Mixed model formulations for multi-environment trials

When studying genotype X environment interaction in multi-environment trials, plant breeders and geneticists often consider one of the effects, environments or genotypes, to be fixed and the other to be random. However, there are two main formulations for variance component estimation for the mixed model situation, referred to as the unconstrained-parameters (UP) and constrained-parameters (CP) formulations. These formulations give different estimates of genetic correlation and heritability as well as different tests of significance for the random effects factor. The definition of main effects and interactions and the consequences of such definitions should be clearly understood, and the selected formulation should be consistent for both fixed and random effects. A discussion of the practical outcomes of using the two formulations in the analysis of balanced data from multi-environment trials is presented. It is recommended that the CP formulation be used because of the meaning of its parameters and the corresponding variance components. When managed (fixed) environments are considered, users will have more confidence in prediction for them but will not be overconfident in prediction in the target (random) environments. Genetic gain (predicted response to selection in the target environments from the managed environments) is independent of formulation.

Phylogeography of an east Australian wet-forest bird, the satin bowerbird (Ptilonorhynchus violaceus), derived from mtDNA, and its relationship to morphology

Australian wet forests have undergone a contraction in range since the mid-Tertiary, resulting in a fragmented distribution along the east Australian coast incorporating several biogeographical barriers. Variation in mitochondrial DNA and morphology within the satin bowerbird was used to examine biogeographical structure throughout almost the entire geographical extent of these wet forest fragments. We used several genetic analysis techniques, nested clade and barrier analyses, that use patterns inherent in the data to describe the spatial structuring. We also examined the validity of the two previously described satin bowerbird subspecies that are separated by well-defined biogeographical barriers and tested existing hypotheses that propose divergence occurs within each subspecies across two other barriers, the Black Mountain corridor and the Hunter Valley. Our data showed that the two subspecies were genetically and morphologically divergent. The northern subspecies, found in the Wet Tropics region of Queensland, showed little divergence across the Black Mountain corridor, a barrier found to be significant in other Wet Tropics species. Biogeographical structure was found through southeastern Australia; three geographically isolated populations showed genetic differentiation, although minimal divergence was found across the proposed Hunter Valley barrier. A novel barrier was found separating inland and coastal populations in southern New South Wales. Little morphological divergence was observed within subspecies, bar a trend for birds to be larger in the more southerly parts of the species' range. The results from both novel and well-established genetic analyses were similar, providing greater confidence in the conclusions about spatial divergence and supporting the validity of these new techniques.

English teachers' choice of language for publication: Qualitative insights from Bangladesh

The aim of this small-scale research was to gain some understanding of Bangladeshi English language teachers' language preference for publication purposes & the extent of the use of Bangla (Bengali), the L1, in their professional practice. Qualitative data for the study were gathered by means of a self-produced questionnaire. Results show that about three-quarters of the teachers published or would publish entirely in English because they believed that it was, among other reasons, the usual professional practice. More importantly, a number of teachers stated that they felt more comfortable writing academic essays in English. Regarding the use of L1, all 37 respondents pointed out that they used it sparingly in the classroom, & only a small number considered it a barrier in learning English, the L2. While emphasising the study's limitations, the paper suggests that English teachers' lack of confidence in L1 academic writing may be seen as indicating the potential direction of a slowly emerging individual bilingualism among university teachers of English. However, the paper also argues that the emergence of this potential bilingualism can be seen only at the individual rather than societal level, &, within the academic context, only in the limited domain of academic writing. Figures, References. Adapted from the source document

Crisis management and risk communication: Why the food industry must get it right

There is public unease about food-related issues including food additives, food poisoning bacteria and GM ingredients. The public wants evidence of no risks, but all regulators can ever offer is no evidence of risk or evidence of a very small risk. The situation is complex because experts and non-experts can perceive the same risk in vastly different ways. The way in which the food industry manages crises and communicates risks will determine the public acceptance and success of new technologies such as GM foods and nanomaterials. There is a need for the food industry (including regulators and scientific experts) to sharpen up their risk communication skills to ensure that technical innovations are accepted by consumers, and crises such as food recalls do not undermine the public's confidence in the food industry. The AIFST has a key role to play in driving the risk communication process and allaying public unease about food-related issues.

Virtual training environments to improve train driver's crisis decision making

This paper reports on a current research project in which virtual reality simulators are being investigated as a means of simulating hazardous Rail work conditions in order to allow train drivers to practice decision-making under stress. When working under high stress conditions train drivers need to move beyond procedural responses into a response activated through their own problem-solving and decision-making skills. This study focuses on the use of stress inoculation training which aims to build driver’s confidence in the use of new decision-making skills by being repeatedly required to respond to hazardous driving conditions. In particular, the study makes use of a train cab driving simulator to reproduce potentially stress inducing real-world scenarios. Initial pilot research has been undertaken in which drivers have experienced the training simulation and subsequently completed surveys on the level of immersion experienced. Concurrently drivers have also participated in a velocity perception experiment designed to objectively measure the fidelity of the virtual training environment. Baseline data, against which decision-making skills post training will be measured, is being gathered via cognitive task analysis designed to identify primary decision requirements for specific rail events. While considerable efforts have been invested in improving Virtual Reality technology, little is known about how to best use this technology for training personnel to respond to workplace conditions in the Rail Industry. To enable the best use of simulators for training in the Rail context the project aims to identify those factors within virtual reality that support required learning outcomes and use this information to design training simulations that reliably and safely train staff in required workplace accident response skills.

Commercial-in-confidence: An obituary to transparency?

This article addresses the issue of accountability and transparency in relation to the use of commercial-in-confidence clauses to withhold information. The issue is contentious. On the one hand some like the Senate Finance and Public Administration Reference Committee (SFPARC) argue that: 'Put simply there can be no accountability if there is no information' (SFPARC 2000). On the other hand, an alternative view is: 'I think that the sanctity of contract... [is] a fundamental pillar of our legal system, and if private businesses enter into contracts with governments that specify confidentiality, then that ought to be respected' (Paterson 1999). This paper is an abridged version of a keynote address to CPA Australia (Queensland Division) Audit Intensive Day 2000, Brisbane Hilton, 10 November 2000.

Impact of an intensive nursing education course on nurses' knowledge, confidence, attitudes, and perceived skills in the care of patients with cancer

Purpose/Objectives: To evaluate the impact of a cancer nursing education course on RNs. Design: Quasi-experimental, longitudinal, pretest/post-test design, with a follow-up assessment six weeks after the completion of the nursing education course. Setting: Urban, nongovernment, cancer control agency in Australia. Sample: 53 RNs, of whom 93% were female, with a mean age of 44.6 years and a mean of 16.8 years of experience in nursing; 86% of the nurses resided and worked in regional areas outside of the state capital. Methods: Scales included the Intervention With Psychosocial Needs: Perceived Importance and Skill Level Scale, Palliative Care Quiz for Nurses, Breast Cancer Knowledge, Preparedness for Cancer Nursing, and Satisfaction With Learning. Data were analyzed using multiple analysis of variance and paired t tests. Main Research Variables: Cancer nursing-related knowledge, preparedness for cancer nursing, and attitudes toward and perceived skills in the psychosocial care of patients with cancer and their families. Findings: Compared to nurses in the control group, nurses who attended the nursing education course improved in their cancer nursing-related knowledge, preparedness for cancer nursing, and attitudes toward and perceived skills in the psychosocial care of patients with cancer and their families. Improvements were evident at course completion and were maintained at the six-week follow-up assessment. Conclusions: The nursing education course was effective in improving nurses' scores on all outcome variables. Implications for Nursing: Continuing nursing education courses that use intensive mode timetabling, small group learning, and a mix of teaching methods, including didactic and interactive approaches and clinical placements, are effective and have the potential to improve nursing practice in oncology.

Australian and New Zealand practice in intensive care (ANZPIC II): Predictors of physician confidence to diagnose pneumonia and determine illness severity in ventilated patients

The manner in which elements of clinical history, physical examination and investigations influence subjectively assessed illness severity and outcome prediction is poorly understood. This study investigates the relationship between clinician and objectively assessed illness severity and the factors influencing clinician's diagnostic confidence and illness severity rating for ventilated patients with suspected pneumonia in the intensive care unit (ICU). A prospective study of fourteen ICUs included all ventilated admissions with a clinical diagnosis of pneumonia. Data collection included pneumonia type - community-acquired (CAP), hospital-acquired (HAP) and ventilator-associated (VAP), clinician determined illness severity (CDIS), diagnostic methods, clinical diagnostic confidence (CDC), microbiological isolates and antibiotic use. For 476 episodes of pneumonia (48% CAP, 24% HAP, 28% VAP), CDC was greatest for CAP (64% CAP, 50% HAP and 49% VAP, P < 0.01) or when pneumonia was considered life-threatening (84% high CDC, 13% medium CDC and 3% low CDC, P < 0.001). Life-threatening pneumonia was predicted by worsening gas exchange (OR 4.8, CI 95% 2.3-10.2, P < 0.001), clinical signs of consolidation (OR 2.0, CI 95% 1.2-3.2, P < 0.01) and the Sepsis-Related Organ Failure Assessment (SOFA) Score (OR 1.1, CI 95% 1.1-1.2, P < 0.001). Diagnostic confidence increased with CDIS (OR 163, CI 95% 8.4-31.4, P < 0.001), definite pathogen isolation (OR 3.3, CI 95% 2.0-5.6) and clinical signs of consolidation (OR 2.1, CI 95% 1.3-3.3, P = 0.001). Although the CDIS, SOFA Score and the Simplified Acute Physiologic Score (SAPS II) were all associated with mortality, the SAPS II Score was the best predictor of mortality (P = 0.02). Diagnostic confidence for pneumonia is moderate but increases with more classical presentations. A small set of clinical parameters influence subjective assessment. Objective assessment using SAPS II Scoring is a better predictor of mortality.

Won't pay or can't pay? Exploring the use of fines as a sentencing alternative for public nuisance type offences in Queensland

The complex relationship between marginalized people, 'public nuisance type offences' and fines law is explored. Court observation research conducted in Brisbane is reported which suggests that indigent people are more likely than others to appear before the court on charges related to public space offences, and that they are just as likely as others to receive a fine in response to their offending behaviour despite the legislative provisions aimed at avoiding this

A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

A two-phase strategy for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We previously evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach to delineate breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

Interval breast cancers in an Australian mammographic screening program

Objective: To determine the incidence of interval cancers which occurred in the first 12 months after mammographic screening at a mammographic screening service. Design: Retrospective analysis of data obtained by crossmatching the screening Service and the New South Wales Central Cancer Registry databases. Setting: The Central & Eastern Sydney Service of BreastScreen NSW. Participants: Women aged 40-69 years at first screen, who attended for their first or second screen between 1 March 1988 and 31 December 1992. Main outcome measures: Interval-cancer rates per 10 000 screens and as a proportion of the underlying incidence of breast cancer (as estimated by the underlying rate in the total NSW population). Results: The 12-month interval-cancer incidence per 10 000 screens was 4.17 for the 40-49 years age group (95% confidence interval [CI], 1.35-9.73) and 4.64 for the 50-69 years age group (95% CI, 2.47-7.94). Proportional incidence rates were 30.1% for the 40-49 years age group (95% CI, 9.8-70.3) and 22% for the 50-69 years age group (95% CI, 11.7-37.7). There was no significant difference between the proportional incidence rate for the 50-69 years age group for the Central & Eastern Sydney Service and those of major successful overseas screening trials. Conclusion: Screening quality was acceptable and should result in a significant mortality reduction in the screened population. Given the small number of cancers involved, comparison of interval-cancer statistics of mammographic screening programs with trials requires age-specific or age-adjusted data, and consideration of confidence intervals of both program and trial data.