Family-level relationships among the Australasian marsupial “herbivores” (Diprotodontia: Koala, wombats, kangaroos and possums)

The marsupial order Diprotodontia includes 10 extant families, which occupy all terrestrial habitats across Australia and New Guinea and have evolved remarkable dietary and locomotory diversity. Despite considerable attention, the interrelations of these families have for the most part remained elusive. In this study, we separately model mitochondrial RNA and protein-coding sequences in addition to nuclear protein-coding sequences to provide near-complete resolution of diprotodontian family-level phylogeny. We show that alternative topologies inferred in some previous studies are likely to be artifactual, resulting from branch-length and compositional biases. Subordinal groupings resolved herein include Vombatiformes (wombats and koala) and Phalangerida, which in turn comprises Petauroidea (petaurid gliders and striped, feathertail, ringtail and honey possums) and a clade whose plesiomorphic members possess blade-like premolars (phalangerid possums, kangaroos and their allies and most likely, pygmy possums). The topology resolved reveals ecological niche structuring among diprotodontians that has likely been maintained for more than 40 million years.

Multi-method, multi-theoretical, multi-level research in the learning sciences

We examine methodologies and methods that apply to multi-level research in the learning sciences. In so doing we describe how multiple theoretical frameworks informs the use of different methods that apply to social levels involving space-time relationships that are not accessible consciously as social life is enacted. Most of the methods involve analyses of video and audio files. Within a framework of interpretive research we present a methodology of event-oriented social science, which employs video ethnography, narrative, conversation analysis, prosody analysis, and facial expression analysis. We illustrate multi-method research in an examination of the role of emotions in teaching and learning. Conversation and prosody analyses augment facial expression analysis and ethnography. We conclude with an exploration of ways in which multi-level studies can be complemented with neural level analyses.

Socioeconomic inequalities in weight status among mid-aged adults : the contribution of perceptions of weight status and weight-control behaviours

Background Socioeconomically-disadvantaged adults in developed countries experience a higher prevalence of a number of chronic diseases, such as cardiovascular disease, type 2 diabetes, osteoarthritis and some forms of cancer. Overweight and obesity are major risk factors for these diseases. Lower socioeconomic groups have a greater prevalence of overweight and obesity and this may contribute to their higher morbidity and mortality. International studies suggest that socioeconomic groups may differ in their self-perceptions of weight status and their engagement in weightcontrol behaviours (WCBs). Research has shown that lower socioeconomic adults are more likely to underestimate their weight status, and are less likely to engage in WCBs. This may contribute (in part) to the marked inequalities in weight status observed at the population level. There are few, and somewhat limited, Australian studies that have examined the types of weight-control strategies people adopt, the barriers to their weight control, the determinants of their perceived weight status and WCBs. Furthermore, there are no known Australian studies that have examined socioeconomic differences in these factors to better understand the reasons for socioeconomic inequalities in weight status. Hence, the overall aim of this Thesis is to examine why socioeconomically-disadvantaged group experience a greater prevalence of overweight and obesity than their more-advantaged counterparts. Methods This Thesis used data from two sources. Men and women aged 45 to 60 years were examined from both data source. First, the longitudinal Australian Diabetes, Obesity and Lifestyle (AusDiab) Study were used to advance our knowledge and understanding of socioeconomic differences in weight change, perceived weight status and WCBs. A total of 2753 participants with measured weights at both baseline (1999-2000) and follow-up (2004-2005) were included in the analyses. Percent weight change over the five-year interval was calculated and perceived weight status, WCBs and highest attained education were collected at baseline. Second, the Candidate conducted a postal questionnaire from 1013 Brisbane residents (69.8 % response rate) to investigate the relationship between socioeconomic position, determinants of perceived weight status, WCBs, and barriers and reasons to weight control. A test-retest reliability study was conducted to determine the reliability of the new measures used in the questionnaire. Most new measures had substantial to almost perfect reliability when considering either kappa coefficient or crude agreement. Results The findings from the AusDiab Study (accepted for publication in the Australian and New Zealand Journal of Public Health) showed that low-educated men and women were more likely to be obese at baseline compared to their higheducated respondents (O.R. = 1.97, 95 % C.I. = 1.30-2.98 and O.R. = 1.52, 95 % C.I. = 1.03-2.25, respectively). Over the five year follow-up period (1999-2000 to 2004- 05) there were no socioeconomic differences in weight change among men, however socioeconomically-disadvantaged women had greater weight gains. Participants perceiving themselves as overweight gained less weight than those who saw themselves as underweight or normal weight. There was no relationship between engaging in WCBs and five-year weight change. The postal questionnaire data showed that socioeconomically-disadvantaged groups were less likely to engage in WCBs. If they did engage in weight control, they were less likely to adopt exercise strategies, including moderate and vigorous physical activities but were more likely to decrease their sitting time to control their weight. Socioeconomically-disadvantaged adults reported more barriers to weight control; such as perceiving weight loss as expensive, requiring a lot of cooking skills, not being a high priority and eating differently from other people in the household. These results have been accepted for publication in Public Health Nutrition. The third manuscript (under review in Social Science and Medicine) examined socioeconomic differences in determinants of perceived weight status and reasons for weight control. The results showed that lower socioeconomic adults were more likely to specify the following reasons for weight control: they considered themselves to be too heavy, for occupational requirements, on recommendation from their doctor, family members or friends. Conversely, high-income adults were more likely to report weight control to improve their physical condition or to look more attractive compared with those on lower-incomes. There were few socioeconomic differences in the determinants of perceived weight status. Conclusions Education inequalities in overweight/obesity among men and women may be due to mis-perceptions of weight status; overweight or obese individuals in loweducated groups may not perceive their weight as problematic and therefore may not pay attention to their energy-balance behaviours. Socioeconomic groups differ in WCBs, and their reasons and perceived barriers to weight control. Health promotion programs should encourage weight control among lower socioeconomic groups. More specifically, they should encourage the engagement of physical activity or exercise and dietary strategies among disadvantaged groups. Furthermore, such programs should address potential barriers for weight control that disadvantaged groups may encounter. For example, disadvantaged groups perceive that weight control is expensive, requires cooking skills, not a high priority and eating differently from other people in the household. Lastly, health promotion programs and policies aimed at reducing overweight and obesity should be tailored to the different reasons and motivations to weight control experienced by different socioeconomic groups. Weight-control interventions targeted at higher socioeconomic groups should use improving physical condition and attractiveness as motivational goals; while, utilising social support may be more effective for encouraging weight control among lower socioeconomic groups.

An analysis of holding cost impact on housing affordability in relation to midsized Greenfield residential property developments in South East Queensland

The position of housing demand and supply is not consistent. The Australian situation counters the experience demonstrated in many other parts of the world in the aftermath of the Global Financial Crisis, with residential housing prices proving particularly resilient. A seemingly inexorable housing demand remains a critical issue affecting the socio-economic landscape. Underpinned by high levels of population growth fuelled by immigration, and further buoyed by sustained historically low interest rates, increasing income levels, and increased government assistance for first home buyers, this strong housing demand level ensures problems related to housing affordability continue almost unabated. A significant, but less visible factor impacting housing affordability relates to holding costs. Although only one contributor in the housing affordability matrix, the nature and extent of holding cost impact requires elucidation: for example, the computation and methodology behind the calculation of holding costs varies widely - and in some instances completely ignored. In addition, ambiguity exists in terms of the inclusion of various elements that comprise holding costs, thereby affecting the assessment of their relative contribution. Such anomalies may be explained by considering that assessment is conducted over time in an ever-changing environment. A strong relationship with opportunity cost - in turn dependant inter alia upon prevailing inflation and / or interest rates - adds further complexity. By extending research in the general area of housing affordability, this thesis seeks to provide a detailed investigation of those elements related to holding costs specifically in the context of midsized (i.e. between 15-200 lots) greenfield residential property developments in South East Queensland. With the dimensions of holding costs and their influence over housing affordability determined, the null hypothesis H0 that holding costs are not passed on can be addressed. Arriving at these conclusions involves the development of robust economic and econometric models which seek to clarify the componentry impacts of holding cost elements. An explanatory sequential design research methodology has been adopted, whereby the compilation and analysis of quantitative data and the development of an economic model is informed by the subsequent collection and analysis of primarily qualitative data derived from surveying development related organisations. Ultimately, there are significant policy implications in relation to the framework used in Australian jurisdictions that promote, retain, or otherwise maximise, the opportunities for affordable housing.

Adoption of low-cost rail level crossing warning devices : an Australian case study

The objective of this chapter is to provide rail practitioners with a practical approach for determining safety requirements of low-cost level crossing warning devices (LCLCWDs) on an Australian railway by way of a case study. LCLCWDs, in theory, allow railway operators to improve the safety of passively controlled crossing by upgrading a larger number of level crossings with the same budget that would otherwise be used to upgrade these using the conventional active level crossing control technologies, e.g. track circuit initiated flashing light systems. The chapter discusses the experience and obstacles of adopting LCLCWDs in Australia, and demonstrates how the risk-based approach may be used to make the case for LCLCWDs.

Family literacy practices and home literacy resources : an Australian pilot study

The combined impact of social class, cultural background and experience upon early literacy achievement in the first year of schooling is among the most durable questions in educational research. Links have been established between social class and achievement but literacy involves complex social and cognitive practices that are not necessarily reflected in the connections that have been made. The complexity of relationships between social class, cultural background and experience, and their impact on early literacy achievement have received little research attention. Recent refinements of the broad terms of social class or socioeconomic status have questioned the established links between social class and achievement. Nevertheless, it remains difficult to move beyond deficit and mismatch models of explaining and understanding the underperformance of children from lower socioeconomic and cultural minority groups when conventional measures are used. The data from an Australian pilot study reported here add to the increasing evidence that income is not necessarily related directly to home literacy resources or to how those resources are used. Further, the data show that the level of print resources in the home may not be a good indicator of the level of use of those resources.

Viruses of banana in East Africa

Bananas are one of the world's most important food crops, providing sustenance and income for millions of people in developing countries and supporting large export industries. Viruses are considered major constraints to banana production, germplasm multiplication and exchange, and to genetic improvement of banana through traditional breeding. In Africa, the two most important virus diseases are bunchy top, caused by Banana bunchy top virus (BBTV), and banana streak disease, caused by Banana streak virus (BSV). BBTV is a serious production constraint in a number of countries within/bordering East Africa, such as Burundi, Democratic Republic of Congo, Malawi, Mozambique, Rwanda and Zambia, but is not present in Kenya, Tanzania and Uganda. Additionally, epidemics of banana streak disease are occurring in Kenya and Uganda. The rapidly growing tissue culture (TC) industry within East Africa, aiming to provide planting material to banana farmers, has stimulated discussion about the need for virus indexing to certify planting material as virus-free. Diagnostic methods for BBTV and BSV have been reported and, for BBTV, PCR-based assays are reliable and relatively straightforward. However for BSV, high levels of serological and genetic variability and the presence of endogenous virus sequences within the banana genome complicate diagnosis. Uganda has been shown to contain the greatest diversity in BSV isolates found anywhere in the world. A broad-spectrum diagnostic test for BSV detection, which can discriminate between endogenous and episomal BSV sequences, is a priority. This PhD project aimed to establish diagnostic methods for banana viruses, with a particular focus on the development of novel methods for BSV detection, and to use these diagnostic methods for the detection and characterisation of banana viruses in East Africa. A novel rolling-circle amplification (RCA) method was developed for the detection of BSV. Using samples of Banana streak MY virus (BSMYV) and Banana streak OL virus (BSOLV) from Australia, this method was shown to distinguish between endogenous and episomal BSV sequences in banana plants. The RCA assay was used to screen a collection of 56 banana samples from south-west Uganda for BSV. RCA detected at least five distinct BSV isolates in these samples, including BSOLV and Banana streak GF virus (BSGFV) as well as three BSV isolates (Banana streak Uganda-I, -L and -M virus) for which only partial sequences had been previously reported. These latter three BSV had only been detected using immuno-capture (IC)-PCR and thus were possible endogenous sequences. In addition to its ability to detect BSV, the RCA protocol was also demonstrated to detect other viruses within the family Caulimoviridae, including Sugar cane bacilliform virus, and Cauliflower mosaic virus. Using the novel RCA method, three distinct BSV isolates from both Kenya and Uganda were identified and characterised. The complete genome of these isolates was sequenced and annotated. All six isolates were shown to have a characteristic badnavirus genome organisation with three open reading frames (ORFs) and the large polyprotein encoded by ORF 3 was shown to contain conserved amino acid motifs for movement, aspartic protease, reverse transcriptase and ribonuclease H activities. As well, several sequences important for expression and replication of the virus genome were identified including the conserved tRNAmet primer binding site present in the intergenic region of all badnaviruses. Based on the International Committee on Taxonomy of Viruses (ICTV) guidelines for species demarcation in the genus Badnavirus, these six isolates were proposed as distinct species, and named Banana streak UA virus (BSUAV), Banana streak UI virus (BSUIV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), Banana streak CA virus (BSCAV) and Banana streak IM virus (BSIMV). Using PCR with species-specific primers designed to each isolate, a genotypically diverse collection of 12 virus-free banana cultivars were tested for the presence of endogenous sequences. For five of the BSV no amplification was observed in any cultivar tested, while for BSIMV, four positive samples were identified in cultivars with a B-genome component. During field visits to Kenya, Tanzania and Uganda, 143 samples were collected and assayed for BSV. PCR using nine sets of species-specific primers, and RCA, were compared for BSV detection. For five BSV species with no known endogenous counterpart (namely BSCAV, BSUAV, BSUIV, BSULV and BSUMV), PCR was used to detect 30 infections from the 143 samples. Using RCA, 96.4% of these samples were considered positive, with one additional sample detected using RCA which was not positive using PCR. For these five BSV, PCR and RCA were both useful for identifying infected samples, irrespective of the host cultivar genotype (Musa A- or B-genome components). For four additional BSV with known endogenous counterparts in the M. balbisiana genome (BSOLV, BSGFV, BSMYV and BSIMV), PCR was shown to detect 75 infections from the 143 samples. In 30 samples from cultivars with an A-only genome component there was 96.3% agreement between PCR positive samples and detection using RCA, again demonstrating either PCR or RCA are suitable methods for detection. However, in 45 samples from cultivars with some B-genome component, the level of agreement between PCR positive samples and RCA positive samples was 70.5%. This suggests that, in cultivars with some B-genome component, many infections were detected using PCR which were the result of amplification of endogenous sequences. In these latter cases, RCA or another method which discriminates between endogenous and episomal sequences, such as immuno-capture PCR, is needed to diagnose episomal BSV infection. Field visits were made to Malawi and Rwanda to collect local isolates of BBTV for validation of a PCR-based diagnostic assay. The presence of BBTV in samples of bananas with bunchy top disease was confirmed in 28 out of 39 samples from Malawi and all nine samples collected in Rwanda, using PCR and RCA. For three isolates, one from Malawi and two from Rwanda, the complete nucleotide sequences were determined and shown to have a similar genome organisation to previously published BBTV isolates. The two isolates from Rwanda had at least 98.1% nucleotide sequence identity between each of the six DNA components, while the similarity between isolates from Rwanda and Malawi was between 96.2% and 99.4% depending on the DNA component. At the amino acid level, similarities in the putative proteins encoded by DNA-R, -S, -M, - C and -N were found to range between 98.8% to 100%. In a phylogenetic analysis, the three East African isolates clustered together within the South Pacific subgroup of BBTV isolates. Nucleotide sequence comparison to isolates of BBTV from outside Africa identified India as the possible origin of East African isolates of BBTV.

Drivers’ inability to assess their level of alertness on monotonous highways

Decline of alertness constitutes a normal physiological phenomenon but could be aggravated when drivers operate in monotonous environments, even in rested individuals. Driving performance is impaired and this increases crash risk due to inattention. This paper aims to show that road characteristics - namely road design (road geometry) and road side variability (signage and buildings) – influence subjective assessment of alertness by drivers. This study used a driving simulator to investigate the drivers’ ability to subjectively detect periods of time when their alertness is importantly reduced by varying road geometry and road environment. Driver’s EEG activity is recorded as a reference to evaluate objectively driver's alertness and is compared to self-reported alertness by participants. Twenty-five participants drove on four different scenarios (varying road design and road environment monotony) for forty minutes. It was observed that participants were significantly more accurate in their assessment before the driving task as compared to after (90% versus 60%). Errors in assessment were largely underestimations of their real alertness rather than over-estimations. The ability to detect low alertness as assessed with an EEG was highly dependent on the road monotony. Scenarios with low roadside variability resulted in high overestimation of the real alertness, which was not observed on monotonous road design. The findings have consequences for road safety and suggest that countermeasures to lapses of alertness cannot rely solely on self-assessment from drivers and road design should reduce environments with low variability.

Sustainable Road Management in Texas : network-level flexible pavement structural condition analysis using data mining techniques

The research team recognized the value of network-level Falling Weight Deflectometer (FWD) testing to evaluate the structural condition trends of flexible pavements. However, practical limitations due to the cost of testing, traffic control and safety concerns and the ability to test a large network may discourage some agencies from conducting the network-level FWD testing. For this reason, the surrogate measure of the Structural Condition Index (SCI) is suggested for use. The main purpose of the research presented in this paper is to investigate data mining strategies and to develop a prediction method of the structural condition trends for network-level applications which does not require FWD testing. The research team first evaluated the existing and historical pavement condition, distress, ride, traffic and other data attributes in the Texas Department of Transportation (TxDOT) Pavement Maintenance Information System (PMIS), applied data mining strategies to the data, discovered useful patterns and knowledge for SCI value prediction, and finally provided a reasonable measure of pavement structural condition which is correlated to the SCI. To evaluate the performance of the developed prediction approach, a case study was conducted using the SCI data calculated from the FWD data collected on flexible pavements over a 5-year period (2005 – 09) from 354 PMIS sections representing 37 pavement sections on the Texas highway system. The preliminary study results showed that the proposed approach can be used as a supportive pavement structural index in the event when FWD deflection data is not available and help pavement managers identify the timing and appropriate treatment level of preventive maintenance activities.