Beyond barcoding : a mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117–200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.

Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution

Background Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA. Results Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots - of the breakpoints required to re-create MSV-MatA. Although the MSV-sensitive maize genotype gave rise to the greatest variety of recombinants, the measured fitness of each of these recombinants correlated with their similarity to MSV-MatA. Conclusions The mechanistic predispositions of different MSV genomic regions to recombination can strongly influence the accessibility of high-fitness MSV recombinants. The frequency with which the fittest recombinant MSV genomes arise also correlates directly with the escalating selection pressures imposed by increasingly MSV-resistant maize hosts.

The trials and tribulations of a BYOD science classroom

The increase in the availability and use of portable mobile devices has had a number of impacts on society. In particular, this impact has been seen within Higher Education Institutions where staff and students are using these devices for both simple and complex tasks. Within undergraduate teacher education courses there is an expectation that students will be fully prepared for teaching their respective areas of expertise as well as having the ability to use ICT, and in particular portable mobile devices, to support teaching and learning. This paper reports on a small case study into the use of portable mobile devices in a science unit, where the students (N=16) bring their own devices into the classroom and use them in lectures, tutorials and workshops. The study highlights the changing nature of classroom practice within the university setting and the challenges faced by teaching staff and students when using these devices.

The legitimation and reproduction of discourse-practice gaps in work-life balance

Purpose - Critical scholarship on work-life balance (WLB) and its associated practices maintains that workplace flexibility is more than a quasi-functionalist response to contemporary problems faced by individuals, families or organisations. Beginning with Fleetwood’s contention that WLB discourses have become "detached" from their associated practices, this paper explores how workplace practices support or challenge dominant WLB discourses evident in socio-cultural, political and organisational sources. Design/methodology/approach - We analyse individual and group interview transcripts derived from 122 white-collar employees in two different organisational contexts (one public, one private) in the construction industry in Australia. Findings - Four major themes were identified in the data which illustrate discourse practice gaps. First, the demands facing this particular industry/ sector were framed as heightened and unique. Second, productivity was prioritised, dominating employees’ care-giving and lifestyle concerns. Third, employees’ caring responsibilities were communicated as personal and individual choices. Fourth, commitment and efficiency were judged on the basis of presence in the workplace. Research limitations/implications - Even in industries that have embraced WLB, workplace practices legitimate and reinforce the status quo, and maintain a gap between the promises of WLB and its potential to ameliorate conflict and assist workers to span the boundaries of paid work and other life domains. Originality/value - While the practices demonstrated in the research are focused on one industry, the study provides a critical analysis of how the contextually-influenced meaning of WLB is constructed, created and contested in these workplaces and the effects it produces.

Collective sampling and analysis of high order tensors for chatroom communications

This work investigates the accuracy and efficiency tradeoffs between centralized and collective (distributed) algorithms for (i) sampling, and (ii) n-way data analysis techniques in multidimensional stream data, such as Internet chatroom communications. Its contributions are threefold. First, we use the Kolmogorov-Smirnov goodness-of-fit test to show that statistical differences between real data obtained by collective sampling in time dimension from multiple servers and that of obtained from a single server are insignificant. Second, we show using the real data that collective data analysis of 3-way data arrays (users x keywords x time) known as high order tensors is more efficient than centralized algorithms with respect to both space and computational cost. Furthermore, we show that this gain is obtained without loss of accuracy. Third, we examine the sensitivity of collective constructions and analysis of high order data tensors to the choice of server selection and sampling window size. We construct 4-way tensors (users x keywords x time x servers) and analyze them to show the impact of server and window size selections on the results.

Urban transit quality of service : user perception and behaviour

Despite its potential multiple contributions to sustainable policy objectives, urban transit is generally not widely used by the public in terms of its market share compared to that of automobiles, particularly in affluent societies with low-density urban forms like Australia. Transit service providers need to attract more people to transit by improving transit quality of service. The key to cost-effective transit service improvements lies in accurate evaluation of policy proposals by taking into account their impacts on transit users. If transit providers knew what is more or less important to their customers, they could focus their efforts on optimising customer-oriented service. Policy interventions could also be specified to influence transit users’ travel decisions, with targets of customer satisfaction and broader community welfare. This significance motivates the research into the relationship between urban transit quality of service and its user perception as well as behaviour. This research focused on two dimensions of transit user’s travel behaviour: route choice and access arrival time choice. The study area chosen was a busy urban transit corridor linking Brisbane central business district (CBD) and the St. Lucia campus of The University of Queensland (UQ). This multi-system corridor provided a ‘natural experiment’ for transit users between the CBD and UQ, as they can choose between busway 109 (with grade-separate exclusive right-of-way), ordinary on-street bus 412, and linear fast ferry CityCat on the Brisbane River. The population of interest was set as the attendees to UQ, who travelled from the CBD or from a suburb via the CBD. Two waves of internet-based self-completion questionnaire surveys were conducted to collect data on sampled passengers’ perception of transit service quality and behaviour of using public transit in the study area. The first wave survey is to collect behaviour and attitude data on respondents’ daily transit usage and their direct rating of importance on factors of route-level transit quality of service. A series of statistical analyses is conducted to examine the relationships between transit users’ travel and personal characteristics and their transit usage characteristics. A factor-cluster segmentation procedure is applied to respodents’ importance ratings on service quality variables regarding transit route preference to explore users’ various perspectives to transit quality of service. Based on the perceptions of service quality collected from the second wave survey, a series of quality criteria of the transit routes under study was quantitatively measured, particularly, the travel time reliability in terms of schedule adherence. It was proved that mixed traffic conditions and peak-period effects can affect transit service reliability. Multinomial logit models of transit user’s route choice were estimated using route-level service quality perceptions collected in the second wave survey. Relative importance of service quality factors were derived from choice model’s significant parameter estimates, such as access and egress times, seat availability, and busway system. Interpretations of the parameter estimates were conducted, particularly the equivalent in-vehicle time of access and egress times, and busway in-vehicle time. Market segmentation by trip origin was applied to investigate the difference in magnitude between the parameter estimates of access and egress times. The significant costs of transfer in transit trips were highlighted. These importance ratios were applied back to quality perceptions collected as RP data to compare the satisfaction levels between the service attributes and to generate an action relevance matrix to prioritise attributes for quality improvement. An empirical study on the relationship between average passenger waiting time and transit service characteristics was performed using the service quality perceived. Passenger arrivals for services with long headways (over 15 minutes) were found to be obviously coordinated with scheduled departure times of transit vehicles in order to reduce waiting time. This drove further investigations and modelling innovations in passenger’ access arrival time choice and its relationships with transit service characteristics and average passenger waiting time. Specifically, original contributions were made in formulation of expected waiting time, analysis of the risk-aversion attitude to missing desired service run in the passengers’ access time arrivals’ choice, and extensions of the utility function specification for modelling passenger access arrival distribution, by using complicated expected utility forms and non-linear probability weighting to explicitly accommodate the risk of missing an intended service and passenger’s risk-aversion attitude. Discussions on this research’s contributions to knowledge, its limitations, and recommendations for future research are provided at the concluding section of this thesis.

A micro-level indexing model for the assessment of sustainable urban ecosystems

During the last several decades, the quality of natural resources and their services have been exposed to significant degradation from increased urban populations combined with the sprawl of settlements, development of transportation networks and industrial activities (Dorsey, 2003; Pauleit et al., 2005). As a result of this environmental degradation, a sustainable framework for urban development is required to provide the resilience of natural resources and ecosystems. Sustainable urban development refers to the management of cities with adequate infrastructure to support the needs of its population for the present and future generations as well as maintain the sustainability of its ecosystems (UNEP/IETC, 2002; Yigitcanlar, 2010). One of the important strategic approaches for planning sustainable cities is „ecological planning‟. Ecological planning is a multi-dimensional concept that aims to preserve biodiversity richness and ecosystem productivity through the sustainable management of natural resources (Barnes et al., 2005). As stated by Baldwin (1985, p.4), ecological planning is the initiation and operation of activities to direct and control the acquisition, transformation, disruption and disposal of resources in a manner capable of sustaining human activities with a minimum disruption of ecosystem processes. Therefore, ecological planning is a powerful method for creating sustainable urban ecosystems. In order to explore the city as an ecosystem and investigate the interaction between the urban ecosystem and human activities, a holistic urban ecosystem sustainability assessment approach is required. Urban ecosystem sustainability assessment serves as a tool that helps policy and decision-makers in improving their actions towards sustainable urban development. There are several methods used in urban ecosystem sustainability assessment among which sustainability indicators and composite indices are the most commonly used tools for assessing the progress towards sustainable land use and urban management. Currently, a variety of composite indices are available to measure the sustainability at the local, national and international levels. However, the main conclusion drawn from the literature review is that they are too broad to be applied to assess local and micro level sustainability and no benchmark value for most of the indicators exists due to limited data availability and non-comparable data across countries. Mayer (2008, p. 280) advocates that by stating "as different as the indices may seem, many of them incorporate the same underlying data because of the small number of available sustainability datasets". Mori and Christodoulou (2011) also argue that this relative evaluation and comparison brings along biased assessments, as data only exists for some entities, which also means excluding many nations from evaluation and comparison. Thus, there is a need for developing an accurate and comprehensive micro-level urban ecosystem sustainability assessment method. In order to develop such a model, it is practical to adopt an approach that uses a method to utilise indicators for collecting data, designate certain threshold values or ranges, perform a comparative sustainability assessment via indices at the micro-level, and aggregate these assessment findings to the local level. Hereby, through this approach and model, it is possible to produce sufficient and reliable data to enable comparison at the local level, and provide useful results to inform the local planning, conservation and development decision-making process to secure sustainable ecosystems and urban futures. To advance research in this area, this study investigated the environmental impacts of an existing urban context by using a composite index with an aim to identify the interaction between urban ecosystems and human activities in the context of environmental sustainability. In this respect, this study developed a new comprehensive urban ecosystem sustainability assessment tool entitled the „Micro-level Urban-ecosystem Sustainability IndeX‟ (MUSIX). The MUSIX model is an indicator-based indexing model that investigates the factors affecting urban sustainability in a local context. The model outputs provide local and micro-level sustainability reporting guidance to help policy-making concerning environmental issues. A multi-method research approach, which is based on both quantitative analysis and qualitative analysis, was employed in the construction of the MUSIX model. First, a qualitative research was conducted through an interpretive and critical literature review in developing a theoretical framework and indicator selection. Afterwards, a quantitative research was conducted through statistical and spatial analyses in data collection, processing and model application. The MUSIX model was tested in four pilot study sites selected from the Gold Coast City, Queensland, Australia. The model results detected the sustainability performance of current urban settings referring to six main issues of urban development: (1) hydrology, (2) ecology, (3) pollution, (4) location, (5) design, and; (6) efficiency. For each category, a set of core indicators was assigned which are intended to: (1) benchmark the current situation, strengths and weaknesses, (2) evaluate the efficiency of implemented plans, and; (3) measure the progress towards sustainable development. While the indicator set of the model provided specific information about the environmental impacts in the area at the parcel scale, the composite index score provided general information about the sustainability of the area at the neighbourhood scale. Finally, in light of the model findings, integrated ecological planning strategies were developed to guide the preparation and assessment of development and local area plans in conjunction with the Gold Coast Planning Scheme, which establishes regulatory provisions to achieve ecological sustainability through the formulation of place codes, development codes, constraint codes and other assessment criteria that provide guidance for best practice development solutions. These relevant strategies can be summarised as follows: • Establishing hydrological conservation through sustainable stormwater management in order to preserve the Earth’s water cycle and aquatic ecosystems; • Providing ecological conservation through sustainable ecosystem management in order to protect biological diversity and maintain the integrity of natural ecosystems; • Improving environmental quality through developing pollution prevention regulations and policies in order to promote high quality water resources, clean air and enhanced ecosystem health; • Creating sustainable mobility and accessibility through designing better local services and walkable neighbourhoods in order to promote safe environments and healthy communities; • Sustainable design of urban environment through climate responsive design in order to increase the efficient use of solar energy to provide thermal comfort, and; • Use of renewable resources through creating efficient communities in order to provide long-term management of natural resources for the sustainability of future generations.

“Would you; could you; on a boat?” Wait-time and travel-time activities during river ferry journeys and their relationship to overall satisfaction in Brisbane Queensland

This study investigates travel behaviour and wait-time activities as a component of passenger satisfaction with public transport in Brisbane, Australia. Australian transport planners recognise a variety of benefits to encouraging a mode shift away from automobile travel in favour of active and public transport use. Efforts to increase public transport ridership have included introducing state of the art passenger information systems, improving physical station access, and integrating system pricing, routes and scheduling for train, bus and ferry. Previous research regarding satisfaction with public transport emphasizes technical dimensions of service quality, including the timing and reliability of service. Those factors might be especially significant for frequent (commuting) travellers who look to balance the cost and efficiency of their travel options. In contrast, infrequent (leisure) passengers may be more concerned with way finding and the sensory experience of the journey. Perhaps due to the small relative proportion of trips made by river ferry compared to bus and rail, this mode of public transport has not received as much attention in travel-behaviour research. This case study of Brisbane’s river ferry system examines ferry passengers at selected terminals during peak and off-peak travel times to find out how travel behaviours and activities correlate to satisfaction with ferry travel. Data include 416 questionnaires completed by passengers intercepted during wait times at seven CityCat terminals in Brisbane. Descriptive statistical analysis revealed associations between specific wait time activities and satisfaction levels that could inform planners seeking to increase ridership and quality of life through ferry-oriented development.

Financial Markets, Institutions and Money [3rd ed.]

"The financial system is a key influencer of the health and efficiency of an economy. The role of the financial system is to gather money from people and businesses that currently have more money than they need and transfer it to those that can use it for either business or consumer expenditures. This flow of funds through financial markets and institutions in the Australian economy is huge (in the billions of dollars), affecting business profits, the rate of inflation, interest rates and the production of goods and services. In general, the larger the flow of funds and the more efficient the financial system, the greater the economic output and welfare in the economy. It is not possible to have a modern, complex economy such as that in Australia, without an efficient and sound financial system. The global financial crisis (GFC) of late 2007–09 (and the ensuing European debt crisis), where the global financial market was on the brink of collapse with only significant government intervention stopping a catastrophic global failure of the market, illustrated the importance of the financial system. Financial Markets, Institutions and Money 3rd edition introduces students to the financial system, its operations, and participants. The text offers a fresh, succinct analysis of the financial markets and discusses how the many participants in the financial system interrelate. This includes coverage of regulators, regulations and the role of the Reserve Bank of Australia, that ensure the system’s smooth running, which is essential to a modern economy. The text has been significantly revised to take into account changes in the financial world."---publisher website Table of Contents 1. The financial system - an overview 2. The Monetary Authorities 3. The Reserve Bank of Australia and interest rates 4. The level of interest rates 5. Mathematics of finance 6. Bond Prices and interest rate risk 7. The Structure of Interest Rates 8. Money Markets 9. Bond Markets 10. Equity Markets

Condition monitoring and operational decision making in semiconductor manufacturing

Today, the majority of semiconductor fabrication plants (fabs) conduct equipment preventive maintenance based on statistically-derived time- or wafer-count-based intervals. While these practices have had relative success in managing equipment availability and product yield, the cost, both in time and materials, remains high. Condition-based maintenance has been successfully adopted in several industries, where costs associated with equipment downtime range from potential loss of life to unacceptable affects to companies’ bottom lines. In this paper, we present a method for the monitoring of complex systems in the presence of multiple operating regimes. In addition, the new representation of degradation processes will be used to define an optimization procedure that facilitates concurrent maintenance and operational decision-making in a manufacturing system. This decision-making procedure metaheuristically maximizes a customizable cost function that reflects the benefits of production uptime, and the losses incurred due to deficient quality and downtime. The new degradation monitoring method is illustrated through the monitoring of a deposition tool operating over a prolonged period of time in a major fab, while the operational decision-making is demonstrated using simulated operation of a generic cluster tool.

A proposed approach to monitor private-sector policies and practices related to food environments, obesity and non-communicable disease prevention

Private-sector organizations play a critical role in shaping the food environments of individuals and populations. However, there is currently very limited independent monitoring of private-sector actions related to food environments. This paper reviews previous efforts to monitor the private sector in this area, and outlines a proposed approach to monitor private-sector policies and practices related to food environments, and their influence on obesity and non-communicable disease (NCD) prevention. A step-wise approach to data collection is recommended, in which the first (‘minimal’) step is the collation of publicly available food and nutrition-related policies of selected private-sector organizations. The second (‘expanded’) step assesses the nutritional composition of each organization's products, their promotions to children, their labelling practices, and the accessibility, availability and affordability of their products. The third (‘optimal’) step includes data on other commercial activities that may influence food environments, such as political lobbying and corporate philanthropy. The proposed approach will be further developed and piloted in countries of varying size and income levels. There is potential for this approach to enable national and international benchmarking of private-sector policies and practices, and to inform efforts to hold the private sector to account for their role in obesity and NCD prevention.

Selection and monitoring of navigation modes for an autonomous rover

Considering the wide spectrum of situations that it may encounter, a robot navigating autonomously in outdoor environments needs to be endowed with several operating modes, for robustness and efficiency reasons. Indeed, the terrain it has to traverse may be composed of flat or rough areas, low cohesive soils such as sand dunes, concrete road etc... Traversing these various kinds of environment calls for different navigation and/or locomotion functionalities, especially if the robot is endowed with different locomotion abilities, such as the robots WorkPartner, Hylos [4], Nomad or the Marsokhod rovers.

Selection and monitoring of navigation modes for an autonomous rover

Considering the wide spectrum of situations that it may encounter, a robot navigating autonomously in outdoor environments needs to be endowed with several operating modes, for robustness and efficiency reasons. Indeed, the terrain it has to traverse may be composed of flat or rough areas, low cohesive soils such as sand dunes, concrete road etc. . .Traversing these various kinds of environment calls for different navigation and/or locomotion functionalities, especially if the robot is endowed with different locomotion abilities, such as the robots WorkPartner, Hylos [4], Nomad or the Marsokhod rovers. Numerous rover navigation techniques have been proposed, each of them being suited to a particular environment context (e.g. path following, obstacle avoidance in more or less cluttered environments, rough terrain traverses...). However, seldom contributions in the literature tackle the problem of selecting autonomously the most suited mode [3]. Most of the existing work is indeed devoted to the passive analysis of a single navigation mode, as in [2]. Fault detection is of course essential: one can imagine that a proper monitoring of the Mars Exploration Rover Opportunity could have avoided the rover to be stuck during several weeks in a dune, by detecting non-nominal behavior of some parameters. But the ability to recover the anticipated problem by switching to a better suited navigation mode would bring higher autonomy abilities, and therefore a better overall efficiency. We propose here a probabilistic framework to achieve this, which fuses environment related and robot related information in order to actively control the rover operations.

Handmade clay balls and recycled crush glass as alternative media in water filtration

For many years materials such as quarried sand, anthracite, and granular activated carbon have been the principal media-products traditionally used in water and wastewater filtration plants. Pebble Matrix Filtration (PMF) is a novel non-chemical, sustainable pre-treatment method of protecting Slow Sand Filters (SSF) from high turbidity during heavy monsoon periods. PMF uses sand and pebbles as the filter media and the sustainability of this new technology might depend on availability and supply of pebbles and sand, both finite resources. In many countries there are two principal methods of obtaining pebbles and sand, namely dredging from rivers and beaches, and due to the scarcity of these resources in some countries the cost of pebbles is often 4-5 times higher than that of sand. In search for an alternative medium to pebbles after some preliminary laboratory tests conducted in Colombo-Sri Lanka, Poznan-Poland and Cambridge-UK, a 100-year-old brick factory near Sudbury, Suffolk, has produced hand-made clay pebbles satisfying the PMF quality requirements. As an alternative to sand, crushed recycled glass from a UK supplier was used and the PMF system was operated together with hand-made clay balls in the laboratory for high turbidity removal effectively. The results of laboratory experiments with alternative media are presented in this paper. There are potential opportunities for recycled crushed glass and clay ball manufacturing processes in some countries where they can be used as filter media.

Secure and safe water supplies in remote Australian and rural Sri Lankan regions : common issues and emerging responses

Most urban dwelling Australians take secure and safe water supplies for granted. That is, they have an adequate quantity of water at a quality that can be used by people without harm from human and animal wastes, salinity and hardness or pollutants from agriculture and manufacturing industries. Australia wide urban and peri-urban dwellers use safe water for all domestic as well as industrial purposes. However, this is not the situation remote regions in Australia where availability and poor quality water can be a development constraint. Nor is it the case in Sri Lanka where people in rural regions are struggling to obtain a secure supply of water, irrespective of it being safe because of the impact of faecal and other contaminants. The purposes of this paper are to overview: the population and environmental health challenges arising from the lack of safe water in rural and remote communities; response pathways to address water quality issues; and the status of and need for integrated catchment management (ICM) in selected remote regions of Australia and vulnerable and lagging rural regions in Sri Lanka. Conclusions are drawn that focus on the opportunity for inter-regional collaborations between Australia and Sri Lanka for the delivery of safe water through ICM.