Ecological aspects of biosecurity surveillance design for the detection of multiple invasive animal species

Complex surveillance problems are common in biosecurity, such as prioritizing detection among multiple invasive species, specifying risk over a heterogeneous landscape, combining multiple sources of surveillance data, designing for specified power to detect, resource management, and collateral effects on the environment. Moreover, when designing for multiple target species, inherent biological differences among species result in different ecological models underpinning the individual surveillance systems for each. Species are likely to have different habitat requirements, different introduction mechanisms and locations, require different methods of detection, have different levels of detectability, and vary in rates of movement and spread. Often there is a further challenge of a lack of knowledge, literature, or data, for any number of the above problems. Even so, governments and industry need to proceed with surveillance programs which aim to detect incursions in order to meet environmental, social and political requirements. We present an approach taken to meet these challenges in one comprehensive and statistically powerful surveillance design for non-indigenous terrestrial vertebrates on Barrow Island, a high conservation nature reserve off the Western Australian coast. Here, the possibility of incursions is increased due to construction and expanding industry on the island. The design, which includes mammals, amphibians and reptiles, provides a complete surveillance program for most potential terrestrial vertebrate invaders. Individual surveillance systems were developed for various potential invaders, and then integrated into an overall surveillance system which meets the above challenges using a statistical model and expert elicitation. We discuss the ecological basis for the design, the flexibility of the surveillance scheme, how it meets the above challenges, design limitations, and how it can be updated as data are collected as a basis for adaptive management.

Towards the adoption of low-cost rail level crossing warning devices in regional areas of Australia : a review of current technologies and reliability issues

This paper discusses major obstacles for the adoption of low cost level crossing warning devices (LCLCWDs) in Australia and reviews those trialed in Australia and internationally. The argument for the use of LCLCWDs is that for a given investment, more passive level crossings can be treated, therefore increasing safety benefits across the rail network. This approach, in theory, reduces risk across the network by utilizing a combination of low-cost and conventional level crossing interventions, similar to what is done in the road environment. This paper concludes that in order to determine if this approach can produce better safety outcomes than the current approach, involving the incremental upgrade of level crossings with conventional interventions, it is necessary to perform rigorous risk assessments and cost-benefit analyses of LCLCWDs. Further research is also needed to determine how best to differentiate less reliable LCCLWDs from conventional warning devices through the use of different warning signs and signals. This paper presents a strategy for progressing research and development of LCLCWDs and details how the Cooperative Research Centre (CRC) for Rail Innovation is fulfilling this strategy through the current and future affordable level crossing projects.

Using GIS to visualise and evaluate student travel behaviour

Using GIS to evaluate travel behaviour is an important technique to increase our understanding of the relationship between accessibility and transport demand. In this paper, the activity space concept was used to identify the nature of participation in activities (or lack of it) amongst a group of students using a 2 day travel-activity diary. Three different indicators such as the number of unique locations visited, average daily distance travelled, and average daily activity duration were used to measure the size of activity spaces. These indicators reflect levels of accessibility, personal mobility, and the extent of participation respectively. Multiple regression analyses were used to assess the impacts of students socio-economic status and the spatial characteristics of home location. Although no differences were found in the levels of accessibility and the extent of participation measures, home location with respect to a demand responsive transport (DRT) service was found to be the most important determinant of their mobility patterns. Despite being able to travel longer distances, students who live outside of the DRT service area were found to be temporally excluded from some opportunities. Student activity spaces were also visualised within a GIS environment and a spatial analysis was conducted to underpin the evaluation of the performance of the DRT. This approach was also used to identify the activity spaces of individuals that are geographically excluded from the service. Evaluation of these results indicated that although the service currently covers areas of high demand, 90% of the activity spaces remained un-served by the DRT service. Using this data six new routes were designed to meet the coverage goal of public transport based on a measure of network impedance based on inverse activity density. Following assessment of public transport service coverage, the study was extended using a Spatial Multi Criteria Evaluation (SMCE) technique to assess the effect of service provision on patronage.

Identifying rural disadvantage using a multiday travel diary

This paper identifies transport disadvantage using a 7 day activity-travel diary data from two rural case study areas. A composite participation index (PI) measure was developed for this study based on six indices measuring elements of travel and activity participation. Using the index the paper then goes on to compare these results, with the results obtained from other more traditional indicators used to identify transport disadvantage. These indicators are related to the size of activity space such as unique network distance travelled, number of unique locations visited, activity space area, activity duration, and fullness (shape) of activity spaces. The weaknesses of these indicator based measures are that: firstly, they do not take into account the relativity of the measure between different areas i.e. travel distance in terms of the wider context of available activities within an area; and secondly, these indicators are multi-dimensional and each represents a different qualitative aspect of travel and activity participation. As a result, six individual indices were developed to overcome these problems. These include: participation count index, participation length index, participation area index, participation duration index, participation type index, and participation frequency index. These are then aggregated to assess the relative performance in terms of these different indices and identify the nature of transport disadvantage. GIS was used to visualise individual travel patterns and to derive scores for both the indicator based measures and the index based measures. Factor analysis was conducted to derive weights of the individual indices to form the composite index measure. From this analysis, two intermediate indices were also derived using the underlying factors of the data related to these indices. Using the scores of all these measures, multiple regression analyses were conducted to identify patterns of transport disadvantage.

Mobility, accessibility and activity participation : a comparative assessment of methods to identify rural transport disadvantage

Traditionally, transport disadvantage has been identified using accessibility analysis although the effectiveness of the accessibility planning approach to improving access to goods and services is not known. This paper undertakes a comparative assessment of measures of mobility, accessibility, and participation used to identify transport disadvantage using the concept of activity spaces. A 7 day activity-travel diary data for 89 individuals was collected from two case study areas located in rural Northern Ireland. A spatial analysis was conducted to select the case study areas using criteria derived from the literature. The criteria are related to the levels of area accessibility and area mobility which are known to influence the nature of transport disadvantage. Using the activity-travel diary data individuals weekly as well as day to day variations in activity-travel patterns were visualised. A model was developed using the ArcGIS ModelBuilder tool and was run to derive scores related to individual levels of mobility, accessibility, and participation in activities from the geovisualisation. Using these scores a multiple regression analysis was conducted to identify patterns of transport disadvantage. This study found a positive association between mobility and accessibility, between mobility and participation, and between accessibility and participation in activities. However, area accessibility and area mobility were found to have little impact on individual mobility, accessibility, and participation in activities. Income vis-àvis ´ car-ownership was found to have a significant impact on individual levels of mobility, and accessibility; whereas participation in activities were found to be a function of individual levels of income and their occupational status.

Evolutionary biology of Gondwanan non-biting midges (Diptera: Chironomidae)

The potential restriction to effective dispersal and gene flow caused by habitat fragmentation can apply to multiple levels of evolutionary scale; from the fragmentation of ancient supercontinents driving diversification and speciation on disjunct landmasses, to the isolation of proximate populations as a result of their inability to cross intervening unsuitable habitat. Investigating the role of habitat fragmentation in driving diversity within and among taxa can thus include inferences of phylogenetic relationships among taxa, assessments of intraspecific phylogeographic structure and analyses of gene flow among neighbouring populations. The proposed Gondwanan clade within the chironomid (non-biting midge) subfamily Orthocladiinae (Diptera: Chironomidae) represents a model system for investigating the role that population fragmentation and isolation has played at different evolutionary scales. A pilot study by Krosch et al (2009) indentified several highly divergent lineages restricted to ancient rainforest refugia and limited gene flow among proximate sites within a refuge for one member of this clade, Echinocladius martini Cranston. This study provided a framework for investigating the evolutionary history of this taxon and its relatives more thoroughly. Populations of E. martini were sampled in the Paluma bioregion of northeast Queensland to investigate patterns of fine-scale within- and among-stream dispersal and gene flow within a refuge more rigorously. Data was incorporated from Krosch et al (2009) and additional sites were sampled up- and downstream of the original sites. Analyses of genetic structure revealed strong natal site fidelity and high genetic structure among geographically proximate streams. Little evidence was found for regular headwater exchange among upstream sites, but there was distinct evidence for rare adult flight among sites on separate stream reaches. Overall, however, the distribution of shared haplotypes implied that both larval and adult dispersal was largely limited to the natal stream channel. Patterns of regional phylogeographic structure were examined in two related austral orthoclad taxa – Naonella forsythi Boothroyd from New Zealand and Ferringtonia patagonica Sæther and Andersen from southern South America – to provide a comparison with patterns revealed in their close relative E. martini. Both taxa inhabit tectonically active areas of the southern hemisphere that have also experienced several glaciation events throughout the Plio-Pleistocene that are thought to have affected population structure dramatically in many taxa. Four highly divergent lineages estimated to have diverged since the late Miocene were revealed in each taxon, mirroring patterns in E. martini; however, there was no evidence for local geographical endemism, implying substantial range expansion post-diversification. The differences in pattern evident among the three related taxa were suggested to have been influenced by variation in the responses of closed forest habitat to climatic fluctuations during interglacial periods across the three landmasses. Phylogeographic structure in E. martini was resolved at a continental scale by expanding upon the sampling design of Krosch et al (2009) to encompass populations in southeast Queensland, New South Wales and Victoria. Patterns of phylogeographic structure were consistent with expectations and several previously unrecognised lineages were revealed from central- and southern Australia that were geographically endemic to closed forest refugia. Estimated divergence times were congruent with the timing of Plio-Pleistocene rainforest contractions across the east coast of Australia. This suggested that dispersal and gene flow of E. martini among isolated refugia was highly restricted and that this taxon was susceptible to the impacts of habitat change. Broader phylogenetic relationships among taxa considered to be members of this Gondwanan orthoclad group were resolved in order to test expected patterns of evolutionary affinities across the austral continents. The inferred phylogeny and estimated divergence times did not accord with expected patterns based on the geological sequence of break-up of the Gondwanan supercontinent and implied instead several transoceanic dispersal events post-vicariance. Difficulties in appropriate taxonomic sampling and accurate calibration of molecular phylogenies notwithstanding, the sampling regime implemented in the current study has been the most intensive yet performed for austral members of the Orthocladiinae and unsurprisingly has revealed both novel taxa and phylogenetic relationships within and among described genera. Several novel associations between life stages are made here for both described and previously unknown taxa. Investigating evolutionary relationships within and among members of this clade of proposed Gondwanan orthoclad taxa has demonstrated that a complex interaction between historical population fragmentation and dispersal at several levels of evolutionary scale has been important in driving diversification in this group. While interruptions to migration, colonisation and gene flow driven by population fragmentation have clearly contributed to the development and maintenance of much of the diversity present in this group, long-distance dispersal has also played a role in influencing diversification of continental biotas and facilitating gene flow among disjunct populations.

Sustainable assessment for large science classes : non-multiple choice, randomised assignments through a Learning Management System

This paper reports on the development of a tool that generates randomised, non-multiple choice assessment within the BlackBoard Learning Management System interface. An accepted weakness of multiple-choice assessment is that it cannot elicit learning outcomes from upper levels of Biggs’ SOLO taxonomy. However, written assessment items require extensive resources for marking, and are susceptible to copying as well as marking inconsistencies for large classes. This project developed an assessment tool which is valid, reliable and sustainable and that addresses the issues identified above. The tool provides each student with an assignment assessing the same learning outcomes, but containing different questions, with responses in the form of words or numbers. Practice questions are available, enabling students to obtain feedback on their approach before submitting their assignment. Thus, the tool incorporates automatic marking (essential for large classes), randomised tasks to each student (reducing copying), the capacity to give credit for working (feedback on the application of theory), and the capacity to target higher order learning outcomes by requiring students to derive their answers rather than choosing them. Results and feedback from students are presented, along with technical implementation details.

Multiple evolutionary rate classes in animal genome evolution

The proportion of functional sequence in the human genome is currently a subject of debate. The most widely accepted figure is that approximately 5% is under purifying selection. In Drosophila, estimates are an order of magnitude higher, though this corresponds to a similar quantity of sequence. These estimates depend on the difference between the distribution of genomewide evolutionary rates and that observed in a subset of sequences presumed to be neutrally evolving. Motivated by the widening gap between these estimates and experimental evidence of genome function, especially in mammals, we developed a sensitive technique for evaluating such distributions and found that they are much more complex than previously apparent. We found strong evidence for at least nine well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least seven classes in an alignment of four mammals, including human. We also identified at least three rate classes in human ancestral repeats. By positing that the largest of these ancestral repeat classes is neutrally evolving, we estimate that the proportion of nonneutrally evolving sequence is 30% of human ancestral repeats and 45% of the aligned portion of the genome. However, we also question whether any of the classes represent neutrally evolving sequences and argue that a plausible alternative is that they reflect variable structure-function constraints operating throughout the genomes of complex organisms.

Children with special health care needs : social and learning competence in the early years

The number of children with special health care needs surviving infancy and attending school has been increasing. Due to their health status, these children may be at risk of low social-emotional and learning competencies (e.g., Lightfoot, Mukherjee, & Sloper, 2000; Zehnder, Landolt, Prchal, & Vollrath, 2006). Early social problems have been linked to low levels of academic achievement (Ladd, 2005), inappropriate behaviours at school (Shiu, 2001) and strained teacher-child relationships (Blumberg, Carle, O‘Connor, Moore, & Lippmann, 2008). Early learning difficulties have been associated with mental health problems (Maughan, Rowe, Loeber, & Stouthamer-Loeber, 2003), increased behaviour issues (Arnold, 1997), delinquency (Loeber & Dishion, 1983) and later academic failure (Epstein, 2008). Considering the importance of these areas, the limited research on special health care needs in social-emotional and learning domains is a factor driving this research. The purpose of the current research is to investigate social-emotional and learning competence in the early years for Australian children who have special health care needs. The data which informed this thesis was from Growing up in Australia: The Longitudinal Study of Australian Children. This is a national, longitudinal study being conducted by the Commonwealth Department of Families, Housing, Community Services and Indigenous Affairs. The study has a national representative sample, with data collection occurring biennially, in 2004 (Wave 1), 2006 (Wave 2) and 2008 (Wave 3). Growing up in Australia uses a cross-sequential research design involving two cohorts, an Infant Cohort (0-1 at recruitment) and a Kindergarten Cohort (4-5 at recruitment). This study uses the Kindergarten Cohort, for which there were 4,983 children at recruitment. Three studies were conducted to address the objectives of this thesis. Study 1 used Wave 1 data to identify and describe Australian children with special health care needs. Children who identified as having special health care needs through the special health care needs screener were selected. From this, descriptive analyses were run. The results indicate that boys, children with low birth weight and children from families with low levels of maternal education are likely to be in the population of children with special health care needs. Further, these children are likely to be using prescription medications, have poor general health and are likely to have specific condition diagnoses. Study 2 used Wave 1 data to examine differences between children with special health care needs and their peers in social-emotional competence and learning competence prior to school. Children identified by the special health care needs screener were chosen for the case group (n = 650). A matched case control group of peers (n = 650), matched on sex, cultural and linguistic diversity, family socioeconomic position and age, were the comparison group. Social-emotional competence was measured through Social/Emotional Domain scores taken from the Growing up in Australia Outcome Index, with learning competence measured through Learning Domain scores. Results suggest statistically significant differences in scores between the two groups. Children with special health care needs have lower levels of social-emotional and learning competence prior to school compared to their peers. Study 3 used Wave 1 and Wave 2 data to examine the relationship between special health care needs at Wave 1 and social-emotional competence and learning competence at Wave 2, as children started school. The sample for this study consisted of children in the Kindergarten Cohort who had teacher data at Wave 2. Results from multiple regression models indicate that special health care needs prior to school (Wave 1) significantly predicts social-emotional competence and learning competence in the early years of school (Wave 2). These results indicate that having special health care needs prior to school is a risk factor for the social-emotional and learning domains in the early years of school. The results from these studies give valuable insight into Australian children with special health care needs and their social-emotional and learning competence in the early years. The Australia population of children with special health care needs were primarily male children, from families with low maternal education, were likely to be of poor health and taking prescription medications. It was found that children with special health care needs were likely to have lower social-emotional competence and learning competence prior to school compared to their peers. Results indicate that special health care needs prior to school were predictive of lower social-emotional and learning competencies in the early years of school. More research is required into this unique population and their competencies over time. However, the current research provides valuable insight into an under researched 'at risk' population.

Multiple analysis of three common genetic alterations associated with thrombophilia

We have previously reported the use of a novel mini-sequencing protocol for detection of the factor V Leiden variant, the first nucleotide change (FNC) technology. This technology is based on a single nucleotide extension of a primer, which is hybridized immediately adjacent to the site of mutation. The extended nucleotide that carries a reporter molecule (fluorescein) has the power to discriminate the genotype at the site of mutation. More recently, the prothrombin 20210 and thermolabile methylene tetrahydrofolate reductase (MTHFR) 677 variants have been identified as possible risk factors associated with thrombophilia. This study describes the use of the FNC technology in a combined assay to detect factor V, prothrombin and MTHFR variants in a population of Australian blood donors, and describes the objective numerical methodology used to determine genotype cut-off values for each genetic variation. Using FNC to test 500 normal blood donors, the incidence of Factor V Leiden was 3.6% (all heterozygous), that of prothrombin 20210 was 2.8% (all heterozygous) and that of MTHFR was 10% (homozygous). The combined FNC technology offers a simple, rapid, automatable DNA-based test for the detection of these three important mutations that are associated with familial thrombophilia. (C) 2000 Lippincott Williams and Wilkins.

Assessment of pre- and post-flood groundwater recharge via 3D visualisation, Lockyer Valley, southeast Queensland

The Lockyer Valley in southeast Queensland supports important and intensive irrigation which is dependant on the quality and availability of groundwater. Prolonged drought conditions from ~1997 resulted in a depletion of the alluvial aquifers, and concern for the long-term sustainability of this resource. By 2008, many areas of the valley were at < 20% of storage. Some relief occurred with rain events in early 2009, then in December 2010 - January 2011, most of southeast Queensland experienced unprecedented flooding. These storm-based events have caused a shift in research focus from investigations of drought conditions and mitigation to flood response analysis. For the alluvial aquifer system of the valley, a preliminary assessment of groundwater observation bore data, prior to and during the flood, indicates that there is a spatially variable aquifer response. While water levels in some bores screened in unconfined shallow aquifers have recovered by more than 10 m within a short period of time (months), others show only a small or moderate response. Measurements of pre- and post-flood groundwater levels and high-resolution time-series records from data loggers are considered within the framework of a 3D geological model of the Lockyer Valley using Groundwater Visualisation System(GVS). Groundwater level fluctuations covering both drought and flood periods are used to estimate groundwater recharge using the water table fluctuation method (WTF), supplemented by estimates derived using chloride mass balance. The presentation of hydraulic and recharge information in a 3D format has considerable advantages over the traditional 2D presentation of data. The 3D approach allows the distillation of multiple types of information(topography, geological, hydraulic and spatial) into one representation that provides valuable insights into the major controls of groundwater flow and recharge. The influence of aquifer lithology on the spatial variability of groundwater recharge is also demonstrated.