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.

The Cannabis Expectancy Questionnaire for Men who have Sex with Men (CEQ-MSM): A measure of substance-related beliefs

Objective Substance-related expectancies are associated with substance use and post-substance use thoughts, feelings and behaviours. The expectancies held by specific cultural or sub-cultural groups have rarely been investigated. This research maps expectancies specific to gay and other men who have sex with men (MSM) and their relationship with substance patterns and behaviours following use, including sexual practices (e.g., unprotected anal intercourse). This study describes the development of a measure of such beliefs for cannabis, the Cannabis Expectancy Questionnaire for Men who have Sex with Men (CEQ-MSM). Method Items selected through a focus group and interviews were piloted on 180 self-identified gay or other MSM via an online questionnaire. Results Factor analysis revealed six distinct substance reinforcement domains (“Enhanced sexual experience”, “Sexual negotiation”, “Cognitive impairment”, “Social and emotional facilitation”, “Enhanced sexual desire”, and “Sexual inhibition”). The scale was associated with consumption patterns of cannabis, and in a crucial test of discriminant validity not with the consumption of alcohol or stimulants. Conclusions The CEQ-MSM represents a reliable and valid measure of outcome expectancies, related to cannabis among MSM. Future applications of the CEQ-MSM in health promotion, clinical settings and research may contribute to reducing harm associated with substance use among MSM, including HIV transmission.

Hypercapitalism : a political economy of informational idealism

In this this paper I identify specific historical trajectories that are directly contingent upon the deployment and use of new media, but which are actually hidden by a focus on the purely technological. They are: the increasingly abstract and alienated nature of economic value; the subsumption of all labour - material and intellectual - under systemic capital; and the convergence of formerly distinct spheres of analysis –the spheres of production, circulation, and consumption. This paper examines the implications of the knowledge economy from an historical materialist perspective. I synthesise the systemic views of Marx (1846/1972, 1875/1972 1970 1973 1976 1978 1981), Adorno (1951/1974 1964/1973 1991; Horkheimer and Adorno 1944/1998; Jarvis 1998), and Bourdieu (1991 1998) to argue for a language-focused approach to new media research and suggest aspects of Marxist thought which might be useful in researching emergent socio-technical domains. I also identify specific categories in the Marxist tradition which may no longer be analytically useful for researching the effects of new media.

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.

Reflections, successes and pitfalls of coordinating online discussion forums in a foreign language

The advent of e-learning has seen the adaptation and use of a plethora of educational techniques. Of these, online discussion forums have met with success and been used widely in both undergraduate and postgraduate education. The authors of this paper, having previously used online discussion forums in the postgraduate arena with success, adopted this approach for the design and subsequent delivery of a learning and teaching subject. This learning and teaching subject, however, was part of an international collaboration and designed for nurse academics in another country – Vietnam. With the nursing curriculum in Vietnam currently moving to adopt a competency based approach, two learning and teaching subjects were designed by an Australian university for Vietnamese nurse academics. Subject materials constituted a DVD which arrived by post and access to an online platform. Assessment for the subject included (but was not limited to) mandatory participation in online discussion with the other nurse academics enrolled in the subject. The purpose behind the online discussion was to generate discourse between the Vietnamese nurse academics located across Vietnam. Consequently the online discussions occurred in both Vietnamese and English; the Australian academic moderating the discussion did so in Australia with a Vietnamese translator. For the Australian University delivering this subject the difference between this and past online discussions were twofold: delivery was in a foreign language; and the teaching experience of the Vietnamese nurse teachers was mixed and frequently very limited. This paper will provide a discussion addressing the design of an online learning environment for foreign correspondents, the resources and translation required to maximise the success of the online discussion, the lessons learnt and consequent changes made, as well as the rationale of delivering complex content in a foreign language. While specifically addressing the first iteration of the first learning module designed, this paper will also address subsequent changes made for the second iteration of the first module and comment on their success. While a translator is clearly a key component of success, the elements of simplicity and clarity in hand with supportive online moderation must not be overlooked.

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.

Risk of falls, injurious falls, and other injuries resulting from visual impairment among older adults with age-related macular degeneration

Purpose: Age-related macular degeneration (AMD) is the leading cause of irreversible visual impairment among older adults. This study explored the relationship between AMD, falls risk and other injuries and identified visual risk factors for these adverse events. Methods: Participants included 76 community-dwelling individuals with a range of severity of AMD (mean age, 77.0±6.9 years). Baseline assessment included binocular visual acuity, contrast sensitivity and merged visual fields. Participants completed monthly falls and injury diaries for one year following the baseline assessment. Results: Overall, 74% of participants reported having either a fall, injurious fall or other injury. Fifty-four percent of participants reported a fall and 30% reported more than one fall; of the 102 falls reported, 63% resulted in an injury. Most occurred outdoors (52%), between late morning and late afternoon (61%) and when navigating on level ground (62%). The most common non-fall injuries were lacerations (36%) and collisions with an object (35%). Reduced contrast sensitivity and visual acuity were associated with increased fall rate, after controlling for age, gender, cognitive function, cataract severity and self-reported physical function. Reduced contrast sensitivity was the only significant predictor of falls and other injuries. Conclusion: Among older adults with AMD, increased visual impairment was significantly associated with an increased incidence of falls and other injuries. Reduced contrast sensitivity was significantly associated with increased rates of falls, injurious falls and injuries, while reduced visual acuity was only associated with increased falls risk. These findings have important implications for the assessment of visually impaired older adults.

Scoping work integrated learning purposes, practices and issues

A range of terms is used in Australian higher education institutions to describe learning approaches and teaching models that provide students with opportunities to engage in learning connected to the world of work. The umbrella term currently being used widely is Work Integrated Learning (WIL). The common aim of approaches captured under the term WIL is to integrate discipline specific knowledge learnt in university setting with that learnt in the practice of work through purposefully designed curriculum. In endeavours to extend WIL opportunities for students, universities are currently exploring authentic learning experiences, both within and outside of university settings. Some universities describe these approaches as ‘real world learning’ or ‘professional learning’. Others refer to ‘social engagement’ with the community and focus on building social capital and citizenship through curriculum design that enables students to engage with the professions through a range of learning experiences. This chapter discusses the context for, the scope, purposes, characteristics and effectiveness of WIL across Australian universities as derived from a national scoping study. This study, undertaken in response to a high level of interest in WIL, involved data collection from academic and professional staff, and students at nearly all Australian universities. Participants in the study consistently reported the benefits, especially in relation to the student learning experience. Responses highlight the importance of strong partnerships between stakeholders to facilitate effective learning outcomes and a range of issues that shape the quality of approaches and models being adopted, in promoting professional learning.

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.