Stability of Dimeric Interface in Banana Lectin: Insight from Molecular Dynamics Simulations

Banana lectin (Banlec) is a homodimeric non-glycosylated protein. It exhibits the b-prism I structure. High-temperature molecular dynamics simulations have been utilized to monitor and understand early stages of thermally induced unfolding of Banlec. The present study elucidates the behavior of the dimeric protein at four different temperatures and compares the structural and conformational changes to that of the minimized crystal structure. The process of unfolding was monitored by following the radius of gyration, the rms deviation of each residue, change in relative solvent accessibility and the pattern of inter- and intra-subunit interactions. The overall study demonstrates that the Banlec dimer is a highly stable structure, and the stability is mostly contributed by interfacial interactions. It maintains its overall conformation during high-temperature (400–500 K) simulations, with only the unstructured loop regions acquiring greater momentum under such condition. Nevertheless, at still higher temperatures (600 K) the tertiary structure is gradually lost which later extends to loss of secondary structural elements. The pattern of hydrogen bonding within the subunit and at the interface across different stages has been analyzed and has provided rationale for its intrinsic high stability.

A Proposal for Concurrent Estimation of Static and Dynamic Nonlinearity of ADC

Despite great advances in very large scale integrated-circuit design and manufacturing, performance of even the best available high-speed, high-resolution analog-to-digital converter (ADC) is known to deteriorate while acquiring fast-rising, high-frequency, and nonrepetitive waveforms. Waveform digitizers (ADCs) used in high-voltage impulse recordings and measurements are invariably subjected to such waveforms. Errors resulting from a lowered ADC performance can be unacceptably high, especially when higher accuracies have to be achieved (e.g., when part of a reference measuring system). Static and dynamic nonlinearities (estimated independently) are vital indices for evaluating performance and suitability of ADCs to be used in such environments. Typically, the estimation of static nonlinearity involves 10-12 h of time or more (for a 12-b ADC) and the acquisition of millions of samples at high input frequencies for dynamic characterization. ADCs with even higher resolution and faster sampling speeds will soon become available. So, there is a need to reduce testing time for evaluating these parameters. This paper proposes a novel and time-efficient method for the simultaneous estimation of static and dynamic nonlinearity from a single test. This is achieved by conceiving a test signal, comprised of a high-frequency sinusoid (which addresses dynamic assessment) modulated by a low-frequency ramp (relevant to the static part). Details of implementation and results on two digitizers are presented and compared with nonlinearities determined by the existing standardized approaches. Good agreement in results and time savings achievable indicates its suitability.

A Proposal for Concurrent Estimation of Static and Dynamic Nonlinearity of ADC

Despite great advances in very large scale integrated-circuit design and manufacturing, performance of even the best available high-speed, high-resolution analog-to-digital converter (ADC) is known to deteriorate while acquiring fast-rising, high-frequency, and nonrepetitive waveforms. Waveform digitizers (ADCs) used in high-voltage impulse recordings and measurements are invariably subjected to such waveforms. Errors resulting from a lowered ADC performance can be unacceptably high, especially when higher accuracies have to be achieved (e.g., when part of a reference measuring system). Static and dynamic nonlinearities (estimated independently) are vital indices for evaluating performance and suitability of ADCs to be used in such environments. Typically, the estimation of static nonlinearity involves 10-12 h of time or more (for a 12-b ADC) and the acquisition of millions of samples at high input frequencies for dynamic characterization. ADCs with even higher resolution and faster sampling speeds will soon become available. So, there is a need to reduce testing time for evaluating these parameters. This paper proposes a novel and time-efficient method for the simultaneous estimation of static and dynamic nonlinearity from a single test. This is achieved by conceiving a test signal, comprised of a high-frequency sinusoid (which addresses dynamic assessment) modulated by a low-frequency ramp (relevant to the static part). Details of implementation and results on two digitizers are presented and compared with nonlinearities determined by the existing standardized approaches. Good agreement in results and time savings achievable indicates its suitability.

Sequence generator for periodic sampling of transient phenomena

A simple instrument that can provide a sequence of timed pulses for first initiating a transient process and then enabling sampling and recording periodically during the course of the transient event is described. The time delay between the first of these sampling pulses and the start of the transient event is adjustable. This sequence generator has additional features that make it ideal for use in acquiring the waveforms when a storage oscilloscope is used as the recording device. For avoiding the clutter caused by many waveforms being recorded at the same place on an oscilloscope screen such features as displacements of waveforms in the X and Y directions and trace blanking at places where the waveform is not required, have been incorporated. This sequence generator has been employed to acquire a sequence of Raman scattered radiation signals from an adiabatically expanding saturated vapour probed by a flashlamp-pumped dye laser.

Improved k-t BLAST for fast fMR imaging

A popular dynamic imaging technique, k-t BLAST (ktB) is studied here for BAR imaging. ktB utilizes correlations in k-space and time, to reconstruct the image time series with only a fraction of the data. The algorithm works by unwrapping the aliased Fourier conjugate space of k-t (y-f-space). The unwrapping process utilizes the estimate of the true y-f-space, by acquiring densely sampled low k-space data. The drawbacks of this method include separate training scan, blurred training estimates and aliased phase maps. The proposed changes are incorporation of phase information from the training map and using generalized-series-extrapolated training map. The proposed technique is compared with ktB on real fMRI data. The proposed changes allow for ktB to operate at an acceleration factor of 6. Performance is evaluated by comparing activation maps obtained using reconstructed images. An improvement of up to 10 dB is observed in thePSNR of activation maps. Besides, a 10% reduction in RMSE is obtained over the entire time series of fMRI images. Peak improvement of the proposed method over ktB is 35%, averaged over five data sets. (C)2010 Elsevier Inc. All rights reserved.

Analysis of the beta-glucoside utilization (bgl) genes of Shigella sonnei: evolutionary implications for their maintenance in a cryptic state

The pattern of expression of the genes involved in the utilization of aryl beta-glucosides such as arbutin and salicin is different in the genus Shigella compared to Escherichia coli. The results presented here indicate that the homologue of the cryptic bgl operon of E. coli is conserved in Shigella sonnei and is the primary system involved in beta-glucoside utilization in the organism. The organization of the bgl genes in 5. sonnei is similar to that of E. coli; however there are three major differences in terms of their pattern of expression. (i) The bglB gene, encoding phospho-beta-glucosidase B, is insertionally inactivated in 5. sonnei. As a result, mutational activation of the silent bgl promoter confers an Arbutin-positive (Arb(+)) phenotype to the cells in a single step; however, acquiring a Salicin-positive (Sal(+)) phenotype requires the reversion or suppression of the bglB mutation in addition. (ii) Unlike in E. coli, a majority of the activating mutations (conferring the Arb(+) phenotype) map within the unlinked hns locus, whereas activation of the E. coli bgl operon under the same conditions is predominantly due to insertions within the bglR locus. (iii) Although the bgl promoter is silent in the wild-type strain of 5. sonnei (as in the case of E. coli), transcriptional and functional analyses indicated a higher basal level of transcription of the downstream genes. This was correlated with a 1 bp deletion within the putative Rho-independent terminator present in the leader sequence preceding the homologue of the bglG gene. The possible evolutionary implications of these differences for the maintenance of the genes in the cryptic state are discussed.

Imaging in vivo Neuronal Transport in Genetic Model Organisms Using Microfluidic Devices

Microfluidic devices have been developed for imaging behavior and various cellular processes in Caenorhabditis elegans, but not subcellular processes requiring high spatial resolution. In neurons, essential processes such as axonal, dendritic, intraflagellar and other long-distance transport can be studied by acquiring fast time-lapse images of green fluorescent protein (GFP)-tagged moving cargo. We have achieved two important goals in such in vivo studies namely, imaging several transport processes in unanesthetized intact animals and imaging very early developmental stages. We describe a microfluidic device for immobilizing C. elegans and Drosophila larvae that allows imaging without anesthetics or dissection. We observed that for certain neuronal cargoes in C. elegans, anesthetics have significant and sometimes unexpected effects on the flux. Further, imaging the transport of certain cargo in early developmental stages was possible only in the microfluidic device. Using our device we observed an increase in anterograde synaptic vesicle transport during development corresponding with synaptic growth. We also imaged Q neuroblast divisions and mitochondrial transport during early developmental stages of C. elegans and Drosophila, respectively. Our simple microfluidic device offers a useful means to image high-resolution subcellular processes in C. elegans and Drosophila and can be readily adapted to other transparent or translucent organisms.

Review of hypersonic research investigations in IISc shock tunnel (HST1)

Real gas effects dominate the hypersonic flow fields encountered by modem day hypersonic space vehicles. Measurement of aerodynamic data for the design applications of such aerospace vehicles calls for special kinds of wind tunnels capable of faithfully simulating real gas effects. A shock tunnel is an established facility commonly used along with special instrumentation for acquiring the data for this purpose within a short time period. The hypersonic shock tunnel (HST1), established at the Indian Institute of Science (IISc) in the early 1970s, has been extensively used to measure the aerodynamic data of various bodies of interest at hypersonic Mach numbers in the range 4 to 13. Details of some important measurements made during the period 1975-1995 along with the performance capabilities of the HST1 are presented in this review. In view of the re-emergence of interest in hypersonics across the globe in recent times, the present review highlights the Suitability of the hypersonic shock tunnel at the IISc for future space application studies in India.

A Profilometric Approach to 3D Face Reconstruction and Its Application to Face Recognition

3D Face Recognition is an active area of research for past several years. For a 3D face recognition system one would like to have an accurate as well as low cost setup for constructing 3D face model. In this paper, we use Profilometry approach to obtain a 3D face model.This method gives a low cost solution to the problem of acquiring 3D data and the 3D face models generated by this method are sufficiently accurate. We also develop an algorithm that can use the 3D face model generated by the above method for the recognition purpose.

The Future of Computation

The purpose of life is to obtain knowledge, use it to live with as much satisfaction as possible, and pass it on with improvements and modifications to the next generation.'' This may sound philosophical, and the interpretation of words may be subjective, yet it is fairly clear that this is what all living organisms--from bacteria to human beings--do in their life time. Indeed, this can be adopted as the information theoretic definition of life. Over billions of years, biological evolution has experimented with a wide range of physical systems for acquiring, processing and communicating information. We are now in a position to make the principles behind these systems mathematically precise, and then extend them as far as laws of physics permit. Therein lies the future of computation, of ourselves, and of life.

Performance Analysis of a Cooperative System with Rateless Codes and Buffered Relays

In a cooperative relay-assisted communication system that uses rateless codes, packets get transmitted from a source to a destination at a rate that depends on instantaneous channel states of the wireless links between nodes. When multiple relays are present, the relay with the highest channel gain to the source is the first to successfully decode a packet from the source and forward it to the destination. Thus, the unique properties of rateless codes ensure that both rate adaptation and relay selection occur without the transmitting source or relays acquiring instantaneous channel knowledge. In this paper, we show that in such cooperative systems, buffering packets at relays significantly increases throughput. We develop a novel analysis of these systems that combines the communication-theoretic aspects of cooperation over fading channels with the queuing-theoretic aspects associated with buffering. Closed-form expressions are derived for the throughput and end-to-end delay for the general case in which the channels between various nodes are not statistically identical. Corresponding results are also derived for benchmark systems that either do not exploit spatial diversity or do not buffer packets. Altogether, our results show that buffering - a capability that will be commonly available in practical deployments of relays - amplifies the benefits of cooperation.

Rationalization and prediction of drug resistant mutations in targets for clinical anti-tubercular drugs

Resistance to therapy limits the effectiveness of drug treatment in many diseases. Drug resistance can be considered as a successful outcome of the bacterial struggle to survive in the hostile environment of a drug-exposed cell. An important mechanism by which bacteria acquire drug resistance is through mutations in the drug target. Drug resistant strains (multi-drug resistant and extensively drug resistant) of Mycobacterium tuberculosis are being identified at alarming rates, increasing the global burden of tuberculosis. An understanding of the nature of mutations in different drug targets and how they achieve resistance is therefore important. An objective of this study is to first decipher sequence as well as structural bases for the observed resistance in known drug resistant mutants and then to predict positions in each target that are more prone to acquiring drug resistant mutations. A curated database containing hundreds of mutations in the 38 drug targets of nine major clinical drugs, associated with resistance is studied here. Mutations have been classified into those that occur in the binding site itself, those that occur in residues interacting with the binding site and those that occur in outer zones. Structural models of the wild type and mutant forms of the target proteins have been analysed to seek explanations for reduction in drug binding. Stability analysis of an entire array of 19 mutations at each of the residues for each target has been computed using structural models. Conservation indices of individual residues, binding sites and whole proteins are computed based on sequence conservation analysis of the target proteins. The analyses lead to insights about which positions in the polypeptide chain have a higher propensity to acquire drug resistant mutations. Thus critical insights can be obtained about the effect of mutations on drug binding, in terms of which amino acid positions and therefore which interactions should not be heavily relied upon, which in turn can be translated into guidelines for modifying the existing drugs as well as for designing new drugs. The methodology can serve as a general framework to study drug resistant mutants in other micro-organisms as well.

Context aware M-commerce services: C-IOB model approach

Context-aware computing is useful in providing individualized services focusing mainly on acquiring surrounding context of user. By comparison, only very little research has been completed in integrating context from different environments, despite of its usefulness in diverse applications such as healthcare, M-commerce and tourist guide applications. In particular, one of the most important criteria in providing personalized service in a highly dynamic environment and constantly changing user environment, is to develop a context model which aggregates context from different domains to infer context of an entity at the more abstract level. Hence, the purpose of this paper is to propose a context model based on cognitive aspects to relate contextual information that better captures the observation of certain worlds of interest for a more sophisticated context-aware service. We developed a C-IOB (Context-Information, Observation, Belief) conceptual model to analyze the context data from physical, system, application, and social domains to infer context at the more abstract level. The beliefs developed about an entity (person, place, things) are primitive in most theories of decision making so that applications can use these beliefs in addition to history of transaction for providing intelligent service. We enhance our proposed context model by further classifying context information into three categories: a well-defined, a qualitative and credible context information to make the system more realistic towards real world implementation. The proposed model is deployed to assist a M-commerce application. The simulation results show that the service selection and service delivery of the system are high compared to traditional system.

An adaptation framework for head-pose classification in dynamic multi-view scenarios

Multi-view head-pose estimation in low-resolution, dynamic scenes is difficult due to blurred facial appearance and perspective changes as targets move around freely in the environment. Under these conditions, acquiring sufficient training examples to learn the dynamic relationship between position, face appearance and head-pose can be very expensive. Instead, a transfer learning approach is proposed in this work. Upon learning a weighted-distance function from many examples where the target position is fixed, we adapt these weights to the scenario where target positions are varying. The adaptation framework incorporates reliability of the different face regions for pose estimation under positional variation, by transforming the target appearance to a canonical appearance corresponding to a reference scene location. Experimental results confirm effectiveness of the proposed approach, which outperforms state-of-the-art by 9.5% under relevant conditions. To aid further research on this topic, we also make DPOSE- a dynamic, multi-view head-pose dataset with ground-truth publicly available with this paper.

Microstructure Development, Nanomechanical, and Dynamic Compression Properties of Spark Plasma Sintered TiB2-Ti-Based Homogeneous and Bi-layered Composites

The growing threats due to increased use of small-caliber armor piercing projectiles demand the development of new light-weight body armor materials. In this context, TiB2 appears to be a promising ceramic material. However, poor sinterability and low fracture toughness remain two major issues for TiB2. In order to address these issues together, Ti as a sinter-aid is used to develop TiB2-(x wt pct Ti), (x = 10, 20) homogeneous composites and a bi-layered composite (BLC) with each layer having Ti content of 10 and 20 wt pct. The present study uniquely demonstrates the efficacy of two-stage spark plasma sintering route to develop dense TiB2-Ti composites with an excellent combination of nanoscale hardness (similar to 36 GPa) and indentation fracture toughness (similar to 12 MPa m(1/2)). In case of BLC, these properties are not compromised w.r.t. homogeneous composites, suggesting the retention of baseline material properties even in the bi-layer design due to optimal relief of residual stresses. The better indentation toughness of TiB2-(10 wt pct Ti) and TiB2-(20 wt pct Ti) composites can be attributed to the observed crack deflection/arrest, indicating better damage tolerance. Transmission electron microscope investigation reveals the presence of dense dislocation networks and deformation twins in alpha-Ti at the grain boundaries and triple pockets, surrounded by TiB2 grains. The dynamic strength of around 4 GPa has been measured using Split Hopkinson Pressure Bar tests in a reproducible manner at strain rates of the order of 600 s(-1). The damage progression under high strain rate has been investigated by acquiring real time images for the entire test duration using ultra-high speed imaging. An attempt has been made to establish microstructure-property correlation and a simple analysis based on Mohr-Coulomb theory is used to rationalize the measured strength properties.