Structure of Atomic and Molecular Adsorbates on Low-Miller-Index ZnO Surfaces Using X-ray Absorption Spectroscopy

We review our X-ray absorption spectroscopy studies of adsorbate geometries on the O-terminated (000 ) and Zn-terminated (0001) basel faces, as well as the non-polar (10 0) prism face of ZnO. Studies employing near-edge X-ray absorption fine-structure (NEXAFS) and surface X-ray absorption fine-structure (SEXAFS) are included.     

A study of structural determinants in the interleukin-1 fold

The structures of interleukin-1ß, basic fibroblastgrowth factor and Erythrina trypsin inhibitor have been analysedin order to determine whether the hydrophobic core remains conserved,even when the structures have extremely low sequence similarities.We find that there are significant differences in the way eachprotein achieves a satisfactory arrangement of core residuesand that positions which contribute to the core of one structureare not guaranteed to contribute to the integrity of another.Furthermore, the side-chain packing arrangements of these coreresidues vary significantly between the three structures. Duringthis analysis the side-chain rotamers for three independentlydetermined interleukin-1ß structures were also compared.It was found that although buried residues are generally inagreement the remaining residues frequently occupy differentrotamers in the three structures. This suggests that althoughmeaningful studies are possible for buried side-chains the resultsobtained from equivalent analyses of accessible residues shouldbe treated with caution. These results are discussed with specificreference to the optimization of side-chain packing in proteinsof known structure.     

Substitutional diffusion and Kirkendall effect in binary crystalline solids containing discrete vacancy sources and sinks

We investigate vacancy-mediated diffusion in a binary substitutional alloy by explicitly accounting for discrete vacancy sources and sinks. The regions between sources and sinks are treated as binary crystals with a perfect lattice structure containing a dilute concentration of vacancies. The sources and sinks are assumed ideal, maintaining an equilibrium vacancy concentration in their immediate vicinity. Diffusion within the perfect lattice is described with a diffusion-coefficient matrix determined by kinetic Monte Carlo simulations for a binary, thermodynamically ideal alloy in which the components have different vacancy-exchange frequencies. Continuum simulations are performed for diffusion couples with discrete grain boundaries acting as vacancy sources and sinks. Effective grain coarsening due to the Kirkendall effect is observed even in the absence of Gibbs-Thomson driving forces. As in standard ternary systems, uphill diffusion is observed. We also find that the drift of the lattice frame of reference as a result of the Kirkendall effect increases with the source/sink density. Upon increasing the density of vacancy sources and sinks, we recover the conventional treatment of substitutional diffusion, which assumes a dense and uniform distribution of vacancy sources and sinks that maintain an equilibrium vacancy concentration throughout the solid. The inverse Kirkendall effect, where the slower component segregates at grain boundaries acting as vacancy sinks, is also observed in the simulations.     

A bayesian approach to deformed pattern matching of iris images

We describe a general probabilistic framework for matching patterns that experience in-plane nonlinear deformations, such as iris patterns. Given a pair of images, we derive a maximum a posteriori probability (MAP) estimate of the parameters of the relative deformation between them. Our estimation process accomplishes two things simultaneously: it normalizes for pattern warping and it returns a distortion-tolerant similarity metric which can be used for matching two nonlinearly deformed image patterns. The prior probability of the deformation parameters is specific to the pattern-type and, therefore, should result in more accurate matching than an arbitrary general distribution. We show that the proposed method is very well suited for handling iris biometrics, applying it to two databases of iris images which contain real instances of warped patterns. We demonstrate a significant improvement in matching accuracy using the proposed deformed Bayesian matching methodology. We also show that the additional computation required to estimate the deformation is relatively inexpensive, making it suitable for real-time applications     

Visual signatures in video visualization

Video visualization is a computation process that extracts meaningful information from original video data sets and conveys the extracted information to users in appropriate visual representations. This paper presents a broad treatment of the subject, following a typical research pipeline involving concept formulation, system development, a path-finding user study, and a field trial with real application data. In particular, we have conducted a fundamental study on the visualization of motion events in videos. We have, for the first time, deployed flow visualization techniques in video visualization. We have compared the effectiveness of different abstract visual representations of videos. We have conducted a user study to examine whether users are able to learn to recognize visual signatures of motions, and to assist in the evaluation of different visualization techniques. We have applied our understanding and the developed techniques to a set of application video clips. Our study has demonstrated that video visualization is both technically feasible and cost-effective. It has provided the first set of evidence confirming that ordinary users can be accustomed to the visual features depicted in video visualizations, and can learn to recognize visual signatures of a variety of motion events.     

Ion-pairs in proteins

A "working definition" for an ion-pair has been derived based upon analysis of the distance distributions for like- and oppositely charged groups in 38 proteins. Ion-pairs defined according to this criterion (less than or equal to 4 A between charged groups) have been analysed in respect of: (1) the frequencies of different pair types; (2) the residue separations and secondary structural locations of the residues involved; (3) the flexibility of the side-chains involved; (4) their conformation; (5) their environment (accessibility to solvent and proximity to active site or ligand binding regions); and (6) their conservation in related proteins. The results obtained indicate that on average one-third of the charged residues in a protein are involved in ion-pairs and 76% of these are concerned with stabilizing the tertiary (rather than the secondary) structure. Only 17% of ion-pairs are buried, and conservation of the interactions is generally low unless the residues involved have more specific functions to perform. In the light of the results obtained, the role of ion pairs in globular proteins is discussed.     

Hyperinsulinemic Hypoglycemia Associated with a CaV1.2 Variant with Mixed Gain- and Loss-of-Function Effects

The voltage-dependent L-type calcium channel isoform Ca_V1.2 is critically involved in many physiological processes, e.g., in cardiac action potential formation, electromechanical coupling and regulation of insulin secretion by beta cells. Gain-of-function mutations in the calcium voltage-gated channel subunit alpha 1 C (CACNA1C) gene, encoding the Ca_V1.2 α₁-subunit, cause Timothy syndrome (TS), a multisystemic disorder that includes autism spectrum disorders and long QT (LQT) syndrome. Strikingly, TS patients frequently suffer from hypoglycemia of yet unproven origin. Using next-generation sequencing, we identified a novel heterozygous CACNA1C mutation in a patient with congenital hyperinsulinism (CHI) and associated hypoglycemic episodes. We characterized the electrophysiological phenotype of the mutated channel using voltage-clamp recordings and in silico action potential modeling experiments. The identified Ca_V1.2^L566P mutation causes a mixed electrophysiological phenotype of gain- and loss-of-function effects. In silico action potential modeling supports that this mixed electrophysiological phenotype leads to a tissue-specific impact on beta cells compared to cardiomyocytes. Thus, CACNA1C variants may be associated with non-syndromic hyperinsulinemic hypoglycemia without long-QT syndrome, explained by very specific electrophysiological properties of the mutated channel. We discuss different biochemical characteristics and clinical impacts of hypoglycemia in the context of CACNA1C variants and show that these may be associated with significant morbidity for Timothy Syndrome patients. Our findings underline that the potential of hypoglycemia warrants careful attention in patients with CACNA1C variants, and such variants should be included in the differential diagnosis of non-syndromic congenital hyperinsulinism.     

Fluid Flow and Defect Formation in the Three-Dimensional Dendritic Structure of Nickel-Based Single Crystals

Fluid flow within the dendritic structure at the solid–liquid interface in nickel-based superalloys has been studied in two directionally solidified alloy systems. Millimeter-scale, three-dimensional (3D) datasets of dendritic structure have been collected by serial sectioning, and the reconstructed mushy zones have been used as domains for fluid-flow modeling. Flow permeability and the influence of dendritic structure on flow patterns have been investigated. Permeability analyses indicate that the cross flow normal to the withdrawal direction limits the development of flow instabilities. Local Rayleigh numbers calculated using the permeabilities extracted from the 3D dataset are higher than predicted by conventional empirical calculations in the regions of the mushy zone that are prone to the onset of convective instabilities. The ability to measure dendrite surface area in 3D volumes permit improved prediction of permeability as well.