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.

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.

Commuting mode choice in transit oriented development: Disentangling the effects of competitive neighbourhoods, travel attitudes, and self-selection

This research identifies the commuting mode choice behaviour of 3537 adults living in different types of transit oriented development (TOD) in Brisbane by disentangling the effects of their “evil twin” transit adjacent developments (TADs), and by also controlling for residential self-selection, travel attitudes and preferences, and socio-demographic effects. A TwoStep cluster analysis was conducted to identify the natural groupings of respondents’ living environment based on six built environment indicators. The analysis resulted in five types of neighbourhoods: urban TODs, activity centre TODs, potential TODs, TADs, and traditional suburbs. HABITAT survey data were used to derive the commute mode choice behaviour of people living in these neighbourhoods. In addition, statements reflecting both respondents’ travel attitudes and living preferences were also collected as part of the survey. Factor analyses were conducted based on these statements and these derived factors were then used to control for residential self-selection. Four binary logistic regression models were estimated, one for each of the travel modes used (e.g. public transport, active transport, less sustainable transport such as the car/taxi, and other), to differentiate between the commuting behaviour of people living in the five types of neighbourhoods. The findings verify that urban TODs enhance the use of public transport and reduce car usage. No significant difference was found in the commuting behaviour between respondents living in traditional suburbs and TADs. The results confirm the hypothesis that TADs are the “evil twin” of TODs. The data indicates that TADs and the mode choices of residents in these neighbourhoods is a missed transport policy opportunity. Further policy efforts are required for a successive transition of TADs into TODs in order to realise the full benefits of these. TOD policy should also be integrated with context specific TOD design principles.

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.

A new twist on mode indicator functions

Mode indicator functions (MIFs) are used in modal testing and analysis as a means of identifying modes of vibration, often as a precursor to modal parameter estimation. Various methods have been developed since the MIF was introduced four decades ago. These methods are quite useful in assisting the analyst to identify genuine modes and, in the case of the complex mode indicator function, have even been developed into modal parameter estimation techniques. Although the various MIFs are able to indicate the existence of a mode, they do not provide the analyst with any descriptive information about the mode. This paper uses the simple summation type of MIF to develop five averaged and normalised MIFs that will provide the analyst with enough information to identify whether a mode is longitudinal, vertical, lateral or torsional. The first three functions, termed directional MIFs, have been noted in the literature in one form or another; however, this paper introduces a new twist on the MIF by introducing two MIFs, termed torsional MIFs, that can be used by the analyst to identify torsional modes and, moreover, can assist in determining whether the mode is of a pure torsion or sway type (i.e., having a rigid cross-section) or a distorted twisting type. The directional and torsional MIFs are tested on a finite element model based simulation of an experimental modal test using an impact hammer. Results indicate that the directional and torsional MIFs are indeed useful in assisting the analyst to identify whether a mode is longitudinal, vertical, lateral, sway, or torsion.

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.

Tuning the resonance properties of 2D carbon nanotube networks towards a mechanical resonator

The capabilities of the mechanical resonator-based nanosensors in detecting ultra-small mass or force shifts have driven a continuing exploration of the palette of nanomaterials for such application purposes. Based on large-scale molecular dynamics simulations, we have assessed the applicability of a new class of carbon nanomaterials for nanoresonator usage, i.e. the single-wall carbon nanotube (SWNT) network. It is found that SWNT networks inherit excellent mechanical properties from the constituent SWNTs, possessing a high natural frequency. However, although a high quality factor is suggested from the simulation results, it is hard to obtain an unambiguous Q-factor due to the existence of vibration modes in addition to the dominant mode. The nonlinearities resulting from these extra vibration modes are found to exist uniformly under various testing conditions including different initial actuations and temperatures. Further testing shows that these modes can be effectively suppressed through the introduction of axial strain, leading to an extremely high quality factor in the order of 109 estimated from the SWNT network with 2% tensile strain. Additional studies indicate that the carbon rings connecting the SWNTs can also be used to alter the vibrational properties of the resulting network. This study suggests that the SWNT network can be a good candidate for applications as nanoresonators.

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.

IdeaWall: Mixed mode distributed collaboration in enterprise environments

In early stages of design and modeling, computers and computer applications are often considered an obstacle, rather than a facilitator of the process. Most notably, brainstorms, process modeling with business experts, or development planning, are often performed by a team in front of a whiteboard. While "whiteboarding" is recognized as an effective tool, low-tech solutions that allow remote participants to contribute are still not generally available. This is a striking observation, considering that vast majority of teams in large organizations are distributed teams. And this has also been one of the key triggers behind the project described in this article, where a team of corporate researchers decided to identify state of the art technologies that could facilitate the scenario mentioned above. This paper is an account of a research project in the area of enterprise collaboration, with a strong focus on the aspects of human computer interaction in mixed mode environments, especially in areas of collaboration where computers still play a secondary role. It is describing a currently running corporate research project. © 2012 Springer-Verlag.