Strategies for identifying and predicting islet autoantigen T-cell epitopes in insulin-dependent diabetes mellitus

T cells recognize peptide epitopes bound to major histocompatibility complex molecules. Human T-cell epitopes have diagnostic and therapeutic applications in autoimmune diseases. However, their accurate definition within an autoantigen by T-cell bioassay, usually proliferation, involves many costly peptides and a large amount of blood, We have therefore developed a strategy to predict T-cell epitopes and applied it to tyrosine phosphatase IA-2, an autoantigen in IDDM, and HLA-DR4(*0401). First, the binding of synthetic overlapping peptides encompassing IA-2 was measured directly to purified DR4. Secondly, a large amount of HLA-DR4 binding data were analysed by alignment using a genetic algorithm and were used to train an artificial neural network to predict the affinity of binding. This bioinformatic prediction method was then validated experimentally and used to predict DR4 binding peptides in IA-2. The binding set encompassed 85% of experimentally determined T-cell epitopes. Both the experimental and bioinformatic methods had high negative predictive values, 92% and 95%, indicating that this strategy of combining experimental results with computer modelling should lead to a significant reduction in the amount of blood and the number of peptides required to define T-cell epitopes in humans.

Fast evolution strategies

Evolution strategies are a class of general optimisation algorithms which are applicable to functions that are multimodal, nondifferentiable, or even discontinuous. Although recombination operators have been introduced into evolution strategies, the primary search operator is still mutation. Classical evolution strategies rely on Gaussian mutations. A new mutation operator based on the Cauchy distribution is proposed in this paper. It is shown empirically that the new evolution strategy based on Cauchy mutation outperforms the classical evolution strategy on most of the 23 benchmark problems tested in this paper. The paper also shows empirically that changing the order of mutating the objective variables and mutating the strategy parameters does not alter the previous conclusion significantly, and that Cauchy mutations with different scaling parameters still outperform the Gaussian mutation with self-adaptation. However, the advantage of Cauchy mutations disappears when recombination is used in evolution strategies. It is argued that the search step size plays an important role in determining evolution strategies' performance. The large step size of recombination plays a similar role as Cauchy mutation.

Identification of two novel mutations in the hydroxymethylbilane synthase gene in three patients from two unrelated families with acute intermittent porphyria

We have screened the hydroxymethylbilane synthase cDNAs of 3 patients from 2 families suffering from acute intermittent porphyria (AIP) from Scotland and South Africa using heteroduplex and chemical cleavage of mismatch analyses, Direct sequencing was used to characterise the mutations, The two novel mutations identified were a missense mutation at nucleotide position 64 in exon 3 (R22C) and a single base-pair deletion in exon 15, These mutations are predicted to affect the normal function of the enzyme and, therefore, are expected to be the primary cause of disease in these patients.

Two-body and three-body abrasion: A critical discussion

It is argued that the common classification of abrasive wear into 'two-body abrasion' and 'three-body abrasion' is seriously flawed. No definitions have been agreed upon for these terms, and indeed there are two quite different interpretations, the implications of which are mutually inconsistent. In the dominant interpretation, the primary thrust of the two-body/three-body concept is to describe whether the abrasive particles are constrained (two-body) or free to roll (three-body). In this view, two-body abrasion is generally much more severe than three-body. The alternative interpretation emphasises the presence (three-body) or absence (two-body) of a rigid counterface backing the abrasive. In this view, three-body abrasion is equated to high-stress (or grinding) abrasion and is generally more severe than two-body (low-stress) abrasion. This paper recommends that the 'two-body/three-body' terminology be abandoned, to be replaced by an alternative classification scheme based directly upon the manifest severity of wear. (C) 1998 Elsevier Science S.A.

Neuroleptic management of schizophrenia: A survey and commentary on Australian psychiatric practice

Objective: We seek to assess Australian psychiatrists' views and practices concerning provision of neuroleptic medication to patients with schizophrenia, and to determine whether such management strategies are likely to have changed over time and the extent to which they correspond to published treatment guidelines. Method: A sample of 139 psychiatrists based in three Australian capital cities was derived, with respondents completing a brief questionnaire by choosing from a limited-option answer set. Co-authors of this paper comment on the extent to which responses are in line with contemporary recommendations driven by experts or empirical studies. Results: Overall, survey findings indicate that there has been considerable change in clinical practice over the last decade and provide some estimate of the extent to which Australian management practices are congruent with contemporary recommendations. We identify a number of issues of concern (more in relation to dose levels of neuroleptic medication rather than treatment duration) revealed by survey data and make recommendations for addressing a number of practical clinical issues. Conclusions: As this report focuses on central issues involved in managing schizophrenia, and integrates a number of treatment guidelines, we suggest that it should be of assistance for practice review by clinicians.

Pinch my wig or winch my pig: Spelling, spoonerisms and other language skills

Phonological processing skills have often been assumed to play a minimal role in skilled adult spelling despite evidence showing their importance in the development of spelling skills. The present study investigated the relationship between phonological awareness and spelling in adults. It was hypothesised that subjects demonstrating higher levels of spelling proficiency would also show superior phonological processing skills. This relationship was expected to be mediated by sound-spelling mapping knowledge. Given the irregularities of sound-spelling correspondences in English, it was also predicted that knowledge of orthographic conventions would be related to spelling competency. Two measures of each component skill were used on seventy three university students. As predicted, the importance of spelling-sound mapping skills in spelling were demonstrated, as was a relationship between phonological awareness and spelling-sound correspondences. In addition a moderate correlation was found between orthographic tasks and spelling performance. It was concluded that, among university students at least, phonological ability makes an important contribution to skilled adult spelling.

Analysis and application of an equilibrium model for in vitro bioassay systems with three components: Receptor, hormone and hormone-binding-protein

A simple theoretical framework is presented for bioassay studies using three component in vitro systems. An equilibrium model is used to derive equations useful for predicting changes in biological response after addition of hormone-binding-protein or as a consequence of increased hormone affinity. Sets of possible solutions for receptor occupancy and binding protein occupancy are found for typical values of receptor and binding protein affinity constants. Unique equilibrium solutions are dictated by the initial condition of total hormone concentration. According to the occupancy theory of drug action, increasing the affinity of a hormone for its receptor will result in a proportional increase in biological potency. However, the three component model predicts that the magnitude of increase in biological potency will be a small fraction of the proportional increase in affinity. With typical initial conditions a two-fold increase in hormone affinity for its receptor is predicted to result in only a 33% increase in biological response. Under the same conditions an Ii-fold increase in hormone affinity for receptor would be needed to produce a two-fold increase in biological potency. Some currently used bioassay systems may be unrecognized three component systems and gross errors in biopotency estimates will result if the effect of binding protein is not calculated. An algorithm derived from the three component model is used to predict changes in biological response after addition of binding protein to in vitro systems. The algorithm is tested by application to a published data set from an experimental study in an in vitro system (Lim et al., 1990, Endocrinology 127, 1287-1291). Predicted changes show good agreement (within 8%) with experimental observations. (C) 1998 Academic Press Limited.

Analytical solution for the Mollow and Autler-Townes probe absorption spectra of a three-level atom in a squeezed vacuum

The Mellow and Autler-Townes probe absorption spectra of a three-level atom in a cascade configuration with the lower transition coherently driven and also coupled to a narrow bandwidth squeezed-vacuum field are studied. Analytical studies of the modifications caused by the finite squeezed-vacuum bandwidth to the spectra are made for the case when the Rabi frequency of the driving field is much larger than the natural linewidth. The squeezed vacuum center frequency and the driving laser frequency are assumed equal. We show that the spectral features depend on the bandwidth of a squeezed vacuum field and whether the sources of the squeezing field are degenerate (DPA) or nondegenerate (NDPA) parametric amplifiers. In a broadband or narrow bandwidth squeezed vacuum generated by a NDPA, the central component of the Mellow spectrum can be significantly narrower than that in the normal vacuum. When the source of the squeezed vacuum is a DPA, the central feature is insensitive to squeezing. The Rabi sidebands, however, can be significantly narrowed only in the squeezed vacuum produced by the DPA. The two lines of the Autler-Townes absorption spectrum can be narrowed only in a narrow bandwidth squeezed vacuum, whereas they are independent of the phase and are always broadened in a broadband squeezed vacuum.

An open-boundary integrable model of three coupled XY spin chains

The integrable open-boundary conditions for the model of three coupled one-dimensional XY spin chains are considered in the framework of the quantum inverse scattering method. The diagonal boundary K-matrices are found and a class of integrable boundary terms is determined. The boundary model Hamiltonian is solved by using the coordinate space Bethe ansatz technique and Bethe ansatz equations are derived. (C) 1998 Elsevier Science B.V.

Structure determination of the three disulfide bond isomers of alpha-conotoxin GI: A model for the role of disulfide bonds in structural stability

The three possible disulfide bonded isomers of alpha-conotoxin GI have been selectively synthesised and their structures determined by H-1 NMR spectroscopy. alpha-Conotoxin GI derives from the venom of Conus geographus and is a useful neuropharmacological tool as it selectively binds to the nicotinic acetylcholine receptor (nAChR), a ligand-gated ion channel involved in nerve signal transmission. The peptide has the sequence ECCNPACGRHYSC-NH2, and the three disulfide bonded isomers are referred to as GI(2-7;3-13), GI(2-13;3-7) and GI(2-3;7-13). The NMR structure for the native isomer GI(2-7;3-13) is of excellent quality, with a backbone pairwise RMSD of 0.16 Angstrom for a family of 35 structures, and comprises primarily a distorted 3(10),, helix between residues 5 to 11. The two non-native isomers exhibit multiple conformers in solution, with the major populated forms being different in structure both from each other and from the native form. Structure-activity relationships for the native GI(2-7;3-13) as well as the role of the disulfide bonds on folding and stability of the three isomers are examined. It is concluded that the disulfide bonds in alpha-conotoxin GI play a crucial part in determining both the structure and stability of the peptide. A trend for increased conformational heterogeneity was observed in the order of GI(2-7;3-13) < GI(2-13;3-7) < GI(2-3;7-13). It was found that the peptide bond joining Cys2 to Cys3 in GI(2-3;7-13) is predominantly trans, rather than cis as theoretically predicted. These structural data are used to interpret the varying nAChR binding of the non-native forms. A model for the binding of native GI(2-7;3-13) to the mammalian nAChR is proposed, with an alpha-subunit binding face made up of Cys2, Asn4, Pro5, Ala6 and Cys7 and a selectivity face, comprised of Arg9 and His10. These two faces orient the molecule between the alpha and delta subunits of the receptor. The structure of the CCNPAC sequence of the native GI(2-7;3-13) is compared to the structure of the identical sequence from the toxic domain of heat-stable enterotoxins, which forms part of the receptor binding region of the enterotoxins, but which has a different disulfide connectivity. (C) 1998 Academic Press Limited.

Incorporating cognitive-behavioral therapy with occupational therapy: A comparative study with patients with low back pain

This paper reports on the implementation of a psychoeducational program utilizing cognitive-behavioral principles. The efficacy of this psychoeducational treatment program in modifying dysfunctional attitudes in patients with chronic low back pain was examined using a two-group pretest posttest design with a follow-lip at 3 months Thirty patients (average age = 44.37 SD = 13.71) participated in the study, with 15 in the psychoeducational treatment group and 15 in the placebo control group. These two conditions were added on to an existing eclectic inpatient pain management program. After assessment on the IPAM (The Integrated Psychosocial Assessment Model), scores were reduced to multivariate composite scores on the factors of illness behavior depressed and negative cognitions, and acute pain strategies. Results of a group x time repeated measures analysis of variance for the three pain factors revealed a significant main effect for group (F(23,1) = 5.00 p < .04), tempered by a significant interaction between group and rime on the 'depressed and negative' pain factor (F(23,1) = 4.77 p < .04). Patients in the treatment group improved significantly over time and significantly more than the placebo control group patients at posttreatment. Results provide support for the program in increasing patients' feelings of control over their pain and the use of positive coping strategies, while reducing perceived helplessness, depression, disability, and pain intensity.

Changes in three-dimensional architecture of microfilaments in cultured vascular smooth muscle cells during phenotypic modulation

To investigate changes in the three-dimensional microfilament architecture of vascular smooth muscle cells (SMC) during the process of phenotypic modulation, rabbit aortic SMCs cultured under different conditions and at different time points were either labelled with fluorescein-conjugated probes to cytoskeletal and contractile proteins for observation by confocal laser scanning microscopy, or extracted with Triton X-100 for scanning electron microscopy. Densely seeded SMCs in primary culture, which maintain a contractile phenotype, display prominent linear myofilament bundles (stress fibres) that are present throughout the cytoplasm with alpha-actin filaments predominant in the central part and beta-actin filaments in the periphery of the cell. Intermediate filaments form a meshed network interconnecting the stress fibres and linking directly to the nucleus. Moderately and sparsely seeded SMCs, which modulate toward the synthetic phenotype during the first 5 days of culture, undergo a gradual redistribution of intermediate filaments from the perinuclear region toward the peripheral cytoplasm and a partial disassembly of stress fibres in the central part of the upper cortex of the cytoplasm, with an obvious decrease in alpha-actin and myosin staining. These changes are reversed in moderately seeded SMCs by day 8 of culture when they have reached confluence. The results reveal two changes in microfilament architecture in SMCs as they undergo a change in phenotype: the redistribution of intermediate filaments probably due to an increase in synthetic organelles in the perinuclear area, and the partial disassembly of stress fibres which may reflect a degradation of contractile components.

Three-dimensional quantum solitons with parametric coupling

We consider the quantum field theory of two bosonic fields interacting via both parametric (cubic) and quartic couplings. In the case of photonic fields in a nonlinear optical medium, this corresponds to the process of second-harmonic generation (via chi((2)) nonlinearity) modified by the chi((3)) nonlinearity. The quantum solitons or energy eigenstates (bound-state solutions) are obtained exactly in the simplest case of two-particle binding, in one, two, and three space dimensions. We also investigate three-particle binding in one space dimension. The results indicate that the exact quantum solitons of this field theory have a singular, pointlike structure in two and three dimensions-even though the corresponding classical theory is nonsingular. To estimate the physically accessible radii and binding energies of the bound states, we impose a momentum cutoff on the nonlinear couplings. In the case of nonlinear optical interactions, the resulting radii and binding energies of these photonic particlelike excitations in highly nonlinear parametric media appear to be close to physically observable values.

Reputations, self-concepts and coping strategies of volatile solvent users

Data pertaining to the reputations, self-concepts and coping strategies of thirty-one secondary school Volatile Solvent Users (VSUs), forty-four ex-VSUs, and forty-eight non-VSUs in the Perth Metropolitan area of Western Australia were obtained using the High School Student Activity Questionnaire. Findings revealed that significant differences between current VSUs, ex-VSUs, and non-VSUs were more attributable to factors of reputation enhancement than to factors of either self-concept or coping strategies. Current VSUs identified themselves as both having and wanting to have a more non-confronting reputation, and as admiring drug-related activities significantly more than both ex-VSUs and non-VSUs. Two coping variables were also found to be significant indicating that females use more nonproductive coping strategies and external coping strategies than males. No interaction effects were identified. The implications for drug education and further research are discussed.

Three-dimensional solution structure of alpha-conotoxin MII by NMR spectroscopy: Effects of solution environment on helicity

alpha-Conotoxin MII, a 16-residue polypeptide from the venom of the piscivorous cone snail Conus magus, is a potent and highly specific blocker of mammalian neuronal nicotinic acetylcholine receptors composed of alpha 3 beta 2 subunits. The role of this receptor type in the modulation of neurotransmitter release and its relevance to the problems of addiction and psychosis emphasize the importance of a structural understanding of the mode of interaction of MII with the alpha 3 beta 2 interface. Here we describe the three-dimensional solution structure of MIT determined using 2D H-1 NMR spectroscopy. Structural restraints consisting of 376 interproton distances inferred from NOEs and 12 dihedral restraints derived from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimization in the program X-PLOR. The final set of 20 structures is exceptionally well-defined with mean pairwise rms differences over the whole molecule of 0.07 Angstrom for the backbone atoms and 0.34 Angstrom for all heavy atoms. MII adopts a compact structure incorporating a central segment of alpha-helix and beta-turns at the N- and C-termini. The molecule is stabilized by two disulfide bonds, which provide cross-links between the N-terminus and both the middle and C-terminus of the structure. The susceptibility of the structure to conformational change was examined using several different solvent conditions. While the global fold of MII remains the same, the structure is stabilized in a more hydrophobic environment provided by the addition of acetonitrile or trifluoroethanol to the aqueous solution. The distribution of amino acid side chains in MII creates distinct hydrophobic and polar patches on its surface that may be important for the specific interaction with the alpha 3 beta 2 neuronal nAChR. A comparison of the structure of MII with other neuronal-specific alpha-conotoxins provides insights into their mode of interaction with these receptors.