Geometric criteria of hydrogen bonds in proteins and identification of `bifurcated' hydrogen bonds

Empirical criteria for identification of hydrogen bonds wereanalyzed to produce a set of geometrically consistent criteria.For a data set of 30 structures, application of a set of purelygeometrical criteria, along with exclusion of abnormal backboneconformations, also excluded a common interaction of Ser/Thrside chains with Asp/Glu side chains ([ST]/[DE] pairs). Theseinteractions were termed `bifurcated hydrogen bonds/', whichimplies delocalization of a positively charged hydrogen of hydroxylbetween the two acceptor atoms of the carboxylic group. These`bifurcated/' interactions are among the most common packingpatterns for [ST]/[DE] pairs of side chains. Therefore, theidentification of hydrogen bonds cannot be based on geometricalcriteria only and requires introduction of some physico-chemicalcriteria.     

How disorder can diminish avalanche risks: effect of size distribution

We study the behavior of disk assemblies with a variable disorder distribution. The packing is first consolidated and then continuously tilted very slowly. The amount of displaced disks for each tilted angle is recorded. Large displacements of the disks can occur due to some local or global mechanical instabilities. The definition of neighboring disks is based on radical (extension of Voronoï) tessellation rules to decompose, in a unique and perfectly defined manner, the two-dimensional space for polydisperse disks. In this way, by comparing the characteristics of stability for one disk to the neighboring ones for local ordered cluster, we can predict the global amount of displaced disks. Some tilting cycles have been performed to check the correlation between the instability of the packing structure (collective displacements) with micro and macro order parameters.     

Melanin Distribution in Human Skin: Influence of Cytoskeletal,Polarity, and Centrosome-Related Machinery of Stratum basale Keratinocytes

Melanin granules cluster within supra-nuclear caps in basal keratinocytes (KCs) of the human epidermis, where they protect KC genomic DNA against ultraviolet radiation (UVR) damage. While much is known about melanogenesis in melanocytes (MCs) and a moderate amount about melanin transfer from MC to KC, we know little about the fate of melanin once inside KCs. We recently reported that melanin fate in progenitor KCs is regulated by rare asymmetric organelle movement during mitosis. Here, we explore the role of actin, microtubules, and centrosome-associated machinery in distributing melanin within KCs. Short-term cultures of human skin explants were treated with cytochalasin-B and nocodazole to target actin filaments and microtubules, respectively. Treatment effects on melanin distribution were assessed by the Warthin–Starry stain, on centrosome-associated proteins by immunofluorescence microscopy, and on co-localisation with melanin granules by brightfield microscopy. Cytochalasin-B treatment disassembled supra-nuclear melanin caps, while nocodazole treatment moved melanin from the apical to basal KC domain. Centrosome and centriolar satellite-associated proteins showed a high degree of co-localisation with melanin. Thus, once melanin granules are transferred to KCs, their preferred apical distribution appears to be facilitated by coordinated movement of centrosomes and centriolar satellites. This mechanism may control melanin’s strategic position within UVR-exposed KCs.     

Synthesis and properties of aminopropyl nucleic acids

Oligonucleotides that contain up to three aminopropyl nucleoside analogues have been synthesized. Dimers of aminopropyl adenine and thymidine were prepared and used as building blocks by applying phosphoramidite chemistry. Both R and S isomers of the aminopropyl nucleosides were used. This incorporation led to a reduction of thermal stability of double-stranded DNA. Furthermore, the (R)-adenine analogue, which yielded (S)-APNA, can be considered as a candidate for universal base pairing.     

Texture and shape information fusion for facial expression and facial action unit recognition

A novel method based on fusion of texture and shape information is proposed for facial expression and Facial Action Unit (FAU) recognition from video sequences. Regarding facial expression recognition, a subspace method based on Discriminant Non-negative Matrix Factorization (DNMF) is applied to the images, thus extracting the texture information. In order to extract the shape information, the system firstly extracts the deformed Candide facial grid that corresponds to the facial expression depicted in the video sequence. A Support Vector Machine (SVM) system designed on an Euclidean space, defined over a novel metric between grids, is used for the classification of the shape information. Regarding FAU recognition, the texture extraction method (DNMF) is applied on the differences images of the video sequence, calculated taking under consideration the neutral and the expressive frame. An SVM system is used for FAU classification from the shape information. This time, the shape information consists of the grid node coordinate displacements between the neutral and the expressed facial expression frame. The fusion of texture and shape information is performed using various approaches, among which are SVMs and Median Radial Basis Functions (MRBFs), in order to detect the facial expression and the set of present FAUs. The accuracy achieved using the Cohn–Kanade database is 92.3% when recognizing the seven basic facial expressions (anger, disgust, fear, happiness, sadness, surprise and neutral), and 92.1% when recognizing the 17 FAUs that are responsible for facial expression development.     

A JESS-enabled context elicitation system for providing context-aware Web services

Providing context-aware Web services is an adaptive process of delivering contextually matched Web services to meet service requesters’ needs. We define the term “context” from two perspectives: one from service requesters; and the other from Web services. From the former perspective, context is defined as the surrounding environment affecting requesters’ services discovery and access, such as requesters’ preferences, locations, activities, and accessible network and devices. From the latter perspective, context is defined as the surrounding environment affecting Web services delivery and execution, such as networks and protocols for service binding, devices and platforms for service execution, and so on. This paper presents a Java Expert System Shell (JESS)-enabled context elicitation system featuring an ontology-based context model that formally describes and acquires contextual information pertaining to service requesters and Web services. Based on the context elicitation system, we present a context-aware services-oriented architecture for providing context-aware Web service request, publication, and discovery. Implementation details of the context elicitation system and the evaluation results of context-aware service provision are also reported.     

New approach for optimizing the interpretation and representation of the degree of historical-archaeological evidence in the virtual reconstructions

Virtual Reality - Virtual reconstruction is defined as the visual recovery of a building or object through the creation of a three-dimensional model of the asset to be reconstructed, in a...     

A discontinuous Galerkin solver for Boltzmann–Poisson systems in nano devices

In this paper, we present results of a discontinuous Galerkin (DG) scheme applied to deterministic computations of the transients for the Boltzmann–Poisson system describing electron transport in semiconductor devices. The collisional term models optical-phonon interactions which become dominant under strong energetic conditions corresponding to nano-scale active regions under applied bias. The proposed numerical technique is a finite element method using discontinuous piecewise polynomials as basis functions on unstructured meshes. It is applied to simulate hot electron transport in bulk silicon, in a silicon n⁺–n–n⁺ diode and in a double gated 12 nm MOSFET. Additionally, the obtained results are compared to those of a high order WENO scheme simulation and DSMC (Discrete Simulation Monte Carlo) solvers.