CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone H-1(alpha) and C-13' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to alpha-helical/beta-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment.

Linear Coding Schemes for the Distributed Computation of Subspaces

Let X-1,..., X-m be a set of m statistically dependent sources over the common alphabet F-q, that are linearly independent when considered as functions over the sample space. We consider a distributed function computation setting in which the receiver is interested in the lossless computation of the elements of an s-dimensional subspace W spanned by the elements of the row vector X-1,..., X-m]Gamma in which the (m x s) matrix Gamma has rank s. A sequence of three increasingly refined approaches is presented, all based on linear encoders. The first approach uses a common matrix to encode all the sources and a Korner-Marton like receiver to directly compute W. The second improves upon the first by showing that it is often more efficient to compute a carefully chosen superspace U of W. The superspace is identified by showing that the joint distribution of the {X-i} induces a unique decomposition of the set of all linear combinations of the {X-i}, into a chain of subspaces identified by a normalized measure of entropy. This subspace chain also suggests a third approach, one that employs nested codes. For any joint distribution of the {X-i} and any W, the sum-rate of the nested code approach is no larger than that under the Slepian-Wolf (SW) approach. Under the SW approach, W is computed by first recovering each of the {X-i}. For a large class of joint distributions and subspaces W, the nested code approach is shown to improve upon SW. Additionally, a class of source distributions and subspaces are identified, for which the nested-code approach is sum-rate optimal.

The credit risk(+) model with general sector correlations

We consider an enhancement of the credit risk+ model to incorporate correlations between sectors. We model the sector default rates as linear combinations of a common set of independent variables that represent macro-economic variables or risk factors. We also derive the formula for exact VaR contributions at the obligor level.

Cochannel Interference in Partially Coherent Communication

Effects of cochannel interference and synchronization error of the carrier phase on the probability of error in binary communications are considered. Several bounds on the probability of error are proposed. The bounds are easy to compute and do not require complete statistical characterization of the errors. They turn out to be simple linear combinations of error probabilities with no cochannel interferences and no phase errors. Several illustrative examples are given which show that the bounds can be tight.

On the maximal rate of non-square STBCs from complex orthogonal designs

A Linear Processing Complex Orthogonal Design (LPCOD) is a p x n matrix epsilon, (p >= n) in k complex indeterminates x(1), x(2),..., x(k) such that (i) the entries of epsilon are complex linear combinations of 0, +/- x(i), i = 1,..., k and their conjugates, (ii) epsilon(H)epsilon = D, where epsilon(H) is the Hermitian (conjugate transpose) of epsilon and D is a diagonal matrix with the (i, i)-th diagonal element of the form l(1)((i))vertical bar x(1)vertical bar(2) + l(2)((i))vertical bar x(2)vertical bar(2)+...+ l(k)((i))vertical bar x(k)vertical bar(2) where l(j)((i)), i = 1, 2,..., n, j = 1, 2,...,k are strictly positive real numbers and the condition l(1)((i)) = l(2)((i)) = ... = l(k)((i)), called the equal-weights condition, holds for all values of i. For square designs it is known. that whenever a LPCOD exists without the equal-weights condition satisfied then there exists another LPCOD with identical parameters with l(1)((i)) = l(2)((i)) = ... = l(k)((i)) = 1. This implies that the maximum possible rate for square LPCODs without the equal-weights condition is the same as that or square LPCODs with equal-weights condition. In this paper, this result is extended to a subclass of non-square LPCODs. It is shown that, a set of sufficient conditions is identified such that whenever a non-square (p > n) LPCOD satisfies these sufficient conditions and do not satisfy the equal-weights condition, then there exists another LPCOD with the same parameters n, k and p in the same complex indeterminates with l(1)((i)) = l(2)((i)) = ... = l(k)((i)) = 1.

On the maximal rate of (n+1) x n and (n+2) x n complex orthogonal designs

For p x n complex orthogonal designs in k variables, where p is the number of channels uses and n is the number of transmit antennas, the maximal rate L of the design is asymptotically half as n increases. But, for such maximal rate codes, the decoding delay p increases exponentially. To control the delay, if we put the restriction that p = n, i.e., consider only the square designs, then, the rate decreases exponentially as n increases. This necessitates the study of the maximal rate of the designs with restrictions of the form p = n+1, p = n+2, p = n+3 etc. In this paper, we study the maximal rate of complex orthogonal designs with the restrictions p = n+1 and p = n+2. We derive upper and lower bounds for the maximal rate for p = n+1 and p = n+2. Also for the case of p = n+1, we show that if the orthogonal design admit only the variables, their negatives and multiples of these by root-1 and zeros as the entries of the matrix (other complex linear combinations are not allowed), then the maximal rate always equals the lower bound.

Symmetry adaptation of correlated states in the valence bond basis

Symmetry?adapted linear combinations of valence?bond (VB) diagrams are constructed for arbitrary point groups and total spin S using diagrammatic VB methods. VB diagrams are related uniquely to invariant subspaces whose size reflects the number of group elements; their nonorthogonality leads to sparser matrices and is fully incorporated into a binary integer representation. Symmetry?adapated linear combinations of VB diagrams are constructed for the 1764 singlets of a half?filled cube of eight sites, the 2.8 million ??electron singlets of anthracene, and for illustrative S?0 systems.

Network Error Correction for Unit-Delay, Memory-Free Networks Using Convolutional Codes

A single source network is said to be memory-free if all of the internal nodes (those except the source and the sinks) do not employ memory but merely send linear combinations of the symbols received at their incoming edges on their outgoing edges. In this work, we introduce network-error correction for single source, acyclic, unit-delay, memory-free networks with coherent network coding for multicast. A convolutional code is designed at the source based on the network code in order to correct network- errors that correspond to any of a given set of error patterns, as long as consecutive errors are separated by a certain interval which depends on the convolutional code selected. Bounds on this interval and the field size required for constructing the convolutional code with the required free distance are also obtained. We illustrate the performance of convolutional network error correcting codes (CNECCs) designed for the unit-delay networks using simulations of CNECCs on an example network under a probabilistic error model.

Single-Generation Network Coding for Networks with Delay

A single-source network is said to be memory-free if all of the internal nodes (those except the source and the sinks) do not employ memory but merely send linear combinations of the incoming symbols (received at their incoming edges) on their outgoing edges. Memory-free networks with delay using network coding are forced to do inter-generation network coding, as a result of which the problem of some or all sinks requiring a large amount of memory for decoding is faced. In this work, we address this problem by utilizing memory elements at the internal nodes of the network also, which results in the reduction of the number of memory elements used at the sinks. We give an algorithm which employs memory at all the nodes of the network to achieve single- generation network coding. For fixed latency, our algorithm reduces the total number of memory elements used in the network to achieve single- generation network coding. We also discuss the advantages of employing single-generation network coding together with convolutional network-error correction codes (CNECCs) for networks with unit- delay and illustrate the performance gain of CNECCs by using memory at the intermediate nodes using simulations on an example network under a probabilistic network error model.

Quantum stochastic calculus associated with quadratic quantum noises

We first study a class of fundamental quantum stochastic processes induced by the generators of a six dimensional non-solvable Lie dagger-algebra consisting of all linear combinations of the generalized Gross Laplacian and its adjoint, annihilation operator, creation operator, conservation, and time, and then we study the quantum stochastic integrals associated with the class of fundamental quantum stochastic processes, and the quantum Ito formula is revisited. The existence and uniqueness of solution of a quantum stochastic differential equation is proved. The unitarity conditions of solutions of quantum stochastic differential equations associated with the fundamental processes are examined. The quantum stochastic calculus extends the Hudson-Parthasarathy quantum stochastic calculus. (C) 2016 AIP Publishing LLC.

A fast algorithm for speech polarity detection using long-term linear prediction

Speech polarity detection is a crucial first step in many speech processing techniques. In this paper, an algorithm is proposed that improvises the existing technique using the skewness of the voice source (VS) signal. Here, the integrated linear prediction residual (ILPR) is used as the VS estimate, which is obtained using linear prediction on long-term frames of the low-pass filtered speech signal. This excludes the unvoiced regions from analysis and also reduces the computation. Further, a modified skewness measure is proposed for decision, which also considers the magnitude of the skewness of the ILPR along with its sign. With the detection error rate (DER) as the performance metric, the algorithm is tested on 8 large databases and its performance (DER=0.20%) is found to be comparable to that of the best technique (DER=0.06%) on both clean and noisy speech. Further, the proposed method is found to be ten times faster than the best technique.

Constrained Linear Spectral Unmixing Technique for Regional Land Cover Mapping Using MODIS Data

Over the last few decades, there has been a significant land cover (LC) change across the globe due to the increasing demand of the burgeoning population and urban sprawl. In order to take account of the change, there is a need for accurate and up-to-date LC maps. Mapping and monitoring of LC in India is being carried out at national level using multi-temporal IRS AWiFS data. Multispectral data such as IKONOS, Landsat-TM/ETM+, IRS-ICID LISS-III/IV, AWiFS and SPOT-5, etc. have adequate spatial resolution (similar to 1m to 56m) for LC mapping to generate 1:50,000 maps. However, for developing countries and those with large geographical extent, seasonal LC mapping is prohibitive with data from commercial sensors of limited spatial coverage. Superspectral data from the MODIS sensor are freely available, have better temporal (8 day composites) and spectral information. MODIS pixels typically contain a mixture of various LC types (due to coarse spatial resolution of 250, 500 and 1000 in), especially in more fragmented landscapes. In this context, linear spectral unmixing would be useful for mapping patchy land covers, such as those that characterise much of the Indian subcontinent. This work evaluates the existing unmixing technique for LC mapping using MODIS data, using end-members that are extracted through Pixel Purity Index (PPI), Scatter plot and N-dimensional visualisation. The abundance maps were generated for agriculture, built up, forest, plantations, waste land/others and water bodies. The assessment of the results using ground truth and a LISS-III classified map shows 86% overall accuracy, suggesting the potential for broad-scale applicability of the technique with superspectral data for natural resource planning and inventory applications. Index Terms-Remote sensing, digital

A new load distribution strategy for linear network with communication delays

In this paper, we propose a new load distribution strategy called `send-and-receive' for scheduling divisible loads, in a linear network of processors with communication delay. This strategy is designed to optimally utilize the network resources and thereby minimizes the processing time of entire processing load. A closed-form expression for optimal size of load fractions and processing time are derived when the processing load originates at processor located in boundary and interior of the network. A condition on processor and link speed is also derived to ensure that the processors are continuously engaged in load distributions. This paper also presents a parallel implementation of `digital watermarking problem' on a personal computer-based Pentium Linear Network (PLN) topology. Experiments are carried out to study the performance of the proposed strategy and results are compared with other strategies found in literature.

Conformation-activity correlations for chemotactic tripeptide analogs incorporating dialkyl residues with linear and cyclic alkyl sidechains at position 2

Five stereochemically constrained analogs of the chemotactic tripeptide incorporating 1-aminocycloalkane-1-carboxylic acid (Ac(n)c) and alpha,alpha-dialkylglycines (Deg, diethylglycine; Dpg, n,n-dipropylglycine and Dbg, n,n-dibutylglycine) at position 2 have been synthesized. NMR studies of peptides For-Met-Xxx-Phe-OMe (Xxx = Ac(7)c, I; Ac(8)c, II; Deg, III; Dpg, IV and Dbg, V; For, formyl) establish that peptides with cycloalkyl residues, I and II, adopt folded beta-turn conformations in CDCl3 and (CD3)(2)SO. In contrast, analogs with linear alkyl sidechains, III-V, favour fully extended (C-5) conformations in solution. Peptides I-V exhibit high activity in inducing beta-glucosaminidase release from rabbit neutrophils, with ED(50) values ranging from 1.4-8.0 x 10(-11)M. In human neutrophils the Dxg peptides III-V have ED(50) values ranging from 2.3 x 10(-8) to 5.9 x 10(-10) M, with the activity order being V > IV > III. While peptides I-IV are less active than the parent. For-Met-Leu-Phe-OH, in stimulating histamine release from human basophils, the Dbg peptide V is appreciably more potent, suggesting its potential utility as a probe for formyl peptide receptors.

An Efficient Load Distribution Strategy for a Distributed Linear Network of Processors with Communication Delays

In this paper, we present an improved load distribution strategy, for arbitrarily divisible processing loads, to minimize the processing time in a distributed linear network of communicating processors by an efficient utilization of their front-ends. Closed-form solutions are derived, with the processing load originating at the boundary and at the interior of the network, under some important conditions on the arrangement of processors and links in the network. Asymptotic analysis is carried out to explore the ultimate performance limits of such networks. Two important theorems are stated regarding the optimal load sequence and the optimal load origination point. Comparative study of this new strategy with an earlier strategy is also presented.