Testing an alternative search algorithm for compound identification with the ‘Wiley Registry of Tandem Mass Spectral Data,MSforID’

A tandem mass spectral database system consists of a library of reference spectra and a search program. State‐of‐the‐art search programs show a high tolerance for variability in compound‐specific fragmentation patterns produced by collision‐induced decomposition and enable sensitive and specific ‘identity search’. In this communication, performance characteristics of two search algorithms combined with the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ (Wiley Registry MSMS, John Wiley and Sons, Hoboken, NJ, USA) were evaluated. The search algorithms tested were the MSMS search algorithm implemented in the NIST MS Search program 2.0g (NIST, Gaithersburg, MD, USA) and the MSforID algorithm (John Wiley and Sons, Hoboken, NJ, USA). Sample spectra were acquired on different instruments and, thus, covered a broad range of possible experimental conditions or were generated in silico. For each algorithm, more than 30 000 matches were performed. Statistical evaluation of the library search results revealed that principally both search algorithms can be combined with the Wiley Registry MSMS to create a reliable identification tool. It appears, however, that a higher degree of spectral similarity is necessary to obtain a correct match with the NIST MS Search program. This characteristic of the NIST MS Search program has a positive effect on specificity as it helps to avoid false positive matches (type I errors), but reduces sensitivity. Thus, particularly with sample spectra acquired on instruments differing in their setup from tandem‐in‐space type fragmentation, a comparably higher number of false negative matches (type II errors) were observed by searching the Wiley Registry MSMS. Copyright © 2013 John Wiley & Sons, Ltd.     

Identification of wild collected mosquito vectors of diseases using gas chromatography–mass spectrometry in Jazan Province,Saudi Arabia

Thirty‐three species of mosquitoes have been reported from the Kingdom of Saudi Arabia. Several of these mosquitoes, Anopheles gambiae Giles s.l., Anopheles stephensi Liston, Culex pipiens Linnaeus, Culex quinquefasciatus Say, Culex tritaeniorhynchus Giles, Stegomyia aegypti (Linnaeus) and Aedimorphus vexans arabiensis (Patton) are known vectors of human and animal diseases. In this study, the cuticular hydrocarbon profiles of eight mosquito species using gas chromatography–mass spectrometry were analyzed. Wild collected fourth‐instar larvae were reared, and single, newly emerged, unfed adult females were used for the analysis. A total of 146–160 peaks were detected from the cuticular extracts by gas chromatography. Repeated analysis of variance (ANOVA) and Tukey HSD Post Hoc test was used to test for quantitative differences in relative hydrocarbon quantity. In addition, a linear regression model was applied using Enter method to determine the diagnostic peaks for the eight mosquito specimens. The ANOVA test indicated that relative peaks were significant (P < 0.05) when selected pairs of peaks were compared. Also, seven compounds showed qualitative differences among the five mosquito vectors tested. The classes of constituents present were n‐alkanes, monomethylalkanes, dimethylalkanes, trimethylalkanes, alkenes, branched aromatic hydrocarbons, aldehydes and esters. These compounds have a carbon chain length ranging from 8 to 18 carbons. The most abundant compound in all adult mosquito specimens was n‐hexylacrylate [retention time (RT) 6.73 min], which was not detected in Cx. pipiens. In Cx. pipiens, the most abundant peak was benzaldehyde (RT 2.98 min). Gas chromatography–mass spectrometry is a suitable method to identify adult mosquitoes, especially from focal areas of public health concern such as Jazan Province, Saudi Arabia. This method allows a wide range of adult collected material to be identified with high accuracy. Copyright © 2013 John Wiley & Sons, Ltd.     

Electrochemical Characterization of Egyptian Blue Pigment in Wall Paintings Using the Voltammetry of Microparticles Methodology

The solid state voltammetric response of Egypt blue, Han blue and ploss blue pigments upon attachment to graphite electrodes in contact with aqueous phosphate buffer at pH 7.0 is studied by voltammetry of microparticles and scanning electrochemical microscopy. Such voltammetric responses, combined with those for synthetic specimens consisting of binary mixtures of the pigment and SiO₂ or CaCO₃ as well as ternary ones of CaCO₃ and SiO₂ mixtures allow for the identification of the pigment and the support in samples from wall paintings using different electrochemical parameters, in particular upon performing the Tafel and modified Tafel analysis of voltammetric peaks. Identification of Egypt blue in microsamples of murals from a Roman archaeological site in Castulo (Jaén, Spain) is discussed.     

Mutation scanning analysis of genetic variation within and among Echinococcus species: Implications and future prospects

Adult tapeworms of the genus Echinococcus (family Taeniidae) occur in the small intestines of carnivorous definitive hosts and are transmitted to particular intermediate mammalian hosts, in which they develop as fluid‐filled larvae (cysts) in internal organs (usually lung and liver), causing the disease echinococcosis. Echinococcus species are of major medical importance and also cause losses to the meat and livestock industries, mainly due to the condemnation of infected offal. Decisions regarding the treatment and control of echinococcosis rely on the accurate identification of species and population variants (strains). Conventional, phenetic methods for specific identification have some significant limitations. Despite advances in the development of molecular tools, there has been limited application of mutation scanning methods to species of Echinococcus. Here, we briefly review key genetic markers used for the identification of Echinococcus species and techniques for the analysis of genetic variation within and among populations, and the diagnosis of echinococcosis. We also discuss the benefits of utilizing mutation scanning approaches to elucidate the population genetics and epidemiology of Echinococcus species. These benefits are likely to become more evident following the complete characterization of the genomes of E. granulosus and E. multilocularis.     

Ethylene Glycol as New Mobile Phase for Resolution of Two-Component Mixture of Cationic Surfactants on Alumina Surface

Aqueous ethylene glycol (ethane 1,2 diol) as a green mobile phase has been used for thin layer chromatographic (TLC) studies of cationic surfactants on alumina layers. Nineteen solvent systems were used to examine the mobility of the surfactants and to discover the best TLC system for the selective separation of dodecyl trimethylammonium bromide (DTAB) from multi-component mixture of other surfactants. Among the TLC systems studied, M₃ (ethylene glycol: water, 8:2) was best for achieving the selective separation of DTAB from multi-component mixture of other surfactants because in this mobile phase mobility of all surfactants except DTAB were insignificant. Effect of organic additives in aqueous ethylene glycol mobile phase on the mobility of surfactants was examined. The results obtained on laboratory made alumina TLC plates and commercially available precoated alumina HPTLC plates were compared. The lower limits of detection of DTAB, CPC, CTAB, HDTAC, and TTAB were 0.02, 0.05, 0.04, 0.06, or 0.08 µg per zone respectively. The resolution of mixture of cationic surfactants was also examined in the presence metal cations as an impurity in the analyzed sample.     

水声通信中基于信道辨识的盲turbo均衡方法

水声信道多途效应明显,造成接收信号存在严重的码间干扰(ISI,Intersymbol interference)。基于最小均方误差(MMSE,Minimum mean square error)准则的turbo均衡器级联了均衡和信道译码,能够有效去除ISI,并获得优良的性能。由于水声信道的时变性,传统MMSE-turbo均衡需要周期性的训练序列,以实现连续可靠的通信。训练序列虽然提高了通信的可靠性,但降低了信息的有效传输速率。因此,为提高通信效率,本文提出了一种盲turbo均衡方法,该方法通过引入新的盲信道辨识器来同时获得信道估计响应和已去除部分ISI的初步均衡输出信号,并为turbo均衡提供初始的响应参数和比特软信息。与水声通信中应用较多的盲判决反馈均衡器(DFE,Decision feedback equalizer)相比,海上实验结果证明本文提出的盲turbo均衡方法抗信道多途衰落的能力较强,并且与传统MMSE-turbo均衡相比无需训练序列,因此提高了信息的有效传输速率。     

Numerical discretization-based kernel type estimation methods for ordinary differential equation models

We consider the problem of parameter estimation in both linear and nonlinear ordinary differential equation(ODE) models. Nonlinear ODE models are widely used in applications. But their analytic solutions are usually not available. Thus regular methods usually depend on repetitive use of numerical solutions which bring huge computational cost. We proposed a new two-stage approach which includes a smoothing method(kernel smoothing or local polynomial fitting) in the first stage, and a numerical discretization method(Eulers discretization method, the trapezoidal discretization method,or the Runge–Kutta discretization method) in the second stage. Through numerical simulations, we find the proposed method gains a proper balance between estimation accuracy and computational cost.Asymptotic properties are also presented, which show the consistency and asymptotic normality of estimators under some mild conditions. The proposed method is compared to existing methods in term of accuracy and computational cost. The simulation results show that the estimators with local linear smoothing in the first stage and trapezoidal discretization in the second stage have the lowest average relative errors. We apply the proposed method to HIV dynamics data to illustrate the practicability of the estimator.     

Neuroprotective glucosides of magnolol and honokiol from microbial-specific glycosylation

Thirteen new glucosides (1–13) of magnolol and honokiol were obtained from specific O-glycosylation by two filamentous fungi, Cunninghamella echinulata AS 3.3400 and Rhizopus japonicus ZW-4. The glucosides' structures were determined on the basis of extensive spectroscopic (HRESIMS, 1D and 2D NMR, and CD) analyses and a chemical method. C. echinulata appeared to transfer a glucosyl moiety to 2-OH of magnolol and honokiol, whereas R. japonicus preferred to regio-specifically transfer a glucosyl moiety to 4′-OH when honokiol was as the substrate. In addition, hydroxylation by C. echinulata and specific 6″-O-acylation of the introduced glucosyl moiety by R. japonicus were observed as minor reactions. Bioassay results indicated that glucosides 1–12 together with magnolol and honokiol at 10 μM attenuated the glutamate-induced toxicity in SK-N-SH cells to levels comparable to the results for MK-801, a positive control. However, the water-solubility of major glucosylated products (1, 8, and 11) increased greatly.     

GPCR A2A AR腺苷受体蛋白的激动剂结合及其诱导的蛋白活性开关构象变化

运用分子动力学模拟,研究了腺苷酸（激动剂）与A2AAR腺苷受体蛋白的相互作用和配体结合诱导的蛋白动力学变化．识别了与腺苷酸结合力强于0．5kcal／mol的关键基团：A63^2．61,I66^2．64,V84^3.32,L85^3.33,T88^3.36,F168^5.29,M177^5.38,L249^6.51,H250^6.52和N253^6.55,观察到腺苷酸没有与L167^5.28相互作用,这一结果支持了L167^5.28是抑制剂特异性结合位点,不与激动剂结合．未结合配体（激动剂或抑制剂）的单体A2AAR和腺苷酸结合后的A2AAR在构象上有三个不同功能性开关．腺苷酸结合可以诱导A2AAR腺苷受体蛋白的构象调整,使得三个功能性开关器件的构象与单体A2AAR不同．     

Approximate chemical analysis of volcanic glasses using Raman spectroscopy

The effect of chemical composition on the Raman spectra of a series of natural calcalkaline silicate glasses has been quantified by performing electron microprobe analyses and obtaining Raman spectra on glassy filaments (~450 µm) derived from a magma mingling experiment. The results provide a robust compositionally‐dependent database for the Raman spectra of natural silicate glasses along the calcalkaline series. An empirical model based on both the acquired Raman spectra and an ideal mixing equation between calcalkaline basaltic and rhyolitic end‐members is constructed enabling the estimation of the chemical composition and degree of polymerization of silicate glasses using Raman spectra. The model is relatively insensitive to acquisition conditions and has been validated using the MPI‐DING geochemical standard glasses 1 as well as further samples. The methods and model developed here offer several advantages compared with other analytical and spectroscopic methods such as infrared spectroscopy, X‐ray fluorescence spectroscopy, electron and ion microprobe analyses, inasmuch as Raman spectroscopy can be performed with a high spatial resolution (1 µm²) without the need for any sample preparation as a nondestructive technique. This study represents an advance in efforts to provide the first database of Raman spectra for natural silicate glasses and yields a new approach for the treatment of Raman spectra, which allows us to extract approximate information about the chemical composition of natural silicate glasses using Raman spectroscopy. We anticipate its application in handheld in situ terrestrial field studies of silicate glasses under extreme conditions (e.g. extraterrestrial and submarine environments). © 2015 The Authors Journal of Raman Spectroscopy Published by John Wiley & Sons Ltd