Inferring phylogenies of evolving sequences without multiple sequence alignment

Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics.

Emotional expressions preferentially elicit implicit evaluations of faces also varying in race or age

Both facial cues of group membership (race, age, and sex) and emotional expressions can elicit implicit evaluations to guide subsequent social behavior. There is, however, little research addressing whether group membership cues or emotional expressions are more influential in the formation of implicit evaluations of faces when both cues are simultaneously present. The current study aimed to determine this. Emotional expressions but not race or age cues elicited implicit evaluations in a series of affective priming tasks with emotional Caucasian and African faces (Experiments 1 and 2) and young and old faces (Experiment 3). Spontaneous evaluations of group membership cues of race and age only occurred when those cues were task relevant, suggesting the preferential influence of emotional expressions in the formation of implicit evaluations of others when cues of race or age are not salient. Implications for implicit prejudice, face perception, and person construal are discussed.

Enterprise business technology governance: A validation of three technology-governance competencies for boards of directors

The competent leadership and governance of digital transformation needs to involve the board of directors. The reported lack of such capability in boards is becoming a pressing issue. Underpinning leadership in such transformation are the competencies to effectively govern Enterprise Technology (ETG). In this paper we take the position that ETG competencies are essential in boards because competent enterprise business technology governance has been shown to contribute to increased revenue, profit, and returns. We report the industry validation processes of a set of three board-of-director competencies needed for effective ETG related to strategy and planning; investment and risk; and, innovation and value creation. We conclude that gaps in board ETG competence remain.

Working on the edge : Exploring the creative tensions experienced by practitioners facilitating participatory media projects with refugees and asylum seekers in Australia

This paper aims to provide a contextualised and embedded exploration of how the notions of "practice" and "participation", key concepts in the study of culture and media, are manifest in an example of a complex creative project. This project aimed to engage with refugees and asylum seekers through the co-creation of cultural material and is an outcome of an? ethnographic action research (Tacchi et al. 2003) partnership involving a community development worker in a settlement support agency and a storytelling/community media researcher (the author), along with other project collaborators. The discussion of this project focuses on the role of the facilitator and illustrates the processes of orchestrating a complex project involving a series of linked stages with cumulative effect. As practitioners at this site we are working in the space where personal narratives, participatory arts and media, and the staging of intercultural, civic dialogue events, intersect. Co-creative media facilitation in these contexts involves both managing hybrid communicative spaces and (re)combining the "integrative practices" (Schatzki 1996) of a range of professional approaches and creative roles. This is liminal work, located on the boundaries of several disciplines and practices. Drawing on reflections gathered from collaborative ethnographic descriptions (Bhattacharya 2008), this paper traces moments of practitioner uncertainty that can be linked to the way "practice" and “participation” is problematised within the community cultural development field in a way that is at times an uneasy fit with conventional ways of operating in social service roles. These moments of tension also indicate where this project pushed practitioners into spaces of improvisation and new learning. Keywords: Youth, refugees, community cultural development, co-creative media facilitation, ethnographic action research, intercultural dialogue.

Émile Durkheim and Thomas Luckmann: Religion, spirituality and mental health

This chapter examines connections between religion, spirituality and mental health. Religion and spirituality influence the way people conceive themselves, others and the world around them, as well as how they behave – and are strongly associated with numerous mental health outcomes. Religion and spirituality therefore demand the attention of those who seek a comprehensive understanding of the factors that affect mental health. Mental health professionals are increasingly being asked to consider their clients’ religious and/or spiritual beliefs when devising their treatment plans, making the study of religion and spirituality an essential area of learning for those working in the mental health field. Initial discussion in this chapter will focus on the different approaches taken by sociologists in studying mental health. Emile Durkheim, one of the founders of sociology, proposed that religion was fundamental to societal wellbeing and was the first to demonstrate a link between religion and mental health at a population level in the late 19th century. Durkheim’s classic theory of religion, together with the work of Thomas Luckmann and other contemporary social theorists who have sought to explain widespread religious change in Western countries since World War II will be examined. Two key changes during this period are the shift away from mainstream Christian religions and the widespread embracing of ‘spirituality’ as an alternative form of religious expression. In combination, the theories of Durkheim, Luckmann and other sociologists provide a platform from which to consider reasons for variations in rates of mental health problems observed in contemporary Western societies according to people’s religious/spiritual orientation. This analysis demonstrates the relevance of both classic and contemporary sociological theories to issues confronting societies in the present day.

Injecting Creative Commons Licensing into university policy and publishing

Australian universities are publishing previously unpublished works such as theses in institutional repositories or by publishing scholarly journals on their own presses. This re-invented role of publisher is due in part, to the availability of digital age technologies which scaffold the publishing process and facilitate inexpensive production of digital-only journals. The global push for Open Access to the outputs of publicly-funded research has also been a major driver. Research funder mandates and institutional Open Access policies apply only to publications for which the authors have no expectation of commercial gain. In all cases the primary motivation is to disseminate widely for maximum uptake with attribution to the author thereby increasing impact. This makes works published in institutional repositories and on university presses ideal candidates for Creative Commons licences.

A conjugative plasmid carrying the carbapenem resistance gene blaOXA-23 in AbaR4 in an extensively resistant GC1 Acinetobacter baumannii isolate

OBJECTIVES: To locate the acquired bla(OXA-23) carbapenem resistance gene in an Australian A. baumannii global clone 1 (GC1) isolate. METHODS: The genome of the extensively antibiotic-resistant GC1 isolate A85 harbouring bla(OXA-23) in Tn2006 was sequenced using Illumina HiSeq, and the reads were used to generate a de novo assembly. PCR was used to assemble relevant contigs. Sequences were compared with ones in GenBank. Conjugation experiments were conducted. RESULTS: The sporadic GC1 isolate A85, recovered in 2003, was extensively resistant, exhibiting resistance to imipenem, meropenem and ticarcillin/clavulanate, to cephalosporins and fluoroquinolones and to the older antibiotics gentamicin, kanamycin and neomycin, sulfamethoxazole, trimethoprim and tetracycline. Genes for resistance to older antibiotics are in the chromosome, in an AbaR3 resistance island. A second copy of the ampC gene in Tn6168 confers cephalosporin resistance and the gyrA and parC genes have mutations leading to fluoroquinolone resistance. An 86 335 bp repAci6 plasmid, pA85-3, carrying bla(OXA-23) in Tn2006 in AbaR4, was shown to transfer imipenem, meropenem and ticarcillin/clavulanate resistance into a susceptible recipient. A85 also contains two small cryptic plasmids of 2.7 and 8.7 kb. A85 is sequence type ST126 (Oxford scheme) and carries a novel KL15 capsule locus and the OCL3 outer core locus. CONCLUSIONS: A85 represents a new GC1 lineage identified by the novel capsule locus but retains AbaR3 carrying genes for resistance to older antibiotics. Resistance to imipenem, meropenem and ticarcillin/clavulanate has been introduced into A85 by pA85-3, a repAci6 conjugative plasmid carrying Tn2006 in AbaR4.

Exploration of diarrhoea seasonality and its drivers in China

This study investigated the diarrhoea seasonality and its potential drivers as well as potential opportunities for future diarrhoea control and prevention in China. Data on weekly infectious diarrhoea cases in 31 provinces of China from 2005 to 2012, and data on demographic and geographic characteristics, as well as climatic factors, were complied. A cosinor function combined with a Poisson regression was used to calculate the three seasonal parameters of diarrhoea in different provinces. Regression tree analysis was used to identify the predictors of diarrhoea seasonality. Diarrhoea cases in China showed a bimodal distribution. Diarrhoea in children <5 years was more likely to peak in fall-winter seasons, while diarrhoea in persons > = 5 years peaked in summer. Latitude was significantly associated with spatial pattern of diarrhoea seasonality, with peak and trough times occurring earlier at high latitudes (northern areas), and later at low latitudes (southern areas). The annual amplitudes of diarrhoea in persons > = 5 years increased with latitude (r = 0.62, P<0.001). Latitude 27.8° N and 38.65° N were the latitudinal thresholds for diarrhoea seasonality in China. Regional-specific diarrhoea control and prevention strategies may be optimal for China. More attention should be paid to diarrhoea in children <5 years during fall-winter seasons.

The ghost in the machine: Legal challenges of neural interface devices

Neural interface devices and the melding of mind and machine, challenge the law in determining where civil liability for injury, damage or loss should lie. The ability of the human mind to instruct and control these devices means that in a negligence action against a person with a neural interface device, determining the standard of care owed by him or her will be of paramount importance. This article considers some of the factors that may influence the court’s determination of the appropriate standard of care to be applied in this situation, leading to the conclusion that a new standard of care might evolve.

Being here: Designing for distributed hands-on collaboration in blended interaction spaces

This paper describes a concept for supporting distributed hands-on collaboration through interaction design for the physical and the digital workspace. The Blended Interaction Spaces concept creates distributed work environments in which collaborating parties all feel that they are present “here” rather than “there”. We describe thinking and inspirations behind the Blended Interaction Spaces concept, and summarize findings from fieldwork activities informing our design. We then exemplify the Blended Interaction Spaces concept through a prototype implementation of one of four concepts.

Discrete families of Saffman–Taylor fingers with exotic shapes

The mathematical problem of determining the shape of a steadily propagating Saffman–Taylor finger in a rectangular Hele-Shaw cell is known to have a countably infinite number of solutions for each fixed surface tension value. For sufficiently large surface tension values, we find that fingers on higher solution branches are non-convex. The tips of the fingers have increasingly exotic shapes as the branch number increases.

Comparative analysis reveals loss of the appetite-regulating peptide hormone ghrelin in falcons

Ghrelin and leptin are key peripherally secreted appetite-regulating hormones in vertebrates. Here we consider the ghrelin gene (GHRL) of birds (class Aves), where it has been reported that ghrelin inhibits rather than augments feeding. Thirty-one bird species were compared, revealing that most species harbour a functional copy of GHRL and the coding region for its derived peptides ghrelin and obestatin. We provide evidence for loss of GHRL in saker and peregrine falcons, and this is likely to result from the insertion of an ERVK retrotransposon in intron 0. We hypothesise that the loss of anorexigenic ghrelin is a predatory adaptation that results in increased food-seeking behaviour and feeding in falcons.

Canadian rhapsody: Copyright law and research libraries

This article considers the ground-breaking Supreme Court of Canada decision in The Law Society of Upper Canada v CCH Canadian Limited. The matter involved legal publishers bringing an action for copyright infringement against the Law Society of Upper Canada for operating a photocopy and custom copy service at the Great Library of Osgoode Hall. The Supreme Court of Canada decision laid down important precedents in relation to originality, authorisation, and the defence of fair dealing. The ruling has been hailed as ’one of the strongest pro-user rights decisions from any high court in the world, showing what it means to do more than pay mere lip service to balance in copyright'. This decision will have important implications for the regulation of new technologies. The approach has been applied in two decisions dealing copyright law and the Internet - the Canadian Federal Court case of BMG Canada v John Doe, and the Supreme Court of Canada ’Tariff 22' case. The Supreme Court of Canada decision in The Law Society of Upper Canada v CCH Canadian Limited provides an impetus to reconsider the judicial interpretation of user rights in Australian jurisprudence.

Bibliometric study of the reverse salient concept

In the development of technological systems the focus of system analysis is often on the sub-system that delivers insufficient performance – i.e. the reverse salient – which subsequently limits the performance of the system in its entirety. The reverse salient is therefore a useful concept in the study of technological systems and while the literature holds numerous accounts of its use, it is not known how often, in which streams of literature, and in what type of application the concept has been utilized by scholars since its introduction by Thomas Hughes in 1983. In this paper we employ bibliometric citation analysis between 1983 and 2008, inclusively, to study the impact of the reverse salient concept in the literature at large as well as study the dissemination of the concept into different fields of research. The study results show continuously growing number of concept citations in the literature over time as well as increasing concept diffusion into different research areas. The analysis of article contents additionally suggests the opportunity for scholars to engage in deeper conceptual application. Finally, the continuing increase in the number of citations highlights the importance of the reverse salient concept to scholars and practitioners.