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.     

Interface and defects engineering for multilayer laser coatings

High-reflective multilayer laser coatings are widely used in advanced optical systems from high power laser facilities to high precision metrology systems. However, the real interface quality and defects will significantly affect absorption/scattering losses and laser induced damage thresholds of multilayer coatings. With the recent advances in the control of coating design and deposition processes, these coating properties can be significantly improved when properly engineered the interface and defects. This paper reviews the recent progress in the physics of laser damage, optical losses and environmental stability involved in multilayer reflective coatings for high power nanosecond near-infrared lasers. We first provide an overview of the layer growth mechanisms, ways to control the microstructures and reduce layer roughness, as well as the nature of defects which are critical to the optical loss and laser induced damage. Then an overview of interface engineering based on the design of coating structure and the regulation of deposition materials reveals their ability to improve the laser induced damage threshold, reduce the backscattering, and realize the desirable properties of environmental stability and exceptional multifunctionality. Moreover, we describe the recent progress in the laser damage and scattering mechanism of nodule defects and give the approaches to suppress the defect-induced damage and scattering of the multilayer laser coatings. Finally, the present challenges and limitations of high-performance multilayer laser coatings are highlighted, along with the comments on likely trends in future.     

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.     

Design of a novel optical sensor for determination of trace amounts of copper by UV–visible spectrophotometry in real samples

A new optical chemical sensor is established for sensitive and selective spectrophotometric detection of copper based on the immobilization of 3‐(2‐methyl‐2,3‐dihydro‐1,3‐benzothiezol‐2‐yl)‐2H‐chromen‐2‐one on a triacetylcellulose membrane. Copper ions react with the immobilized ligand and cause an increase in the absorption of the membrane at 550 nm in universal buffer solution at pH = 6. The effects of pH, indicator concentration and reaction time on the immobilization of the ligand were studied. This optode exhibits a linear range of 7.0 × 10^?7 to 1 × 10^?4 mol l^?1 of copper ion concentration with a limit of detection of 3.0 × 10^?7 mol l^?1. The response time of the newly designed optode is within 3 min. The effect of different possible interfering species was investigated and it was found that the sensor has very good selectivity. The proposed sensor benefits from advantages such as low cost, high stability, low detection limit, fast response time, reproducibility, relatively long lifetime, and good selectivity for Cu²⁺ ion determination among a large number of alkali, alkaline earth, transition and heavy metal ions. The sensor can readily be regenerated with thiourea solution and its response is reversible and reproducible (relative standard deviation < 1.4%). The proposed optode was applied successfully for the determination of Cu(II) in various samples.     

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.     

Promising photoluminescence optical approach for triiodothyronine hormone determination based on smart copper metal–organic framework nanoparticles

A copper metal–organic framework nanoparticles (Cu‐MOF‐NPs) synthesized via simple technique. The prepared Cu‐MOF‐NPs nanoparticles were further characterized using ¹H‐NMR, FE‐SEM/EDX and thermal study (DSC/TGA). The FE‐SEM/EDX, thermal analysis, and NMR spectrum data with the other analysis support the nano‐Cu‐MOF structure and the monomeric unit (n[Cu (AIP)₂(APY)(H₂O)₂].4H₂O) of Cu‐MOF‐NPs. The photoluminescence (PL) studies of triiodothyronine hormone (T3) based on the prepared Cu‐MOF‐NPs investigated. The results revealed that the Cu‐MOF‐NPs might be used as a biosensor in the determination of triiodothyronine hormone (T3) in biological fluids through a significant quenching of the photoluminescence intensity of Cu‐MOF‐NPs at excitation wavelength 492 nm. The calibration plot achieved over the concentration range 0.0–200.0 ng/dL T3 hormone with a correlation coefficient 0.996 and limit of detection (LOD) and quantification (LOQ) 0.198 and 0.60 ng/dL, respectively. The PL spectra are indicating that Cu‐MOF‐NPs has highly selective sensing properties for T3 hormone without interfering with other human many hormones types. This approach considered a promising analytical tool for early diagnosis of the cases of thyroid disease. The mechanism of quenching between the Cu‐MOF‐NPs, and T3 hormone studied. The mechanism was a dynamic type and obtained due to the energy transfer mechanism.     

An easily organic–inorganic hybrid optical sensor based on dithizone impregnation on mesoporous SBA‐15 for simultaneous detection and removal of Pb(II) ions from water samples: Response‐surface methodology

In this study, a novel organic–inorganic hybrid adsorbent for single‐step detection and removal of Pb(II) ions based on dithizone (DZ) anchored on mesoporous SBA‐15 was fabricated. The designed solid optical sensor revealed rapid colorimetric responses and high selectivity. Central composite design (CCD) combined with desirability function (DF) was applied to evaluate the interactive effects and optimization of important variables such as pH value, mesoporous SBA‐15 dosage, contact time and initial concentration of Pb(II) ions and optimum conditions for each of the factors were obtained 6.0, 25 mg, 30 min and 20 μg ml^{− 1}, respectively. This adsorbent or solid optical chemo sensor exhibited a linear range of 1.0 to 100.0 μg ml⁻¹ of Pb(II) ion concentration with a detection limit of 0.07 μg ml⁻¹. This adsorbent was applied to determine and remove the Pb(II) in spiked samples. Various isotherm models such as Langmuir, Freundlich, Temkin and Dubinin–Radushkevich were studied for fitting the experimental equilibrium data. Langmuir model was chosen as an efficient model. Various kinetic models such as pseudo‐first, second order intraparticle, diffusion models were studied for analysis of experimental adsorption data and the pseudo second order model was chosen as an efficient model.