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.

Designing hubs for connected learning: social, spatial and technological insights from Coworking, Hackerspaces and Meetup groups

Connected learning, as a design approach, does not restrict learning to a dedicated learning space (school, university, etc.), but considers it to be an aggregation of individual experiences made through intrinsically motivated, active participation in and across various socio-cultural, every-day life environments. Urban places for meeting, interacting and connected learning with people from diverse backgrounds, cultures and areas of expertise are highly significant in the knowledge economy of our 21st century. However, little is yet known about best practices to design and curate such hubs that attract and support interest-driven and socially embedded learning experiences. The research study presented in this paper investigates design aspects that contribute to successful place-based spaces for connected learning. The paper reports findings from observations as well as interviews with users and managers of three different types of local, community-led learning environments, i.e., coworking spaces, hackerspaces, and meetup groups across Australia. The findings reveal social, spatial and technological interventions that these spaces apply to nourish a culture of connected learning, sharing and peer interaction. The discussion suggests a set of design implications for designers, managers and decision makers that have an interest in nourishing a connected learning culture among their user community.

The good, the bad, and the efficient: Productivity, efficiency, and technical change in the airline industry, 2004–11

This study models the joint production of desirable and undesirable output production (that is, CO2 emissions) of airlines. The Malmquist–Luenberger productivity index is employed to measure productivity growth when undesirable output production is incorporated into the production model. The results show that pollution abatement activities of airlines lowers productivity growth, which suggests that the traditional approach of measuring productivity growth, which ignores CO2 emissions, overstates ‘true’ productivity growth. The reliability of the results is also tested and verified using confidence intervals based on bootstrapping.

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.

Perceived safety, quality and cultural competency of maternity care for culturally and linguistically diverse women in Queensland

Various policies, plans, and initiatives have been implemented to provide safe, quality, and culturally competent care to patients within Queensland’s healthcare system. A series of models of maternity care are available in Queensland that range from standard public care to private midwifery care. The current study aimed to determine whether identifying as Culturally or Linguistically Diverse (CALD) was associated with the perceived safety, quality, and cultural competency of maternity care from a consumer perspective, and to identify specific needs and preferences of CALD maternity care consumers. Secondary analysis of data collected in the Having a Baby in Queensland Survey 2012 was used to compare the experiences of 655 CALD women to those of 4049 non-CALD women in Queensland, Australia, across three stages of maternity care: pregnancy, labour and birth, and after birth. After adjustment for model of maternity care received and socio-demographic characteristics, CALD women were significantly more likely than non-CALD women to experience suboptimal staff technical competence in pregnancy, overall perceived safety in pregnancy and labour/birth, and interpersonal sensitivity in pregnancy and labour/birth. Approximately 50% of CALD women did not have the choice to use a translator or interpreter, or the gender of their care provider, during labour and birth. Thirteen themes of preferences and needs of CALD maternity care consumers based on ethnicity, cultural beliefs, or traditions were identified, however, these were rarely met. Findings imply that CALD women in Queensland experience disadvantageous maternity care with regards to perceived staff technical competence, safety, and interpersonal sensitivity, and receive care that lacks cultural competence. Improved access to support persons, continuity and choice of carer, and staff availability and training is recommended.

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 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.

Hierarchical clustering of the genetic connectivity matrix reveals the network topology of gene action on brain microstructure: An N=531 twin study

Genetic correlation (rg) analysis determines how much of the correlation between two measures is due to common genetic influences. In an analysis of 4 Tesla diffusion tensor images (DTI) from 531 healthy young adult twins and their siblings, we generalized the concept of genetic correlation to determine common genetic influences on white matter integrity, measured by fractional anisotropy (FA), at all points of the brain, yielding an NxN genetic correlation matrix rg(x,y) between FA values at all pairs of voxels in the brain. With hierarchical clustering, we identified brain regions with relatively homogeneous genetic determinants, to boost the power to identify causal single nucleotide polymorphisms (SNP). We applied genome-wide association (GWA) to assess associations between 529,497 SNPs and FA in clusters defined by hubs of the clustered genetic correlation matrix. We identified a network of genes, with a scale-free topology, that influences white matter integrity over multiple brain regions.

Gene network effects on brain microstructure and intellectual performance identified in 472 twins

A major challenge in neuroscience is finding which genes affect brain integrity, connectivity, and intellectual function. Discovering influential genes holds vast promise for neuroscience, but typical genome-wide searches assess approximately one million genetic variants one-by-one, leading to intractable false positive rates, even with vast samples of subjects. Even more intractable is the question of which genes interact and how they work together to affect brain connectivity. Here, we report a novel approach that discovers which genes contribute to brain wiring and fiber integrity at all pairs of points in a brain scan. We studied genetic correlations between thousands of points in human brain images from 472 twins and their nontwin siblings (mean age: 23.7 2.1 SD years; 193 male/279 female).Wecombined clustering with genome-wide scanning to find brain systems withcommongenetic determination.Wethen filtered the image in a new way to boost power to find causal genes. Using network analysis, we found a network of genes that affect brain wiring in healthy young adults. Our new strategy makes it computationally more tractable to discover genes that affect brain integrity. The gene network showed small-world and scale-free topologies, suggesting efficiency in genetic interactions and resilience to network disruption. Genetic variants at hubs of the network influence intellectual performance by modulating associations between performance intelligence quotient and the integrity of major white matter tracts, such as the callosal genu and splenium, cingulum, optic radiations, and the superior longitudinal fasciculus.

Hierarchical topological network analysis of anatomical human brain connectivity and differences related to sex and kinship

Modern non-invasive brain imaging technologies, such as diffusion weighted magnetic resonance imaging (DWI), enable the mapping of neural fiber tracts in the white matter, providing a basis to reconstruct a detailed map of brain structural connectivity networks. Brain connectivity networks differ from random networks in their topology, which can be measured using small worldness, modularity, and high-degree nodes (hubs). Still, little is known about how individual differences in structural brain network properties relate to age, sex, or genetic differences. Recently, some groups have reported brain network biomarkers that enable differentiation among individuals, pairs of individuals, and groups of individuals. In addition to studying new topological features, here we provide a unifying general method to investigate topological brain networks and connectivity differences between individuals, pairs of individuals, and groups of individuals at several levels of the data hierarchy, while appropriately controlling false discovery rate (FDR) errors. We apply our new method to a large dataset of high quality brain connectivity networks obtained from High Angular Resolution Diffusion Imaging (HARDI) tractography in 303 young adult twins, siblings, and unrelated people. Our proposed approach can accurately classify brain connectivity networks based on sex (93% accuracy) and kinship (88.5% accuracy). We find statistically significant differences associated with sex and kinship both in the brain connectivity networks and in derived topological metrics, such as the clustering coefficient and the communicability matrix.

Brain network efficiency and topology depend on the fiber tracking method: 11 tractography algorithms compared in 536 subjects

As connectivity analyses become more popular, claims are often made about how the brain's anatomical networks depend on age, sex, or disease. It is unclear how results depend on tractography methods used to compute fiber networks. We applied 11 tractography methods to high angular resolution diffusion images of the brain (4-Tesla 105-gradient HARDI) from 536 healthy young adults. We parcellated 70 cortical regions, yielding 70×70 connectivity matrices, encoding fiber density. We computed popular graph theory metrics, including network efficiency, and characteristic path lengths. Both metrics were robust to the number of spherical harmonics used to model diffusion (4th-8th order). Age effects were detected only for networks computed with the probabilistic Hough transform method, which excludes smaller fibers. Sex and total brain volume affected networks measured with deterministic, tensor-based fiber tracking but not with the Hough method. Each tractography method includes different fibers, which affects inferences made about the reconstructed networks.

Studying relationships in project management through social network analysis

Successful project management depends upon forming and maintaining relationships between and among project team members and stakeholder groups. The nature of these relationships and the patterns that they form affect communication, collaboration and resource flows. Networks affect us directly, and we use them to influence people and processes. Social Network Analysis (SNA) can be an extremely valuable research tool to better understand how critical social networks develop and influence work processes, particularly as projects become larger and more complex. This chapter introduces foundational network concepts, helps you determine if SNA could help you answer your research questions, and explains how to design and implement a social network study. At the end of this chapter, the reader can: understand foundational concepts about social networks; decide if SNA is an appropriate research methodology to address particular questions or problems; design and implement a basic social network study.

On food security and alternative food networks: Understanding and performing food security in the context of urban bias

This paper offers one explanation for the institutional basis of food insecurity in Australia, and argues that while alternative food networks and the food sovereignty movement perform a valuable function in building forms of social solidarity between urban consumers and rural producers, they currently make only a minor contribution to Australia’s food and nutrition security. The paper begins by identifying two key drivers of food security: household incomes (on the demand side) and nutrition-sensitive, ‘fair food’ agriculture (on the supply side). We focus on this second driver and argue that healthy populations require an agricultural sector that delivers dietary diversity via a fair and sustainable food system. In order to understand why nutrition-sensitive, fair food agriculture is not flourishing in Australia we introduce the development economics theory of urban bias. According to this theory, governments support capital intensive rather than labour intensive agriculture in order to deliver cheap food alongside the transfer of public revenues gained from rural agriculture to urban infrastructure, where the majority of the voting public resides. We chart the unfolding of the Urban Bias across the twentieth century and its consolidation through neo-liberal orthodoxy, and argue that agricultural policies do little to sustain, let alone revitalize, rural and regional Australia. We conclude that by observing food system dynamics through a re-spatialized lens, Urban Bias Theory is valuable in highlighting rural–urban socio-economic and political economy tensions, particularly regarding food system sustainability. It also sheds light on the cultural economy tensions for alternative food networks as they move beyond niche markets to simultaneously support urban food security and sustainable rural livelihoods.