in protein sequences. The software utilizes various sequence characteristics to assess the local propensity of a protein to be disordered or ordered in terms of local structure stability. These disordered parts of a protein are likely to create interdomain spacers. Because of its speed and portability, the method was successfully applied to several genome-wide fold annotation experiments. The user can run an automated analysis of sets of proteins or perform semi-automated multiple user projects (saving the results on the server). Additionally the sequences of predicted domains can be sent to the Bioinfo.PL Protein Structure Prediction Meta-Server for further protein three-dimensional structure and function prediction. The program is freely accessible as a web service at http://lucjan.bioinfo.pl/proteinsplit together with detailed benchmark results on the critical assessment of a fully automated structure prediction (CAFASP) set of sequences. The source code of the local version of protein domain boundary prediction is available upon request from the authors

Genetic variability of Echinococcus granulosus complex in various geographical populations of Iran inferred by mitochondrial DNA sequences.

Science.gov (United States)

Spotin, Adel; Mahami-Oskouei, Mahmoud; Harandi, Majid Fasihi; Baratchian, Mehdi; Bordbar, Ali; Ahmadpour, Ehsan; Ebrahimi, Sahar

2017-01-01

To investigate the genetic variability and population structure of Echinococcus granulosus complex, 79 isolates were sequenced from different host species covering human, dog, camel, goat, sheep and cattle as of various geographical sub-populations of Iran (Northwestern, Northern, and Southeastern). In addition, 36 sequences of other geographical populations (Western, Southeastern and Central Iran), were directly retrieved from GenBank database for the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The confirmed isolates were grouped as G1 genotype (n=92), G6 genotype (n=14), G3 genotype (n=8) and G2 genotype (n=1). 50 unique haplotypes were identified based on the analyzed sequences of cox1. A parsimonious network of the sequence haplotypes displayed star-like features in the overall population containing IR23 (22: 19.1%) as the most common haplotype. According to the analysis of molecular variance (AMOVA) test, the high value of haplotype diversity of E. granulosus complex was shown the total genetic variability within populations while nucleotide diversity was low in all populations. Neutrality indices of the cox1 (Tajima's D and Fu's Fs tests) were shown negative values in Western-Northwestern, Northern and Southeastern populations which indicating significant divergence from neutrality and positive but not significant in Central isolates. A pairwise fixation index (Fst) as a degree of gene flow was generally low value for all populations (0.00647-0.15198). The statistically Fst values indicate that Echinococcus sensu stricto (genotype G1-G3) populations are not genetically well differentiated in various geographical regions of Iran. To appraise the hypothetical evolutionary scenario, further study is needed to analyze concatenated mitogenomes and as well a panel of single locus nuclear markers should be considered in wider areas of Iran and neighboring countries. Copyright © 2016 Elsevier B.V. All rights reserved.

Syntheses and structures of technetium(V) and rhenium(V) oxo complexes of peptide having KYC-sequence

International Nuclear Information System (INIS)

Takayama, T.; Suzuki, K.; Sekine, T.; Kudo, H.

2000-01-01

Technetium(V) and rhenium(V) oxo complexes of a peptide having a KYC-sequence such as KYCAR (H 3 L 5 ) and KYCAREPPTRTNAYQGQG-NH 2 (H 3 L 18 ) were synthesized, and structures of the complexes were characterized by spectroscopic techniques. All of the complexes were synthesized by the ligand exchange reaction of [(n-C 4 H 9 ) 4 N][MOCl 4 ] (M = 99 Tc, Re) with peptide in methanol or dimethylformamide solution. These complexes have a square pyramidal structure with an oxo ligand at the apical position. The peptide is coordinated to a metal atom through N amine of lysine. S thiol of cysteine, and N amide of tyrosine and cysteine in the equatorial plane. A lysine (CH 2 ) 4 NH 2 group of the L 5 ligand has the syn conformation with respect to metal-oxo bonding in the complex. The syn isomer was selectively formed in the ligand exchange reaction. The conversion of the syn isomer to the anti isomer was observed only for syn-[ReO(L 5 )], in which the coordination of water to the trans position of the oxo ligand was involved. (orig.)

Multimodal sequence learning.

Science.gov (United States)

Kemény, Ferenc; Meier, Beat

2016-02-01

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

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

Science.gov (United States)

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

2012-10-04

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

The Teaching of Biochemistry: An Innovative Course Sequence Based on the Logic of Chemistry

Science.gov (United States)

Jakubowski, Henry V.; Owen, Whyte G.

1998-06-01

An innovative course sequence for the teaching of biochemistry is offered, which more truly reflects the common philosophy found in biochemistry texts: that the foundation of biological phenomena can best be understood through the logic of chemistry. Topic order is chosen to develop an emerging understanding that is based on chemical principles. Preeminent biological questions serve as a framework for the course. Lipid and lipid-aggregate structures are introduced first, since it is more logical to discuss the intermolecular association of simple amphiphiles to form micelle and bilayer formations than to discuss the complexities of protein structure/folding. Protein, nucleic acid, and carbohydrate structures are studied next. Binding, a noncovalent process and the simplest expression of macromolecular function, follows. The physical (noncovalent) transport of solute molecules across a biological membrane is studied next, followed by the chemical transformation of substrates by enzymes. These are logical extensions of the expression of molecular function, first involving a simpler (physical transport) and second, a more complex (covalent transformation) process. The final sequence involves energy and signal transduction. This unique course sequence emerges naturally when chemical logic is used as an organizing paradigm for structuring a biochemistry course. Traditional order, which seems to reflect historic trends in research, or even an order derived from the central dogma of biology can not provide this logical framework.

Reproductive biology and variation of nuclear ribosomal ITS and ETS sequences in the Calligonum mongolicum complex (Polygonaceae

Directory of Open Access Journals (Sweden)

Wei Shi

2017-01-01

Full Text Available To explore the biosystematics of the Calligonum mongolicum complex (Polygonaceae, the flowering phenological period, breeding and pollination characters and seed set of the complex (C. Mongolicum Turze, C. chinense A. Los., C. gobicum A. Los., C. pumilum A. Los. and C. zaidamense A. Los. were documented in the Turpan Eremophyte Botanical Garden, China. The sequences of the nuclear ribosomal ITS and ETS region were employed to differentiate the C. mongolicum complex and other species in sect. Medusae. The results showed species of the C. mongolicum complex occupied overlapping flowering periods and had consistent pollination agents. Their breeding systems are all self-compatible, tend to be out-crossing and they interbreed amongst each other (out-crossing index, OCI = 4.The crosses within and amongst species had high seed sets (44 - 65%. Phylogenetic analyses of Calligonum sect. Medusae and the network analysis of nrDNA (ITS and ETS in the complex suggest interbreeding amongst “species” within the complex and provide evidence for taxonomically merging the five species in the complex. The detected hybridisation, occurring within the complex, suggests the need to improve traditional methods of ex situ plant conservation in botanical gardens for maintaining genetic diversity of Calligonum within and amongst species from different geographic areas.

Effects of order and sequence of resistance and endurance training on body fat in elementary school-aged girls

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Ana R. Alves

2017-12-01

Full Text Available The purpose of this study was to analyse the effects of order and sequence of concurrent resistance and endurance training on body fat percentage (BFP in a large sample of elementary school-aged girls. One hundred and twenty-six healthy girls, aged 10-11 years (10.95 ± 0.48 years, were randomly assigned to six groups to perform different training protocols per week for 8 weeks: Resistance-only (R, Endurance-only (E, Concurrent Distinct Endurance-Resistance (CDER, Concurrent Parallel Endurance-Resistance (CPER, Concurrent Parallel Resistance-Endurance (CPRE, and a Control group (C. In R and E, the subjects performed single sessions of resistance or endurance exercises, respectively (two days per week. In CDER, resistance-endurance training was performed on different days each week (four days per week. CPER and CPRE performed single-session combined endurance-resistance training or combined resistance-endurance training, respectively, each week (two days per week. After an 8-week training period, BFP decreased in all experimental groups (CPER: 13.3%, p0.05; and CDER: 5.6%, p>0.05. However, a significant difference was found in CPER and CPRE when compared to CDER, E, and R, indicating that training sequence may influence BFP. All programmes were effective, but CPER and CPRE obtained better results for BFP than CDER, E, or R. The effects of concurrent resistance and endurance training on body fat percentage can be mediated by order and sequence of exercise. These results provide insight into optimization of school-based fat loss exercise programmes in childhood.

A look at the effect of sequence complexity on pressure destabilisation of DNA polymers.

Science.gov (United States)

Rayan, Gamal; Macgregor, Robert B

2015-04-01

Our previous studies on the helix-coil transition of double-stranded DNA polymers have demonstrated that molar volume change (ΔV) accompanying the thermally-induced transition can be positive or negative depending on the experimental conditions, that the pressure-induced transition is more cooperative than the heat-induced transition [Rayan and Macgregor, J Phys Chem B2005, 109, 15558-15565], and that the pressure-induced transition does not occur in the absence of water [Rayan and Macgregor, Biophys Chem, 2009, 144, 62-66]. Additionally, we have shown that ΔV values obtained by pressure-dependent techniques differ from those obtained by ambient pressure techniques such as PPC [Rayan et al. J Phys Chem B2009, 113, 1738-1742] thus shedding light on the effects of pressure on DNA polymers. Herein, we examine the effect of sequence complexity, and hence cooperativity on pressure destabilisation of DNA polymers. Working with Clostridium perfringes DNA under conditions such that the estimated ΔV of the helix-coil transition corresponds to -1.78 mL/mol (base pair) at atmospheric pressure, we do not observe the pressure-induced helix-coil transition of this DNA polymer, whereas synthetic copolymers poly[d(A-T)] and poly[d(I-C)] undergo cooperative pressure-induced transitions at similar ΔV values. We hypothesise that the reason for the lack of pressure-induced helix-coil transition of C. perfringens DNA under these experimental conditions lies in its sequence complexity. Copyright © 2015 Elsevier B.V. All rights reserved.

Progress on resolving the Gonatocerus tuberculifemur complex: neither COI nor ITS2 sequence data alone can discriminate all the species within the complex, whereas, ISSR-PCR DNA fingerprinting can

Science.gov (United States)

We utilized two molecular methods to aid in resolving the Gonatocerus tuberculifemur complex, potential glassy-winged sharpshooter (GWSS) biological control candidate agents from South America. The two methods used were DNA sequencing of both the mitochondrial cytochrome oxidase subunit 1 gene (COI...

Hyers-Ulam stability of linear second-order differential equations in complex Banach spaces

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Yongjin Li

2013-08-01

Full Text Available We prove the Hyers-Ulam stability of linear second-order differential equations in complex Banach spaces. That is, if y is an approximate solution of the differential equation $y''+ alpha y'(t +eta y = 0$ or $y''+ alpha y'(t +eta y = f(t$, then there exists an exact solution of the differential equation near to y.

Prediction of Human Activity by Discovering Temporal Sequence Patterns.

Science.gov (United States)

Li, Kang; Fu, Yun

2014-08-01

Early prediction of ongoing human activity has become more valuable in a large variety of time-critical applications. To build an effective representation for prediction, human activities can be characterized by a complex temporal composition of constituent simple actions and interacting objects. Different from early detection on short-duration simple actions, we propose a novel framework for long -duration complex activity prediction by discovering three key aspects of activity: Causality, Context-cue, and Predictability. The major contributions of our work include: (1) a general framework is proposed to systematically address the problem of complex activity prediction by mining temporal sequence patterns; (2) probabilistic suffix tree (PST) is introduced to model causal relationships between constituent actions, where both large and small order Markov dependencies between action units are captured; (3) the context-cue, especially interactive objects information, is modeled through sequential pattern mining (SPM), where a series of action and object co-occurrence are encoded as a complex symbolic sequence; (4) we also present a predictive accumulative function (PAF) to depict the predictability of each kind of activity. The effectiveness of our approach is evaluated on two experimental scenarios with two data sets for each: action-only prediction and context-aware prediction. Our method achieves superior performance for predicting global activity classes and local action units.

Development of taxon-specific sequence characterized amplified region (SCAR) markers based on actin sequences and DNA amplification fingerprinting (DAF): a case study in the Phoma exigua species complex.

Science.gov (United States)

Aveskamp, Maikel M; Woudenberg, Joyce H C; de Gruyter, Johannes; Turco, Elena; Groenewald, Johannes Z; Crous, Pedro W

2009-05-01

Phoma exigua is considered to be an assemblage of at least nine varieties that are mainly distinguished on the basis of host specificity and pathogenicity. However, these varieties are also reported to be weak pathogens and secondary invaders on non-host tissue. In practice, it is difficult to distinguish P. exigua from its close relatives and to correctly identify isolates up to the variety level, because of their low genetic variation and high morphological similarity. Because of quarantine issues and phytosanitary measures, a robust DNA-based tool is required for accurate and rapid identification of the separate taxa in this species complex. The present study therefore aims to develop such a tool based on unique nucleotide sequence identifiers. More than 60 strains of P. exigua and related species were compared in terms of partial actin gene sequences, or analysed using DNA amplification fingerprinting (DAF) with short, arbitrary, mini-hairpin primers. Fragments in the fingerprint unique to a single taxon were identified, purified and sequenced. Alignment of the sequence data and subsequent primer trials led to the identification of taxon-specific sequence characterized amplified regions (SCARs), and to a set of specific oligonucleotide combinations that can be used to identify these organisms in plant quarantine inspections.

The development of second-order social cognition and its relation with complex language understanding and working memory

NARCIS (Netherlands)

Arslan, Burcu; Hohenberger, Annette; Verbrugge, Rineke

2012-01-01

In this study, the development of second-order social cognition and its possible relationship with language and memory were investigated. For this reason two second-order false belief tasks (FBT_2), a short term memory task (WST), a complex working memory task (LST), a linguistic perspective-taking

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

Energy Technology Data Exchange (ETDEWEB)

White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya; Zucker, Jeremy D.; Brislawn, Colin J.; Nicora, Carrie D.; Fansler, Sarah J.; Glaesemann, Kurt R.; Glass, Kevin; Jansson, Janet K.; Langille, Morgan

2016-06-28

Soil metagenomics has been touted as the “grand challenge” for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87.7 Gbp of rapid-mode read data (~250 bp), plus 69.6 Gbp (>1.5 kbp) from Moleculo sequencing. The Moleculo data alone yielded over 5,600 reads of >10 kbp in length, and over 95% of the unassembled reads mapped to contigs of >1.5 kbp. Hybrid assembly of all data resulted in more than 10,000 contigs over 10 kbp in length. We mapped three replicate metatranscriptomes derived from the same parent soil to the Moleculo subassembly and found that 95% of the predicted genes, based on their assignments to Enzyme Commission (EC) numbers, were expressed. The Moleculo subassembly also enabled binning of >100 microbial genome bins. We obtained via direct binning the first complete genome, that of “CandidatusPseudomonas sp. strain JKJ-1” from a native soil metagenome. By mapping metatranscriptome sequence reads back to the bins, we found that several bins corresponding to low-relative-abundanceAcidobacteriawere highly transcriptionally active, whereas bins corresponding to high-relative-abundanceVerrucomicrobiawere not. These results demonstrate that Moleculo sequencing provides a significant advance for resolving complex soil microbial communities.

IMPORTANCESoil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients and supporting growth of plants. However, there is poor molecular-level understanding of their

Unsplit complex frequency shifted perfectly matched layer for second-order wave equation using auxiliary differential equations.

Science.gov (United States)

Gao, Yingjie; Zhang, Jinhai; Yao, Zhenxing

2015-12-01

The complex frequency shifted perfectly matched layer (CFS-PML) can improve the absorbing performance of PML for nearly grazing incident waves. However, traditional PML and CFS-PML are based on first-order wave equations; thus, they are not suitable for second-order wave equation. In this paper, an implementation of CFS-PML for second-order wave equation is presented using auxiliary differential equations. This method is free of both convolution calculations and third-order temporal derivatives. As an unsplit CFS-PML, it can reduce the nearly grazing incidence. Numerical experiments show that it has better absorption than typical PML implementations based on second-order wave equation.

Time spans and spacers: Molecular phylogenetic explorations in the Cladophora complex (Chlorophyta) from the perspective of rDNA gene and spacer sequences

OpenAIRE

Bakker, Frederik Theodoor

1995-01-01

In this study, phylogenetic relationships among genera, species and biogeographic representatives of single Cladophora species within the Cladophorales were analyzed using rDNA gene and spacer sequences. Based on phylogenetic analysis of 18S rRNA gene sequences, the Cladophora complex is shown to be paraphyletic with respect to Cladophora species and includes several genera shich werde traditionally ascribed to the Siphonocladales (Chapter 3). ... Zie: Summary/Samenvatting

Sequence Design for a Test Tube of Interacting Nucleic Acid Strands.

Science.gov (United States)

Wolfe, Brian R; Pierce, Niles A

2015-10-16

We describe an algorithm for designing the equilibrium base-pairing properties of a test tube of interacting nucleic acid strands. A target test tube is specified as a set of desired "on-target" complexes, each with a target secondary structure and target concentration, and a set of undesired "off-target" complexes, each with vanishing target concentration. Sequence design is performed by optimizing the test tube ensemble defect, corresponding to the concentration of incorrectly paired nucleotides at equilibrium evaluated over the ensemble of the test tube. To reduce the computational cost of accepting or rejecting mutations to a random initial sequence, the structural ensemble of each on-target complex is hierarchically decomposed into a tree of conditional subensembles, yielding a forest of decomposition trees. Candidate sequences are evaluated efficiently at the leaf level of the decomposition forest by estimating the test tube ensemble defect from conditional physical properties calculated over the leaf subensembles. As optimized subsequences are merged toward the root level of the forest, any emergent defects are eliminated via ensemble redecomposition and sequence reoptimization. After successfully merging subsequences to the root level, the exact test tube ensemble defect is calculated for the first time, explicitly checking for the effect of the previously neglected off-target complexes. Any off-target complexes that form at appreciable concentration are hierarchically decomposed, added to the decomposition forest, and actively destabilized during subsequent forest reoptimization. For target test tubes representative of design challenges in the molecular programming and synthetic biology communities, our test tube design algorithm typically succeeds in achieving a normalized test tube ensemble defect ≤1% at a design cost within an order of magnitude of the cost of test tube analysis.

SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes

Energy Technology Data Exchange (ETDEWEB)

Drmanac, R.; Drmanac, S.; Labat, I.; Vicentic, A.; Gemmell, A.; Stavropoulos, N.; Jarvis, J.

1992-01-01

A variant of sequencing by hybridization (SBH) is being developed with a potential to inexpensively determine up to 100 million base pairs per year. The method comprises (1) arraying short clones in 864-well plates; (2) growth of the M13 clones or PCR of the inserts; (3) automated spotting of DNAs by corresponding pin-arrays; (4) hybridization of dotted samples with 200-3000 [sup 32]P- or [sup 33]P-labeled 6- to 8-mer probes; and (5) scoring hybridization signals using storage phosphor plates. Some 200 7- to 8-mers can provide an inventory of the genes if CDNA clones are hybridized, or can define the order of 2-kb genomic clones, creating physical and structural maps with 100-bp resolution; the distribution of G+C, LINEs, SINEs, and gene families would be revealed. cDNAs that represent new genes and genomic clones in regions of interest selected by SBH can be sequenced by a gel method. Uniformly distributed clones from the previous step will be hybridized with 2000--3000 6- to 8-mers. As a result, approximately 50--60% of the genomic regions containing members of large repetitive and gene families and those families represented in GenBank would be completely sequenced. In the less redundant regions, every base pair is expected to be read with 3-4 probes, but the complete sequence can not be reconstructed. Such partial sequences allow the inference of similarity and the recognition of coding, regulatory, and repetitive sequences, as well as study of the evolutionary processes all the way up to the species delineation.

SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes

Energy Technology Data Exchange (ETDEWEB)

Drmanac, R.; Drmanac, S.; Labat, I.; Vicentic, A.; Gemmell, A.; Stavropoulos, N.; Jarvis, J.

1992-12-01

A variant of sequencing by hybridization (SBH) is being developed with a potential to inexpensively determine up to 100 million base pairs per year. The method comprises (1) arraying short clones in 864-well plates; (2) growth of the M13 clones or PCR of the inserts; (3) automated spotting of DNAs by corresponding pin-arrays; (4) hybridization of dotted samples with 200-3000 {sup 32}P- or {sup 33}P-labeled 6- to 8-mer probes; and (5) scoring hybridization signals using storage phosphor plates. Some 200 7- to 8-mers can provide an inventory of the genes if CDNA clones are hybridized, or can define the order of 2-kb genomic clones, creating physical and structural maps with 100-bp resolution; the distribution of G+C, LINEs, SINEs, and gene families would be revealed. cDNAs that represent new genes and genomic clones in regions of interest selected by SBH can be sequenced by a gel method. Uniformly distributed clones from the previous step will be hybridized with 2000--3000 6- to 8-mers. As a result, approximately 50--60% of the genomic regions containing members of large repetitive and gene families and those families represented in GenBank would be completely sequenced. In the less redundant regions, every base pair is expected to be read with 3-4 probes, but the complete sequence can not be reconstructed. Such partial sequences allow the inference of similarity and the recognition of coding, regulatory, and repetitive sequences, as well as study of the evolutionary processes all the way up to the species delineation.

SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes

International Nuclear Information System (INIS)

Drmanac, R.; Drmanac, S.; Labat, I.; Vicentic, A.; Gemmell, A.; Stavropoulos, N.; Jarvis, J.

1992-01-01

A variant of sequencing by hybridization (SBH) is being developed with a potential to inexpensively determine up to 100 million base pairs per year. The method comprises (1) arraying short clones in 864-well plates; (2) growth of the M13 clones or PCR of the inserts; (3) automated spotting of DNAs by corresponding pin-arrays; (4) hybridization of dotted samples with 200-3000 32 P- or 33 P-labeled 6- to 8-mer probes; and (5) scoring hybridization signals using storage phosphor plates. Some 200 7- to 8-mers can provide an inventory of the genes if CDNA clones are hybridized, or can define the order of 2-kb genomic clones, creating physical and structural maps with 100-bp resolution; the distribution of G+C, LINEs, SINEs, and gene families would be revealed. cDNAs that represent new genes and genomic clones in regions of interest selected by SBH can be sequenced by a gel method. Uniformly distributed clones from the previous step will be hybridized with 2000--3000 6- to 8-mers. As a result, approximately 50--60% of the genomic regions containing members of large repetitive and gene families and those families represented in GenBank would be completely sequenced. In the less redundant regions, every base pair is expected to be read with 3-4 probes, but the complete sequence can not be reconstructed. Such partial sequences allow the inference of similarity and the recognition of coding, regulatory, and repetitive sequences, as well as study of the evolutionary processes all the way up to the species delineation

Syntheses and structures of technetium(V) and rhenium(V) oxo complexes of peptide having KYC-sequence

Energy Technology Data Exchange (ETDEWEB)

Takayama, T.; Suzuki, K.; Sekine, T.; Kudo, H. [Dept. of Chemistry, Tohoku Univ., Sendai (Japan)

2000-07-01

Technetium(V) and rhenium(V) oxo complexes of a peptide having a KYC-sequence such as KYCAR (H{sub 3}L{sup 5}) and KYCAREPPTRTNAYQGQG-NH{sub 2} (H{sub 3}L{sup 18}) were synthesized, and structures of the complexes were characterized by spectroscopic techniques. All of the complexes were synthesized by the ligand exchange reaction of [(n-C{sub 4}H{sub 9}){sub 4}N][MOCl{sub 4}] (M = {sup 99}Tc, Re) with peptide in methanol or dimethylformamide solution. These complexes have a square pyramidal structure with an oxo ligand at the apical position. The peptide is coordinated to a metal atom through N{sub amine} of lysine. S{sub thiol} of cysteine, and N{sub amide} of tyrosine and cysteine in the equatorial plane. A lysine (CH{sub 2}){sub 4}NH{sub 2} group of the L{sup 5} ligand has the syn conformation with respect to metal-oxo bonding in the complex. The syn isomer was selectively formed in the ligand exchange reaction. The conversion of the syn isomer to the anti isomer was observed only for syn-[ReO(L{sup 5})], in which the coordination of water to the trans position of the oxo ligand was involved. (orig.)

Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.

Directory of Open Access Journals (Sweden)

Jie Qiu

Full Text Available Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou and a wild line (Lanxi 1 collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1 no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2 besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3 high heterozygous rates (0.19-0.49 were observed in several semi-wild lines; and (4 over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.

Second Order Ideal-Ward Continuity

Directory of Open Access Journals (Sweden)

Bipan Hazarika

2014-01-01

Full Text Available The main aim of the paper is to introduce a concept of second order ideal-ward continuity in the sense that a function f is second order ideal-ward continuous if I-limn→∞Δ2f(xn=0 whenever I-limn→∞Δ2xn=0 and a concept of second order ideal-ward compactness in the sense that a subset E of R is second order ideal-ward compact if any sequence x=(xn of points in E has a subsequence z=(zk=(xnk of the sequence x such that I-limk→∞Δ2zk=0 where Δ2zk=zk+2-2zk+1+zk. We investigate the impact of changing the definition of convergence of sequences on the structure of ideal-ward continuity in the sense of second order ideal-ward continuity and compactness of sets in the sense of second order ideal-ward compactness and prove related theorems.

Partially ordered sets in complex networks

International Nuclear Information System (INIS)

Xuan Qi; Du Fang; Wu Tiejun

2010-01-01

In this paper, a partial-order relation is defined among vertices of a network to describe which vertex is more important than another on its contribution to the connectivity of the network. A maximum linearly ordered subset of vertices is defined as a chain and the chains sharing the same end-vertex are grouped as a family. Through combining the same vertices appearing in different chains, a directed chain graph is obtained. Based on these definitions, a series of new network measurements, such as chain length distribution, family diversity distribution, as well as the centrality of families, are proposed. By studying the partially ordered sets in three kinds of real-world networks, many interesting results are revealed. For instance, the similar approximately power-law chain length distribution may be attributed to a chain-based positive feedback mechanism, i.e. new vertices prefer to participate in longer chains, which can be inferred by combining the notable preferential attachment rule with a well-ordered recommendation manner. Moreover, the relatively large average incoming degree of the chain graphs may indicate an efficient substitution mechanism in these networks. Most of the partially ordered set-based properties cannot be explained by the current well-known scale-free network models; therefore, we are required to propose more appropriate network models in the future.

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

Directory of Open Access Journals (Sweden)

Ren Jian

2004-01-01

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

Quantum Image Encryption Algorithm Based on Image Correlation Decomposition

Science.gov (United States)

Hua, Tianxiang; Chen, Jiamin; Pei, Dongju; Zhang, Wenquan; Zhou, Nanrun

2015-02-01

A novel quantum gray-level image encryption and decryption algorithm based on image correlation decomposition is proposed. The correlation among image pixels is established by utilizing the superposition and measurement principle of quantum states. And a whole quantum image is divided into a series of sub-images. These sub-images are stored into a complete binary tree array constructed previously and then randomly performed by one of the operations of quantum random-phase gate, quantum revolving gate and Hadamard transform. The encrypted image can be obtained by superimposing the resulting sub-images with the superposition principle of quantum states. For the encryption algorithm, the keys are the parameters of random phase gate, rotation angle, binary sequence and orthonormal basis states. The security and the computational complexity of the proposed algorithm are analyzed. The proposed encryption algorithm can resist brute force attack due to its very large key space and has lower computational complexity than its classical counterparts.

eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.

Directory of Open Access Journals (Sweden)

Michal Brylinski

2014-09-01

Full Text Available Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.

Th unnatural order of things: A history of the high school science sequence

Science.gov (United States)

Robbins, Dennis M.

Historical studies of US high school science education are rare. This study examines the historical origins of a unique characteristic of the secondary science curriculum, the Biology-Chemistry-Physics (B-C-P) order of courses. Statements from scientists, educators and the media claim that B-C-P has been the traditional curriculum sequence for over a century and can be traced back to the influential educational commission known as the Committee of Ten (CoT) of 1893. This study examines the history of the ordering of high school science subjects over the last 150 years. The reports and primary documents of important national educational commissions, such as the CoT, were searched for their recommendations on secondary science, particularly on course ordering. These recommendations were then compared to national, state and local statistical data on subject offerings and student enrollments to measure the effect of these national commissions on school policy. This study concludes that the Committee of Ten did not create B-P-C. The CoT made six recommendations, five placed Chemistry before Physics (P-C). One recommendation for C-P met with strong disagreement because it was thought an illogical order. Biology as a "uniform" course did not exist at this time and so the CoT made no recommendations for its grade placement. Statistical data shows that B-C-P evolved over many decades. From 1860 up to 1920 most schools used a P-C curriculum believing Physics was a foundational prerequisite of Chemistry. Biology was introduced in the early 1900s and it assumed a position before the physical sciences. Through the 1920s Chemistry and Physics were placed equally likely in 11th or 12 th grades and Biology was in the 10th grade. After World War II, B-C-P became the dominant pattern, exhibited in over 90% of schools. But up to this point in time no educational body or national commission had recommended B-C-P. The Biology-Chemistry-Physics order of courses is a product of many

Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

Directory of Open Access Journals (Sweden)

Bharti Arvind K

2008-12-01

epigenetic boundaries are barely understood at this time, MSLL technology flags both approximate boundaries and methylated genes that deserve additional investigation. MSLL and HMPR sequences provide a valuable resource for maize genome annotation, and are a uniquely valuable complement to any plant genome sequencing project. In order to make these results fully accessible to the community, a web display was developed that shows the alignment of MSLL, HMPR, and other gene-rich sequences to the BACs; this display is continually updated with the latest ESTs and BAC sequences.

Decoding the cognitive map: ensemble hippocampal sequences and decision making

OpenAIRE

Wikenheiser, Andrew M.; Redish, A. David

2014-01-01

Tolman proposed that complex animal behavior is mediated by the cognitive map, an integrative learning system that allows animals to reconfigure previous experience in order to compute predictions about the future. The discovery of place cells in the rodent hippocampus immediately suggested a plausible neural mechanism to fulfill the “map” component of Tolman’s theory. Recent work examining hippocampal representations occurring at fast time scales suggests that these sequences might be import...

Reduced-order modeling of piezoelectric energy harvesters with nonlinear circuits under complex conditions

Science.gov (United States)

Xiang, Hong-Jun; Zhang, Zhi-Wei; Shi, Zhi-Fei; Li, Hong

2018-04-01

A fully coupled modeling approach is developed for piezoelectric energy harvesters in this work based on the use of available robust finite element packages and efficient reducing order modeling techniques. At first, the harvester is modeled using finite element packages. The dynamic equilibrium equations of harvesters are rebuilt by extracting system matrices from the finite element model using built-in commands without any additional tools. A Krylov subspace-based scheme is then applied to obtain a reduced-order model for improving simulation efficiency but preserving the key features of harvesters. Co-simulation of the reduced-order model with nonlinear energy harvesting circuits is achieved in a system level. Several examples in both cases of harmonic response and transient response analysis are conducted to validate the present approach. The proposed approach allows to improve the simulation efficiency by several orders of magnitude. Moreover, the parameters used in the equivalent circuit model can be conveniently obtained by the proposed eigenvector-based model order reduction technique. More importantly, this work establishes a methodology for modeling of piezoelectric energy harvesters with any complicated mechanical geometries and nonlinear circuits. The input load may be more complex also. The method can be employed by harvester designers to optimal mechanical structures or by circuit designers to develop novel energy harvesting circuits.

A comparative study of three ternary complexes prepared in different mixing orders of siRNA/redox-responsive hyperbranched poly (amido amine/hyaluronic acid

Directory of Open Access Journals (Sweden)

Chen CJ

2012-07-01

Full Text Available Cheng-Jun Chen,1 Zhi-Xia Zhao,1 Jian-Cheng Wang,1 En-Yu Zhao,1 Ling-Yan Gao,1 Shu-Feng Zhou,2 Xiao-Yan Liu,1 Wan-Liang Lu,1 Qiang Zhang11State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmaceutics, School of Pharmaceutical Science, Peking University, Beijing, People’s Republic of China; 2Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USAAbstract: In this study, a novel redox-responsive hyperbranched poly(amido amine (named PCD was synthesized and used as a cationic polymer to form a ternary complex with small interfering RNA (siRNA and hyaluronic acid (HA for siRNA delivery. Here, it is hypothesized that different mixing orders result in different assembly structures, which may affect the siRNA delivery efficiency. To investigate the effects of mixing orders on siRNA delivery efficiency in two human breast cancer cell lines, three ternary complexes with different mixing orders of siRNA/PCD/HA were prepared and characterized: mixing order I (initially prepared siRNA/PCD binary complex further coated by negatively charged HA, mixing order II (initially prepared HA/PCD binary complex further incubated with siRNA, and mixing order III (initially prepared siRNA/HA mixture further electrostatically compacted by positively charged PCD. With an optimized siRNA/PCD/HA charge ratio of 1/20/16, the particle sizes and zeta potentials of these ternary complexes were 124.8 nm and 27.3 mV (mixing order I, 147.5 nm and 29.9 mV (mixing order II, and 128.8 nm and 19.4 mV (mixing order III. Also, the effects on stability, cellular uptake, and gene silencing efficiency of siRNA formulated in ternary complexes with different mixing orders were investigated. The results showed that mixing orders I and III displayed better siRNA transfection and protection than mixing order II in human breast cancer MCF-7 and MDA-MB-231 cells. More interesting, at the siRNA/PCD/HA charge ratio of 1/20/16, the

Getting complete genomes from complex samples using nanopore sequencing

DEFF Research Database (Denmark)

Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Albertsen, Mads

Background Short read DNA sequencing and metagenomic binning workflows have made it possible to extract bacterial genome bins from environmental microbial samples containing hundreds to thousands of different species. However, these genome bins often do not represent complete genomes......, as they are mostly fragmented, incomplete and often contaminated with foreign DNA. The value of these `draft genomes` have limited, lasting value to the scientific community, as gene synteny is broken and there is some uncertainty of what is missing1. The genetic material most often missed is important multi......-copy and/or conserved marker genes such as the 16S rRNA gene, as sequence micro-heterogeneity prevents assembly of these genes in the de novo assembly. However, long read sequencing technologies are emerging promising an end to fragmented genome assemblies2. Experimental design We extracted DNA from a full...

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

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Wadim L. Matochko

2013-01-01

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

Exome Sequencing in Suspected Monogenic Dyslipidemias

Science.gov (United States)

Stitziel, Nathan O.; Peloso, Gina M.; Abifadel, Marianne; Cefalu, Angelo B.; Fouchier, Sigrid; Motazacker, M. Mahdi; Tada, Hayato; Larach, Daniel B.; Awan, Zuhier; Haller, Jorge F.; Pullinger, Clive R.; Varret, Mathilde; Rabès, Jean-Pierre; Noto, Davide; Tarugi, Patrizia; Kawashiri, Masa-aki; Nohara, Atsushi; Yamagishi, Masakazu; Risman, Marjorie; Deo, Rahul; Ruel, Isabelle; Shendure, Jay; Nickerson, Deborah A.; Wilson, James G.; Rich, Stephen S.; Gupta, Namrata; Farlow, Deborah N.; Neale, Benjamin M.; Daly, Mark J.; Kane, John P.; Freeman, Mason W.; Genest, Jacques; Rader, Daniel J.; Mabuchi, Hiroshi; Kastelein, John J.P.; Hovingh, G. Kees; Averna, Maurizio R.; Gabriel, Stacey; Boileau, Catherine; Kathiresan, Sekar

2015-01-01

Background Exome sequencing is a promising tool for gene mapping in Mendelian disorders. We utilized this technique in an attempt to identify novel genes underlying monogenic dyslipidemias. Methods and Results We performed exome sequencing on 213 selected family members from 41 kindreds with suspected Mendelian inheritance of extreme levels of low-density lipoprotein (LDL) cholesterol (after candidate gene sequencing excluded known genetic causes for high LDL cholesterol families) or high-density lipoprotein (HDL) cholesterol. We used standard analytic approaches to identify candidate variants and also assigned a polygenic score to each individual in order to account for their burden of common genetic variants known to influence lipid levels. In nine families, we identified likely pathogenic variants in known lipid genes (ABCA1, APOB, APOE, LDLR, LIPA, and PCSK9); however, we were unable to identify obvious genetic etiologies in the remaining 32 families despite follow-up analyses. We identified three factors that limited novel gene discovery: (1) imperfect sequencing coverage across the exome hid potentially causal variants; (2) large numbers of shared rare alleles within families obfuscated causal variant identification; and (3) individuals from 15% of families carried a significant burden of common lipid-related alleles, suggesting complex inheritance can masquerade as monogenic disease. Conclusions We identified the genetic basis of disease in nine of 41 families; however, none of these represented novel gene discoveries. Our results highlight the promise and limitations of exome sequencing as a discovery technique in suspected monogenic dyslipidemias. Considering the confounders identified may inform the design of future exome sequencing studies. PMID:25632026

Sequence-specific capture of protein-DNA complexes for mass spectrometric protein identification.

Directory of Open Access Journals (Sweden)

Cheng-Hsien Wu

Full Text Available The regulation of gene transcription is fundamental to the existence of complex multicellular organisms such as humans. Although it is widely recognized that much of gene regulation is controlled by gene-specific protein-DNA interactions, there presently exists little in the way of tools to identify proteins that interact with the genome at locations of interest. We have developed a novel strategy to address this problem, which we refer to as GENECAPP, for Global ExoNuclease-based Enrichment of Chromatin-Associated Proteins for Proteomics. In this approach, formaldehyde cross-linking is employed to covalently link DNA to its associated proteins; subsequent fragmentation of the DNA, followed by exonuclease digestion, produces a single-stranded region of the DNA that enables sequence-specific hybridization capture of the protein-DNA complex on a solid support. Mass spectrometric (MS analysis of the captured proteins is then used for their identification and/or quantification. We show here the development and optimization of GENECAPP for an in vitro model system, comprised of the murine insulin-like growth factor-binding protein 1 (IGFBP1 promoter region and FoxO1, a member of the forkhead rhabdomyosarcoma (FoxO subfamily of transcription factors, which binds specifically to the IGFBP1 promoter. This novel strategy provides a powerful tool for studies of protein-DNA and protein-protein interactions.

Complex-plane strategy for computing rotating polytropic models - efficiency and accuracy of the complex first-order perturbation theory

International Nuclear Information System (INIS)

Geroyannis, V.S.

1988-01-01

In this paper, a numerical method is developed for determining the structure distortion of a polytropic star which rotates either uniformly or differentially. This method carries out the required numerical integrations in the complex plane. The method is implemented to compute indicative quantities, such as the critical perturbation parameter which represents an upper limit in the rotational behavior of the star. From such indicative results, it is inferred that this method achieves impressive improvement against other relevant methods; most important, it is comparable to some of the most elaborate and accurate techniques on the subject. It is also shown that the use of this method with Chandrasekhar's first-order perturbation theory yields an immediate drastic improvement of the results. Thus, there is no neeed - for most applications concerning rotating polytropic models - to proceed to the further use of the method with higher order techniques, unless the maximum accuracy of the method is required. 31 references

Strategies for Reduced-Order Models in Uncertainty Quantification of Complex Turbulent Dynamical Systems

Science.gov (United States)

Qi, Di

Turbulent dynamical systems are ubiquitous in science and engineering. Uncertainty quantification (UQ) in turbulent dynamical systems is a grand challenge where the goal is to obtain statistical estimates for key physical quantities. In the development of a proper UQ scheme for systems characterized by both a high-dimensional phase space and a large number of instabilities, significant model errors compared with the true natural signal are always unavoidable due to both the imperfect understanding of the underlying physical processes and the limited computational resources available. One central issue in contemporary research is the development of a systematic methodology for reduced order models that can recover the crucial features both with model fidelity in statistical equilibrium and with model sensitivity in response to perturbations. In the first part, we discuss a general mathematical framework to construct statistically accurate reduced-order models that have skill in capturing the statistical variability in the principal directions of a general class of complex systems with quadratic nonlinearity. A systematic hierarchy of simple statistical closure schemes, which are built through new global statistical energy conservation principles combined with statistical equilibrium fidelity, are designed and tested for UQ of these problems. Second, the capacity of imperfect low-order stochastic approximations to model extreme events in a passive scalar field advected by turbulent flows is investigated. The effects in complicated flow systems are considered including strong nonlinear and non-Gaussian interactions, and much simpler and cheaper imperfect models with model error are constructed to capture the crucial statistical features in the stationary tracer field. Several mathematical ideas are introduced to improve the prediction skill of the imperfect reduced-order models. Most importantly, empirical information theory and statistical linear response theory are

Excitonic magnet in external field: Complex order parameter and spin currents

Science.gov (United States)

Geffroy, D.; Hariki, A.; Kuneš, J.

2018-04-01

We investigate spin-triplet exciton condensation in the two-orbital Hubbard model close to half-filling by means of dynamical mean-field theory. Employing an impurity solver that handles complex off-diagonal hybridization functions, we study the behavior of excitonic condensate in stoichiometric and doped systems subject to external magnetic field. We find a general tendency of the triplet order parameter to lie perpendicular with the applied field and identify exceptions from this rule. For solutions exhibiting k -odd spin textures, we discuss the Bloch theorem, which, in the absence of spin-orbit coupling, forbids the appearance of spontaneous net spin current. We demonstrate that the Bloch theorem is not obeyed by the dynamical mean-field theory.

On the multi-index (3 m-parametric) Mittag-Leffler functions, fractional calculus relations and series convergence

Science.gov (United States)

Paneva-Konovska, Jordanka

2013-10-01

In this paper we consider a family of 3 m-indices generalizations of the classical Mittag-Leffler function, called multi-index (3 m-parametric) Mittag-Leffler functions. We survey the basic properties of these entire functions, find their order and type, and new representations by means of Mellin-Barnes type contour integrals, Wright p Ψ q -functions and Fox H-functions, asymptotic estimates. Formulas for integer and fractional order integration and differentiations are found, and these are extended also for the operators of the generalized fractional calculus (multiple Erdélyi-Kober operators). Some interesting particular cases of the multi-index Mittag-Leffler functions are discussed. The convergence of series of such type functions in the complex plane is considered, and analogues of the Cauchy-Hadamard, Abel, Tauber and Littlewood theorems are provided.

A Simple and High Performing Rate Control Initialization Method for H.264 AVC Coding Based on Motion Vector Map and Spatial Complexity at Low Bitrate

Directory of Open Access Journals (Sweden)

Yalin Wu

2014-01-01

Full Text Available The temporal complexity of video sequences can be characterized by motion vector map which consists of motion vectors of each macroblock (MB. In order to obtain the optimal initial QP (quantization parameter for the various video sequences which have different spatial and temporal complexities, this paper proposes a simple and high performance initial QP determining method based on motion vector map and temporal complexity to decide an initial QP in given target bit rate. The proposed algorithm produces the reconstructed video sequences with outstanding and stable quality. For any video sequences, the initial QP can be easily determined from matrices by target bit rate and mapped spatial complexity using proposed mapping method. Experimental results show that the proposed algorithm can show more outstanding objective and subjective performance than other conventional determining methods.

Optimization of parameter values for complex pulse sequences by simulated annealing: application to 3D MP-RAGE imaging of the brain.

Science.gov (United States)

Epstein, F H; Mugler, J P; Brookeman, J R

1994-02-01

A number of pulse sequence techniques, including magnetization-prepared gradient echo (MP-GRE), segmented GRE, and hybrid RARE, employ a relatively large number of variable pulse sequence parameters and acquire the image data during a transient signal evolution. These sequences have recently been proposed and/or used for clinical applications in the brain, spine, liver, and coronary arteries. Thus, the need for a method of deriving optimal pulse sequence parameter values for this class of sequences now exists. Due to the complexity of these sequences, conventional optimization approaches, such as applying differential calculus to signal difference equations, are inadequate. We have developed a general framework for adapting the simulated annealing algorithm to pulse sequence parameter value optimization, and applied this framework to the specific case of optimizing the white matter-gray matter signal difference for a T1-weighted variable flip angle 3D MP-RAGE sequence. Using our algorithm, the values of 35 sequence parameters, including the magnetization-preparation RF pulse flip angle and delay time, 32 flip angles in the variable flip angle gradient-echo acquisition sequence, and the magnetization recovery time, were derived. Optimized 3D MP-RAGE achieved up to a 130% increase in white matter-gray matter signal difference compared with optimized 3D RF-spoiled FLASH with the same total acquisition time. The simulated annealing approach was effective at deriving optimal parameter values for a specific 3D MP-RAGE imaging objective, and may be useful for other imaging objectives and sequences in this general class.

An Analysis of Delay-based and Integrator-based Sequence Detectors for Grid-Connected Converters

DEFF Research Database (Denmark)

Khazraj, Hesam; Silva, Filipe Miguel Faria da; Bak, Claus Leth

2017-01-01

-signal cancellation operators are the main members of the delay-based sequence detectors. The aim of this paper is to provide a theoretical and experimental comparative study between integrator and delay based sequence detectors. The theoretical analysis is conducted based on the small-signal modelling......Detecting and separating positive and negative sequence components of the grid voltage or current is of vital importance in the control of grid-connected power converters, HVDC systems, etc. To this end, several techniques have been proposed in recent years. These techniques can be broadly...... classified into two main classes: The integrator-based techniques and Delay-based techniques. The complex-coefficient filter-based technique, dual second-order generalized integrator-based method, multiple reference frame approach are the main members of the integrator-based sequence detector and the delay...

Integrated sequence analysis. Final report

International Nuclear Information System (INIS)

Andersson, K.; Pyy, P.

1998-02-01

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

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

Anatomy of extremely thin marine sequences landward of a passive-margin hinge zone: Neogene Calvert Cliffs succession, Maryland, U.S.A.

Energy Technology Data Exchange (ETDEWEB)

Kidwell, S.M. [Univ. of Chicago, IL (United States). Dept. of Geophysical Sciences

1997-03-01

Detailed examination of Neogene strata in cliffs 25--35 m high along the western shore of Chesapeake Bay, Maryland, reveals the complexity of the surviving record of siliciclastic sequences {approximately}150 km inland of the structural hinge zone of the Atlantic passive margin. Previous study of the lower to middle Miocene Calvert (Plum Point Member) and Choptank Formations documented a series of third-order sequences 7--10 m thick in which lowstand deposits are entirely lacking, transgressive tracts comprise a mosaic of condensed bioclastic facies, and regressive (highstand) tracts are present but partially truncated by the next sequence boundary; smaller-scale (fourth-order) cyclic units could not be resolved. Together, these sequences constitute the transgressive and early highstand tracts of a larger (second-order Miocene) composite sequence. The present paper documents stratigraphic relations higher in the Calvert Cliffs succession, including the upper Miocene St. Marys Formation, which represents late highstand marine deposits of the Miocene second-order sequence, and younger Neogene fluvial and tidal-inlet deposits representing incised-valley deposits of the succeeding second-order cycle. The St. Marys Formation consists of a series of tabular units 2--5 m thick, each with an exclusively transgressive array of facies and bounded by stranding surfaces of abrupt shallowing. These units, which are opposite to the flooding-surface-bounded regressive facies arrays of model parasequences, are best characterized as shaved sequences in which only the transgressive tract survives, and are stacked into larger transgressive, highstand, and forced-regression sets.

Multilocus sequence typing scheme for the Mycobacterium abscessus complex.

Science.gov (United States)

Macheras, Edouard; Konjek, Julie; Roux, Anne-Laure; Thiberge, Jean-Michel; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby E; Bodmer, Thomas; Jarlier, Vincent; Cambau, Emmanuelle; Brisse, Sylvain; Caro, Valérie; Rastogi, Nalin; Gaillard, Jean-Louis; Heym, Beate

2014-01-01

We developed a multilocus sequence typing (MLST) scheme for Mycobacterium abscessus sensu lato, based on the partial sequencing of seven housekeeping genes: argH, cya, glpK, gnd, murC, pta and purH. This scheme was used to characterize a collection of 227 isolates recovered between 1994 and 2010 in France, Germany, Switzerland and Brazil. We identified 100 different sequence types (STs), which were distributed into three groups on the tree obtained by concatenating the sequences of the seven housekeeping gene fragments (3576bp): the M. abscessus sensu stricto group (44 STs), the "M. massiliense" group (31 STs) and the "M. bolletii" group (25 STs). SplitTree analysis showed a degree of intergroup lateral transfers. There was also evidence of lateral transfer events involving rpoB. The most prevalent STs in our collection were ST1 (CC5; 20 isolates) and ST23 (CC3; 31 isolates). Both STs were found in Europe and Brazil, and the latter was implicated in a large post-surgical procedure outbreak in Brazil. Respiratory isolates from patients with cystic fibrosis belonged to a large variety of STs; however, ST2 was predominant in this group of patients. Our MLST scheme, publicly available at www.pasteur.fr/mlst, offers investigators a valuable typing tool for M. abscessus sensu lato in future epidemiological studies throughout the world. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers

Directory of Open Access Journals (Sweden)

Kuzin Alexander

2008-08-01

Full Text Available Abstract Background The presence of highly conserved sequences within cis-regulatory regions can serve as a valuable starting point for elucidating the basis of enhancer function. This study focuses on regulation of gene expression during the early events of Drosophila neural development. We describe the use of EvoPrinter and cis-Decoder, a suite of interrelated phylogenetic footprinting and alignment programs, to characterize highly conserved sequences that are shared among co-regulating enhancers. Results Analysis of in vivo characterized enhancers that drive neural precursor gene expression has revealed that they contain clusters of highly conserved sequence blocks (CSBs made up of shorter shared sequence elements which are present in different combinations and orientations within the different co-regulating enhancers; these elements contain either known consensus transcription factor binding sites or consist of novel sequences that have not been functionally characterized. The CSBs of co-regulated enhancers share a large number of sequence elements, suggesting that a diverse repertoire of transcription factors may interact in a highly combinatorial fashion to coordinately regulate gene expression. We have used information gained from our comparative analysis to discover an enhancer that directs expression of the nervy gene in neural precursor cells of the CNS and PNS. Conclusion The combined use EvoPrinter and cis-Decoder has yielded important insights into the combinatorial appearance of fundamental sequence elements required for neural enhancer function. Each of the 30 enhancers examined conformed to a pattern of highly conserved blocks of sequences containing shared constituent elements. These data establish a basis for further analysis and understanding of neural enhancer function.

One size does not fit all: On how Markov model order dictates performance of genomic sequence analyses

Science.gov (United States)

Narlikar, Leelavati; Mehta, Nidhi; Galande, Sanjeev; Arjunwadkar, Mihir

2013-01-01

The structural simplicity and ability to capture serial correlations make Markov models a popular modeling choice in several genomic analyses, such as identification of motifs, genes and regulatory elements. A critical, yet relatively unexplored, issue is the determination of the order of the Markov model. Most biological applications use a predetermined order for all data sets indiscriminately. Here, we show the vast variation in the performance of such applications with the order. To identify the ‘optimal’ order, we investigated two model selection criteria: Akaike information criterion and Bayesian information criterion (BIC). The BIC optimal order delivers the best performance for mammalian phylogeny reconstruction and motif discovery. Importantly, this order is different from orders typically used by many tools, suggesting that a simple additional step determining this order can significantly improve results. Further, we describe a novel classification approach based on BIC optimal Markov models to predict functionality of tissue-specific promoters. Our classifier discriminates between promoters active across 12 different tissues with remarkable accuracy, yielding 3 times the precision expected by chance. Application to the metagenomics problem of identifying the taxum from a short DNA fragment yields accuracies at least as high as the more complex mainstream methodologies, while retaining conceptual and computational simplicity. PMID:23267010

Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

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.

Nonparametric combinatorial sequence models.

Science.gov (United States)

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

2011-11-01

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

Anatomically ordered tapping interferes more with one-digit addition than two-digit addition: a dual-task fMRI study.

Science.gov (United States)

Soylu, Firat; Newman, Sharlene D

2016-02-01

Fingers are used as canonical representations for numbers across cultures. In previous imaging studies, it was shown that arithmetic processing activates neural resources that are known to participate in finger movements. Additionally, in one dual-task study, it was shown that anatomically ordered finger tapping disrupts addition and subtraction more than multiplication, possibly due to a long-lasting effect of early finger counting experiences on the neural correlates and organization of addition and subtraction processes. How arithmetic task difficulty and tapping complexity affect the concurrent performance is still unclear. If early finger counting experiences have bearing on the neural correlates of arithmetic in adults, then one would expect anatomically and non-anatomically ordered tapping to have different interference effects, given that finger counting is usually anatomically ordered. To unravel these issues, we studied how (1) arithmetic task difficulty and (2) the complexity of the finger tapping sequence (anatomical vs. non-anatomical ordering) affect concurrent performance and use of key neural circuits using a mixed block/event-related dual-task fMRI design with adult participants. The results suggest that complexity of the tapping sequence modulates interference on addition, and that one-digit addition (fact retrieval), compared to two-digit addition (calculation), is more affected from anatomically ordered tapping. The region-of-interest analysis showed higher left angular gyrus BOLD response for one-digit compared to two-digit addition, and in no-tapping conditions than dual tapping conditions. The results support a specific association between addition fact retrieval and anatomically ordered finger movements in adults, possibly due to finger counting strategies that deploy anatomically ordered finger movements early in the development.

Decoding the cognitive map: ensemble hippocampal sequences and decision making.

Science.gov (United States)

Wikenheiser, Andrew M; Redish, A David

2015-06-01

Tolman proposed that complex animal behavior is mediated by the cognitive map, an integrative learning system that allows animals to reconfigure previous experience in order to compute predictions about the future. The discovery of place cells in the rodent hippocampus immediately suggested a plausible neural mechanism to fulfill the 'map' component of Tolman's theory. Recent work examining hippocampal representations occurring at fast time scales suggests that these sequences might be important for supporting the inferential mental operations associated with the cognitive map function. New findings that hippocampal sequences play an important causal role in mediating adaptive behavior on a moment-by-moment basis suggest specific neural processes that may underlie Tolman's cognitive map framework. Copyright © 2014 Elsevier Ltd. All rights reserved.

Stability and Hopf Bifurcation of Fractional-Order Complex-Valued Single Neuron Model with Time Delay

Science.gov (United States)

Wang, Zhen; Wang, Xiaohong; Li, Yuxia; Huang, Xia

2017-12-01

In this paper, the problems of stability and Hopf bifurcation in a class of fractional-order complex-valued single neuron model with time delay are addressed. With the help of the stability theory of fractional-order differential equations and Laplace transforms, several new sufficient conditions, which ensure the stability of the system are derived. Taking the time delay as the bifurcation parameter, Hopf bifurcation is investigated and the critical value of the time delay for the occurrence of Hopf bifurcation is determined. Finally, two representative numerical examples are given to show the effectiveness of the theoretical results.

Counterbalancing for Serial Order Carryover Effects in Experimental Condition Orders

Science.gov (United States)

Brooks, Joseph L.

2012-01-01

Reactions of neural, psychological, and social systems are rarely, if ever, independent of previous inputs and states. The potential for serial order carryover effects from one condition to the next in a sequence of experimental trials makes counterbalancing of condition order an essential part of experimental design. Here, a method is proposed…

OD (order-disorder) character of the crystal structure of godlevskite Ni9S8

DEFF Research Database (Denmark)

Merlino, Stefano; Makovicky, Emil

2009-01-01

Godlevskite Ni9S8 has been found to be an OD (order-disorder) structure consisting of two kinds of OD layers in strict alternation; these layers display stacking disorder. They have layer symmetries P( )2m and P212(2), respectively (symmetry elements in parentheses are perpendicular to OD layers......). Two structures with maximum degree of order (MDO polytypes), with space-group symmetries A222 and I4122, respectively, exist, together with more complex polytypes or disordered sequences. The OD character is in keeping with the frequent twinning of godlevskite....

Ordered Pooling of Optical Flow Sequences for Action Recognition

OpenAIRE

Wang, Jue; Cherian, Anoop; Porikli, Fatih

2017-01-01

Training of Convolutional Neural Networks (CNNs) on long video sequences is computationally expensive due to the substantial memory requirements and the massive number of parameters that deep architectures demand. Early fusion of video frames is thus a standard technique, in which several consecutive frames are first agglomerated into a compact representation, and then fed into the CNN as an input sample. For this purpose, a summarization approach that represents a set of consecutive RGB fram...

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 ...

Extending generalized Fibonacci sequences and their binet-type formula

Directory of Open Access Journals (Sweden)

Saeki Osamu

2006-01-01

Full Text Available We study the extension problem of a given sequence defined by a finite order recurrence to a sequence defined by an infinite order recurrence with periodic coefficient sequence. We also study infinite order recurrence relations in a strong sense and give a complete answer to the extension problem. We also obtain a Binet-type formula, answering several open questions about these sequences and their characteristic power series.

Finite-part integration of the generalized Stieltjes transform and its dominant asymptotic behavior for small values of the parameter. I. Integer orders

Science.gov (United States)

Tica, Christian D.; Galapon, Eric A.

2018-02-01

The paper addresses the exact evaluation of the generalized Stieltjes transform Sn[f ] =∫0∞f (x ) (ω+x ) -nd x of integral order n = 1, 2, 3, … about ω = 0 from which the asymptotic behavior of Sn[f] for small parameters ω is directly extracted. An attempt to evaluate the integral by expanding the integrand (ω + x)-n about ω = 0 and then naively integrating the resulting infinite series term by term leads to an infinite series whose terms are divergent integrals. Assigning values to the divergent integrals, say, by analytic continuation or by Hadamard's finite part is known to reproduce only some of the correct terms of the expansion but completely misses out a group of terms. Here we evaluate explicitly the generalized Stieltjes transform by means of finite-part integration recently introduced in Galapon [Proc. R. Soc. A 473, 20160567 (2017)]. It is shown that, when f(x) does not vanish or has zero of order m at the origin such that (n - m) ≥ 1, the dominant terms of Sn[f] as ω → 0 come from contributions arising from the poles and branch points of the complex valued function f(z)(ω + z)-n. These dominant terms are precisely the terms missed out by naive term by term integration. Furthermore, it is demonstrated how finite-part integration leads to new series representations of special functions by exploiting their known Stieltjes integral representations. Finally, the application of finite part integration in obtaining asymptotic expansions of the effective diffusivity in the limit of high Peclet number, the Green-Kubo formula for the self-diffusion coefficient, and the antisymmetric part of the diffusion tensor in the weak noise limit is discussed.

Novel algorithms for protein sequence analysis

NARCIS (Netherlands)

Ye, Kai

2008-01-01

Each protein is characterized by its unique sequential order of amino acids, the so-called protein sequence. Biology”s paradigm is that this order of amino acids determines the protein”s architecture and function. In this thesis, we introduce novel algorithms to analyze protein sequences. Chapter 1

MIMO processing based on higher-order Poincaré spheres

Science.gov (United States)

Fernandes, Gil M.; Muga, Nelson J.; Pinto, Armando N.

2017-08-01

A multi-input multi-output (MIMO) algorithm based on higher-order Poincaré spheres is demonstrated for space-division multiplexing (SDM) systems. The MIMO algorithm is modulation format agnostic, robust to frequency offset and does not require training sequences. In this approach, the space-multiplexed signal is decomposed in sets of two tributary signals, with each set represented in a higher-order Poincaré sphere. For any arbitrary complex modulation format, the samples of two tributaries can be represented in a given higher-order Poincaré sphere with a symmetry plane. The crosstalk along propagation changes the spatial orientation of this plane and, therefore, it can be compensated by computing and realigning the best fit plane. We show how the transmitted signal can be successfully recovered using this procedure for all possible combinations of tributaries. Moreover, we analyze the convergence speed for the MIMO technique considering several optical-to-noise ratios.

Methylene blue binding to DNA with alternating AT base sequence: minor groove binding is favored over intercalation.

Science.gov (United States)

Rohs, Remo; Sklenar, Heinz

2004-04-01

The results presented in this paper on methylene blue (MB) binding to DNA with AT alternating base sequence complement the data obtained in two former modeling studies of MB binding to GC alternating DNA. In the light of the large amount of experimental data for both systems, this theoretical study is focused on a detailed energetic analysis and comparison in order to understand their different behavior. Since experimental high-resolution structures of the complexes are not available, the analysis is based on energy minimized structural models of the complexes in different binding modes. For both sequences, four different intercalation structures and two models for MB binding in the minor and major groove have been proposed. Solvent electrostatic effects were included in the energetic analysis by using electrostatic continuum theory, and the dependence of MB binding on salt concentration was investigated by solving the non-linear Poisson-Boltzmann equation. We find that the relative stability of the different complexes is similar for the two sequences, in agreement with the interpretation of spectroscopic data. Subtle differences, however, are seen in energy decompositions and can be attributed to the change from symmetric 5'-YpR-3' intercalation to minor groove binding with increasing salt concentration, which is experimentally observed for the AT sequence at lower salt concentration than for the GC sequence. According to our results, this difference is due to the significantly lower non-electrostatic energy for the minor groove complex with AT alternating DNA, whereas the slightly lower binding energy to this sequence is caused by a higher deformation energy of DNA. The energetic data are in agreement with the conclusions derived from different spectroscopic studies and can also be structurally interpreted on the basis of the modeled complexes. The simple static modeling technique and the neglect of entropy terms and of non-electrostatic solute

Complexities of sibling analysis when exposures and outcomes change with time and birth order

OpenAIRE

Sudan, M; Kheifets, LI; Arah, OA; Divan, HA; Olsen, J

2014-01-01

In this study, we demonstrate the complexities of performing a sibling analysis with a re-examination of associations between cell phone exposures and behavioral problems observed previously in the Danish National Birth Cohort. Children (52,680; including 5441 siblings) followed up to age 7 were included. We examined differences in exposures and behavioral problems between siblings and non-siblings and by birth order and birth year. We estimated associations between cell phone exposures and b...

STRATEGIC SEQUENCES IN POLICE INTERVIEWS AND THE IMPORTANCE OF ORDER AND CULTURAL FIT

NARCIS (Netherlands)

Beune, Karlijn; Giebels, Ellen; Adair, Wendi L.; Fennis, Bob M.; Van Der Zee, Karen I.

This study introduces the concept of strategic sequences to police interviews and concentrates on the impact of active listening behavior and rational arguments. To test the authors' central assumption that the effectiveness of strategic sequences is dependent on cultural fit (i.e., the match with

Strategic sequences in police interviews and the importance of order and cultural fit

NARCIS (Netherlands)

Beune, K.; Giebels, Ellen; Adair, Wendi L.; Fennis, B.M.; van der Zee, Karen; van der Zee, Karin I.

2011-01-01

This study introduces the concept of strategic sequences to police interviews and concentrates on the impact of active listening behavior and rational arguments. To test the authors’ central assumption that the effectiveness of strategic sequences is dependent on cultural fit (i.e., the match with

Strategic sequences in police interviews and the importance of order and cultural fit

NARCIS (Netherlands)

Beune, Karlijn; Giebels, Ellen; Adair, Wendi L.; Fennis, Bob M.; van der Zee, Karen I.

This study introduces the concept of strategic sequences to police interviews and concentrates on the impact of active listening behavior and rational arguments. To test the authors' central assumption that the effectiveness of strategic sequences is dependent on cultural fit (i.e., the match with

Lessons learned from whole exome sequencing in multiplex families affected by a complex genetic disorder, intracranial aneurysm.

Directory of Open Access Journals (Sweden)

Janice L Farlow

Full Text Available Genetic risk factors for intracranial aneurysm (IA are not yet fully understood. Genomewide association studies have been successful at identifying common variants; however, the role of rare variation in IA susceptibility has not been fully explored. In this study, we report the use of whole exome sequencing (WES in seven densely-affected families (45 individuals recruited as part of the Familial Intracranial Aneurysm study. WES variants were prioritized by functional prediction, frequency, predicted pathogenicity, and segregation within families. Using these criteria, 68 variants in 68 genes were prioritized across the seven families. Of the genes that were expressed in IA tissue, one gene (TMEM132B was differentially expressed in aneurysmal samples (n=44 as compared to control samples (n=16 (false discovery rate adjusted p-value=0.023. We demonstrate that sequencing of densely affected families permits exploration of the role of rare variants in a relatively common disease such as IA, although there are important study design considerations for applying sequencing to complex disorders. In this study, we explore methods of WES variant prioritization, including the incorporation of unaffected individuals, multipoint linkage analysis, biological pathway information, and transcriptome profiling. Further studies are needed to validate and characterize the set of variants and genes identified in this study.

Intelligibility in microbial complex systems: Wittgenstein and the score of life.

Science.gov (United States)

Baquero, Fernando; Moya, Andrés

2012-01-01

Knowledge in microbiology is reaching an extreme level of diversification and complexity, which paradoxically results in a strong reduction in the intelligibility of microbial life. In our days, the "score of life" metaphor is more accurate to express the complexity of living systems than the classic "book of life." Music and life can be represented at lower hierarchical levels by music scores and genomic sequences, and such representations have a generational influence in the reproduction of music and life. If music can be considered as a representation of life, such representation remains as unthinkable as life itself. The analysis of scores and genomic sequences might provide mechanistic, phylogenetic, and evolutionary insights into music and life, but not about their real dynamics and nature, which is still maintained unthinkable, as was proposed by Wittgenstein. As complex systems, life or music is composed by thinkable and only showable parts, and a strategy of half-thinking, half-seeing is needed to expand knowledge. Complex models for complex systems, based on experiences on trans-hierarchical integrations, should be developed in order to provide a mixture of legibility and imageability of biological processes, which should lead to higher levels of intelligibility of microbial life.

Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.

Science.gov (United States)

Gilbert, Jack A; Field, Dawn; Huang, Ying; Edwards, Rob; Li, Weizhong; Gilna, Paul; Joint, Ian

2008-08-22

Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with >100 members, approximately 91% of which were novel. This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities--if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families.

Universal sequence map (USM of arbitrary discrete sequences

Directory of Open Access Journals (Sweden)

Almeida Jonas S

2002-02-01

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

Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR.

Science.gov (United States)

Tyson, Jess; Armour, John A L

2012-12-11

Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in) regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR

Directory of Open Access Journals (Sweden)

Tyson Jess

2012-12-01

Full Text Available Abstract Background Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. Results In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. Conclusion This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

Isolation of a new two-dimensional honeycomb carbonato-bridged copper(II) complex exhibiting long-range ferromagnetic ordering.

Science.gov (United States)

Majumder, Arpi; Choudhury, Chirantan Roy; Mitra, Samiran; Rosair, Georgina M; El Fallah, M Salah; Ribas, Joan

2005-04-28

Atmospheric CO2 fixation by an aqueous solution containing Cu(ClO4)2.6H2O and 4-aminopyridine (4-apy) yields a novel example of a two-dimensional mu3-CO3 bridged copper(II) complex {[Cu(4-apy)2]3(mu3-CO3)2(ClO4)2.(1/2)CH3OH}n that has been characterized by IR, UV and X-ray crystallography; preliminary magnetic measurements show that complex exhibits long-range ordered ferromagnetic coupling.

Spatial serial order processing in schizophrenia.

Science.gov (United States)

Fraser, David; Park, Sohee; Clark, Gina; Yohanna, Daniel; Houk, James C

2004-10-01

The aim of this study was to examine serial order processing deficits in 21 schizophrenia patients and 16 age- and education-matched healthy controls. In a spatial serial order working memory task, one to four spatial targets were presented in a randomized sequence. Subjects were required to remember the locations and the order in which the targets were presented. Patients showed a marked deficit in ability to remember the sequences compared with controls. Increasing the number of targets within a sequence resulted in poorer memory performance for both control and schizophrenia subjects, but the effect was much more pronounced in the patients. Targets presented at the end of a long sequence were more vulnerable to memory error in schizophrenia patients. Performance deficits were not attributable to motor errors, but to errors in target choice. The results support the idea that the memory errors seen in schizophrenia patients may be due to saturating the working memory network at relatively low levels of memory load.

Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity.

OpenAIRE

Mulligan, M E; Hawley, D K; Entriken, R; McClure, W R

1984-01-01

We describe a simple algorithm for computing a homology score for Escherichia coli promoters based on DNA sequence alone. The homology score was related to 31 values, measured in vitro, of RNA polymerase selectivity, which we define as the product KBk2, the apparent second order rate constant for open complex formation. We found that promoter strength could be predicted to within a factor of +/-4.1 in KBk2 over a range of 10(4) in the same parameter. The quantitative evaluation was linked to ...

Step out - Step in Sequencing Games

NARCIS (Netherlands)

Musegaas, M.; Borm, P.E.M.; Quant, M.

2014-01-01

In this paper a new class of relaxed sequencing games is introduced: the class of Step out - Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order.

A pedagogical example of second-order arithmetic sequences applied to the construction of computer passwords by upper elementary grade students

Science.gov (United States)

Coggins, Porter E.

2015-04-01

The purpose of this paper is (1) to present how general education elementary school age students constructed computer passwords using digital root sums and second-order arithmetic sequences, (2) argue that computer password construction can be used as an engaging introduction to generate interest in elementary school students to study mathematics related to computer science, and (3) share additional mathematical ideas accessible to elementary school students that can be used to create computer passwords. This paper serves to fill a current gap in the literature regarding the integration of mathematical content accessible to upper elementary school students and aspects of computer science in general, and computer password construction in particular. In addition, the protocols presented here can serve as a hook to generate further interest in mathematics and computer science. Students learned to create a random-looking computer password by using biometric measurements of their shoe size, height, and age in months and to create a second-order arithmetic sequence, then converted the resulting numbers into characters that become their computer passwords. This password protocol can be used to introduce students to good computer password habits that can serve a foundation for a life-long awareness of data security. A refinement of the password protocol is also presented.

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.

λ (Δim) -statistical convergence of order α

Science.gov (United States)

Colak, Rifat; Et, Mikail; Altin, Yavuz

2017-09-01

In this study, using the generalized difference operator Δim and a sequence λ = (λn) which is a non-decreasing sequence of positive numbers tending to ∞ such that λn+1 ≤ λn+1, λ1 = 1, we introduce the concepts of λ (Δim) -statistical convergence of order α (α ∈ (0, 1]) and strong λ (Δim) -Cesàro summablility of order α (α > 0). We establish some connections between λ (Δim) -statistical convergence of order α and strong λ (Δim) -Cesàro summablility of order α. It is shown that if a sequence is strongly λ (Δim) -Cesàro summable of order α, then it is λ (Δim) -statistically convergent of order β in case 0 < α ≤ β ≤ 1.

Taxonomy and phylogeny of Pluteus glaucotinctus sensu lato (Agaricales, Basidiomycota), a multicontinental species complex

Science.gov (United States)

Nelson Menolli; Alfredo Justo; Pedro Arrillaga; C.K. Pradeep; Andrew M. Minnis; Marina. Capelari

2014-01-01

In order to better understand species delimitation in the Pluteus glaucotinctus species complex, we present a detailed study based on morphological and DNA sequence (nrITS + tef1) data. Pluteus glaucotinctus sensu stricto is known only from the type collection (Democratic Republic of the Congo), which is re-...

A REVIEW OF ORDER PICKING IMPROVEMENT METHODS

Directory of Open Access Journals (Sweden)

Johan Oscar Ong

2014-09-01

Full Text Available As a crucial and one of the most important parts of warehousing, order picking often raises discussion between warehousing professionals, resulting in various studies aiming to analyze how order picking activity can be improved from various perspective. This paper reviews various past researches on order picking improvement, and the various methods those studies analyzed or developed. This literature review is based on twenty research articles on order picking improvement viewed from four different perspectives: Automation (specifically, stock-to-picker system, storage assignment policy, order batching, and order picking sequencing. By reviewing these studies, we try to identify the most prevalent order picking improvement approach to order picking improvement. Keywords: warehousing; stock-to-picker; storage assignment; order batching; order picking sequencing; improvement

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.

Algebraic Number Precoded OFDM Transmission for Asynchronous Cooperative Multirelay Networks

Directory of Open Access Journals (Sweden)

Hua Jiang

2014-01-01

Full Text Available This paper proposes a space-time block coding (STBC transmission scheme for asynchronous cooperative systems. By combination of rotated complex constellations and Hadamard transform, these constructed codes are capable of achieving full cooperative diversity with the analysis of the pairwise error probability (PEP. Due to the asynchronous characteristic of cooperative systems, orthogonal frequency division multiplexing (OFDM technique with cyclic prefix (CP is adopted for combating timing delays from relay nodes. The total transmit power across the entire network is fixed and appropriate power allocation can be implemented to optimize the network performance. The relay nodes do not require decoding and demodulation operation, resulting in a low complexity. Besides, there is no delay for forwarding the OFDM symbols to the destination node. At the destination node the received signals have the corresponding STBC structure on each subcarrier. In order to reduce the decoding complexity, the sphere decoder is implemented for fast data decoding. Bit error rate (BER performance demonstrates the effectiveness of the proposed scheme.

Phylogenetic relationships in the Festuca-Lolium complex (Loliinae; Poaceae: New insights from chloroplast sequences

Directory of Open Access Journals (Sweden)

Yajuan Cheng

2016-07-01

Full Text Available The species within the Lolium/Festuca grass complex have dispersed and colonized large areas of temperate global grasslands both naturally and by human intervention. The species within this grass complex represent some of the most important grass species both for amenity and agricultural use worldwide. There has been renewed interest by grass breeders in producing hybrid combinations between these species and several countries now market Festulolium varieties as a combination of genes from both genera. The two genera have been differentiated by their inflorescence structure, but controversy has surrounded the taxonomic classification of the Lolium-Festuca complex species for several decades. In order to better understand the complexities within the Lolium/Festuca complex and their genetic background, the phylogeny of important examplers from the Lolium-Festuca complex were reconstructed. In total 40 taxa representing the Festuca and Lolium species with Vulpia myuros and Brachypodium distachyon as outgroups were sampled, using two noncoding intergenic spacers (trnQ-rps16, trnH-psbA and one coding gene (rbcL. Maximum parsimony (MP, Bayesian inference (BI analyses based on each partition and combined plastid DNA dataset, and median-jointing network analysis were employed. The outcomes strongly suggested that the subgen. Schedonorus has a close relationship to Lolium, and it is also proposed to move the sect. Leucopoa from subgen. Leucopoa to Subgen. Schedonorus and to separate sect. Breviaristatae from the subgen. Leucopoa. We found that F. californica could be a lineage of hybrid origin because of its intermediate placement between the broad-leaved and fine-leaved clade.

Step out-step in sequencing games

NARCIS (Netherlands)

Musegaas, Marieke; Borm, Peter; Quant, Marieke

2015-01-01

In this paper a new class of relaxed sequencing games is introduced: the class of Step out–Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order. First,

Long-range order in canary song.

Science.gov (United States)

Markowitz, Jeffrey E; Ivie, Elizabeth; Kligler, Laura; Gardner, Timothy J

2013-01-01

Bird songs range in form from the simple notes of a Chipping Sparrow to the rich performance of the nightingale. Non-adjacent correlations can be found in the syntax of some birdsongs, indicating that the choice of what to sing next is determined not only by the current syllable, but also by previous syllables sung. Here we examine the song of the domesticated canary, a complex singer whose song consists of syllables, grouped into phrases that are arranged in flexible sequences. Phrases are defined by a fundamental time-scale that is independent of the underlying syllable duration. We show that the ordering of phrases is governed by long-range rules: the choice of what phrase to sing next in a given context depends on the history of the song, and for some syllables, highly specific rules produce correlations in song over timescales of up to ten seconds. The neural basis of these long-range correlations may provide insight into how complex behaviors are assembled from more elementary, stereotyped modules.

Real and complex analysis

CERN Document Server

Apelian, Christopher; Taft, Earl; Nashed, Zuhair

2009-01-01

The Spaces R, Rk, and CThe Real Numbers RThe Real Spaces RkThe Complex Numbers CPoint-Set Topology Bounded SetsClassification of Points Open and Closed SetsNested Intervals and the Bolzano-Weierstrass Theorem Compactness and Connectedness Limits and Convergence Definitions and First Properties Convergence Results for SequencesTopological Results for Sequences Properties of Infinite SeriesManipulations of Series in RFunctions: Definitions and Limits DefinitionsFunctions as MappingsSome Elementary Complex FunctionsLimits of FunctionsFunctions: Continuity and Convergence Continuity Uniform Continuity Sequences and Series of FunctionsThe DerivativeThe Derivative for f: D1 → RThe Derivative for f: Dk → RThe Derivative for f: Dk → RpThe Derivative for f: D → CThe Inverse and Implicit Function TheoremsReal IntegrationThe Integral of f: [a, b] → RProperties of the Riemann Integral Further Development of Integration TheoryVector-Valued and Line IntegralsComplex IntegrationIntroduction to Complex Integrals Fu...

Asymptotically stable fourth-order accurate schemes for the diffusion equation on complex shapes

International Nuclear Information System (INIS)

Abarbanel, S.; Ditkowski, A.

1997-01-01

An algorithm which solves the multidimensional diffusion equation on complex shapes to fourth-order accuracy and is asymptotically stable in time is presented. This bounded-error result is achieved by constructing, on a rectangular grid, a differentiation matrix whose symmetric part is negative definite. The differentiation matrix accounts for the Dirichlet boundary condition by imposing penalty-like terms. Numerical examples in 2-D show that the method is effective even where standard schemes, stable by traditional definitions, fail. The ability of the paradigm to be applied to arbitrary geometric domains is an important feature of the algorithm. 5 refs., 14 figs

Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

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Joern Toedling

Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

Spectral representation of the particle production out of equilibrium—Schwinger mechanism in pulsed electric fields

International Nuclear Information System (INIS)

Fukushima, Kenji

2014-01-01

We develop a formalism to describe the particle production out of equilibrium in terms of dynamical spectral functions, i.e. Wigner transformed Pauli–Jordan's and Hadamard's functions. We take an explicit example of a spatially homogeneous scalar theory under pulsed electric fields and investigate the time evolution of the spectral functions. In the out-state we find an oscillatory peak in Hadamard's function as a result of the mixing between positive- and negative-energy waves. The strength of this peak is of the linear order of the Bogoliubov mixing coefficient, whereas the peak corresponding to the Schwinger mechanism is of the quadratic order. Between the in- and the out-states we observe a continuous flow of the spectral peaks together with two transient oscillatory peaks. We also discuss the medium effect at finite temperature and density. We emphasize that the entire structure of the spectral functions conveys rich information on real-time dynamics including the particle production. (paper)

Forward Genetics by Sequencing EMS Variation-Induced Inbred Lines

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Charles Addo-Quaye

2017-02-01

Full Text Available In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of ethyl methanesulfonate (EMS-mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error-prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequences in wild-type siblings and heterozygous in segregating families. This region contained a single nonsynonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the Sorghum ortholog encoding the gibberellic acid (GA biosynthetic enzyme ent-kaurene oxidase. Application of exogenous GA rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models. This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks cosegregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extension of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.

Yeast genome sequencing:

DEFF Research Database (Denmark)

Piskur, Jure; Langkjær, Rikke Breinhold

2004-01-01

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

The role of consolidation in learning context-dependent phonotactic patterns in speech and digital sequence production.

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Anderson, Nathaniel D; Dell, Gary S

2018-04-03

Speakers implicitly learn novel phonotactic patterns by producing strings of syllables. The learning is revealed in their speech errors. First-order patterns, such as "/f/ must be a syllable onset," can be distinguished from contingent, or second-order, patterns, such as "/f/ must be an onset if the vowel is /a/, but a coda if the vowel is /o/." A metaanalysis of 19 experiments clearly demonstrated that first-order patterns affect speech errors to a very great extent in a single experimental session, but second-order vowel-contingent patterns only affect errors on the second day of testing, suggesting the need for a consolidation period. Two experiments tested an analogue to these studies involving sequences of button pushes, with fingers as "consonants" and thumbs as "vowels." The button-push errors revealed two of the key speech-error findings: first-order patterns are learned quickly, but second-order thumb-contingent patterns are only strongly revealed in the errors on the second day of testing. The influence of computational complexity on the implicit learning of phonotactic patterns in speech production may be a general feature of sequence production.

Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae.

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Blake T Hovde

Full Text Available Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales, is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales, and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb, compact (∼ 40% of the genome is protein coding and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two "red" RuBisCO activases that are shared across many algal lineages. The Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes.

A linguistic representation of the regulation of transcription initiation. I. An ordered array of complex symbols with distinctive features.

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Collado-Vides, J

1993-01-01

The inadequacy of context-free grammars in the description of regulatory information contained in DNA gave the formal justification for a linguistic approach to the study of gene regulation. Based on that result, we have initiated a linguistic formalization of the regulatory arrays of 107 sigma 70 E. coli promoters. The complete sequences of promoter (Pr), operator (Op) and activator binding sites (I) have previously been identified as the smallest elements, or categories, for a combinatorial analysis of the range of transcription initiation of sigma 70 promoters. These categories are conceptually equivalent to phonemes of natural language. Several features associated with these categories are required in a complete description of regulatory arrays of promoters. We have to select the best way to describe the properties that are pertinent for the description of such regulatory regions. In this paper we define distinctive features of regulatory regions based on the following criteria: identification of subclasses of substitutable elements, simplicity, selection of the most directly related information, and distinction of one array among the whole set of promoters. Alternative ways to represent distances in between regulatory sites are discussed, permitting, together with a principle of precedence, the identification of an ordered set of complex symbols as a unique representation for a promoter and its associated regulatory sites. In the accompanying paper additional distinctive features of promoters and regulatory sites are identified.

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

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Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

2017-07-01

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

Crystal structure of importin-{alpha} complexed with a classic nuclear localization sequence obtained by oriented peptide library screening

Energy Technology Data Exchange (ETDEWEB)

Takeda, A.A.S.; Fontes, M.R.M. [UNESP, Universidade Estadual Paulista, Botucatu, SP (Brazil); Yang, S.N.Y. [University of Melbourne, Melbourne (Australia); Harris, J.M. [Queensland University of Technology, Brisbane (Australia); Jans, D.A. [Monash University, Clayton (Australia); Kobe, B. [University of Queensland, Brisbane, QU (Australia)

2012-07-01

Full text: Importin-{alpha} (Imp{alpha}) plays a role in the classical nuclear import pathway, binding to cargo proteins with activities in the nucleus. Different Imp{alpha} paralogs responsible for specific cargos can be found in a single organism. The cargos contain nuclear localization sequences (NLSs), which are characterized by one or two clusters of basic amino acids (monopartite and bipartite NLSs, respectively). In this work we present the crystal structure of Imp{alpha} from M. musculus (residues 70-529, lacking the auto inhibitory domain) bound to a NLS peptide (pepTM). The peptide corresponds to the optimal sequence obtained by an oriented peptide library experiment designed to probe the specificity of the major NLS binding site. The peptide library used five degenerate positions and identified the sequence KKKRR as the optimal sequence for binding to this site for mouse Imp{alpha} (70-529). The protein was obtained using an E. coli expression system and purified by affinity chromatography followed by an ion exchange chromatography. A single crystal of Imp{alpha} -pepTM complex was grown by the hanging drop method. The data were collected using the Synchrotron Radiation Source LNLS, Brazil and processed to 2.3. Molecular replacement techniques were used to determine the crystal structure. Electron density corresponding to the peptide was present in both major and minor binding sites The peptide is bound to Imp{alpha} similar as the simian virus 40 (SV40) large tumour (T)-antigen NLS. Binding assays confirmed that the peptide bound to Imp{alpha} with low nM affinities. This is the first time that structural information has been linked to an oriented peptide library screening approach for importin-{alpha}; the results will contribute to understanding of the sequence determinants of classical NLSs, and may help identify as yet unidentified classical NLSs in novel proteins. (author)

Ultrashort optical solitons in the cubic-quintic complex Ginzburg-Landau equation with higher-order terms

International Nuclear Information System (INIS)

Fewo, Serge I.; Kofane, Timoleon C.; Ngabireng, Claude M.

2008-01-01

With the help of the Maxwell equations, a basic equation modeling the propagation of ultrashort optical solitons in optical fiber is derived, namely the higher-order complex Ginzburg-Landau equation (HCGLE). Considering this one-dimensional HCGLE, we obtain a set of differential equations characterizing the variation of the pulse parameters called collective variables (CVs), of a pulse propagating in dispersion-managed (DM) fiber optic-links. Equations obtained are investigated numerically in order to observe the behaviour of pulse parameters along the optical fiber. A fully numerical simulation of the one-dimensional HCGLE finally tests the results of the CV theory. A good agreement between both methods is observed. Among various behaviours, chaotic pulses, attenuate pulses and stable pulses can be obtained under certain parameter values. (author)

COULCC: A continued-fraction algorithm for Coulomb functions of complex order with complex arguments

International Nuclear Information System (INIS)

Thompson, I.J.; Barnett, A.R.

1985-01-01

The routine COULCC calculates both the oscillating and the exponentially varying Coulomb wave functions, and their radial derivations, for complex eta(Sommerfeld parameter), complex energies and complex angular momenta. The functions for uncharged scattering (spherical Bessels) and cylindrical Bessel functions are special cases which are more easily solved. Two linearly independent solutions are found, in general, to the differential equation f''(x)+g(x)f(x)=0, where g(x) has x 0 , x -1 and x -2 terms, with coefficients 1, -2eta and -lambda(lambda+1), respectively. (orig.)

Analysis of the first and second internal transcribed spacer sequences of the ribosomal DNA in Biomphalaria tenagophila complex (Mollusca: Planorbidae

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Teofânia HDA Vidigal

2004-03-01

Full Text Available The first and second internal transcribed spacer regions (ITS1 and ITS2 of the ribosomal DNA of Biomphalaria tenagophila complex (B. tenagophila, B. occidentalis, and B. t. guaibensis were sequenced and compared. The alignment lengths of these regions were about 655 bp and 481 bp, respectively. Phylogenetic relationships among the Biomphalaria species were inferred by Maximum Parsimony and Neighbor-joining methods. The phylogenetic trees produced, in most of the cases, were in accordance with morphological systematics and other molecular data previously obtained by polymerase chain reaction and restriction fragment length polymorphism analysis. The present results provide support for the proposal that B. tenagophila represents a complex comprising B. tenagophila, B. occidentalis and B. t. guaibensis.

Getting complete genomes from complex samples using nanopore sequencing

DEFF Research Database (Denmark)

Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Albertsen, Mads

Short read sequencing and metagenomic binning workflows have made it possible to extract bacterial genome bins from environmental microbial samples containing hundreds to thousands of different species. However, these genome bins often do not represent complete genomes, as they are mostly...... fragmented, incomplete and often contaminated with foreign DNA and with no robust strategies to validate the quality. The value of these `draft genomes` have limited, lasting value to the scientific community, as gene synteny is broken and the uncertainty of what is missing. The genetic material most often...... missed is important multi-copy and/or conserved marker genes such as the 16S rRNA gene, as sequence micro-heterogeneity prevents assembly of these genes in the de novo assembly. We demonstrate that using nanopore long reads it is now possible to overcome these issues and make complete genomes from...

Ordering within Moral Orders to Manage Classroom Trouble

Science.gov (United States)

Doherty, Catherine; McGregor, Rowena; Shield, Paul

2016-01-01

This paper demonstrates how classroom trouble warranting teacher intervention can stem from transgressions in different layers of the complex moral order regulating classroom interactions. The paper builds from Durkheim's treatment of schooling as the institution responsible for the inculcation of a shared moral order, Bernstein's distinction…

Feynman propagator for spin foam quantum gravity.

Science.gov (United States)

Oriti, Daniele

2005-03-25

We link the notion causality with the orientation of the spin foam 2-complex. We show that all current spin foam models are orientation independent. Using the technology of evolution kernels for quantum fields on Lie groups, we construct a generalized version of spin foam models, introducing an extra proper time variable. We prove that different ranges of integration for this variable lead to different classes of spin foam models: the usual ones, interpreted as the quantum gravity analogue of the Hadamard function of quantum field theory (QFT) or as inner products between quantum gravity states; and a new class of causal models, the quantum gravity analogue of the Feynman propagator in QFT, nontrivial function of the orientation data, and implying a notion of "timeless ordering".

A Novel Method for Decoding Any High-Order Hidden Markov Model

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Fei Ye

2014-01-01

Full Text Available This paper proposes a novel method for decoding any high-order hidden Markov model. First, the high-order hidden Markov model is transformed into an equivalent first-order hidden Markov model by Hadar’s transformation. Next, the optimal state sequence of the equivalent first-order hidden Markov model is recognized by the existing Viterbi algorithm of the first-order hidden Markov model. Finally, the optimal state sequence of the high-order hidden Markov model is inferred from the optimal state sequence of the equivalent first-order hidden Markov model. This method provides a unified algorithm framework for decoding hidden Markov models including the first-order hidden Markov model and any high-order hidden Markov model.

Crystallinity and order of poly(ethylene oxide)/lithium triflate complex confined in nanoporous membranes

International Nuclear Information System (INIS)

Bishop, Christina; Teeters, Dale

2009-01-01

The confinement of poly(ethylene oxide), PEO, electrolyte in pores of 13, 35, 55 and 100 nm in diameter in nanoporous alumina membranes was seen to have effects on the ionic conduction properties. Specific conductivity values for the PEO/lithium triflate complex in the 13 and 35 nm pores, for temperatures below the melt temperatures, were increased by a factor of four compared to the non-confined polymer and the 55 and 100 nm pore systems. Thermal analysis data indicate the melting temperature for the PEO electrolyte in the pores is directly proportional to the pore size such that as the pore size of confinement is decreased, the T m decreases as well. The same behavior is seen for the amount of crystallinity, with less crystallinity being observed as the pores become smaller. Perhaps the observed conduction behavior could be attributed to less crystallinity. However, it is known that confinement of polyethers in pores results in stretching and ordering of the backbone and that such ordering can increase ion conduction. This ordering would seem to be the major factor involved in these results. The enhanced conduction only being seen in the 13 and 35 nm pores and not the 55 and 100 nm pores is attributed to the larger size for the latter which allows a more bulk-like behavior with less ordering.

Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns

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Alexander H. Li

2017-10-01

Full Text Available Abstract Background Left-sided lesions (LSLs account for an important fraction of severe congenital cardiovascular malformations (CVMs. The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. Methods Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF, and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. Results Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1 as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2. We also identified two genes (DNAH5, OFD1 with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5–6.5. Conclusions Our analytical strategy highlights the utility of bioinformatic resources, including human

PsB multiprotein complex of Dictyostelium discoideum. Demonstration of cellulose binding activity and order of protein subunit assembly.

Science.gov (United States)

McGuire, V; Alexander, S

1996-06-14

The differentiated spores of Dictyostelium are surrounded by an extracellular matrix, the spore coat, which protects them from environmental factors allowing them to remain viable for extended periods of time. This presumably is a major evolutionary advantage. This unique extracellular matrix is composed of cellulose and glycoproteins. Previous work has shown that some of these spore coat glycoproteins exist as a preassembled multiprotein complex (the PsB multiprotein complex) which is stored in the prespore vesicles (Watson, N., McGuire, V., and Alexander, S (1994) J. Cell Sci. 107, 2567-2579). Later in development, the complex is synchronously secreted from the prespore vesicles and incorporated into the spore coat. We now have shown that the PsB complex has a specific in vitro cellulose binding activity. The analysis of mutants lacking individual subunits of the PsB complex revealed the relative order of assembly of the subunit proteins and demonstrated that the protein subunits must be assembled for cellulose binding activity. These results provide a biochemical explanation for the localization of this multiprotein complex in the spore coat.

n-Order and maximum fuzzy similarity entropy for discrimination of signals of different complexity: Application to fetal heart rate signals.

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Zaylaa, Amira; Oudjemia, Souad; Charara, Jamal; Girault, Jean-Marc

2015-09-01

This paper presents two new concepts for discrimination of signals of different complexity. The first focused initially on solving the problem of setting entropy descriptors by varying the pattern size instead of the tolerance. This led to the search for the optimal pattern size that maximized the similarity entropy. The second paradigm was based on the n-order similarity entropy that encompasses the 1-order similarity entropy. To improve the statistical stability, n-order fuzzy similarity entropy was proposed. Fractional Brownian motion was simulated to validate the different methods proposed, and fetal heart rate signals were used to discriminate normal from abnormal fetuses. In all cases, it was found that it was possible to discriminate time series of different complexity such as fractional Brownian motion and fetal heart rate signals. The best levels of performance in terms of sensitivity (90%) and specificity (90%) were obtained with the n-order fuzzy similarity entropy. However, it was shown that the optimal pattern size and the maximum similarity measurement were related to intrinsic features of the time series. Copyright © 2015 Elsevier Ltd. All rights reserved.

Image correlation method for DNA sequence alignment.

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Curilem Saldías, Millaray; Villarroel Sassarini, Felipe; Muñoz Poblete, Carlos; Vargas Vásquez, Asticio; Maureira Butler, Iván

2012-01-01

The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

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

Science.gov (United States)

Lynch, Brighid; Beukema, Patrick; Verstynen, Timothy

2017-01-01

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

Fractionalization of the complex-valued Brownian motion of order n using Riemann-Liouville derivative. Applications to mathematical finance and stochastic mechanics

International Nuclear Information System (INIS)

Jumarie, Guy

2006-01-01

The (complex-valued) Brownian motion of order n is defined as the limit of a random walk on the complex roots of the unity. Real-valued fractional noises are obtained as fractional derivatives of the Gaussian white noise (or order two). Here one combines these two approaches and one considers the new class of fractional noises obtained as fractional derivative of the complex-valued Brownian motion of order n. The key of the approach is the relation between differential and fractional differential provided by the fractional Taylor's series of analytic function f(z+h)=E α (h α D z α ).f(z), where E α is the Mittag-Leffler function on the one hand, and the generalized Maruyama's notation, on the other hand. Some questions are revisited such as the definition of fractional Brownian motion as integral w.r.t. (dt) α , and the exponential growth equation driven by fractional Brownian motion, to which a new solution is proposed. As a first illustrative example of application, in mathematical finance, one proposes a new approach to the optimal management of a stochastic portfolio of fractional order via the Lagrange variational technique applied to the state moment dynamical equations. In the second example, one deals with non-random Lagrangian mechanics of fractional order. The last example proposes a new approach to fractional stochastic mechanics, and the solution so obtained gives rise to the question as to whether physical systems would not have their own internal random times

The synthesis and complex anion-vacancy ordered structure of La0.33Sr0.67MnO2.42

International Nuclear Information System (INIS)

Dixon, Edward; Hadermann, Joke; Hayward, Michael A.

2011-01-01

The low-temperature topotactic reduction of La 0.33 Sr 0.67 MnO 3 with NaH results in the formation of La 0.33 Sr 0.67 MnO 2.42 . A combination of neutron powder and electron diffraction data show that La 0.33 Sr 0.67 MnO 2.42 adopts a novel anion-vacancy ordered structure with a 6-layer OOTOOT' stacking sequence of the 'octahedral' and tetrahedral layers (Pcmb, a=5.5804(1) A, b=23.4104(7) A, c=11.2441(3) A). A significant concentration of anion vacancies at the anion site, which links neighbouring 'octahedral' layers means that only 25% of the 'octahedral' manganese coordination sites actually have 6-fold MnO 6 coordination, the remainder being MnO 5 square-based pyramidal sites. The chains of cooperatively twisted apex-linked MnO 4 tetrahedra adopt an ordered -L-R-L-R- arrangement within each tetrahedral layer. This is the first published example of a fully refined structure of this type which exhibits such intralayer ordering of the twisted tetrahedral chains. The rationale behind the contrasting structures of La 0.33 Sr 0.67 MnO 2.42 and other previously reported reduced La 1-x Sr x MnO 3-y phases is discussed. - Graphical Abstract: The topotactic reduction of the perovskite phase La 0.33 Sr 0.67 MnO 3 with NaH yields La 0.33 Sr 0.67 MnO 2.42(3) , which adopts a novel anion vacancy ordered structure with a 6-layer OOTOOT' stacking sequence of the 'octahedral' and tetrahedral layers. The anion site that links the neighbouring octahedral layers is partially occupied so only 25% of the 'octahedral' manganese sites actually have 6-fold MnO 6 coordination. Highlights: → Topotactic reduction with NaH to form a mixed valent Mn 2+ /Mn 3+ phase. → Novel layered anion-vacancy ordered structure. → Comparison to related brownmillerite structure types.

A dimer of the lymphoid protein RAG1 recognizes the recombination signal sequence and the complex stably incorporates the high mobility group protein HMG2.

Science.gov (United States)

Rodgers, K K; Villey, I J; Ptaszek, L; Corbett, E; Schatz, D G; Coleman, J E

1999-07-15

RAG1 and RAG2 are the two lymphoid-specific proteins required for the cleavage of DNA sequences known as the recombination signal sequences (RSSs) flanking V, D or J regions of the antigen-binding genes. Previous studies have shown that RAG1 alone is capable of binding to the RSS, whereas RAG2 only binds as a RAG1/RAG2 complex. We have expressed recombinant core RAG1 (amino acids 384-1008) in Escherichia coli and demonstrated catalytic activity when combined with RAG2. This protein was then used to determine its oligomeric forms and the dissociation constant of binding to the RSS. Electrophoretic mobility shift assays show that up to three oligomeric complexes of core RAG1 form with a single RSS. Core RAG1 was found to exist as a dimer both when free in solution and as the minimal species bound to the RSS. Competition assays show that RAG1 recognizes both the conserved nonamer and heptamer sequences of the RSS. Zinc analysis shows the core to contain two zinc ions. The purified RAG1 protein overexpressed in E.coli exhibited the expected cleavage activity when combined with RAG2 purified from transfected 293T cells. The high mobility group protein HMG2 is stably incorporated into the recombinant RAG1/RSS complex and can increase the affinity of RAG1 for the RSS in the absence of RAG2.

Learning word order at birth: A NIRS study

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Silvia Benavides-Varela

2017-06-01

Full Text Available In language, the relative order of words in sentences carries important grammatical functions. However, the developmental origins and the neural correlates of the ability to track word order are to date poorly understood. The current study therefore investigates the origins of infants’ ability to learn about the sequential order of words, using near-infrared spectroscopy (NIRS with newborn infants. We have conducted two experiments: one in which a word order change was implemented in 4-word sequences recorded with a list intonation (as if each word was a separate item in a list; list prosody condition, Experiment 1 and one in which the same 4-word sequences were recorded with a well-formed utterance-level prosodic contour (utterance prosody condition, Experiment 2. We found that newborns could detect the violation of the word order in the list prosody condition, but not in the utterance prosody condition. These results suggest that while newborns are already sensitive to word order in linguistic sequences, prosody appears to be a stronger cue than word order for the identification of linguistic units at birth.

The presence of five nifH-like sequences in Clostridium pasteurianum: sequence divergence and transcription properties.

OpenAIRE

Wang, S Z; Chen, J S; Johnson, J L

1988-01-01

The nifH gene encodes the iron protein (component II) of the nitrogenase complex. We have previously shown the presence in Clostridium pasteurianum of two nifH-like sequences in addition to the nifH1 gene which codes for a protein identical to the isolated iron protein. In the present study, we report that there are at least five nifH-like sequences in C. pasteurianum. DNA sequencing data indicate that the six nifH (nifH1) and nifH-like (nifH2, nifH3, nifH4, nifH5 and nifH6) sequences are not...

Purification, crystallization and preliminary X-ray crystallographic analysis of the ETS domain of human Ergp55 in complex with the cfos promoter DNA sequence

International Nuclear Information System (INIS)

Gangwar, Shanti P.; Meena, Sita R.; Saxena, Ajay K.

2012-01-01

The ETS domain of human Ergp55 was purified and crystallized in native, complexes with E74, and cfos promoter DNA sequences. The X-ray intensity data set was collected on ETS–cfos promoter DNA complex crystal at 3.1 Å resolution to analyze the structure by molecular replacement technique. The Ergp55 protein belongs to the Ets family of transciption factors. The Ets transcription factors are involved in various developmental processes and the regulation of cancer metabolism. They contain a highly similar DNA-binding domain known as the ETS domain and have diverse functions in oncogenesis and physiology. The Ets transcription factors differ in their DNA-binding preference at the ETS site and the mechanisms by which they target genes are not clearly understood. To understand its DNA-binding mechanism, the ETS domain of Ergp55 was expressed and purified. The ETS domain was crystallized in the native form and in complex forms with DNA sequences from the E74 and cfos promoters. An X-ray diffraction data set was collected from an ETS–cfos DNA complex crystal at a wavelength of 0.9725 Å on the BM14 synchrotron beamline at the ESRF, France. The ETS–cfos DNA complex crystal belonged to space group C222 1 , with four molecules in the asymmetric unit. For structure analysis, initial phases for the ETS–cfos DNA complex were obtained by the molecular-replacement technique with Phaser in the CCP4 suite using the coordinates of Fli-1 protein and cfos DNA as search models. Structure analysis of the ETS–cfos DNA complex may possibly explain the DNA-binding specificity and its mechanism of interaction with the ETS domain of Ergp55

Permutation Entropy for Random Binary Sequences

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Lingfeng Liu

2015-12-01

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

Systems genetics of complex diseases using RNA-sequencing methods

DEFF Research Database (Denmark)

Mazzoni, Gianluca; Kogelman, Lisette; Suravajhala, Prashanth

2015-01-01

Next generation sequencing technologies have enabled the generation of huge quantities of biological data, and nowadays extensive datasets at different ‘omics levels have been generated. Systems genetics is a powerful approach that allows to integrate different ‘omics level and understand the bio...

Regularization of divergent integrals

OpenAIRE

Felder, Giovanni; Kazhdan, David

2016-01-01

We study the Hadamard finite part of divergent integrals of differential forms with singularities on submanifolds. We give formulae for the dependence of the finite part on the choice of regularization and express them in terms of a suitable local residue map. The cases where the submanifold is a complex hypersurface in a complex manifold and where it is a boundary component of a manifold with boundary, arising in string perturbation theory, are treated in more detail.

An alignment-free method to find similarity among protein sequences via the general form of Chou's pseudo amino acid composition.

Science.gov (United States)

Gupta, M K; Niyogi, R; Misra, M

2013-01-01

In this paper, we propose a method to create the 60-dimensional feature vector for protein sequences via the general form of pseudo amino acid composition. The construction of the feature vector is based on the contents of amino acids, total distance of each amino acid from the first amino acid in the protein sequence and the distribution of 20 amino acids. The obtained cosine distance metric (also called the similarity matrix) is used to construct the phylogenetic tree by the neighbour joining method. In order to show the applicability of our approach, we tested it on three proteins: 1) ND5 protein sequences from nine species, 2) ND6 protein sequences from eight species, and 3) 50 coronavirus spike proteins. The results are in agreement with known history and the output from the multiple sequence alignment program ClustalW, which is widely used. We have also compared our phylogenetic results with six other recently proposed alignment-free methods. These comparisons show that our proposed method gives a more consistent biological relationship than the others. In addition, the time complexity is linear and space required is less as compared with other alignment-free methods that use graphical representation. It should be noted that the multiple sequence alignment method has exponential time complexity.

Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

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Morozov Alexandre V

2009-08-01

Full Text Available Abstract Background The reaction of HIV protease to inhibitor therapy is characterized by the emergence of complex mutational patterns which confer drug resistance. The response of HIV protease to drugs often involves both primary mutations that directly inhibit the action of the drug, and a host of accessory resistance mutations that may occur far from the active site but may contribute to restoring the fitness or stability of the enzyme. Here we develop a probabilistic approach based on connected information that allows us to study residue, pair level and higher-order correlations within the same framework. Results We apply our methodology to a database of approximately 13,000 sequences which have been annotated by the treatment history of the patients from which the samples were obtained. We show that including pair interactions is essential for agreement with the mutational data, since neglect of these interactions results in order-of-magnitude errors in the probabilities of the simultaneous occurence of many mutations. The magnitude of these pair correlations changes dramatically between sequences obtained from patients that were or were not exposed to drugs. Higher-order effects make a contribution of as much as 10% for residues taken three at a time, but increase to more than twice that for 10 to 15-residue groups. The sequence data is insufficient to determine the higher-order effects for larger groups. We find that higher-order interactions have a significant effect on the predicted frequencies of sequences with large numbers of mutations. While relatively rare, such sequences are more prevalent after multi-drug therapy. The relative importance of these higher-order interactions increases with the number of drugs the patient had been exposed to. Conclusion Correlations are critical for the understanding of mutation patterns in HIV protease. Pair interactions have substantial qualitative effects, while higher-order interactions are

Tournaments, oriented graphs and football sequences

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Pirzada S.

2017-08-01

Full Text Available Consider the result of a soccer league competition where n teams play each other exactly once. A team gets three points for each win and one point for each draw. The total score obtained by each team vi is called the f-score of vi and is denoted by fi. The sequences of all f-scores [fi]i=1n$\\left[ {{\\rm{f}}_{\\rm{i}} } \\right]_{{\\rm{i}} = 1}^{\\rm{n}} $ arranged in non-decreasing order is called the f-score sequence of the competition. We raise the following problem: Which sequences of non-negative integers in non-decreasing order is a football sequence, that is the outcome of a soccer league competition. We model such a competition by an oriented graph with teams represented by vertices in which the teams play each other once, with an arc from team u to team v if and only if u defeats v. We obtain some necessary conditions for football sequences and some characterizations under restrictions.

Temporal correlation of fluvial and alluvial sequences in the Makran Range, SE-Iran

Science.gov (United States)

Kober, F.; Zeilinger, G.; Ivy-Ochs, S.; Dolati, A.; Smit, J.; Burg, J.-P.; Bahroudi, A.; Kubik, P. W.; Baur, H.; Wieler, R.; Haghipour, N.

2009-04-01

The Makran region of southeastern Iran is an active accretionary wedge with a partially subaerial component. New investigations have revealed a rather complex geodynamic evolution of the Makran active accretionary wedge that is not yet fully understood in its entity. Ongoing convergence between the Arabian and Eurasian plates and tectonic activity since the late Mesozoic has extended all trough the Quaternary. We focus here on fluvial and alluvial sequences in tectonically separated basins that have been deposited probably in the Pliocene/Quaternary, based on stratigraphic classification in official geological maps, in order to understand the climatic and tectonic forces occurring during the ongoing accretionary wegde formation. Specifically, we investigate the influence of Quaternary climate variations (Pleistocene cold period, monsoonal variations) on erosional and depositional processes in the (semi)arid Makran as well as local and regional tectonic forces in the Coastal and Central Makran Range region. Necessary for such an analysis is a temporal calibration of alluvial and fluvial terrace sequences that will allow an inter-basin correlation. We utilize the exposure age dating method using terrestrial cosmogenic nuclides (TCN) due to the lack of otherwise datatable material in the arid Makran region. Limited radiocarbon data are only available for marine terraces (wave-cut platforms). Our preliminary 21Ne and 10Be TCN-ages of amalgamated clast samples from (un)deformed terrace and alluvial sequences range from ~250 ky to present day (modern wash). These ages agree in relative terms with sequences previously assigned by other investigations through correlation of Quaternary sequences from Central and Western Iran regions. However, our minimum ages suggest that all age sequences are of middle to late Pleistocene age, compared to Pliocene age estimates previously assigned for the oldest units. Although often suggested, a genetical relation and connection of those

Diagnostics of Primary Immunodeficiencies through Next Generation Sequencing

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Vera Gallo

2016-11-01

Full Text Available Background: Recently, a growing number of novel genetic defects underlying primary immunodeficiencies (PID have been identified, increasing the number of PID up to more than 250 well-defined forms. Next-generation sequencing (NGS technologies and proper filtering strategies greatly contributed to this rapid evolution, providing the possibility to rapidly and simultaneously analyze large numbers of genes or the whole exome. Objective: To evaluate the role of targeted next-generation sequencing and whole exome sequencing in the diagnosis of a case series, characterized by complex or atypical clinical features suggesting a PID, difficult to diagnose using the current diagnostic procedures.Methods: We retrospectively analyzed genetic variants identified through targeted next-generation sequencing or whole exome sequencing in 45 patients with complex PID of unknown etiology. Results: 40 variants were identified using targeted next-generation sequencing, while 5 were identified using whole exome sequencing. Newly identified genetic variants were classified into 4 groups: I variations associated with a well-defined PID; II variations associated with atypical features of a well-defined PID; III functionally relevant variations potentially involved in the immunological features; IV non-diagnostic genotype, in whom the link with phenotype is missing. We reached a conclusive genetic diagnosis in 7/45 patients (~16%. Among them, 4 patients presented with a typical well-defined PID. In the remaining 3 cases, mutations were associated with unexpected clinical features, expanding the phenotypic spectrum of typical PIDs. In addition, we identified 31 variants in 10 patients with complex phenotype, individually not causative per se of the disorder.Conclusion: NGS technologies represent a cost-effective and rapid first-line genetic approaches for the evaluation of complex PIDs. Whole exome sequencing, despite a moderate higher cost compared to targeted, is

Multiscale high-order/low-order (HOLO) algorithms and applications

International Nuclear Information System (INIS)

Chacón, L.; Chen, G.; Knoll, D.A.; Newman, C.; Park, H.; Taitano, W.; Willert, J.A.; Womeldorff, G.

2017-01-01

We review the state of the art in the formulation, implementation, and performance of so-called high-order/low-order (HOLO) algorithms for challenging multiscale problems. HOLO algorithms attempt to couple one or several high-complexity physical models (the high-order model, HO) with low-complexity ones (the low-order model, LO). The primary goal of HOLO algorithms is to achieve nonlinear convergence between HO and LO components while minimizing memory footprint and managing the computational complexity in a practical manner. Key to the HOLO approach is the use of the LO representations to address temporal stiffness, effectively accelerating the convergence of the HO/LO coupled system. The HOLO approach is broadly underpinned by the concept of nonlinear elimination, which enables segregation of the HO and LO components in ways that can effectively use heterogeneous architectures. The accuracy and efficiency benefits of HOLO algorithms are demonstrated with specific applications to radiation transport, gas dynamics, plasmas (both Eulerian and Lagrangian formulations), and ocean modeling. Across this broad application spectrum, HOLO algorithms achieve significant accuracy improvements at a fraction of the cost compared to conventional approaches. It follows that HOLO algorithms hold significant potential for high-fidelity system scale multiscale simulations leveraging exascale computing.

Multiscale high-order/low-order (HOLO) algorithms and applications

Energy Technology Data Exchange (ETDEWEB)

Chacón, L., E-mail: chacon@lanl.gov [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Chen, G.; Knoll, D.A.; Newman, C.; Park, H.; Taitano, W. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Willert, J.A. [Institute for Defense Analyses, Alexandria, VA 22311 (United States); Womeldorff, G. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

2017-02-01

We review the state of the art in the formulation, implementation, and performance of so-called high-order/low-order (HOLO) algorithms for challenging multiscale problems. HOLO algorithms attempt to couple one or several high-complexity physical models (the high-order model, HO) with low-complexity ones (the low-order model, LO). The primary goal of HOLO algorithms is to achieve nonlinear convergence between HO and LO components while minimizing memory footprint and managing the computational complexity in a practical manner. Key to the HOLO approach is the use of the LO representations to address temporal stiffness, effectively accelerating the convergence of the HO/LO coupled system. The HOLO approach is broadly underpinned by the concept of nonlinear elimination, which enables segregation of the HO and LO components in ways that can effectively use heterogeneous architectures. The accuracy and efficiency benefits of HOLO algorithms are demonstrated with specific applications to radiation transport, gas dynamics, plasmas (both Eulerian and Lagrangian formulations), and ocean modeling. Across this broad application spectrum, HOLO algorithms achieve significant accuracy improvements at a fraction of the cost compared to conventional approaches. It follows that HOLO algorithms hold significant potential for high-fidelity system scale multiscale simulations leveraging exascale computing.

Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

DEFF Research Database (Denmark)

Karlskov-Mortensen, Peter; Hu, Z.L.; Gorodkin, Jan

2007-01-01

the human genome (BLAST cut-off threshold = 1 x 10-5). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html . These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude...

Impact of Different Spreading Codes Using FEC on DWT Based MC-CDMA System

OpenAIRE

Masum, Saleh; Kabir, M. Hasnat; Islam, Md. Matiqul; Shams, Rifat Ara; Ullah, Shaikh Enayet

2012-01-01

The effect of different spreading codes in DWT based MC-CDMA wireless communication system is investigated. In this paper, we present the Bit Error Rate (BER) performance of different spreading codes (Walsh-Hadamard code, Orthogonal gold code and Golay complementary sequences) using Forward Error Correction (FEC) of the proposed system. The data is analyzed and is compared among different spreading codes in both coded and uncoded cases. It is found via computer simulation that the performance...

HEURISTIC METHODS FOR TEST SEQUENCING IN TELECOMMUNICATION SATELLITES

OpenAIRE

Boche-Sauvan , Ludivine; Cabon , Bertrand; Huguet , Marie-José; Hébrard , Emmanuel

2014-01-01

Colloque avec actes et comité de lecture. internationale.; International audience; The increasing complexity in telecommunication satellite payload design demands new test sequencing approaches to face the induced increase of validation complexity. In such a sequencing problem, each test requires specific payload equipment states at a dedicated temperature range. The industrial objectives are both to reduce the total time of tests and to keep the thermal stability of the payload. For solving ...

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

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Ren Jian

2004-01-01

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

Pairwise Sequence Alignment Library

Energy Technology Data Exchange (ETDEWEB)

2015-05-20

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

The recurrence sequences via Sylvester matrices

Science.gov (United States)

Karaduman, Erdal; Deveci, Ömür

2017-07-01

In this work, we define the Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by using the Slyvester matrices which are obtained from the characteristic polynomials of the Pell and Jacobsthal sequences and then, we study the sequences defined modulo m. Also, we obtain the cyclic groups and the semigroups from the generating matrices of these sequences when read modulo m and then, we derive the relationships among the orders of the cyclic groups and the periods of the sequences. Furthermore, we redefine Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by means of the elements of the groups and then, we examine them in the finite groups.

Learning predictive statistics from temporal sequences: Dynamics and strategies.

Science.gov (United States)

Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E; Kourtzi, Zoe

2017-10-01

Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics-that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments.

Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

Directory of Open Access Journals (Sweden)

Xu Xiangming

2010-12-01

Full Text Available Abstract Background Determining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method. Results The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps. Conclusions We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.

Characteristics of MHC class I genes in house sparrows Passer domesticus as revealed by long cDNA transcripts and amplicon sequencing.

Science.gov (United States)

Karlsson, Maria; Westerdahl, Helena

2013-08-01

In birds the major histocompatibility complex (MHC) organization differs both among and within orders; chickens Gallus gallus of the order Galliformes have a simple arrangement, while many songbirds of the order Passeriformes have a more complex arrangement with larger numbers of MHC class I and II genes. Chicken MHC genes are found at two independent loci, classical MHC-B and non-classical MHC-Y, whereas non-classical MHC genes are yet to be verified in passerines. Here we characterize MHC class I transcripts (α1 to α3 domain) and perform amplicon sequencing using a next-generation sequencing technique on exon 3 from house sparrow Passer domesticus (a passerine) families. Then we use phylogenetic, selection, and segregation analyses to gain a better understanding of the MHC class I organization. Trees based on the α1 and α2 domain revealed a distinct cluster with short terminal branches for transcripts with a 6-bp deletion. Interestingly, this cluster was not seen in the tree based on the α3 domain. 21 exon 3 sequences were verified in a single individual and the average numbers within an individual were nine and five for sequences with and without a 6-bp deletion, respectively. All individuals had exon 3 sequences with and without a 6-bp deletion. The sequences with a 6-bp deletion have many characteristics in common with non-classical MHC, e.g., highly conserved amino acid positions were substituted compared with the other alleles, low nucleotide diversity and just a single site was subject to positive selection. However, these alleles also have characteristics that suggest they could be classical, e.g., complete linkage and absence of a distinct cluster in a tree based on the α3 domain. Thus, we cannot determine for certain whether or not the alleles with a 6-bp deletion are non-classical based on our present data. Further analyses on segregation patterns of these alleles in combination with dating the 6-bp deletion through MHC characterization across the

Orders out of chaos--molecular phylogenetics reveals the complexity of shark and stingray tapeworm relationships.

Science.gov (United States)

Caira, Janine N; Jensen, Kirsten; Waeschenbach, Andrea; Olson, Peter D; Littlewood, D Timothy J

2014-01-01

Novel molecular data are presented to resolve the long-standing issue of the non-monophyly of the elasmobranch-hosted tapeworm order Tetraphyllidea relative to the other acetabulate eucestode orders. Bayesian inference analyses of various combinations of full ssrDNA, and full or partial lsrDNA (D1-D3), sequence data, which included 134 species representing 97 genera across the 15 eucestode orders, were conducted. New ssrDNA data were generated for 82 species, partial lsrDNA data for 53 species, and full lsrDNA data for 29 species. The monophyly of each of the elasmobranch-hosted orders Cathetocephalidea, Litobothriidea, Lecanicephalidea and Rhinebothriidea was confirmed, as was the non-monophyly of the Tetraphyllidea. Two relatively stable groups of tetraphyllidean taxa emerged and are hereby designated as new orders. The Onchoproteocephalidea n. ord. is established to recognise the integrated nature of one undescribed and 10 described genera of hook-bearing tetraphyllideans, previously placed in the family Onchobothriidae, with the members of the order Proteocephalidea. The Phyllobothriidea n. ord. is established for a subset of 12 non-hooked genera characterised by scoleces bearing four bothridia each with an anterior accessory sucker; most parasitise sharks and have been assigned to the Phyllobothriidae at one time or another. Tentative ordinal placements are suggested for eight additional genera; placements for the remaining tetraphyllidean genera have not yet emerged. We propose that these 17 genera remain in the "Tetraphyllidea". Among these, particularly labile across analyses were Anthobothrium, Megalonchos, Carpobothrium, Calliobothrium and Caulobothrium. The unique association of Chimaerocestus with holocephalans, rather than with elasmobranchs, appears to represent a host-switching event. Both of the non-elasmobranch hosted clades of acetabulate cestodes (i.e. Proteocephalidea and Cyclophyllidea and their kin) appear to have had their origins with

Entropic Movement Complexity Reflects Subjective Creativity Rankings of Visualized Hand Motion Trajectories

Science.gov (United States)

Peng, Zhen; Braun, Daniel A.

2015-01-01

In a previous study we have shown that human motion trajectories can be characterized by translating continuous trajectories into symbol sequences with well-defined complexity measures. Here we test the hypothesis that the motion complexity individuals generate in their movements might be correlated to the degree of creativity assigned by a human observer to the visualized motion trajectories. We asked participants to generate 55 novel hand movement patterns in virtual reality, where each pattern had to be repeated 10 times in a row to ensure reproducibility. This allowed us to estimate a probability distribution over trajectories for each pattern. We assessed motion complexity not only by the previously proposed complexity measures on symbolic sequences, but we also propose two novel complexity measures that can be directly applied to the distributions over trajectories based on the frameworks of Gaussian Processes and Probabilistic Movement Primitives. In contrast to previous studies, these new methods allow computing complexities of individual motion patterns from very few sample trajectories. We compared the different complexity measures to how a group of independent jurors rank ordered the recorded motion trajectories according to their personal creativity judgment. We found three entropic complexity measures that correlate significantly with human creativity judgment and discuss differences between the measures. We also test whether these complexity measures correlate with individual creativity in divergent thinking tasks, but do not find any consistent correlation. Our results suggest that entropic complexity measures of hand motion may reveal domain-specific individual differences in kinesthetic creativity. PMID:26733896

Quantitative phenotyping via deep barcode sequencing.

Science.gov (United States)

Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

2009-10-01

Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

Learning word order at birth: A NIRS study.

Science.gov (United States)

Benavides-Varela, Silvia; Gervain, Judit

2017-06-01

In language, the relative order of words in sentences carries important grammatical functions. However, the developmental origins and the neural correlates of the ability to track word order are to date poorly understood. The current study therefore investigates the origins of infants' ability to learn about the sequential order of words, using near-infrared spectroscopy (NIRS) with newborn infants. We have conducted two experiments: one in which a word order change was implemented in 4-word sequences recorded with a list intonation (as if each word was a separate item in a list; list prosody condition, Experiment 1) and one in which the same 4-word sequences were recorded with a well-formed utterance-level prosodic contour (utterance prosody condition, Experiment 2). We found that newborns could detect the violation of the word order in the list prosody condition, but not in the utterance prosody condition. These results suggest that while newborns are already sensitive to word order in linguistic sequences, prosody appears to be a stronger cue than word order for the identification of linguistic units at birth. Copyright © 2017. Published by Elsevier Ltd.

Identifying driver mutations in sequenced cancer genomes

DEFF Research Database (Denmark)

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

2014-01-01

High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the measurement of the somatic mutations that drive cancer development. However, the resulting sequencing datasets are large and complex, obscuring the clinically important mutations in a background of errors, nois...... patterns of mutual exclusivity. These techniques, coupled with advances in high-throughput DNA sequencing, are enabling precision medicine approaches to the diagnosis and treatment of cancer....

Pade approximants for entire functions with regularly decreasing Taylor coefficients

International Nuclear Information System (INIS)

Rusak, V N; Starovoitov, A P

2002-01-01

For a class of entire functions the asymptotic behaviour of the Hadamard determinants D n,m as 0≤m≤m(n)→∞ and n→∞ is described. This enables one to study the behaviour of parabolic sequences from Pade and Chebyshev tables for many individual entire functions. The central result of the paper is as follows: for some sequences {(n,m(n))} in certain classes of entire functions (with regular Taylor coefficients) the Pade approximants {π n,m(n) }, which provide the locally best possible rational approximations, converge to the given function uniformly on the compact set D={z:|z|≤1} with asymptotically best rate

Genomic sequencing in clinical trials

OpenAIRE

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

2011-01-01

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

Lactation transcriptomics in the Australian marsupial, Macropus eugenii: transcript sequencing and quantification

Directory of Open Access Journals (Sweden)

Whitley Jane C

2007-11-01

Full Text Available Abstract Background Lactation is an important aspect of mammalian biology and, amongst mammals, marsupials show one of the most complex lactation cycles. Marsupials, such as the tammar wallaby (Macropus eugenii give birth to a relatively immature newborn and progressive changes in milk composition and milk production regulate early stage development of the young. Results In order to investigate gene expression in the marsupial mammary gland during lactation, a comprehensive set of cDNA libraries was derived from lactating tissues throughout the lactation cycle of the tammar wallaby. A total of 14,837 express sequence tags were produced by cDNA sequencing. Sequence analysis and sequence assembly were used to construct a comprehensive catalogue of mammary transcripts. Sequence data from pregnant and early or late lactating specific cDNA libraries and, data from early or late lactation massively parallel sequencing strategies were combined to analyse the variation of milk protein gene expression during the lactation cycle. Conclusion Results show a steady increase in expression of genes coding for secreted protein during the lactation cycle that is associated with high proportion of transcripts coding for milk proteins. In addition, genes involved in immune function, translation and energy or anabolic metabolism are expressed across the lactation cycle. A number of potential new milk proteins or mammary gland remodelling markers, including noncoding RNAs have been identified.

Structural organization and spectroscopy of peptide-actinide(IV) complexes

International Nuclear Information System (INIS)

Dahou, S.

2010-01-01

The contamination of living organisms by actinide elements is at the origin of both radiological and chemical toxicity that may lead to severe dysfunction. Most of the data available on the actinide interaction with biological systems are macroscopic physiological measurements and are lacking a molecular description of the systems. Because of the intricacy of these systems, classical biochemical methods are difficult to implement. Our strategy consisted in designing simplified biomimetic peptides, and describing the corresponding intramolecular interactions with actinides. A carboxylic pentapeptide of the form DDPDD has been at the starting point of this work in order to further assess the influence of the peptide sequence on the topology of the complexes.To do so, various linear (Asp/Ala permutations, peptoids) and cyclic analogues have been synthesized. Furthermore, in order to include the hydroxamic function (with a high affinity for Fe(III)) in the peptide, both desferrioxamine and acetohydroxamic acid have been investigated. However because of difficulties in synthesis, we have not been able to test these peptides. Three actinide cations have been considered at oxidation state +IV (Th, Np, Pu) and compared to Fe(III), often considered as a biological surrogate of Pu(IV). The spatial arrangement of the peptide around the cation has been probed by spectrophotometry and X-ray Absorption Spectroscopy. The spectroscopic data and EXAFS data adjustment lead us to rationalize the topology of the complexes as a function of the peptide sequence: mix hydroxy polynuclear species for linear and cyclic peptides, mononuclear for the desferrioxamine complexes. Furthermore, significant differences have appeared between Fe(III) and actinide(IV), related to differences of reactivity in aqueous medium. (author)

Geology and geochemistry of Massangana Granitoid Complex, Brazil, and its relation with tin mineralization

International Nuclear Information System (INIS)

Romanini, S.J.

1982-01-01

The geochemical and petroLogical characteristics of the Massangana Granitoid Complex, situated in the Rondonia Federal Territory, Brazil, aiming to discriminate the tin mineralized granitic rocks from the no mineralized ones. The collected samples consists of examples in tin mineralized and sterile phases. The elements traces were determined by x-ray fluorescence analysis, emission spectrography, molecular absorption spectrophotometry and atomic absorption spectrophotometry. The complex edifying evolved in four sucessive episodes called Massangana Phase, Bom Jardim Phase, Sao domingos Phase and Taboca Phase ordered stratigraphycally in this sequence. (author/M.C.K.) [pt

Sequencing of BAC pools by different next generation sequencing platforms and strategies

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Scholz Uwe

2011-10-01

Full Text Available Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.

Compositional segmentation and complexity measurement in stock indices

Science.gov (United States)

Wang, Haifeng; Shang, Pengjian; Xia, Jianan

2016-01-01

In this paper, we introduce a complexity measure based on the entropic segmentation called sequence compositional complexity (SCC) into the analysis of financial time series. SCC was first used to deal directly with the complex heterogeneity in nonstationary DNA sequences. We already know that SCC was found to be higher in sequences with long-range correlation than those with low long-range correlation, especially in the DNA sequences. Now, we introduce this method into financial index data, subsequently, we find that the values of SCC of some mature stock indices, such as S & P 500 (simplified with S & P in the following) and HSI, are likely to be lower than the SCC value of Chinese index data (such as SSE). What is more, we find that, if we classify the indices with the method of SCC, the financial market of Hong Kong has more similarities with mature foreign markets than Chinese ones. So we believe that a good correspondence is found between the SCC of the index sequence and the complexity of the market involved.

Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients.

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Matthias Merker

Full Text Available Multidrug-resistant (MDR Mycobacterium tuberculosis complex (MTBC strains represent a major threat for tuberculosis (TB control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A and nine (Patient B polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and

Multi-locus sequence typing provides epidemiological insights for diseased sharks infected with fungi belonging to the Fusarium solani species complex.

Science.gov (United States)

Desoubeaux, Guillaume; Debourgogne, Anne; Wiederhold, Nathan P; Zaffino, Marie; Sutton, Deanna; Burns, Rachel E; Frasca, Salvatore; Hyatt, Michael W; Cray, Carolyn

2018-07-01

Fusarium spp. are saprobic moulds that are responsible for severe opportunistic infections in humans and animals. However, we need epidemiological tools to reliably trace the circulation of such fungal strains within medical or veterinary facilities, to recognize environmental contaminations that might lead to infection and to improve our understanding of factors responsible for the onset of outbreaks. In this study, we used molecular genotyping to investigate clustered cases of Fusarium solani species complex (FSSC) infection that occurred in eight Sphyrnidae sharks under managed care at a public aquarium. Genetic relationships between fungal strains were determined by multi-locus sequence typing (MLST) analysis based on DNA sequencing at five loci, followed by comparison with sequences of 50 epidemiologically unrelated FSSC strains. Our genotyping approach revealed that F. keratoplasticum and F. solani haplotype 9x were most commonly isolated. In one case, the infection proved to be with another Hypocrealian rare opportunistic pathogen Metarhizium robertsii. Twice, sharks proved to be infected with FSSC strains with the same MLST sequence type, supporting the hypothesis the hypothesis that common environmental populations of fungi existed for these sharks and would suggest the longtime persistence of the two clonal strains within the environment, perhaps in holding pools and life support systems of the aquarium. This study highlights how molecular tools like MLST can be used to investigate outbreaks of microbiological disease. This work reinforces the need for regular controls of water quality to reduce microbiological contamination due to waterborne microorganisms.

On a class of fourth order linear recurrence equations

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Sui-Sun Cheng

1984-01-01

Full Text Available This paper is concerned with sequences that satisfy a class of fourth order linear recurrence equations. Basic properties of such sequences are derived. In addition, we discuss the oscillatory and nonoscillatory behavior of such sequences.

Rhipicephalus microplus dataset of nonredundant raw sequence reads from 454 GS FLX sequencing of Cot-selected (Cot = 660) genomic DNA

Science.gov (United States)

A reassociation kinetics-based approach was used to reduce the complexity of genomic DNA from the Deutsch laboratory strain of the cattle tick, Rhipicephalus microplus, to facilitate genome sequencing. Selected genomic DNA (Cot value = 660) was sequenced using 454 GS FLX technology, resulting in 356...

Grammatical complexity for two-dimensional maps

International Nuclear Information System (INIS)

Hagiwara, Ryouichi; Shudo, Akira

2004-01-01

We calculate the grammatical complexity of the symbol sequences generated from the Henon map and the Lozi map using the recently developed methods to construct the pruning front. When the map is hyperbolic, the language of symbol sequences is regular in the sense of the Chomsky hierarchy and the corresponding grammatical complexity takes finite values. It is found that the complexity exhibits a self-similar structure as a function of the system parameter, and the similarity of the pruning fronts is discussed as an origin of such self-similarity. For non-hyperbolic cases, it is observed that the complexity monotonically increases as we increase the resolution of the pruning front

Grammatical complexity for two-dimensional maps

Energy Technology Data Exchange (ETDEWEB)

Hagiwara, Ryouichi; Shudo, Akira [Department of Physics, Tokyo Metropolitan University, Minami-Ohsawa, Hachioji, Tokyo 192-0397 (Japan)

2004-11-05

We calculate the grammatical complexity of the symbol sequences generated from the Henon map and the Lozi map using the recently developed methods to construct the pruning front. When the map is hyperbolic, the language of symbol sequences is regular in the sense of the Chomsky hierarchy and the corresponding grammatical complexity takes finite values. It is found that the complexity exhibits a self-similar structure as a function of the system parameter, and the similarity of the pruning fronts is discussed as an origin of such self-similarity. For non-hyperbolic cases, it is observed that the complexity monotonically increases as we increase the resolution of the pruning front.

Grammatical complexity for two-dimensional maps

Science.gov (United States)

Hagiwara, Ryouichi; Shudo, Akira

2004-11-01

We calculate the grammatical complexity of the symbol sequences generated from the Hénon map and the Lozi map using the recently developed methods to construct the pruning front. When the map is hyperbolic, the language of symbol sequences is regular in the sense of the Chomsky hierarchy and the corresponding grammatical complexity takes finite values. It is found that the complexity exhibits a self-similar structure as a function of the system parameter, and the similarity of the pruning fronts is discussed as an origin of such self-similarity. For non-hyperbolic cases, it is observed that the complexity monotonically increases as we increase the resolution of the pruning front.

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

Directory of Open Access Journals (Sweden)

Nicholas J Schurch

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

Thread extraction for polyadic instruction sequences

NARCIS (Netherlands)

Bergstra, J.; Middelburg, C.

2011-01-01

In this paper, we study the phenomenon that instruction sequences are split into fragments which somehow produce a joint behaviour. In order to bring this phenomenon better into the picture, we formalize a simple mechanism by which several instruction sequence fragments can produce a joint

Complexities of sibling analysis when exposures and outcomes change with time and birth order.

Science.gov (United States)

Sudan, Madhuri; Kheifets, Leeka I; Arah, Onyebuchi A; Divan, Hozefa A; Olsen, Jørn

2014-01-01

In this study, we demonstrate the complexities of performing a sibling analysis with a re-examination of associations between cell phone exposures and behavioral problems observed previously in the Danish National Birth Cohort. Children (52,680; including 5441 siblings) followed up to age 7 were included. We examined differences in exposures and behavioral problems between siblings and non-siblings and by birth order and birth year. We estimated associations between cell phone exposures and behavioral problems while accounting for the random family effect among siblings. The association of behavioral problems with both prenatal and postnatal exposure differed between siblings (odds ratio (OR): 1.07; 95% confidence interval (CI): 0.69-1.66) and non-siblings (OR: 1.54; 95% CI: 1.36-1.74) and within siblings by birth order; the association was strongest for first-born siblings (OR: 1.72; 95% CI: 0.86-3.42) and negative for later-born siblings (OR: 0.63; 95% CI: 0.31-1.25), which may be because of increases in cell phone use with later birth year. Sibling analysis can be a powerful tool for (partially) accounting for confounding by invariant unmeasured within-family factors, but it cannot account for uncontrolled confounding by varying family-level factors, such as those that vary with time and birth order.

Parallel motif extraction from very long sequences

KAUST Repository

Sahli, Majed

2013-01-01

Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

Quantitative measure of randomness and order for complete genomes

Science.gov (United States)

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

2009-06-01

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

LPTAU, Quasi Random Sequence Generator

International Nuclear Information System (INIS)

Sobol, Ilya M.

1993-01-01

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

Arbitrarily accurate twin composite π -pulse sequences

Science.gov (United States)

Torosov, Boyan T.; Vitanov, Nikolay V.

2018-04-01

We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .

Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing

Directory of Open Access Journals (Sweden)

Miri eMichaeli

2012-12-01

Full Text Available High throughput sequencing (HTS yields tens of thousands to millions of sequences that require a large amount of pre-processing work to clean various artifacts. Such cleaning cannot be performed manually. Existing programs are not suitable for immunoglobulin (Ig genes, which are variable and often highly mutated. This paper describes Ig-HTS-Cleaner (Ig High Throughput Sequencing Cleaner, a program containing a simple cleaning procedure that successfully deals with pre-processing of Ig sequences derived from HTS, and Ig-Indel-Identifier (Ig Insertion – Deletion Identifier, a program for identifying legitimate and artifact insertions and/or deletions (indels. Our programs were designed for analyzing Ig gene sequences obtained by 454 sequencing, but they are applicable to all types of sequences and sequencing platforms. Ig-HTS-Cleaner and Ig-Indel-Identifier have been implemented in Java and saved as executable JAR files, supported on Linux and MS Windows. No special requirements are needed in order to run the programs, except for correctly constructing the input files as explained in the text. The programs' performance has been tested and validated on real and simulated data sets.

Harmonic spectral components in time sequences of Markov correlated events

Science.gov (United States)

Mazzetti, Piero; Carbone, Anna

2017-07-01

The paper concerns the analysis of the conditions allowing time sequences of Markov correlated events give rise to a line power spectrum having a relevant physical interest. It is found that by specializing the Markov matrix in order to represent closed loop sequences of events with arbitrary distribution, generated in a steady physical condition, a large set of line spectra, covering all possible frequency values, is obtained. The amplitude of the spectral lines is given by a matrix equation based on a generalized Markov matrix involving the Fourier transform of the distribution functions representing the time intervals between successive events of the sequence. The paper is a complement of a previous work where a general expression for the continuous power spectrum was given. In that case the Markov matrix was left in a more general form, thus preventing the possibility of finding line spectra of physical interest. The present extension is also suggested by the interest of explaining the emergence of a broad set of waves found in the electro and magneto-encephalograms, whose frequency ranges from 0.5 to about 40Hz, in terms of the effects produced by chains of firing neurons within the complex neural network of the brain. An original model based on synchronized closed loop sequences of firing neurons is proposed, and a few numerical simulations are reported as an application of the above cited equation.

On symmetric structures of order two

Directory of Open Access Journals (Sweden)

Michel Bousquet

2008-04-01

Full Text Available Let (ω n 0 < n be the sequence known as Integer Sequence A047749 http://www.research.att.com/ njas/sequences/A047749 In this paper, we show that the integer ω n enumerates various kinds of symmetric structures of order two. We first consider ternary trees having a reflexive symmetry and we relate all symmetric combinatorial objects by means of bijection. We then generalize the symmetric structures and correspondences to an infinite family of symmetric objects.

Optimization of sequence alignment for simple sequence repeat regions

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Ogbonnaya Francis C

2011-07-01

Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes.

Science.gov (United States)

Kachhap, Sangita; Singh, Balvinder

2015-01-01

In most of homeodomain-DNA complexes, glutamine or lysine is present at 50th position and interacts with 5th and 6th nucleotide of core recognition region. Molecular dynamics simulations of Msx-1-DNA complex (Q50-TG) and its variant complexes, that is specific (Q50K-CC), nonspecific (Q50-CC) having mutation in DNA and (Q50K-TG) in protein, have been carried out. Analysis of protein-DNA interactions and structure of DNA in specific and nonspecific complexes show that amino acid residues use sequence-dependent shape of DNA to interact. The binding free energies of all four complexes were analysed to define role of amino acid residue at 50th position in terms of binding strength considering the variation in DNA on stability of protein-DNA complexes. The order of stability of protein-DNA complexes shows that specific complexes are more stable than nonspecific ones. Decomposition analysis shows that N-terminal amino acid residues have been found to contribute maximally in binding free energy of protein-DNA complexes. Among specific protein-DNA complexes, K50 contributes more as compared to Q50 towards binding free energy in respective complexes. The sequence dependence of local conformation of DNA enables Q50/Q50K to make hydrogen bond with nucleotide(s) of DNA. The changes in amino acid sequence of protein are accommodated and stabilized around TAAT core region of DNA having variation in nucleotides.

An efficient approach to BAC based assembly of complex genomes.

Science.gov (United States)

Visendi, Paul; Berkman, Paul J; Hayashi, Satomi; Golicz, Agnieszka A; Bayer, Philipp E; Ruperao, Pradeep; Hurgobin, Bhavna; Montenegro, Juan; Chan, Chon-Kit Kenneth; Staňková, Helena; Batley, Jacqueline; Šimková, Hana; Doležel, Jaroslav; Edwards, David

2016-01-01

There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.

Use of amplicon sequencing to improve sensitivity in PCR-based detection of microbial pathogen in environmental samples.

Science.gov (United States)

Saingam, Prakit; Li, Bo; Yan, Tao

2018-06-01

DNA-based molecular detection of microbial pathogens in complex environments is still plagued by sensitivity, specificity and robustness issues. We propose to address these issues by viewing them as inadvertent consequences of requiring specific and adequate amplification (SAA) of target DNA molecules by current PCR methods. Using the invA gene of Salmonella as the model system, we investigated if next generation sequencing (NGS) can be used to directly detect target sequences in false-negative PCR reaction (PCR-NGS) in order to remove the SAA requirement from PCR. False-negative PCR and qPCR reactions were first created using serial dilutions of laboratory-prepared Salmonella genomic DNA and then analyzed directly by NGS. Target invA sequences were detected in all false-negative PCR and qPCR reactions, which lowered the method detection limits near the theoretical minimum of single gene copy detection. The capability of the PCR-NGS approach in correcting false negativity was further tested and confirmed under more environmentally relevant conditions using Salmonella-spiked stream water and sediment samples. Finally, the PCR-NGS approach was applied to ten urban stream water samples and detected invA sequences in eight samples that would be otherwise deemed Salmonella negative. Analysis of the non-target sequences in the false-negative reactions helped to identify primer dime-like short sequences as the main cause of the false negativity. Together, the results demonstrated that the PCR-NGS approach can significantly improve method sensitivity, correct false-negative detections, and enable sequence-based analysis for failure diagnostics in complex environmental samples. Copyright © 2018 Elsevier B.V. All rights reserved.

Cloning and sequencing of the bovine gastrin gene

DEFF Research Database (Denmark)

Lund, T; Rehfeld, J F; Olsen, Jørgen

1989-01-01

In order to deduce the primary structure of bovine preprogastrin we therefore sequenced a gastrin DNA clone isolated from a bovine liver cosmid library. Bovine preprogastrin comprises 104 amino acids and consists of a signal peptide, a 37 amino acid spacer-sequence, the gastrin-34 sequence followed...

The evolutionary sequence: origin and emergences

Science.gov (United States)

Fox, S. W.

1986-01-01

The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

The evolutionary sequence: origin and emergences.

Science.gov (United States)

Fox, S W

1986-03-01

The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

Reducing assembly complexity of microbial genomes with single-molecule sequencing

Science.gov (United States)

Genome assembly algorithms cannot fully reconstruct microbial chromosomes from the DNA reads output by first or second-generation sequencing instruments. Therefore, most genomes are left unfinished due to the significant resources required to manually close gaps left in the draft assemblies. Single-...

Phase transition type change in order-order and order-disorder transformations of LaH2+c-like superstoichiometric dihydrides

International Nuclear Information System (INIS)

Ratishvili, I.G.

1999-01-01

Phase transformations in metal-hydrogen systems associated with the ordering processes in the subsystem of interstitial hydrogen atoms are considered. It is shown that in a particular class of superstoichiometric rare-earth dihydrides, where the ordering subsystem is characterized by two long-range-order parameters η 1 , η 2 and the energy parameter p 0 (1) (p) ≤ c ≤ c 0 (2) (p), it becomes discontinuous outside of this region. Dependence of critical concentrations c 0 (1) and c 0 (2) upon the energy parameter p is deduced. It is shown, as well, that there exists a second sequence of critical concentrations, c 1 (1) (p) and c 1 (2) (p), denoting the boundaries between the regions of continuous and discontinuous order-disorder transformations. (orig.)

Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

Science.gov (United States)

Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

2016-11-01

It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

Thermodynamics of complexity and pattern manipulation

Science.gov (United States)

Garner, Andrew J. P.; Thompson, Jayne; Vedral, Vlatko; Gu, Mile

2017-04-01

Many organisms capitalize on their ability to predict the environment to maximize available free energy and reinvest this energy to create new complex structures. This functionality relies on the manipulation of patterns—temporally ordered sequences of data. Here, we propose a framework to describe pattern manipulators—devices that convert thermodynamic work to patterns or vice versa—and use them to build a "pattern engine" that facilitates a thermodynamic cycle of pattern creation and consumption. We show that the least heat dissipation is achieved by the provably simplest devices, the ones that exhibit desired operational behavior while maintaining the least internal memory. We derive the ultimate limits of this heat dissipation and show that it is generally nonzero and connected with the pattern's intrinsic crypticity—a complexity theoretic quantity that captures the puzzling difference between the amount of information the pattern's past behavior reveals about its future and the amount one needs to communicate about this past to optimally predict the future.

A measurement of disorder in binary sequences

Science.gov (United States)

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

2015-03-01

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

A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data.

Science.gov (United States)

Heinrich, Verena; Kamphans, Tom; Mundlos, Stefan; Robinson, Peter N; Krawitz, Peter M

2017-01-01

Next generation sequencing technology considerably changed the way we screen for pathogenic mutations in rare Mendelian disorders. However, the identification of the disease-causing mutation amongst thousands of variants of partly unknown relevance is still challenging and efficient techniques that reduce the genomic search space play a decisive role. Often segregation- or linkage analysis are used to prioritize candidates, however, these approaches require correct information about the degree of relationship among the sequenced samples. For quality assurance an automated control of pedigree structures and sample assignment is therefore highly desirable in order to detect label mix-ups that might otherwise corrupt downstream analysis. We developed an algorithm based on likelihood ratios that discriminates between different classes of relationship for an arbitrary number of genotyped samples. By identifying the most likely class we are able to reconstruct entire pedigrees iteratively, even for highly consanguineous families. We tested our approach on exome data of different sequencing studies and achieved high precision for all pedigree predictions. By analyzing the precision for varying degrees of relatedness or inbreeding we could show that a prediction is robust down to magnitudes of a few hundred loci. A java standalone application that computes the relationships between multiple samples as well as a Rscript that visualizes the pedigree information is available for download as well as a web service at www.gene-talk.de CONTACT: heinrich@molgen.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Can you sequence ecology? Metagenomics of adaptive diversification.

Science.gov (United States)

Marx, Christopher J

2013-01-01

Few areas of science have benefited more from the expansion in sequencing capability than the study of microbial communities. Can sequence data, besides providing hypotheses of the functions the members possess, detect the evolutionary and ecological processes that are occurring? For example, can we determine if a species is adapting to one niche, or if it is diversifying into multiple specialists that inhabit distinct niches? Fortunately, adaptation of populations in the laboratory can serve as a model to test our ability to make such inferences about evolution and ecology from sequencing. Even adaptation to a single niche can give rise to complex temporal dynamics due to the transient presence of multiple competing lineages. If there are multiple niches, this complexity is augmented by segmentation of the population into multiple specialists that can each continue to evolve within their own niche. For a known example of parallel diversification that occurred in the laboratory, sequencing data gave surprisingly few obvious, unambiguous signs of the ecological complexity present. Whereas experimental systems are open to direct experimentation to test hypotheses of selection or ecological interaction, the difficulty in "seeing ecology" from sequencing for even such a simple system suggests translation to communities like the human microbiome will be quite challenging. This will require both improved empirical methods to enhance the depth and time resolution for the relevant polymorphisms and novel statistical approaches to rigorously examine time-series data for signs of various evolutionary and ecological phenomena within and between species.

Study of event sequence database for a nuclear power domain

International Nuclear Information System (INIS)

Kusumi, Yoshiaki

1998-01-01

A retrieval engine developed to extract event sequences from an accident information database using a time series retrieval formula expressed with ordered retrieval terms is explored. This engine outputs not only a sequence which completely matches with a time series retrieval formula, but also sequence which approximately matches the formula (fuzzy retrieval). An event sequence database in which records consist of three ordered parameters, namely the causal event, the process and result. Then the database is used to assess the feasibility of this engine and favorable results were obtained. (author)

Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: the role of mixing statistics and frame shift of neighboring genes.

Science.gov (United States)

Cocho, Germinal; Miramontes, Pedro; Mansilla, Ricardo; Li, Wentian

2014-12-01

We examine the relationship between exponential correlation functions and Markov models in a bacterial genome in detail. Despite the well known fact that Markov models generate sequences with correlation function that decays exponentially, simply constructed Markov models based on nearest-neighbor dimer (first-order), trimer (second-order), up to hexamer (fifth-order), and treating the DNA sequence as being homogeneous all fail to predict the value of exponential decay rate. Even reading-frame-specific Markov models (both first- and fifth-order) could not explain the fact that the exponential decay is very slow. Starting with the in-phase coding-DNA-sequence (CDS), we investigated correlation within a fixed-codon-position subsequence, and in artificially constructed sequences by packing CDSs with out-of-phase spacers, as well as altering CDS length distribution by imposing an upper limit. From these targeted analyses, we conclude that the correlation in the bacterial genomic sequence is mainly due to a mixing of heterogeneous statistics at different codon positions, and the decay of correlation is due to the possible out-of-phase between neighboring CDSs. There are also small contributions to the correlation from bases at the same codon position, as well as by non-coding sequences. These show that the seemingly simple exponential correlation functions in bacterial genome hide a complexity in correlation structure which is not suitable for a modeling by Markov chain in a homogeneous sequence. Other results include: use of the (absolute value) second largest eigenvalue to represent the 16 correlation functions and the prediction of a 10-11 base periodicity from the hexamer frequencies. Copyright © 2014 Elsevier Ltd. All rights reserved.

A reduced-order filtering approach for 3D dynamical electrical impedance tomography

International Nuclear Information System (INIS)

Voutilainen, A; Lehikoinen, A; Vauhkonen, M; Kaipio, J P

2011-01-01

Recently, it has been shown that the state estimation approach to process tomography can provide estimates that are significantly better than (a sequence of) conventional stationary snapshot estimates. One of the main obstacles of the adoption of the recursive state estimation algorithms, most commonly different versions of the Kalman filter, is the computational complexity. This is due to both the required large dimension for the state variable and the need to use iterative versions of the Kalman filter in such cases in which there are large contrasts or varying background. In this paper, we propose to use a reduced-order representation for the state variable. In particular, we propose to use the proper orthogonal decomposition-related basis for the state. We consider a simulation study with fluctuating background conductivity, and, in particular, with fluctuating contact impedances. We compare the proposed approach to three different versions of the Kalman filter having different computational complexities. We show that this approach allows the reduction of the dimension of the problem approximately by an order of magnitude and yields essentially as accurate estimates as the most accurate traditional Kalman filter version, the iterated extended Kalman filter

Optimization of micropillar sequences for fluid flow sculpting

Energy Technology Data Exchange (ETDEWEB)

Stoecklein, Daniel; Ganapathysubramanian, Baskar [Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011 (United States); Wu, Chueh-Yu; Kim, Donghyuk; Di Carlo, Dino [Department of Bioengineering, University of California at Los Angeles, Los Angeles, California 90095 (United States)

2016-01-15

Inertial fluid flow deformation around pillars in a microchannel is a new method for controlling fluid flow. Sequences of pillars have been shown to produce a rich phase space with a wide variety of flow transformations. Previous work has successfully demonstrated manual design of pillar sequences to achieve desired transformations of the flow cross section, with experimental validation. However, such a method is not ideal for seeking out complex sculpted shapes as the search space quickly becomes too large for efficient manual discovery. We explore fast, automated optimization methods to solve this problem. We formulate the inertial flow physics in microchannels with different micropillar configurations as a set of state transition matrix operations. These state transition matrices are constructed from experimentally validated streamtraces for a fixed channel length per pillar. This facilitates modeling the effect of a sequence of micropillars as nested matrix-matrix products, which have very efficient numerical implementations. With this new forward model, arbitrary micropillar sequences can be rapidly simulated with various inlet configurations, allowing optimization routines quick access to a large search space. We integrate this framework with the genetic algorithm and showcase its applicability by designing micropillar sequences for various useful transformations. We computationally discover micropillar sequences for complex transformations that are substantially shorter than manually designed sequences. We also determine sequences for novel transformations that were difficult to manually design. Finally, we experimentally validate these computational designs by fabricating devices and comparing predictions with the results from confocal microscopy.

COMPUTER-IMPLEMENTED METHOD OF PERFORMING A SEARCH USING SIGNATURES

DEFF Research Database (Denmark)

2017-01-01

A computer-implemented method of processing a query vector and a data vector), comprising: generating a set of masks and a first set of multiple signatures and a second set of multiple signatures by applying the set of masks to the query vector and the data vector, respectively, and generating...... candidate pairs, of a first signature and a second signature, by identifying matches of a first signature and a second signature. The set of masks comprises a configuration of the elements that is a Hadamard code; a permutation of a Hadamard code; or a code that deviates from a Hadamard code...

Neural correlates of skill acquisition: decreased cortical activity during a serial interception sequence learning task.

Science.gov (United States)

Gobel, Eric W; Parrish, Todd B; Reber, Paul J

2011-10-15

Learning of complex motor skills requires learning of component movements as well as the sequential structure of their order and timing. Using a Serial Interception Sequence Learning (SISL) task, participants learned a sequence of precisely timed interception responses through training with a repeating sequence. Following initial implicit learning of the repeating sequence, functional MRI data were collected during performance of that known sequence and compared with activity evoked during novel sequences of actions, novel timing patterns, or both. Reduced activity was observed during the practiced sequence in a distributed bilateral network including extrastriate occipital, parietal, and premotor cortical regions. These reductions in evoked activity likely reflect improved efficiency in visuospatial processing, spatio-motor integration, motor planning, and motor execution for the trained sequence, which is likely supported by nondeclarative skill learning. In addition, the practiced sequence evoked increased activity in the left ventral striatum and medial prefrontal cortex, while the posterior cingulate was more active during periods of better performance. Many prior studies of perceptual-motor skill learning have found increased activity in motor areas of the frontal cortex (e.g., motor and premotor cortex, SMA) and striatal areas (e.g., the putamen). The change in activity observed here (i.e., decreased activity across a cortical network) may reflect skill learning that is predominantly expressed through more accurate performance rather than decreased reaction time. Copyright © 2011 Elsevier Inc. All rights reserved.

Detecting change in stochastic sound sequences.

Directory of Open Access Journals (Sweden)

Benjamin Skerritt-Davis