Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments

Modern multicapillary devices allow researchers to address increasingly complex biological questions involving comparisons of gene expression patterns across electrophoretic samples under various experimental conditions. As labor-intensive visual evaluation of the electrophoretic results is often the bottleneck of large-scale differential display (DD) studies, one way to further streamline this process is to focus only on a highly compressed list of the most potential patterns that are likely to provide reliable findings. To enable the identification of such candidate patterns, we present a computer-assisted method for objective ranking of multitrace peak patterns in DD experiments. The fundamental component of the multitrace pattern ranking method (MRANK) is the multiple alignment algorithm that allows for discovery of patterns involving sets of peak complexes from various electrophoretic samples. A score value is attached to each detected pattern which characterizes how accurately the pattern resembles the desired pattern query, freely defined by the researcher. The ranked pattern list produced by MRANK is validated against visual evaluation in terms of detecting and ranking a group of relevant patterns in a DD analysis of T-helper cell differentiation. We demonstrate high enrichment of the desired patterns on top of the score-ranked list (e.g., 90% of the visually selected patterns are discovered by looking through the first 3% of patterns in the ranked list of all patterns). The results suggest that a substantial amount of manual labor can be saved without compromising the accuracy of the findings by prioritizing the patterns according to MRANK output in the visual confirmation phase.     

Glass microfabricated nebulizer chip for mass spectrometry

A microfluidic nebulizer chip for mass spectrometry is presented. It is an all-glass device which consists of fusion bonded Pyrex wafers with embedded flow channels and a nozzle at the chip edge. A platinum heater is located on the wafer backside. Fabrication of the chip is detailed, especially glass deep etching, wafer bonding, and metal patterning. Various process combinations of bonding and metallization have been considered (anodic bonding vs. fusion bonding; heater inside/outside channel; metallization before/after bonding; platinum lift-off vs. etching). The chip vaporizes the liquid sample (0.1-10 microL min(-1)) and mixes it with a nebulizer gas (ca. 100 sccm N2). Operating temperatures can go up to 500 degrees C ensuring efficient vaporization. Thermal insulation of the glass ensures low temperatures at the far end of the chip, enabling easy interconnections.     

On-line monitoring of continuous beer fermentation process using automatic membrane inlet mass spectrometric system

A fully automatic membrane inlet mass spectrometric (MIMS) on-line instrumentation for the analysis of aroma compounds in continuous beer fermentation processes was constructed and tested. The instrumentation includes automatic filtration of the sample stream, flushing of all tubing between samples and pH control. The calibration standards can be measured periodically. The instrumentation has also an extra sample line that can be used for off-line sample collection or it can be connected to another on-line method. Detection limits for ethanol, acetic acid and eight organic beer aroma compounds were from μg l⁻¹ to low mg l⁻¹ levels and the standard deviations were less than 3.4%. The method has a good repeatability and linearity in the measurement range. Response times are shorter than or equal to 3 min for all compounds except for ethyl caproate, which has a response time of 8 min. In beer aroma compound analysis a good agreement between MIMS and static headspace gas chromatographic (HSGC) measurements was found. The effects of different matrix compounds commonly present in the fermentation media on the MIMS response to acetaldehyde, ethyl acetate and ethanol were studied. Addition of yeast did not have any effect on the MIMS response of ethanol or ethyl acetate. Sugars, glucose and xylose, increased the MIMS response of all studied analytes only slightly, whereas salts, ammonium chloride, ammonium nitrate and sodium chloride, increased the MIMS response of all three studied compounds prominently. The system was used for on-line monitoring of continuous beer fermentation with immobilised yeast. The results show that with MIMS it is possible to monitor the changes in the continuous process as well as delays in the two-phase process.     

A Density Result for Homogeneous Sobolev Spaces on Planar Domains

Potential Analysis - We show that in a bounded simply connected planar domain Ω the smooth Sobolev functions Wk,∞(Ω) ∩ C∞(Ω) are dense in the homogeneous Sobolev...     

Thermal risk assessment for the epoxidation of linseed oil by classical Prisleschajew epoxidation and by direct epoxidation by H2O2 on alumina

Journal of Thermal Analysis and Calorimetry - Substitution of fossil feedstock by vegetable oils is growing due to environmental constraints and oil depletion. Among the different valorization...     

Adduct formed by chromium trioxide and zwitterionic quinolinic acid

Chromium trioxide forms an adduct with zwitterionic quinolinic acid. The structure of the product was found to be (quinolinium-3-carboxylato-O)trioxidochromium(VI), determined by single-crystal X-ray diffraction methods. To evaluate the bonding properties of the compound, its structure was optimized at the B3LYP/6-311G* level of theory. The electronic characteristics were investigated by topological methods applied to the total charge density in various model compounds including the title compound, title compound with a HF molecule presenting a hydrogen bonding and anionic moiety. Calculated aromaticity indices indicate that the quinolinic rings tend to conserve their degree of aromaticity against hydrogen bonding. However, when there is hydrogen bonding involving an N-H bond or when the quinolinium zwitterion is deprotonated, there are clear changes in the interaction between chromium trioxide and the quinolinic moiety.      

Salvia officinalis L.: composition and antioxidant-related activities of a crude extract and selected sub-fractions

The composition and antioxidant properties of a methanol: acetic acid (99:1, v/v) soluble crude extract isolated from S. officinalis L. leaves through maceration and selected fractions isolated thereof are presented in this study. The total phenol content was estimated as gallic acid equivalents, whilst qualitative-quantitative phenolic content was determined using high performance liquid chromatography with photodiode array detection. Antioxidant evaluation consisted of ferric reductive capacity and 1,1-diphenyl-2-picrylhydrazyl and hydroxyl free radical scavenging determinations. The crude extract contained hydroxybenzoic acids, hydroxycinnamic acids, flavonoids and diterpenoids, whilst caffeic acid, carnosic acid, luteolin, luteolin-7-O-glucoside and rosmarinic acid were identified from their chromatographic and spectral characteristics and quantified from their respective calibration curves. The crude extract and sub-fractions demonstrated varying degrees of efficacy in the antioxidant-related assays used, except the n-hexane fraction, which was unable to reduce iron(III) at reasonable concentrations. Although the positive controls, ascorbic acid, BHA and BHT, were more potent than the S. officinalis samples, two fractions were significantly (p < 0.05) more potent iron(III) reducing agents than pycnogenol, a proanthocyanidin-rich commercial preparation.     

Stability of hydrogen peroxide during perhydrolysis of carboxylic acids on acidic heterogeneous catalysts

This paper describes a study of the stability of hydrogen peroxide in the presence of different aluminosilicate materials, in connection with an investigation of carboxylic acid perhydrolysis. During the reaction, aluminosilicate materials such as H-β zeolites, mesoporous material H-MCM-41 and alumina initiate the decomposition of hydrogen peroxide. The reason of the spontaneous decomposition of H₂O₂ is related to the partial dealumination of these zeolites. However, in the case of experiments carried out with H-ZSM-5 zeolite catalysts, a slight catalytic effect on the perhydrolysis and no spontaneous decomposition of hydrogen peroxide were noticed. The use of cation exchange resins as catalysts is more kinetically beneficial than H-ZSM-5 zeolite catalysts.     

Mechanism of the chemo–bio catalyzed cascade synthesis of <Emphasis Type="Italic">R</Emphasis>-1-phenylethyl acetate over Pd/Al<Subscript>2</Subscript>O<Subscript>3</Subscript>, lipase,and Ru-catalysts

One-pot synthesis of R-1-phenylethyl acetate was investigated starting from acetophenone hydrogenation performed over Pd/Al₂O₃ and PdZn/Al₂O₃ catalysts followed by acylation of the intermediate secondary alcohol, R-1-phenylethanol, over an immobilized lipase. Furthermore, the performance of a third type of catalyst, Ru supported on hydroxyapatite (HAP) was evaluated for racemization of S-1-phenylethanol in one pot together with the two other catalysts. The main objectives of this work were to separate the effects of different catalysts and to reveal the reaction mechanism. For this purpose not only acetophenone, but also (R,S)-1-phenylethanol, S-1-phenylethanol, R-1-phenylethyl acetate, and styrene were used as reactants in combination with Pd/Al₂O₃, lipase and Ru/HAP as catalysts. The results revealed that the main side product, ethylbenzene, was formed in two different ways, via dehydration of (R,S)-1-phenylethanol to styrene, followed by its rapid hydrogenation to ethylbenzene, and via debenzylation of the desired product, R-1-phenylethyl acetate to ethylbenzene. The true one-pot synthesis, however, was demonstrated over Shvo’s catalyst, but Ru/HAP was not sufficiently active in the racemization step. Ru/Al₂O₃ was a promising catalyst for racemization of S-1-phenylethanol and for dynamic kinetic resolution of (R,S)-1-phenylethanol, when using only small amounts of the acyl donor ethyl acetate. The challenge in racemization is that the activity of heterogeneous Ru catalysts was inhibited by esters.     

Method to determine critical current of poorly cooled short sample

Superconducting wire characterization can fail owing to many reasons. For example, unintentional sample heating may distort voltage–current-data, i.e. decrease the critical current and increase the n-value. This occurs rarely if a sample is immersed into liquid cryogen, but in conduction cooled measurements, constant sample temperature is difficult to achieve. Ohmic losses are generated at current contacts as well as inside the sample even at subcritical currents. Most of these losses can be extracted using a well designed sample holder, but in any case, significant amount of heat is generated rapidly when critical current is approached and overstepped, especially if n-value is low. Then, heat has no time to conduct away, and thus, the sample will warm up distorting the measurement. In this paper, we present a computational post-processing method to reduce the effect of heating on measured voltage–current characteristics. Simulations are performed for a Bi-2223/Ag tape, but the model can be applied to any other superconductor as well.