Stacking Interactions in RNA and DNA: Roll-Slide Energy Hyperspace for Ten Unique Dinucleotide Steps

Understanding dinucleotide sequence directed structures of nuleic acids and their variability from experimental observation remained ineffective due to unavailability of statistically meaningful data. We have attempted to understand this from energy scan along twist, roll, and slide degrees of freedom which are mostly dependent on dinucleotide sequence using ab initio density functional theory. We have carried out stacking energy analysis in these dinucleotide parameter phase space for all ten unique dinucleotide steps in DNA and RNA using DFT-D by B97X-D/6-31G(2d,2p), which appears to satisfactorily explain conformational preferences for AU/AU step in our recent study. We show that values of roll, slide, and twist of most of the dinucleotide sequences in crystal structures fall in the low energy region. The minimum energy regions with large twist values are associated with the roll and slide values of B-DNA, whereas, smaller twist values correspond to higher stability to RNA and A-DNA like conformations. Incorporation of solvent effect by CPCM method could explain the preference shown by some sequences to occur in B-DNA or A-DNA conformations. Conformational preference of BII sub-state in B-DNA is preferentially displayed mainly by pyrimidine-purine steps and partly by purine-purine steps. The purine-pyrimidine steps show largest effect of 5-methyl group of thymine in stacking energy and the introduction of solvent reduces this effect significantly. These predicted structures and variabilities can explain the effect of sequence on DNA and RNA functionality. (c) 2014 Wiley Periodicals, Inc. Biopolymers 103: 134-147, 2015.

Effect of viscosity contrast on plume formation in density stratified fluids

We perform two and three dimensional numerical simulations of plume formation in density and viscosity stratified fluid systems. We show that the ambient to plume fluid viscosity ratio strongly affects the near wall plume structures (line or sheet plumes) such as plume spacing and shape of plumes. We observe that where mushroom-like plumes are observed for lower viscosity ratios, taller plumes with bulbous heads form for high viscosity ratios. Plume structure and spacing are in good agreement with experimental results. By studying the geometry of the line plumes and the flow in the circulation cells, we discuss the mechanisms of their formation and the dynamics of merging. We show that an increase in the viscosity ratio decreases the total length of line plumes in the planform which indicates a decreased mixing at higher viscosity ratios. (C) 2015 Elsevier Ltd. All rights reserved.

The two-component signalling networks of Mycobacterium tuberculosis display extensive cross-talk in vitro

Two-component systems (TCSs), which contain paired sensor kinase and response regulator proteins, form the primary apparatus for sensing and responding to environmental cues in bacteria. TCSs are thought to be highly specific, displaying minimal cross-talk, primarily due to the co-evolution of the participating proteins. To assess the level of cross-talk between the TCSs of Mycobacterium tuberculosis, we mapped the complete interactome of the M. tuberculosis TCSs using phosphotransfer profiling. Surprisingly, we found extensive crosstalk among the M. tuberculosis TCSs, significantly more than that in the TCSs in Escherichia coli or Caulobacter crescentus, thereby offering an alternate to specificity paradigm in TCS signalling. Nearly half of the interactions we detected were significant novel cross-interactions, unravelling a potentially complex signalling landscape. We classified the TCSs into specific `one-to-one' and promiscuous `one-to-many' and `many-to-one' circuits. Using mathematical modelling, we deduced that the promiscuous signalling observed can explain several currently confounding observations about M. tuberculosis TCSs. Our findings suggest an alternative paradigm of bacterial signalling with significant cross-talk between TCSs yielding potentially complex signalling landscapes.

Ag-doped hydroxyapatite as efficient adsorbent for removal of Congo red dye from aqueous solution: Synthesis, kinetic and equilibrium adsorption isotherm analysis

In the present study a versatile and efficient adsorbent with high adsorption capacity for adsorption of Congo red dye in aqueous solution at ambient temperature without adjusting any pH is presented over the Ag modified calcium hydroxyapatite (CaHAp). CaHAp and Ag-doped CaHAp materials were synthesized using facile aqueous precipitation method. The physico-chemical properties of the materials were determined by powder X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, Transmission electron microscopy (TEM), UV-Visible spectroscopy, N-2 physisorption and acidity was determined by n-butylamine titration and pyridine adsorption methods. XRD analysis confirmed all adsorbents exhibit hexagonal CaHAp structure with P6(3)/m space group. TEM analysis confirms the rod like morphology of the adsorbents and the average length of the rods were in the range of 40-45 nm. Pyridine adsorption results indicate increase in number of Lewis acid sites with Ag doping in CaHAp. Adsorption capacity of CaHAp was found increased with Ag content in the adsorbents. Ag (10): CaHAp adsorbent showed superior adsorption performance among all the adsorbents for various concentrations of Congo red (CR) dye in aqueous solutions. The amount of CR dye adsorbed on Ag (10): CaHAp was found to be 49.89-267.81 mg g(-1) for 50-300 ppm in aqueous solution. A good correlation between adsorption capacity and acidity of the adsorbents was observed. The adsorption kinetic data of adsorbents fitted well with pseudo second-order kinetic model with correlation coefficients ranged from 0.998 to 0.999. The equilibrium adsorption data was found to best fit to the Langmuir adsorption isotherm model. (C) 2015 Elsevier Inc. All rights reserved.

In-plane elastic responses of circular cell honeycombs and bundled circular tubes in a diamond array structure

Assemblages of circular tubes and circular honeycombs in close packed arrangement are presently both competing and complementing regular honeycomb structures (HCS). The intrinsic isotropy of bundled tubes/rings in hexagonal arrays restricts their use to applications with isotopic need. With the aim of extending the utility of tubes/rings assemblages to anisotropic needs, this paper explores the prospects of bundled tubes and circular honeycombs in a general diamond array structure (DAS) to cater these needs. To this end, effective transverse Young's moduli and Poisson's ratio for thick/thin DAS are obtained theoretically. Analysis frameworks including thin ring theory (TRT), curved beam theory (CBT) and elasticity formulations are tested and corroborated by FEA employing contact elements. Results indicate that TRT and CBT are reasonable for thin tubes and honeycombs. Nevertheless, TRT yields compact formulae to study the anisotropy ratio, moduli spectrum and sensitivity of the assemblage as a function of thicknesses and array structure. These formulae supplement designers as a guide to tailor the structures. On the other hand, elasticity formulation can estimate over a larger range including very thick tubes/rings. In addition, this formulation offers to estimate refined transverse strengths of assemblages. (C) 2015 Elsevier Ltd. All rights reserved.

Role of upward leaders in modifying the induced currents in solitary down-conductors during a nearby lightning strike to ground

Electromagnetic field produced by a lightning strike to ground causes significant induction to tall objects in the vicinity. The frequency of occurrence of such nearby ground strikes can be higher than the number of direct strikes. Therefore, a complete knowledge on these induced currents is of practical relevance. However, limited efforts towards the characterisation of such induced currents in tall down-conductors could be seen in the literature. Due to the intensification of the background field caused by the descending stepped leader, tall towers/down-conductors can launch upward leaders of significant length. The nonlinearity in the conductance of upward leader and the surrounding corona sheath can alter the characteristics of the induced currents. Preliminary aspects of this phenomenon have been studied by the author previously and the present work aims to perform a detailed investigation on the role of upward leaders in modifying the characteristics of the induced currents. A consistent model for the upward leader, which covers all the essential electrical aspects of the phenomena, is employed. A first order arc model for representing the conductance of upward leader and a field dependant quadratic conductivity model for the corona sheath is employed. The initial gradient in the upward leader and the field produced by the return stroke forms the excitation. The dynamic electromagnetic response is determined by solving the wave equation using thin-wire time-domain formulation. Simulations are carried out initially to ascertain the role of individual parameters, including the length of the upward leader. Based on the simulation results, it is shown that the upward leader enhances the induced current, and when significant in length, can alter the waveshape of induced current from bipolar oscillatory to unipolar. The duration of the induced current is governed by the length of upward leader, which in turn is dependant on the return stroke current and the effective length of the down-conductor. If the current during the upward leader developmental phase is considered along with that after the stroke termination to ground, it would present a bipolar current pulse. (C) 2015 Elsevier Ltd. All rights reserved.

CheepSync: A Time Synchronization Service for Resource Constrained Bluetooth LE Advertisers

Clock synchronization is highly desirable in distributed systems, including many applications in the Internet of Things and Humans. It improves the efficiency, modularity, and scalability of the system, and optimizes use of event triggers. For IoTH, BLE - a subset of the recent Bluetooth v4.0 stack - provides a low-power and loosely coupled mechanism for sensor data collection with ubiquitous units (e.g., smartphones and tablets) carried by humans. This fundamental design paradigm of BLE is enabled by a range of broadcast advertising modes. While its operational benefits are numerous, the lack of a common time reference in the broadcast mode of BLE has been a fundamental limitation. This article presents and describes CheepSync, a time synchronization service for BLE advertisers, especially tailored for applications requiring high time precision on resource constrained BLE platforms. Designed on top of the existing Bluetooth v4.0 standard, the CheepSync framework utilizes low-level time-stamping and comprehensive error compensation mechanisms for overcoming uncertainties in message transmission, clock drift, and other system-specific constraints. CheepSync was implemented on custom designed nRF24Cheep beacon platforms (as broadcasters) and commercial off-the-shelf Android ported smartphones (as passive listeners). We demonstrate the efficacy of CheepSync by numerous empirical evaluations in a variety of experimental setups, and show that its average (single-hop) time synchronization accuracy is in the 10 mu s range.

A nano-scale instability in the beta phase of dilute Ti-Mo alloys

A nano-scale instability in the beta phase resulting in the formation of the disordered orthorhombic O' phase has been discovered in a fairly dilute binary Ti-Mo alloy, using selected area electron diffraction and high resolution scanning transmission electron microscopy. The O' phase informed in the alloy when the Mo content exceeds a critical value. The instability occurs in beta-solutionized samples that have been quenched to room temperature and is found to co-exist with athermal omega to phase. Interestingly, this nano-scale instability, involving the {110}<1<(1)over bar>0> soft-phonon shuffle, occurs in the beta phase without deliberate additions of either interstitial or substitutional solutes. (C) 2016 Elsevier Ltd. All rights reserved.

Effects of Microstructural Heterogeneity on the Spallation Behavior of Materials

It is of utmost importance to understand the spallation behaviour of heterogeneous materials. In this paper, a driven nonlinear threshold model with stress fluctuation is presented to study the effects of microstructural heterogeneity on continuum damage evolution. The spallation behavior of heterogeneity material is analyzed with this model. The heterogeniety of mesoscopic units is characterized in terms of Weibull modulus m of strength distibution and stress fluctuation parameter k. At high stress, the maximum damage increases with m; while at low stress, the maximum damage decreases. In addition, for low stress, severe stress fluctuation causes higher damage; while for high stress, causes lower damage.

Microcracks Propagation in One Al/SiCp under Impact Loading

Numerous microcracks propagation in one metal matrix composite, Al/SiCp under impact loading was investigated. The test data was got with a specially designed impact experimental approach. The analysis to the density, nucleating locations and distributions of the microcracks as well as microstructure effects of the original composite was received particular emphasis. The types of microcracks or debonding nucleated in the tested composite were dependent on the stress level and its duration. Distributions of the microcracks were depended on that of microstructures of the tested composite while total number of microcracks in unit area and unit duration, was controlled by the stress levels. Also, why the velocity was much lower than theoretical estimations for elastic solids and why the microcracks propagating velocities increased with the stress levels' increasing in current experiments were analysed and explained.

High speed liquid crystal over silicon display based on the flexoelectro-optic effect.

One of the key technologies to evolve in the displays market in recent years is liquid crystal over silicon (LCOS) microdisplays. Traditional LCOS devices and applications such as rear projection televisions, have been based on intensity modulation electro-optical effects, however, recent developments have shown that multi-level phase modulation from these devices is extremely sought after for applications such as holographic projectors, optical correlators and adaptive optics. Here, we propose alternative device geometry based on the flexoelectric-optic effect in a chiral nematic liquid crystal. This device is capable of delivering a multilevel phase shift at response times less than 100 microsec which has been verified by phase shift interferometry using an LCOS test device. The flexoelectric on silicon device, due to its remarkable characteristics, enables the next generation of holographic devices to be realized.

Real-Time Measurement on Deformation Fields of Hole-Excavated Samples under Impact Tension

In this paper, the real-time deformation fields are observed in two different kinds of hole-excavated dog-bone samples loaded by an SHTB, including single hole sample and dual holes sample with the aperture size of 0.8mm. The testing system consists of a high-speed camera, a He-Ne laser, a frame grabber and a synchronization device with the controlling accuracy of I microsecond. Both the single hole expanding process and the interaction of the two holes are recorded with the time interval of 10 mu s. The observed images on the sample surface are analyzed by newly developed software based on digital correlation theory and a modified image processing method. The 2-D displacement fields in plane are obtained with a resolution of 50 mu m and an accuracy of 0.5 mu m. Experimental results obtained in this paper are proofed, by compared with FEM numerical simulations.

Efecto de tres niveles de proteína sobre los rendimientos productivos en conejos de engorde

El presente trabajo experimental se realizó con el objetivo de estudiar el efecto de la variación proteica sobre los rendimientos productivos en conejos de engorde y la evaluación económica de los Tratamientos. Se utilizarán 27 gazapos de 40 días de edad, de la raza Neozelandés Blanco (NB), con un peso vivo inicial promedio de 0.612 Kg. Se realizó sexaje de los animales resultando 12 hembras y 15 machos. Se utilizaron tres tratamientos. A los animales del grupo uno (T1) se les suministró pellet con 13% PB. En el segundo grupo (T2) o testigo se suministró pellet con 15% PB y el tercer tratamiento se suministró pellet con 17% PB. Para las evaluaciones estadísticas se empleó un diseño completamente aleatorio (DCA), con tres tratamientos y tres repeticiones por tratamiento. Cada repetición estaba constituida por tres gazapos distribuidos aleatoriamente a los que se le registraron diariamente consumo de alimento y semanalmente aumento de peso vivo, ganancia media diaria e índice de conversión alimenticia. Las variables analizadas estadísticamente por medio del análisis de varianza (ANDEVA) fueron la Consumo Promedio de Alimento (Kg/día), Ganancia Media Diaria (Gr/día) y el índice de conversión por cada tratamiento, Duración del período de Ceba y los Costos Totales por Tratamiento. Para las variables dependientes se obtuvieron los siguientes valores : %P T1. 13%; T2. 15%; T3. 17% CA(Kg) T1: 0.0757 %; T2: 0.0785; T3: 0.0945 GMD (Gr/Dia) T1: 18.874; T2:17.990; T3: 17.902 ICA (Kg A/Kg PV)T1: 4.01; T2: 4.36; T3: 5.28 lnc. Peso (Kg) T1: 1.189; T2: 1.134; T3: 1.128 Durante el ensayo los animales del tratamiento T1 (13 16 PB) fueron los primeros en alcanzar el peso comercial (1.872 Kg) a los 63 días del engorde. En tanto en los tratamientos T2 (15 % PB) y T3 (17 % PB) los pesos finales registrados fueron 1.850 y 1.833 Kg de PV respectivamente. En el ANDEVA realizado para las diferentes variables, se observó que el efecto de los tratamientos sobre Consumo alimenticio, Ganancia Media Diaria e índice de Conversión Alimenticia resultó no significativo concluyendo que no existe diferencia entre los tratamientos. Sin embargo el Tratamiento con13% de PB (T1) fue el que presentó menor consumo, mayor ganancia de peso y mejor conversión Con la realización del análisis de los costos totales para un gazapo en engorde se determinaron valores de $20.01(T1),20.45 (T2) y 21.55 (T3). Al determinar los costos de alimentación por tratamiento se obtuvieron valores de C$ 27.91 para el13% de PB (T1), C$ 30.86 para el15% de PB (T2) y C$ 43.53 para el 17% de PB (T3). Pudiendo concluir que el tratamiento con 13% de PB (T1) fue el que presentó menores costos de alimentación y por lo tanto se obtuvo mayor utilidad.

Parámetros y evaluación genética preliminar de hembras de un hato criollo reyna en el Trópico Seco, Rivas, Nicaragua

Con el objetivo de evaluar el efecto de distintos factores ambientales (año de parto, época de parto y número de parto) sobre el comportamiento productivo de un hato Criollo Reyna y su preliminar categorización genética bajo condiciones de trópico seco en la finca "El Pino" Rivas Nicaragua. En general, se analizaron 470 lactancias provenientes de 155 vacas en el periodo 1998-2005. Las características Producción de leche a 305 días (PL305), producción de leche por día a 305 días (PLDL305) y largo de lactancia (LARLA) fueron analizadas mediante la utilización de modelos lineales fijos que en general incluyeron efectos de año de parto (APART), número de parto (NUMPA), época de parto (EP), Manejo del ordeño (MAN). Los índices de herencia (h2) y constancia (r) para PL305, PLD305 Y LARLA se obtuvieron a partir de modelos lineales mixtos que incluyeron efectos aleatorios de semental (S) y vaca (V), así como los efectos fijos APART, NUMPA, EP, MAN. De los factores ambientales se encontró efecto significativo del APART (P< 0.01) para todas las características al igual que NUMPA, EP y la interacción APART* EP, exceptuando MAN el cual afectó únicamente a LARLA P< 0.01). Se obtuvieron medias de mínimos cuadrados de 1630.56±59.56 kg. 260.24±6.39 días y 5.34±0.19 para (PL305), (LARLA) y PLD305, respectivamente. El parto número 3 mostró los máximos valores (1804.04±67.46) para PL305 días y parto 8 con 273.90±17.49 días para LARLA respectivamente. La EP 2 presentó máximos valores de 1707.93±67.00 kg., 5.59±0.21 kg. y 266.66±7.19 días para PL305, PLDL305 y LARLA, respectivamente. Los APART 1998, 2000 y 2001 mostraron los mayores promedios para PL305, PLDL305, con 1896.37±97.71 kg., 6.21±0.32 kg.; 1963.77±112.65 kg., 6.43 ± 0.36 kg; 1884.90±107.95 kg., 6.18±0.35 kg. respectivamente. El MAN no presentó tendencia definida en su comportamiento. Los valores de repetitividad fueron 0.46±0.05, 0.46±0.05 y 0.078±0.05 y los heredabilidad de 0.25±0.13, 0.253±0.134 y 0.002±0.083, para PL305, PLD305 y LARLA, respectivamente. Del valor genético se pudo constatar la normalidad y distribución de los valores; las vacas en producción con valores genéticos superiores en parte ya estaban identificadas por el productor en su proceso de selección, reflejando así que el sistema de selección del productor ha sido relativamente efectivo. Los promedios de producción de leche obtenidos demuestran la capacidad del Reyna para su explotación en condiciones similares al del lugar de estudio y los parámetros r y h2 revelan claramente la existencia de variabilidad genética, posible de utilizar en mejoramiento genético a mediano y largo plazo para producción de leche.