A novel approach to design of cis-acting DNA structural element for regulation of gene expression in vivo

Taking advantage of the degeneracy of the genetic code we have developed a novel approach to introduce, within a gene, DNA sequences capable of adopting unusual structures and to investigate the role of such sequences in regulation of gene expression in vivo. We used a computer program that generates alternative codon sequences for the same amino-acid sequence to convert a stretch of nucleotides into an inverted-repeat sequence with the potential to adopt cruciform structure. This approach was used to replace a 51-base-pair EcoRI-HindIII segment in the N-terminal region of the beta-galactosidase gene in plasmid pUC19 with a 51-bp synthetic oligonucleotide sequence with the potential to adopt a cruciform structure with 18 bp in the stem region. In selecting the 51-bp sequence, care was taken to include those codons that are preferred in E. coli. E. coli DH5-alpha cells harbouring the plasmid containing the redesigned sequence showed drastic reduction in expression of the beta-galactosidase gene compared to cells harbouring the plasmid with the native sequence. This approach demonstrates the possibility of introducing DNA secondary-structure elements to alter regulation of gene expression in vivo.

Curved composite beams—optimum lay-up for buckling by ranking

Instability of laminated curved composite beams made of repeated sublaminate construction is studied using finite element method. In repeated sublaminate construction, a full laminate is obtained by repeating a basic sublaminate which has a smaller number of plies. This paper deals with the determination of optimum lay-up for buckling by ranking of such composite curved beams (which may be solid or sandwich). For this purpose, use is made of a two-noded, 16 degress of freedom curved composite beam finite element. The displacements u, v, w of the element reference axis are expressed in terms of one-dimensional first-order Hermite interpolation polynomials, and line member assumptions are invoked in formulation of the elastic stiffness matrix and geometric stiffness matrix. The nonlinear expressions for the strains, occurring in beams subjected to axial, flexural and torsional loads, are incorporated in a general instability analysis. The computer program developed has been used, after extensive checking for correctness, to obtain optimum orientation scheme of the plies in the sublaminate so as to achieve maximum buckling load for typical curved solid/sandwich composite beams.

Flow-Acoustic Performance of Perforated Element Mufflers With Application to Design

A fairly comprehensive computer program incorporating explicit expressions for the four-pole parameters of concentric-tube resonators, plug mufflers, and three-duct cross-flow perforated elements has been used for parametric studies. The parameters considered are hole diameter, the center-to-center distance between consecutive holes (which decides porosity), the incoming mean flow Mach number, the area expansion ratio, the number of partitions of chambers within a given overall shell length, and the relative lengths of these partitions or chambers, all normalized with respect to the exhaust pipe diameter. Transmission loss has been plotted as a function of a normalized frequency parameter. Additionally, the effect of the tail pipe length on insertion loss for an anechoic source has also been studied. These studies have been supplemented by empirical expressions for the normalized static pressure drop for different types of perforated-element mufflers developed from experimental observations.

Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and edothelin I

A general procedure for arriving at 3-D models of disulphiderich olypeptide systems based on the covalent cross-link constraints has been developed. The procedure, which has been coded as a computer program, RANMOD, assigns a large number of random, permitted backbone conformations to the polypeptide and identifies stereochemically acceptable structures as plausible models based on strainless disulphide bridge modelling. Disulphide bond modelling is performed using the procedure MODIP developed earlier, in connection with the choice of suitable sites where disulphide bonds could be engineered in proteins (Sowdhamini,R., Srinivasan,N., Shoichet,B., Santi,D.V., Ramakrishnan,C. and Balaram,P. (1989) Protein Engng, 3, 95-103). The method RANMOD has been tested on small disulphide loops and the structures compared against preferred backbone conformations derived from an analysis of putative disulphide subdatabase and model calculations. RANMOD has been applied to disulphiderich peptides and found to give rise to several stereochemically acceptable structures. The results obtained on the modelling of two test cases, a-conotoxin GI and endothelin I, are presented. Available NMR data suggest that such small systems exhibit conformational heterogeneity in solution. Hence, this approach for obtaining several distinct models is particularly attractive for the study of conformational excursions.

A bicharacteristic formulation of the ideal MHD equations

On a characteristic surface Omega of a hyperbolic system of first-order equations in multi-dimensions (x, t), there exits a compatibility condition which is in the form of a transport equation along a bicharacteristic on Omega. This result can be interpreted also as a transport equation along rays of the wavefront Omega(t) in x-space associated with Omega. For a system of quasi-linear equations, the ray equations (which has two distinct parts) and the transport equation form a coupled system of underdetermined equations. As an example of this bicharacteristic formulation, we consider two-dimensional unsteady flow of an ideal magnetohydrodynamics gas with a plane aligned magnetic field. For any mode of propagation in this two-dimensional flow, there are three ray equations: two for the spatial coordinates x and y and one for the ray diffraction. In spite of little longer calculations, the final four equations (three ray equations and one transport equation) for the fast magneto-acoustic wave are simple and elegant and cannot be derived in these simple forms by use of a computer program like REDUCE.

A hybrid technique of modeling of cracks using displacement discontinuity and direct boundary element method

A hybrid technique to model two dimensional fracture problems which makes use of displacement discontinuity and direct boundary element method is presented. Direct boundary element method is used to model the finite domain of the body, while displacement discontinuity elements are utilized to represent the cracks. Thus the advantages of the component methods are effectively combined. This method has been implemented in a computer program and numerical results which show the accuracy of the present method are presented. The cases of bodies containing edge cracks as well as multiple cracks are considered. A direct method and an iterative technique are described. The present hybrid method is most suitable for modeling problems invoking crack propagation.

Genome analysis: A new approach for visualization of sequence organization in genomes

In this article we describe and demonstrate the versatility of a computer program, GENOME MAPPING, that uses interactive graphics and runs on an IRIS workstation. The program helps to visualize as well as analyse global and local patterns of genomic DNA sequences. It was developed keeping in mind the requirements of the human genome sequencing programme, which requires rapid analysis of the data. Using GENOME MAPPING one can discern signature patterns of different kinds of sequences and analyse such patterns for repetitive as well as rare sequence strings. Further, one can visualize the extent of global homology between different genomic sequences. An application of our method to the published yeast mitochondrial genome data shows similar sequence organizations in the entire sequence and in smaller subsequences.

Stiffened composite cylindrical panels�Optimum lay-up for buckling by ranking

Buckling of discretely stiffened composite cylindrical panels made of repeated sublaminate construction is studied using a finite element method. In repeated sublaminate construction, a full laminate is obtained by repeating a basic sublaminate, which has a smaller number of plies. This paper deals with the determination of the optimum lay-up for buckling by ranking of such stiffened (longitudinal and hoop) composite cylindrical panels. For this purpose we use the particularized form of a four-noded, 48 degrees of freedom doubly curved quadrilateral thin shell finite element together with a fully compatible two-noded, 16 degrees of freedom composite stiffener element. The computer program developed has been used, after extensive checking for correctness, to obtain an optimum orientation scheme of the plies in the sublaminate so as to achieve maximum buckling load for a specified thickness of typical stiffened composite cylindrical panels.

A checking method for probabilistic seismic-hazard assessment: case studies on three cities

The conventional Cornell's source-based approach of probabilistic seismic-hazard assessment (PSHA) has been employed all around the world, whilst many studies often rely on the use of computer packages such as FRISK (McGuire FRISK-a computer program for seismic risk analysis. Open-File Report 78-1007, United States Geological Survey, Department of Interior, Washington 1978) and SEISRISK III (Bender and Perkins SEISRISK III-a computer program for seismic hazard estimation, Bulletin 1772. United States Geological Survey, Department of Interior, Washington 1987). A ``black-box'' syndrome may be resulted if the user of the software does not have another simple and robust PSHA method that can be used to make comparisons. An alternative method for PSHA, namely direct amplitude-based (DAB) approach, has been developed as a heuristic and efficient method enabling users to undertake their own sanity checks on outputs from computer packages. This paper experiments the application of the DAB approach for three cities in China, Iran, and India, respectively, and compares with documented results computed by the source-based approach. Several insights regarding the procedure of conducting PSHA have also been obtained, which could be useful for future seismic-hazard studies.

A new parallel overlapped domain decomposition method for nonlinear dynamic finite element analysis

In this paper a new parallel algorithm for nonlinear transient dynamic analysis of large structures has been presented. An unconditionally stable Newmark-beta method (constant average acceleration technique) has been employed for time integration. The proposed parallel algorithm has been devised within the broad framework of domain decomposition techniques. However, unlike most of the existing parallel algorithms (devised for structural dynamic applications) which are basically derived using nonoverlapped domains, the proposed algorithm uses overlapped domains. The parallel overlapped domain decomposition algorithm proposed in this paper has been formulated by splitting the mass, damping and stiffness matrices arises out of finite element discretisation of a given structure. A predictor-corrector scheme has been formulated for iteratively improving the solution in each step. A computer program based on the proposed algorithm has been developed and implemented with message passing interface as software development environment. PARAM-10000 MIMD parallel computer has been used to evaluate the performances. Numerical experiments have been conducted to validate as well as to evaluate the performance of the proposed parallel algorithm. Comparisons have been made with the conventional nonoverlapped domain decomposition algorithms. Numerical studies indicate that the proposed algorithm is superior in performance to the conventional domain decomposition algorithms. (C) 2003 Elsevier Ltd. All rights reserved.

Calculating the Effect of Uneven Terrain on Glide Path Signals

A method for calculating the bends in the glide slope due to uneven terrain is presented. A computer program written for the purpose enables the calculation of the difference in depth of modulation (DDM) at any point, taking into account the effect of uneven terrain. Results are presented for a hypothetical case of a hill in front of the runway. The program enables us to predict the glide slope bends due to irregular terrain, so that proper selection of glide slope antenna location can be made.

Root cause diagnostics using temporal data mining

A method, system, and computer program product for fault data correlation in a diagnostic system are provided. The method includes receiving the fault data including a plurality of faults collected over a period of time, and identifying a plurality of episodes within the fault data, where each episode includes a sequence of the faults. The method further includes calculating a frequency of the episodes within the fault data, calculating a correlation confidence of the faults relative to the episodes as a function of the frequency of the episodes, and outputting a report of the faults with the correlation confidence.

A mode-shape classification technique for robust speech rate estimation and syllable nuclei detection

Acoustic feature based speech (syllable) rate estimation and syllable nuclei detection are important problems in automatic speech recognition (ASR), computer assisted language learning (CALL) and fluency analysis. A typical solution for both the problems consists of two stages. The first stage involves computing a short-time feature contour such that most of the peaks of the contour correspond to the syllabic nuclei. In the second stage, the peaks corresponding to the syllable nuclei are detected. In this work, instead of the peak detection, we perform a mode-shape classification, which is formulated as a supervised binary classification problem - mode-shapes representing the syllabic nuclei as one class and remaining as the other. We use the temporal correlation and selected sub-band correlation (TCSSBC) feature contour and the mode-shapes in the TCSSBC feature contour are converted into a set of feature vectors using an interpolation technique. A support vector machine classifier is used for the classification. Experiments are performed separately using Switchboard, TIMIT and CTIMIT corpora in a five-fold cross validation setup. The average correlation coefficients for the syllable rate estimation turn out to be 0.6761, 0.6928 and 0.3604 for three corpora respectively, which outperform those obtained by the best of the existing peak detection techniques. Similarly, the average F-scores (syllable level) for the syllable nuclei detection are 0.8917, 0.8200 and 0.7637 for three corpora respectively. (C) 2016 Elsevier B.V. All rights reserved.

Numerical simulation of an adaptive optics system with laser propagation in the atmosphere

A comprehensive model of laser propagation in the atmosphere with a complete adaptive optics (AO) system for phase compensation is presented, and a corresponding computer program is compiled. A direct wave-front gradient control method is used to reconstruct the wave-front phase. With the long-exposure Strehl ratio as the evaluation parameter, a numerical simulation of an AO system in a stationary state with the atmospheric propagation of a laser beam was conducted. It was found that for certain conditions the phase screen that describes turbulence in the atmosphere might not be isotropic. Numerical experiments show that the computational results in imaging of lenses by means of the fast Fourier transform (FFT) method agree well with those computed by means of an integration method. However, the computer time required for the FFT method is 1 order of magnitude less than that of the integration method. Phase tailoring of the calculated phase is presented as a means to solve the problem that variance of the calculated residual phase does not correspond to the correction effectiveness of an AO system. It is found for the first time to our knowledge that for a constant delay time of an AO system, when the lateral wind speed exceeds a threshold, the compensation effectiveness of an AO system is better than that of complete phase conjugation. This finding indicates that the better compensation capability of an AO system does not mean better correction effectiveness. (C) 2000 Optical Society of America.

Effects of Noise and Detection Error in a Dynamic Adaptive Optics System

It is well known that noise and detection error can affect the performances of an adaptive optics (AO) system. Effects of noise and detection error on the phase compensation effectiveness in a dynamic AO system are investigated by means of a pure numerical simulation in this paper. A theoretical model for numerically simulating effects of noise and detection error in a static AO system and a corresponding computer program were presented in a previous article. A numerical simulation of effects of noise and detection error is combined with our previous numeral simulation of a dynamic AO system in this paper and a corresponding computer program has been compiled. Effects of detection error, readout noise and photon noise are included and investigated by a numerical simulation for finding the preferred working conditions and the best performances in a practical dynamic AO system. An approximate model is presented as well. Under many practical conditions such approximate model is a good alternative to the more accurate one. A simple algorithm which can be used for reducing the effect of noise is presented as well. When signal to noise ratio is very low, such method can be used to improve the performances of a dynamic AO system.