Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Walking with another : rural nurses' experiences of mentoring

The aim of this constructivist grounded theory study was to explore rural nurses' experiences of mentoring. Mentoring is often proposed as a solution to the problem of nursing workforce shortages. The global problem of workforce for nurses can be defined using the parameters of recruitment and retention rates, 'problems' with which result in staff shortages, particularly of experienced nurses. Constructivist grounded theory has its foundations in relativism and an appreciation of the multiple truths and realities of subjectivism. Seven Australian rural nurses were interviewed. To ensure data saturation of particular categories and the fit of tentative theoretical conceptualisations, two participants were interviewed twice with no new codes identified from the subsequent interviews. Cultivating and growing new or novice rural nurses was the core category which conceptualised a two-part process consisting of getting to know a stranger and walking with another. Supportive relationships such as mentoring were found to be an existing, integral part of experienced rural nurses' practice - initiated by living and working in the same community. In this grounded theory, cultivating and growing is conceptualised as the core category. A two-part process was identified - getting to know a stranger and walking with another. This paper examines one of these subcategories, walking with another, relating the ways in which experienced rural nurses walk with another by firstly keeping things in perspective for new or novice rural nurses, and secondly using a particular form of language called nurse chat. For experienced rural nurses, mentoring in this way delivers a number of different outcomes with various nurses. Because it is a part of the experienced rural nurse's practice on an ongoing basis, individual mentoring relationships do not provide an end in relation to this nurse's experiences of mentoring, rather they are part of an ongoing experience. Creating supportive environments that include developing relationships such as mentoring is a potential solution to local staffing needs that does not require intensive resources. Experienced nurses engaged in clinical practice have the potential to cultivate and grow new or novice nurses - many already do so. Recognising their role and providing support as well as development opportunities will bring about a cycle of mentoring within the workplace. © 2008 Sage Publications.

A case for addressing the literacy demands of student assessment

The development and implementation of the Australian Curriculum together with national testing of students and the publication of school results place new demands on teachers. In this article we address the importance of teachers becoming attuned to the silent assessors in assessment generally and in the National Literacy and Numeracy Program (NAPLAN) more specifically. Using the concept of literacies, we develop a method to conduct a literacy audit of assessment tasks that teachers can use to help both themselves and their students. Providing assistance to students as a consequence of such an audit is imperative to improve the outcomes for students and to address issues of equity.

Heidegger's hippies : a dissenting voice on "the problem of the subject"

This is a deliberately contentious paper about the future of the socio-political sphere in the West based on what we know about its past. I argue that the predominant public discourse in Western countries is best characterised as one of selective forgetfulness; a semi-blissful, amnesiacal state of collective dementia that manifests itself in symbolic idealism: informationalism. Informationalism is merely the latest form of idealism. It is a lot like religion insofar as it causally relates abstract concepts with reality and, consequently, becomes confused between the two. Historically, this has proven to be a dangerous state of affairs, especially when elites becomes confused between ideas about how a society should work, and the way it actually does work. Central to the idealism of the information age, at least in intellectual spheres, is the so called "problem of the subject". I argue that the "problem of the subject" is a largely synthetic, destabilising, and ultimately fruitless theoretical abstraction which turns on a synthetically derived, generalised intradiscursive space; existentialist nihilism; and the theoretical baubles of ontological metaphysics. These philosophical aberrations are, in turn, historically concomitant with especially destructive political and social configurations. This paper sketches a theoretical framework for identity formation which rejects the problem of the subject, and proposes potential resources, sources, and strategies with which to engage the idealism that underpins this obfuscating problematic in an age of turbulent social uncertainty. Quite simply, I turn to history as the source of human identity. While informationalism, like religion, is mostly focused on utopian futures, I assert that history, not the future, holds the solutions for substantive problematics concerning individual and social identities. I argue here that history, language, thought, and identity are indissolubly entangled and so should be understood as such: they are the fundamental parts of 'identities in action'. From this perspective, the ‘problem of the subject’ becomes less a substantive intellectual problematic and more a theoretical red herring.

Autopoiesis, language, literacy and the brain

When we attempt to speak about the relationship between language, literacy, and the brain, we find ourselves ill equipped to deal with these conceptually and qualitatively different phenomena. Immediately we must straddle different academic traditions that treat each of these as separate “things”. Broadly speaking, the study of language firstly belongs to the domain of biology, then to anthropology, sociology, and linguistics. At its most functional, a study of literacy education is a study of a particular technology, its diffusion techniques, and the abilities and motivations of people to adopt, or adapt themselves to, this technology. The brain is most commonly studied in the field of neurology, which is also a sub-discipline of biology, biochemistry, and medicine.

Here’s a story : using student podcasts to raise awareness of language

Thirty-five years ago, a landmark article entitled 'What The "Good Language Learner" Can Teach Us' suggested that if more was known about what 'successful learners' did, then those strategies could be taught to poorer learners to enhance learning (Rubin, 1975, p. 42). Since publication of Rubin's article, language instruction has begun to encompass technological applications (Chinnery, 2006) through mobile-assisted language learning (MALL or m-learning) like podcasts. Podcasting extends the classroom, offers convenience for diverse learners, and provides authentic listening opportunities. Although the effects of podcasting in higher education have yet to be investigated (Educause, 2007), this article describes how action research lead to the creation of a student learning strategy webpage featuring peer podcasts and successful language learning strategies in higher education.

Doorway to research : Issues in the development of an interactive website for international graduate students

This paper describes results of a study evaluating the content, functionality and design features of an innovative online website called the Doorway to Research (http://rsc.acid.net.au/Main.aspx) , which was developed to support international graduate students studying at universities in Australia. First, the key features of the website are described. Second, the result of a pilot study involving 12 students and faculty members who tested key aspects of the design, content and functionality of the website and provided written and oral feedback base on task-based questions and focus group discussions are explored. Finally, recommendations for future development are presented. Results of the study indicate general student satisfaction with the website and its design, content and functionality, with specific areas identified for further development.

Domestication to crop improvement: Genetic resources for sorghum and saccharum (Andropogoneae)

Background Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe in the Poaceae and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programmes to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species. Genetic Resources The genome of sorghum has recently been sequenced providing a great boost to our knowledge of the evolution of grass genomes and the wealth of diversity within S. bicolor taxa. Molecular analysis of the Sorghum genus has identified close relatives of S. bicolor with novel traits, endosperm structure and composition that may be used to expand the cultivated gene pool. Mutant populations (including TILLING populations) provide a useful addition to genetic resources for this species. Sugarcane is a complex polyploid with a large and variable number of copies of each gene. The wild relatives of sugarcane represent a reservoir of genetic diversity for use in sugarcane improvement. Techniques for quantitative molecular analysis of gene or allele copy number in this genetically complex crop have been developed. SNP discovery and mapping in sugarcane has been advanced by the development of high-throughput techniques for ecoTILLING in sugarcane. Genetic linkage maps of the sugarcane genome are being improved for use in breeding selection. The improvement of both sorghum and sugarcane will be accelerated by the incorporation of more diverse germplasm into the domesticated gene pools using molecular tools and the improved knowledge of these genomes.

Theorising a model for teaching and assessing reflective learning in higher education

The importance of reflection in higher education, and across disciplinary fields is widely recognised; it is generally included in university graduate attributes, professional standards and program objectives. Furthermore, reflection is commonly embedded into assessment requirements in higher education subjects, often without necessary scaffolding or clear expectations for students. Despite the rhetoric around the importance of reflection for ongoing learning, there is scant literature on any systematic, developmental approach to teaching reflective learning across higher education programs/courses. Given that professional or academic reflection is not intuitive, and requires specific pedagogic intervention to do well, a program/course-wide approach is essential. This paper draws on current literature to theorise a new, transferable and customisable model for teaching and assessing reflective learning across higher education, which foregrounds and explains the pedagogic field of higher education as a multi-dimensional space. We argue that explicit and strategic pedagogic intervention, supported by dynamic resources, is necessary for successful, broad-scale approaches to reflection in higher education.

High-Order Concept Associations Mining and Inferential Language Modeling for Online Review Spam Detection

Despite many incidents about fake online consumer reviews have been reported, very few studies have been conducted to date to examine the trustworthiness of online consumer reviews. One of the reasons is the lack of an effective computational method to separate the untruthful reviews (i.e., spam) from the legitimate ones (i.e., ham) given the fact that prominent spam features are often missing in online reviews. The main contribution of our research work is the development of a novel review spam detection method which is underpinned by an unsupervised inferential language modeling framework. Another contribution of this work is the development of a high-order concept association mining method which provides the essential term association knowledge to bootstrap the performance for untruthful review detection. Our experimental results confirm that the proposed inferential language model equipped with high-order concept association knowledge is effective in untruthful review detection when compared with other baseline methods.