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.     

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.     

OptaDOS: A tool for obtaining density of states,core-level and optical spectra from electronic structure codes

We present OptaDOS, a program for calculating core-electron and low-loss electron energy loss spectra (EELS) and optical spectra along with total-, projected- and joint-density of electronic states (DOS) from single-particle eigenenergies and dipole transition coefficients. Energy-loss spectroscopy is an important tool for probing bonding within a material. Interpreting these spectra can be aided by first principles calculations. The spectra are generated from the eigenenergies through integration over the Brillouin zone. An important feature of this code is that this integration is performed using a choice of adaptive or linear extrapolation broadening methods which we show produces higher accuracy spectra than standard fixed-width Gaussian broadening. OptaDOS  may be straightforwardly interfaced to any electronic structure code. OptaDOS  is freely available under the GNU General Public licence from http://www.optados.org.     

Use of laser scanning confocal microscopy for characterizing changes in film thickness and local surface morphology of UV-exposed polymer coatings

Laser scanning confocal microscopy (LSCM) has been used to characterize the changes in film thickness and local surface morphology of polymer coatings during the UV degradation process. With the noninvasive feature of LSCM, one can obtain thickness information directly and nondestructively at various exposure times without destroying the specimens or deriving the thickness values from IR measurement by assuming uniform film ablation. Two acrylic polymer coatings were chosen for the study, and the physical and chemical changes of the two systems at various exposure times were measured and analyzed. Those measurable physical changes caused by UV exposure include film ablation, formation of pits and other surface defects, and increases in surface roughness. It was found in both coatings that changes in measured film thickness by LSCM were not correlated linearly to the predicted thickness loss using the changes in the CH band obtained by the Fourier Transform Infrared (FTIR) spectroscopy measurements in the later degradation stages. This result suggested it was not a uniform film ablation process during the UV degradation. At later stages, where surface deformation became severe, surface roughness and profile information using LSCM were also proven to be useful for analyzing the surface degradation process Presented at the 81st Annual Meeting of the Federation of Societies for Coatings Technology, November 13–14, 2004 in Philadelphia, PA.     

Inhibition of lipid peroxidation in UVA‐treated skin fibroblasts by luteolin and its glucosides

Ultraviolet A (UVA) radiation causes oxidative damage to human skin cells. This damage may be reduced or prevented using plant compounds as photoprotectants. To investigate the relationship between chemical structure and UVA‐protective activity, three structurally related flavonoids, namely luteolin, luteolin‐7‐O‐glucoside (both present in artichoke) and luteolin‐4'‐O‐glucoside (present in wild carrot), were studied. Human skin fibroblasts exposed to UVA (250 and 500 kJ/m²) were treated with each flavonoid (30 µM) for 18 h prior to irradiation. The extent of lipid peroxidation in the cellular extracts was assessed as lipid peroxides and malondialdehyde (MDA). Luteolin and luteolin‐7‐O‐glucoside both prevented a significant increase in lipid peroxides at 250 kJ/m², but at 500 kJ/m² their effectiveness was clearly attenuated. Contrastingly, luteolin‐4'‐O‐glucoside was pro‐oxidant at both radiation doses. Measurements of MDA levels highlighted that luteolin was clearly more effective than the two glucosides at both 250 and 500 kJ/m². Overall, these results show clear differences between the three flavonoids and suggest that the B ring 3',4'‐dihydroxy group, lacking in luteolin‐4'‐O‐glucoside, may be particularly important. Flavonoid: transition metal ion chelation studies confirmed the influence of the 3',4'‐dihydroxy group, which is also relevant to the quenching of singlet oxygen. These features as well as the greater lipophilic nature of luteolin together explain the superior activity of this flavonoid which may be potentially useful as a supplement in photoprotective skin preparations.     

Automatic dimensional reduction and meshing of stiffened thin-wall structures

The creation of idealised, dimensionally reduced meshes for preliminary design and optimisation remains a time-consuming, manual task. A dimensionally reduced model is ideal for assessing design changes through modification of element properties without the need to create a new geometry or mesh. In this paper, a novel approach for automating the creation of mixed dimensional meshes is presented. The input to the process is a solid model which has been decomposed into a non-manifold assembly of smaller volumes with different meshing significance. Associativity between the original solid model and the dimensionally reduced equivalent is maintained. The approach is validated by means of a free-free modal analysis on an output mesh of a gas turbine engine component of industrial complexity. Extensions and enhancements to this work are also discussed.     

Distributed Learning for Planning Under Uncertainty Problems with Heterogeneous Teams

This paper considers the problem of multiagent sequential decision making under uncertainty and incomplete knowledge of the state transition model. A distributed learning framework, where each agent learns an individual model and shares the results with the team, is proposed. The challenges associated with this approach include choosing the model representation for each agent and how to effectively share these representations under limited communication. A decentralized extension of the model learning scheme based on the Incremental Feature Dependency Discovery (Dec-iFDD) is presented to address the distributed learning problem. The representation selection problem is solved by leveraging iFDD’s property of adjusting the model complexity based on the observed data. The model sharing problem is addressed by having each agent rank the features of their representation based on the model reduction error and broadcast the most relevant features to their teammates. The algorithm is tested on the multi-agent block building and the persistent search and track missions. The results show that the proposed distributed learning scheme is particularly useful in heterogeneous learning setting, where each agent learns significantly different models. We show through large-scale planning under uncertainty simulations and flight experiments with state-dependent actuator and fuel-burn- rate uncertainty that our planning approach can outperform planners that do not account for heterogeneity between agents.     

Potassium sorbate solutions as copper chemical mechanical planarization (CMP) based slurries

Copper depassivation and repassivation characteristics in potassium sorbate solutions, subsequent to mechanical abrading are reported. The identification of copper repassivation kinetics obtained subsequent to mechanical damage of copper protective films formed in sorbate based solutions is discussed. The repassivation rate of copper in sorbate based solutions was measured by means of a slurryjet system capable of measuring single particle impingments on microelectrodes. Copper repassivation rates measured by this slurryjet system in sulfate solutions containing 10 g L⁻¹ potassium sorbate were found to be in the range of 0.5-1.5 ms. An increase in the potassium sorbate concentration leads to a decrease in copper repassivation time at potentials ranging from 200 to 600 mV_Ag/AgCl. The impingement angle between the copper surface and a single abrasive particle has no impact on copper repassivation time nor peak current (I_max) values. XPS studies revealed that copper passivation in potassium based solution was due to the formation of a thin film which is constituted of: Cu₂O, Cu(OH)₂ and Cu(II)-sorbate, while copper(II)-sorbate is mainly present at the top levels of the passive film. It is therefore recommended that the use of potassium sorbate as a passivating component in conjunction with the addition of strong oxidizing agents in chemical mechanical planarization (CMP) slurry design should be considered.     

Microstructure and Microchemistry of Polymer-Derived Crystalline SiC Fibers

Stoichiometric and near-stoichiometric silicon carbide fibers, derived from the polymer polycarbosilane, have been characterized by scanning Auger and transmission electron microscope techniques. Excess carbon usually appeared in the fibers, but it could be eliminated by controlling processing conditions. The fibers consisted mainly of submicrometer-sized SiC microcrystals, with a considerably twinned and stacking-faulted β-SiC structure. Free carbon, which appeared in the form of graphite, was the only detectable intergranular phase in the nonstoichioinetric SiC fibers, while the stoichiometric SiC fibers contained no detectable second phase whatsoever.     

Ammoxidation of toluene over Y-Ba-Cu-Co-O perovskites

Ammoxidation of toluene over the perovskites YBa₂Cu₃O_6.1, YBa₂Cu₂CoO_6.7 and YBaCuCoO_4.9 was investigated at 400 °C. At low partial pressures of O₂ benzonitrile was selectively formed, while CO₂ was the main product at high pressures of O₂. Systematic differences in activity were observed for the three phases and are related to the crystal contents of Cu and Co. At low O₂ pressures, Cu-sites are active for nitrile formation, while Co-sites give CO₂. At high O₂ pressures, the activity for CO₂ of Cu-sites increases more than that of Co-sites due to filling of near-surface oxygen vacancies.