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.

What the evolution of the amyloid protein precursor supergene family tells us about its function

The Alzheimer's disease amyloid protein precursor (APP) gene is part of a multi-gene super-family from which sixteen homologous amyloid precursor-like proteins (APLP) and APP species homologues have been isolated and characterised. Comparison of exon structure (including the uncharacterised APL-1 gene), construction of phylogenetic trees, and analysis of the protein sequence alignment of known homologues of the APP super-family were performed to reconstruct the evolution of the family and to assess the functional significance of conserved protein sequences between homologues. This analysis supports an adhesion function for all members of the APP super family, with specificity determined by those sequences which are not conserved between APLP lineages, and provides evidence for an increasingly complex APP superfamily during evolution. The analysis also suggests that Drosophila APPL and Caenorhabdotids elegans APL-1 may be a fourth APLP lineage indicating that these proteins, while not functional homologues of human APP, are similarly likely to regulate cell adhesion. Furthermore, the beta A4 sequence is highly conserved only in APP orthologues, strongly suggesting this sequence is of significant functional importance in this lineage. (C) 2000 Elsevier Science Ltd. All rights reserved.

Sausage: protein threading with flexible force fields

Sausage is a protein sequence threading program, but with remarkable run-time flexibility. Using different scripts, it can calculate protein sequence-structure alignments, search structure libraries, swap force fields, create models form alignments, convert file formats and analyse results. There are several different force fields which might be classed as knowledge-based, although they do not rely on Boltzmann statistics. Different force fields are used for alignment calculations and subsequent ranking of calculated models.

Prejudiced attitudes, group norms, and discriminatory behaviour

Most current attitude research focuses on range of non-social attitudinal targets, including health-related and consumer outcomes. In this paper, a program of research that considers the relations among intergroup attitudes, group norms, and behavior will be described. The first study examined the effect of ingroup norms relating to multiculturalism on the extent to wich participants hehaviourally enacted their attitudes. Consistent with social identity theory, attitudebehaviour consistency in relation was influenced by ingroup norms, particularly when national identity was salient. The results of a large scale field study that essential replicated this pattern of results will also be discussed.

Volunteer decision making by older people: A test of a revised theory of planned behavior

This study was designed to test the utility of a revised theory of planned behavior in the prediction of intentions to volunteer among older people. Such a perspective allowed for the consideration of a broader range of social and contextual factors than has been examined in previous research on volunteer decision making among older people. The article reports the findings from a study that investigated volunteer intentions and behavior in a random sample of older people aged 65 to 74 years living in an Australian capital city. Results showed that, as predicted by the revised theory of planned behavior, intention to volunteer predicted subsequent reported volunteer behavior. Intention was, in turn, predicted by social norms (both subjective and behavioral), perceived behavioral control, and moral obligation, with the effect of attitude being mediated through moral obligation.

Syndrome packets and health worker training improve sexually transmitted disease case management in rural South Africa: randomized controlled trial

Background: Sexually transmitted diseases (STD) are important co-factors in HIV transmission. We studied the impact of health worker training and STD syndrome packets (containing recommended drugs, condoms, partner notification cards and information leaflets) on the quality of STD case management in primary care clinics in rural South Africa. Methods: A randomized controlled trial of five matched pairs of clinics compared the intervention with routine syndromic management. Outcomes were measured by simulated patients using standardized scripts, and included the proportion given recommended drugs; correctly case managed (given recommended drugs plus condoms and partner cards); adequately counselled; reporting good staff attitude; and consulted in privacy. Results: At baseline, the quality of STD case management was similarly poor in both groups. Only 36 and 46% of simulated patients visiting intervention and control clinics, respectively, were given recommended drugs. After the intervention, intervention clinics provided better case management than controls: 88 versus 50% (P < 0.01) received recommended drugs; 83 versus 12% (P < 0.005) were correctly case managed; 68 versus 46% (P = 0.06) were adequately counselled; 84 versus 58% experienced good staff attitude (P = 0.07); and 92 versus 86% (P = 0.4) were consulted privately. A syndrome packet cost US$1.50; the incremental cost was US$6.80. The total intervention cost equalled 0.3% of annual district health expenditure. Interpretation: A simple and affordable health service intervention achieved substantial improvements in STD case management. Although this is a critical component of STD control and can reduce HIV transmission, community-level interventions to influence health-seeking behaviour are also needed. (C) 2000 Lippincott Williams & Wilkins.

Undergraduate student experience in dental service delivery in rural South Australia: An analysis of costs and benefits

Background, Rural experience for dental students can provide valuable clinical education, change attitudes to rural practice, and make a valuable contribution to clinical service provision. The aim of this paper is to assess the costs and benefits of service delivery by students through rural training programmes Methods: Groups of two students worked in the public dental clinics in adjacent rural centres where there had been long-term difficulties in recruiting staff. The costs and benefits of the programme were assessed by the impact on waiting lists, the total cost per patient of, a course of care and by the marginal cost of adding service provision by students to existing arrangements. Results: The total costs of emergency and complete treatment provided by students were greater than the costs of treatment provided by public-sector dentists but less than the costs of private providers treating public patients. However, the value of services were greater when care was provided by students or private providers and the marginal cost of students providing services was 50-70 per cent of the cost of care provided by public dentists. Conclusion: This assessment suggests that the service benefits achieved compliment the primary objective of influencing the attitude of students to rural practice.

Bioinformatics for characterisation of allergens, allergenicity and allergic crossreactivity

Allergies are a major cause of chronic ill health in industrialised countries with the incidence of reported cases steadily increasing. This Research Focus details how bioinformatics is transforming the field of allergy through providing databases for management of allergen data, algorithms for characterisation of allergic crossreactivity, structural motifs and B- and T-cell epitopes, tools for prediction of allergenicity and techniques for genomic and proteomic analysis of allergens.

Anisotropic convection model for the earth's mantle

The paper presents a theory for modeling flow in anisotropic, viscous rock. This theory has originally been developed for the simulation of large deformation processes including the folding and kinking of multi-layered visco-elastic rock (Muhlhaus et al. [1,2]). The orientation of slip planes in the context of crystallographic slip is determined by the normal vector - the director - of these surfaces. The model is applied to simulate anisotropic mantle convection. We compare the evolution of flow patterns, Nusselt number and director orientations for isotropic and anisotropic rheologies. In the simulations we utilize two different finite element methodologies: The Lagrangian Integration Point Method Moresi et al [8] and an Eulerian formulation, which we implemented into the finite element based pde solver Fastflo (www.cmis.csiro.au/Fastflo/). The reason for utilizing two different finite element codes was firstly to study the influence of an anisotropic power law rheology which currently is not implemented into the Lagrangian Integration point scheme [8] and secondly to study the numerical performance of Eulerian (Fastflo)- and Lagrangian integration schemes [8]. It turned out that whereas in the Lagrangian method the Nusselt number vs time plot reached only a quasi steady state where the Nusselt number oscillates around a steady state value the Eulerian scheme reaches exact steady states and produces a high degree of alignment (director orientation locally orthogonal to velocity vector almost everywhere in the computational domain). In the simulations emergent anisotropy was strongest in terms of modulus contrast in the up and down-welling plumes. Mechanisms for anisotropic material behavior in the mantle dynamics context are discussed by Christensen [3]. The dominant mineral phases in the mantle generally do not exhibit strong elastic anisotropy but they still may be oriented by the convective flow. Thus viscous anisotropy (the main focus of this paper) may or may not correlate with elastic or seismic anisotropy.

Computational tools for the study of allergens

Allergy is a major cause of morbidity worldwide. The number of characterized allergens and related information is increasing rapidly creating demands for advanced information storage, retrieval and analysis. Bioinformatics provides useful tools for analysing allergens and these are complementary to traditional laboratory techniques for the study of allergens. Specific applications include structural analysis of allergens, identification of B- and T-cell epitopes, assessment of allergenicity and cross-reactivity, and genome analysis. In this paper, the most important bioinformatic tools and methods with relevance to the study of allergy have been reviewed.

Slant or occlusion: global factors resolve stereoscopic ambiguity in sets of horizontal lines

Perceived slant was measured for horizontal lines aligned on one side and of varying lengths whose length disparity was either a constant linear amount for all lines (consistent with uniocular occlusion) or proportional to line length (consistent with global slant). Although the disparity of any line was ambiguous with respect to these two possibilities, slant of individual lines did not occur in the former case, but a subjective contour in depth was reported along the alignment. For proportional disparity of the set, global slant was seen. Adding a constant length to each line on the invalid eye for occlusion resulted in multiple slants. Smooth uniocular variations in alignment shape elicited subjective contours slanting or curving in depth. Global context can disambiguate the depth status of individual disparate lines. (C) 2004 Elsevier Ltd. All rights reserved.

Royal Australian and New Zealand College of Psychiatrists clinical practice guidelines for the treatment of schizophrenia and related disorders

Background: The Royal Australian and New Zealand College of Psychiatrists is co-ordinating the development of clinical practice guidelines (CPGs) in psychiatry, funded under the National Mental Health Strategy (Australia) and the New Zealand Health Funding Authority. This paper presents CPGs for schizophrenia and related disorders. Over the past decade schizophrenia has become more treatable than ever before. A new generation of drug therapies, a renaissance of psychological and psychosocial interventions and a first generation of reform within the specialist mental health system have combined to create an evidence-based climate of realistic optimism. Progressive neuroscientific advances hold out the strong possibility of more definitive biological treatments in the near future. However, this improved potential for better outcomes and quality of life for people with schizophrenia has not been translated into reality in Australia. The efficacy-effectiveness gap is wider for schizophrenia than any other serious medical disorder. Therapeutic nihilism, under-resourcing of services and a stalling of the service reform process, poor morale within specialist mental health services, a lack of broad-based recovery and life support programs, and a climate of tenacious stigma and consequent lack of concern for people with schizophrenia are the contributory causes for this failure to effectively treat. These guidelines therefore tackle only one element in the endeavour to reduce the impact of schizophrenia. They distil the current evidence-base and make recommendations based on the best available knowledge. Method: A comprehensive literature review (1990-2003) was conducted, including all Cochrane schizophrenia reviews and all relevant meta-analyses, and a number of recent international clinical practice guidelines were consulted. A series of drafts were refined by the expert committee and enhanced through a bi-national consultation process. Treatment recommendations: This guideline provides evidence-based recommendations for the management of schizophrenia by treatment type and by phase of illness. The essential features of the guidelines are: (i) Early detection and comprehensive treatment of first episode cases is a priority since the psychosocial and possibly the biological impact of illness can be minimized and outcome improved. An optimistic attitude on the part of health professionals is an essential ingredient from the outset and across all phases of illness. (ii) Comprehensive and sustained intervention should be assured during the initial 3-5 years following diagnosis since course of illness is strongly influenced by what occurs in this 'critical period'. Patients should not have to 'prove chronicity' before they gain consistent access and tenure to specialist mental health services. (iii) Antipsychotic medication is the cornerstone of treatment. These medicines have improved in quality and tolerability, yet should be used cautiously and in a more targeted manner than in the past. The treatment of choice for most patients is now the novel antipsychotic medications because of their superior tolerability and, in particular, the reduced risk of tardive dyskinesia. This is particularly so for the first episode patient where, due to superior tolerability, novel agents are the first, second and third line choice. These novel agents are nevertheless associated with potentially serious medium to long-term side-effects of their own for which patients must be carefully monitored. Conventional antipsychotic medications in low dosage may still have a role in a small proportion of patients, where there has been full remission and good tolerability; however, the indications are shrinking progressively. These principles are now accepted in most developed countries. (vi) Clozapine should be used early in the course, as soon as treatment resistance to at least two antipsychotics has been demonstrated. This usually means incomplete remission of positive symptomatology, but clozapine may also be considered where there are pervasive negative symptoms or significant or persistent suicidal risk is present. (v) Comprehensive psychosocial interventions should be routinely available to all patients and their families, and provided by appropriately trained mental health professionals with time to devote to the task. This includes family interventions, cognitive-behaviour therapy, vocational rehabilitation and other forms of therapy, especially for comorbid conditions, such as substance abuse, depression and anxiety. (vi) The social and cultural environment of people with schizophrenia is an essential arena for intervention. Adequate shelter, financial security, access to meaningful social roles and availability of social support are essential components of recovery and quality of life. (vii) Interventions should be carefully tailored to phase and stage of illness, and to gender and cultural background. (viii) Genuine involvement of consumers and relatives in service development and provision should be standard. (ix) Maintenance of good physical health and prevention and early treatment of serious medical illness has been seriously neglected in the management of schizophrenia, and results in premature death and widespread morbidity. Quality of medical care for people with schizophrenia should be equivalent to the general community standard. (x) General practitioners (GPs)s should always be closely involved in the care of people with schizophrenia. However, this should be truly shared care, and sole care by a GP with minimal or no special Optimal treatment of schizophrenia requires a multidisciplinary team approach with a consultant psychiatrist centrally involved.

The link between prejudiced attitudes and discriminatory behaviour: The role of ingroup norms

In the present research, a reconceptualisation of the role of norms in the link between prejudiced attitudes and discriminatory behaviour — along the lines suggested by the social identity perspective — was tested. In the first study, group salience and group norm were manipulated. As expected, participants ascribed negative traits to significantly fewer Asian university students when they had received consensus information along these lines from a salient ingroup rather than from a salient outgroup. These results were replicated on a measure of strength of motivation to appear nonprejudiced. In a second study, group salience and norm were once again manipulated and strength of attitude and perceived group threat were measured. As predicted, people's negative attitudes towards globalisation were more likely to predict congruent behavioural responses to the extent that the group norm supported the attitude and group salience was high, particularly when high levels of group threat were perceived.

Survey of countertrade practices in Australia

This empirical exploratory study is part of a larger comprehensive study of countertrade practices in the Asia-Pacific region. A mail survey of 600 Australian international trading firms reveals that a positive attitude toward countertrade exists among both countertraders and non-countertraders in Australia. Further the study reveals the major motivating factors, the benefits derived difficulties faced and reasons for not countertrading by Australian firms. In addition, the study identifies the forms of countertrade used, the countries sewed, and the product and service categories countertraded. The results are compared to earlier studies of UK and Canadian firms, and the implications for international marketing managers are discussed. (C) Elsevier Science Inc., 1997.

How can and do Australian doctors promote physical activity?

Background. Physical inactivity is recognized as an important public health issue. Yet little is known about doctors' knowledge, attitude, skills, and resources specifically relating to the promotion of physical activity. Our survey assessed the current practice, perceived desirable practice, confidence, and barriers related to the promotion of physical activity in family practice, Methods. A questionnaire was developed and distributed to all 1,228 family practitioners in Perth, Western Australia. Results. We received a 71% response (n = 789). Family practitioners are most likely to recommend walking to sedentary adults to improve fitness and they are aware of the major barriers to patients participating in physical activity. Doctors are less confident at providing specific advice on exercise and may require further skills, knowledge, and experience, Although they promote exercise to patients through verbal advice in the consultation, few use written materials or referral systems, Conclusions. There are significant differences between self-reports of current practice and perceived desirable practice in the promotion of physical activity by doctors, Future strategies need to address the self-efficacy of family physicians and involve resources of proven effectiveness. The potential of referral systems for supporting efforts to increase physical activity by Australians should be explored. (C) 1997 Academic Press.