BLAST Atlas : a function based multiple genome browser

BLAST Atlas is a visual analysis system for comparative genomics that supports genome-wide gene characterisation, functional assignment and function-based browsing of one or more chromosomes. Inspired by applications such as the WorldWide Telescope, Bing Maps 3D and Google Earth, BLAST Atlas uses novel three-dimensional gene and function views that provide a highly interactive and intuitive way for scientists to navigate, query and compare gene annotations. The system can be used for gene identification and functional assignment or as a function-based multiple genome comparison tool which complements existing position based comparison and alignment viewers.

From Jindabyne to 'Jindabyne' : immigrant and indigenous specters

This paper reads Ray Lawrence's film Jindabyne (2006) in order to consider how "Australian" connotes as "immigrant" or "Indigenous" in contemporary Australia. Although the film is an adaptation of an American short story, it exploits an existing grammar of place in Australian cultural production in order to interrogate this very culture. If questions of race, gender, and class have haunted post-settlement Australia, Lawrence's film simultaneously stages these spectres and gestures towards the necessary failure of any attempt to exorcise them in a place where indigeneity is invisible. Thus, the location of Jindabyne, the town drowned in the name of progress, offers an exemplary visual metaphor for the failed project of identity formation in a place where forgetting is a survival tool.

The play's the thing? : Hamlet, Slings & Arrows, and the authority of theatrical consumption

This paper reads season 1 of the critically-acclaimed Canadian television series “Slings & Arrows” (2003). This six-episode series is set in a fictionalised version of the Stratford Festival, and tells the story of a plagued production of Shakespeare’s Hamlet. It follows the play’s rehearsal after the death of the festival’s artistic director; Geoffrey Tennant (himself a plagued Hamlet) takes over the role of director, and must face his past in order to produce a Hamlet that will save the festival, redeem his reputation, and repair his interpersonal relationships. Drawing on popular and theatrical understandings of Shakespeare’s play, the series negotiates tropes of metatheatre, filiality, cultural production and consumption, in order to demonstrate the ongoing relevance and legitimacy of “Shakespeare” in the twenty-first century. The “Slings & Arrows” narrative revolves around the doubled-plot of Hamlet and the experiences of the company mounting Hamlet. In quite obvious ways, the show thus thematises ways in which Shakespeare can be used to read one’s own life and world. In the broader sense, however, the show also offers theatre/performance as a catalyst for affect. In doing so, the show functions as a relatively straight adaptation of Hamlet, and a metatheatrical/metafictional commentary on the functions of Hamlet within contemporary culture. In Shakespeare’s play, the production of “The Mouse-Trap” proves, both to Hamlet and the audience, the legitimacy of the ghost’s claims. Similarly, in “Slings & Arrows”, the successful performance of Hamlet legitimises Geoffrey’s position as artistic director of the festival, and affirms for the viewer the value of Shakespearean production in contemporary culture. In each text, theatre/performance enables and legitimises a son carrying out a dead father’s wishes in order to restore or reproduce socio-cultural order. The metatheatrics of these gestures engage the reader/viewer in a self-reflexive process whereby the ‘value’ of theatre is thematised and performed, and the consumer is positioned as the arbiter and agent of that value: complicit in its production even as they are the site of its consumption.

Blast atlas: a virtual observatory for genomes

Following the completion of the draft Human Genome in 2001, genomic sequence data is becoming available at an accelerating rate, fueled by advances in sequencing and computational technology. Meanwhile, large collections of astronomical and geospatial data have allowed the creation of virtual observatories, accessible throughout the world and requiring only commodity hardware. Through a combination of advances in data management, data mining and visualization, this infrastructure enables the development of new scientific and educational applications as diverse as galaxy classification and real-time tracking of earthquakes and volcanic plumes. In the present paper, we describe steps taken along a similar path towards a virtual observatory for genomes – an immersive three-dimensional visual navigation and query system for comparative genomic data.

Longitudinal investigation of wandering behavior in department of veterans affairs nursing home care units

Objectives To explore the extent of and factors associated with male residents who change wandering status post nursing home admission. Design Longitudinal design with secondary data analyses. Admissions over a 4-year period were examined using repeat assessments with the Minimum Data Set (MDS) to formulate a model understanding the development of wandering behavior. Setting One hundred thirty-four Veterans Administration (VA) nursing homes throughout the United States. Participants: Included 6673 residents admitted to VA nursing homes between October 2000 and October 2004. Measurements MDS variables (cognitive impairment, mood, behavior problems, activities of daily living and wandering) included ratings recorded at residents’ admission to the nursing home and a minimum of two other time points at quarterly intervals. Results The majority (86%) of the sample were classified as non wanderers at admission and most of these (94%) remained non wanderers until discharge or the end of the study. Fifty one per cent of the wanderers changed status to non wanderers with 6% of these residents fluctuating in status more than two times. Admission variables associated with an increased risk of changing status from non-wandering to wandering included older age, greater cognitive impairment, more socially inappropriate behavior, resisting care, easier distractibility, and needing less help with personal hygiene. Requiring assistance with locomotion and having three or more medical comorbidities were associated with a decreased chance of changing from non-wandering to wandering status. Conclusion A resident’s change from non-wandering to wandering status may reflect an undetected medical event that affects cognition, but spares mobility.

Wireless mobility usage: a preliminary study for management in two Australian university settings

Wireless Mobility Usage: A Preliminary Qualitative Study for Management in Two Australian University Settings, Neville Meyers, Heather Gray, Greg Hearn, Louis Sanzogni, and Sandra Lawrence.

Bow and stern flows with constant vorticity

Free surface flows of a rotational fluid past a two-dimensional semi-infinite body are considered. The fluid is assumed to be inviscid, incompressible, and of finite depth. A boundary integral method is used to solve the problem for the case where the free surface meets the body at a stagnation point. Supercritical solutions which satisfy the radiation condition are found for various values of the Froude number and the dimensionless vorticity. Subcritical solutions are also found; however these solutions violate the radiation condition and are characterized by a train of waves upstream. It is shown numerically that the amplitude of these waves increases as each of the Froude number, vorticity and height of the body above the bottom increases.

Optimal fluid injection strategies for in situ mineral leaching in two-dimensions

This paper examines the ground-water flow problem associated with the injection and recovery of certain corrosive fluids into mineral bearing rock. The aim is to dissolve the minerals in situ, and then recover them in solution. In general, it is not possible to recover all the injected fluid, which is of concern economically and environmentally. However, a new strategy is proposed here, that allows all the leaching fluid to be recovered. A mathematical model of the situation is solved approximately using an asymptotic solution, and exactly using a boundary integral approach. Solutions are shown for two-dimensional flow, which is of some practical interest as it is achievable in old mine tunnels, for example.

Smoothly attaching bow flows with constant vorticity

The free surface flow of a finite depth fluid past a semi-infinite body is considered. The fluid is assumed to have constant vorticity throughout and the free surface is assumed to attach smoothly to the front face of the body. Numerical solutions are found using a boundary integral method in the physical plane and it is shown that solutions exist for all supercritical Froude numbers. The related problem of the cusp-like flow due to a submerged sink in a corner is also considered. Vorticity is included in the flow and it is shown that the behaviour of the solutions is qualitatively the same as that found in the problem described above.

Workplace emotion : fear and anger

This original screen drama functioned as the stimulus in an audience response experiment, undertaken as part of research into workplace emotion. Commissioned and scripted by researchers at the University of Queensland and Griffith University, the film portrays the same narrative (a workplace conflict) twice, but played differently each time. The first version is intended to evince in viewers a fear response, and the second, an anger response. In preparing and rehearsing their performance choices, the actors utilised established taxonomies of fear and anger, in order to produce the optimum stimulus for conducting the experiment.

Ureaplasma parvum and ureaplasma urealyticum detected in semen after washing prior to assisted reproductive technology procedures

Objective: This study investigated: (i) the prevalence of ureaplasmas in semen and washed semen and (ii) the effect of ureaplasmas on semen andrology parameters. Design: Prospective study. Setting: IVF unit -private hospital, Brisbane, Australia. Patient(s): Three hundred and forty three men participating in an assisted reproductive technology (ART) treatment cycle. Intervention(s): Semen and washed semen tested by culture, PCR assays and indirect immunofluorescent antibody assays. Statistical differences were determined by a t-test, Wilcoxon or Pearson’s Chi- square test where appropriate. Main Outcome Measure(s): The prevalence of ureaplasmas in semen and washed semen and the effect of these microorganisms on semen andrology parameters. Result(s): Ureaplasmas were detected in 73/343 (22%) semen samples and 29/343 (8.5%) washed semen samples. Ureaplasmas adherent to the surface of spermatozoa were demonstrated by indirect immunofluorescent antibody testing. U. parvum serovar 6 (36.6%) and U. urealyticum (30%) were the most prevalent isolates in washed semen. A comparison of the semen andrology parameters of washed semen ureaplasma positive and negative groups demonstrated a lower proportion of non-motile sperm in the washed semen ureaplasma positive group. Conclusion(s): Ureaplasmas are not always removed from semen by a standard ART washing procedure and can remain adherent to the surface of spermatozoa.

Strategies for managing osteoarthritis

Background Although there are recommendations for the management of osteoarthritis (OA), little is known about how people with OA actually manage this chronic condition. Purpose The aims of this study were to identify the non-pharmacological and pharmacological therapies most commonly used for the management of hip or knee OA, in a community-based sample of adults, and to compare these with evidence-based recommendations. Methods A questionnaire was mailed to 2200 adult members of Arthritis Queensland living in Brisbane, Australia. It included questions about OA symptoms, management therapies and demographic characteristics. Results Of the 485 participants (192 men, 293 women) with hip or knee OA who completed the questionnaire, most had mild to moderate symptoms. Ninety-six percent of participants (aged 27–95 years) reported using at least one non-pharmacological therapy, and 78% reported using at least one pharmacological therapy. The most common currently used non-pharmacological strategy was range-of-motion exercises (men 52%, women 61%, p=0.05) and the most common frequently used pharmacological strategy was glucosamine/chondroitin (men 51%, women 60%, ns). For the most highly recommended strategies, 65% of men and 54% of women had never attended an information/education course (p=0.04), and fewer than half (46% of women and 42% of men, p=0.03) were frequent users of anti-inflammatory agents. Conclusion The findings suggest that many people with knee or hip OA do not follow the most highly endorsed of the OARSI (Osteoarthritis Research Society International) recommendations for management of OA. Health professionals should be encouraged to recommend evidence-based therapies to their patients.

Copyright future copyright freedom

If copyright law does not liberate us from restrictions on the dissemination of knowledge, if it does not encourage expressive freedom, what is its purpose? This volume offers the thinking and suggestions of some of the finest minds grappling with the future of copyright regulation. The Copyright Future Copyright Freedom conference held in 2009 at Old Parliament House Canberra brought together Lawrence Lessig, Julie Cohen, Leslie Zines, Adrian Sterling, Sam Ricketson, Graham Greenleaf, Anne Fitzgerald, Susy Frankel, John Gilchrist, Michael Kirby and others to share the rich fruits of their experience and analysis. Zines, Sterling and Gilchrist outline their roles in the genesis and early growth of Australian copyright legislation, enriching the knowledge of anyone asking urgent questions about the future of information regulation.

A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells

In humans, more than 30,000 chimeric transcripts originating from 23,686 genes have been identified. The mechanisms and association of chimeric transcripts arising from chromosomal rearrangements with cancer are well established, but much remains unknown regarding the biogenesis and importance of other chimeric transcripts that arise from nongenomic alterations. Recently, a SLC45A3–ELK4 chimera has been shown to be androgen-regulated, and is overexpressed in metastatic or high-grade prostate tumors relative to local prostate cancers. Here, we characterize the expression of a KLK4 cis sense–antisense chimeric transcript, and show other examples in prostate cancer. Using non-protein-coding microarray analyses, we initially identified an androgen-regulated antisense transcript within the 3′ untranslated region of the KLK4 gene in LNCaP cells. The KLK4 cis-NAT was validated by strand-specific linker-mediated RT-PCR and Northern blotting. Characterization of the KLK4 cis-NAT by 5′ and 3′ rapid amplification of cDNA ends (RACE) revealed that this transcript forms multiple fusions with the KLK4 sense transcript. Lack of KLK4 antisense promoter activity using reporter assays suggests that these transcripts are unlikely to arise from a trans-splicing mechanism. 5′ RACE and analyses of deep sequencing data from LNCaP cells treated ±androgens revealed six high-confidence sense–antisense chimeras of which three were supported by the cDNA databases. In this study, we have shown complex gene expression at the KLK4 locus that might be a hallmark of cis sense–antisense chimeric transcription.