Genomic splice site prediction algorithm based on nucleotide sequence pattern for RNA viruses

Splice site prediction on an RNA virus has two potential difficulties seriously degrading the performance of most conventional splice site predictors. One is a limited number of strains available for a virus species and the other is the diversified sequence patterns around the splice sites caused by the high mutation frequency. To overcome these two difficulties, a new algorithm called Genomic Splice Site Prediction (GSSP) algorithm, was proposed for splice site prediction of RNA viruses. The key idea of the GSSP algorithm was to characterize the interdependency among the nucleotides and base positions based on the eigen-patterns. Identified by a sequence pattern mining technique, each eigen-pattern specified a unique composition of the base positions and the nucleotides occurring at the positions. To remedy the problem of insufficient training data due to the limited number of strains for an RNA virus, a cross-species strategy was employed in this study. The GSSP algorithm was shown to be effective and superior to two conventional methods in predicting the splice sites of five RNA species in the Orthomyxoviruses family. The sensitivity and specificity achieved by the GSSP algorithm was higher than 99 and 94%, respectively, for the donor sites, and was higher than 96 and 92%, respectively, for the acceptor sites. Supplementary data associated with this work are freely available for academic use at http://homepage.ntu.edu.tw/ approximately d91548013/.     

Atomic scale control of catalytic process in oxidation of Pb thin films

Using scanning tunneling microscopy (STM), we demonstrate that oxidation on Pb films is greatly enhanced by atomic Cs catalysts. With only a minute concentration of isolated Cs substitutional atoms in the surface layer (0.004 ML coverage), surface oxidation rates are greatly enhanced. First-principles density functional theory (DFT) calculations reveal that a substitutional Cs atom strongly increases O₂ binding on the surface. Then, with additional oxygen exposure this substitutional Cs-initiated oxidation process results in growth of PbO layers in an auto-catalytic manner. Furthermore, we investigate the role of temperature in the oxidation of the Pb films with and without Cs, and we explore the overall morphology of the resultant oxide layers.     

Flexible optitrode for localized light delivery and electrical recording

We present optitrode, a miniaturized flexible probe for integrated, localized light delivery and electrical recording. This device features an annular light guide with transparent polymer and fused silica layers surrounding a twisted-wire tetrode. We have developed a novel fabrication process, V-groove guided capillary assembly, to achieve high-precision, coaxial alignment of the various layers of the device. Optitrode with a length-to-diameter ratio ～500 (5 cm long, 100 μm diameter) has been fabricated, and both the electrical and optical functions have been characterized. The prototype can deliver 11% (110 mW) of the total laser power under abrupt bending angle ～25°.     

Kinetic analysis of the hydrogen oxidation reaction on Pt-black/Nafion electrode

The hydrogen oxidation reaction on Pt-black/Nafion electrode was investigated using a rotating disk electrode and cyclic voltammetry technique. The voltammetric results demonstrated that the electrode can be prepared with good reproducibility and that Pt-black particles without direct contact with Nafion were still electrochemically active in taking part in the H-adsorption/desorption process. For hydrogen oxidation, the limiting current density was reduced by the presence of Nafion coating. The H₂ diffusion resistance in Nafion film was avoided when the film thickness was less than 0.2 μm for a Pt-black loading of 20 μg. Moreover, the uncertainties in the kinetic results were discussed.     

Morphological development in water assisted injection molded polyethylene/polyamide‐6 blends

Water assisted injection molding (WAIM) has gradually become one of the most important polymer processing methods for making hollowed parts. This study examined the morphological development in water assisted injection molded high density polyethylene (HDPE)/polyamide‐6 (PA‐6) blends. Samples for microscopic observation were prepared by an 80‐ton injection‐molding machine equipped with a tube cavity and with a water injection unit. A distinct skin layer, core region, and channel layer were observed across the thickness. The shape and size of the dispersed phase depended on the position both across the part thickness and along the flow direction. Small and large particles coexisted in the skin and channel layers, indicating that both coalescence and disintegration of the dispersed phase occurred in these layers. High water pressures were found to mold parts with smaller polyamide particle distributions. Additionally, the morphology of water assisted injection molded parts was compared to that of gas assisted injection molded products. It was found that water molded parts exhibit a smaller polyamide particle distribution than their gas counterparts. Copyright © 2010 John Wiley & Sons, Ltd.     

Catalytic asymmetric Staudinger reactions to form beta-lactams: an unanticipated dependence of diastereoselectivity on the choice of the nitrogen substituent

There are relatively few methods for the catalytic asymmetric synthesis of beta-lactams, and those that have been reported are generally cis selective. This communication describes the first catalytic enantioselective Staudinger reactions that preferentially furnish trans beta-lactams (trans = relationship of Ph to R1). The key to this method is the use of an N-triflyl protecting group for the imine. Along with serving as interesting targets in their own right, N-triflyl beta-lactams readily react with nucleophiles to generate useful families of compounds, such as gamma-amino alcohols and beta-amino acids.     

Synthesis and redox behavior of biferrocenyl-functionalized ruthenium(II) terpyridine gold clusters

Spectroscopic and electrochemical characterizations of ferrocene- and biferrocene-functionalized terpyridine octanethiolate monolayer-protected clusters were investigated and reported. The electrochemical measurements of Ru2+ coordinated with 4'-ferrocenyl-2,2':6',2' '-terpyridine and 4'-biferrocenyl-2,2':6',2' '-terpyridine complexes were dominated by the Ru2+/Ru3+ redox couple (E(1/2) at approximately 1.3 V), Fe(2+)/Fe(3+) redox couples (E(1/2) from approximately 0.6 to approximately 0.9 V), and terpy/terpy-/terpy2- redox couples (E(1/)(2) at ca. -1.2 and ca. -1.4 V). The substantial appreciable variations detected in the Ru2+/Ru3+ and Fe2+/Fe3+ oxidation potentials indicate that there is an interaction between the Ru2+ and Fe2+ metal centers. The coordination of the Ru2+ metal center with 4'-ferrocenyl-2,2':6',2' '-terpyridine and 4'-biferrocenyl-2,2':6',2' '-terpyridine leads to an intense 1[(d(pi)Fe)6] --> 1[d(pi)Fe)5(pi*terpyRu)1] transition in the visible region. The 1[(d(pi)Fe)6] -->1[d(pi)Fe)5(pi*terpyRu)1] transition observed at approximately 510 nm revealed that there was a qualitative electronic coupling between metal centers. The coordination of the Ru2+ transition metal center lowers the energy of the pi*terpy orbitals, causing this transition.     

Micellar Formation Study of Crown Ether Surfactants

Fluorescence probe and nuclear magnetic resonance (NMR) methods were employed to investigate the micellation of prepared crown ether surfactants, e.g. decyl 15‐crown‐5 and decyl 18‐crown‐6. Pyrene was employed as the fluorescence probe to evaluate the critical micellar concentration (CMC) of these surfactants in aqueous solutions while spin lattice relaxation times (T₁) and chemical shifts of H‐1 NMR were applied in non‐aqueous solutions. Decyl 15‐crown‐5 with lower CMC forms micelles much easier than decyl 18‐crown‐6 with higher CMC in aqueous solutions, whereas decyl 18‐crown‐6 forms micelles easier than decyl 15‐crown‐5 in nonaqueous solutions. Comparison of the CMC of crown ether surfactants and other polyoxyethylene surfactants such as decylhexaethylene glycol was made. Effects of salts and solvents on the micellar formation were also investigated. In general, additions of both alkali metal salts and polar organic solvents into the aqueous surfactant solutions increased in the CMC of these surfactants. The formation of micelles in organic solvents such as methanol and acetonitrile was successfully observed by the NMR method while it was difficult to study these surfactants in organic solutions by the pyrene fluorescence probe method. The NMR study revealed that the formation of micelles resulted in the decrease in all H‐1 spin lattice relaxation times (T₁) of hydrophobic groups, e.g. CH₃ and CH₂, and hydrophilic group OCH₂ of these surfactants. However, upon the micellar formation, the H‐1 chemical shifts (δ) of these surfactant hydrophobic groups were found to shift to downfield (increased δ) while the chemical shift of the hydrophilic group OCH₂ moved to up‐field. Comparison of the spin lattice relaxation time and H‐1 chemical shift methods was also made and discussed.     

Determining eight colorants in milk beverages by capillary electrophoresis

Milk beverages are popular because of their high nutritional value, and milk products that are enhanced with various fruit flavors are especially in high demand in Asia. Colorants are usually added to fruit flavored milk in order to increase its attraction and appearance, therefore, the detection and measurement of colorants in this type of beverage are relatively important for health issue reasons. Carminic acid, a natural colorant, along with tartrazine, Fast green FCF, Brilliant blue FCF, Allura Red AC, Indigo carmine, Sunset yellow FCF, and New coccine, which are seven different synthetic food colorants, are commonly used as food additives, therefore, this study would focus on the development of an analytical method for the detection of these common colorants in milk beverages. A high efficiency capillary electrophoresis separation method was finished by a pH 10.0 running buffer containing 7.0 mM beta-cyclodextrin, and the eight colorants were separated with baseline resolution within 9 min. In order to reduce the matrix interference resulting from the constituents of milk, a suitable polyamide column solid-phase extraction (SPE) was also investigated for milk sample pretreatment. The combination of the simple SPE pretreatment and the fast separation method of capillary electrophoresis, was able to determine successfully without matrix interference the content of these colorant additives in commercial milk beverages. The recoveries of the eight food colorants in milk beverages were better than 85% and the detection limits were also lower than 0.5 microg/ml by the developed method.     

Access to the syntheses of sydnonyl-substituted α,β-unsaturated ketones and 1,3-dihydro-indol-2-ones by modified Knoevenagel reaction

A convenient method for the preparation of sydnonyl-substituted α, β-unsaturated ketones, based on Knoevenagel condensation, is presented. Although well known, this reaction has never been utilized in the condensation involving sydnone derivatives. Thus, 3-aryl-4-formylsydnones (1) are reacted with active methylene compounds such as acetylacetone (2a), ethyl acetoacetate (2b), diethyl malonate (2c), malononitrile (4a), ethyl cyanoacetate (4b) and cyanoacetamide (4c) by modified Knoevenagel condensation to afford multifunctional derivatives. Also, sydnonyl-substituted 1,3-dihydro-indol-2-one derivatives 10 were synthesized successfully by condensing 3-aryl-4-formylsydnones (1) with oxindoles 9.