Algebraic methods for inferring biochemical networks: A maximum likelihood approach

We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current method, unlike some of the graphical approaches proposed in the literature, uses the values of the experimental measurements only relative to the geometry of the biochemical reactions under the assumption that the underlying reaction network is the same for all the experiments. The proposed approach utilizes algebraic statistical methods in order to parametrize the set of possible reactions so as to identify the most likely network structure, and is easily scalable to very complicated biochemical systems involving a large number of species and reactions. The method is illustrated with a numerical example of a hypothetical network arising from a “mass transfer”-type model.     

A simplified mass transfer analysis for multicomponent condensation

This paper considers the problem of calculating the condensation fluxes N_i for n-component vapour mixtures, taking account of diffusional interactions in the vapour phase. A simplified method for the flux calculation is suggested requiring the assumption that the matrix of multicomponent mass transfer coefficients [W], defined by the n-1 dimensional matrix relation (N) = [W](Δx), is constant along the diffusion path. This assumption allows the calculation of the steady-state fluxes N_i in an explicit manner without iterations. For conditions of equimolar diffusion, the simplified method developed here coincides with the linearized theory development of Toor and Stewart and Prober. For other cases involving diffusion through an inert gas, for example, the method suggested here is simpler than the Toor-Stewart-Prober approach. The accuracy of the simplified method is demonstrated with a few typical examples involving mass transfer in a ternary gas phase. Though condensation in the presence of an inert gas has been treated explicitly here, the developed simplified method should find application in other mass transfer processes such as distillation, absorption and extraction.     

A new matching algorithm for high resolution mass spectra

We present a new matching algorithm designed to compare high-resolution spectra. Whereas existing methods are bound to compare fixed intervals of ion masses, the accurate mass spectrum (AMS) distance method presented here is independent of any alignment. Based on the Jeffreys-Matusitas (JM) distance, a difference between observed peaks across pairs of spectra can be calculated, and used to find a unique correspondence between the peaks. The method takes into account that there may be differences in resolution of the spectra. The algorithm is used for indexing in a database containing 80 accurate mass spectra from an analysis of extracts of 80 isolates representing the nine closely related species in the Penicillium series Viridicata. Using this algorithm we can obtain a retrieval performance of approximately 97-98% that is comparable with the best of the existing methods (e.g., the dot-product distance). Furthermore, the presented method is independent of any variable alignment procedures or binning.     

A new multicomponent approach to highly functionalized 2,3-dihydroisoxazoles

The synthesis of highly functionalized 2,3-dihydroisoxazoles by a one-pot multicomponent reaction of an aldehyde, hydroxamic acid, and malononitrile or methyl cyanoacetate is described.     

A new convenient asymmetric approach to herbarumin Ⅲ

The asymmetric total synthesis of herbarumin Ⅲ 3, a naturally occurred phytotoxin, along with 8-epi-herbarumin Ⅲ 22, was succeeded in 12 steps from n-butyraldehyde based on Brown's asymmetric allylation, taking modified Julia olefination and Yamaguchi's macro-lactonization as key steps.     

A maximum information utilization approach in X-ray fluorescence analysis

X-ray fluorescence data bases have significant contradictions, and inconsistencies. We have identified that the main source of the contradictions, after the human factors, is rooted in the signal processing approaches. We have developed signal processors to overcome many of the problems by maximizing the information available to the analyst. These non-paralyzable, fully digital signal processors have yielded improved resolution, line shape, tailing and pile up recognition. The signal processors account for and register all events, sorting them into two spectra, one spectrum for the desirable or accepted events, and one spectrum for the rejected events. The information contained in the rejected spectrum is mandatory to have control over the measurement and to make a proper accounting and allocation of the events. It has established the basis for the application of the fundamental parameter method approach. A fundamental parameter program was also developed. The primary X-ray line shape (Lorentzian) is convoluted with a system line shape (Gaussian) and corrected for the sample material absorption, X-ray absorbers and detector efficiency. The peaks also can have, a lower and upper energy side tailing, including the physical interaction based long range functions. It also employs a peak and continuum pile up and can handle layered samples of up to five layers. The application of a fundamental parameter method demands the proper equipment characterization. We have also developed an inverse fundamental parameter method software package for equipment characterisation. The program calculates the excitation function at the sample position and the detector efficiency, supplying an internally consistent system.     

Carbon nanocoatings: A new approach to recording mass spectra of low-molecular compounds using surface-assisted laser desorption/ionization mass spectrometry

A simple and rapid approach to obtaining target plates for the investigation of low-molecularweight compounds by surface-assisted laser desorption/ionization (SALDI) mass spectrometry is proposed. It consists in the vacuum sputtering of a carbon layer with a thickness of about 50 nm onto a metal surface. The resulting coatings are characterized by homogeneity, hydrophobicity, and high mechanical strength, which eliminates a possibility of mass spectrometer contamination. A comparison of the SALDI mass spectra of test compounds recorded using conventional carbon materials and carbon nanocoatings demonstrates advantages of the last named materials, such as high spectral resolution and the absence of spectral interferences at low m/z values.     

A new approach to processing electronic diffuse reflectance spectra

The fundamental absorption band edge in the diffuse reflectance spectra can be represented as the superposition of bands described by the Fermi-Dirac distribution to determine the coordination state of element-containing structures formed on the surface of a matrix. The suggested procedure is compared with the other spectrum processing methods (the determination of the position of the absorption band edge and transformation in the Gurevich-Kubelka-Munk or (αhν) ^m coordinates). It was shown that the use of the Fermi-Dirac distribution allows not only experimental data to be correctly described but also separation of complex spectra to be performed with isolating the contribution of surface structures containing atom-modifiers in various coordination states. Original Russian Text ? E.A. Sosnov, A.A. Malkov, A.A. Malygin, 2009, published in Zhurnal Fizicheskoi Khimii, 2009, Vol. 83, No. 4, pp. 746–752.     

A simple asymmetric lineshape for fitting infrared absorption spectra

Almost exclusively, lineshape functions used to model infrared (IR) absorption peaks are based on symmetric frequency distributions. However, in complex systems such as large biological macromolecules in aqueous solutions, the distribution of vibrational frequencies may in fact be asymmetric. In this communication, we show that asymmetry can be introduced to the standard symmetric Lorentzian and Gaussian lineshapes using a simple, easy to implement method. Our technique involves replacing the static width parameter of the symmetric profiles with a smoothly varying function that is wave number dependent. In this way, the width varies across the IR band resulting in an asymmetric peak. In our model, the width varies sigmoidally with wave number. As a demonstration, we fit experimental spectra of adenosine 5′-monophosphate (AMP).     

A new analytical system for multicomponent gas-chromatographic analysis of metabolites in biological material

Summary A new method for the gas-chromatographic multicomponent analysis of metabolites in biological material is described. It is an analytical procedure involving several extractions carried out under different conditions. In this procedure the metabolites are divided according to their functional groups and specific chemical behaviours into eight main fractions: lipids, hydrocarbons, organic acids, neutral substances, phenols, amines, amino acids and carbohydrates. Each of these fractions is derivatized; the components are separated and estimated by gas chromatography. This analytical system was applied to the determination of a number of metabolites in serum, urine, amniotic fluid, sperma, tissues and other biological materials.

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Neues Analysensystem zur Multikomponenten-GC-Analyse von Metaboliten in biologischem Material

Zusammenfassung Eine Methode für die Multikomponenten-GC-Analyse von Metaboliten in Biomaterialien wird beschrieben. Das Verfahren umfaßt mehrere Extraktionen, die unter verschiedenen Bedingungen durchgeführt werden. Die Komponenten werden in Abhängigkeit von ihren funktionellen Gruppen und spezifischem chemischen Verhalten in acht Hauptfraktionen geteilt: Lipide, Kohlenwasserstoffe, organische Säuren, neutrale Substanzen, Phenole, Amine, Aminosäuren und Kohlenhydrate. Die Komponenten jeder Gruppe werden nach spezieller Derivatisierung gaschromatographisch getrennt und bestimmt. Dieses neue System ist bei verschiedenen biologischen Materialien (klinische Proben, Pflanzen- und Tiergewebe) angewandt worden.

     

A peptide bromoiodinane approach for asymmetric bromolactonization

A series of 37 peptides containing an iodo-aryl amide active site were generated by means of both solid phase and conventional synthesis. These peptides were screened for asymmetric induction in the bromolactonization of 4-phenyl-4-pentenoic acid based on the generation of chiral bromoiodinane bromenium sources. The study culminated in the discovery of a tri-peptide iodo-aryl amide that effected the desired bromolactonization in quantitative conversion with 24% ee. The experiments disclosed herein provided valuable insight that ultimately facilitated the development of more synthetically useful enantioselective halocyclization methodology.     

Hybrid approach combining chemometrics and likelihood ratio framework for reporting the evidential value of spectra

Many chemometric tools are invaluable and have proven effective in data mining and substantial dimensionality reduction of highly multivariate data. This becomes vital for interpreting various physicochemical data due to rapid development of advanced analytical techniques, delivering much information in a single measurement run. This concerns especially spectra, which are frequently used as the subject of comparative analysis in e.g. forensic sciences. In the presented study the microtraces collected from the scenarios of hit-and-run accidents were analysed. Plastic containers and automotive plastics (e.g. bumpers, headlamp lenses) were subjected to Fourier transform infrared spectrometry and car paints were analysed using Raman spectroscopy. In the forensic context analytical results must be interpreted and reported according to the standards of the interpretation schemes acknowledged in forensic sciences using the likelihood ratio approach. However, for proper construction of LR models for highly multivariate data, such as spectra, chemometric tools must be employed for substantial data compression. Conversion from classical feature representation to distance representation was proposed for revealing hidden data peculiarities and linear discriminant analysis was further applied for minimising the within-sample variability while maximising the between-sample variability. Both techniques enabled substantial reduction of data dimensionality. Univariate and multivariate likelihood ratio models were proposed for such data. It was shown that the combination of chemometric tools and the likelihood ratio approach is capable of solving the comparison problem of highly multivariate and correlated data after proper extraction of the most relevant features and variance information hidden in the data structure.     

Siscom — a new library search system for mass spectra

SISCOM is a library search system for mass spectrometry which is based on a new method of coding spectra by selecting the most important peaks within homologous ion series, and on a multiple factor assessment of the result. Examples demonstrate the ability of the system to identify various compounds, even from mixtures or by reference spectra which differ from those measured. SISCOM is especially suitable for detecting structural similarities like common substructures, even in cases where no similarity can be recognized by visual comparison of patterns or by human interpretation of the spectrum.     

A quality index for reference mass spectra

A numerical rating for evaluating the quality of reference mass spectra used for retrieval and interpretive applications is proposed. The overall quality index is the product of seven quality factors: (1) source of the spectrum; (2) ionization conditions; (3) higher molecular weight impurities; (4) illogical neutral losses; (5) isotopic abundance accuracy; (6) number of peaks; and (7) lower mass limit of peaks. For quality factor 6 the number of peaks of abundances ≥1% was found to correspond to 15 more than the number of atoms in the molecule with a correlation coefficient of 0.482. The program has been found useful in preparing a data base of 41429 mass spectra; for the majority of spectra judged to be unsatisfactory by the program this arose from a low quality factor 6 value (too few peaks).     

A new modeling of asymmetric membrane formation in rapid mass transfer system

Mass transfer process involved in the immersion precipitation of polyurethane/dimethylformamide (DMF)/water system was investigated. The set of diffusion equations describing the local composition of the membrane solution as a function of space coordinate and time were solved by numerical method, and the composition path in the phase diagram was obtained. Instead of boundary conditions based on the instantaneous equilibrium assumption between membrane solution and coagulation bath, new boundary conditions were set up by using mass transfer formalism at the interface which is especially valid in the condition that the mass transfer rate is extremely rapid. Phase separation phenomena during immersion precipitation were taken into account to continue the calculation after phase separation. The calculated results showed that the chance of phase separation via spinodal decomposition increases with the strength of nonsolvent, addition of nonsolvent to the dope solution, and the use of more hydrophobic polymer. The proposed model is the improvement of the previous works eliminating the equilibrium assumption at the interface and extending the calculation after phase separation.     

Band composition analysis: a new procedure for deconvolution of the mass spectra of organometallic compounds

A new chemometric procedure called band composition analysis (BCA) designed for the deconvolution of mass spectra of organometallics is proposed. BCA generates theoretical bands T(i), then combines them to obtain a model band M, which is finally compared with the experimental band E. All of these steps are realized with computer assistance. This modeling yields four parameters characterizing the experimental band: theoretical and model variances s(2) (theor) and s(2) (model), a fit factor alpha and a contribution x(i) from the theoretical band. If s(2) (theor) > 20 the band is deemed complex and needs modeling. The values alpha > 90 indicate that there is good agreement between the experimental and model bands. BCA is particularly effective for the modeling of complex isotopic bands often present in organometallics. Two illustrations of BCA for tetrabutyltin, C(16)H(36)Sn, and 1,1',2,2',3,3'-hexachloroferrocene, C(10)H(4)Cl(6)Fe, are shown.