miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

miRDeep and its varieties are widely used to quantify known and novel micro RNA (miRNA) from small RNA sequencing (RNAseq). This article describes miRDeep*, our integrated miRNA identification tool, which is modeled off miRDeep, but the precision of detecting novel miRNAs is improved by introducing new strategies to identify precursor miRNAs. miRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and Sequence Alignment Map (SAM) or the binary equivalent (BAM) format. Known and novel miRNA expression levels, as measured by the number of reads, are displayed in an interface, which shows each RNAseq read relative to the pre-miRNA hairpin. The secondary pre-miRNA structure and read locations for each predicted miRNA are shown and kept in a separate figure file. Moreover, the target genes of known and novel miRNAs are predicted using the TargetScan algorithm, and the targets are ranked according to the confidence score. miRDeep* is an integrated standalone application where sequence alignment, pre-miRNA secondary structure calculation and graphical display are purely Java coded. This application tool can be executed using a normal personal computer with 1.5 GB of memory. Further, we show that miRDeep* outperformed existing miRNA prediction tools using our LNCaP and other small RNAseq datasets. miRDeep* is freely available online at http://www.australianprostatecentre.org/research/software/mirdeep-star

Avoiding road rage

Road Rage describes a range of aggressive and dangerous driving behaviours directed at other road users. The phrase involves images of uncontrolled temper and the open display of anger and frustration. A common alternative term is “aggressive driving” with road rage seen to be a manifestation of extreme aggressive driving.

Organotypic culture of normal, dysplastic and squamous cell carcinoma-derived oral cell lines reveals loss of spatial regulation of CD44 and p75(NTR) in malignancy

Oral squamous cell carcinomas (OSCC) often arise from dysplastic lesions. The role of cancer stem cells in tumour initiation is widely accepted, yet the potential existence of pre-cancerous stem cells in dysplastic tissue has received little attention. Cell lines from oral diseases ranging in severity from dysplasia to malignancy provide opportunity to investigate the involvement of stem cells in malignant progression from dysplasia. Stem cells are functionally defined by their ability to generate hierarchical tissue structures in consortium with spatial regulation. Organotypic cultures readily display tissue hierarchy in vitro; hence, in this study, we compared hierarchical expression of stem cell-associated markers in dermis-based organotypic cultures of oral epithelial cells from normal tissue (OKF6-TERT2), mild dysplasia (DOK), severe dysplasia (POE-9n) and OSCC (PE/CA P J15). Expression of CD44, p75NTR, CD24 and ALDH was studied in monolayers by flow cytometry and in organotypic cultures by immunohistochemistry. Spatial regulation of CD44 and p75NTR was evident for organotypic cultures of normal (OKF6-TERT2) and dysplasia (DOK and POE-9n) but was lacking for OSCC (PE/CA PJ15)-derived cells. Spatial regulation of CD24 was not evident. All monolayer cultures exhibited CD44, p75NTR, CD24 antigens and ALDH activity (ALDEFLUOR® assay), with a trend towards loss of population heterogeneity that mirrored disease severity. In monolayer, increased FOXA1 and decreased FOXA2 expression correlated with disease severity, but OCT3/4, Sox2 and NANOG did not. We conclude that dermis-based organotypic cultures give opportunity to investigate the mechanisms that underlie loss of spatial regulation of stem cell markers seen with OSCC-derived cells.

Changing lanes

The purpose of Changing Lanes was to question the identity of Brisbane laneways through the collaboration of local stakeholders by promoting design. Community partners provided design briefs for student work from Architecture and Interior Design to be included in a design competition. Shortlisted student projects were featured in the Changing Lanes event during which the winners were announced. In addition to student work from Architecture and Interior Design, the five other disciplines from QUT's School of Design also exhibited samples of student work. The engagement of local stakeholders; architectural practice, interior designers, engineers, and a media and publication agency was fundamental to the success of this event. The design work on display provided creative expression for the potential of Brisbane Laneways to bring communities together through the language of design. An underutilised area of Fortitude Valley was activated through a combination of media including drawings, videos, street furniture, and music.

Classification—Content Regulation and Convergent Media

On 24 March 2011, Attorney-General Robert McClelland referred the National Classification Scheme to the ALRC and asked it to conduct widespread public consultation across the community and industry. The review considered issues including: existing Commonwealth, State and Territory classification laws the current classification categories contained in the Classification Act, Code and Guidelines the rapid pace of technological change the need to improve classification information available to the community the effect of media on children and the desirability of a strong content and distribution industry in Australia. During the inquiry, the ALRC conducted face-to-face consultations with stakeholders, hosted two online discussion forums, and commissioned pilot community and reference group forums into community attitudes to higher level media content. The ALRC published two consultation documents—an Issues Paper and a Discussion Paper—and invited submissions from the public. The Final Report was tabled in Parliament on 1 March 2012. Recommendations: The report makes 57 recommendations for reform. The net effect of the recommendations would be the establishment of a new National Classification Scheme that: applies consistent rules to content that are sufficiently flexible to be adaptive to technological change; places a regulatory focus on restricting access to adult content, helping to promote cyber-safety and protect children from inappropriate content across media platforms; retains the Classification Board as an independent classification decision maker with an essential role in setting benchmarks; promotes industry co-regulation, encouraging greater industry content classification, with government regulation more directly focused on content of higher community concern; provides for pragmatic regulatory oversight, to meet community expectations and safeguard community standards; reduces the overall regulatory burden on media content industries while ensuring that content obligations are focused on what Australians most expect to be classified; and harmonises classification laws across Australia, for the benefit of consumers and content providers.

The fishtown series

Fishtown is a series of mediated animated works which embody artistic conceptions of ambience and explore the interplay between foreground and background. The series draws upon a representation of natural patterns and rhythms in the ambient environment and is produced using a hybrid style of animation process that incorporates motion capture, dynamics and keyframe animation to construct a biomemtic peripheral rhythm. The display of the work is a crucial part of the project, and contributes a considerable amount to the reception of the work. Based on the ambient conceptions defined by Cage, Eno and Bizzocchi, ambient animation should incorporate some form of ambient display. As Eno (1978) states, it should be as ignorable as it is interesting. The ultimate intention is to place the work outside the gallery setting, to provide a more neutral ambient setting for the viewing of the work, and therefore the use of an ambient display is necessary if the work is to be situated in an ambient setting. Craig Walsh is a contemporary artist producing work for large scale projections in ambient settings. Completing Walsh's masterclass in 2011 (Tanawha Arts and Ecology Centre) has been an important factor in arriving at a strategy for the display of the Fishtown series. The most recent work in the Fishtown series was developed during a residency at the Crane Arts studios in Philadelphia USA in August 2012, and is comprised of a screen based animated work, utilizing large scale digital projection. Documentation of this work can be found at the Crane Arts Residency Website: http://cranearts.qcagriffith.com/crane-arts-residency-chris-denaro

Shift

Shift was an exhibition held in October 2008, and was the culmination of a 10 month artist in residence held at Metro Arts, Brisbane in 2008. A number of works were produced and exhibited, and were a response to the ambient urban landscape of inner city Brisbane. The research component contributes to the discussion of the form and display of digital animation, and builds upon strategies of presentation developed from series of works completed in 2005-2007 as part of an MA (research) at QUT, Brisbane. For the two week exhibition, one interactive kiosk and several large scale digital prints were produced, and also a site specific digital animation sequence was projected onto urban landscape features next to the gallery.

A Material Reverie

excerpt: from soil and stone is a work consisting of fifty drawings on paper organised in a grid. Each drawing is small, only 19 by 14 centimetres, and set out in portrait format. They each reference, either explicitly or abstractly, natural phenomena. These include plant forms, pollens, seeds, pods, and leaf shapes and each is painted with a dizzying and liquid array of techniques and technical finesse. Colour is used sparingly but tellingly, and all are generously and wetly composed, with each seeming to flow into the necessary rightness of composition. Within the overall work the feel is sometimes of the archive, a personal kind where pressed flowers are stumbled upon within a book. At other times they seem to image the stellar as one confronts the immensity of some planet suspended in the void. Again, as a recurring theme in Reynolds’ oeuvre, the notion of the taxonomy is sounded. The drawings are laid out to display difference and reveal through contrast essence. It is a mapping that illuminates a generous plentitude.

Were intercalated komatiites and dacites at the Black Swan nickel sulphide mine, Yilgarn Craton, Western Australia, emplaced as extrusive lavas or intrusive bodies? The significance of breccia textures and contact relationships

Intercalated Archean komatiites and dacites sit above a thick footwall dacite unit in the host rock succession at the Black Swan Nickel Mine, north of Kalgoorlie in the Yilgarn Craton, Western Australia. Both lithofacies occur in units that vary in scale from laterally extensive at the scale of the mine lease to localized, thin, irregular bodies, from > 100 m thick to only centimetres thick. Some dacites are only slightly altered and deformed, and are interpreted to post-date major deformation and alteration (late porphyries). However, the majority of the dacites display evidence of deformation, especially at contacts, and metamorphism, varying from silicification and chlorite alteration at contacts to pervasive low grade regional metamorphic alteration represented by common assemblages of chlorite, sericite and albite. Texturally, the dacites vary from entirely massive and coherent to partially brecciated to totally brecciated. Strangely, some dacites are coherent at the margins and brecciated internally. Breccia textures vary from cryptically defined, to blocky, closely packed, in situ jig-saw fit textures with secondary minerals in fractures between clasts, to more apparent matrix rich textures with round clast forms, giving apparent conglomerate textures. Some clast zones have multi-coloured clasts, giving the impression of varied provenance. Strangely however, all these textural variants have gradational relationships with each other, and no bedding or depositional structures are present. This indicates that all textures have an in situ origin. The komatiites are generally altered and pervasively carbonate veined. Preservation of original textures is patchy and local, but includes coarse adcumulate, mesocumulate, orthocumulate, crescumulate-harrisite and occasionally spinifex textures. Where original contacts between komatiites and dacites are preserved intact (i.e. not sheared or overprinted by alteration), the komatiites have chilled margins, whereas the dacites do not. The margins of the dacites are commonly silicified, and inclusions of dacite occur in komatiite, even at the top contacts of komatiite units, but komatiite clasts do not occur in the dacites. The komatiites therefore were emplaced as sills into the dacites, and the intercalated relationships are interpreted as intrusive. The brecciation and alteration in the dacites are interpreted as being largely due to hydraulic fracturing and alteration induced by contact metamorphic effects and hydrothermal alteration deriving from the intrusion of komatiites into the felsic pile. The absence of autobreccia and hyaloclastite textures in the dacites suggest that they were emplaced as an earlier intrusive (sill?) complex at a high level in the crust.

Starter packs : a good start to therapy?

Samples of drugs are often given to doctors by pharmaceutical representatives as part of a marketing strategy. Despite the well described advantages of drug samples, little has been published on the potential adverse outcomes. A series of consumer calls to the Adverse Medicine Events Line has highlighted concerns regarding the quality use of medicines associated with drug samples. The most commonly reported problems were drug samples being supplied to patients with inadequate information regarding dosage, administration, storage and possible adverse effects. In addition, some patients were given excessive quantities of a drug. To reduce such adverse outcomes, the drug industry, health professionals and consumers should be aware of the potential problems associated with starter packs.

Goodbye TAIS and thanks for all the information

The Therapeutic Advice and Information Service was funded by the National Prescribing Service to provide a national drug information service for health professionals working in the community. For ten years the service achieved high levels of client satisfaction, and reached its contracted target of 6000 enquiries about medicines per year, however the service ceased on 30 June 2010.

A coupled SPH/FEM analysis of portable water filled barriers

Portable water filled barriers (PWFB) are semi-rigid roadside barriers which have the potential to display good crash attenuation characteristics at low and moderate impact speeds. The traditional mesh based numerical methods alone fail to simulate this type of impact with precision, stability and efficiency. This paper proposes to develop an advanced simulation model based on the combination of Smoothed Particles Hydrodynamics (SPH), a meshless method, and finite element method (FEM) for fluid-structure analysis using the commercially available software package LS-Dyna. The interaction between SPH particles and FEA elements is studied in this paper. Two methods of element setup at the element boundary were investigated. The response of the impacted barrier and fluid inside were analysed and compared. The system response and lagging were observed and reported in this paper. It was demonstrated that coupled SPH/FEM can be used in full scale PWFB modelling application. This will aid the research in determining the best initial setup to couple FEA and SPH in road safety barrier for impact response and safety analysis in the future.

Ruthenium(II) dichloro or dithiocyanato complexes with 4,4′:2′,2″:4″,4‴-quaterpyridinium ligands : towards photosensitisers with enhanced low-energy absorption properties

Fourteen new complexes of the form cis-\[RuIIX2(R2qpy2+)2]4+ (R2qpy2+ = a 4,4′:2′,2″:4″,4‴-quaterpyridinium ligand, X = Cl− or NCS−) have been prepared and isolated as their PF6− salts. Characterisation involved various techniques including 1H NMR spectroscopy and +electrospray or MALDI mass spectrometry. The UV–Vis spectra display intense intraligand π → π∗ absorptions, and also metal-to-ligand charge-transfer (MLCT) bands with two resolved maxima in the visible region. Red-shifts in the MLCT bands occur as the electron-withdrawing strength of the pyridinium groups increases, while replacing Cl− with NCS− causes blue-shifts. Cyclic voltammograms show quasi-reversible or reversible RuIII/II oxidation waves, and several ligand-based reductions that are irreversible. The variations in the redox potentials correlate with changes in the MLCT energies. A single-crystal X-ray structure has been obtained for a protonated form of a proligand salt, \[(4-(CO2H)Ph)2qpyH3+]\[HSO4]3·3H2O. Time-dependent density functional theory calculations give adequate correlations with the experimental UV–Vis spectra for the two carboxylic acid-functionalised complexes in DMSO. Despite their attractive electronic absorption spectra, these dyes are relatively inefficient photosensitisers on electrodes coated with TiO2 or ZnO. These observations are attributed primarily to weak electronic coupling with the surfaces, since the DFT-derived LUMOs include no electron density near the carboxylic acid anchors.

Using ‘think aloud’ as a strategy for improving clinical reasoning in high fidelity case-based simulation for undergraduate nursing students.

Theme Paper for Curriculum innovation and enhancement theme AIM: This paper reports on a research project that trialled an educational strategy implemented in an undergraduate nursing curriculum. The project aimed to explore the effectiveness of ‘think aloud’ as a strategy for improving clinical reasoning for students in simulated clinical settings. BACKGROUND: Nurses are required to apply and utilise critical thinking skills to enable clinical reasoning and problem solving in the clinical setting (Lasater, 2007). Nursing students are expected to develop and display clinical reasoning skills in practice, but may struggle articulating reasons behind decisions about patient care. The ‘think aloud’ approach is an innovative learning/teaching method which can create an environment suitable for developing clinical reasoning skills in students (Banning, 2008, Lee and Ryan-Wenger, 1997). This project used the ‘think aloud’ strategy within a simulation context to provide a safe learning environment in which third year students were assisted to uncover cognitive approaches to assist in making effective patient care decisions, and improve their confidence, clinical reasoning and active critical reflection about their practice. MEHODS: In semester 2 2011 at QUT, third year nursing students undertook high fidelity simulation (some for the first time), commencing in September of 2011. There were two cohorts for strategy implementation (group 1= used think aloud as a strategy within the simulation, group 2= no specific strategy outside of nursing assessment frameworks used by all students) in relation to problem solving patient needs. The think aloud strategy was described to students in their pre-simulation briefing and allowed time for clarification of this strategy. All other aspects of the simulations remained the same, (resources, suggested nursing assessment frameworks, simulation session duration, size of simulation teams, preparatory materials). Ethics approval has been obtained for this project. RESULTS: Results of a qualitative analysis (in progress- will be completed by March 2012) of student and facilitator reports on students’ ability to meet the learning objectives of solving patient problems using clinical reasoning and experience with the ‘think aloud’ method will be presented. A comparison of clinical reasoning learning outcomes between the two groups will determine the effect on clinical reasoning for students responding to patient problems. CONCLUSIONS: In an environment of increasingly constrained clinical placement opportunities, exploration of alternate strategies to improve critical thinking skills and develop clinical reasoning and problem solving for nursing students is imperative in preparing nurses to respond to changing patient needs.