Quantification of secondary structure prediction improvement using multiple alignments

The use of multiple sequence alignments for secondary structurepredictions is analysed. Seven different protein families, containingonly sequences of known structure, were considered to providea range of alignment and prediction conditions. Using alignmentsobtained by spatial superposition of main chain atoms in knowntertiary protein structures allowed a mean of 8% in secondarystructure prediction accuracy, when compared to those obtainedfrom the individual sequences. Substitution of these alignmentsby those determined directly from an automated sequence alignmentalgorithm showed variations in the prediction accuracy whichcorrelated with the quality of the multiple alignments and distanceof the primary sequence. Secondary structure predictions canbe reliably improved using alignments from an automatic alignmentprocedure with a mean increase of 6.87percnt;, giving an overallprediction accuracy of 68.5%, if there is a minimum of 25% sequenceidentity between all sequences in a family.     

Energetics of Defect Fluorite and Pyrochlore Phases in Lanthanum and Gadolinium Hafnates

Aerodynamic levitation combined with laser heating was used to prepare melts in the HfO₂–La₂O₃ (–Gd₂O₃) systems. All melts crystallized upon quenching in oxygen. Hf₂La₂O₇ pyrochlore and Gd_0.5Hf_0.5O_1.75 fluorite phases were identified. Gd_0.5Hf_0.5O_1.75 fluorite was transformed into the pyrochlore structure by annealing at 1450°C. Pyrochlore that crystallized from HfO₂- La₂O₃ melts contained 31.6–34.2 mol% La₂O₃. The unit cell parameter increased linearly with La content from 10.736 to 10.789 Å. Drop solution calorimetric experiments were performed in 3Na₂O·4MoO₃ melt at 702°C. The enthalpies of formation from the oxides for pyrochlore phases are −107.0±5.0 kJ/mol for Hf₂La₂O₇ and −48.8±4.7 kJ/mol for Hf₂Gd₂O₇. The enthalpy of the pyrochlore–fluorite phase transition in Hf₂Gd₂O₇ is 23.6±3.1 kJ/mol.     

A Multi-Channel Pulse-Coded Multiplexing and Demodulating Telemetry System

A multiplexing, demodulating, and recording telemetry system designed to process multiple pulse-coded temperature channels is described. The system provides complete control of recording and multiplexing sequences and timing, and gives a single analog signal in response to each sample of pulse-coded data. It identifies all channels and indicates to a computer when a new data sample is to be processed. The system is self-calibrating to maintain accuracy over extended data collection periods, and is inexpensive.     

Miniemulsion and conventional emulsion copolymerization of styrene and butadiene: Effect of process on gel content

The properties of styrene/butadiene copolymers obtained by conventional emulsion and miniemulsion polymerizations were studied. Thin layer chromatography with flame ionization detection was used to determine the gel fraction of the copolymer in the latex particles as a function of conversion. It was found that the gel formation began at a higher conversion in the miniemulsion polymerization when compared with that in the conventional process. Also, a lower glass transition temperature was noted at the lowest conversion sampled (～25%), implying a higher initial butadiene monomer concentration within the nucleated miniemulsion monomer droplets when compared with particles formed conventionally. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102: 4616–4622, 2006     

THE “UCKRON-1” TEST PROBLEM FOR REACTION ENGINEERING MODELING

Testing kinetic models against a “true” and detailed kinetic expression was the aim of the Workshop on Kinetic Model Development at the Denver AIChE Meeting in August, 1983. For this purpose an artificial reaction mechanism was created, based on the known thermodynamics of the methanol synthesis as a framework. The kinetic rate laws, that were derived from this mechanism, were made thermodynamically consistent by achieving agreement between equilibrium constants calculated at various temperatures from the given, real original thermodynamic relationship and those calculated from the detailed reversible kinetic expressions.

Using the artificial kinetics as the "true" one, CSTR experiments were simulated. The results of a statistically designed set of experiments were published after 5% random error was added to the data. Participation was invited for all interested to correlate the data, develop kinetic models and to calculate the performance of the specified reactor.

The results of 19 submitted entries are summarized with the conclusion that the models had more differences than were expected, but their predictive values were not as different as was anticipated, if the extreme high production rates due to thermal runaways are not considered. This in turn points out the necessity to check models experimentally, in pilot plant, not only for predicted optimum, but also for calculated runaway conditions. Models which did not capture the true character of this reaction failed to predict the onset of runaway reactions.     

Elucidation of the miniemulsion stabilization mechanism and polymerization kinetics

Styrene/hexadecane miniemulsions were polymerized at 50°C using a redox initiator. The miniemulsions and their corresponding latexes were characterized in terms of size, polymerization rate, and surface properties. The resulting data were analyzed to elucidate the miniemulsion stabilization and polymerization mechanisms. It was found that the free surfactant concentration exceeded the critical micelle concentration when large amounts of surfactant (60 mM sodium lauryl sulfate) were used, resulting in simultaneous micellar and droplet nucleation. Most surfactant was on the surface of the droplets (85%) or particles (95%). The fractional surface coverage was proportional to the surfactant concentration to the 0.55 power. Using a particle diameter equation, the number of particles was calculated to be proportional to the surfactant concentration to the 1.35 power. Through direct particle size measurements, a power of 1.38 was confirmed. The rate of polymerization was determined by reaction calorimetry to be proportional to the number of particles to the 0.59 power, in contrast to classical Smith–Ewart kinetics for conventional emulsions (1.0 power). The average number of radicals per particle was estimated from the rate and number data, and varied with the particle diameter to the 0.97 power. The observed kinetic dependencies were validated through an extension of Smith–Ewart theory. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3987–3993, 2003     

Microstructure and morphology of amine-cured epoxy coatings before and after outdoor exposures—An AFM study

Atomic force microscopy (AFM) has been used to study the morphology and microstructure of an amine-cured epoxy before and after outdoor exposure. Measurements were made from samples prepared in an essentially CO₂-free, H₂O-free glove box and from samples prepared in ambient conditions. For those prepared in a CO₂-free glove box, AFM imaging was conducted on (1) an unexposed air/coating surface, (2) an unexposed coating bulk, (3) an unexposed coating/substrate interface, and (4) a field exposed air/coating surface. For samples prepared in ambient conditions, only the unexposed air/coating surface was investigated. The same regions of the exposed samples were scanned periodically by the AFM to monitor changes in the surface morphology of the coating as UV exposure progressed. Small angle neutron scattering and Fourier transform infrared spectroscopy (FTIR) studies were performed to verify the microstructure and to follow chemical changes during outdoor exposure, respectively. The results have shown that amine blushing, which occurs only under ambient conditions, had a significant effect on the surface morphology and microstructure of the epoxy. The surface morphology of the samples prepared under CO₂-free, dry conditions was generally smooth and homogeneous. However, the interface and the bulk samples clearly revealed a two-phase structure consisting of bright nodular domains and dark interstitial regions, indicating an inhomogeneous microstructure. Such heterogeneous structure of the bulk was in good agreement with results obtained by small angle neutron scattering of unexposed samples and by AFM phase imaging of the degraded sample surface. The relationship between submicrometer physical changes and molecular chemical degradation is discussed. Presented at the 82nd Annual Meeting of the Federation of Societies for Coatings Technology, October 27–29, 2004, in Chicago, IL.     

Effect of dietary n−3 and n−6 polyunsaturated fatty acids on lipid-metabolizing enzymes in obese rat liver

This study was designed to examine whether n−3 and n−6 polyunsaturated fatty acids at a very low dietary level (about 0.2%) would alter liver activities in respect to fatty acid oxidation. Obese Zucker rats were used because of their low level of fatty acid oxidation, which would make increases easier to detect. Zucker rats were fed diets containing different oil mixtures (5%, w/w) with the same ratio of n−6/n−3 fatty acids supplied either as fish oil or arachidonic acid concentrate. Decreased hepatic triacylglycerol levels were observed only with the diet containing fish oil. In mitochondrial outer membranes, which support carnitine palmitoyltransferase I activity, cholesterol content was similar for all diets, while the percentage of 22∶6n−3 and 20∶4n−6 in phospholipids was enhanced about by 6 and 3% with the diets containing fish oil and arachidonic acid, respectively. With the fish oil diet, the only difference found in activities related to fatty acid oxidation was the lower sensitivity of carnitine palmitoyltransferase I to malonyl-CoA inhibition. With the diet containing arachidonic acid, peroxisomal fatty acid oxidation and carnitine palmitoyltransferase I activity were markedly depressed. Compared with the control diet, the diets enriched in fish oil and in arachidonic acid gave rise to a higher specific activity of aryl-ester hydrolase in microsomal fractions. We suggest that slight changes in composition of n−3 or n−6 polyunsaturated fatty acids in mitochondrial outer membranes may alter carnitine palmitoyltransferase I activity.     

RF MEMS continuous reversible variable inductor based on a microfluidic network

In this work, RF MEMS continuous reversible variable inductor has been fabricated by using microelectronic technology and lamination process. We review, evaluate and compare this variable inductor with other work. The proposed inductor is a dual circular coil and has an inductance of few nH. The fundamental idea is to place a liquid droplet between the metal turns of a coil in order to modify the capacitive/resistive coupling between metal tracks and hence to change the stored magnetic energy. The SU-8 resin was used to realize the microfluidic channels and Au as metallic tracks. To prove the reversibility of the inductor, two cases were studied: filling and emptying of channels. The tuning range of the inductance is approximately 107 % at 1.6 GHz, making these devices very suitable as building blocks in many RF applications.