Maximum Margin Classifiers with Specified False Positive and False Negative Error Rates

This paper addresses the problem of maximum margin classification given the moments of class conditional densities and the false positive and false negative error rates. Using Chebyshev inequalities, the problem can be posed as a second order cone programming problem. The dual of the formulation leads to a geometric optimization problem, that of computing the distance between two ellipsoids, which is solved by an iterative algorithm. The formulation is extended to non-linear classifiers using kernel methods. The resultant classifiers are applied to the case of classification of unbalanced datasets with asymmetric costs for misclassification. Experimental results on benchmark datasets show the efficacy of the proposed method.

Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS-alpha method

Biochemical pathways involving chemical kinetics in medium concentrations (i.e., at mesoscale) of the reacting molecules can be approximated as chemical Langevin equations (CLE) systems. We address the physically consistent non-negative simulation of the CLE sample paths as well as the issue of non-Lipschitz diffusion coefficients when a species approaches depletion and any stiffness due to faster reactions. The non-negative Fully Implicit Stochastic alpha (FIS alpha) method in which stopped reaction channels due to depleted reactants are deleted until a reactant concentration rises again, for non-negativity preservation and in which a positive definite Jacobian is maintained to deal with possible stiffness, is proposed and analysed. The method is illustrated with the computation of active Protein Kinase C response in the Protein Kinase C pathway. (C) 2011 Elsevier Inc. All rights reserved.

Degrees of freedom of relay aided MIMO X network with orthogonal components

We consider the one-way relay aided MIMO X fading Channel where there are two transmitters and two receivers along with a relay with M antennas at every node. Every transmitter wants to transmit messages to every other receiver. The relay broadcasts to the receivers along a noisy link which is independent of the transmitters channel. In literature, this is referred to as a relay with orthogonal components. We derive an upper bound on the degrees of freedom of such a network. Next we show that the upper bound is tight by proposing an achievability scheme based on signal space alignment for the same for M = 2 antennas at every node.

Ion-Acoustic Solitary Waves in Multicomponent Plasmas with Negative Ions

By using the perturbation technique, a Kortewege-de-Vries (K-dV) equation for a multicomponent plasma with negative ions and isothermal electrons has been derived. We have discussed the stationary solutions of K-dV equation and it has shown that in the presece of multiple ions, the amplitude of solitons exhibits interesting behaviour, especiallY when the negative ions are present.

Crystallographic Study of Novel Transthyretin Ligands Exhibiting Negative-Cooperativity between Two Thyroxine Binding Sites

Background: Transthyretin (TTR) is a homotetrameric serum and cerebrospinal fluid protein that transports thyroxine (T4) and retinol by binding to retinol binding protein. Rate-limiting tetramer dissociation and rapid monomer misfolding and disassembly of TTR lead to amyloid fibril formation in different tissues causing various amyloid diseases. Based on the current understanding of the pathogenesis of TTR amyloidosis, it is considered that the inhibition of amyloid fibril formation by stabilization of TTR in native tetrameric form is a viable approach for the treatment of TTR amyloidosis. Methodology and Principal Findings: We have examined interactions of the wtTTR with a series of compounds containing various substitutions at biphenyl ether skeleton and a novel compound, previously evaluated for binding and inhibiting tetramer dissociation, by x-ray crystallographic approach. High resolution crystal structures of five ligands in complex with wtTTR provided snapshots of negatively cooperative binding of ligands in two T4 binding sites besides characterizing their binding orientations, conformations, and interactions with binding site residues. In all complexes, the ligand has better fit and more potent interactions in first T4 site i.e. (AC site) than the second T4 site (BD site). Together, these results suggest that AC site is a preferred ligand binding site and retention of ordered water molecules between the dimer interfaces further stabilizes the tetramer by bridging a hydrogen bond interaction between Ser117 and its symmetric copy. Conclusion: Novel biphenyl ether based compounds exhibit negative-cooperativity while binding to two T4 sites which suggests that binding of only single ligand molecule is sufficient to inhibit the TTR tetramer dissociation.

On the generalized degrees of freedom of the K-user symmetric MIMO Gaussian interference channel

This work derives inner and outer bounds on the generalized degrees of freedom (GDOF) of the K-user symmetric MIMO Gaussian interference channel. For the inner bound, an achievable GDOF is derived by employing a combination of treating interference as noise, zero-forcing at the receivers, interference alignment (IA), and extending the Han-Kobayashi (HK) scheme to K users, depending on the number of antennas and the INR/SNR level. An outer bound on the GDOF is derived, using a combination of the notion of cooperation and providing side information to the receivers. Several interesting conclusions are drawn from the bounds. For example, in terms of the achievable GDOF in the weak interference regime, when the number of transmit antennas (M) is equal to the number of receive antennas (N), treating interference as noise performs the same as the HK scheme and is GDOF optimal. For K >; N/M+1, a combination of the HK and IA schemes performs the best among the schemes considered. However, for N/M <; K ≤ N/M+1, the HK scheme is found to be GDOF optimal.

A soluble-lead redox flow battery with corrugated graphite sheet and reticulated vitreous carbon as positive and negative current collectors

A soluble-lead redox flow battery with corrugated-graphite sheet and reticulated-vitreous carbon as positive and negative current collectors is assembled and performance tested. In the cell, electrolyte comprising of 1 center dot 5 M lead (II) methanesulfonate and 0 center dot 9 M methanesulfonic acid with sodium salt of lignosulfonic acid as additive is circulated through the reaction chamber at a flow rate of 50 ml min (-aEuro parts per thousand 1). During the charge cycle, pure lead (Pb) and lead dioxide (PbO2) from the soluble lead (II) species are electrodeposited onto the surface of the negative and positive current collectors, respectively. Both the electrodeposited materials are characterized by XRD, XPS and SEM. Phase purity of synthesized lead (II) methanesulfonate is unequivocally established by single crystal X-ray diffraction followed by profile refinements using high resolution powder data. During the discharge cycle, electrodeposited Pb and PbO2 are dissolved back into the electrolyte. Since lead ions are produced during oxidation and reduction at the negative and positive plates, respectively there is no risk of crossover during discharge cycle, preventing the possibility of lowering the overall efficiency of the cell. As the cell employs a common electrolyte, the need of employing a membrane is averted. It has been possible to achieve a capacity value of 114 mAh g (-aEuro parts per thousand 1) at a load current-density of 20 mA cm (-aEuro parts per thousand 2) with the cell at a faradaic efficiency of 95%. The cell is tested for 200 cycles with little loss in its capacity and efficiency.

Hybrid online non-negative matrix factorization for clustering of documents

When document corpus is very large, we often need to reduce the number of features. But it is not possible to apply conventional Non-negative Matrix Factorization(NMF) on billion by million matrix as the matrix may not fit in memory. Here we present novel Online NMF algorithm. Using Online NMF, we reduced original high-dimensional space to low-dimensional space. Then we cluster all the documents in reduced dimension using k-means algorithm. We experimentally show that by processing small subsets of documents we will be able to achieve good performance. The method proposed outperforms existing algorithms.

Analysis of the degrees-of-freedom of spatial parallel manipulators in regular and singular configurations

This paper presents a study of the nature of the degrees-of-freedom of spatial manipulators based on the concept of partition of degrees-of-freedom. In particular, the partitioning of degrees-of-freedom is studied in five lower-mobility spatial parallel manipulators possessing different combinations of degrees-of-freedom. An extension of the existing theory is introduced so as to analyse the nature of the gained degree(s)-of-freedom at a gain-type singularity. The gain of one- and two-degrees-of-freedom is analysed in several well-studied, as well as newly developed manipulators. The formulations also present a basis for the analysis of the velocity kinematics of manipulators of any architecture. (C) 2013 Elsevier Ltd. All rights reserved.

Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Negative differential resistance and effect of defects and deformations in MoS2 armchair nanoribbon metal-oxide-semiconductor field effect transistor

In this work, we present a study on the negative differential resistance (NDR) behavior and the impact of various deformations (like ripple, twist, wrap) and defects like vacancies and edge roughness on the electronic properties of short-channel MoS2 armchair nanoribbon MOSFETs. The effect of deformation (3 degrees-7 degrees twist or wrap and 0.3-0.7 angstrom ripple amplitude) and defects on a 10 nm MoS2 ANR FET is evaluated by the density functional tight binding theory and the non-equilibrium Green's function approach. We study the channel density of states, transmission spectra, and the I-D-V-D characteristics of such devices under the varying conditions, with focus on the NDR behavior. Our results show significant change in the NDR peak to valley ratio and the NDR window with such minor intrinsic deformations, especially with the ripple. (C) 2013 AIP Publishing LLC.

Metal-organic chemical vapor-deposited cobalt oxide films as negative electrodes for thin film Li-ion battery

In this study, thin films of cobalt oxide (Co3O4) have been grown by the metal-organic chemical vapor deposition (MOCVD) technique on stainless steel substrate at two preferred temperatures (450 degrees C and 500 degrees C), using cobalt acetylacetonate dihydrate as precursor. Spherical as well as columnar microstructures of Co3O4 have been observed under controlled growth conditions. Further investigations reveal these films are phase-pure, well crystallized and carbon-free. High-resolution TEM analysis confirms that each columnar structure is a continuous stack of minute crystals. Comparative study between these Co3O4 films grown at 450 degrees C and 500 degrees C has been carried out for their application as negative electrodes in Li-ion batteries. Our method of electrode fabrication leads to a coating of active material directly on current collector without any use of external additives. A high specific capacity of 1168 micro Ah cm(-2) mu m(-1) has been measured reproducibly for the film deposited at 500 degrees C with columnar morphology. Further, high rate capability is observed when cycled at different current densities. The Co3O4 electrode with columnar structure has a specific capacity 38% higher than the electrode with spherical microstructure (grown at 450 degrees C). Impedance measurements on the Co3O4 electrode grown at 500 degrees C also carried out to study the kinetics of the electrode process. (C) 2014 Published by Elsevier B.V.

Demonstration of helicase activity in the nonstructural protein, NSs, of the negative-sense RNA virus, Groundnut bud necrosis virus

The nonstructural protein NSs, encoded by the S RNA of groundnut bud necrosis virus (GBNV) (genus Tospovirus, family Bunyaviridae) has earlier been shown to possess nucleic-acid-stimulated NTPase and 50 a phosphatase activity. ATP hydrolysis is an essential function of a true helicase. Therefore, NSs was tested for DNA helicase activity. The results demonstrated that GBNV NSs possesses bidirectional DNA helicase activity. An alanine mutation in the Walker A motif (K189A rNSs) decreased DNA helicase activity substantially, whereas a mutation in the Walker B motif resulted in a marginal decrease in this activity. The parallel loss of the helicase and ATPase activity in the K189A mutant confirms that NSs acts as a non-canonical DNA helicase. Furthermore, both the wild-type and K189A NSs could function as RNA silencing suppressors, demonstrating that the suppressor activity of NSs is independent of its helicase or ATPase activity. This is the first report of a true helicase from a negative-sense RNA virus.

Negative hyperconjugation and red-, blue- or zero-shift in X-Z center dot center dot center dot Y complexes

A generalized explanation is provided for the existence of the red-and blue-shifting nature of X-Z bonds (Z = H, halogens, chalcogens, pnicogens, etc.) in X-Z center dot center dot center dot Y complexes based on computational studies on a selected set of weakly bonded complexes and analysis of existing literature data. The additional electrons and orbitals available on Z in comparison to H make for dramatic differences between the H-bond and the rest of the Z-bonds. The nature of the X-group and its influence on the X-Z bond length in the parent X-Z molecule largely controls the change in the X-Z bond length on X-Z center dot center dot center dot Y bond formation; the Y-group usually influences only the magnitude of the effects controlled by X. The major factors which control the X-Z bond length change are: (a) negative hyperconjugative donation of electron density from X-group to X-Z sigma* antibonding molecular orbital (ABMO) in the parent X-Z, (b) induced negative hyperconjugation from the lone pair of electrons on Z to the antibonding orbitals of the X-group, and (c) charge transfer (CT) from the Y-group to the X-Z sigma* orbital. The exchange repulsion from the Y-group that shifts partial electron density at the X-Z sigma* ABMO back to X leads to blue-shifting and the CT from the Y-group to the sigma* ABMO of X-Z leads to red-shifting. The balance between these two opposing forces decides red-, zero- or blue-shifting. A continuum of behaviour of X-Z bond length variation is inevitable in X-Z center dot center dot center dot Y complexes.