Analysis of UDP-galactose 4'-epimerase mutations associated with the intermediate form of type III galactosaemia

Type III galactosaemia is a hereditary disease caused by reduced activity in the Leloir pathway enzyme, UDP-galactose 4'-epimerase (GALE). Traditionally, the condition has been divided into two forms-a mild, or peripheral, form and a severe, or generalized, form. Recently it has become apparent that there are disease states which are intermediate between these two extremes. Three mutations associated with this intermediate form (S81R, T150M and P293L) were analysed for their kinetic and structural properties in vitro and their effects on galactose-sensitivity of Saccharomyces cerevisiae cells that were deleted for the yeast GALE homologue Gal10p. All three mutations result in impairment of the kinetic parameters (principally the turnover number, k(cat)) compared with the wild-type enzyme. However, the degree of impairment was mild compared with that seen with the mutation (V94M) associated with the generalized form of epimerase deficiency galactosaemia. None of the three mutations tested affected the ability of the protein to dimerize in solution or its susceptibility to limited proteolysis in vitro. Finally, in the yeast model, each of the mutated patient alleles was able to complement the galactose-sensitivity of gal10 Delta cells as fully as was the wild-type human allele. Furthermore, there was no difference from control in metabolite profile following galactose exposure for any of these strains. Thus we conclude that the subtle biochemical and metabolic abnormalities detected in patients expressing these GALE alleles likely reflect, at least in part, the reduced enzymatic activity of the encoded GALE proteins.

Analysing orchestrations with risk profiles and angel-daemon games

In this paper game theory is used to analyse the effect of a number of service failures during the execution of a grid orchestration. A service failure may be catastrophic in that it causes an entire orchestration to fail. Alternatively, a grid manager may utilise alternative services in the case of failure, allowing an orchestration to recover, A risk profile provides a means of modelling situations in a way that is neither overly optimistic nor overly pessimistic. Risk profiles are analysed using angel and daemon games. A risk profile can be assigned a valuation through an analysis of the structure of its associated Nash equilibria. Some structural properties of valuation functions, that show their validity as a measure for risk, are given. Two main cases are considered, the assessment of Orc expressions and the arrangement of a meeting using reputations.

Probing warm dense lithium by inelastic X-ray scattering

One of the grand challenges of contemporary physics is understanding strongly interacting quantum systems comprising such diverse examples as ultracold atoms in traps, electrons in high-temperature superconductors and nuclear matter. Warm dense matter, defined by temperatures of a few electron volts and densities comparable with solids, is a complex state of such interacting matter. Moreover, the study of warm dense matter states has practical applications for controlled thermonuclear fusion, where it is encountered during the implosion phase, and it also represents laboratory analogues of astrophysical environments found in the core of planets and the crusts of old stars, Here we demonstrate how warm dense matter states can be diagnosed and structural properties can be obtained by inelastic X-ray scattering measurements on a compressed lithium sample. Combining experiments and ab initio simulations enables us to determine its microscopic state and to evaluate more approximate theoretical models for the ionic structure.

Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae

Background: Gene networks are a representation of molecular interactions among genes or products thereof and, hence, are forming causal networks. Despite intense studies during the last years most investigations focus so far on inferential methods to reconstruct gene networks from experimental data or on their structural properties, e.g., degree distributions. Their structural analysis to gain functional insights into organizational principles of, e.g., pathways remains so far under appreciated.

Interstitial cells of blood vessels

Blood vessels are made up of several distinct cell types. Although it was originally thought that the tunica media of blood vessels was composed of a homogeneous population of fully differentiated smooth muscle cells, more recent data suggest the existence of multiple smooth muscle cell subpopulations in the vascular wall. One of the cell types contributing to this heterogeneity is the novel, irregularly shaped, noncontractile cell with thin processes, termed interstitial cell, found in the tunica media of both veins and arteries. While the principal role of interstitial cells in veins seems to be pacemaking, the role of arterial interstitial cells is less clear. This review summarises the knowledge of the functional and structural properties of vascular interstitial cells accumulated so far, offers hypotheses on their physiological role, and proposes directions for future research.

A similarity measure for graphs with low computational complexity

We present and analyze an algorithm to measure the structural similarity of generalized trees, a new graph class which includes rooted trees. For this, we represent structural properties of graphs as strings and define the similarity of two Graphs as optimal alignments of the corresponding property stings. We prove that the obtained graph similarity measures are so called Backward similarity measures. From this we find that the time complexity of our algorithm is polynomial and, hence, significantly better than the time complexity of classical graph similarity methods based on isomorphic relations. (c) 2006 Elsevier Inc. All rights reserved.

Shell Model Study of Local and Global Energy Barriers in KDP

We perform a study of the energetics of KH2PO4 (KDP) by using a shell model (SM) which was constructed by adjusting the interaction parameters to ab initio calculations, and was fitted to reproduce phonons, polarization-inversion energies and structural properties. We calculate the energy profiles by performing global displacements and local distortions following the ferroelectric (FE) mode pattern in clusters of different sizes embedded in a paraelectric (PE) phase matrix. These properties are expected to be relevant to the PE-FE phase transition. The obtained SM results are compared to corresponding ab initio (AI) data. The global instabilities are found in good agreement for both KDP and DKDP. We also find qualitative good agreement in the KDP structure and even quantitative agreement in the expanded DKDP structure for the local distortions. The SM results reproduce well different trends like increasing instabilities as the cluster sizes grows, as the heavier atoms are included, and as the volume is increased, in accordance with the corresponding data from AI calculations.

Networks for systems biology: conceptual connection of data and function

The purpose of this study is to survey the use of networks and network-based methods in systems biology. This study starts with an introduction to graph theory and basic measures allowing to quantify structural properties of networks. Then, the authors present important network classes and gene networks as well as methods for their analysis. In the last part of this study, the authors review approaches that aim at analysing the functional organisation of gene networks and the use of networks in medicine. In addition to this, the authors advocate networks as a systematic approach to general problems in systems biology, because networks are capable of assuming multiple roles that are very beneficial connecting experimental data with a functional interpretation in biological terms.

Dynamic pricing for used products in remanufacturing with back orders(ABS 3* Journal, Accepted with Revision on 2nd December 2011).

In remanufacturing, the supply of used products and the demand for remanufactured products are usually mismatched because of the great uncertainties on both sides. In this paper, we propose a dynamic pricing policy to balance this uncertain supply and demand. Specifically, we study a remanufacturer’s problem of pricing a single class of cores with random price-dependent returns and random demand for the remanufactured products with backlogs. We model this pricing task as a continuous-time Markov decision process, which addresses both the finite and infinite horizon problems, and provide managerial insights by analyzing the structural properties of the optimal policy. We then use several computational examples to illustrate the impacts of particular system parameters on pricing policy.

Exploring statistical and population aspects of network complexity

The characterization and the definition of the complexity of objects is an important but very difficult problem that attracted much interest in many different fields. In this paper we introduce a new measure, called network diversity score (NDS), which allows us to quantify structural properties of networks. We demonstrate numerically that our diversity score is capable of distinguishing ordered, random and complex networks from each other and, hence, allowing us to categorize networks with respect to their structural complexity. We study 16 additional network complexity measures and find that none of these measures has similar good categorization capabilities. In contrast to many other measures suggested so far aiming for a characterization of the structural complexity of networks, our score is different for a variety of reasons. First, our score is multiplicatively composed of four individual scores, each assessing different structural properties of a network. That means our composite score reflects the structural diversity of a network. Second, our score is defined for a population of networks instead of individual networks. We will show that this removes an unwanted ambiguity, inherently present in measures that are based on single networks. In order to apply our measure practically, we provide a statistical estimator for the diversity score, which is based on a finite number of samples.

Electromagnetic rogue waves in beam-plasma interactions

The occurrence of rogue waves (freak waves) associated with electromagnetic pulse propagation interacting with a plasma is investigated, from first principles. A multiscale technique is employed to solve the fluid Maxwell equations describing weakly nonlinear circularly polarized electromagnetic pulses in magnetized plasmas. A nonlinear Schrödinger (NLS) type equation is shown to govern the amplitude of the vector potential. A set of non-stationary envelope solutions of the NLS equation are considered as potential candidates for the modeling of rogue waves (freak waves) in beam-plasma interactions, namely in the form of the Peregrine soliton, the Akhmediev breather and the Kuznetsov-Ma breather. The variation of the structural properties of the latter structures with relevant plasma parameters is investigated, in particular focusing on the ratio between the (magnetic field dependent) cyclotron (gyro-)frequency and the plasma frequency. © 2013 IOP Publishing Ltd.

Multiferroic PbZrxTi1-xO3/Fe3O4 epitaxial sub-micron sized structures

Large range well ordered epitaxial ferrimagnetic nominally Fe3O4 structures were fabricated by pulsed-laser deposition and embedded in ferroelectric PbZrxTi1-xO3 (x = 0.2, 0.52) epitaxial films. Magnetite dots were investigated by magnetic force microscopy and exhibited magnetic domain contrast at room temperature (RT). Embedding ferroelectric PbZrxTi1-xO3 layers exhibit remnant polarization values close to the values of single epitaxial layers. Transmission electron microscopy demonstrated the epitaxial growth of the composites and the formation of the ferrimagnetic and ferroelectric phases. Physical and structural properties of these composites recommend them for investigations of stress mediated magneto-electric coupling at room temperature. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3692583]

Advanced Modelling and Optimization of Infared Oven in Injection Stretch Blow-moulding for Energy Saving

In the production process of polyethylene terephthalate (PET) bottles, the initial temperature of preforms plays a central role on the final thickness, intensity and other structural properties of the bottles. Also, the difference between inside and outside temperature profiles could make a significant impact on the final product quality. The preforms are preheated by infrared heating oven system which is often an open loop system and relies heavily on trial and error approach to adjust the lamp power settings. In this paper, a radial basis function (RBF) neural network model, optimized by a two-stage selection (TSS) algorithm combined with partial swarm optimization (PSO), is developed to model the nonlinear relations between the lamp power settings and the output temperature profile of PET bottles. Then an improved PSO method for lamp setting adjustment using the above model is presented. Simulation results based on experimental data confirm the effectiveness of the modelling and optimization method.

Analysing Web-Orchestrations Under Stress Using Uncertainty Profiles

An orchestration is a multi-threaded computation that invokes a number of remote services. In practice, the responsiveness of a web-service fluctuates with demand; during surges in activity service responsiveness may be degraded, perhaps even to the point of failure. An uncertainty profile formalizes a user's perception of the effects of stress on an orchestration of web-services; it describes a strategic situation, modelled by a zero-sum angel–daemon game. Stressed web-service scenarios are analysed, using game theory, in a realistic way, lying between over-optimism (services are entirely reliable) and over-pessimism (all services are broken). The ‘resilience’ of an uncertainty profile can be assessed using the valuation of its associated zero-sum game. In order to demonstrate the validity of the approach, we consider two measures of resilience and a number of different stress models. It is shown how (i) uncertainty profiles can be ordered by risk (as measured by game valuations) and (ii) the structural properties of risk partial orders can be analysed.

Robust Room Temperature Hysteresis in an FeIII Spin Crossover Metallomesogen

The high temperature magnetic and structural properties of an amphiphilic iron(III) spin crossover complex are reported. Thermal cycling reveals a scan rate-dependent 20 K thermal hysteresis in the mT vs. T data close to room temperature. A fast scan rate is essential for the hysteresis but it is robust and reproducible after multiple thermal cycles. Differential scanning calorimetry and cross polarized microscopy are used to show that the magnetic switching aligns with a material state change from solid to ordered liquid phase on warming.