Feature based fuzzy matching of 2D gel electrophoresis images

Automatic alignment (matching) of two-dimensional gel electrophoresis images is of primary interest in the evolving field of proteomics. In the present study, feature-based matching techniques, in their classical and robust versions, are described, and an automatic method of fuzzy alignment (FA) is introduced. This method allows automatic matching of two gel images with different numbers of features with unknown correspondence. Performance of FA is tested on simulated and real data sets.     

New Tricyclic Amides. Synthesis,Structure, and Oxidation with Peroxyphthalic Acid

4-Azatricyclo[5.2.1.0^2,6]dec-8-ene was synthesized and brought into reactions with benzoyl, o-chlorobenzoyl, p-bromobenzoyl, p-, m-, and o-nitrobenzoyl, and bicyclo[2.2.1]hept-2-ene-endo-5,endo-6-dicarboximidoacetyl chlorides in chloroform in the presence of pyridine. The tricyclic amides thus obtained were epoxidated with peroxyphthalic acid prepared in situ by reaction of phthalic anhydride with a 35% aqueous solution of hydrogen peroxide. The structure of newly synthesized compounds was confirmed by IR and ¹H and ¹³C NMR spectroscopy and mass spectrometry. Their NMR spectra were compared with those of previously synthesized N-arylsulfonyl-4-azatricyclo[5.2.1.0^2,6]dec-8-enes on the basis of conformational composition of the corresponding p-nitrophenyl-substituted derivatives, which was determined by PM3 semi-empirical quantum-chemical calculations.__________Translated from Zhurnal Organicheskoi Khimii, Vol. 41, No. 6, 2005, pp. 837–845.Original Russian Text Copyright © 2005 by L. Kas’yan, Okovityi, Tarabara, A. Kas’yan, Bondarenko.     

Spectroscopic study of low temperature interactions in metal-organic co-condensates

The results on spectroscopic study of low temperature interactions of metal atoms, small clusters and nanoparticles with different organic and inorganic substances in the temperature range 12-300 K are presented. Complexation and reactions of atoms and clusters of magnesium, samarium and silver with carbon dioxide, ethylene and some mesogenic cyanophenyls were studied by the technique of matrix isolation and low temperature co-condensation of metal and ligand vapors, low temperature UV-Vis, IR- and ESR-spectroscopy in combination with quantum chemistry calculations. It was shown that cryochemical reactions of metal particles of different sizes reflected the system's redundant energy.     

Mass spectra of halogenated esters. 7. Methyl esters of 2-chloro C2?C20 n-alkanoic acids

The mass spectral fragmentation of a homologous series of methyl esters of 2-chloro n-alkanoic acids ranging from acetic (C₂) to eicosanoic (C₂₀) acid on electron impact has been investigated. The fragmentation pathways were elucidated with the aid of the first field-free region metastable ions, the results being presented with one compound, i.e. with ionized methyl 2-chloro-octauoate. Owing to the Cl/H exchanges and to the formation of the non-chlorinated parent esters prior to the fragmentations the spectra show the peak pairs with and without the chlorine atom. The effects become more evident with increasing chain length; shown most visually by the abundance ratios of the McLafferty rearrangement ions atm/z108/110 and 74, and fragments at m/z121/123 and 87.     

Fluorine-containing azoles. 2. Reaction of imidazole,benzimidazoles, and perimidines with difluorocarbene

The reaction of difluorocarbene, generated from difluorochloromethane in an alkaline medium or from sodium trifluoroacetate in a neutral medium, with imidazole, tetrahydrobenzimidazole, benzimidazoles, and perimidines leads to the production of their N-difluoromethyl-substituted derivatives.See [1] for communication 1.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 520–523, April, 1984.     

Quinoid pigments of echinodermata III. Minor pigments of the sea urchin Strongylocentrotus nudus

Summary 1. 3-Acetyl-2,7-dihydroxy-6-methylnaphthazarin, not previously described, has been isolated from the test and needles of the sea urchinStronglyocentrotus nudus.2. The pigments of this sea urchin have been shown to include 2,7-dihydroxynaphthazarin and spinochrome E.3. A number of minor pigments forming naphthazarin derivatives has been isolated. One of them is connected with spinochrome C by mutual transformations.The subject matter of the present paper was given in part at the All-Union Conference on Biological Resources of the Seas of the Far East (Vladivostok, 1975).Pacific Ocean Institute of Bioorganic Chemistry, Far Eastern Scientific Center of the Academy of Sciences of the USSR, Vladivostok. Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 202–207, March–April, 1977.     

Polystyrene resins with immobilized polyamines: Preparation,characterization, and ability to bind Cu(II) ions

Three polyamine ligands, ethylenediamine (EDA), diethylenetriamine (DTA), and triethylenetetramine (TETA), were bound to three chloromethylated “popcorn” polystyrene resins (16, 50, and 100% phenyl ring substitution) with the use of pyridine as the reaction medium. The rate of chloride displacement decreased with increasing molecular weight of the amine and higher degree of resin chloromethylation, while the extent of multiple attachments to the polymer matrix increased. The additional crosslinking, a result of multiple attachments, caused the polyamine resins to swell to a lesser extent in pyridine and water. The ability of the insoluble polyamine–polystyrene resins to chelate Cu²⁺ ions from dilute solutions (200 ppm) was determined at pH 5. With EDA resins the capacity for Cu²⁺ increased with increasing amount of the bound polyamine, with DTA it remained unchanged, while with TETA it was found to decrease.     

Chromatographic analysis of hydrocarbons in marine sediments and seawater.

The low concentration of hydrocarbons anticipated in pollution baseline studies necessitates the development of analytical techniques sensitive at the sub-microgram per kilogram concentration level. The method of analysis developed in this laboratory involves dynamic headspace sampling for volatile hydrocarbon components of the sample, followed by coupled-column liquid chromatography for the non-volatile components. These techniques require minimal sample handling, reducing the risk of sample component loss and/or sample contamination. Volatile sample components are separated from the matrix in a closed system and concentrated on a TENAX-GC packed pre-column, free from large amounts of solvent and ready for GC/GC-MS analysis. Non-volatile compounds, such as the benzpyrenes, may be extracted from large volumes of water and concentrated on a Bondapak C18 packed pre-column for coupled-column liquid chromatographic separation and analysis. Results of the application of these techniques to the analysis of samples from sites of known low level hydrocarbon contamination are presented and discussed.     

Acetylation of lagochilin

The acetylation of lagochilin and its derivatives with acetic anhydride in the presence of pyridine has been studied by PMR spectroscopy. It has been shown that the manifestation of the polyfunctionality of lagochilin in acetylation reactions with acetic anhydride is connected with a change in the nature of the process of solvation of the reaction forms with the subsequent replacement of the hydrogen atoms of the hydroxy groups by acetyl groups.V. I. Lenin Tashkent State University. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 46–49, January–February, 1980.     

Electrochemical investigations of amino acids at solid electrodes: Part I. Sulfur components: Cystine,cysteine, methionine

The electrochemical oxidation of sulfur amino acids has been investigated by ac measurements and cyclic voltammetry at solid electrodes (Au, vitreous carbon). Electrochemical oxidation proceeds first in the adsorbed state and second by diffusion at metal electrodes. Electrochemical oxidation is catalyzed by a labile metal oxide. At vitreous carbon electrode oxidation in the adsorbed state is only present in the case of methionine. XPS studies have shown the presence of

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as intermediate species. To explain the experimental results a reaction path is proposed.