Protein fold recognition score functions: Unusual construction strategies

We describe two ways of optimizing score functions for protein sequence to structure threading. The first method adjusts parameters to improve sequence to structure alignment. The second adjusts parameters so as to improve a score function's ability to rank alignments calculated in the first score function. Unlike those functions known as knowledge-based force fields, the resulting parameter sets do not rely on Boltzmann statistics, have no claim to representing free energies and are purely constructions for recognizing protein folds. The methods give a small improvement, but suggest that functions can be profitably optimized for very specific aspects of protein fold recognition, Proteins 1999;36:454-461. (C) 1999 Wiley-Liss, Inc.

Absorption spectrum of a strongly driven atom in a detuned squeezed vacuum

We present numerical and analytical results for the Mollow probe absorption spectrum of a coherently driven two-level system in a narrow bandwidth squeezed vacuum field. The spectra are calculated for the case where the Rabi frequency of the driving field is much larger than the natural linewidth and the squeezed vacuum carrier frequency is detuned from the driving laser frequency. The driving laser is on resonance. We show that in a detuned squeezed vacuum the standard Mellow features are each split into triplets. The central components of each triplet are weakly dependent on the squeezing phase but the sidebands strongly depend on the phase and can have dispersive or absorptive/emissive profiles. We also derive approximate analytical expressions for the spectral features and find that the multi-peak structure of the spectrum can be interpreted either via the eigenfrequencies of a generalized Floquet Hamiltonian or in terms of three-photon transitions between dressed stales involving a probe field photon and a correlated photon pair from the squeezed vacuum field.

Finite element modeling of fluid-rock interaction problems in pore-fluid saturated hydrothermal/sedimentary basins

In order to use the finite element method for solving fluid-rock interaction problems in pore-fluid saturated hydrothermal/sedimentary basins effectively and efficiently, we have presented, in this paper, the new concept and numerical algorithms to deal with the fundamental issues associated with the fluid-rock interaction problems. These fundamental issues are often overlooked by some purely numerical modelers. (1) Since the fluid-rock interaction problem involves heterogeneous chemical reactions between reactive aqueous chemical species in the pore-fluid and solid minerals in the rock masses, it is necessary to develop the new concept of the generalized concentration of a solid mineral, so that two types of reactive mass transport equations, namely, the conventional mass transport equation for the aqueous chemical species in the pore-fluid and the degenerated mass transport equation for the solid minerals in the rock mass, can be solved simultaneously in computation. (2) Since the reaction area between the pore-fluid and mineral surfaces is basically a function of the generalized concentration of the solid mineral, there is a definite need to appropriately consider the dependence of the dissolution rate of a dissolving mineral on its generalized concentration in the numerical analysis. (3) Considering the direct consequence of the porosity evolution with time in the transient analysis of fluid-rock interaction problems; we have proposed the term splitting algorithm and the concept of the equivalent source/sink terms in mass transport equations so that the problem of variable mesh Peclet number and Courant number has been successfully converted into the problem of constant mesh Peclet and Courant numbers. The numerical results from an application example have demonstrated the usefulness of the proposed concepts and the robustness of the proposed numerical algorithms in dealing with fluid-rock interaction problems in pore-fluid saturated hydrothermal/sedimentary basins. (C) 2001 Elsevier Science B.V. All rights reserved.

Modelling the Distribution of Ischaemic Stroke-Specific Survival Time Using an EM-based Mixture Approach with Random Effects Adjustment

A two-component survival mixture model is proposed to analyse a set of ischaemic stroke-specific mortality data. The survival experience of stroke patients after index stroke may be described by a subpopulation of patients in the acute condition and another subpopulation of patients in the chronic phase. To adjust for the inherent correlation of observations due to random hospital effects, a mixture model of two survival functions with random effects is formulated. Assuming a Weibull hazard in both components, an EM algorithm is developed for the estimation of fixed effect parameters and variance components. A simulation study is conducted to assess the performance of the two-component survival mixture model estimators. Simulation results confirm the applicability of the proposed model in a small sample setting. Copyright (C) 2004 John Wiley Sons, Ltd.

A comparison of the expressive communication skills of triplet, twin and singleton children

Few studies have focused on the language acquisition of higher multiple birth sets. In this study, the communication skills of 51 triplet children are described. The measures used were: mean length of utterance; type-token ratio; conversational nets; phoneme repertoire; and number of different types of phonological processes used. The data gained were used to compare the communication skills of triplets with those of twins, singletons and normative data available in the literature. Siblings within triplet sets were also compared using language samples obtained from adult-child interactions and when the three children were playing together. The results indicated that the triplets' early communication skills were different from those of both singletons and twins. The triplets' difficulties included delayed syntactic development, limited use of different language functions and delayed phonological development. In contrast, twins' communication profile is characterised by disordered phonological development.

Do generalized visual training programmes for sport really work? An experimental investigation

We assessed the effectiveness of two generalized visual training programmes in enhancing visual and motor performance for racquet sports. Forty young participants were assigned equally to groups undertaking visual training using Revien and Gabor's Sports Vision programme (Group 1), visual training using Revien's Eyerobics (Group 2), a placebo condition involving reading (Group 3) and a control condition involving physical practice only (Group 4). Measures of basic visual function and of sport-specific motor performance were obtained from all participants before and immediately after a 4-week training period. Significant pre- to post-training differences were evident on some of the measures; however, these were not group-dependent. Contrary to the claims made by proponents of generalized visual training, we found no evidence that the visual training programmes led to improvements in either vision or motor performance above and beyond those resulting simply from test familiarity.

Adult mouse intrinsic laryngeal muscles express high levels of the myogenic regulatory factor, MYF-5

The intrinsic laryngeal muscles display unique structural and functional characteristics that distinguish them from the skeletal muscle of the trunk and limbs. These features include relatively small muscle fibers, super-fast contraction speed, and fatigue resistance. The molecular basis of tissue-specific functions and other characteristics is differential gene expression. Accordingly, we have investigated the molecular basis of the functional specialization of the intrinsic laryngeal muscles by examining the expression of two key genes in the larynx, known to be important for skeletal muscle development and function: (a) the muscle regulatory factor, Myf-5, and (b) the superfast-contracting myosin heavy chain (EO-MyHC). We have found that the adult thyroarytenoid muscles express much higher levels of both Myf-5 and EO-MyHC messenger ribonucleic acid (mRNA), compared to lower hindlimb skeletal muscle where Myf-5 mRNA levels are very low and EO-MyHC is not detectable. These findings suggest that the unique functional characteristics of the intrinsic laryngeal muscles may be based in laryngeal muscle-specific gene expression directed by a unique combination of muscle regulatory factors. Such laryngeal muscle-specific genes may allow the future development of new treatments for laryngeal muscle dysfunction.

On the nonlocality of the quantum channel in the standard teleportation protocol

By exhibiting a violation of a novel form of the Bell-CHSH inequality, Żukowski has recently established that the quantum correlations exploited in the standard perfect teleportation protocol cannot be recovered by any local hidden variables model. In the case of imperfect teleportation, we show that a violation of a generalized form of Żukowski's teleportation inequality can only occur if the channel state, considered by itself, already violates a Bell-CHSH inequality. On the other hand, the fact that the channel state violates a Bell-CHSH inequality is not sufficient to imply a violation of Żukowski's teleportation inequality (or any of its generalizations). The implication does hold, however, if the fidelity of the teleportation exceeds ≈ 0.90. © 2001 Elsevier Science B.V. All rights reserved.

Complex language functions and subcortical mechanisms: evidence from Huntington's disease and patients with non-thalamic subcortical lesions

The neuropathological changes associated with Huntington's disease (HD) are most marked in the head of the caudate nucleus and, to a lesser extent, in the putamen and globus pallidus, suggesting that at least part of the language impairments found in patients with HD may result from non-thalamic subcortical (NTS) pathology. The present study aimed to test the hypothesis that a signature profile of impaired language functions is found in patients who have sustained damage to the non-thalamic subcortex, either focally induced or resulting from neurodegenerative pathology. The language abilities of a group of patients with Huntington's disease (n=13) were compared with those of an age- and education-matched group of patients with chronic NTS lesions following stroke (n=13) and a non-neurologically impaired control group (n=13). The three groups were compared on language tasks that assessed both primary and more complex language abilities. The primary language battery consisted of The Western Aphasia Battery and The Boston Naming Test, whilst the more complex cognitive-linguistic battery employed selected subtests from The Test of Language Competence-Expanded, The Test of Word Knowledge and The Word Test-Revised. On many of the tests of primary language function from the Western Aphasia Battery, both the HD and NTS participants performed in a similar manner to the control participants. The language performances of the HD participants were significantly more impaired (p<0.05 using modified Bonferroni adjustments) than the control group, however, on various lexico-semantic tasks (e. g. the Boston Naming Test and providing definitions), on both single-word and sentence-level generative tasks (e. g. category fluency and formulating sentences), and on tasks which required interpretation of ambiguous, figurative and inferential meaning. The difficulties that patients with HD experienced with tasks assessing complex language abilities were strikingly similar, both qualitatively and quantitatively, to the language profile produced by NTS participants. The results provide evidence to suggest that a signature language profile is associated with damage to the non-thalamic subcortex resulting from either focal neurological insult or a degenerative disease.

Application of the maximum entropy method to the (2 + 1)D four-fermion model

We investigate spectral functions extracted using the maximum entropy method from correlators measured in lattice simulations of the (2+1)-dimensional four-fermion model. This model is particularly interesting because it has both a chirally broken phase with a rich spectrum of mesonic bound states and a symmetric phase where there are only resonances. In the broken phase we study the elementary fermion, pion, sigma, and massive pseudoscalar meson; our results confirm the Goldstone nature of the π and permit an estimate of the meson binding energy. We have, however, seen no signal of σ→ππ decay as the chiral limit is approached. In the symmetric phase we observe a resonance of nonzero width in qualitative agreement with analytic expectations; in addition the ultraviolet behavior of the spectral functions is consistent with the large nonperturbative anomalous dimension for fermion composite operators expected in this model.

The Relative Frequency of the Synthetic End Composite Futures in the Newspaper Quest-France and some Observations on Distribution

Figures on the relative frequency of synthetic and composite future forms in Ouest-France are presented and compared with those of earlier studies on the passé simple and passé composé. The synthetic future is found to be dominant. Possible formal explanations for distribution are found to be inconclusive. Distribution across different text-types is found to be more promising, since contrastive functions of the two forms can be identified in texts where they co-occur. The composite future typically reports new proposals or plans as current news, while the synthetic future outlines details that will be realised at the time of implementation. Both functions are important in dailies, but current news is more often expressed in the present tense at the expense of the composite future.

Identification of T cell epitopes on the 33-kDa fragment of Plasmodium yoelii merozoite surface protein 1 and their antibody-independent protective role in immunity to blood stage malarial

Merozoite surface protein 1 (MSP1) of malaria parasites undergoes proteolytic processing at least twice before invasion into a new RBC. The 42-kDa fragment, a product of primary processing, is cleaved by proteolytic enzymes giving rise to MSP1(33), which is shed from the merozoite surface, and MSP1(19), which is the only fragment carried into a new RBC. In this study, we have identified T cell epitopes on MSP1(33) of Plasmodium yoelii and have examined their function in immunity to blood stage malaria. Peptides 20 aa in length, spanning the length of MSP1(33) and overlapping each other by 10 aa, were analyzed for their ability to induce T cell proliferation in immunized BALB/c and C57BL/6 mice. Multiple epitopes were recognized by these two strains of mice. Effector functions of the dominant epitopes were then investigated. Peptides Cm15 and Cm21 were of particular interest as they were able to induce effector T cells capable of delaying growth of lethal P. yoelii YM following adoptive transfer into immuno-deficient mice without inducing detectable Ab responses. Homologs of these epitopes could be candidates for inclusion in a subunit vaccine.

Effects of rosiglitazone and linoleic acid on human preadipocyte differentiation

Background Peroxisome proliferator activated receptor gamma (PPARgamma) is a ligand-activated transcription factor known to be central to both adipose tissue development and insulin action. Growth of adipose tissue requires differentiation of preadipocytes with acquisition of specific cellular functions including insulin sensitivity, leptin secretion and the capacity to store triglyceride. Dietary fatty acids and members of the thiazolidinedione class of compounds have been reported to influence adipogenesis at the transcriptional level. Here, we compare the effects of a dietary fatty acid, linoleic acid, and a thiazolidinedione, rosiglitazone, on biochemical and functional aspects of human preadipocyte differentiation in vitro . Materials and methods Human omental and subcutaneous preadipocytes were subcultured 2-3 times and subsequently differentiated for 21 days in the presence of either linoleic acid or rosiglitazone. Differentiation was assessed using a number of biochemical and functional parameters. Results Omental and subcutaneous preadipocytes differentiated in the presence of linoleic acid showed marked cytoplasmic triacylglycerol accumulation however, no biochemical markers of differentiation (LPL expression, G3PDH gene expression and enzyme activity and leptin expression or secretion) were detected. In contrast, treatment of these cells with rosiglitazone induced full biochemical differentiation as judged by all markers assessed, despite comparatively little lipid accumulation. The rosiglitazone effects were subcutaneous depot-specific. Cells treated with linoleic acid showed decreased glucose uptake cf rosiglitazone-treated cells. A luciferase reporter assay demonstrated that rosiglitazone potently activates h-peroxisome proliferator activated receptor gamma while linoleic acid had no effect. Conclusions These studies demonstrate that (a) human preadipocytes have the potential to accumulate triacylglycerol irrespective of their stage of biochemical differentiation; (b) while omental preadipocytes are refractory to biochemical differentiation in vitro , they are able to accumulate triacylglycerol; and (c) rosiglitazone and linoleic acid may exert their effects via different biochemical pathways.

Is maximizing resilience compatible with established ecological goal functions?

Cropp and Gabric [Ecosystem adaptation: do ecosystems maximise resilience? Ecology. In press] used a simple phytoplanktonzooplankton-nutrient model and a genetic algorithm to determine the parameter values that would maximize the value of certain goal functions. These goal functions were to maximize biomass, maximize flux, maximize flux to biomass ratio, and maximize resilience. It was found that maximizing goal functions maximized resilience. The objective of this study was to investigate whether the Cropp and Gabric [Ecosystem adaptation: do ecosystems maximise resilience? Ecology. In press] result was indicative of a general ecosystem principle, or peculiar to the model and parameter ranges used. This study successfully replicated the Cropp and Gabric [Ecosystem adaptation: do ecosystems maximise resilience? Ecology. In press] experiment for a number of different model types, however, a different interpretation of the results is made. A new metric, concordance, was devised to describe the agreement between goal functions. It was found that resilience has the highest concordance of all goal functions trialled. for most model types. This implies that resilience offers a compromise between the established ecological goal functions. The parameter value range used is found to affect the parameter versus goal function relationships. Local maxima and minima affected the relationship between parameters and goal functions, and between goal functions. (C) 2003 Elsevier B.V. All rights reserved.

Mapping the royal road and other hierarchical functions

In this paper we present a technique for visualising hierarchical and symmetric, multimodal fitness functions that have been investigated in the evolutionary computation literature. The focus of this technique is on landscapes in moderate-dimensional, binary spaces (i.e., fitness functions defined over {0, 1}(n), for n less than or equal to 16). The visualisation approach involves an unfolding of the hyperspace into a two-dimensional graph, whose layout represents the topology of the space using a recursive relationship, and whose shading defines the shape of the cost surface defined on the space. Using this technique we present case-study explorations of three fitness functions: royal road, hierarchical-if-and-only-if (H-IFF), and hierarchically decomposable functions (HDF). The visualisation approach provides an insight into the properties of these functions, particularly with respect to the size and shape of the basins of attraction around each of the local optima.