Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

Aberration measurement of projection optics in lithographic tools based on two-beam interference theory

The degradation of image quality caused by aberrations of projection optics in lithographic tools is a serious problem in optical lithography. We propose what we believe to be a novel technique for measuring aberrations of projection optics based on two-beam interference theory. By utilizing the partial coherent imaging theory, a novel model that accurately characterizes the relative image displacement of a fine grating pattern to a large pattern induced by aberrations is derived. Both even and odd aberrations are extracted independently from the relative image displacements of the printed patterns by two-beam interference imaging of the zeroth and positive first orders. The simulation results show that by using this technique we can measure the aberrations present in the lithographic tool with higher accuracy. (c) 2006 Optical Society of America.

Spatiotemporal segmentation based on two-dimensional spatiotemporal entropic thresholding

A novel spatiotemporal segmentation technique is further developed for extracting uncovered background and moving objects from the image sequences, then the following motion estimation is performed only on the regions corresponding to moving objects. The frame difference contrast (FCON) and local variance contrast (LCON), which are related to the temporal and spatial homogeneity of the image sequence, are selected to form the 2-D spatiotemporal entropy. Then the spatial segmentation threshold is determined by maximizing the 2-D spatiotemporal entropy, and the temporal segmentation point is selected to minimize the complexity measure for image sequence coding. Since both temporal and spatial correlation of an image sequence are exploited, this proposed spatiotemporal segmentation technique can further be used to determine the positions of reference frames adaptively, hence resulting in a low bit rate. Experimental results show that this segmentation-based coding scheme is more efficient than usual fixed-size coding algorithms. (C) 1997 Society of Photo-Optical Instrumentation Engineers.

Gain and noise figure of a double-pass waveguide amplifier based on Er/Yb-doped phosphate glass

A waveguide amplifier is fabricated by Ag+-Na+ two-step ion exchange on Er/Yb-doped phosphate glass. The spectroscopic performance of glass and the properties of channel waveguide are characterized. A double-pass configuration is adopted to measure the gain and noise figure (NF) of the waveguide amplifier, and the comparison of gain and NF for the single and double-pass configuration of the waveguide amplifier is presented. The results show that the double-pass configuration can make the gain increase from 8.8dB (net gain 2.2dB/cm) of the single-pass one to 14.6 dB (net gain 3.65 dB/cm) for small input power at 1534 nm, and the NF are all lower than 5.5dB for both the configurations.

The junction temperature and forward voltage relationship of GaN-based laser diode

In GaAs-based light-emitting diode (LED) or laser diode (LD), the forward voltage (V) will decrease linearly with the increasing junction temperature (T). This can be used as a convenient method to measure the junction temperature. In GaN-based LED, the relationship is linear too. But in GaN-based LD, the acceptor M (g) in p-GaN material can not ionize completely at-room temperature, and the carrier density will change with temperature. But we find finally that, this change won't lead to a nonlinear relationship of V-T. Our experiments show that it is Linear too.

Light-propagation characteristics of photonic crystal waveguide based on SOI materials at different polarized states

Straight single-line defect optical waveguides in photonic crystal slabs are designed by the plane wave expansion method and fabricated into silicon-on-insulator (SOI) wafer by 248-nm deep UV lithography. We present an efficient way to measure the light transmission spectrum of the photonic crystal waveguide (PhC WG) at given polarization states. By employing the Mueller/Stokes method, we measure and analyse the light propagation properties of the PhC WG at different polarized states. It is shown that experimental results are in agreement with the simulation results of the three-dimensional finite-difference-time-domain method.

Experiment on Qinghai-Tibet railroad subgrade temperature monitoring based on FBG sensors

Qinghai-Tibet Railway is the longest and highest plateau railway in the world. A long term monitoring system of the stability of the subgrade in the permafrost regions should be put forward immediately to prevent damage to the railway. As it's very difficult to set up the long-distance automatic monitoring system which contains a lot of measure points along the 550 kilometers railway in the permafrost area, we present a subgrade temperature monitor system based on fiber Bragg grating (FBG). In this paper the principles of the FBG was presented, and the feasibility of the FBG sensors in the permafrost area of Qinghai-Tibet plateau was analysized. We embedded fifteen FBG temperature sensors and thermal resistance temperature sensors. A contrast experiment is made while the two kinds of sensors are arranged in the same position. The result of the experiment shows that the accuracy of the FBG temperature sensors is less than 0.1 degrees C. and the FBG sensors can do well in the measurement of pattern which the temperature varies with the depth of the permafrost soil. The result also shows the stability of the FBG sensors in the bad environmental condition of Qinghai-Tibet plateau, which proves the feasibility of the application of FBG sensors and our monitoring system on the Qinghai-Tibet railway.

semantic oriented ontology cohesion metrics for ontology-based systems

Ontologies play a core role to provide shared knowledge models to semantic-driven applications targeted by Semantic Web. Ontology metrics become an important area because they can help ontology engineers to assess ontology and better control project management and development of ontology based systems, and therefore reduce the risk of project failures. In this paper, we propose a set of ontology cohesion metrics which focuses on measuring (possibly inconsistent) ontologies in the context of dynamic and changing Web. They are: Number of Ontology Partitions (NOP), Number of Minimally Inconsistent Subsets (NMIS) and Average Value of Axiom Inconsistencies (AVAI). These ontology metrics are used to measure ontological semantics rather than ontological structure. They are theoretically validated for ensuring their theoretical soundness, and further empirically validated by a standard test set of debugging ontologies. The related algorithms to compute these ontology metrics also are discussed. These metrics proposed in this paper can be used as a very useful complementarity of existing ontology cohesion metrics.

THEORETICAL AND EXPERIMENTAL STUDY OF POLARIZATION CHARACTERISTICS OF POLARIZATION MAINTAINING FIBER BASED ON WAVELENGTH-SWEEPING MODULATION

We analyze theoretically the polarization characteristics of polarization maintaining fiber and study the basic measurement principles of beat length and polarization extinction ratio of this kind of optical fiber. According, to the dependence of the phase difference between two orthogonally polarized modes (denoted Os HE(11)(x) and HE(11)(y)) transmitted in the polarization maintaining fiber on the light wavelength, we propose the wavelength-sweeping modulation method to measure the beat length and the model birefringence. Based on this technique, the hew length and polarization extinction ratio of the PANDA polarization maintaining fibers (PMFs) (provided by Yangtze Optical Fiber and Cable Company, Wuhan, China) were investigated in detail. Experimental results show good consistent with the theoretical ones. We find that this method shows high measurement precision with the advantages of clear measurement principle and easy to operate. 2010 Wiley Periodicals, Inc. Microwave Opt Technol Lett 52: 1466-1469, 2010; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.25244

Anticancer Drug-DNA Interactions Measured Using a Photoinduced Electron-Transfer Mechanism Based on Luminescent Quantum Dots

A sensing system based on the photoinduced electron transfer of quantum dots (QDs) was designed to measure the interaction of anticancer drug and DNA, taking mitoxantrone (MTX) as a model drug. MTX adsorbed on the surface of QDs can quench the photoluminescence (PL) of QDs through the photoinduced electron-transfer process; and then the addition of DNA will bring the restoration of QDs PL intensity, as DNA can bind with MTX and remove it from QDs. Sensitive detection of MTX with the detection limit of 10 nmol L-1 and a linear detection range from 10 nmol L-1 to 4.5 mu mol L-1 was achieved. The dependence of PL intensity on DNA amount was successfully utilized to investigate the interactions between MTX and DNA. Both the binding constants and the sizes of binding site of MTX-DNA interactions were calculated based on the equations deduced for the PL recovery process. The binding constant obtained in our experiment was generally consistent with previous reports. The sensitive and speedy detection of MTX as well as the avoidance of modification or immobilization process made this system suitable and promising in the drug-DNA interaction studies.

Chemical environment code and measure of molecular similarity

A new scheme for the code of chemical environments of compounds is described in this paper, and three molecular similarity methods have been used to select nearest neighbors from four different types of probe compounds. One of the methods is based on the C-13 NMR spectra. The second method is based on the code of chemical environments and molecular topological index A(x). The third approach, i.e. the Tanimoto coefficient, is also based on the code of chemical environments, but not to use the topological index. Five nearest neighbors for each probe compound using these three molecular similarity methods were determined and taken from the database of 7309 structures. The results indicate that the scheme of the chemical environment code and the method for similarity measure of intermolecules suggested in this study are reasonable. (C) 1998 Published by Elsevier Science Ltd. All rights reserved.