Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A(2)

Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A(2) have been determined at around 1.9 Angstrom resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P2(1)2(1)2(1), The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3(1)21, The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.

Risk-sensitive optimal control for Markov decision processes with monotone cost

The existence of an optimal feedback law is established for the risk-sensitive optimal control problem with denumerable state space. The main assumptions imposed are irreducibility and a near monotonicity condition on the one-step cost function. A solution can be found constructively using either value iteration or policy iteration under suitable conditions on initial feedback law.

Ellipsometry as a Sensitive Technique to Probe film -Substrate Interfaces: Al2O3 on Si(100)

An attempt has been made to study the film-substrate interface by using a sensitive, non- conventional tool. Because of the prospective use of gate oxide in MOSFET devices, we have chosen to study alumina films grown on silicon. Film-substrate interface of alumina grown by MOCVD on Si(100) was studied systematically using spectroscopic ellipsometry in the range 1.5-5.0 eV, supported by cross-sectional SEM, and SIMS. The (ε1,ε2) versus energy data obtained for films grown at 600°C, 700°C, and 750°C were modeled to fit a substrate/interface/film “sandwich”. The experimental results reveal (as may be expected) that the nature of the substrate -film interface depends strongly on the growth temperature. The simulated (ε1,ε2) patterns are in excellent agreement with observed ellipsometric data. The MOCVD precursors results the presence of carbon in the films. Theoretical simulation was able to account for the ellipsometry data by invoking the presence of “free” carbon in the alumina films.

Scalable Context-Sensitive Points-To Analysis Using Multi-Dimensional Bloom Filters

Context-sensitive points-to analysis is critical for several program optimizations. However, as the number of contexts grows exponentially, storage requirements for the analysis increase tremendously for large programs, making the analysis non-scalable. We propose a scalable flow-insensitive context-sensitive inclusion-based points-to analysis that uses a specially designed multi-dimensional bloom filter to store the points-to information. Two key observations motivate our proposal: (i) points-to information (between pointer-object and between pointer-pointer) is sparse, and (ii) moving from an exact to an approximate representation of points-to information only leads to reduced precision without affecting correctness of the (may-points-to) analysis. By using an approximate representation a multi-dimensional bloom filter can significantly reduce the memory requirements with a probabilistic bound on loss in precision. Experimental evaluation on SPEC 2000 benchmarks and two large open source programs reveals that with an average storage requirement of 4MB, our approach achieves almost the same precision (98.6%) as the exact implementation. By increasing the average memory to 27MB, it achieves precision upto 99.7% for these benchmarks. Using Mod/Ref analysis as the client, we find that the client analysis is not affected that often even when there is some loss of precision in the points-to representation. We find that the NoModRef percentage is within 2% of the exact analysis while requiring 4MB (maximum 15MB) memory and less than 4 minutes on average for the points-to analysis. Another major advantage of our technique is that it allows to trade off precision for memory usage of the analysis.

A near-singular, flexure jointed, moment sensitive Stewart platform based fore-torque sensor

A force-torque sensor capable of accurate measurement of the three components of externally applied forces and moments is required for force control in robotic applications involving assembly operations. The goal in this paper is to design a Stewart platform based force torque sensor at a near-singular configuration sensitive to externally applied moments. In such a configuration, we show an enhanced mechanical amplification of leg forces and thereby higher sensitivity for the applied external moments. In other directions, the sensitivity will be that of a normal load sensor determined by the sensitivity of the sensing element and the associated electronic amplification, and all the six components of the force and torque can be sensed. In a sensor application, the friction, backlash and other non-linearities at the passive spherical joints of the Stewart platform will affect the measurements in unpredictable ways. In this sensor, we use flexural hinges at the leg interfaces of the base and platform of the sensor. The design dimensions of the flexure joints in the sensor have been arrived at using FEA. The sensor has been fabricated, assembled and instrumented. It has been calibrated for low level loads and is found to show linearity and marked sensitivity to moments about the three orthogonal X, Y and Z axes. This sensor is compatible for usage as a wrist sensor for a robot under development at ISRO Satellite Centre.

Output-Sensitive Construction of Reeb Graphs

The Reeb graph of a scalar function represents the evolution of the topology of its level sets. This paper describes a near-optimal output-sensitive algorithm for computing the Reeb graph of scalar functions defined over manifolds or non-manifolds in any dimension. Key to the simplicity and efficiency of the algorithm is an alternate definition of the Reeb graph that considers equivalence classes of level sets instead of individual level sets. The algorithm works in two steps. The first step locates all critical points of the function in the domain. Critical points correspond to nodes in the Reeb graph. Arcs connecting the nodes are computed in the second step by a simple search procedure that works on a small subset of the domain that corresponds to a pair of critical points. The paper also describes a scheme for controlled simplification of the Reeb graph and two different graph layout schemes that help in the effective presentation of Reeb graphs for visual analysis of scalar fields. Finally, the Reeb graph is employed in four different applications-surface segmentation, spatially-aware transfer function design, visualization of interval volumes, and interactive exploration of time-varying data.

UDP-glucose 4, 6-dehydratase Activity Plays an Important Role in Maintaining Cell Wall Integrity and Virulence of Candida albicans

Candida albicans, a human fungal pathogen, undergoes morphogenetic changes that are associated with virulence. We report here that GAL102 in C. albicans encodes a homolog of dTDP-glucose 4,6-dehydratase, an enzyme that affects cell wall properties as well as virulence of many pathogenic bacteria. We found that GAL102 deletion leads to greater sensitivity to antifungal drugs and cell wall destabilizing agents like Calcofluor white and Congo red. The mutant also formed biofilms consisting mainly of hyphal cells that show less turgor. The NMR analysis of cell wall mannans of gal102 deletion strain revealed that a major constituent of mannan is missing and the phosphomannan component known to affect virulence is greatly reduced. We also observed that there was a substantial reduction in the expression of genes involved in biofilm formation but increase in the expression of genes encoding glycosylphosphatidylinositol-anchored proteins in the mutant. These, along with altered mannosylation of cell wall proteins together might be responsible for multiple phenotypes displayed by the mutant. Finally, the mutant was unable to grow in the presence of resident peritoneal macrophages and elicited a weak pro-inflammatory cytokine response in vitro. Similarly, this mutant elicited a poor serum pro-inflammatory cytokine response as judged by IFN gamma and TNF alpha levels and showed reduced virulence in a mouse model of systemic candidiasis. Importantly, an Ala substitution for a conserved Lys residue in the active site motif YXXXK, that abrogates the enzyme activity also showed reduced virulence and increased filamentation similar to the gal102 deletion strain. Since inactivating the enzyme encoded by GAL102 makes the cells sensitive to antifungal drugs and reduces its virulence, it can serve as a potential drug target in combination therapies for C. albicans and related pathogens.

Measurement of probability-distribution functions sensitive technique for the study of conduction phenomena in liquid dielectrics

The paper outlines a technique for sensitive measurement of conduction phenomena in liquid dielectrics. The special features of this technique are the simplicity of the electrical system, the inexpensive instrumentation and the high accuracy. Detection, separation and analysis of a random function of current that is superimposed on the prebreakdown direct current forms the basis of this investigation. In this case, prebreakdown direct current is the output data of a test cell with large electrodes immersed in a liquid medium subjected to high direct voltages. Measurement of the probability-distribution function of a random fluctuating component of current provides a method that gives insight into the mechanism of conduction in a liquid medium subjected to high voltages and the processes that are responsible for the existence of the fluctuating component of the current.

Preparation of a thermally sensitive ammonium perchlorate

The effect of ultrasound on the thermal decomposition behaviour of ammonium perchlorate (AP) has been investigated. It was observed that significant changes in the thermal behaviour of A-P, followed using differential thermal analysis and thermogravimetry, was observed when AP was subjected to power ultrasound in water saturated with oxygen-nitrogen mixture. The decomposition temperature of AP was found to have been lowered by nearly 25degreesC. A similar thermal sensitization was observed in AP when subjected to sonication in the presence of transition metal oxides. Kinetic parameters were calculated for AP, modified AP and catalyzed AP decomposition using non-isothermal kinetics. The activation energy for the decomposition of the sonicated AP samples were found to be lower than normal AP.

Sampling disturbances of soft sensitive clays

Sampling disturbance is unavoidable and hence the laboratory testing most often is on partially disturbed samples. This paper deals with the development of a simple method to assess degree of sample disturbance from the prediction of yield stress due to cementation and comparison of yield stress in compression of partially disturbed sample with reference to a predicted compression path of the clay devoid of any mechanical disturbance. The method uses simple parameters which are normally determined in routine investigations.

Quasi-static crack tip fields in rate-sensitive FCC single crystals

In this work, the effects of loading rate, material rate sensitivity and constraint level on quasi-static crack tip fields in a FCC single crystal are studied. Finite element simulations are performed within a mode I, plane strain modified boundary layer framework by prescribing the two term (K-T) elastic crack tip field as remote boundary conditions. The material is assumed to obey a rate-dependent crystal plasticity theory. The orientation of the single crystal is chosen so that the crack surface coincides with the crystallographic (010) plane and the crack front lies along 101] direction. Solutions corresponding to different stress intensity rates K., T-stress values and strain rate exponents m are obtained. The results show that the stress levels ahead of the crack tip increase with K. which is accompanied by gradual shrinking of the plastic zone size. However, the nature of the shear band patterns around the crack tip is not affected by the loading rate. Further, it is found that while positive T-stress enhances the opening and hydrostatic stress levels ahead of crack tip, they are considerably reduced with imposition of negative T-stress. Also, negative T-stress promotes formation of shear bands in the forward sector ahead of the crack tip and suppresses them behind the tip.

Females of a tree cricket prefer larger males but not the lower frequency male calls that indicate large body size

In the tree cricket Oecanthus henryi, females are attracted by male calls and can choose between males. To make a case for female choice based on male calls, it is necessary to examine male call variation in the field and identify repeatable call features that are reliable indicators of male size or symmetry. Female preference for these reliable call features and the underlying assumption behind this choice, female preference for larger males, also need to be examined. We found that females did prefer larger males during mating, as revealed by the longer mating durations and longer spermatophore retention times. We then examined the correlation between acoustic and morphological features and the repeatability of male calls in the field across two temporal scales, within and across nights. We found that carrier frequency was a reliable indicator of male size, with larger males calling at lower frequencies at a given temperature. Simultaneous playback of male calls differing in frequency, spanning the entire range of natural variation at a given temperature, revealed a lack of female preference for low carrier frequencies. The contrasting results between the phonotaxis and mating experiments may be because females are incapable of discriminating small differences in frequency or because the change in call carrier frequency with temperature renders this cue unreliable in tree crickets. (C) 2012 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Sensitive Liquid Chromatography-Tandem Mass Spectrometry Method for the Determination of Olanzapine in Human Urine

A sensitive and selective liquid chromatographic-tandem mass spectrometric (LC-MS-MS) method was developed to determine olanzapine (OLZ) in human urine. After solid-phase extraction with SPE cartridge, the urine sample was analysed on a C-18 column (Symmetry 3.5 mu m, 50 x 4.6 mm i.d) interfaced with a triple quadrupole tandem mass spectrometer. Positive electrospray ionization was employed as the ionization source. The mobile phase consisted of ammonium acetate (pH 7.8)-acetonitrile (10:90, v/v). The method was linear over a concentration range of 1-100 ngml(-1). The lower limit of quantitation was 1 ngml(-1). The intra-day and inter-day relative standard deviation across three validation runs over the entire concentration range was < 11.5 %. The accuracy determined at three concentrations (8.0, 50.0 and 85.0 ngml(-1) OLZ) was within +/- 1.21 % in terms of relative errors.

Pressure-sensitive paint on a truncated cone in hypersonic flow at incidences

The flow over a truncated cone is a classical and fundamental problem for aerodynamic research due to its three-dimensional and complicated characteristics. The flow is made more complex when examining high angles of incidence. Recently these types of flows have drawn more attention for the purposes of drag reduction in supersonic/hypersonic flows. In the present study the flow over a truncated cone at various incidences was experimentally investigated in a Mach 5 flow with a unit Reynolds number of 13.5�10 6m -1. The cone semi-apex angle is 15° and the truncation ratio (truncated length/cone length) is 0.5. The incidence of the model varied from -12° to 12° with 3° intervals relative to the freestream direction. The external flow around the truncated cone was visualised by colour Schlieren photography, while the surface flow pattern was revealed using the oil flow method. The surface pressure distribution was measured using the anodized aluminium pressure-sensitive paint (AA-PSP) technique. Both top and sideviews of the pressure distribution on the model surface were acquired at various incidences. AA-PSP showed high pressure sensitivity and captured the complicated flow structures which correlated well with the colour Schlieren and oil flow visualisation results. © 2012 Elsevier Inc.