Fundamentals of modelling concurrency using discrete relational structures

We consider relational structures such that is a set and are two binary relations on . For a number of different classes of structures we show that any structure can be represented as the intersection of its maximal extensions. Such a property – called extension completeness – can be seen as a generalisation of Szpilrajn's theorem which states that each partial order is the intersection of its total order extensions. When can be interpreted as causality and as ‘weak’ causality we obtain a model of concurrent histories generalising that based on causal partial orders. Received 1 February 1994 / 6 May 1996     

A Multiplex Assay to Assess the Transaminase Activity toward Chemically Diverse Amine Donors

The development of methods to engineer and immobilize amine transaminases (ATAs) to improve their functionality and operational stability is gaining momentum. The quest for robust, fast, and easy-to-use methods to screen the activity of large collections of transaminases, is essential. This work presents a novel and multiplex fluorescence-based kinetic assay to assess ATA activity using 4-dimethylamino-1-naphthaldehyde as an amine acceptor. The developed assay allowed us to screen a battery of amine donors using free and immobilized ATAs from different microbial sources as biocatalysts. As a result, using chromatographic methods, 4-hydroxybenzylamine was identified as the best amine donor for the amination of 5-(hydroxymethyl)furfural. Finally, we adapted this method to determine the apparent Michaelis-Menten parameters of a model immobilized ATA at the microscopic (single-particle) level. Our studies promote the use of this multiplex, multidimensional assay to screen ATAs for further improvement.     

A new generation of fibers from alginic acid for dressing materials

We developed and elaborated manufacturing conditions for the production of alginic acid fibers with high sorption properties. The fibers' tenacity obtained at a level of 16 cN/tex is suitable for textile processing these fibers, and will make it possible to produce a new generation of highly absorptive dressing materials. The presence of acid groups in the fiber‐forming material allows us to use them for the addition of new generation antibiotics, which makes it possible to extend the antibacterial effects of these fibers. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2008     

Label-Free Quantitative Proteomics Reveals Differences in Molecular Mechanism of Atherosclerosis Related and Non-Related to Chronic Kidney Disease

The major cause of mortality in patients with chronic kidney disease (CKD) is atherosclerosis related to traditional and non-traditional risk factors. However, the understanding of the molecular specificity that distinguishes the risk factors for classical cardiovascular disease (CVD) and CKD-related atherosclerosis (CKD-A) is far from complete. In this study we investigated the disease-related differences in the proteomes of patients with atherosclerosis related and non-related to CKD. Plasma collected from patients in various stages of CKD, CVD patients without symptoms of kidney dysfunction, and healthy volunteers (HVs), were analyzed by a coupled label-free and mass spectrometry approach. Dysregulated proteins were confirmed by an enzyme-linked immunosorbent assay (ELISA). All proteomic data were correlated with kidney disease development and were subjected to bioinformatics analysis. One hundred sixty-two differentially expressed proteins were identified. By directly comparing the plasma proteomes from HVs, CKD, and CVD patients in one study, we demonstrated that proteins involved in inflammation, blood coagulation, oxidative stress, vascular damage, and calcification process exhibited greater alterations in patients with atherosclerosis related with CKD. These data indicate that the above nontraditional risk factors are strongly specific for CKD-A and appear to be less essential for the development of “classical” CVD.     

The Semantic Web: Collective Intelligence on the Web

The World Wide Web has turned hypertext into a success story by enabling world-wide sharing of unstructured information and informal knowledge. The Semantic Web targets the sharing of structured information and formal knowledge pursuing objectives of achieving collective intelligence on the Web. Germane to the structure of the Semantic Web is a layering and standardization of concerns. These concerns are reflected by an architecture of the Semantic Web that we present through a common use case. Semantic Web data for the use case is now found on the Web and is part of a quickly growing set of Semantic Web resources available for formal processing.     

Multipose Binding in Molecular Docking

Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.     

Catalytic graphene formation in coal tar pitch- derived carbon structure in the presence of SiO2 nanoparticles

A simple and effective way to manufacture graphene from a coal tar pitch (CTP) is demonstrated. Silica (SiO₂) nanoparticles were used to modify the CTP as carbon precursor. A silica nanofiller introduced into the CTP matrix underwent carboreduction during heat treatment to 2000 °C, resulting in the formation of silicon carbide. Surfaces of SiC grains were sites for graphene formation. The influence of SiO₂ on the structure and microstructure of CTP- based carbon matrix, after annealing up to 2800 °C, was studied. Carbon samples were analyzed using X- ray Diffraction (XRD), Transmission Electron Microscopy (TEM) and Raman Spectroscopy. Crystallite sizes (L_a, L_c) and interplanar distance (d₀₀₂) were determined. The presence of SiO₂ in CTP carbon precursor favored the crystallites’ growth in the ‘a′ crystallographic graphite direction, and inhibited their growth on the ‘c′ axis. The crystallites composing of graphene layers, were characterized by an elongated dimension in the ‘a′ axis direction. Above 2000 °C silicon carbide decomposed, followed by the sublimation of silicon from the carbon matrix.     

Non-minimum-phase property of N-trailer kinematics resulting from off-axle interconnections

Off-axle interconnections between segments of N-trailer vehicles may imply specific oscillatory behaviour of trailers during vehicle manoeuvres. The paper reveals that this kind of oscillations is a direct consequence of the non-minimum-phase property of vehicle kinematics resulting from application of off-axle interconnections between vehicle segments. First we show the non-minimum-phase property for dynamics of a single pair of interconnected segments, and then how it propagates along the N-trailers equipped with arbitrary number of off-axle interconnections. By referring to available results for linear systems, we locally analyse linearly approximated vehicle kinematics around selected steady-motion conditions. We focus on the time-response effects like undershooting, zero-crossing, and overshooting caused by off-axle interconnections. We show how the number and type of interconnections influence the non-minimum-phase effects. Numerical results obtained for three-trailer kinematics validate theoretical considerations providing some quantitative view of the problem. Short discussion has been provided on the possible control-level consequences resulting from the non-minimum-phase property of N-trailers.