CONFORMATIONAL FEATURES OF SIGMA FACTOR/ANTI-SIGMA COMPLEXES

The association of a factors with the RNA polymerase dictates the expression profile of a bacterial cell. Major changes to the transcription profile are achieved by the use of multiple sigma factors that confer distinct promoter selectivity to the holoenzyme. The cellular concentration of a sigma factor is regulated by diverse mechanisms involving transcription, translation and post-translational events. The number of sigma factors varies substantially across bacteria. The diversity in the interactions between sigma factors also vary-ranging from collaboration, competition or partial redundancy in some cellular or environmental contexts. These interactions can be rationalized by a mechanistic model referred to as the partitioning of a space model of bacterial transcription. The structural similarity between different sigma/anti-sigma complexes despite poor sequence conservation and cellular localization reveals an elegant route to incorporate diverse regulatory mechanisms within a structurally conserved scaffold. These features are described here with a focus on sigma/anti-sigma complexes from Mycobacterium tuberculosis. In particular, we discuss recent data on the conditional regulation of sigma/anti-sigma factor interactions. Specific stages of M. tuberculosis infection, such as the latent phase, as well as the remarkable adaptability of this pathogen to diverse environmental conditions can be rationalized by the synchronized action of different a factors.

Extended liaison as an interface between product and process model in assembly

This paper describes the use of liaison to better integrate product model and assembly process model so as to enable sharing of design and assembly process information in a common integrated form and reason about them. Liaison can be viewed as a set, usually a pair, of features in proximity with which process information can be associated. A liaison is defined as a set of geometric entities on the parts being assembled and relations between these geometric entities. Liaisons have been defined for riveting, welding, bolt fastening, screw fastening, adhesive bonding (gluing) and blind fastening processes. The liaison captures process specific information through attributes associated with it. The attributes are associated with process details at varying levels of abstraction. A data structure for liaison has been developed to cluster the attributes of the liaison based on the level of abstraction. As information about the liaisons is not explicitly available in either the part model or the assembly model, algorithms have been developed for extracting liaisons from the assembly model. The use of liaison is proposed to enable both the construction of process model as the product model is fleshed out, as well as maintaining integrity of both product and process models as the inevitable changes happen to both design and the manufacturing environment during the product lifecycle. Results from aerospace and automotive domains have been provided to illustrate and validate the use of liaisons. (C) 2014 Elsevier Ltd. All rights reserved.

Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

D Regulatory information for transcription initiation is present in a stretch of genomic DNA, called the promoter region that is located upstream of the transcription start site (TSS) of the gene. The promoter region interacts with different transcription factors and RNA polymerase to initiate transcription and contains short stretches of transcription factor binding sites (TFBSs), as well as structurally unique elements. Recent experimental and computational analyses of promoter sequences show that they often have non-B-DNA structural motifs, as well as some conserved structural properties, such as stability, bendability, nucleosome positioning preference and curvature, across a class of organisms. Here, we briefly describe these structural features, the differences observed in various organisms and their possible role in regulation of gene expression.

Microstructural Features of Hot Deformed Nb-1Zr-0.1C Alloy

Niobium-based alloys are well-established refractory materials; as a result of their high melting temperature and good creep properties, these alloys find their applications in nuclear reactors. The present study deals with a microstructural response of these materials during hot working. The evolution of microstructure and texture during high-temperature deformation has been investigated in the temperature range 1500-1700A degrees C and strain rate range of 0.001-0.1 s(-1). For each deformed sample, the microstructure has been examined in detail. The microstructural features clearly revealed the formation of a substructure and the occurrence of dynamic recrystallization in a proper temperature-strain rate window. At low strain rates, the necklace structure formation was more prominent.

A Short-Channel Common Double-Gate MOSFET Model Adapted to Gate Oxide Thickness Asymmetry

Existing compact models for common double-gate (CDG) MOSFETs are based on the fundamental assumption of having symmetric gate oxide thickness. In this paper, we demonstrate that using the unique quasi-linear relationship between the surface potentials, it is possible to develop compact model for CDG-MOSFETs without such approximation while preserving the mathematical complexity at the same level of the existing models. In the proposed model, the surface potential relationship is used to include the drain-induced barrier lowering, channel length modulation, velocity saturation, and quantum mechanical effect in the long-channel model and good agreement is observed with the technology computer aided design simulation results.

Sequence and conformational preferences at termini of alpha-helices in membrane proteins: Role of the helix environment

-helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These -helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze -helices in a high-resolution dataset of integral -helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. Proteins 2014; 82:3420-3436. (c) 2014 Wiley Periodicals, Inc.

Common-Mode Injection PWM for Parallel Converters

The ac-side terminal voltages of parallel-connected converters are different if the line reactive drops of the individual converters are different. This could result either from differences in per-phase inductances or from differences in the line currents of the converters. In such cases, the modulating signals are different for the converters. Hence, the common-mode (CM) voltages for the converters, injected by conventional space vector pulsewidth modulation (CSVPWM) to increase dc-bus utilization, are different. Consequently, significant low-frequency zero-sequence circulating currents result. This paper proposes a new modulation method for parallel-connected converters with unequal terminal voltages. This method does not cause low-frequency zero-sequence circulating currents and is comparable with CSVPWM in terms of dc-bus utilization and device power loss. Experimental results are presented at a power level of 150 kVA from a circulating-power test setup, where the differences in converter terminal voltages are quite significant.

A model for the classification and survey of clock synchronization protocols in WSNs

Clock synchronization in wireless sensor networks (WSNs) assures that sensor nodes have the same reference clock time. This is necessary not only for various WSN applications but also for many system level protocols for WSNs such as MAC protocols, and protocols for sleep scheduling of sensor nodes. Clock value of a node at a particular instant of time depends on its initial value and the frequency of the crystal oscillator used in the sensor node. The frequency of the crystal oscillator varies from node to node, and may also change over time depending upon many factors like temperature, humidity, etc. As a result, clock values of different sensor nodes diverge from each other and also from the real time clock, and hence, there is a requirement for clock synchronization in WSNs. Consequently, many clock synchronization protocols for WSNs have been proposed in the recent past. These protocols differ from each other considerably, and so, there is a need to understand them using a common platform. Towards this goal, this survey paper categorizes the features of clock synchronization protocols for WSNs into three types, viz, structural features, technical features, and global objective features. Each of these categories has different options to further segregate the features for better understanding. The features of clock synchronization protocols that have been used in this survey include all the features which have been used in existing surveys as well as new features such as how the clock value is propagated, when the clock value is propagated, and when the physical clock is updated, which are required for better understanding of the clock synchronization protocols in WSNs in a systematic way. This paper also gives a brief description of a few basic clock synchronization protocols for WSNs, and shows how these protocols fit into the above classification criteria. In addition, the recent clock synchronization protocols for WSNs, which are based on the above basic clock synchronization protocols, are also given alongside the corresponding basic clock synchronization protocols. Indeed, the proposed model for characterizing the clock synchronization protocols in WSNs can be used not only for analyzing the existing protocols but also for designing new clock synchronization protocols. (C) 2014 Elsevier B.V. All rights reserved.

Designing Elastic Organic Crystals: Highly Flexible Polyhalogenated N-Benzylideneanilines

The intermolecular interactions and structural features in crystals of seven halogenated N-benzylideneanilines (Schiff bases), all of which exhibit remarkable flexibility, were examined to identify the common packing features that are the raison d'etre for the observed elasticity. The following two features, in part related, were identified as essential to obtain elastic organic crystals: 1)A multitude of weak and dispersive interactions, including halogen bonds, which may act as structural buffers for deformation through easy rupture and reformation during bending; and 2)corrugated packing patterns that would get interlocked and, in the process, prevent long-range sliding of molecular planes.

Small signal Nonquasi-Static Model for Common Double-Gate MOSFETs Adapted to Gate Oxide Thickness Asymmetry

We present a physics-based closed form small signal Nonquasi-static (NQS) model for a long channel Common Double Gate MOSFET (CDG) by taking into account the asymmetry that may prevail between the gate oxide thickness. We use the unique quasi-linear relationship between the surface potentials along the channel to solve the governing continuity equation (CE) in order to develop the analytical expressions for the Y parameters. The Bessel function based solution of the CE is simplified in form of polynomials so that it could be easily implemented in any circuit simulator. The model shows good agreement with the TCAD simulation at-least till 4 times of the cut-off frequency for different device geometries and bias conditions.

A common stochastic accumulator with effector-dependent noise can explain eye-hand coordination

The computational architecture that enables the flexible coupling between otherwise independent eye and hand effector systems is not understood. By using a drift diffusion framework, in which variability of the reaction time (RT) distribution scales with mean RT, we tested the ability of a common stochastic accumulator to explain eye-hand coordination. Using a combination of behavior, computational modeling and electromyography, we show how a single stochastic accumulator to threshold, followed by noisy effector-dependent delays, explains eye-hand RT distributions and their correlation, while an alternate independent, interactive eye and hand accumulator model does not. Interestingly, the common accumulator model did not explain the RT distributions of the same subjects when they made eye and hand movements in isolation. Taken together, these data suggest that a dedicated circuit underlies coordinated eye-hand planning.

A comparative study of failure features in aerospace grade unidirectional and bidirectional woven CFRP composite laminates under four-point bend fatigue loads

Damage mechanisms in unidirectional (UD) and bi-directional (BD) woven carbon fiber reinforced polymer (CFRP) laminates subjected to four point flexure, both in static and fatigue loadings, were studied. The damage progression in composites was monitored by observing the slopes of the load vs. deflection data that represent the stiffness of the given specimen geometry over a number of cycles. It was observed that the unidirectional composites exhibit gradual loss in stiffness whereas the bidirectional woven composites show a relatively quicker loss during stage II of fatigue damage progression. Both, the static and the fatigue failures in unidirectional carbon fiber reinforced polymer composites originates due to generation of cracks on compression face while in bidirectional woven composites the damage ensues from both the compression and the tensile faces. These observations are supported by a detailed fractographic analysis.

Investigation of orographic features influencing spatial distribution of rainfall over the Western Ghats of India using satellite data

Using remotely sensed Tropical Rainfall Measuring Mission (TRMM) 3B42 rainfall and topographic data from the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) Digital Elevation Model (DEM), the impact of oroghraphical aspects such as topography, spatial variability of elevation and altitude of apexes are examined to investigate capacious summer monsoon rainfall over the Western Ghats (WG) of India. TRMM 3B42 v7 rainfall data is validated with Indian Meteorological Department (IMD) gridded rainfall data at 0.5 degrees resolution over the WG. The analysis of spatial pattern of monsoon rainfall with orography of the WG ascertains that the grade of orographic precipitation depends mainly on topography of the mountain barrier followed by steepness of windward side slope and altitude of the mountain. Longer and broader, i.e. cascaded topography, elevated summits and gradually increasing slopes impel the enhancement in precipitation. Comparing topography of various states of the WG, it has been observed that windward side of Karnataka receives intense rainfall in the WG during summer monsoon. It has been observed that the rainfall is enhanced before the peak of the mountain and confined up to the height about 800m over the WG. In addition to this, the spatial distribution of heavy and very heavy rainfall events in the last 14 years has also been explored. Heavy and very heavy rain events on this hilly terrain are categorized with a threshold of precipitation (R) in the range 150>R>120mmday(-1) and exceeding 150mmday(-1) using probability distribution of TRMM 3B42 v7 rainfall. The areas which are prone to heavy precipitation are identified. The study would help policy makers to manage the hazard scenario and, to improve weather predictions on mountainous terrain of the WG.

Multifarious facets of sugar-derived molecular gels: molecular features, mechanisms of self-assembly and emerging applications

The remarkable capability of nature to design and create excellent self-assembled nano-structures, especially in the biological world, has motivated chemists to mimic such systems with synthetic molecular and supramolecular systems. The hierarchically organized self-assembly of low molecular weight gelators (LMWGs) based on non-covalent interactions has been proven to be a useful tool in the development of well-defined nanostructures. Among these, the self-assembly of sugar-derived LMWGs has received immense attention because of their propensity to furnish biocompatible, hierarchical, supramolecular architectures that are macroscopically expressed in gel formation. This review sheds light on various aspects of sugar-derived LMWGs, uncovering their mechanisms of gelation, structural analysis, and tailorable properties, and their diverse applications such as stimuli-responsiveness, sensing, self-healing, environmental problems, and nano and biomaterials synthesis.

Analysis of Wrist Pulse Signals Using Spatial Features in Time Domain

Wrist pulse signal contains more important information about the health status of a person and pulse signal diagnosis has been employed in oriental medicine since very long time. In this paper we have used signal processing techniques to extract information from wrist pulse signals. For this purpose we have acquired radial artery pulse signals at wrist position noninvasively for different cases of interest. The wrist pulse waveforms have been analyzed using spatial features. Results have been obtained for the case of wrist pulse signals recorded for several subjects before exercise and after exercise. It is shown that the spatial features show statistically significant changes for the two cases and hence they are effective in distinguishing the changes taking place due to exercise. Support vector machine classifier is used to classify between the groups, and a high classification accuracy of 99.71% is achieved. Thus this paper demonstrates the utility of the spatial features in studying wrist pulse signals obtained under various recording conditions. The ability of the model to distinguish changes occurring under two different recording conditions can be potentially used for health care applications.