Universality in protein residue networks

Residue networks representing 595 nonhomologous proteins are studied. These networks exhibit universal topological characteristics as they belong to the topological class of modular networks formed by several highly interconnected clusters separated by topological cavities. There are some networks which tend to deviate from this universality. These networks represent small-size proteins having less than 200 residues. We explain such differences in terms of the domain structure of these proteins. On the other hand, we find that the topological cavities characterizing proteins residue networks match very well with protein binding sites. We then investigate the effect of the cutoff value used in building the residue network. For small cutoff values, less than 5Å, the cavities found are very large corresponding almost to the whole protein surface. On the contrary, for large cutoff value, more than 10.0 Å, only very large cavities are detected and the networks look very homogeneous. These findings are useful for practical purposes as well as for identifying "protein-like" complex networks. Finally, we show that the main topological class of residue networks is not reproduced by random networks growing according to Erdös-Rényi model or the preferential attachment method of Barabási-Albert. However, the Watts-Strogatz (WS) model reproduces very well the topological class as well as other topological properties of residue network. We propose here a more biologically appealing modification of the WS model to describe residue networks

Commercial fire-retarded PET formulations - relationship between thermal degradation behaviour and fire-retardant action

Many types of fire-retardants are used in poly(ethylene terephthalate), PET, formulations, and two commercial fire retardants, Ukanol(TM) and Phosgard(TM), have been shown to improve significantly PET flame-retardancy when used as comonomers. Phosgard incorporates a phosphorus atom within the main chain whereas Ukanol incorporates a phosphorus atom as a pendent substituent. Despite their acknowledged effectiveness, the mode of action of these fire retardants remains unclear, and in this paper we present a comparison of the overall thermal degradation behaviour of PET and Ukanol and Phosgard fire retarded formulations. DSC and particularly TGA data show that both Ukanol and Phosgard have some stabilising influence on PET degradation, especially under oxidative conditions. TGA and pyrolysis experiments both clearly indicate that neither additive acts as a char promoter. Only the Phosgard formulation shows any release of volatile phosphorus species which could act in the gas phase. On the other hand, the most striking feature of the pyrolysis experiments is the macroscopic structure of the chars produced by the fire-retarded formulations, which hints at their fire-retardancy action - an open-cell charred foam was obtained upon charring at 400°C or 600°C. This foaming layer between the degrading melt and the flame would lower the amount of fuel available for combustion, and would also limit the feedback of heat to the condensed phase

Mathematical modelling of internal HIV dynamics

We study a mathematical model for the viral dynamics of HIV in an infected individual in the presence of HAART. The paper starts with a literature review and then formulates the basic mathematical model. An expression for R0, the basic reproduction number of the virus under steady state application of HAART, is derived followed by an equilibrium and stability analysis. There is always a disease-free equilibrium (DFE) which is globally asymptotically stable for R0 1 then some simulations will die out whereas others will not. Stochastic simulations suggest that if R0 > 1 those which do not die out approach a stochastic quasi-equilibrium consisting of random uctuations about the non-trivial deterministic equilibrium levels, but the amplitude of these uctuations is so small that practically the system is at the non-trivial equilibrium. A brief discussion concludes the paper

The guitar music of Heitor Villa-Lobos : challenging common assumptions regarding idiomatic fingerings, shapes and gestures as used in selected preludes and etudesc

The lecture explores the idiomatic "guitaristic" gestures used by Villa-Lobos in selected Etudes and Preludes focusing on the relationships between both the "idiomatic" fingerings/shapes employed by Villa-Lobos and their the harmonic and formal design of each composition. The emphasis is emphasis on Etude number 12, though there is further discussion of how early twentieth century compositional trends were incorporated in the Etudes, Preludes and Choros of Villa-Lobos. Audio/visual recording of a lecture-presentation given for the Big Guitar Weekend event at the Royal Scottish Academy of Music and Drama 10 November 2009

A triangulation approach for design research

Triangulation has been adopted in social science in the study of the same phenomenon through applying and combining several data sources, research methods, investigators, and theoretical schemes. From a post-positivism view point, this paper presents a triangulation approach in design research from two perspectives, data sources and research methods. Data triangulation was achieved through collecting data from multiple sources including company design documents, student design projects, and company design projects. Different research methods, e.g. interview, content analysis, protocol analysis, and questionnaire, were used to conduct data collection and analysis into a particular aspect of design, the nature of coupling design artefact and process knowledge. It was found that triangulation can provide an effective means for design research

Anisotropic creep model for soft soils

In this paper a new anisotropic model for time-dependent behaviour of soft soils is presented. The formulation is based on a previously developed isotropic creep model, assuming rotated Modified Cam Clay ellipses as contours of volumetric creep strain rates. A rotational hardening law is adopted to account for changes in anisotropy due to viscous strains. Although this will introduce some new soil parameters, they do not need calibration as they can be expressed as functions of basic soil parameters through simple analytical expressions. To start with, the one-dimensional response of the model is discussed, making it possible to explore how the model is capable of capturing key features of viscous soft soil behaviour. Subsequently, the three-dimensional generalisation of the model is presented, followed by comparison with experimental data, showing good agreement in both triaxial undrained compression and extension. In the authors' opinion, the simple formulation of the model makes it attractive for use in engineering practice

Plastic anisotropy of soft reconstituted clays

The aim of the paper is to extend the experimental validation of the S-CLAY1 model, which is a recently proposed elastoplastic constitutive model that accounts for initial and plastic strain-induced anisotropy. Drained stress path controlled tests were performed on reconstituted samples of four Finnish clays to study the effects of anisotropy in the absence of the complexities of structure present in natural undisturbed clays. Each test involved several loading, unloading, and reloading stages with different values of stress ratio and, hence, induced noticeable changes in the fabric anisotropy. Comparisons between test results and model predictions with the S-CLAY1 model and the modified Cam clay model demonstrate that despite its simplicity, the S-CLAY1 model can provide excellent predictions of the behaviour of unstructured soil

Understanding and promoting student mental health in Scottish higher education - a mapping exercise

There has been an increase in the incidence of mental health difficulties among HE students over the past decade. Official statistics show that the proportion of undergraduates declaring a mental health difficulty on entry to HE rose from 5 in every 10,000 in 1994-5 to 30 in every 10,000 in 2004-5. Incidence of severe psychological problems has increased, and student mental health is generally worse than that of the general population (for agematched populations). Anxiety and depression are the most commonly noted difficulties. The research review identified a relationship between mental health and the following factors: finances, accommodation, academic issues, university systems and social factors. Academic issues, and specifically coursework, emerged as particularly related to stress levels and mental health issues

Micromechanical analysis of kinematic hardening in natural clay

This paper presents a micromechanical analysis of the macroscopic behaviour of natural clay. A microstructural stress-strain model for clayey material has been developed which considers clay as a collection of clusters. The deformation of a representative volume of the material is generated by mobilizing and compressing all the clusters along their contact planes. Numerical simulations of multistage drained triaxial stress paths on Otaniemi clay have been performed and compared the numerical results to the experimental ones in order to validate the modelling approach. Then, the numerical results obtained at the microscopic level were analysed in order to explain the induced anisotropy observed in the clay behaviour at the macroscopic level. The evolution of the state variables at each contact plane during loading can explain the changes in shape and position in the stress space of the yield surface at the macroscopic level, as well as the rotation of the axes of anisotropy of the material

Fast Track Children's Hearings Pilot : Final Report of the Evaluation of the Pilot

The Scottish Executive decided that a Fast Track approach to the children's hearings system would be introduced in early 2003 on a pilot basis in selected parts of Scotland. The aim was to improve practice and outcomes with respect to the ways that the hearings system and associated services dealt with young people who persistently offend. Particular objectives were to: • reduce the time taken both overall and at each stage of decision-making • promote more comprehensive assessments which include appraisals of offending risk • ensure that all young people who persistently offend and who require an appropriate programme have access to one • reduce re-offending rates as a result of the concerted efforts made in such cases