Adaptive window zero-crossing-based instantaneous frequency estimation

We address the problem of estimating instantaneous frequency (IF) of a real-valued constant amplitude time-varying sinusoid. Estimation of polynomial IF is formulated using the zero-crossings of the signal. We propose an algorithm to estimate nonpolynomial IF by local approximation using a low-order polynomial, over a short segment of the signal. This involves the choice of window length to minimize the mean square error (MSE). The optimal window length found by directly minimizing the MSE is a function of the higher-order derivatives of the IF which are not available a priori. However, an optimum solution is formulated using an adaptive window technique based on the concept of intersection of confidence intervals. The adaptive algorithm enables minimum MSE-IF (MMSE-IF) estimation without requiring a priori information about the IF. Simulation results show that the adaptive window zero-crossing-based IF estimation method is superior to fixed window methods and is also better than adaptive spectrogram and adaptive Wigner-Ville distribution (WVD)-based IF estimators for different signal-to-noise ratio (SNR).

Mutations in hpyAVIBM, C5 cytosine DNA methyltransferase from Helicobacter pylori result in relaxed specificity

The genome of Helicobacter pylori is rich in restrictionmodification (RM) systems. Approximately 4% of the genome codes for components of RM systems. hpyAVIBM, which codes for a phase-variable C5 cytosine methyltransferase (MTase) from H. pylori, lacks a cognate restriction enzyme. Over-expression of M.HpyAVIB in Escherichia coli enhances the rate of mutations. However, when the catalytically inactive F9N or C82W mutants of M.HpyAVIB were expressed in E. coli, mutations were not observed. The M.HpyAVIB gene itself was mutated to give rise to different variants of the MTase. M.HpyAVIB variants were purified and differences in kinetic properties and specificity were observed. Intriguingly, purified MTase variants showed relaxed substrate specificity. Homologues of hpyAVIBM homologues amplified and sequenced from different clinical isolates showed similar variations in sequence. Thus, hpyAVIBM presents an interesting example of allelic variations in H. pylori where changes in the nucleotide sequence result in proteins with new properties.

Residual strength evaluation of concrete structural components under fatigue loading

This paper presents methodologies for residual strength evaluation of concrete structural components using linear elastic and nonlinear fracture mechanics principles. The effect of cohesive forces due to aggregate bridging has been represented mathematically by employing tension softening models. Various tension softening models such as linear, bilinear, trilinear, exponential and power curve have been described with appropriate expressions. These models have been validated by predicting the remaining life of concrete structural components and comparing with the corresponding experimental values available in the literature. It is observed that the predicted remaining life by using power model and modified bi-linear model is in good agreement with the corresponding experimental values. Residual strength has also been predicted using these tension softening models and observed that the predicted residual strength is in good agreement with the corresponding analytical values in the literature. In general, it is observed that the variation of predicted residual moment with the chosen tension softening model follows the similar trend as in the case of remaining life. Linear model predicts large residual moments followed by trilinear, bilinear and power models.

Incremental Cycle Detection, Topological Ordering, and Strong Component Maintenance

We present two online algorithms for maintaining a topological order of a directed n-vertex acyclic graph as arcs are added, and detecting a cycle when one is created. Our first algorithm handles m arc additions in O(m(3/2)) time. For sparse graphs (m/n = O(1)), this bound improves the best previous bound by a logarithmic factor, and is tight to within a constant factor among algorithms satisfying a natural locality property. Our second algorithm handles an arbitrary sequence of arc additions in O(n(5/2)) time. For sufficiently dense graphs, this bound improves the best previous bound by a polynomial factor. Our bound may be far from tight: we show that the algorithm can take Omega(n(2)2 root(2lgn)) time by relating its performance to a generalization of the k-levels problem of combinatorial geometry. A completely different algorithm running in Theta (n(2) log n) time was given recently by Bender, Fineman, and Gilbert. We extend both of our algorithms to the maintenance of strong components, without affecting the asymptotic time bounds.

Sequence-Structure Similarity: Do Sequentially Identical Peptide Fragments have Similar Three-Dimensional Structures?

The rapidly growing structure databases enhance the probability of finding identical sequences sharing structural similarity. Structure prediction methods are being used extensively to abridge the gap between known protein sequences and the solved structures which is essential to understand its specific biochemical and cellular functions. In this work, we plan to study the ambiguity between sequence-structure relationships and examine if sequentially identical peptide fragments adopt similar three-dimensional structures. Fragments of varying lengths (five to ten residues) were used to observe the behavior of sequence and its three-dimensional structures. The STAMP program was used to superpose the three-dimensional structures and the two parameters (Sequence Structure Similarity Score (Sc) and Root Mean Square Deviation value) were employed to classify them into three categories: similar, intermediate and dissimilar structures. Furthermore, the same approach was carried out on all the three-dimensional protein structures solved in the two organisms, Mycobacterium tuberculosis and Plasmodium falciparum to validate our results.

Regulation of lipid biosynthesis by phosphatidylinositol-specific phospholipase C through the transcriptional repression of upstream activating sequence inositol containing genes

The regulation of phospholipid biosynthesis in Saccharomyces cerevisiae through cis-acting upstream activating sequence inositol (UAS(ino)) and trans-acting elements, such as the INO2-INO4 complex and OPI1 by inositol supplementation in growth is thoroughly studied. In this study, we provide evidence for the regulation of lipid biosynthesis by phosphatidylinositol-specific phospholipase C (PLC) through UAS(ino) and the trans-acting elements. Gene expression analysis and radiolabelling experiments demonstrated that the overexpression of rice PLC in yeast cells altered phospholipid biosynthesis at the levels of transcriptional and enzyme activity. This is the first report implicating PLC in the direct regulation of lipid biosynthesis. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Draft Genome Sequence of Staphylococcus aureus 118 (ST772), a Major Disease Clone from India

We report the draft genome sequence of an ST772 Staphylococcus aureus disease isolate carrying staphylococcal cassette chromosome mec (SCCmec) type V from a pyomyositis patient. Our de novo short read assembly is similar to 2.8 Mb and encodes a unique Panton-Valentine leukocidin (PVL) phage with structural genes similar to those of phi 7247PVL and novel lysogenic genes at the N termini.

Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins

Over the past two decades, many ingenious efforts have been made in protein remote homology detection. Because homologous proteins often diversify extensively in sequence, it is challenging to demonstrate such relatedness through entirely sequence-driven searches. Here, we describe a computational method for the generation of `protein-like' sequences that serves to bridge gaps in protein sequence space. Sequence profile information, as embodied in a position-specific scoring matrix of multiply aligned sequences of bona fide family members, serves as the starting point in this algorithm. The observed amino acid propensity and the selection of a random number dictate the selection of a residue for each position in the sequence. In a systematic manner, and by applying a `roulette-wheel' selection approach at each position, we generate parent family-like sequences and thus facilitate an enlargement of sequence space around the family. When generated for a large number of families, we demonstrate that they expand the utility of natural intermediately related sequences in linking distant proteins. In 91% of the assessed examples, inclusion of designed sequences improved fold coverage by 5-10% over searches made in their absence. Furthermore, with several examples from proteins adopting folds such as TIM, globin, lipocalin and others, we demonstrate that the success of including designed sequences in a database positively sensitized methods such as PSI-BLAST and Cascade PSI-BLAST and is a promising opportunity for enormously improved remote homology recognition using sequence information alone.

Analysis of Conformational Variation in Macromolecular Structural Models

Experimental conditions or the presence of interacting components can lead to variations in the structural models of macromolecules. However, the role of these factors in conformational selection is often omitted by in silico methods to extract dynamic information from protein structural models. Structures of small peptides, considered building blocks for larger macromolecular structural models, can substantially differ in the context of a larger protein. This limitation is more evident in the case of modeling large multi-subunit macromolecular complexes using structures of the individual protein components. Here we report an analysis of variations in structural models of proteins with high sequence similarity. These models were analyzed for sequence features of the protein, the role of scaffolding segments including interacting proteins or affinity tags and the chemical components in the experimental conditions. Conformational features in these structural models could be rationalized by conformational selection events, perhaps induced by experimental conditions. This analysis was performed on a non-redundant dataset of protein structures from different SCOP classes. The sequence-conformation correlations that we note here suggest additional features that could be incorporated by in silico methods to extract dynamic information from protein structural models.

Evolution of quantum discord and its stability in two-qubit NMR systems

We investigate evolution of quantum correlations in ensembles of two-qubit nuclear spin systems via nuclear magnetic resonance techniques. We use discord as a measure of quantum correlations and the Werner state as an explicit example. We, first, introduce different ways of measuring discord and geometric discord in two-qubit systems and then describe the following experimental studies: (a) We quantitatively measure discord for Werner-like states prepared using an entangling pulse sequence. An initial thermal state with zero discord is gradually and periodically transformed into a mixed state with maximum discord. The experimental and simulated behavior of rise and fall of discord agree fairly well. (b) We examine the efficiency of dynamical decoupling sequences in preserving quantum correlations. In our experimental setup, the dynamical decoupling sequences preserved the traceless parts of the density matrices at high fidelity. But they could not maintain the purity of the quantum states and so were unable to keep the discord from decaying. (c) We observe the evolution of discord for a singlet-triplet mixed state during a radio-frequency spin-lock. A simple relaxation model describes the evolution of discord, and the accompanying evolution of fidelity of the long-lived singlet state, reasonably well.

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a ID sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. (C) 2012 Elsevier Masson SAS. All rights reserved.

Zero-Sum Risk-Sensitive Stochastic Differential Games

We study zero-sum risk-sensitive stochastic differential games on the infinite horizon with discounted and ergodic payoff criteria. Under certain assumptions, we establish the existence of values and saddle-point equilibria. We obtain our results by studying the corresponding Hamilton-Jacobi-Isaacs equations. Finally, we show that the value of the ergodic payoff criterion is a constant multiple of the maximal eigenvalue of the generators of the associated nonlinear semigroups.

Experimental Investigation on the Effect of Advanced Bus-Clamping Pulsewidth Modulation on Motor Acoustic Noise

Voltage source inverters (VSIs) supply nonsinusoidal voltages to induction motor drives, leading to line current distortion and torque pulsation. Conventional space vector pulsewidth modulation (PWM) techniques are widely used in VSIs on the account of good waveform quality and high dc bus utilization. In a conventional space vector PWM technique, the switching sequence begins with one zero state and ends with the other zero state in a subcycle. Some novel switching sequences have been proposed, which employ only one zero state but apply one of the two active states twice in a subcycle. One pair of such special switching sequences has recently been shown to reduce the pulsating torque considerably. In this paper, the conventional and special switching sequences are compared experimentally in terms of acoustic noise. In the low-and medium-speed ranges, the special switching sequence is seen to reduce the amplitude of the tonal component of noise at the switching frequency considerably and is also found to result in spread spectrum.

Zero-crossing approach to high-resolution reconstruction in frequency-domain optical-coherence tomography

We address the problem of high-resolution reconstruction in frequency-domain optical-coherence tomography (FDOCT). The traditional method employed uses the inverse discrete Fourier transform, which is limited in resolution due to the Heisenberg uncertainty principle. We propose a reconstruction technique based on zero-crossing (ZC) interval analysis. The motivation for our approach lies in the observation that, for a multilayered specimen, the backscattered signal may be expressed as a sum of sinusoids, and each sinusoid manifests as a peak in the FDOCT reconstruction. The successive ZC intervals of a sinusoid exhibit high consistency, with the intervals being inversely related to the frequency of the sinusoid. The statistics of the ZC intervals are used for detecting the frequencies present in the input signal. The noise robustness of the proposed technique is improved by using a cosine-modulated filter bank for separating the input into different frequency bands, and the ZC analysis is carried out on each band separately. The design of the filter bank requires the design of a prototype, which we accomplish using a Kaiser window approach. We show that the proposed method gives good results on synthesized and experimental data. The resolution is enhanced, and noise robustness is higher compared with the standard Fourier reconstruction. (c) 2012 Optical Society of America

Sequence and structural basis for chromosomal fragility during translocations in cancer

Chromosomal aberration is considered to be one of the major characteristic features in many cancers. Chromosomal translocation, one type of genomic abnormality, can lead to deregulation of critical genes involved in regulating important physiological functions such as cell proliferation and DNA repair. Although chromosomal translocations were thought to be random events, recent findings suggest that certain regions in the human genome are more susceptible to breakage than others. The possibility of deviation from the usual B-DNA conformation in such fragile regions has been an active area of investigation. This review summarizes the factors that contribute towards the fragility of these regions in the chromosomes, such as DNA sequences and the role of different forms of DNA structures. Proteins responsible for chromosomal fragility, and their mechanism of action are also discussed. The effect of positioning of chromosomes within the nucleus favoring chromosomal translocations and the role of repair mechanisms are also addressed.