Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences

Genome sequences contain a number of patterns that have biomedical significance. Repetitive sequences of various kinds are a primary component of most of the genomic sequence patterns. We extended the suffix-array based Biological Language Modeling Toolkit to compute n-gram frequencies as well as n-gram language-model based perplexity in windows over the whole genome sequence to find biologically relevant patterns. We present the suite of tools and their application for analysis on whole human genome sequence.

Chiral discrimination and the measurement of enantiomeric excess from a severely overcrowded NMR spectrum

NMR spectroscopic chiral visualization, unambiguous assignment of peaks pertaining to R and S enantiomers and the subsequent measurement of enantiomeric composition demands a highly resolved spectrum. The method fails when the spectrum is severely overcrowded or highly complex, thereby hampering the determination of enantiomeric excess. In order to circumvent such problems we propose the utility of pure shift spectrum obtained by resolving the chemical shift and coupling information in two orthogonal dimensions. The skew projected spectrum yields singlet's at the respective chemical shift positions, permitting the unravelling of the superimposed spectral transitions for each enantiomer and measurement of enantiomeric composition. (C) 2012 Elsevier B. V. All rights reserved.

Statistical Methods for Accelerated Life Testing with Particular Reference to Resin Impregnated Paper Bushings

Electrical failure of insulation is known to be an extremal random process wherein nominally identical pro-rated specimens of equipment insulation, at constant stress fail at inordinately different times even under laboratory test conditions. In order to be able to estimate the life of power equipment, it is necessary to run long duration ageing experiments under accelerated stresses, to acquire and analyze insulation specific failure data. In the present work, Resin Impregnated Paper (RIP) a relatively new insulation system of choice used in transformer bushings, is taken as an example. The failure data has been processed using proven statistical methods, both graphical and analytical. The physical model governing insulation failure at constant accelerated stress has been assumed to be based on temperature dependent inverse power law model.

Computational tools for mechanistic discrimination in the reductive and metathesis coupling reactions mediated by titanium(IV) isopropoxide

A theoretical study has been carried out at the B3LYP/LANL2DZ level to compare the reactivity of phenyl isocyanate and phenyl isothiocyanate towards titanium(IV) alkoxides. Isocyanates are shown to favour both mono insertion and double insertion reactions. Double insertion in a head-to-tail fashion is shown to be more exothermic than double insertion in a head-to-head fashion. The head-to-head double insertion leads to the metathesis product, a carbodiimide, after the extrusion of carbon dioxide. In the case of phenyl isothiocyanate, calculations favour the formation of only mono insertion products. Formation of a double insertion product is highly unfavourable. Further, these studies indicate that the reverse reaction involving the metathesis of N,N-'-diphenyl carbodiimide with carbon dioxide is likely to proceed more efficiently than the metathesis reaction with carbon disulphide. This is in excellent agreement with experimental results as metathesis with carbon disulphide fails to occur. In a second study, multilayer MM/QM calculations are carried out on intermediates generated from reduction of titanium(IV) alkoxides to investigate the effect of alkoxy bridging on the reactivity of multinuclear Ti species. Bimolecular coupling of imines initiated by Ti(III) species leads to a mixture of diastereomers and not diastereoselective coupling of the imine. However if the reaction is carried out by a trimeric biradical species, diastereoselective coupling of the imine is predicted. The presence of alkoxy bridges greatly favours the formation of the d,l (+/-) isomer, whereas the intermediate without alkoxy bridges favours the more stable meso isomer. As a bridged trimeric species, stabilized by bridging alkoxy groups, correctly explains the diastereoselective reaction, it is the most likely intermediate in the reaction.

Device oriented statistical modeling method for process variability in 45nm analog CMOS technology

With the rapid scaling down of the semiconductor process technology, the process variation aware circuit design has become essential today. Several statistical models have been proposed to deal with the process variation. We propose an accurate BSIM model for handling variability in 45nm CMOS technology. The MOSFET is designed to meet the specification of low standby power technology of International Technology Roadmap for Semiconductors (ITRS).The process parameters variation of annealing temperature, oxide thickness, halo dose and title angle of halo implant are considered for the model development. One parameter variation at a time is considered for developing the model. The model validation is done by performance matching with device simulation results and reported error is less than 10%.© (2012) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

Discrimination of alpha-Amino Acids Using Green Tea Flavonoid (-)-Epigallocatechin Gallate as a Chiral Solvating Agent

We report a special, hitherto-unexplored property of (-)-epigallocatechin gallate (EGCG) as a chiral solvating agent for enantiodiscrimination of alpha-amino acids in the polar solvent DMSO. This phenomenon has been investigated by H-1 NMR spectroscopy. The mechanism of the interaction property of EGCG with alpha-amino acids has been understood as arising out of hydrogen-bonded noncovalent interactions, where the -OH groups of two phenyl rings of EGCG play dominant roles. The conversion of the enantiomeric mixture into diastereomers yielded well-resolved peaks for D and L amino acids permitting the precise measurement of enantiomeric composition. Often one encounters complex situations when the spectra are severely overlapped or partially resolved hampering the testing of enantiopurity and the precise measurement of enantiomeric excess (ee). Though higher concentration of EGCG yielded better discrimination, the use of lower concentration being economical, we have exploited an appropriate 2D NMR experiment in overcoming such problems. Thus, in the present study we have successfully demonstrated the utility of the bioflavonoid (-)-EGCG, a natural product as a chiral solvating agent for the discrimination of large number of alpha-amino acids in a polar solvent DMSO. Another significant advantage of this new chiral sensing agent is that it is a natural product and does not require tedious multistep synthesis unlike many other chiral auxiliaries.

Novel piezoelectric thin film impact sensor: application in non-destructive material discrimination

We report on the design, development, and performance study of a packaged piezoelectric thin film impact sensor, and its potential application in non-destructive material discrimination. The impact sensing element employed was a thin circular diaphragm of flexible Phynox alloy. Piezoelectric ZnO thin film as an impact sensing layer was deposited on to the Phynox alloy diaphragm by RF reactive magnetron sputtering. Deposited ZnO thin film was characterized by X-ray diffraction (XRD), Atomic Force Microscopy (AFM), and Scanning Electron Microscopy (SEM) techniques. The d(31) piezoelectric coefficient value of ZnO thin film was 4.7 pm V-1, as measured by 4-point bending method. ZnO film deposited diaphragm based sensing element was properly packaged in a suitable housing made of High Density Polyethylene (HDPE) material. Packaged impact sensor was used in an experimental set-up, which was designed and developed in-house for non-destructive material discrimination studies. Materials of different densities (iron, glass, wood, and plastic) were used as test specimens for material discrimination studies. The analysis of output voltage waveforms obtained reveals lots of valuable information about the impacted material. Impact sensor was able to discriminate the test materials on the basis of the difference in their densities. The output response of packaged impact sensor shows high linearity and repeatability. The packaged impact sensor discussed in this paper is highly sensitive, reliable, and cost-effective.

Ternary ion-pair complexation: a protocol for chiral discrimination and the assignment of absolute configuration of chiral hydroxy acids

The study demonstrates the utility of ternary ion-pair complex formed among BINOL (1,1'-Bi-2-naphthol), a carboxylic acid and an organic base, such as, dimethylpyridine (DMAP), 1,4-diazabicyclo2.2.2]octane (DABCO), as a versatile chiral solvating agent (CSA) for the enantiodiscrimination of carboxylic acids, measurement of enantiomeric excess (ee) and the assignment of absolute configuration of hydroxy acids. The proposed mechanism of ternary complex has wider application for testing the enantiopurity owing to the fact that the binary mixture using BINOL alone does not serve as a solvating agent for their discrimination. In addition, the developed protocol has an excellent utility for the assignment of the absolute configurations of hydroxy acids.

Photocurrent spectroscopic studies of diketopyrrolopyrrole-based statistical copolymers

Diketopyrrolopyrrole (DPP) containing copolymers have gained a lot of interest in organic optoelectronics with great potential in organic photovoltaics. In this work, DPP based statistical copolymers, with slightly different bandgap energies and a varying fraction of donor-acceptor ratio are investigated using monochromatic photocurrent spectroscopy and Fourier-transform photocurrent spectroscopy (FTPS). The statistical copolymer with a lower DPP fraction, when blended with a fullerene derivative, shows the signature of an inter charge transfer complex state in photocurrent spectroscopy. Furthermore, the absorption spectrum of the blended sample with a lower DPP fraction is seen to change as a function of an external bias, qualitatively similar to the quantum confined Stark effect, from where we estimate the exciton binding energy. The statistical copolymer with a higher DPP fraction shows no signal of the inter charge transfer states and yields a higher external quantum efficiency in a photovoltaic structure. In order to gain insight into the origin of the observed charge transfer transitions, we present theoretical studies using density-functional theory and time-dependent density-functional theory for the two pristine DPP based statistical monomers.

Photocurrent spectroscopic studies of diketopyrrolopyrrole-based statistical copolymers

Diketopyrrolopyrrole (DPP) containing copolymers have gained a lot of interest in organic optoelectronics with great potential in organic photovoltaics. In this work, DPP based statistical copolymers, with slightly different bandgap energies and a varying fraction of donor-acceptor ratio are investigated using monochromatic photocurrent spectroscopy and Fourier-transform photocurrent spectroscopy (FTPS). The statistical copolymer with a lower DPP fraction, when blended with a fullerene derivative, shows the signature of an inter charge transfer complex state in photocurrent spectroscopy. Furthermore, the absorption spectrum of the blended sample with a lower DPP fraction is seen to change as a function of an external bias, qualitatively similar to the quantum confined Stark effect, from where we estimate the exciton binding energy. The statistical copolymer with a higher DPP fraction shows no signal of the inter charge transfer states and yields a higher external quantum efficiency in a photovoltaic structure. In order to gain insight into the origin of the observed charge transfer transitions, we present theoretical studies using density-functional theory and time-dependent density-functional theory for the two pristine DPP based statistical monomers.

Nestmate discrimination in the social wasp Ropalidia marginata: chemical cues and chemosensory mechanism

Nestmate discrimination plays an important role in preserving the integrity of social insect colonies. It is known to occur in the primitively eusocial wasp Ropalidia marginata in which non-nestmate conspecifics are not allowed to come near a nest. However, newly eclosed females are accepted in foreign colonies, suggesting that such individuals may not express the cues that permit differentiation between nestmates and non-nestmates. As cuticular hydrocarbons (CHCs) have been implicated as chemosensory cues used in nestmate recognition in other species, we investigated, using bioassays and chemical analyses, whether CHCs can play a role in nestmate recognition in R. marginata. We found that individuals can be differentiated according to colony membership using their CHC profiles, suggesting a role of CHCs in nestmate discrimination. Non-nestmate CHCs of adult females received more aggression than nestmate CHCs, thereby showing that CHCs are used as cues for nestmate recognition. Contrarily, and as expected, CHCs of newly eclosed females were not discriminated against when presented to a foreign colony. Behavioural sequence analysis revealed the behavioural mechanism involved in sensing nestmate recognition cues. We also found that newly eclosed females had a different CHC profile from that of adult females, thereby providing an explanation for why young females are accepted in foreign colonies. (C) 2013 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Free turbulent shear layer in a point vortex gas as a problem in nonequilibrium statistical mechanics

This paper attempts to unravel any relations that may exist between turbulent shear flows and statistical mechanics through a detailed numerical investigation in the simplest case where both can be well defined. The flow considered for the purpose is the two-dimensional (2D) temporal free shear layer with a velocity difference Delta U across it, statistically homogeneous in the streamwise direction (x) and evolving from a plane vortex sheet in the direction normal to it (y) in a periodic-in-x domain L x +/-infinity. Extensive computer simulations of the flow are carried out through appropriate initial-value problems for a ``vortex gas'' comprising N point vortices of the same strength (gamma = L Delta U/N) and sign. Such a vortex gas is known to provide weak solutions of the Euler equation. More than ten different initial-condition classes are investigated using simulations involving up to 32 000 vortices, with ensemble averages evaluated over up to 10(3) realizations and integration over 10(4)L/Delta U. The temporal evolution of such a system is found to exhibit three distinct regimes. In Regime I the evolution is strongly influenced by the initial condition, sometimes lasting a significant fraction of L/Delta U. Regime III is a long-time domain-dependent evolution towards a statistically stationary state, via ``violent'' and ``slow'' relaxations P.-H. Chavanis, Physica A 391, 3657 (2012)], over flow time scales of order 10(2) and 10(4)L/Delta U, respectively (for N = 400). The final state involves a single structure that stochastically samples the domain, possibly constituting a ``relative equilibrium.'' The vortex distribution within the structure follows a nonisotropic truncated form of the Lundgren-Pointin (L-P) equilibrium distribution (with negatively high temperatures; L-P parameter lambda close to -1). The central finding is that, in the intermediate Regime II, the spreading rate of the layer is universal over the wide range of cases considered here. The value (in terms of momentum thickness) is 0.0166 +/- 0.0002 times Delta U. Regime II, extensively studied in the turbulent shear flow literature as a self-similar ``equilibrium'' state, is, however, a part of the rapid nonequilibrium evolution of the vortex-gas system, which we term ``explosive'' as it lasts less than one L/Delta U. Regime II also exhibits significant values of N-independent two-vortex correlations, indicating that current kinetic theories that neglect correlations or consider them as O(1/N) cannot describe this regime. The evolution of the layer thickness in present simulations in Regimes I and II agree with the experimental observations of spatially evolving (3D Navier-Stokes) shear layers. Further, the vorticity-stream-function relations in Regime III are close to those computed in 2D Navier-Stokes temporal shear layers J. Sommeria, C. Staquet, and R. Robert, J. Fluid Mech. 233, 661 (1991)]. These findings suggest the dominance of what may be called the Kelvin-Biot-Savart mechanism in determining the growth of the free shear layer through large-scale momentum and vorticity dispersal.

Dual Binding Site Assisted Chromogenic and Fluorogenic Recognition and Discrimination of Fluoride and Cyanide by a Peripherally Borylated Metalloporphyrin: Overcoming Anion Interference in Organoboron Based Sensors

Peripherally triarylborane decorated porphyrin (2) and its Zn(II) complex (3) have been synthesized. Compound 3 contains of two different Lewis acidic binding sites (Zn(II) and boron center). Unlike all previously known triarylborane based sensors, the optical responses of 3 toward fluoride and cyanide are distinctively different, thus enabling the discrimination of these two interfering anions. Metalloporphyrin 3 shows a multiple channel fluorogenic response toward fluoride and cyanide and also a selective visual colorimetric response toward cyanide. By comparison with model systems and from detailed photophysical studies on 2 and 3, we conclude that the preferential binding of fluoride occurs at the peripheral borane moieties resulting in the cessation of the EET (electronic energy transfer) process from borane to porphyrin core and with negligible negetive cooperative effects. On the other hand, cyanide binding occurs at the Zn(II) core leading to drastic changes in its absorption behavior which can be followed by the naked eye. Such changes are not observed when the boryl substituent is absent (e.g., Zn-TPP and TPP). Compounds 2 and 3 were also found to be capable of extracting fluoride from aqueous medium.

A versatile ternary ionic complex for chiral discrimination of molecules with diverse functionalities using H-1 NMR

This study reports a simple, efficient and versatile protocol developed for NMR spectroscopic enantiodiscrimination of molecules containing diverse functional -groups, such as amino alcohols, secondary alcohols, cyanohydrins, oxazolidones, diols, thiones and epoxides, using a phosphorous based three component mixture. The simple mixing and shaking of enantiopure 1,1'-binaphthyt-2,2'-diyl hydrogenphosphate (BNPA), 4-(dimethylamino)pyridine (DMAP) and a chiral analyte in the solvent CDCl3 served as a chiral solvating agent and resulted in well dispersed peaks for each enantiomer in the H-1 NMR spectrum. Discrimination could be achieved not only for the proton at the chiral centre, but also for multiple proton sites. The devised approach also permitted the precise measurement of the enantiomeric excess (ee).