3D-QSAR studies on 4-Hydroxyphenylpyruvate Dioxygenase inhibitors by comparative molecular field analysis (CoMFA)

A comparative molecular field analysis (CoMFA) of alkanoic acid 3-oxo-cyclohex-1-enyl ester and 2-acylcyclohexane-1,3-dione derivatives of 4-hydroxyphenylpyruvate dioxygenase inhibitors has been performed to determine the factors required for the activity of these compounds. The substrate's conformation abstracted from dynamic modeling of the enzyme-substrate complex was used to build the initial structures of the inhibitors. Satisfactory results were obtained after an all-space searching procedure, performing a leave-one out (LOO) cross-validation study with cross-validation q(2) and conventional r(2) values of 0.779 and 0.989, respectively. The results provide the tools for predicting the affinity of related compounds, and for guiding the design and synthesis of new HPPD ligands with predetermined affinities.

Mean field approach for tracking similar objects

In this paper, we consider the problem of tracking similar objects. We show how a mean field approach can be used to deal with interacting targets and we compare it with Markov Chain Monte Carlo (MCMC). Two mean field implementations are presented. The first one is more general and uses particle filtering. We discuss some simplifications of the base algorithm that reduce the computation time. The second one is based on suitable Gaussian approximations of probability densities that lead to a set of self-consistent equations for the means and covariances. These equations give the Kalman solution if there is no interaction. Experiments have been performed on two kinds of sequences. The first kind is composed of a single long sequence of twenty roaming ants and was previously analysed using MCMC. In this case, our mean field algorithms obtain substantially better results. The second kind corresponds to selected sequences of a football match in which the interaction avoids tracker coalescence in situations where independent trackers fail.

Selectivity fields: comparative molecular field analysis (CoMFA) of the glycine/NMDA and AMPA receptors

An approach for evaluation of binding selectivity was suggested and exemplified using glycine/NMDA and AMPA receptors. For analyzing the pairwise selectivity, we propose to use the difference between biological activities (expressed as -log Ki) of ligands with respect to different receptor subtypes as a dependent variable for building comparative molecular field analysis (CoMFA) models. The resulting fields (which will be referred to as the "selectivity fields") indicate the ways of increasing selectivity of binding, inhibition, etc. As an example, CoMFA of a set of pyrazolo[1,5-c]quinazolines and triazolo[1,5-c]quinazolines was used for considering the binding selectivity with respect to glycine/NMDA and AMPA receptors. In addition, the mapping of these fields onto the molecular models of the corresponding receptors makes it possible to reveal the reasons for experimentally observed selectivity as well as to suggest additional ways of increasing selectivity.

Mutational Analysis of the Rhodopsin Gene in Sector Retinitis Pigmentosa

Background: To determine the role of rhodopsin (RHO) gene mutations in patients with sector retinitis pigmentosa (RP) from Northern Ireland.

Design: A case series of sector RP in a tertiary ocular genetics clinic.

Participants: Four patients with sector RP were recruited from the Royal Victoria Hospital (Belfast, Northern Ireland) and Altnagelvin Hospital (Londonderry, Northern Ireland) following informed consent.

Methods: The diagnosis of sector RP was based on clinical examination, International Society for Clinical Electrophysiology of Vision (ISCEV) standard electrophysiology, and visual field analysis. DNA was extracted from peripheral blood leucocytes and the coding regions and adjacent flanking intronic sequences of the RHO gene were polymerase chain reaction (PCR) amplified and cycle sequenced.

Main Outcome Measure: Rhodopsin mutational status.

Results: A heterozygous missense mutation in RHO (c.173C > T) resulting in a non-conservative substitution of threonine to methionine (p. Thr58Met) was identified in one patient and was absent from 360 control individuals. This non-conservative substitution (p.Thr58Met) replaces a highly evolutionary conserved polar hydrophilic threonine residue with a non-polar hydrophobic methionine residue at position 58 near the cytoplasmic border of helix A of RHO.

Conclusions: The study identified a RHO gene mutation (p.Thr58Met) not previously reported in RP in a patient with sector RP. These findings outline the phenotypic variability associated with RHO mutations. It has been proposed that the regional effects of RHO mutations are likely to result from interplay between mutant alleles and other genetic, epigenetic and environmental factors.

Nonlinear response of permanent dipoles in a uniaxial potential to alternating fields

It is shown how the existing theory of the dynamic Kerr effect and nonlinear dielectric relaxation based on the noninertial Brownian rotation of noninteracting rigid dipolar particles may be generalized to take into account interparticle interactions using the Maier-Saupe mean field potential. The results (available in simple closed form) suggest that the frequency dependent nonlinear response provides a method of measuring the Kramers escape rate (or in the analogous problem of magnetic relaxation of fine single domain ferromagnetic particles, the superparamagnetic relaxation time).

Time-dependent tight binding

Starting from a Lagrangian mean-field theory, a set of time-dependent tight-binding equations is derived to describe dynamically and self-consistently an interacting system of quantum electrons and classical nuclei. These equations conserve norm, total energy and total momentum. A comparison with other tight-binding models is made. A previous tight-binding result for forces on atoms in the presence of electrical current flow is generalized to the time-dependent domain and is taken beyond the limit of local charge neutrality.

Generalized compound transport of charged particles in turbulent magnetized plasmas

The transport of charged particles in partially turbulent magnetic systems is investigated from first principles. A generalized compound transport model is proposed, providing an explicit relation between the mean-square deviation of the particle parallel and perpendicular to a magnetic mean field, and the mean-square deviation which characterizes the stochastic field-line topology. The model is applied in various cases of study, and the relation to previous models is discussed.

The Influence of Point Defects and Inhomogeneous Strain on the Functional Behaviour of Thin film Ferroelectrics

An attempt has been made to unequivocally identify the influence that inhomogeneous strain fields, surrounding point defects, have on the functional properties of thin film ferroelectrics. Single crystal thin film lamellae of BaTiO3 have been integrated into capacitor structures, and the functional differences between those annealed in oxygen and those annealed in nitrogen have been mapped. Key features, such as the change in the paraelectric-ferroelectric phase transition from first to second order were noted and found to be consistent with mean field modeling predictions for the effects of inhomogeneous strain. Switching characteristics appeared to be unaffected, suggesting that point defects have a low efficacy in domain wall pinning.

Nonconservative generalized current-induced forces

A recent result for the curl of forces on ions under steady-state current in atomic wires with noninteracting electrons is extended to generalized forces on classical degrees of freedom in the presence of mean-field electron-electron screening. Current is described within a generic multiterminal picture, forces within the Ehrenfest approximation, and screening within an adiabatic, but not necessarily spatially local, mean-field picture.

Spontaneous spin polarization and charge localization in metal nanowires: the role of a geometric constriction

An idealized jellium model of conducting nanowires with a geometric constriction is investigated by density functional theory (DFT) in the local spin density (LSD) approximation. The results reveal a fascinating variety of spin and charge patterns arising in wires of sufficiently low (r(s) >= 15) average electron density, pinned at the indentation by an apparent attractive interaction with the constriction. The spin-resolved frequency-dependent conductivity shows a marked asymmetry in the two spin channels, reflecting the spontaneous spin polarization around the wire neck. The relevance of the computational results is discussed in relation to the so-called 0.7 anomaly found by experiments in the low-frequency conductivity of nanowires at near-breaking conditions (see 2008 J. Phys.: Condens Matter 20, special issue on the 0.7 anomaly). Although our mean-field approach cannot account for the intrinsic many-body effects underlying the 0.7 anomaly, it still provides a diagnostic tool to predict impending transitions in the electronic structure.

Random neighbor sandpile model with constrained total energy

We propose as energy-constrained sandpile model with random neighbors. The critical behavior of the model is in the same universality class as the mean-field self-organized criticality sandpile. The critical energy E-c depends on the number of neighbors n of each site, but the various exponents do not. For n = 6, we got that E-c = 0.4545; and a self-similar structure of the energy distribution function with five major peaks is also observed. This is a natural result of system dynamics and the way the system is disturbed.

Universality and self-similarity of an energy-constrained sandpile model with random neighbors

We study an energy-constrained sandpile model with random neighbors. The critical behavior of the model is in the same universality class as the mean-field self-organized criticality sandpile. The critical energy E-c depends on the number of neighbors n for each site, but the various exponents are independent of n. A self-similar structure with n-1 major peaks is developed for the energy distribution p(E) when the system approaches its stationary state. The avalanche dynamics contributes to the major peaks appearing at E-Pk = 2k/(2n - 1) with k = 1,2,...,n-1, while the fine self-similar structure is a natural result of the way the system is disturbed. [S1063-651X(99)10307-6].

Low Pay, In-Work Poverty and Economic Vulnerability: A Comparative Aanalysis Using EU-SILC

We explore the potential of data from EU-SILC (Statistics on Income and Living Conditions) for the enlarged European Union for the study of low pay and its relationship to household poverty and vulnerability. Limitations of the earnings data currently available mean the analysis covers only 14 of these countries. For employees who are not low paid, income poverty is seen to be rare. The low paid face a much higher risk of being in a household below relative income poverty thresholds, ranging from 7 per cent in Belgium and the Netherlands up to 1718 per cent in Austria, Estonia and Lithuania. The likelihood of their being in a poor household is clearly linked to gender, age and social class. In most of the countries only a minority of low-paid individuals are in vulnerable households.