Exploration of deleterious single nucleotide polymorphisms in the components of human P bodies: An in silico approach

P bodies are 100-300 nm sized organelles involved in mRNA silencing and degradation. A total of 60 human proteins have been reported to localize to P bodies. Several human SNPs contribute to complex diseases by altering the structure and function of the proteins. Also, SNPs alter various transcription factors binding, splicing and miRNA regulatory sites. Owing to the essential functions of P bodies in mRNA regulation, we explored computationally the functional significance of SNPs in 7 P body components such as XRN1, DCP2, EDC3, CPEB1, GEMIN5, STAU1 and TRIM71. Computational analyses of non-synonymous SNPs of these components was initiated using well utilized publicly available software programs such as the SIFT, followed by PolyPhen, PANTHER, MutPred, I-Mutant-2.0 and PhosSNP 1.0. Functional significance of noncoding SNPs in the regulatory regions were analysed using FastSNP. Utilizing miRSNP database, we explored the role of SNPs in the context that alters the miRNA binding sites in the above mentioned genes. Our in silico studies have identified various deleterious SNPs and this cataloguing is essential and gives first hand information for further analysis by in vitro and in vivo methods for a better understanding of maintenance, assembly and functional aspects of P bodies in both health and disease. (C) 2013 Elsevier B.V. All rights reserved.

Elastic-plastic contact conditions for frictionally constrained bodies under cyclic tangential loading

A Frictionally constrained condition implies dependence of friction force on tangential displacement amplitude. The condition may occur due to chemical, physical, and/or mechanical interaction between the contacting surfaces. The condition, sometimes also referred to as the presliding condition or partial slip condition, is characterized under fretting. Under such conditions, various experimental studies indicate the existence of two distinguishable regions, that is, stick region and slip region. In the present study, frictionally constrained conditions are identified and the evolutions of stick-slip regions are investigated in detail. Investigations have been performed on self-mated stainless steel and chromium carbide coated surfaces mated against stainless steel, under both vacuum and ambient conditions. Contact conditions prevailing at the contact interface were identified based on the mechanical responses and were correlated with the surface damage observed. Surface degradation has been observed in the form of microcracks and material transfer. Detailed numerical analysis has also been performed in order to understand the energy dissipation and the damage mode involved in the surface or subsurface damage. It has been observed that under frictionally constrained conditions, the occurrence of annular slip features are mainly due to the junction growth, resulting from elastic-plastic deformation at the contact interface. Ratcheting has been observed as the governing damage mode under cyclic tangential loading condition.

Seventeen-Level Inverter Formed by Cascading Flying Capacitor and Floating Capacitor H-Bridges

A multilevel inverter for generating 17 voltage levels using a three-level flying capacitor inverter and cascaded H-bridge modules with floating capacitors has been proposed. Various aspects of the proposed inverter like capacitor voltage balancing have been presented in the present paper. Experimental results are presented to study the performance of the proposed converter. The stability of the capacitor balancing algorithm has been verified both during transients and steady-state operation. All the capacitors in this circuit can be balanced instantaneously by using one of the pole voltage combinations. Another advantage of this topology is its ability to generate all the voltages from a single dc-link power supply which enables back-to-back operation of converter. Also, the proposed inverter can be operated at all load power factors and modulation indices. Additional advantage is, if one of the H-bridges fail, the inverter can still be operated at full load with reduced number of levels. This configuration has very low dv/dt and common-mode voltage variation.

Isotopic and geochemical characterization of invader tilapia fishes from water bodies of West Bengal and Karnataka, India

The otoliths (N = 12) of freshwater invasive species tilapia (Tilapia mossambicus) collected from two water bodies located at Kolkata and Bangalore, India, were analyzed for stable isotopes (delta 18O, delta 14C) and major and trace elements in order to assess the suitability of using otoliths as a tracer of aquatic environmental changes. The stable isotope analysis was done using the dual inlet system of a Finnigan-MAT 253 isotope ratio mass spectrometer (Thermo-Fisher, Bremen, Germany). Concentrations of major and trace elements were determined using a Thermo X-Series II quadrupole mass spectrometer. The stable isotope composition in tilapia otolith samples from Bangalore and Kolkata water bodies are quite good agreeing with that of the respective lake/pond and rain water. Elemental composition revealed in a pattern of Ca > Fe > Na > Sr > K > Ba > Cr > Mg > As > Mn > Zn > Co > Cu > Cd > Pb. The otoliths from Kolkata pond water are more enriched in Ba, Zn, Pb, Mn, Se, Cu, Zn, Cd, and Ni whereas Cr and As were found to be higher in otolith samples from Bangalore lake. The enrichment factor (EF) values of Cr were higher for both the sampling location in comparison with other metals, although all the studied metals exhibited EF values >1. The PCA shows clustering of metals in the otolith which are related either with the metabolic and physiological attributes or waterborne source. The study demonstrated the potential of stable isotope techniques to distinguish otolith specimens from varied climatic zone, while elemental composition recorded the quality of water at both the locations. The role of climate driving the quality of water can be understood by detailed and continuous monitoring of otolith specimens in the future. Future method allows reconstruction of climate and water quality from old specimens from field exposures or museum collection.

Influence of Local Magnetic Fields on P-Doped Si Floating Zone Melting Crystal Growth in Microgravity

A two-dimensional axisymmetric numerical model is presented to study the influence of local magnetic fields on P-doped Si floating zone melting crystal growth in microgravity. The model is developed based on the finite difference method in a boundary-fitted curvilinear coordinate system. Extensive numerical simulations are carried out, and parameters studied include the curved growth interface shape and the magnetic field configurations. Computed results show that the local magnetic field is more effective in reducing the impurity concentration nonuniformity at the growth interface in comparison with the longitudinal magnetic field. Moreover, the curved growth interface causes more serious impurity concentration nonuniformity at the growth interface than the case with a planar growth interface.

Effect of non-uniform magnetic field on crystal growth by floating-zone method in microgravity

The magnetic damping effect of the non-uniform magnetic field on the floating-zone crystal growth process in microgravity is studied by numerical simulation. The results show that the non-uniform magnetic field with designed configuration can effectively reduce the flow near the free surface and then in the melt zone. At the same time, the designed magnetic field can improve the impurity concentration non-uniformity along the solidification interface. The primary principles of the magnetic field configuration design are also discussed.

Numerical simulation of magnetic field design for damping thermocapillary convection in a floating half-zone

The magnetic fields produced by electrical coils are designed for damping the the thermocapillary convection in a floating half-zone in microgravity. The fields are designed specially to reduce the flow near the free surface and then in the melt zone by adjusting the longitudinal coil positions close to the melt zone. The effects of the designed magnetic fields on reducing the flow velocity and temperature distribution non-uniformity in the melt zone are stronger than those of the case of an uniform longitudinal magnetic field obtained by numerical simulation, particularly at the melt-rod interface. It brings fundamental insights into the heat and mass transfer control at the solidification interface by the magnetic field design for crystal growth by the floating full-zone method.

Experimental Study on the Transition Process to the Oscillatory Thermocapillary Convections in a Floating Half Zone

The transition process of the thermocapillary convection from a steady and axisymmetric mode to the oscillatory mode in a liquid bridge with a fixed aspect ratio and varied volume ratio was studied experimentally. To ensure the surface tension to play an important role in the ground-based experiment, the geometrical configuration of the liquid bridge was so designed that the associated dynamic Bond number Bd ≈ 1. The velocity fields were measured by Particle Image Velocimetry (PIV) technique to effectively distinguish the different flow modes during the transition period in the experiments. Our experiments showed that as the temperature difference increased the slender and fat bridges presented quite different features on the evolution in their flow feature: for the former the thermocapillary convection transformed from a steady and axisymmetric pattern directly into an oscillatory one; but for the latter a transition flow status, characterized by an axial asymmetric steady convection, appeared before reaching the oscillatory mode. Experimental observations agree with the results of numerical simulations and it is obvious that the volume of liquid bridge is a sensitive geometric parameter. In addition, at the initial stage of the oscillation, for the former a rotating oscillatory convection with azimuthal wave number m = 1 was observed while for the latter a pulsating oscillatory pattern with azimuthal wave number m = 2 emerged, and then with further increase of the temperature difference, the pulsating oscillatory convection with azimuthal wave number m = 2 evolved into a rotating oscillatory pattern with azimuthal wave number m = 2.

Study on Flow Patterns of Oscillatory Thermocapillary Convection In Floating Half Zone by PIV

The velocity fields of oscillatory convection have been measured using the techniques of Particle Image Velocimetry (PIV) in a liquid bridge of half floating zone with small typical scales of a few millimeters for emphasizing the thermocapillary effect in comparison with the effect of buoyancy. The flow patterns of the oscillatory flow have been studied experimentally in a liquid bridge. The flow patterns in the liquid bridge are classified with mode numbers according to oscillatory flow characteristics. Results of the experiment show that the mode depends on the aspect ratio as well as the volume ratio of the liquid bridge. The experimental results are helpful for studying the structure of flow at the onset of oscillatory thermocapillary convection in a liquid bridge.

Dynamic SIF of interface crack between two dissimilar viscoelastic bodies under impact loading

In this paper, the transient dynamic stress intensity factor (SIF) is determined for an interface crack between two dissimilar half-infinite isotropic viscoelastic bodies under impact loading. An anti-plane step loading is assumed to act suddenly on the surface of interface crack of finite length. The stress field incurred near the crack tip is analyzed. The integral transformation method and singular integral equation approach are used to get the solution. By virtue of the integral transformation method, the viscoelastic mixed boundary problem is reduced to a set of dual integral equations of crack open displacement function in the transformation domain. The dual integral equations can be further transformed into the first kind of Cauchy-type singular integral equation (SIE) by introduction of crack dislocation density function. A piecewise continuous function approach is adopted to get the numerical solution of SIE. Finally, numerical inverse integral transformation is performed and the dynamic SIF in transformation domain is recovered to that in time domain. The dynamic SIF during a small time-interval is evaluated, and the effects of the viscoelastic material parameters on dynamic SIF are analyzed.

A simulation model of a floating half zone

A simulation model of a floating half zone was suggested by steady numerical simulation and experiment respectively, in the previous papers [Q.S. Chen, W.R. Hu, Int. J. Mass Heat Transfer 40 (1997) 757; J.H. Han, Y. Ar, R. Zhou, W.R. Hue, Int. J. Mass Heat Transfer 40 (1997) 2671]. In the present paper, the simulation model is studied by using the method of unsteady and three-dimensional numerical simulation, and the transient process from steady convection to oscillatory convection is especially analyzed. Comparison of onsets of oscillation for both simulation model and the usual model were obtained, and the results show that the critical Marangoni number of the simulation model is obviously smaller than that of the usual model for the same slender liquid bridge. This implies that the usual model of a floating half zone gives a lower estimation on the onset of oscillation for floating zone convection.

Magnetic field design for floating zone crystal growth

The magnetic fields produced by electrical coils are designed for P-doped Si crystal growth in a floating full zone in microgravity environment. The fields are designed specially to reduce the how near the free surface and then in the melt zone by adjusting the coil positions near the melt zone. The effects of the designed magnetic fields on reducing the Row velocity and the non-uniformity of the concentration distribution in the melt zone are better than those of the case of a uniform longitudinal magnetic field, obtained by numerical simulation. It is expected to improve the radial macro-segregation and reduce the convection in the crystal growth at the same time by using the designed magnetic field.

The scattering of general SH plane wave by interface crack between two dissimilar viscoelastic bodies

The scattering of general SH plane wave by an interface crack between two dissimilar viscoelastic bodies is studied and the dynamic stress,intensity factor at the crack-tip is computed. The scattering problem can be decomposed into two problems: one is the reflection and refraction problem of general SH plane waves at perfect interface (with no crack); another is the scattering problem due to the existence of crack. For the first problem, the viscoelastic wave equation, displacement and stress continuity conditions across the interface are used to obtain the shear stress distribution at the interface. For the second problem, the integral transformation method is used to reduce the scattering problem into dual integral equations. Then, the dual integral equations are transformed into the Cauchy singular integral equation of first kind by introduction of the crack dislocation density function. Finally, the singular integral equation is solved by Kurtz's piecewise continuous function method. As a consequence, the crack opening displacement and dynamic stress intensity factor are obtained. At the end of the paper, a numerical example is given. The effects of incident angle, incident frequency and viscoelastic material parameters are analyzed. It is found that there is a frequency region for viscoelastic material within which the viscoelastic effects cannot be ignored.

Transition to Chaos in the Floating Half Zone Convection

The transition process from steady convection to chaos is experimentally studied in thermocapillary convections of floating half zone. The onset of temperature oscillations in the liquid bridge of floating half zone and further transitions of the temporal convective behaviour are detected by measuring the temperature in the liquid bridge. The fast Fourier transform reveals the frequency and amplitude characteristics of the flow transition. The experimental results indicate the existence of a sequence of period-doubling bifurcations that culminate in chaos. The measured Feigenbaum numbers are delta(2) = 4.69 and delta(4) = 4.6, which are comparable with the theoretical asymptotic value delta = 4.669.

Two bifurcation transitions of the floating half zone convection in a fat liquid bridge of larger Pr

The transient process of the thermocapillary convection was obtained for the large Pu floating half zone by using the method of three-dimensional and unsteady numerical simulation. The convection transits directly from steady and axisymmetric state to oscillatory flow for slender liquid bridge, and transits first from steady and axisymmetric convection to the steady and non-axisymmetric convection, then, secondly to the oscillatory convection for the fatter liquid bridge. This result implies that the volume of liquid bridge is not only a sensitive critical parameter for the onset of oscillation, but also relates to the new mechanism for the onset of instability in the floating half zone convection even in case of large Prandtl number fluid.