Web tools for the prioritization of candidate disease genes

Despite increasing sequencing capacity, genetic disease investigation still frequently results in the identification of loci containing multiple candidate disease genes that need to be tested for involvement in the disease. This process can be expedited by prioritizing the candidates prior to testing. Over the last decade, a large number of computational methods and tools have been developed to assist the clinical geneticist in prioritizing candidate disease genes. In this chapter, we give an overview of computational tools that can be used for this purpose, all of which are freely available over the web.

Ratio-dependent response of a temperate Australian estuarine system to sustained nitrogen loading

Classical resource- and the less studied ratio-dependent models of predator–prey relationships provide divergent predictions as to the sustained ecological effects of bottom-up forcing. While resource-dependent models, which consider only instantaneous prey density in modelling predator responses, predict community responses that are dependent on the number of trophic levels in a system, ratio-dependent models, which consider the number of prey per consumer, predict proportional increase in each level irrespective of chain length. The two models are only subtly different for systems with two or three trophic levels but in the case of four trophic levels, predict opposite effects of enrichment on primary producers. Despite the poor discriminatory power of tests of the models in systems with two or three trophic levels, field tests in estuarine and marine systems with four trophic levels have been notably absent. Sampling of phytoplankton, macroinvertebrates, invertebrate-feeding fishes, piscivorous fishes in Kooloonbung Creek, Hastings River estuary, eastern Australia, subject to over 20 years of sewage discharge, revealed increased abundances in all four trophic levels at the disturbed location relative to control sites. Increased abundance of phytoplankton at the disturbed site was counter to the predictions of resource-dependent models, which posit a reduction in the first trophic level in response to enrichment. By contrast, the increase in abundance of this first trophic level and the proportionality of increases in abundances of each of the four trophic groups to nitrogen loading provided strong support for ratio dependency. This first evidence of ratio dependence in an estuarine system with four trophic levels not only demonstrates the applicability of ecological theory which seeks to simplify the complexity of systems, but has implications for management. Although large nutrient inputs frequently induce mortality of invertebrates and fish, we have shown that smaller inputs may in fact enhance biomass of all trophic levels.

Improving science uptake in coastal zone management : principles for science engagement and their application in south-eastern Tasmania

Sustainable management of the coastal zone represents a considerable challenge to Australian society. This challenge is rooted in the complexity of the biophysical and sociocultural characteristics of coastal areas, including uncertainty about system characteristics and processes, and the diversity of stakeholders, their interests, values and perspectives, and the jurisdictions involved in coastal governance and management. Given this complexity of coastal zone management, scientific and other forms of knowledge can affect decision-making and human action in diverse ways, which will often depend on the ability of scientists to engage effectively with relevant stakeholders.

Mission fulfilment : the role of the non-profit arts board

This research explores the complexity of establishing mission fulfilment through the performance of non-profit arts boards (NP AB). Since the early 1990s, the non-profit literature has only sporadically focussed on the concept of how board performance contributes to mission fulfilment in the broader non-profit sector. Consequently, in both the empirical and normative literatures there is a dearth of understanding of how the nonprofit arts board performance fulfils the organisation's mission. The lack of exploration is problematic for theory development in contextualising non-profit arts board performance contribution to mission fulfilment. Although research has been undertaken in various areas-such as effective and ineffective board performance practices of non-profit organisations, board performance measurement indicators within the arts sector, and mission fulfilment as a result of non-profit organisational effectiveness-research from an extensive literature search did not reveal empirical evidence of the relationship between board performance and mission fulfilment of non-profit arts boards. Against this background, the research issue for the thesis is: How does board performance contribute to mission fulfilment by the non-profit arts organisation?

Research in action for community informatics : a matter for conversation

In this introduction to the special issue on research in action, we briefly outline an argument concerning the importance of conversation,suggesting that, first, conversational uses of ICTs make them most suitable for community informatic development, and second, that their effective adoption and research requires conversation for that process to be effective.

Functional imaging to understand biomechanics : a critical tool for the study of biology, pathology and the development of pharmacological solutions

We present four case studies of the literature discussing the effects of physical forces on biological function. While the field of biomechanics has existed for many decades, it may be considered by some a poor cousin to biochemistry and other traditional fields of medical research. In these case studies, including cardiovascular and respiratory systems, we demonstrate that, in fact, many systems historically believed to be controlled by biochemistry are dominated by biomechanics. We discuss both the previous paradigms that have advanced research in these fields and the changing paradigms that will define the progressions of these fields for decades to come. In the case of biomechanical effects of flowing blood on the endothelium, this has been well understood for decades. In the cases of platelet activation and liquid clearance from the lungs during birth, these discoveries are far more recent and perhaps not as universally accepted. While only a few specific examples are examined here, it is clear that not enough attention is paid to the possible mechanical links to biological function. The continued development of these research areas, with the inclusion of physical effects, will hopefully provide new insight into disease development, progression, diagnosis and effective therapies.

The multifaith movement : global risks and cosmopolitan solutions

This book documents the ultramodern rise of the multifaith movement, as mulitfaith initiatives have been increasingly deployed as cosmopolitan solutions to counter global risks such as terrorism and climate change at the turn of the 21st century. These projects aim to enhance common security, particularly in Western societies following the events of September 11, 2001 and the July 2005 London bombings, where multifaith engagement has been promoted as a strategy to counter violent extremism. The author draws on interviews with 56 leading figures in the field of multifaith relations, including Paul Knitter, Eboo Patel, Marcus Braybrooke, Katherine Marshall, John Voll and Krista Tippett.
Identifying the principle aims of the multifaith movement, the analysis explores the benefits—and challenges—of multifaith engagement, as well as the effectiveness of multifaith initiatives in countering the process of radicalization. Building on notions of cosmopolitanism, the work proposes a new theoretical framework termed ‘Netpeace’, which recognizes the interconnectedness of global problems and their solutions. In doing so, it acknowledges the capacity of multi-actor peacebuilding networks, including religious and state actors, to address the pressing dilemmas of our times. The primary intention of the book is to assist in the formation of new models of activism and governance, founded on a ‘politics of understanding’ modeled by the multifaith movement.

Faster and parameter-free discord search in quasi-periodic time series

Time series discord has proven to be a useful concept for time-series anomaly identification. To search for discords, various algorithms have been developed. Most of these algorithms rely on pre-building an index (such as a trie) for subsequences. Users of these algorithms are typically required to choose optimal values for word-length and/or alphabet-size parameters of the index, which are not intuitive. In this paper, we propose an algorithm to directly search for the top-K discords, without the requirement of building an index or tuning external parameters. The algorithm exploits quasi-periodicity present in many time series. For quasi-periodic time series, the algorithm gains significant speedup by reducing the number of calls to the distance function.

Unsupervised DRG upcoding detection in healthcare databases

Diagnosis Related Group (DRG) upcoding is an anomaly in healthcare data that costs hundreds of millions of dollars in many developed countries. DRG upcoding is typically detected through resource intensive auditing. As supervised modeling of DRG upcoding is severely constrained by scope and timeliness of past audit data, we propose in this paper an unsupervised algorithm to filter data for potential identification of DRG upcoding. The algorithm has been applied to a hip replacement/revision dataset and a heart-attack dataset. The results are consistent with the assumptions held by domain experts.

Visualising a state-wide patient data collection : a case study to expand the audience for healthcare data

This paper describes the application of existing and novel adaptations of visualisation techniques to routinely collected health data. The aim of this case study is to examine the capacity for visualisation approaches to quickly and e ectively inform clinical, policy, and scal decision making to improve healthcare provision. We demonstrate the use of interactive graphics, fluctuation plots, mosaic plots, time plots, heatmaps, and disease maps to visualise patient admission, transfer, in-hospital mortality, morbidity coding, execution of diagnosis and treatment guidelines, and the temporal and spatial variations of diseases. The relative e ectiveness of these techniques and associated challenges are discussed.

Cultural policy in Australia

 In early 2010, more than 15,000 people gathered on Bourke Street in front of Victoria’s Parliament building to register their protest against an unpopular government decision.1 The colourful crowd chanted and marched, sported placards and banners, and listened to speeches by local identities.

What were they protesting about? Climate change? Refugees? The war in Afghanistan?

No, they were protesting about a decision by Liquor Licensing Victoria to enforce onerous security requirements on live music venues in Melbourne. The new regulations had led to the closure of one of Melbourne’s best-loved rock venues, a Collingwood pub named The Tote. Many other venues were threatened with the same fate.

This was a protest about cultural policy.

Parameter-free search of time-series discord

Time-series discord is widely used in data mining applications to characterize anomalous subsequences in time series. Compared to some other discord search algorithms, the direct search algorithm based on the recurrence plot shows the advantage of being fast and parameter free. The direct search algorithm, however, relies on quasi-periodicity in input time series, an assumption that limits the algorithm's applicability. In this paper, we eliminate the periodicity assumption from the direct search algorithm by proposing a reference function for subsequences and a new sampling strategy based on the reference function. These measures result in a new algorithm with improved efficiency and robustness, as evidenced by our empirical evaluation.