Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage

Background: Development of sensitive sequence search procedures for the detection of distant relationships between proteins at superfamily/fold level is still a big challenge. The intermediate sequence search approach is the most frequently employed manner of identifying remote homologues effectively. In this study, examination of serine proteases of prolyl oligopeptidase, rhomboid and subtilisin protein families were carried out using plant serine proteases as queries from two genomes including A. thaliana and O. sativa and 13 other families of unrelated folds to identify the distant homologues which could not be obtained using PSI-BLAST. Methodology/Principal Findings: We have proposed to start with multiple queries of classical serine protease members to identify remote homologues in families, using a rigorous approach like Cascade PSI-BLAST. We found that classical sequence based approaches, like PSI-BLAST, showed very low sequence coverage in identifying plant serine proteases. The algorithm was applied on enriched sequence database of homologous domains and we obtained overall average coverage of 88% at family, 77% at superfamily or fold level along with specificity of similar to 100% and Mathew's correlation coefficient of 0.91. Similar approach was also implemented on 13 other protein families representing every structural class in SCOP database. Further investigation with statistical tests, like jackknifing, helped us to better understand the influence of neighbouring protein families. Conclusions/Significance: Our study suggests that employment of multiple queries of a family for the Cascade PSI-BLAST searches is useful for predicting distant relationships effectively even at superfamily level. We have proposed a generalized strategy to cover all the distant members of a particular family using multiple query sequences. Our findings reveal that prior selection of sequences as query and the presence of neighbouring families can be important for covering the search space effectively in minimal computational time. This study also provides an understanding of the `bridging' role of related families.

Clay mineral liner system for leachates containing organic contaminants

A conventional liner with a good performance against inorganic contaminants with a minimal hydraulic conductivity does not usually perform well for retention/removal of leachates containing organic contaminants. Organic modification of clay can render the naturally organophobic clay tobe organophilic. Incorporation of modified organo clay along with unmodified inorganic clay in liner systems can overcome the inherent incompatibility of conventional liners to organic contaminants and can increase organic sorption. The performance of commercially available organo clay and natural bentonite and mixtures of them in different pore fluids has been studied. It is found that the properties of mixtures improve with increase in organically modified clay particularly in non aqueous fluids from the considerations of liner application.

A LSQR-type method provides a computationally efficient automated optimal choice of regularization parameter in diffuse optical tomography

Purpose: Developing a computationally efficient automated method for the optimal choice of regularization parameter in diffuse optical tomography. Methods: The least-squares QR (LSQR)-type method that uses Lanczos bidiagonalization is known to be computationally efficient in performing the reconstruction procedure in diffuse optical tomography. The same is effectively deployed via an optimization procedure that uses the simplex method to find the optimal regularization parameter. The proposed LSQR-type method is compared with the traditional methods such as L-curve, generalized cross-validation (GCV), and recently proposed minimal residual method (MRM)-based choice of regularization parameter using numerical and experimental phantom data. Results: The results indicate that the proposed LSQR-type and MRM-based methods performance in terms of reconstructed image quality is similar and superior compared to L-curve and GCV-based methods. The proposed method computational complexity is at least five times lower compared to MRM-based method, making it an optimal technique. Conclusions: The LSQR-type method was able to overcome the inherent limitation of computationally expensive nature of MRM-based automated way finding the optimal regularization parameter in diffuse optical tomographic imaging, making this method more suitable to be deployed in real-time. (C) 2013 American Association of Physicists in Medicine. http://dx.doi.org/10.1118/1.4792459]

Generating string solutions in BTZ

Integrability of classical strings in the BTZ black hole enables the construction and study of classical string propagation in this background. We first apply the dressing method to obtain classical string solutions in the BTZ black hole. We dress time like geodesics in the BTZ black hole and obtain open string solutions which are pinned on the boundary at a single point and whose end points move on time like geodesics. These strings upon regularising their charge and spins have a dispersion relation similar to that of giant magnons. We then dress space like geodesics which start and end on the boundary of the BTZ black hole and obtain minimal surfaces which can penetrate the horizon of the black hole while being pinned at the boundary. Finally we embed the giant gluon solutions in the BTZ background in two different ways. They can be embedded as a spiral which contracts and expands touching the horizon or a spike which originates from the boundary and touches the horizon.

Gene expression in osteoblast cells treated with submicron to nanometer hydroxyapatite-mullite eluate particles

The present research focused on determining the effect of hydroxyapatite-20 wt% mullite (H20M) particle eluates on apoptosis and differentiation of human fetal osteoblast (hFOB) cells. The H20M particles (257 +/- 37 nm) were prepared, starting with the production of a nanocomposite using a unique route of spark plasma sintering, followed by a repeated grinding-cryo treatment and elution process. Tetrazolium based cytotoxicity assay results showed a time-and dose-dependent effect of H20M particle eluates on hFOB cytotoxicity. In particular, the results revealed statistically reduced cell viability after hFOB were exposed to the above 10% H20M (257 +/- 37 nm) eluates for 48 h. The apoptotic cell death triggered by H20M treatment was proven by the analysis of molecular markers of apoptosis, that is, the Bcl-2 family of genes. hFOB expression of Bcl-xL and Bcl-xS significantly increased 25.6- and 25.2-fold for 50% of H20M concentrations, respectively. The ratio of Bcl-xL/Bax (4.01) decreased 2-fold for hFOB exposed to 100% of H20M eluates than that for 10% H20M eluate (7.94) treated hFOB cells. On the other hand, the Bcl-xS/Bax ratio for the 10% H20M eluate was 4.15-fold, whereas for 100% H20M eluates, it was 11.55-fold. Specifically, the anti-apoptotic effect of the H20M particle eluates was corroborated by the up-regulation of bone cell differentiation marker genes such as, collagen type I, cbfa, and osteocalcin. In summary, the present work clearly demonstrated that H20M submicron to nanometer composite particle eluates have a minimal effect on hFOB apoptosis and can even up-regulate the expression of bone cell markers at the molecular level.

Discriminative feature analysis and selection for document classification

Classification of a large document collection involves dealing with a huge feature space where each distinct word is a feature. In such an environment, classification is a costly task both in terms of running time and computing resources. Further it will not guarantee optimal results because it is likely to overfit by considering every feature for classification. In such a context, feature selection is inevitable. This work analyses the feature selection methods, explores the relations among them and attempts to find a minimal subset of features which are discriminative for document classification.

Probing the indefinite CP nature of the Higgs boson through decay distributions in the process e(+)e(-) -> t(t)over-bar Phi

The recently discovered scalar resonance at the Large Hadron Collider is now almost confirmed to be a Higgs boson, whose CP properties are yet to be established. At the International Linear Collider with and without polarized beams, it may be possible to probe these properties at high precision. In this work, we study the possibility of probing departures from the pure CP-even case, by using the decay distributions in the process e(+)e(-) -> t (t) over bar Phi, with Phi mainly decaying into a b (b) over bar pair. We have compared the case of a minimal extension of the Standard Model case (model I) with an additional pseudoscalar degree of freedom, with a more realistic case namely the CP-violating two-Higgs doublet model (model II) that permits a more general description of the couplings. We have considered the International Linear Collider with root s = 800 GeV and integrated luminosity of 300 fb(-1). Our main findings are that even in the case of small departures from the CP-even case, the decay distributions are sensitive to the presence of a CP-odd component in model II, while it is difficult to probe these departures in model I unless the pseudoscalar component is very large. Noting that the proposed degrees of beam polarization increase the statistics, the process demonstrates the effective role of beam polarization in studies beyond the Standard Model. Further, our study shows that an indefinite CP Higgs would be a sensitive laboratory to physics beyond the Standard Model.

Process control of cantilever deflection for sensor application based on optical waveguides

This paper reports on the fabrication of cantilever silicon-on-insulator (SOI) optical waveguides and presents solutions to the challenges of using a very thin 260-nm active silicon layer in the SOI structure to enable single-transverse-mode operation of the waveguide with minimal optical transmission losses. In particular, to ameliorate the anchor effect caused by the mean stress difference between the active silicon layer and buried oxide layer, a cantilever flattening process based on Ar plasma treatment is developed and presented. Vertical deflections of 0.5 mu m for 70-mu m-long cantilevers are mitigated to within few nanometers. Experimental investigations of cantilever mechanical resonance characteristics confirm the absence of significant detrimental side effects. Optical and mechanical modeling is extensively used to supplement experimental observations. This approach can satisfy the requirements for on-chip simultaneous readout of many integrated cantilever sensors in which the displacement or resonant frequency changes induced by analyte absorption are measured using an optical-waveguide-based division multiplexed system.

Revisiting lepton flavor violation in a supersymmetric type II seesaw mechanism

In view of the recent measurement of the reactor mixing angle theta(13) and updated limit on BRd(mu -> e gamma) by the MEG experiment, we reexamine the charged lepton flavor violations in a framework of the supersymmetric type II seesaw mechanism. The supersymmetric type II seesaw predicts a strong correlation between BR(mu -> e gamma) and BR(tau -> mu gamma) mainly in terms of the neutrino mixing angles. We show that such a correlation can be determined accurately after the measurement of theta(13). We compute different factors that can affect this correlation and show that the minimal supergravity-like scenarios, in which slepton masses are taken to be universal at the high scale, predict 3.5 <= BR(tau -> mu gamma)/= BR(mu -> e gamma) <= 30 for normal hierarchical neutrino masses. Any experimental indication of deviation from this prediction would rule out the minimal models of the supersymmetric type II seesaw. We show that the current MEG limit puts severe constraints on the light sparticle spectrum in the minimal supergravity model if the seesaw scale lies within 10(13)-10(15) GeV. It is shown that these constraints can be relaxed and a relatively light sparticle spectrum can be obtained in a class of models in which the soft mass of a triplet scalar is taken to be nonuniversal at the high scale.

Common-mode filter design for PWM rectifier-based motor drives

A common-mode (CM) filter based on the LCL filter topology is proposed in this paper, which provides a parallel path for ground currents and which also restricts the magnitude of the EMI noise injected into the grid. The CM filter makes use of the components of a line to line LCL filter, which is modified to address the CM voltage with minimal additional components. This leads to a compact filtering solution. The CM voltage of an adjustable speed drive using a PWM rectifier is analyzed for this purpose. The filter design is based on the CM equivalent circuit of the drive system. The filter addresses the adverse effects of the PWM rectifier in an adjustable speed drive. Guidelines are provided on the selection of the filter components. Different variants of the filter topology are evaluated to establish the effectiveness of the proposed circuit. Experimental results based on EMI measurement on the grid side and the CM current measurement on the motor side are presented. These results validate the effectiveness of the filter.

Authentication using finger Knuckle prints

Automated security is one of the major concerns of modern times. Secure and reliable authentication systems are in great demand. A biometric trait like the finger knuckle print (FKP) of a person is unique and secure. Finger knuckle print is a novel biometric trait and is not explored much for real-time implementation. In this paper, three different algorithms have been proposed based on this trait. The first approach uses Radon transform for feature extraction. Two levels of security are provided here and are based on eigenvalues and the peak points of the Radon graph. In the second approach, Gabor wavelet transform is used for extracting the features. Again, two levels of security are provided based on magnitude values of Gabor wavelet and the peak points of Gabor wavelet graph. The third approach is intended to authenticate a person even if there is a damage in finger knuckle position due to injury. The FKP image is divided into modules and module-wise feature matching is done for authentication. Performance of these algorithms was found to be much better than very few existing works. Moreover, the algorithms are designed so as to implement in real-time system with minimal changes.

Invisible decays of the lightest Higgs boson in supersymmetric models

We consider supersymmetric models in which the lightest Higgs scalar can decay invisibly consistent with the constraints on the 126 GeV state discovered at the CERN LHC. We consider the invisible decay in the minimal supersymmetric standard model (MSSM), as well its extension containing an additional chiral singlet superfield, the so-called next-to-minimal or nonminimal supersymmetric standard model (NMSSM). We consider the case of MSSM with both universal as well as nonuniversal gaugino masses at the grand unified scale, and find that only an E-6 grand unified model with unnaturally large representation can give rise to sufficiently light neutralinos which can possibly lead to the invisible decay h(0) -> (chi) over tilde (0)(1)(chi) over tilde (0)(1). Following this, we consider the case of NMSSM in detail, where we also find that it is not possible to have the invisible decay of the lightest Higgs scalar with universal gaugino masses at the grand unified scale. We delineate the regions of the NMSSM parameter space where it is possible for the lightest Higgs boson to have a mass of about 126 GeV, and then concentrate on the region where this Higgs can decay into light neutralinos, with the soft gaugino masses M-1 and M-2 as two independent parameters, unconstrained by grand unification. We also consider, simultaneously, the other important invisible Higgs decay channel in the NMSSM, namely the decay into the lightest CP-odd scalars, h(1) -> a(1)a(1), which is studied in detail. With the invisible Higgs branching ratio being constrained by the present LHC results, we find that mu(eff) < 170 GeV and M-1 < 80 GeV are disfavored in NMSSM for fixed values of the other input parameters. The dependence of our results on the parameters of NMSSM is discussed in detail.

Multi-resistance states in the electrical switching behavior of amorphous Si15Te75Ge10 thin films: Possibility of multi-bit storage

Electrical switching studies on amorphous Si15Te75Ge10 thin film devices reveal the existence of two distinct, stable low-resistance, SET states, achieved by varying the electrical input to the device. The multiple resistance levels can be attributed to multi-stage crystallization, as observed from temperature dependant resistance studies. The devices are tested for their ability to be RESET with minimal resistance degradation; further, they exhibit a minimal drift in the SET resistance value even after several months of switching. (c) 2013 Elsevier B.V. All rights reserved.

Resolution of Singularities for a Class of Hilbert Modules

Let M be the completion of the polynomial ring C(z) under bar] with respect to some inner product, and for any ideal I subset of C (z) under bar], let I] be the closure of I in M. For a homogeneous ideal I, the joint kernel of the submodule I] subset of M is shown, after imposing some mild conditions on M, to be the linear span of the set of vectors {p(i)(partial derivative/partial derivative(w) over bar (1),...,partial derivative/partial derivative(w) over bar (m)) K-I] (., w)vertical bar(w=0), 1 <= i <= t}, where K-I] is the reproducing kernel for the submodule 2] and p(1),..., p(t) is some minimal ``canonical set of generators'' for the ideal I. The proof includes an algorithm for constructing this canonical set of generators, which is determined uniquely modulo linear relations, for homogeneous ideals. A short proof of the ``Rigidity Theorem'' using the sheaf model for Hilbert modules over polynomial rings is given. We describe, via the monoidal transformation, the construction of a Hermitian holomorphic line bundle for a large class of Hilbert modules of the form I]. We show that the curvature, or even its restriction to the exceptional set, of this line bundle is an invariant for the unitary equivalence class of I]. Several examples are given to illustrate the explicit computation of these invariants.

Joint Antenna Selection and Frequency-Domain Scheduling in OFDMA Systems with Imperfect Estimates from Dual Pilot Training Scheme

Transmit antenna selection (AS) has been adopted in contemporary wideband wireless standards such as Long Term Evolution (LTE). We analyze a comprehensive new model for AS that captures several key features about its operation in wideband orthogonal frequency division multiple access (OFDMA) systems. These include the use of channel-aware frequency-domain scheduling (FDS) in conjunction with AS, the hardware constraint that a user must transmit using the same antenna over all its assigned subcarriers, and the scheduling constraint that the subcarriers assigned to a user must be contiguous. The model also captures the novel dual pilot training scheme that is used in LTE, in which a coarse system bandwidth-wide sounding reference signal is used to acquire relatively noisy channel state information (CSI) for AS and FDS, and a dense narrow-band demodulation reference signal is used to acquire accurate CSI for data demodulation. We analyze the symbol error probability when AS is done in conjunction with the channel-unaware, but fair, round-robin scheduling and with channel-aware greedy FDS. Our results quantify how effective joint AS-FDS is in dispersive environments, the interactions between the above features, and the ability of the user to lower SRS power with minimal performance degradation.