A novel kernel Fisher discriminant analysis: constructing informative kernel by decision tree ensemble for metabolomics data analysis

Large amounts of data from high-throughput metabolomics experiments become commonly more and more complex, which brings an enormous amount of challenges to existing statistical modeling. Thus there is a need to develop statistically efficient approach for mining the underlying metabolite information contained by metabolomics data under investigation. In the work, we developed a novel kernel Fisher discriminant analysis (KFDA) algorithm by constructing an informative kernel based on decision tree ensemble. The constructed kernel can effectively encode the similarities of metabolomics samples between informative metabolites/biomarkers in specific parts of the measurement space. Simultaneously, informative metabolites or potential biomarkers can be successfully discovered by variable importance ranking in the process of building kernel. Moreover, KFDA can also deal with nonlinear relationship in the metabolomics data by such a kernel to some extent. Finally, two real metabolomics datasets together with a simulated data were used to demonstrate the performance of the proposed approach through the comparison of different approaches.     

L-Proline Functionalized Polymers Prepared by RAFT Polymerization and Their Assemblies as Supported Organocatalysts

We have prepared a range of well-defined copolymers of styrene and L-proline functionalized styrene (5-11 kDa) using reversible addition-fragmentation chain transfer (RAFT) polymerization techniques and explored their use in supported catalysis. Upon deprotection of the L-proline functionalities, the solution self-assembly of these copolymers was investigated in mixed solvent systems. The resulting assemblies were characterized by dynamic light scattering, transmission electron microscopy (on graphene oxide substrates, along with cryo-TEM and tomography), and scanning electron microscopy. The application of these functional assemblies as supported catalysts for the aldol condensation reaction was explored using cyclohexanone and 4-nitrobenzaldehyde. The rate and selectivity of solution catalysis in our self-assembled system were comparable to those of L-proline, and a significant advantage of our system was that the polymer support could be utilized at lower catalyst loadings with comparable activity and also could be recycled a number of times while maintaining activity and selectivity.     

Ring-Opening Polymerization of γ-(4-Vinylbenzyl)-(L)-Glutamate N-Carboxyanhydride for the Synthesis of Functional Polypeptides

Introducing various pendant functional groups and building blocks of interest to polypeptides in a highly efficient, controlled manner is crucial to access polypeptide materials with desired structures and functions. In this study, we synthesized γ-(4-vinylbenzyl)-(L)-glutamate N-carboxyanhydride (VB-Glu-NCA), which was readily obtained and purified in large quantity. VB-Glu-NCA monomer was subsequently used for the synthesis of polypeptides containing conjugation-amenable, pendant vinyl functional groups. Controlled, living polymerizations of VB-Glu-NCA were achieved by using hexamethyldisilazane (HMDS) as the initiator, catalytic amounts of 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) as the co-catalyst, and nitrobenzene as the inhibitor of radical-induced side reactions on the vinyl group of VB-Glu-NCA. The resulting poly(γ-(4-vinylbenzyl)-(L)-glutamate) (PVBLG) gave rise to polypeptides containing pendant functional groups or moieties through various vinyl chemistries.     

Composition dependence of the photocatalytic activities of BiOCl(1-x)Br(x) solid solutions under visible light

We prepared BiOCl(1-x)Br(x) (x=0-1) solid solutions and characterized their structures, morphologies, and photocatalytic properties by X-ray diffraction, diffuse reflectance spectroscopy, scanning electron microscopy, Raman spectroscopy, photocurrent and photocatalytic activity measurements and also by density functional theory calculations for BiOCl, BiOBr, BiOCl(0.5)Br(0.5). Under visible-light irradiation BiOCl(1-x)Br(x) exhibits a stronger photocatalytic activity than do BiOCl and BiOBr, with the activity reaching the maximum at x=0.5 and decreasing gradually as x is increased toward 1 or decreased toward 0. This trend is closely mimicked by the photogenerated current of BiOCl(1-x)Br(x) , indicating that the enhanced photocatalytic activity of BiOCl(1-x)Br(x) with respect to those of BiOCl and BiOBr originates from the trapping of photogenerated carriers. Our electronic structure calculations for BiOCl(0.5)Br(0.5) with the anion (O(2-), Cl(-), Br(-)) and cation (Bi(3+)) vacancies suggest that the trapping of photogenerated carriers is caused most likely by Bi(3+) cation vacancies, which generate hole states above the conduction band maximum.     

Photoelectron imaging and theoretical studies of silver monohalides AgX- (X = Cl, Br, I) and AuCl-

Photodetachment of AgX(-) (X = Cl, Br, I) and AuCl(-) is studied by a photoelectron velocity map imaging technique and theoretical calculations. Photoelectron spectra (PES) and photoelectron angular distributions (PADs) were obtained. The vibrationally resolved spectra provided approximately equal electron affinities (EAs) for AgX: 1.593(22) eV for AgCl, 1.623(21) eV for AgBr, and 1.603(22) eV for AgI, respectively. Franck-Condon simulations of these spectra gave the equilibrium bond lengths and vibrational frequencies of the title anions. Relativistic density functional theory (DFT) calculations using BLYP, PW91, PBE, and BP86 functionals have been performed to predict the EAs of the AgX (X = Cl, Br, I) molecules. The computed EAs at the BP86 level of theory are in good agreement with the experimental values. Energy partitioning analyses (EPA) at the BP86(ZORA)/QZ4P level of theory of both anions and their neutrals were reported.     

Selective electroless deposition of copper on organic thin films with improved morphology

We have investigated the selective electroless deposition (ELD) of Cu on functionalized self-assembled monolayers (SAMs). Previous studies have demonstrated that Cu deposits on -COOH and -CH(3) terminated SAMs using ELD. However, the deposited films were rough and contained irregular crystallites. Further, the copper penetrated through the film. In this Article, we demonstrate that copper can be selectively deposited on -COOH terminated SAMs with improved morphology and without penetration of copper through the organic layer. The method employs a Cu(II) seed layer and an additive, adenine or guanine. We demonstrate the efficacy of the technique on photopatterned -CH(3)/-COOH SAMs. Copper is observed to deposit only atop the -COOH terminated SAM area and not on the -CH(3) terminated SAM. The use of a Cu(II) seed layer increased the Cu ELD rate on both -COOH and -CH(3) terminated SAMs. The deposited copper layer strongly adheres to the -COOH terminated SAMs because the copper layer nucleates at Cu(2+)-carboxylate complexes. In contrast, the deposited copper layer can easily be removed from the -CH(3) terminated SAM surface because there is no specific copper-surface interaction. The additives adenine and guanine mediate the interaction of Cu(2+) and the deprotonated -COOH terminated SAMs via the formation of additive-carboxylate complexes. These complexes lead to significantly reduced copper penetration through the SAM. In the case of adenine, the diffusion of copper through the organic film was eliminated. This new technique for copper deposition will facilitate the development of inexpensive molecular electronics, sensors, and other nanotechological devices.     

A fully automated system with on-line micro solid-phase extraction combined with capillary liquid chromatography-tandem mass spectrometry for high throughput analysis of microcystins and nodularin-R in tap water and lake water

Microcystins and nodularins are cyclic peptide hepatotoxins and tumour promoters from cyanobacteria. The present study describes the development, validation and practical application of a fully automated analytical method based on on-line micro solid-phase extraction-capillary liquid chromatography-tandem mass spectrometry for the simultaneous determination of seven microcystins and nodularin-R in tap water and lake water. Aliquots of just 100 μL of water samples are sufficient for the detection and quantification of all eight toxins. Selected reaction monitoring was used to obtain the highest sensitivity. Good linear calibrations were obtained for microcystins (50-2000ng/L) and nodularin-R (25-1000 ng/L) in spiked tap water and lake water samples. Excellent interday and intraday repeatability were achieved for eight toxins with relative standard deviation less than 15.7% in three different concentrations. Acceptable recoveries were achieved in the three concentrations with both tap water matrix and lake water matrix and no significant matrix effect was found in tap water and lake water except for microcystin-RR. The limits of detection (signal to noise ratio=3) of toxins were lower than 56.6 ng/L which is far below the 1 μg/L defined by the World Health Organization provisional guideline for microcystin-LR. Finally, this method was successfully applied to lake water samples from Tai lake and proved to be useful for water quality monitoring.     

Immunosuppressive activity of 8-gingerol on immune responses in mice

8-gingerol is one of the principal components of ginger, which is widely used in China and elsewhere as a food, spice and herb. It shows immunosuppressive activity on the immune responses to ovalbumin (OVA) in mice. In the present study, we found that 8-gingerol suppressed lipopolysaccharide (LPS) and concanavalin A (ConA)-stimulated splenocyte proliferation in vitro. In vivo, 8-gingerol not only signi?cantly suppressed Con A-, LPS- and OVA-induced splenocyte proliferation (P < 0.05) but also decreased the percentage of CD19+ B cells and CD3+ T cell (P < 0.05) at high doses (50, 100 mg/kg). Moreover, OVA-speci?c IgG, IgG1 and IgG2b levels in OVA-immunized mice were reduced by 8-gingerol at doses of 50, 100 mg/kg. These results suggest that 8-gingerol could suppress humoral and cellular immune responses in mice. The mechanism might be related to direct inhibition of sensitized T and B lymphocytes.     

Approaches towards the core pentasaccharide in N-linked glycans

This review focuses on the progresses and challenges in the preparation of Man3GlcNAc2 (M3) which is the core structure in the N-glycan biological pathway. Representative methods and recent reported findings, especially research advances in chemoenzymatic synthesis, are highlighted.