Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data

Staphylococcus aureus (S. aureus) is a prominent human and livestock pathogen investigated widely using omic technologies. Critically, due to availability, low visibility or scattered resources, robust network and statistical contextualisation of the resulting data is generally under-represented. Here, we present novel meta-analyses of freely-accessible molecular network and gene ontology annotation information resources for S. aureus omics data interpretation. Furthermore, through the application of the gene ontology annotation resources we demonstrate their value and ability (or lack-there-of) to summarise and statistically interpret the emergent properties of gene expression and protein abundance changes using publically available data. This analysis provides simple metrics for network selection and demonstrates the availability and impact that gene ontology annotation selection can have on the contextualisation of bacterial omics data.

Proceedings of the 3rd International Subtropical Cities Conference 2011 Subtropical Cities: Subtropical Urbanism -Beyond Climate Change

Climate has been, throughout modern history, a primary attribute for attracting residents to the “Sunshine States” of Florida (USA) and Queensland (Australia). The first major group of settlers capitalized on the winter growing season to support a year-­‐round agricultural economy. As these economies developed, the climate attracted tourism and retirement industries. Yet as Florida and Queensland have blossomed under beneficial climates, the stresses acting on the natural environment are exacting a toll. Southeast Florida and eastern Queensland are among the most vulnerable coastal metropolitan areas in the world. In these places the certainty of sea level rise is measurable with impacts, empirically observable, that will continue to increase regardless of any climate change mitigation.1 The cities of the subtropics share a series of paradoxes relating to climate, resources, environment, and culture. As the subtropical climate entices new residents and visitors there are increasing costs associated with urban infrastructure and the ravages of violent weather. The carefree lifestyle of subtropical cities is increasingly dependent on scarce water and energy resources and the flow of tangible goods that support a trade economy. The natural environment is no longer exploitable as the survival of the human environment is contingent upon the ability of natural ecosystems to absorb the impact of human actions. The quality of subtropical living is challenged by the mounting pressures of population growth and rapid urbanization yet urban form and contemporary building design fail to take advantage of the subtropical zone’s natural attributes of abundant sunshine, cooling breezes and warm temperatures. Yet, by building a global network of local knowledge, subtropical cities like Brisbane, the City of Gold Coast and Fort Lauderdale, are confidently leading the way with innovative and inventive solutions for building resiliency and adaptation to climate change. The Centre for Subtropical Design at Queensland University of Technology organized the first international Subtropical Cities conference in Brisbane, Australia, where the “fault-­‐lines” of subtropical cities at breaking points were revealed. The second conference, held in 2008, shed a more optimistic light with the theme "From fault-­‐lines to sight-­‐lines -­‐ subtropical urbanism in 20-­‐20" highlighting the leadership exemplified in the vitality of small and large works from around the subtropical world. Yet beyond these isolated local actions the need for more cooperation and collaboration was identified as the key to moving beyond the problems of the present and foreseeable future. The spirit of leadership and collaboration has taken on new force, as two institutions from opposite sides of the globe joined together to host the 3rd international conference Subtropical Cities 2011 -­‐ Subtropical Urbanism: Beyond Climate Change. The collaboration between Florida Atlantic University and the Queensland University of Technology to host this conference, for the first time in the United States, forges a new direction in international cooperative research to address urban design solutions that support sustainable behaviours, resiliency and adaptation to sea level rise, green house gas (GHG) reduction, and climate change research in the areas of architecture and urban design, planning, and public policy. With southeast Queensland and southern Florida as contributors to this global effort among subtropical urban regions that share similar challenges, opportunities, and vulnerabilities our mutual aim is to advance the development and application of local knowledge to the global problems we share. The conference attracted over 150 participants from four continents. Presentations by authors were organized into three sub-­‐themes: Cultural/Place Identity, Environment and Ecology, and Social Economics. Each of the 22 papers presented underwent a double-­‐blind peer review by a panel of international experts among the disciplines and research areas represented. The Centre for Subtropical Design at the Queensland University of Technology is leading Australia in innovative environmental design with a multi-­‐disciplinary focus on creating places that are ‘at home’ in the warm humid subtropics. The Broward Community Design Collaborative at Florida Atlantic University's College for Design and Social Inquiry has built an interdisciplinary collaboration that is unique in the United States among the units of Architecture, Urban and Regional Planning, Social Work, Public Administration, together with the College of Engineering and Computer Science, the College of Science, and the Center for Environmental Studies, to engage in funded action research through design inquiry to solve the problems of development for urban resiliency and environmental sustainment. As we move beyond debates about climate change -­‐ now acting upon us -­‐ the subtropical urban regions of the world will continue to convene to demonstrate the power of local knowledge against global forces, thereby inspiring us as we work toward everyday engagement and action that can make our cities more livable, equitable, and green.

Responding to black markets: Role of IT and network structures

This paper presents the unique black markets of asset pooling and leasing services, which exposes the nature and extent of industry-specific threats. We explore how firms providing such services together with their network structures that constitute the foundations of asset pooling and leasing respond to the threat of black markets. We encapsulate detecting and encountering the threat of black markets through the theoretical lens of agility, which encompasses the elements of sensing and responding (Overby et al. 2006; Roberts and Grover 2012). This novel concept of responding to threats using the agility lens has not been adequately addressed by past studies on enterprise agility. Through a case study of a global asset pooling and leasing company, we reveal the criticality of network structures, the impracticality of IT and inadequate tracking mechanisms that challenge firms in minimizing such threats.

Integrated decoupling and matching network incorporated in the ground plane of a compact monopole array

Compact arrays enable various applications such as antenna beam-forming and multi-input, multi-output (MIMO) schemes on limited-size platforms. The reduced element spacing in compact arrays introduces high levels of mutual coupling which can affect the performance of the adaptive array. This coupling causes a mismatch at the input ports, which disturbs the performance of the individual elements in the array and affects the implementation of beam steering. In this article, a reactive decoupling network for a 3-element monopole array is used to establish port isolation while simultaneously matching input impedance at each port to the system impendence. The integrated decoupling and matching network is incorporated in the ground plane of the monopole array, providing further development scope for beamforming using phase shifters and power splitters in double-layered circuits.

Analysis of distributed beamforming in cooperative communications network with phase shifter based smart antenna nodes

This research study investigates the application of phase shifter-based smart antenna system in distributed beamforming. It examines the way to optimise the transmit power by jointly maximising the directivity of the array antennas and the weight vector for distributed beamforming. This research study concludes that maximising directivity can lead to better transmit power minimisation compared to maximising field intensity. This study also concludes that signal to noise power ratio maximisation subject to a power constraint and power minimisation subject to a signal to noise power ratio constraint yield the same results.

A blended learning approach to the teaching of professional practice in architecture

This paper reports on a number of blended learning activities conducted in two subjects of a Master of Architecture degree at a major Australian university. The subjects were related to “professional practice” and as such represent a little researched area of architectural curriculum. The research provides some insight into the student perceptions of learning opportunity and engagement associated with on-line delivery modes. Students from these two subjects were surveyed for their perceptions about the opportunity for learning afforded by the on-line components, and also for their perceived level of engagement. Responses to these perceptions of traditional and on-line modes of delivery are compared and analysed for significant differences. While students were generally positive in response to the learning experiences, analysis of the results shows that students found the traditional modes to assist in their learning significantly more than on-line modes. Students were neutral regarding the opportunity for engagement that on-line modes provided. Analysis of the students’ gender, age and hours of paid work was also conducted to ascertain any relationship with attitudes to the flexibility of on-line delivery; no significant relationship was detected. This study has shown that students were generally resistant to on-line engagement opportunities and their ability to support learning.

An empirical analysis of the factors and measures of Enterprise Architecture Management success

Enterprise Architecture Management (EAM) is discussed in academia and industry as a vehicle to guide IT implementations, alignment, compliance assessment, or technology management. Still, a lack of knowledge prevails about how EAM can be successfully used, and how positive impact can be realized from EAM. To determine these factors, we identify EAM success factors and measures through literature reviews and exploratory interviews and propose a theoretical model that explains key factors and measures of EAM success. We test our model with data collected from a cross-sectional survey of 133 EAM practitioners. The results confirm the existence of an impact of four distinct EAM success factors, ‘EAM product quality’, ‘EAM infrastructure quality’, ‘EAM service delivery quality’, and ‘EAM organizational anchoring’, and two important EAM success measures, ‘intentions to use EAM’ and ‘Organizational and Project Benefits’ in a confirmatory analysis of the model. We found the construct ‘EAM organizational anchoring’ to be a core focal concept that mediated the effect of success factors such as ‘EAM infrastructure quality’ and ‘EAM service quality’ on the success measures. We also found that ‘EAM satisfaction’ was irrelevant to determining or measuring success. We discuss implications for theory and EAM practice.

Building a better world: Can architecture shape behaviour?

In 1966, a British planner called Maurice Broady came up with a new term for the architectural lexicon: architectural determinism. This was to describe the practice of groundlessly asserting that design solutions would change behaviour in a predictable and positive way. It was a new phrase but the belief system behind it – that buildings shape behaviour – had allowed the heroes of architecture to make all kinds of outlandish claims.

A network DEA quantity and quality-orientated production model: An application to Australian university research services

The motivation for this analysis is the recently developed Excellence in Research for Australia (ERA) program developed to assess the quality of research in Australia. The objective is to develop an appropriate empirical model that better represents the underlying production of higher education research. In general, past studies on university research performance have used standard DEA models with some quantifiable research outputs. However, these suffer from the twin maladies of an inappropriate production specification and a lack of consideration of the quality of output. By including the qualitative attributes of peer-reviewed journals, we develop a procedure that captures both quality and quantity, and apply it using a network DEA model. Our main finding is that standard DEA models tend to overstate the research efficiency of most Australian universities.

Crystal palaces: Copyright law and public architecture

This paper investigates copyright law and public architecture in the context of cultural institutions of Australia. Part 1 examines the case of the Sydney Opera House to illustrate the past position of architects in respect of copyright law. It goes onto consider the framework laid down by the Copyright Amendment (Moral Rights) Act 2000 (Cth) to resolve copyright disputes over moral rights and architecture. Part 2 considers the argument over the proposed renovations to the National Gallery of Australia between Dr Brian Kennedy and the original architect Colin Madigan. Part 3 finally deals with the allegations that Ashton Raggatt McDougall, the architects of the National Museum of Australia, plagiarised the designs of Daniel Libeskind for the Jewish Berlin Museum.

Extending genetic linkage analysis to diffusion tensor images to map single gene effects on brain fiber architecture

We extended genetic linkage analysis - an analysis widely used in quantitative genetics - to 3D images to analyze single gene effects on brain fiber architecture. We collected 4 Tesla diffusion tensor images (DTI) and genotype data from 258 healthy adult twins and their non-twin siblings. After high-dimensional fluid registration, at each voxel we estimated the genetic linkage between the single nucleotide polymorphism (SNP), Val66Met (dbSNP number rs6265), of the BDNF gene (brain-derived neurotrophic factor) with fractional anisotropy (FA) derived from each subject's DTI scan, by fitting structural equation models (SEM) from quantitative genetics. We also examined how image filtering affects the effect sizes for genetic linkage by examining how the overall significance of voxelwise effects varied with respect to full width at half maximum (FWHM) of the Gaussian smoothing applied to the FA images. Raw FA maps with no smoothing yielded the greatest sensitivity to detect gene effects, when corrected for multiple comparisons using the false discovery rate (FDR) procedure. The BDNF polymorphism significantly contributed to the variation in FA in the posterior cingulate gyrus, where it accounted for around 90-95% of the total variance in FA. Our study generated the first maps to visualize the effect of the BDNF gene on brain fiber integrity, suggesting that common genetic variants may strongly determine white matter integrity.

Brain fiber architecture, genetics, and intelligence: a high angular resolution diffusion imaging (HARDI) study

We developed an analysis pipeline enabling population studies of HARDI data, and applied it to map genetic influences on fiber architecture in 90 twin subjects. We applied tensor-driven 3D fluid registration to HARDI, resampling the spherical fiber orientation distribution functions (ODFs) in appropriate Riemannian manifolds, after ODF regularization and sharpening. Fitting structural equation models (SEM) from quantitative genetics, we evaluated genetic influences on the Jensen-Shannon divergence (JSD), a novel measure of fiber spatial coherence, and on the generalized fiber anisotropy (GFA) a measure of fiber integrity. With random-effects regression, we mapped regions where diffusion profiles were highly correlated with subjects' intelligence quotient (IQ). Fiber complexity was predominantly under genetic control, and higher in more highly anisotropic regions; the proportion of genetic versus environmental control varied spatially. Our methods show promise for discovering genes affecting fiber connectivity in the brain.

Mapping genetic influences on brain fiber architecture with high angular resolution diffusion imaging (HARDI)

We report the first 3D maps of genetic effects on brain fiber complexity. We analyzed HARDI brain imaging data from 90 young adult twins using an information-theoretic measure, the Jensen-Shannon divergence (JSD), to gauge the regional complexity of the white matter fiber orientation distribution functions (ODF). HARDI data were fluidly registered using Karcher means and ODF square-roots for interpol ation; each subject's JSD map was computed from the spatial coherence of the ODFs in each voxel's neighborhood. We evaluated the genetic influences on generalized fiber anisotropy (GFA) and complexity (JSD) using structural equation models (SEM). At each voxel, genetic and environmental components of data variation were estimated, and their goodness of fit tested by permutation. Color-coded maps revealed that the optimal models varied for different brain regions. Fiber complexity was predominantly under genetic control, and was higher in more highly anisotropic regions. These methods show promise for discovering factors affecting fiber connectivity in the brain.