Hybrid particle swarm optimization and tabu search approach for selecting genes for tumor classification using gene expression data

Gene expression data are characterized by thousands even tens of thousands of measured genes on only a few tissue samples. This can lead either to possible overfitting and dimensional curse or even to a complete failure in analysis of microarray data. Gene selection is an important component for gene expression-based tumor classification systems. In this paper, we develop a hybrid particle swarm optimization (PSO) and tabu search (HPSOTS) approach for gene selection for tumor classification. The incorporation of tabu search (TS) as a local improvement procedure enables the algorithm HPSOTS to overleap local optima and show satisfactory performance. The proposed approach is applied to three different microarray data sets. Moreover, we compare the performance of HPSOTS on these datasets to that of stepwise selection, the pure TS and PSO algorithm. It has been demonstrated that the HPSOTS is a useful tool for gene selection and mining high dimension data.     

A parallel tabu search for conformational energy optimization of oligopeptides

We have developed and implemented a tabu search heuristic (TS) to determine the best energy minimum for oligopeptides. Our test molecule was Met‐enkephalin, a pentapetide that over the years has been used as a validation model for many global optimizers. The test potential energy function was ECEPP/3. Our tabu search implementation is based on assigning integer values to the variables to be optimized, and in facilitating the diversification and intensification of the search. The final output from the TS is treated with a local optimizer, and our best result competes both in quality and CPU time with those reported in the literature. The results indicate that TS is an efficient algorithm for conformational searches. We present a parallel TS version along with experimental results that show that this algorithm allows significant increases in speed. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 147–156, 2000     

A new room-temperature deposition technique for optical coatings

We describe a new coating method Laminar Flow Coating (LFC) technique developed to obtain highly reflective (HR) laser damage resistant sol-gel multidielectric coatings. Such coatings are used in high-power lasers for inertial confinement fusion experiments (ICF). This technique uses substrates in an upside-down position and a travelling wave of coating solution is transported with a laminar motion under the substrate surface with a tubular dispense unit. This creates a thin-film coating by solvent evaporation. Satisfactory results have been obtained on 20-cm square glass substrates regarding the optical performances, the thickness uniformity, the edge-effects and the laser damage resistance. This deposition technique combines the advantages of both classical techniques: the non-exclusive substrate geometry such as in dip-coating and the small solution consumption such as in spin-coating.The association of sol-gel colloidal suspensions and LFC coating process has been demonstrated as a promising way to produce inexpensive specific optical coatings [1].     

A comparison of heuristic search algorithms for molecular docking

This paper describes the implementation and comparison of four heuristic search algorithms (genetic algorithm, evolutionary programming, simulated annealing and tabu search) and a random search procedure for flexible molecular docking. To our knowledge, this is the first application of the tabu search algorithm in this area. The algorithms are compared using a recently described fast molecular recognition potential function and a diverse set of five protein–ligand systems. Statistical analysis of the results indicates that overall the genetic algorithm performs best in terms of the median energy of the solutions located. However, tabu search shows a better performance in terms of locating solutions close to the crystallographic ligand conformation. These results suggest that a hybrid search algorithm may give superior results to any of the algorithms alone.     

Electrical and optical properties of ceramic–polymer nanocomposite coatings

Transparent, conductive composite coatings were fabricated from suspensions of poly(vinyl acetate‐acrylic) (PVAc‐co‐acrylic) copolymer latices (50–600 nm) and nanosized antimony‐doped tin oxide (ATO) particles (～15 nm). The suspensions were deposited as coatings onto poly(ethylene terephthalate) substrates and dried at 50 °C. Microstructure studies using field emission scanning electron microscopy and tapping‐mode atomic force microscopy (TMAFM) indicated that the latex particles coalesced during drying and forced the ATO particles to segregate into the boundaries between the latex particles. Low phase contrast was observed with TMAFM; this result was consistent with the presence of PVAc‐co‐acrylic in the ATO‐rich phase of the composite. The conductivity of the composite coatings followed a percolation power‐law equation, with the percolation threshold between 0.05 and 0.075 volume fractions of ATO and the critical conductivity exponent ranging from 1.34 to 2.32. The highest direct‐current conductivity of the composite coatings was around 10^?2 S/cm. The optical transmittance and scattering behavior of the coatings were also investigated. Compared with the PVAc‐co‐acrylic coating, the composite coatings had lower transparency because of the Rayleigh scattering. The transparency of the composite coatings was improved by a reduction in the coating thickness. The best transparency for the coatings with a direct‐current conductivity of approximately 10^?2 S/cm was around 85% at a wavelength of 600 nm. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1744–1761, 2003     

PRO_LIGAND: An approach to de novo molecular design. 3. A genetic algorithm for structure refinement

Summary Recently, the development of computer programs which permit the de novo design of molecular structures satisfying a set of steric and chemical constraints has become a burgeoning area of research and many operational systems have been reported in the literature. Experience with PRO_LIGAND—the de novo design methodology embodied in our in-house molecular design and simulation system PRO-METHEUS—has suggested that the addition of a genetic algorithm (GA) structure refinement procedure can add value to an already useful tool. Starting with the set of designed molecules as an initial population, the GA can combine features from both high- and low-scoring structures and, over a number of generations, produce individuals of better score than any of the starting structures. This paper describes how we have implemented such a procedure and demonstrates its efficacy in improving two sets of molecules generated by different de novo design projects.     

Development of soft X-ray multilayer laminar-type plane gratings and varied-line-spacing spherical grating for flat-field spectrograph in the 1–8 keV region

W/C and Co/SiO₂ multilayer laminar-type holographic plane gratings (groove density 1/σ = 1200 lines/mm) in the 1–8 keV region are developed. For the Co/SiO₂ grating the diffraction efficiencies of 0.41 and 0.47 at 4 and 6 keV, respectively, and for the W/C grating 0.38 at 8 keV are observed. Taking advantage of the outstanding high diffraction efficiencies into practical soft X-ray spectrographs a Mo/SiO₂ multilayer varied-line-spacing (VLS) laminar-type spherical grating (1/σ = 2400 lines/mm) is also developed for use with a flat field spectrograph in the region of 1.7 keV. For the Mo/SiO₂ multilayer grating the diffraction efficiencies of 0.05–0.20 at 0.9–1.8 keV are observed. The FWHMs of the measured line profiles of Hf-Mα₁(1644.6 eV), Si-Kα₁(1740.0 eV), and W-Mα₁ (1775.4 eV) are 13.7 eV, 8.0 eV, and 8.7 eV, respectively.     

Phase cycling schemes for two-dimensional optical spectroscopy with a pump–probe beam geometry

We present phase cycling schemes for two-dimensional (2D) optical spectroscopy with a pump–probe beam geometry. We detail the theoretical derivation on how the phase cycling schemes measure a pure absorptive 2D spectrum. The ‘rotating frame’ is inherent in such phase locked phase cycling experiments, and can increase the efficiency of the experiment by reducing the number of data points needed to be collected. 2D optical spectra are simulated for the phase cycling pump–probe experiment by solving the Liouville equation that describes the system-field interaction using a non-perturbative method.     

An emulsifier‐free core–shell polyacrylate/diacetone acrylamide emulsion with nano‐SiO2 for room temperature curable waterborne coatings

An emulsifier‐free core–shell polyacrylate emulsion, containing nano‐SiO₂ nanoparticles in the core and diacetone acrylamide (DAAM) in the shell, has been successfully prepared by emulsifier‐free seeded emulsion polymerization. The effects of reaction temperature, dropping time, nano‐SiO₂ and initiator contents, and variation of the composition of core monomers on the amount of coagulum, particle size, and monomer conversion have been investigated. The particle morphology and the distribution of emulsion particles have been measured by transmission electron microscopy (TEM) and dynamic light scattering. The keto‐carbonyl groups on the surface of the polyacrylate emulsion nanoparticles reacted with adipic dihydrazide (ADH) to form a film with a cross‐linked network structure at room temperature. Therefore, the emulsifier‐free core–shell emulsion could be used as a two‐component room temperature curable waterborne coating. It was also found that the properties of the coating were clearly superior after using the cross‐linker. Copyright © 2009 John Wiley & Sons, Ltd.     

Retrotransposon‐microsatellite amplified polymorphism,an electrophoretic approach for studying genetic variability among Schistosoma japonicum geographical isolates

In the present study, retrotransposon‐microsatellite amplified polymorphism (REMAP) was used to examine genetic variability among Schistosoma japonicum isolates from different endemic provinces in mainland China, using S. japonicum from Japan and the Philippines for comparison. Of the 50 primer combinations screened, eight produced highly reproducible REMAP fragments. Using these primers, 190 distinct DNA fragments were generated in total, of which 147 (77.37%) were polymorphic, indicating considerable genetic variation among the 43 S. japonicum isolates examined. The percentage of polymorphic bands (PPB) among S. japonicum isolates from mainland China, Japan, and the Philippines was 77.37%; PPB values of 18.42% and 53.68% were found among isolates from southwestern (SW) China and the lower Yangtze/Zhejiang province in eastern (E) China, respectively. Based on REMAP profiles, unweighted pair‐group method with arithmetic averages (UPGMA) dendrogram analysis revealed that all of the S. japonicum samples grouped into three distinct clusters: parasites from mainland China, Japan, and the Philippines were clustered in each individual clade. Within the mainland China cluster, SW China isolates (from Sichuan and Yunnan provinces) grouped together, whereas worms from E China (Zhejiang, Anhui, Jiangxi, Jiangsu, Hunan, and Hubei provinces) grouped together. These results demonstrated that the REMAP marker system provides a reliable electrophoretic technique for studying genetic diversity and population structures of S. japonicum isolates from mainland China, and could be applied to other pathogens of human and animal health significance.