Search

• Innovative phenotype-genotype association analysis for categorical genomic data having non-ignorable missing values. • Statistical learning method of random forest is used for variable selection in the analysis. • Weighted logistic ridge regression with EM algorithm is used for missing data imputation in the analysis. • Linear statistical hypothesis testing is used for determining the missingness mechanism in the analysis. • An application to analyzing real data from Australia breast cancer genome-wide association study (GWAS). Genomic data arising from a genome-wide association study (GWAS) are often not only of large-scale, but also incomplete. A specific form of their incompleteness is missing values with non-ignorable missingness mechanism. The intrinsic complications of genomic data present significant challenges in developing an effective and efficient procedure of phenotype-genotype association analysis by a statistical variable selection approach. In this paper we develop a coherent procedure of categorical phenotype-genotype association analysis, in the presence of missing values with non-ignorable missingness mechanism in genomic data. It is developed by integrating the statistical learning methods of random forest for variable selection, joint weighted logistic ridge regression with EM algorithm for missing data imputation, and linear statistical hypothesis testing for determining the missingness mechanism. Two simulated genomic datasets are used to undertake the phenotype-genotype association analysis by the proposed procedure, with the performance validated. The proposed procedure is then applied to analyze a real data set from breast cancer GWAS. [ABSTRACT FROM AUTHOR]

Background: These trials are the first randomised controlled trials of telephone-based weight management and healthy lifestyle interventions for low back pain and knee osteoarthritis. This article describes the protocol and statistical analysis plan. Method: These trials are parallel randomised controlled trials that investigate and compare the effect of a telephone-based weight management and healthy lifestyle intervention for improving pain intensity in overweight or obese patients with low back pain or knee osteoarthritis. The analysis plan was finalised prior to initiation of analyses. All data collected as part of the trial were reviewed, without stratification by group, and classified by baseline characteristics, process of care and trial outcomes. Trial outcomes were classified as primary and secondary outcomes. Appropriate descriptive statistics and statistical testing of between-group differences, where relevant, have been planned and described. Conclusions: A protocol for standard analyses was developed for the results of two randomised controlled trials. This protocol describes the data, and the pre-determined statistical tests of relevant outcome measures. The plan demonstrates transparent and verifiable use of the data collected. This a priori protocol will be followed to ensure rigorous standards of data analysis are strictly adhered to. [ABSTRACT FROM AUTHOR]

Core Goodeniaceae is a clade of ~330 species primarily distributed in Australia. Considerable variation in flower morphology exists within this group and we aim to use geometric morphometrics to characterize this variation across the two major subclades: Scaevola sensu lato (s.l.) and Goodenia s.l., the latter of which was hypothesized to exhibit greater variability in floral symmetry form. We test the hypothesis that floral morphological variation can be adequately characterized by our morphometric approach, and that discrete groups of floral symmetry morphologies exist, which broadly correlate with subjectively determined groups. From 335 images of 44 species in the Core Goodeniaceae, two principal components were computed that describe >98% of variation in all datasets. Increasing values of PC1 ventralize the dorsal petals (increasing the angle between them), whereas increasing values of PC2 primarily ventralize the lateral petals (decreasing the angle between them). Manipulation of these two morphological “axes” alone was sufficient to recreate any of the general floral symmetry patterns in the Core Goodeniaceae. Goodenia s.l. exhibits greater variance than Scaevola s.l. in PC1 and PC2, and has a significantly lower mean value for PC1. Clustering clearly separates fan-flowers (with dorsal petals at least 120° separated) from the others, whereas the distinction between pseudo-radial and bilabiate clusters is less clear and may form a continuum rather than two distinct groups. Transitioning from the average fan-flower to the average non-fan-flower is described almost exclusively by PC1, whereas PC2 partially describes the transition between bilabiate and pseudo-radial morphologies. Our geometric morphometric method accurately models Core Goodeniaceae floral symmetry diversity. [ABSTRACT FROM AUTHOR]

Background: Sitting time questionnaires have largely been validated in small convenience samples. The validity of this multi-context sitting questionnaire against an accurate measure of sitting time is reported in a large demographically diverse sample allowing assessment of validity in varied demographic subgroups. Methods: A subgroup of participants of the third wave of the Australian Diabetes, Obesity, and Lifestyle (AusDiab3) study wore activPAL3™ monitors (7 days, 24 hours/day protocol) and reported their sitting time for work, travel, television viewing, leisure computer use and "other" purposes, on weekdays and weekend days (n = 700, age 36-89 years, 45 % men). Correlations (Pearson's r; Spearman's p) of the self-report measures (the composite total, contextual measures and items) with monitor-assessed sitting time were assessed in the whole sample and separately in socio-demographic subgroups. Agreement was assessed using Bland-Altman plots. Results: The composite total had a correlation with monitor-assessed sitting time of r = 0.46 (95 % confidence interval [CI]: 0.40, 0.52); this correlation did not vary significantly between demographic subgroups (all >0.4). The contextual measure most strongly correlated with monitor-assessed sitting time was work (p = 0.25, 95 % CI: 0.17, 0.31), followed by television viewing (p = 0.16, 95 % CI: 0.09, 0.24). Agreement of the composite total with monitored sitting time was poor, with a positive bias (B = 0.53, SE 0.04, p < 0.001) and wide limits of agreement (±4.32 h). Conclusions: This multi-context questionnaire provides a total sitting time measure that ranks participants well for the purposes of assessing health associations but has limited accuracy relative to activPAL-assessed sitting time. Findings did not differ in demographic subgroups. [ABSTRACT FROM AUTHOR]

Background: Feeding practices are commonly examined as potentially modifiable determinants of children's eating behaviours and weight status. Although a variety of questionnaires exist to assess different feeding aspects, many lack thorough reliability and validity testing. The Feeding Practices and Structure Questionnaire (FPSQ) is a tool designed to measure early feeding practices related to non-responsive feeding and structure of the meal environment. Face validity, factorial validity, internal reliability and cross-sectional correlations with children's eating behaviours have been established in mothers with 2-year-old children. The aim of the present study was to further extend the validity of the FPSQ by examining factorial, construct and predictive validity, and stability. Methods: Participants were from the NOURISH randomised controlled trial which evaluated an intervention with first-time mothers designed to promote protective feeding practices. Maternal feeding practices (FP) and child eating behaviours were assessed when children were aged 2 years and 3.7 years (n = 388). Confirmatory Factor analysis, group differences, predictive relationships, and stability were tested. Results: The original 9-factor structure was confirmed when children were aged 3.7 ± 0.3 years. Cronbach's alpha was above the recommended 0.70 cut-off for all factors except Structured Meal Timing, Over Restriction and Distrust in Appetite which were 0.58, 0.67 and 0.66 respectively. Allocated group differences reflected behaviour consistent with intervention content and all feeding practices were stable across both time points (range of r = 0.45-0.70). There was some evidence for the predictive validity of factors with 2 FP showing expected relationships, 2 FP showing expected and unexpected relationships and 5 FP showing no relationship. Conclusions: Reliability and validity was demonstrated for most subscales of the FPSQ. Future validation is warranted with culturally diverse samples and with fathers and other caregivers. The use of additional outcomes to further explore predictive validity is recommended as well as testing test-retest reliability of the questionnaire. [ABSTRACT FROM AUTHOR]

Background: Delivery of care to people with advanced cancer in the emergency department (ED) is complicated by competing service demands, workloads and physical design constraints. We explored emergency clinicians' attitudes to the ED environment when caring for patients who present with advanced cancer, and how these attitudes are affected by access to palliative care services, palliative care education, staff type, ED experience and patient demographic, hospital type and region. Methods: We electronically surveyed clinicians from the College of Emergency Nursing Australasia, Australian College of Emergency Nursing and Australasian College for Emergency Medicine working in an Australian ED. Results: Respondents were 444 doctors and 237 nurses. They reported overcrowding, noise, lack of time and privacy as barriers to care. Most (93.3%) agreed/strongly agreed that the dying patient should be allocated private space in ED. 73.6% (451) felt unable to provide a desired level of care to advanced cancer patients in ED. Clinician attitudes were affected by staff type, experience, ED demographic and hospital type, but not education in palliative care. Conclusions: ED environments place pressure on clinicians delivering care to people with advanced cancer. Integrating palliative care services in ED and redesigning EDs to better match its multifaceted functions should be considered. [ABSTRACT FROM AUTHOR]

Aim Invasive species are predicted to experience a reduction in genetic diversity during the introduction process because of founder effects, yet they are able to successfully establish in new regions and outcompete the native biota. Admixture has been proposed as a potential solution to this genetic paradox. We adopted a phylogeographic approach to investigate the invasion history of the delicate skink ( Lampropholis delicata) in the Pacific region and test the hypothesis that admixture is important for the success of biological invasions. Location Eastern Australia and the Pacific region ( Lord Howe Island, New Zealand, Hawaii). Methods We obtained mitochondrial DNA sequence data ( ND2, ND4) from across the native Australian range (238 samples, 120 populations) and 371 samples from the introduced range of L. delicata. Genetic distances and Analysis of molecular variance ( AMOVA) were used to examine the level of genetic variation across the native and introduced ranges. Results Fourteen haplotypes were evident in the introduced range (1 in Hawaii, 7 in New Zealand, 7 in Lord Howe Island), with a shared haplotype present in both New Zealand and Lord Howe Island. Five source regions were identified ( Brisbane, Tenterfield, Border Ranges, Yamba- Coffs Harbour, Sydney) from across four distinct native-range genetic lineages. The Hawaiian population stems from a single introduction from Brisbane, whereas one or more introductions from the Tenterfield region led to the New Zealand populations. Multiple introductions from across all five source regions have resulted in extreme admixture (up to 8.3% sequence divergence) within Lord Howe Island. Main Conclusions L. delicata introductions are capable of being successful both in the presence and absence of admixture. Contrary to the predictions of the sequential two-step model, the presence of admixture was not related to the time since initial introduction. We suggest that the importance of admixture in determining the success of biological invasions has been overemphasized. [ABSTRACT FROM AUTHOR]

Background: Goal-directed fluid therapy (GDFT) has been shown to reduce complications and hospital length of stay following major surgery. However, there has been no assessment regarding its use in clinical practice. Methods: An electronic survey was administered to randomly selected anaesthetists from the United Kingdom (UK, n = 2000) and the United States of America (USA, n = 2000), and 500 anaesthetists from Australia/New Zealand (AUS/NZ). Preferences, clinical use and attitudes towards GDFT were investigated. Results were collated to examine regional differences. Results: The response rates from the UK (n = 708) and AUS/NZ (n = 180) were 35%, and 36% respectively. The response rate from the USA was very low (n = 178; 9%). GDFT use was significantly more common in the UK than in AUS/NZ (p < 0.01). The Oesophageal Doppler Monitor was the most preferred instrument in the UK (n = 362; h76%) with no clear preferences in other regions. GDFT was most commonly utilised in major abdominal surgery and for patients with significant comorbidities. The commonest reasons stated for not using GDFT were either lack of availability of monitoring tools (AUS/NZ: 57 (70%); UK: 94 (64%)) or a lack of experience with instruments (AUS/NZ: 43 (53%); UK: 51 (35%)). A subset of respondents (AUS/NZ: 22(27%); UK: 45 (30%)) felt GDFT provided no perceived benefit. Enthusiasm towards the use of GDFT in the absence of existing barriers was high. Conclusion: Several hypotheses were generated regarding important differences in the use of GDFT between anaesthetists from the UK and AUS/NZ. There is significant interest in utilising GDFT in clinical practice and existing barriers should be addressed. [ABSTRACT FROM AUTHOR]

The article presents a study that aimed to describe the local outcomes with major lower limb amputation (LLA) in the Prince of Wales Hospital (POWH) in terms of morbidity, rehabilitation potential, discharge destination, and function in New South Wales between 1994 and 2006. The study found that of 190 patients, 135 were assessed to have a rehabilitation potential and 55 were transferred to nursing homes after stabilization. It discovered that many patients suffered from would infection.

Objective To investigate the effect of immigration on life expectancy in Australia for the period from 1981 to 2003, and to compare life expectancy of the Australian-born population with that of other countries in the Organisation for Economic Cooperation and Development (OECD). Methods Standard life-table methods using age-specific all-cause mortality and population data from 1981 to 2003 were used to calculate life expectancy at birth ( e0) for the total Australian population (including migrants) and for people born in Australia (excluding migrants). Mean differences in life expectancy for each sex were compared using paired t-tests. Rankings of life expectancy among OECD countries were reassessed, and rank changes measured using the Wilcoxon signed rank test. Findings Life expectancy of males and females was significantly lower in the Australian-born group than in the total Australian population. During 1981 to 2003, there was a mean difference in life expectancy of 0.41 years (95% confidence interval, CI: 0.37-0.44; t17 = 27.0; P < 0.0001) in males and 0.29 years (95% CI: 0.26-0.31; t17 = 27.6; P < 0.0001) in females between the Australian-born and the total population. After excluding migrant groups, Australia no longer ranked among the top five OECD countries with the highest life expectancy in the two most recent years examined. Conclusion While Australia has one of the highest life expectancies in the industrialized world, this is partly attributable to immigration of populations with low rates of mortality. This effect needs to be considered in international comparative assessments of mortality levels. [ABSTRACT FROM AUTHOR]

Varanid lizards are difficult to sex in the field because commonly used techniques are not completely reliable and definitive techniques are not logistically or economically feasible for many field-based applications. Previous work has shown that variation in morphometric variables can be used to determine sex in some species of varanid. Here we build on these previous exploratory analyses by developing a set of a priori models (containing morphometric variables) to predict the sex of six species of Australian varanid, and then examining their relative support under the information-theoretic framework. We then use cross-validation procedures to determine the reliability of the best-supported models' predictive ability. Our analysis suggests that a large sample size is required for building models to predict sex in many species. The most important sexually diagnostic features for many species were a number of head variables and (to a lesser extent) scaling of limb proportions. This analysis provides some useful statistical tools for the field-sexing of adult and juvenile Varanus gouldii with a known level of reliability and also serves to highlight the danger of extrapolating from potentially spurious results when using exploratory methods or null hypothesis testing. [ABSTRACT FROM AUTHOR]

Monitoring pregnancy weight can reduce excess gestational weight gain (GWG), and is recommended in clinical practice guidelines as part of routine care. This study aimed to evaluate the implementation of routine weight monitoring using a pregnancy weight gain chart (PWGC), and assess health care professionals (HCPs) and pregnant women's attitudes and practices around its use. A semiquantitative survey was conducted with a consecutive sample of antenatal women at 16 and 36 weeks gestation. Women were weighed, and a PWGC audit done at 36 weeks gestation to assess adherence to chart use and GWG. A cross‐sectional survey of antenatal HCPs at the Australian facility assessed staff attitudes and practices relating to weight monitoring and PWGC use. Of the 291 women surveyed, 68% reported being given a PWGC. Of the audited PWGCs (n = 258), 54% had less than three weights recorded, 36% had errors, and 3% were unused. All HCPs surveyed (n = 42) were aware of the PWGC, 63% reported using it to track GWG regularly and 26% believed it to be only the woman's responsibility (i.e., not the midwife's role) to complete it. Seventy‐six percent reported they needed more training in counselling pregnant women, and insufficient time was a main barrier to weighing and conversing with women. It is feasible to implement a PWGC into routine antenatal care. Clarity over women's and HCPs responsibility for monitoring GWG and completion of the PWGC is needed. Training on correct PWGC use and counselling and workforce engagement are required to overcome barriers and support healthy GWG. [ABSTRACT FROM AUTHOR]

Focuses on the potential problems with management decision errors and their consequences in the monitoring of environmental flow regimes (EFR) in Australia. Effectiveness of the hypothesis-testing framework in monitoring programs for the stream ecology in the region; Constraints in determining the balance between Type 1 and Type II error rates in the program; Details of the decision-making framework for EFR.