Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

Attitude estimation using moment invariants

The problem of estimating the three-dimensional rotational parameters of a rigid body from its monocular image data has been considered using the method of moment invariants. Second- and third-order moment invariants are used to construct the feature vector for the scale and orientation independent identification of the camera view axis direction in the body-fixed reference frame. The camera rotation angle about the view axis is derived from second-order central moments. The relative attitude of the rigid body is then expressed in terms of quaternion parameters to model the outputs of a video sensor in attitude control simulations. Experimental results and simulation outputs are presented using the mathematical model of a spacecraft.

Mobile Base Stations Placement and Energy Aware Routing in Wireless Sensor Networks

Increasing network lifetime is important in wireless sensor/ad-hoc networks. In this paper, we are concerned with algorithms to increase network lifetime and amount of data delivered during the lifetime by deploying multiple mobile base stations in the sensor network field. Specifically, we allow multiple mobile base stations to be deployed along the periphery of the sensor network field and develop algorithms to dynamically choose the locations of these base stations so as to improve network lifetime. We propose energy efficient low-complexity algorithms to determine the locations of the base stations; they include i) Top-K-max algorithm, ii) maximizing the minimum residual energy (Max-Min-RE) algorithm, and iii) minimizing the residual energy difference (MinDiff-RE) algorithm. We show that the proposed base stations placement algorithms provide increased network lifetimes and amount of data delivered during the network lifetime compared to single base station scenario as well as multiple static base stations scenario, and close to those obtained by solving an integer linear program (ILP) to determine the locations of the mobile base stations. We also investigate the lifetime gain when an energy aware routing protocol is employed along with multiple base stations.

Gain calibration of CCD systems at VBO

The system gain of two CCD systems in regular use at the Vainu Bappu Observatory, Kavalur, is determined at a few gain settings. The procedure used for the determination of system gain and base-level noise is described in detail. The Photometrics CCD system at the 1-m reflector uses a Thomson-CSF TH 7882 CDA chip coated for increased ultraviolet sensitivity. The gain is programme-selected through the parameter 'cgain' varying between 0 and 4095 in steps of 1. The inverse system gain for this system varies almost linearly from 27.7 electrons DN-1 at cgain = 0 to 1.5 electrons DN-1 at cgain = 500. The readout noise is less than or similar 11 electrons at cgain = 66. The Astromed CCD system at 2.3-m Vainu Bappu Telescope uses a GEC P8603 chip which is also coated for enhanced ultraviolet sensitivity. The amplifier gain is selected in discrete steps using switches in the controller. The inverse system gain is 4.15 electrons DN-1 at the gain setting of 9.2, and the readout noise approximately 8 electrons.

Intracellular Pathogen Sensor NOD2 Programs Macrophages to Trigger Notch1 Activation

Intracellular pathogen sensor, NOD2, has been implicated in regulation of wide range of anti-inflammatory responses critical during development of a diverse array of inflammatory diseases; however, underlying molecular details are still imprecisely understood. In this study, we demonstrate that NOD2 programs macrophages to trigger Notch1 signaling. Signaling perturbations or genetic approaches suggest signaling integration through cross-talk between Notch1-PI3K during the NOD2-triggered expression of a multitude of immunological parameters including COX-2/PGE(2) and IL-10. NOD2 stimulation enhanced active recruitment of CSL/RBP-Jk on the COX-2 promoter in vivo. Intriguingly, nitric oxide assumes critical importance in NOD2-mediated activation of Notch1 signaling as iNOS(-/-) macrophages exhibited compromised ability to execute NOD2-triggered Notch1 signaling responses. Correlative evidence demonstrates that this mechanism operates in vivo in brain and splenocytes derived from wild type, but not from iNOS(-/-) mice. Importantly, NOD2-driven activation of the Notch1-PI3K signaling axis contributes to its capacity to impart survival of macrophages against TNF-alpha or IFN-gamma-mediated apoptosis and resolution of inflammation. Current investigation identifies Notch1-PI3K as signaling cohorts involved in the NOD2-triggered expression of a battery of genes associated with anti-inflammatory functions. These findings serve as a paradigm to understand the pathogenesis of NOD2-associated inflammatory diseases and clearly pave a way toward development of novel therapeutics.

Particle filters for structural system identification using multiple test and sensor data: A combined computational and experimental study

The problem of structural system identification when measurements originate from multiple tests and multiple sensors is considered. An offline solution to this problem using bootstrap particle filtering is proposed. The central idea of the proposed method is the introduction of a dummy independent variable that allows for simultaneous assimilation of multiple measurements in a sequential manner. The method can treat linear/nonlinear structural models and allows for measurements on strains and displacements under static/dynamic loads. Illustrative examples consider measurement data from numerical models and also from laboratory experiments. The results from the proposed method are compared with those from a Kalman filter-based approach and the superior performance of the proposed method is demonstrated. Copyright (C) 2009 John Wiley & Sons, Ltd.

Model Based Target Tracking in a Wireless Network of Passive Infrared Sensor Nodes

We consider the problem of tracking an intruder in a plane region by using a wireless sensor network comprising motes equipped with passive infrared (PIR) sensors deployed over the region. An input-output model for the PIR sensor and a method to estimate the angular speed of the target from the sensor output are proposed. With the measurement model so obtained, we study the centralized and decentralized tracking performance using the extended Kalman filter.

Tunable Locally-Optimal Geographical Forwarding in Wireless Sensor Networks with Sleep-Wake Cycling Nodes

We consider a wireless sensor network whose main function is to detect certain infrequent alarm events, and to forward alarm packets to a base station, using geographical forwarding. The nodes know their locations, and they sleep-wake cycle, waking up periodically but not synchronously. In this situation, when a node has a packet to forward to the sink, there is a trade-off between how long this node waits for a suitable neighbor to wake up and the progress the packet makes towards the sink once it is forwarded to this neighbor. Hence, in choosing a relay node, we consider the problem of minimizing average delay subject to a constraint on the average progress. By constraint relaxation, we formulate this next hop relay selection problem as a Markov decision process (MDP). The exact optimal solution (BF (Best Forward)) can be found, but is computationally intensive. Next, we consider a mathematically simplified model for which the optimal policy (SF (Simplified Forward)) turns out to be a simple one-step-look-ahead rule. Simulations show that SF is very close in performance to BF, even for reasonably small node density. We then study the end-to-end performance of SF in comparison with two extremal policies: Max Forward (MF) and First Forward (FF), and an end-to-end delay minimising policy proposed by Kim et al. 1]. We find that, with appropriate choice of one hop average progress constraint, SF can be tuned to provide a favorable trade-off between end-to-end packet delay and the number of hops in the forwarding path.

Bounds on the Lifetime of Wireless Sensor Networks Employing Multiple Data Sinks

Employing multiple base stations is an attractive approach to enhance the lifetime of wireless sensor networks. In this paper, we address the fundamental question concerning the limits on the network lifetime in sensor networks when multiple base stations are deployed as data sinks. Specifically, we derive upper bounds on the network lifetime when multiple base stations are employed, and obtain optimum locations of the base stations (BSs) that maximize these lifetime bounds. For the case of two BSs, we jointly optimize the BS locations by maximizing the lifetime bound using a genetic algorithm based optimization. Joint optimization for more number of BSs is complex. Hence, for the case of three BSs, we optimize the third BS location using the previously obtained optimum locations of the first two BSs. We also provide simulation results that validate the lifetime bounds and the optimum locations of the BSs.

C-13 MAS NMR spectra of cis,cis-mucononitrile in liquid-crystalline media and in the solid state. Orientation of the carbon chemical-shift tensors

The spinning sidebands observed in the C-13 MAS NMR spectra of cis,cis-mucononitrile oriented in liquid-crystalline media and of the neat sample in the solid state are studied. There are differences in the sideband intensity patterns in the two cases. These differences arise because the order parameters which characterize the orientation of the solute in the liquid-crystalline media differ for different axes. It is shown that, in general, the relative intensities of the sidebands contain information on the sign and magnitude of an effective chemical-shift parameter which is a function of the sum of the products of the principal components of the chemical-shift tensor and the corresponding order parameters with respect to the director. A method for obtaining the orientation of the carbon chemical-shift tensor is proposed. The carbon chemical-shift tensors obtained from gauge-including atomic orbital calculations are also presented for comparison. (C) 1996 Academic Press, Inc.

Distributed intrusion detection in the presence of correlated sensor readings: Signal-space and communication-complexity view-point

The problem of sensor-network-based distributed intrusion detection in the presence of clutter is considered. It is argued that sensing is best regarded as a local phenomenon in that only sensors in the immediate vicinity of an intruder are triggered. In such a setting, lack of knowledge of intruder location gives rise to correlated sensor readings. A signal-space view-point is introduced in which the noise-free sensor readings associated to intruder and clutter appear as surfaces f(s) and f(g) and the problem reduces to one of determining in distributed fashion, whether the current noisy sensor reading is best classified as intruder or clutter. Two approaches to distributed detection are pursued. In the first, a decision surface separating f(s) and f(g) is identified using Neyman-Pearson criteria. Thereafter, the individual sensor nodes interactively exchange bits to determine whether the sensor readings are on one side or the other of the decision surface. Bounds on the number of bits needed to be exchanged are derived, based on communication-complexity (CC) theory. A lower bound derived for the two-party average case CC of general functions is compared against the performance of a greedy algorithm. Extensions to the multi-party case is straightforward and is briefly discussed. The average case CC of the relevant greaterthan (CT) function is characterized within two bits. Under the second approach, each sensor node broadcasts a single bit arising from appropriate two-level quantization of its own sensor reading, keeping in mind the fusion rule to be subsequently applied at a local fusion center. The optimality of a threshold test as a quantization rule is proved under simplifying assumptions. Finally, results from a QualNet simulation of the algorithms are presented that include intruder tracking using a naive polynomial-regression algorithm. 2010 Elsevier B.V. All rights reserved.

Delay constrained optimal relay placement for planned wireless sensor networks

In this paper, we study the problem of wireless sensor network design by deploying a minimum number of additional relay nodes (to minimize network design cost) at a subset of given potential relay locationsin order to convey the data from already existing sensor nodes (hereafter called source nodes) to a Base Station within a certain specified mean delay bound. We formulate this problem in two different ways, and show that the problem is NP-Hard. For a problem in which the number of existing sensor nodes and potential relay locations is n, we propose an O(n) approximation algorithm of polynomial time complexity. Results show that the algorithm performs efficiently (in over 90% of the tested scenarios, it gave solutions that were either optimal or exceeding optimal just by one relay) in various randomly generated network scenarios.

Conformation and orientation of alkyl chains in the layered organic-inorganic hybrids: (CnH2n+1NH3)(2)PbI4 (n=12,16,18)

Layered organic inorganic hybrids based on perovskite-derived alkylammonium lead halides have been demonstrated as important new materials in the construction of molecular electronic devices. Typical of this class of materials are the single-perovskite slab lead iodides of the general formula (CnH2n+1NH3)(2)PbI4. While for small n, these compounds are amenable to single-crystal structure determination, the increasing degree of disorder in the long chain (n = 12,14...) compounds makes such an analysis difficult. In this study, we use powder X-ray diffraction, and vibrational and C-13 NMR spectroscopies to establish the conformation, orientation and organization of hydrocarbon chains in the series of layered alkylammonium lead iodides (CnH2n+1NH3)(2)PbI4 (n = 12,16,18). We find that the alkyl chains adopt a tilted bilayer arrangement, while the structure of the inorganic layer remains invariant with respect to the value of n. Conformation-sensitive methylene stretching modes in the infrared and Raman spectra, as well as the C-13 NMR spectra indicate that bonds in the methylene chain are in trans configuration. The skeletal modes of the alkyl chain in the Raman spectra establish that there is a high degree of all-trans conformational registry for the values of n studied here. From the orientation dependence of the infrared spectra of crystals of (CnH2n+1NH3)(2)PbI4 ( n = 12,16), we find that the molecular axis of the all-trans alkyl chains are tilted away from the interlayer normal by an angle of 55degrees. This value of this tilt angle is consistent with the dependence of the c lattice expansion as a function of n, as determined from powder X-ray diffraction.

Enhancing lifetime of wireless sensor networks using multiple data sinks

In this paper, we address the fundamental question concerning the limits on the network lifetime in sensor networks when multiple base stations (BSs) are deployed as data sinks. Specifically, we derive upper bounds on the network lifetime when multiple BSs arc employed, and obtain optimum locations of the base stations that maximise these lifetime bounds. For the case of two BSs, we jointly optimise the BS locations by maximising the lifetime bound using genetic algorithm. Joint optimisation for more number of BSs becomes prohibitively complex. Further, we propose a suboptimal approach for higher number of BSs, Individually Optimum method, where we optimise the next BS location using optimum location of previous BSs. Individually Optimum method has advantage of being attractive for solving the problem with more number of BSs at the cost of little compromised accuracy. We show that accuracy degradation is quite small for the case of three BSs.