Development and evaluation of an automated annotation pipeline and cDNA annotation system

Manual curation has long been held to be the gold standard for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed problems with this approach, including inaccurate and inconsistent assignment of gene names, as well as many good assignments that were difficult to reproduce using only computational methods. For the FANTOM2 annotation of more than 60,000 cDNA clones, we developed a number of methods and tools to circumvent some of these problems, including an automated annotation pipeline that provides high-quality preliminary annotation for each sequence by introducing an uninformative filter that eliminates uninformative annotations, controlled vocabularies to accurately reflect both the functional assignments and the evidence supporting them, and a highly refined, Web-based manual annotation tool that allows users to view a wide array of sequence analyses and to assign gene names and putative functions using a consistent nomenclature. The ultimate utility of our approach is reflected in the low rate of reassignment of automated assignments by manual curation. Based on these results, we propose a new standard for large-scale annotation, in which the initial automated annotations are manually investigated and then computational methods are iteratively modified and improved based on the results of manual curation.

Producing computer-generated tailored written information for stroke patients and their carers: System development and preliminary evaluation

Purpose: The aim of this project was to design and evaluate a system that would produce tailored information for stroke patients and their carers, customised according to their informational needs, and facilitate communication between the patient and, health professional. Method: A human factors development approach was used to develop a computer system, which dynamically compiles stroke education booklets for patients and carers. Patients and carers are able to select the topics about which they wish to receive information, the amount of information they want, and the font size of the printed booklet. The system is designed so that the health professional interacts with it, thereby providing opportunities for communication between the health professional and patient/carer at a number of points in time. Results: Preliminary evaluation of the system by health professionals, patients and carers was positive. A randomised controlled trial that examines the effect of the system on patient and carer outcomes is underway. (C) 2004 Elsevier Ireland Ltd. All rights reserved.

Development and evaluation of the Clinician Suicide Risk Assessment Checklist

This paper describes the development and evaluation of a new instrument – the Clinician Suicide Risk Assessment Checklist (CSRAC). The instrument assesses the clinician’s competency in three areas: clinical interviewing, assessment of specific suicide risk factors, and formulating a management plan. A draft checklist was constructed by integrating information from 1) literature review 2) expert clinician focus group and 3) consultation with experts. It was utilised in a simulated clinical scenario with clinician trainees and a trained actor in order to test for inter-rater agreement. Agreement was calculated and the checklist was re-drafted with the aim of maximising agreement. A second phase of simulated clinical scenarios was then conducted and inter-rater agreement was calculated for the revised checklist. In the first phase of the study, 18 of 35 items had inadequate inter-rater agreement (60%>), while in the second phase, using the revised version, only 3 of 39 items failed to achieve adequate inter-rater agreement. Further evidence of reliability and validity are required. Continued development of the CSRAC will be necessary before it can be utilised to assess the effectiveness of risk assessment training programs.

Development and evaluation of a youth mental health community awareness campaign - The Compass Strategy

Background: Early detection and treatment of mental disorders in adolescents and young adults can lead to better health outcomes. Mental health literacy is a key to early recognition and help seeking. Whilst a number of population health initiatives have attempted to improve mental health literacy, none to date have specifically targeted young people nor have they applied the rigorous standards of population health models now accepted as best practice in other health areas. This paper describes the outcomes from the application of a health promotion model to the development, implementation and evaluation of a community awareness campaign designed to improve mental health literacy and early help seeking amongst young people. Method: The Compass Strategy was implemented in the western metropolitan Melbourne and Barwon regions of Victoria, Australia. The Precede-Proceed Model guided the population assessment, campaign strategy development and evaluation. The campaign included the use of multimedia, a website, and an information telephone service. Multiple levels of evaluation were conducted. This included a cross-sectional telephone survey of mental health literacy undertaken before and after 14 months of the campaign using a quasi-experimental design. Randomly selected independent samples of 600 young people aged 12 - 25 years from the experimental region and another 600 from a comparison region were interviewed at each time point. A series of binary logistic regression analyses were used to measure the association between a range of campaign outcome variables and the predictor variables of region and time. Results: The program was judged to have an impact on the following variables, as indicated by significant region-by-time interaction effects ( p < 0.05): awareness of mental health campaigns, self-identified depression, help for depression sought in the previous year, correct estimate of prevalence of mental health problems, increased awareness of suicide risk, and a reduction in perceived barriers to help seeking. These effects may be underestimated because media distribution error resulted in a small amount of print material leaking into the comparison region. Conclusion: We believe this is the first study to apply the rigorous standards of a health promotion model including the use of a control region to a mental health population intervention. The program achieved many of its aims despite the relatively short duration and moderate intensity of the campaign.

Evaluation of different models to describe egg and pupal development of Xyleborus fornicatus Eichh. (Coleoptera: Scolytidae), the shot-hole borer of tea in Sri Lanka

Abstract Development data of eggs and pupae of Xyleborus fornicatus Eichh. (Coleoptera: Scolytidae), the shot-hole borer of tea in Sri Lanka, at constant temperatures were used to evaluate a linear and seven nonlinear models for insect development. Model evaluation was based on fit to data (residual sum of squares and coefficient of determination or coefficient of nonlinear regression), number of measurable parameters, the biological value of the fitted coefficients and accuracy in the estimation of thresholds. Of the nonlinear models, the Lactin model fitted experimental data well and along with the linear model, can be used to describe the temperature-dependent development of this species.