A differential-geometric analysis of singularities of point trajectories of serial and parallel manipulators

In this paper, we present a differential-geometric approach to analyze the singularities of task space point trajectories of two and three-degree-of-freedom serial and parallel manipulators. At non-singular configurations, the first-order, local properties are characterized by metric coefficients, and, geometrically, by the shape and size of a velocity ellipse or an ellipsoid. At singular configurations, the determinant of the matrix of metric coefficients is zero and the velocity ellipsoid degenerates to an ellipse, a line or a point, and the area or the volume of the velocity ellipse or ellipsoid becomes zero. The degeneracies of the velocity ellipsoid or ellipse gives a simple geometric picture of the possible task space velocities at a singular configuration. To study the second-order properties at a singularity, we use the derivatives of the metric coefficients and the rate of change of area or volume. The derivatives are shown to be related to the possible task space accelerations at a singular configuration. In the case of parallel manipulators, singularities may lead to either loss or gain of one or more degrees-of-freedom. For loss of one or more degrees-of-freedom, ther possible velocities and accelerations are again obtained from a modified metric and derivatives of the metric coefficients. In the case of a gain of one or more degrees-of-freedom, the possible task space velocities can be pictured as growth to lines, ellipses, and ellipsoids. The theoretical results are illustrated with the help of a general spatial 2R manipulator and a three-degree-of-freedom RPSSPR-SPR parallel manipulator.

Role of TGF-beta beta and BMP7 in the pathogenesis of oral submucous fibrosis

To understand the molecular pathogenesis of oral submucous fibrosis (OSF), which is a chronic inflammatory disease, gene expression profiling was performed in 10 OSF tissues against 8 pooled normal tissues using oligonucleotide arrays. Microarray results revealed differential expression of 5288 genes (P < a parts per thousand currency sign 0.05 and fold change >= a parts per thousand yen 1.5). Among these, 2884 are upregulated and 2404 are downregulated. Validation employing quantitative real-time PCR and immunohistochemistry confirmed upregulation of transforming growth factor-beta beta 1 (TGF-beta beta 1), TGFBIp, THBS1, SPP1, and TIG1 and downregulation of bone morphogenic protein 7 (BMP7) in OSF tissues. Furthermore, activation of TGF-beta beta pathway was evident in OSF as demonstrated by pSMAD2 strong immunoreactivity. Treatment of keratinocytes and oral fibroblasts by TGF-beta beta confirmed the regulation of few genes identified in microarray including upregulation of connective tissue growth factor, TGM2, THBS1, and downregulation of BMP7, which is a known negative modulator of fibrosis. Taken together, these data suggest activation of TGF-beta beta signaling and suppression of BMP7 expression in the manifestation of OSF.

A gradient PCR-based screen for use in site-directed mutagenesis

Site-directed mutagenesis is widely used to study protein and nucleic acid structure and function. Despite recent advancements in the efficiency of procedures for site-directed mutagenesis, the fraction of site-directed mutants by most procedures rarely exceeds 50% on a routine basis and is never 100%. Hence it is typically necessary to sequence two or three clones each time a site-directed mutant is constructed. We describe a simple and robust gradient-PCR-based screen for distinguishing site-directed mutants from the starting, unmutated plasmid. The procedure can use either purified plasmid DNA or colony PCR, starting from a single colony. The screen utilizes the primer used for mutagenesis and a common outside primer that can be used for all other mutants constructed with the same template. Over 30 site-specific mutants in a variety of templates were successfully screened and all of the mutations detected were subsequently confirmed by DNA sequencing. A single base pair mismatch could be detected in an oligonucleotide of 36 bases. Detection efficiency was relatively independent of starting template concentration and the nature of the outside primer used. (C) 2003 Elsevier Science (USA). All rights reserved.

Development of recombinant coat protein antibody based IC-RT-PCR for detection and discrimination of sugarcane streak mosaic virus isolates from Southern India

Sugarcane streak mosaic virus (SCSMV), causes mosaic disease of sugarcane and is thought to belong to a new undescribed genus in the family Potyviridae. The coat protein (CP) gene from the Andhra Pradesh (AP) isolate of SCSMV (SCSMV AP) was cloned and expressed in Escherichia coli. The recombinant coat protein was used to raise high quality antiserum. The CP antiserum was used to develop an immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) based assay for the detection and discrimination of SCSMV isolates in South India. The sequence of the cloned PCR products encoding 3'untranslated region (UTR) and CP regions of the virus isolates from three different locations in South India viz. Tanuku (Coastal Andhra Pradesh), Coimbatore (Tamil Nadu) and Hospet (Karnataka) was compared with that of SCSMV AP The analysis showed that they share 89.4, 89.5 and 90% identity respectively at the nucleotide level. This suggests that the isolates causing mosaic disease of sugarcane in South India are indeed strains of SCSMV In addition, the sensitivity of the IC-RT-PCR was compared with direct antigen coating-enzyme linked immunosorbent assay (DAC-ELISA) and dot-blot immunobinding assays and was found to be more sensitive and hence could be used to detect the presence of virus in sugarcane breeding, germplasm centres and in quarantine programs.

Direct detection of Salmonella without pre-enrichment in milk, ice-cream and fruit juice by PCR against hilA gene

A novel PCR based assay was devised to specifically detect contamination of any Salmonella serovar in milk, fruit juice and ice-cream without pre-enrichment. This method utilizes primers against hilA gene which is conserved in all Salmonella serovars and absent from the close relatives of Salmonella. An optimized protocol, in terms time and money, is provided for the reduction of PCR contaminants from milk, ice-cream and juice through the use of routine laboratory chemicals. The simplicity, efficiency (time taken 3-4 h) and sensitivity (to about 5-10 CFU/ml) of this technique confers a unique advantage over other previously used time consuming detection techniques. This technique does not involve pre-enrichment of the samples or extensive sample processing, which was a pre-requisite in most of the other reported studies. Hence, this assay can be ideal for adoption, after further fine tuning, by food quality control for timely detection of Salmonella contamination as well as other food-borne pathogens (with species specific primers) in food especially milk, ice-cream and fruit juice. (C) 2011 Elsevier Ltd. All rights reserved.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.

On Convergence of Differential Evolution Over a Class of Continuous Functions With Unique Global Optimum

Differential evolution (DE) is arguably one of the most powerful stochastic real-parameter optimization algorithms of current interest. Since its inception in the mid 1990s, DE has been finding many successful applications in real-world optimization problems from diverse domains of science and engineering. This paper takes a first significant step toward the convergence analysis of a canonical DE (DE/rand/1/bin) algorithm. It first deduces a time-recursive relationship for the probability density function (PDF) of the trial solutions, taking into consideration the DE-type mutation, crossover, and selection mechanisms. Then, by applying the concepts of Lyapunov stability theorems, it shows that as time approaches infinity, the PDF of the trial solutions concentrates narrowly around the global optimum of the objective function, assuming the shape of a Dirac delta distribution. Asymptotic convergence behavior of the population PDF is established by constructing a Lyapunov functional based on the PDF and showing that it monotonically decreases with time. The analysis is applicable to a class of continuous and real-valued objective functions that possesses a unique global optimum (but may have multiple local optima). Theoretical results have been substantiated with relevant computer simulations.

Evidence for a thermally reversing window in bulk Ge–Te–Si glasses revealed by alternating differential scanning calorimetry

Experiments on Ge15Te85− x Si x glasses (2 ≤ x ≤ 12) using alternating differential scanning calorimetry (ADSC) indicate that these glasses exhibit one glass transition and two crystallization reactions upon heating. The glass transition temperature has been found to increase almost linearly with silicon content, in the entire composition tie-line. The first crystallization temperature (T c1) exhibits an increase with silicon content for x < 5; T c1 remains almost a constant in the composition range 5 < x ≤ 10 and it increases comparatively more sharply with silicon content thereafter. The specific heat change (ΔC p) is found to decrease with an increase in silicon content, exhibiting a minimum at x = 5 (average coordination number, r = 2.4); a continuous increase is seen in ΔC p with silicon concentration above x = 5. The effects seen in the variation with composition of T c1 and ΔC p at x = 5, are the specific signatures of the mean-field stiffness threshold at r = 2.4. Furthermore, a broad trough is seen in the enthalpy change (ΔH NR), which is indicative of a thermally reversing window in Ge15Te85− x Si x glasses in the composition range 2 ≤ x ≤ 6 (2.34 ≤ r ≤ 2.42).

Differential Reaction Kinetics, Cleavage Complex Formation, and Nonamer Binding Domain Dependence Dictate the Structure-Specific and Sequence-Specific Nuclease Activity of RAGs

During V(D)J recombination, RAG (recombination-activating gene) complex cleaves DNA based on sequence specificity. Besides its physiological function, RAG has been shown to act as a structure-specific nuclease. Recently, we showed that the presence of cytosine within the single-stranded region of heteroduplex DNA is important when RAGs cleave on DNA structures. In the present study, we report that heteroduplex DNA containing a bubble region can be cleaved efficiently when present along with a recombination signal sequence (RSS) in cis or trans configuration. The sequence of the bubble region influences RAG cleavage at RSS when present in cis. We also find that the kinetics of RAG cleavage differs between RSS and bubble, wherein RSS cleavage reaches maximum efficiency faster than bubble cleavage. In addition, unlike RSS, RAG cleavage at bubbles does not lead to cleavage complex formation. Finally, we show that the ``nonamer binding region,'' which regulates RAG cleavage on RSS, is not important during RAG activity in non-B DNA structures. Therefore, in the current study, we identify the possible mechanism by which RAG cleavage is regulated when it acts as a structure-specific nuclease. (C) 2011 Elsevier Ltd. All rights reserved.

A computational procedure to generate difference equations from differential equations

In this paper we have developed methods to compute maps from differential equations. We take two examples. First is the case of the harmonic oscillator and the second is the case of Duffing's equation. First we convert these equations to a canonical form. This is slightly nontrivial for the Duffing's equation. Then we show a method to extend these differential equations. In the second case, symbolic algebra needs to be used. Once the extensions are accomplished, various maps are generated. The Poincare sections are seen as a special case of such generated maps. Other applications are also discussed.

Enhancement of circular differential deflection of light in an optically active medium

In this letter, we investigate the circular differential deflection of a light beam refracted at the interface of an optically active medium. We show that the difference between the angles of deviation of the two circularly polarized components of the transmitted beam is enhanced manyfold near total internal reflection, which suggests a simple way of increasing the limit of detection of chiro-optical measurements. (C) 2012 Optical Society of America

Differential Diffractive Reflectance Modulation Sensing

We fabricated a reflectance based sensor which relies on the diffraction pattern generated from a bio-microarray where an underlying thin film structure enhances the diffracted intensity from molecular layers. The zero order diffraction represents the background signal and the higher orders represent the phase difference between the array elements and the background. By taking the differential ratio of the first and zero order diffraction signals we get a quantitative measure of molecular binding while simultaneously rejecting common mode fluctuations. We improved the signal-to-noise ratio by an order of magnitude with this ratiometric approach compared to conventional single channel detection. In addition, we use a lithography based approach for fabricating microarrays which results in spot sizes as small as 5 micron diameter unlike the 100 micron spots from inkjet printing and is therefore capable of a high degree of multiplexing. We will describe the real-time measurement of adsorption of charged polymers and bulk refractometry using this technique. The lack of moving parts for point scanning of the microarray and the differential ratiometric measurements using diffracted orders from the same probe beam allows us to make real-time measurements in spite of noise arising from thermal or mechanical fluctuations in the fluid sample above the sensor surface. Further, the lack of moving parts leads to considerable simplification in the readout hardware permitting the use of this technique in compact point of care sensors.