Supplementary information : weighted tree kernels for sequence analysis

Genomic sequences are fundamentally text documents, admitting various representations according to need and tokenization. Gene expression depends crucially on binding of enzymes to the DNA sequence at small, poorly conserved binding sites, limiting the utility of standard pattern search. However, one may exploit the regular syntactic structure of the enzyme's component proteins and the corresponding binding sites, framing the problem as one of detecting grammatically correct genomic phrases. In this paper we propose new kernels based on weighted tree structures, traversing the paths within them to capture the features which underpin the task. Experimentally, we and that these kernels provide performance comparable with state of the art approaches for this problem, while offering significant computational advantages over earlier methods. The methods proposed may be applied to a broad range of sequence or tree-structured data in molecular biology and other domains.

Improved rural health through a collaborative model of care – qualitative findings

INTRODUCTION Health disparity between urban and rural regions in Australia is well-documented. In the Wheatbelt catchments of Western Australia there is higher incidence and rate of avoidable hospitalisation for chronic diseases. Structured care approach to chronic illnesses is not new but the focus has been on single disease state. A recent ARC Discovery Project on general practice nurse-led chronic disease management of diabetes, hypertension and stable ischaemic heart disease reported improved communication and better medical administration.[1] In our study we investigated the sustainability of such a multi-morbidities general practice –led collaborative model of care in rural Australia. METHODS A QUAN(qual) design was utilised. Eight pairs of rural general practices were matched. Inclusion criteria used were >18 years and capable of giving informed consent, at least one identified risk factor or diagnosed with chronic conditions. Patients were excluded if deemed medically unsuitable. A comprehensive care plan was formulated by the respective general practice nurse in consultation with the treating General Practitioner (GP) and patient based on the individual’s readiness to change, and was informed by available local resource. A case management approach was utilised. Shediaz-Rizkallah and Lee’s conceptual framework on sustainability informed our evaluation.[2] Our primary outcome on measures of sustainability was reduction in avoidable hospitalisation. Secondary outcomes were patients and practitioners acceptance and satisfaction, and changes to pre-determined interim clinical and process outcomes. RESULTS The qualitative interviews highlighted the community preference for a ‘sustainable’ local hospital in addition to general practice. Costs, ease of access, low prioritisation of self chronic care, workforce turnover and perception of losing another local resource if underutilised influenced the respondents’ decision to present at local hospital for avoidable chronic diseases regardless. CONCLUSIONS Despite the pragmatic nature of rural general practice in Australia, the sustainability of chronic multi-morbidities management in general practice require efficient integration of primary-secondary health care and consideration of other social determinants of health. What this study adds: What is already known on this subject: Structured approach to chronic disease management is not new and has been shown to be effective for reducing hospitalisation. However, the focus has been on single disease state. What does this study add: Sustainability of collaborative model of multi-morbidities care require better primary-secondary integration and consideration of social determinants of health.

Conceptions of ‘community’ among older adults living in high-density urban areas : an Australian case study

Aim The aim of this study was to explore the social networks of community and its connection to location for older people living in inner city high density (ICHD). Method Using a case study approach employing qualitative (diaries, in-depth interviews) and quantitative (global positioning systems and geographical information systems mapping) methods, this paper explores the everyday interaction and social networks and where they manifest spatially for a group of older ICHD Australians. Results Social networks in two community territories were found to be of particular importance to participants in terms of influencing feelings of well-being, support, social inclusion and cohesion. These two territories include the building where older people reside and the area immediately surrounding the building. Conclusion This study highlights the importance of recognising the spatial aspect to better understand the social networks of community and their effects on well-being and social cohesion for ICHD older people.

A parcel-scale assessment tool to measure sustainability through urban ecosystem components : the MUSIX model

In recent years a number of urban sustainability assessment frameworks are developed to better inform policy formulation and decision-making processes. This paper introduces one of these attempts in developing a comprehensive assessment tool—i.e., Micro-level Urban-ecosystem Sustainability IndeX (MUSIX). Being an indicator-based indexing model, MUSIX investigates the environmental impacts of land-uses on urban sustainability by measuring urban ecosystem components in local scale. The paper presents the methodology of MUSIX and demonstrates the performance of the model in a pilot test-bed—i.e., in Gold Coast, Australia. The model provides useful insights on the sustainability performance of the test-bed area. The parcel-scale findings of the indicators are used to identify local problems considering six main issues of urban development—i.e., hydrology; ecology; pollution; location; design, and; efficiency. The composite index score is used to propose betterment strategies to guide the development of local area plans in conjunction with the City's Planning Scheme. In overall, this study has shown that parcel-scale environmental data provides an overview of the local sustainability in urban areas as in the example of Gold Coast, which can also be used for setting environmental policy, objectives and targets.

Understanding the implications of digital interactions on the design of public urban spaces

This study investigated the impact of digital networked social interactions on the design of public urban spaces. Urban informatics, social media, ubiquitous computing, and mobile technology offer great potential to urban planning, as tools of communication, community engagement, and placemaking. The study considers the function of public spaces as 'third places,' that is, social places that are familiar, comfortable, social and meaningful for everyday life outside the home and work. Libraries were chosen as the study's focus. The study produced findings and insights at the intersection of urban planning (place), cultural geography and urban sociology (people), and information communication technology (technology) – the triad of urban informatics.

Re : Why optometry must work from urban and regional Aboriginal health services

We are writing to support the recent Viewpoint written by Anjou, Boudville and Taylor ‘Why optometry must work in Aboriginal Health Services in urban and regional Australia’.[1] We are a group of optometrists who provide optometric services within Aboriginal Health Services in urban and regional settings and we agree that access to optometry in Aboriginal Health Services should be supported and expanded in an effort to ‘close the gap’ for vision.

Mathematical relationships for metal build-up on urban road surfaces based on traffic and land use characteristics

The study investigated the influence of traffic and land use parameters on metal build-up on urban road surfaces. Mathematical relationships were developed to predict metals originating from fuel combustion and vehicle wear. The analysis undertaken found that nickel and chromium originate from exhaust emissions, lead, copper and zinc from vehicle wear, cadmium from both exhaust and wear and manganese from geogenic sources. Land use does not demonstrate a clear pattern in relation to the metal build-up process, though its inherent characteristics such as traffic activities exert influence. The equation derived for fuel related metal load has high cross-validated coefficient of determination (Q2) and low Standard Error of Cross-Validation (SECV) values indicates that the model is reliable, while the equation derived for wear-related metal load has low Q2 and high SECV values suggesting its use only in preliminary investigations. Relative Prediction Error values for both equations are considered to be well within the error limits for a complex system such as an urban road surface. These equations will be beneficial for developing reliable stormwater treatment strategies in urban areas which specifically focus on mitigation of metal pollution.

Variability of metal composition and concentrations in road dust in the urban environment

Urban road dust comprises of a range of potentially toxic metal elements and plays a critical role in degrading urban receiving water quality. Hence, assessing the metal composition and concentration in urban road dust is a high priority. This study investigated the variability of metal composition and concentrations in road dust in 4 different urban land uses in Gold Coast, Australia. Samples from 16 road sites were collected and tested for selected 12 metal species. The data set was analyzed using both univariate and multivariate techniques. Outcomes of the data analysis revealed that the metal concentrations in road dust differ considerably within and between different land uses. Iron, aluminum, magnesium and zinc are the most abundant in urban land uses. It was also noted that metal species such as titanium, nickel, copper and zinc have the highest concentrations in industrial land use. The study outcomes revealed that soil and traffic related sources as key sources of metals deposited on road surfaces.

Urban Food Security, Urban Resilience and Climate Change

The growing importance of logistics in increasingly globalised production and consumption systems strengthens the case for explicit consideration of the climate risks that may impact on the operation of ports in the future, as well as the formulation of adaptation responses that act to enhance their resilience. Within a logistics chain, seaports are functional nodes of significant strategic importance, and are considered as critical gateways linking local and national supply chains to global markets. However, they are more likely to be exposed to vagaries of climate-related extreme events due to their coastal locations. As such, they need to be adaptive and respond to the projected impacts of climate change, in particular extreme weather events. These impacts are especially important in the logistics context as they could result in varying degrees of business interruption; including business closure in the worst case scenario. Since trans-shipment of freight for both the import and export of goods and raw materials has a significant impact on Australia’s sustained economic growth it was considered important to undertake a study of port functional assets, to assess their vulnerability to climate change, to model the potential impacts of climate-related extreme events, and to highlight possible adaptation responses.

Food in the city : urban food movements and the (re)imagining of urban spaces

Ethical food movements are growing in number throughout Australia. Amongst these diverse movements are urban agriculture initiatives, which articulate a multitude of social and environmental values. Yet, despite the long history of production and exchange of food in urban areas, planners (and others) often overlook its significance. To assist in addressing this oversight, we take the case study of Melbourne to examine the ways in which participants in urban agriculture are re-imagining urban spaces and the future of agriculture and food systems in Australia. We demonstrate that urban food advocates' politics and practices both challenge and resist the enclosure of urban spaces. This creates new frontiers that transgress social, political, ecological and economic boundaries and edges. These transgressions or counter-enclosures articulate new visions for secure and just food systems and, in so doing, offer insights to assist planners in ensuring Australian cities support socially just and environmentally responsible food systems.

Exploring pedestrian accessibility and walkability : insight from public place observations in inner-urban higher density Brisbane, Australia

As planners work to create more sustainable and liveable urban environments, a priority is to transition away from prioritising the automobile and towards enhancing the pedestrian experience. Thus, this research explores the experience of pedestrian accessibility in inner-urban higher-density Brisbane in Australia, drawing on findings from semi-structured in-depth interviews with 24 residents and over 100 hours of public place observations in three case-study neighbourhoods. The interviews took place in residents homes and explored their experience of higher density living and their neighbourhood, whilst observations were recorded through a combination of methods including photographs, sketch maps, recordings and field journals. Observation locations included retail and commercial space, roads, parkland and open space, with multiple observations at each location. A thematic analysis identified common themes in both interviews and the observations, with this paper focusing on residents’ lived experience in urban built environments. This analysis revealed that pedestrian accessibility is linked to access to local amenities and direct routes, aesthetics, sense of community, ownership of space and safety. In particular, observations revealed how pedestrian accessibility and route-taking works with, against or in spite of the design features of urban environments, as well as the importance of the social use of the built environment. Residents spoke about although walking quick and preferred for local amenities, the decision to walk was moderated by factors such as time of day and perceived safety. Measures to ensure and improve the pedestrian accessibility of urban areas needs to take into account the propensity for people to prefer and improvise direct routes (often to the detriment of traffic safety considerations), the importance of ongoing maintenance and upgrading of walking infrastructure and the importance of aesthetically pleasing and safe walking environments. By combining interviews and observations, this research highlights the current dominance of the automobile culture in Brisbane and the layers of meaning, experiences and complexity hidden within the pedestrian experience.

Towards consonance in urban form

By presenting the past as a repository of the characteristics of urban formation, urban morphology utilizes a knowledge platform as the basis for interpretation of accordant architectural responses (Levy, 1999). Operating within this framework at the scale of architectural features of individual buildings, and imbued with reference to the intrinsic architectural elements of both preceding and existing building forms, micro-morphology (Larkham, 2006, p. 126) provides the efficacy for new architecture that emerges from such a manner of composition...

Predicting the likelihood of QA failure using treatment plan accuracy metrics

This study used automated data processing techniques to calculate a set of novel treatment plan accuracy metrics, and investigate their usefulness as predictors of quality assurance (QA) success and failure. 151 beams from 23 prostate and cranial IMRT treatment plans were used in this study. These plans had been evaluated before treatment using measurements with a diode array system. The TADA software suite was adapted to allow automatic batch calculation of several proposed plan accuracy metrics, including mean field area, small-aperture, off-axis and closed-leaf factors. All of these results were compared the gamma pass rates from the QA measurements and correlations were investigated. The mean field area factor provided a threshold field size (5 cm2, equivalent to a 2.2 x 2.2 cm2 square field), below which all beams failed the QA tests. The small aperture score provided a useful predictor of plan failure, when averaged over all beams, despite being weakly correlated with gamma pass rates for individual beams. By contrast, the closed leaf and off-axis factors provided information about the geometric arrangement of the beam segments but were not useful for distinguishing between plans that passed and failed QA. This study has provided some simple tests for plan accuracy, which may help minimise time spent on QA assessments of treatments that are unlikely to pass.

A spatial-indexing model for measuring neighbourhood-level land-use and transport integration

Significant attention has been given in urban policy literature to the integration of land-use and transport planning and policies—with a view to curbing sprawling urban form and diminishing externalities associated with car-dependent travel patterns. By taking land-use and transport interaction into account, this debate mainly focuses on how a successful integration can contribute to societal well-being, providing efficient and balanced economic growth while accomplishing the goal of developing sustainable urban environments and communities. The integration is also a focal theme of contemporary urban development models, such as smart growth, liveable neighbourhoods, and new urbanism. Even though available planning policy options for ameliorating urban form and transport-related externalities have matured—owing to growing research and practice worldwide—there remains a lack of suitable evaluation models to reflect on the current status of urban form and travel problems or on the success of implemented integration policies. In this study we explore the applicability of indicator-based spatial indexing to assess land-use and transport integration at the neighbourhood level. For this, a spatial index is developed by a number of indicators compiled from international studies and trialled in Gold Coast, Queensland, Australia. The results of this modelling study reveal that it is possible to propose an effective metric to determine the success level of city plans considering their sustainability performance via composite indicator methodology. The model proved useful in demarcating areas where planning intervention is applicable, and in identifying the most suitable locations for future urban development and plan amendments. Lastly, we integrate variance-based sensitivity analysis with the spatial indexing method, and discuss the applicability of the model in other urban contexts.