Tandem B1 SINE retro-elements may provide a basis for natural antisense transcription in the Magi1 locus of the mouse (Mus musculus)

Transposable elements, which are DNA sequences that can move between different sites in genomes, comprise approximately 40% of the genome of mammals and are emerging as important contributors to biological diversity. Here we report a transcription unit lying within intron 1 of the murine Magi1 (membrane associated guanylate kinase inverted 1) gene that codes for a cell-cell junction scaffolding protein. The transcription unit, termed Magi1OS (Magi1 Opposite Strand), originates from a region with tandem B1 short interspersed nuclear elements (SINEs) and is an antisense gene to Magi1. Mag1OS transcription initiates in a proximal B1 element that shows only 4% divergence from the consensus sequence, indicating that it has been recently inserted into the mouse genome and could be replication competent. Moreover, a chimaeric transcript may result from intra-chromosomal interaction and trans-splicing of the Magi1 antisense transcript (Magi1OS) and Ghrl, which codes for the multifunctional peptide hormone ghrelin. These two genes are 20 megabases apart on chromosome 6 and are transcribed in opposite directions. We propose that the Magi1OS locus may serve as a useful model system to study exaptation and retrotransposition of B1 SINEs, as well as to examine the mechanisms of intra-chromosomal trans-splicing.

Evaluating NEXUS: A suicide prevention program for young people from refugee backgrounds (2007 – 2009)

Although suicide deaths in Australia continue to decline since the peak of 2,720 suicide deaths in 1997, youth suicide and self-harm are a major health issue. In 2006, in the 20 to 24 year age group, suicide accounted for approximately 21% of all male deaths and 14% of all female deaths. There is a lack of solid data on the rates of suicide and self-harm among young people from refugee backgrounds. However, this population faces a significant number of post-resettlement stressors that may add to their vulnerability and increase their risk of suicide and self-harm. The NEXUS program is an innovative strategy developed by the Queensland Program of Assistance to Survivors of Torture and Trauma (QPASTT) that aims to reduce risk factors for suicide and self-harm and to promote protective factors among youth from refugee backgrounds living in Brisbane and Toowoomba. QPASTT is a non-government organisation that provides culturally appropriate support services to refugee and humanitarian entrants to Australia. QPASTT’s primary function is to provide counselling, advocacy support and community development activities for survivors of torture and trauma at an individual, family and community level. Since 2002 the NEXUS program has been developed and implemented by QPASTT. Since then, this multi-component program has been funded by the Commonwealth Department of Health and Ageing through the National Suicide Prevention Strategy (NSPS). NSPS funding of local community suicide prevention activities will contribute to the outcomes specified in the strategic framework: Living is for Everyone (LIFE): A framework for prevention of suicide and self-harm in Australia. The focus of this report is the evaluation of the NEXUS program conducted by QPASTT between August 2007 and May 2009.

Educational programmes for primary prevention of skin cancer (Protocol)

This is the protocol for a review and there is no abstract. The objectives are as follows: To assess the effects of education programmes for skin cancer prevention in the general population. Description of the condition Skin cancer is a term that includes both melanoma and keratinocyte cancer. Keratinocyte cancer (also known as nonmelanoma skin cancer) generally refers to basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), although it also includes other rare cutaneous neoplasms (Madan 2010). Skin cancer is the most common cancer in populations of predominantly fair-skinned people (Donaldson 2011; Lomas 2012; Stern 2010), with incidence increasing (Garbe 2009; Leiter 2012). There are variations in annual incidence rates between these populations, with Australia reporting the highest rate of skin cancer in the world (Lomas 2012). In 2012, the estimated age-standardised incidence rate for melanoma was almost 63 per 100,000 people for Australian men, and 40 per 100,000 people for Australian women (AIHW 2012). In Europe, incidence rates range from 10 to 15 per 100,000 people (Garbe 2009; Lasithiotakis 2006), with rates highest amongst men (Stang 2006). In the United States, incidence rates are approximately 18 per 100,000 people (Garbe 2009),with the highest rates reported forwomen (Bradford 2010). Keratinocyte cancer is much more common than melanoma. In 2012, the estimated Australian age-standardised rates for BCCand SCC were 884 and 387 per 100,000 people, respectively (Staples 2006). The cumulative three-year risk of developing a subsequent keratinocyte cancer is 18% for SCC and 44% for BCC (Marcil 2000).

Can ginger ameliorate chemotherapy-induced nausea? Protocol of a randomized double blind, placebo-controlled trial

Background Preliminary research shows ginger may be an effective adjuvant treatment for chemotherapy-induced nausea and vomiting but significant limitations need to be addressed before recommendations for clinical practice can be made. Methods/Design In a double–blinded randomised-controlled trial, chemotherapy-naïve patients will be randomly allocated to receive either 1.2 g of a standardised ginger extract or placebo per day. The study medication will be administrated as an adjuvant treatment to standard anti-emetic therapy and will be divided into four capsules per day, to be consumed approximately every 4 hours (300 mg per capsule administered q.i.d) for five days during the first three cycles of chemotherapy. Acute, delayed, and anticipatory symptoms of nausea and vomiting will be assessed over this time frame using a valid and reliable questionnaire, with nausea symptoms being the primary outcome. Quality of life, nutritional status, adverse effects, patient adherence, cancer-related fatigue, and CINV-specific prognostic factors will also be assessed. Discussion Previous trials in this area have noted limitations. These include the inconsistent use of standardized ginger formulations and valid questionnaires, lack of control for anticipatory nausea and prognostic factors that may influence individual CINV response, and the use of suboptimal dosing regimens. This trial is the first to address these issues by incorporating multiple unique additions to the study design including controlling for CINV-specific prognostic factors by recruiting only chemotherapy-naïve patients, implementing a dosing schedule consistent with the pharmacokinetics of oral ginger supplements, and independently analysing ginger supplements before and after recruitment to ensure potency. Our trial will also be the first to assess the effect of ginger supplementation on cancer-related fatigue and nutritional status. Chemotherapy-induced nausea and vomiting are distressing symptoms experienced by oncology patients; this trial will address the significant limitations within the current literature and in doing so, will investigate the effect of ginger supplementation as an adjuvant treatment in modulating nausea and vomiting symptoms. Trial registration

A simple method for EPID-based in vivo dosimetry for radiotherapy treatments of head-and-neck cancers

This study used a homogeneous water-equivalent model of an electronic portal imaging device (EPID), contoured as a structure in a radiotherapy treatment plan, to produce reference dose images for comparison with in vivo EPID dosimetry images. Head and neck treatments were chosen as the focus of this study, due to the heterogeneous anatomies involved and the consequent difficulty of rapidly obtaining reliable reference dose images by other means. A phantom approximating the size and heterogeneity of a typical neck, with a maximum radiological thickness of 8.5 cm, was constructed for use in this study. This phantom was CT scanned and a simple treatment including five square test fields and one off-axis IMRT field was planned. In order to allow the treatment planning system to calculate dose in a model EPID positioned a distance downstream from the phantom to achieve a source-to-detector distance (SDD) of 150 cm, the CT images were padded with air and the phantom’s “body” contour was extended to encompass the EPID contour. Comparison of dose images obtained from treatment planning calculations and experimental irradiations showed good agreement, with more than 90% of points in all fields passing a gamma evaluation, at γ (3%, 3mm )Similar agreement was achieved when the phantom was over-written with air in the treatment plan and removed from the experimental beam, suggesting that water EPID model at 150 cm SDD is capable of providing accurate reference images for comparison with clinical IMRT treatment images, for patient anatomies with radiological thicknesses ranging from 0 up to approximately 9 cm. This methodology therefore has the potential to be used for in vivo dosimetry during treatments to tissues in the neck as well as the oral and nasal cavities, in the head-and-neck region.

Fatty acid uptake and incorporation into phospholipids in the rat lens

PURPOSE. Phospholipids are a major component of lens fiber cells and influence the activity of membrane proteins. Previous investigations of fatty acid uptake by the lens are limited. The purpose of the present study was thus to determine whether exogenous fatty acids could be taken up by the rat lens and incorporated into molecular phospholipids. METHODS. Lenses were incubated with fluorescently labeled palmitic acid and then analyzed by confocal microscopy. Concurrently, lenses incubated with either fluorescently labeled palmitic acid or the more physiologically relevant (13)C(18)-oleic acid were sectioned into nuclear and cortical regions and analyzed by highly sensitive and structurally selective electrospray ionization tandem mass spectrometry techniques. RESULTS. The detection of fluorescently labeled palmitic acid, even after 16 hours of incubation, was limited to approximately the outer 25% to 30% of the rat lens. Mass spectrometry also revealed the presence of free (13)C(18)-oleic acid in the cortex but not the nucleus. No evidence could be found for incorporation of fluorescently labeled palmitic acid into phospholipids; however, a low level of (13)C(18)-oleic acid incorporation into phosphatidylethanolamine (PE), specifically PE (PE 16:0/(13)C(18) 18:1) was detected in the lens cortex after 16 hours. CONCLUSIONS. These data demonstrate that uptake of exogenous (e.g., dietary fatty acids) by the lens and their incorporation into phospholipids is minimal, most likely occurring only during de novo synthesis in the outermost region of the lens. This finding adds support to the hypothesis that once synthesized there is no active remodeling or turnover of fiber cell phospholipids.

H2-O2 porous fuel injection in a radical farming scramjet

This paper reports on the experimental testing of oxygen compatible ceramic matrix composite porous injectors in a nominally two-dimensional hydrogen fuelled and oxygen enriched radical farming scramjet in the T4 shock tunnel facility. All experiments were performed at a dynamic pressure of 146 kPa, an equivalent flight Mach number of 9.7, a stagnation pressure and enthalpy of 40MPa and 4.3 MJ/kg respectively and at a fuelling condition that resulted in an average equivalence ratio of 0.472. Oxygen was pre-mixed with the fuel prior to injection to achieve enrichment percentages of approximately 13%, 15% and 17%. These levels ensured that the hydrogen-oxidiser mix injected into the engine always remained too fuel rich to sustain a flame without any additional mixing with the captured air. Addition of pre-mixed oxygen with the fuel was found to significantly alter the performance of the engine; enhancing both combustion and ignition and converting a previously observed limited combustion condition into one with sustained and noticeable combustion induced pressure rise. Increases in the enrichment percentage lead to further increases in combustion levels and acted to reduce ignition lengths within the engine. Suppressed combustion runs, where a nitrogen test gas was used, confirmed that the pressure rise observed in these experiments as attributed to the oxygen enrichment and not associated with the increased mass injected.

Radiative and total heat transfer measurements to a Titan Explorer model

Radiative and total heat transfer at the flow stagnation point of a 1:40.8 binary scaled model of the Titan Explorer vehicle were measured in the X3 expansion tube. Results from the current study illustrated that with the addition of CH4 into a N2 test gas radiative heat transfer could be detected. For a test gas of 5% CH4 and 95% N2, simulating an atmospheric model for Titanic aerocapture, approximately 4% of the experimentally measured total stagnation point heat transfer was found to be due to radiation. This was in comparison to < 1% measured for a test gas of pure nitrogen. When scaled to the flight vehicle, experimental results indicate a 64% contribution of radiation (test gas 5% CH4/95% N2). Previous numerical results however have predicted this contribution to be between 80-92%. Thus, experimental results from the current study suggest that numerical analyses are over-predicting the radiative heat transfer on the flight vehicle.

Heat transfer measurements on the first experimental layer of the FIRE II reentry vehicle in expansion tubes

The present study focused on simulating a trajectory point towards the end of the first experimental heatshield of the FIRE II vehicle, at a total flight time of 1639.53s. Scale replicas were sized according to binary scaling and instrumented with thermocouples for testing in the X1 expansion tube, located at The University of Queensland. Correlation of flight to experimental data was achieved through the separation, and independent treatment of the heat modes. Preliminary investigation indicates that the absolute value of radiant surface flux is conserved between two binary scaled models, whereas convective heat transfer increases with the length scale. This difference in the scaling techniques result in the overall contribution of radiative heat transfer diminishing to less than 1% in expansion tubes from a flight value of approximately 9-17%. From empirical correlation's it has been shown that the St √Re number decreases, under special circumstances, in expansion tubes by the percentage radiation present on the flight vehicle. Results obtained in this study give a strong indication that the relative radiative heat transfer contribution in the expansion tube tests is less than that in flight, supporting the analysis that the absolute value remains constant with binary scaling.

Residual stresses in rail-ends from the in-service insulated rail joints using neutron diffraction

Insulated rail joints (IRJs) are an integral part of the rail track signaling system and pose significant maintenance and replacement costs due to their low and fluctuating service lives. Failure occurs mainly in rail head region, bolt- holes of fishplates and web-holes of the rails. Propagation of cracks is influenced by the evolution of internal residual stresses in rails during rail manufacturing (hot-rolling, roller-straightening, and head-hardening process), and during service, particularly in heavy rail haul freight systems where loads are high. In this investigation, rail head accumulated residual stresses were analysed using neutron diffraction at the Australian Nuclear Science and Technology Organisation (ANSTO). Two ex-service two head-hardened rail joints damaged under different loading were examined and results were compared with those obtained from an unused rail joint reference sample in order to differentiate the stresses developed during rail manufacturing and stresses accumulated during rail service. Neutron diffraction analyses were carried out on the samples in longitudinal, transverse and vertical directions, and on 5mm thick sliceed samples cut by Electric Discharge Machining (EDM). For the rail joints from the service line, irrespective of loading conditions and in-service times, results revealed similar depth profiles of stress distribution. Evolution of residual stress fields in rails due to service was also accompanied by evidence of larger material flow based on reflected light and scanning electron microscopy studies. Stress evolution in the vicinity of rail ends was characterised by a compressive layer, approximately 5 mm deep, and a tension zone located approximately 5- 15mm below the surfaces. A significant variation of d0 with depth near the top surface was detected and was attributed to decarburization in the top layer induced by cold work. Stress distributions observed in longitudinal slices of the two different deformed rail samples were found to be similar. For the undeformed rail, the stress distributions obtained could be attributed to variations associated with thermo-mechanical history of the rail.

Design Minds Refresh Toolkit

The Design Minds Refresh Toolkit was one of six K7-12 secondary school design toolkits commissioned by the State Library of Queensland (SLQ) Asia Pacific Design Library (APDL), to facilitate the delivery of the Stage 1 launch of its Design Minds online platform (www.designminds.org.au) partnership initiative with Queensland Government Arts Queensland and the Smithsonian Cooper-Hewitt National Design Museum, on June 29, 2012. Design Minds toolkits are practical guides, underpinned by a combination of one to three of the Design Minds model phases of ‘Inquire’, ‘Ideate’ and ‘Implement’ (supported by at each stage with structured reflection), to enhance existing school curriculum and empower students with real life design exercises, within the classroom environment. Toolkits directly identify links to Naplan, National Curriculum, C2C and Professional Standards benchmarks, as well as the student capabilities of successful and creative 21st century citizens they seek to engender through design thinking. Inspired by ideas from a design project for second year Interior Design students at QUT School of Design, this toolkit explores, through five distinct exercises, different design tools and ways to approach the future design of environments (bathrooms) to facilitate the daily washing ritual, while addressing diverse and changing social, cultural, technological and environmental challenges. The Design Minds Refresh Toolkit particularly aims to promote ‘Lateral Thinking’ attitudes and empathy as an approach to create unusual and sustainable solutions to future problems that may affect our daily behavioural routines, and the spaces that facilitate them. More generally, it aims to facilitate awareness in young people, of the role of design in society and the value of design thinking skills in generating strategies to solve basic to complex systemic challenges, as well as to inspire post-secondary pathways and idea generation for education. The toolkit encourages students and teachers to develop sketching, making, communication, presentation and collaboration skills to improve their design process, as well as explore further inquiry (background research) to enhance the ideation exercises. Exercise 1 focuses on the ‘Inquire’ and ‘Ideate’ phases, Exercise 2 and 3 build on ideation skills, and Exercise 4 and 5 concentrate on the ‘Implement’ phase. Depending on the intensity of the focus, the unit of work could be developed over a 4-5 week program (approximately 10-12 x 60 minute lessons/workshops) or as smaller workshops treated as discrete learning experiences. The toolkit is available for public download from http://designminds.org.au/refresh/ on the Design Minds website. Exercise 2 (Other People’s Shoes) and Exercise 3 (The Future Bathroom) of the toolkit were used as content for the inaugural Design Minds Professional Development Workshop on June 28, 2012 to pre-launch the website to Queensland teachers.

Design Minds The Big Picture Toolkit

The Design Minds The Big Picture Toolkit was one of six K7-12 secondary school design toolkits commissioned by the State Library of Queensland (SLQ) Asia Pacific Design Library (APDL), to facilitate the delivery of the Stage 1 launch of its Design Minds online platform (www.designminds.org.au) partnership initiative with Queensland Government Arts Queensland and the Smithsonian Cooper-Hewitt National Design Museum, on June 29, 2012. Design Minds toolkits are practical guides, underpinned by a combination of one to three of the Design Minds model phases of ‘Inquire’, ‘Ideate’ and ‘Implement’ (supported by at each stage with structured reflection), to enhance existing school curriculum and empower students with real life design exercises, within the classroom environment. Toolkits directly identify links to Naplan, National Curriculum, C2C and Professional Standards benchmarks, as well as the student capabilities of successful and creative 21st century citizens they seek to engender through design thinking. Inspired by the Unlimited: Designing for the Asia Pacific Generation Workshop 2010 (http://eprints.qut.edu.au/47762/), this toolkit explores, through three distinct exercises, ‘design for the other 90%’, addressing tools and approaches to diverse and changing social, cultural, technological and environmental challenges. The Design Minds The Big Picture Toolkit challenges students to be active agents for change and to think creatively and optimistically about solutions to future global issues that deliver social, economic and environmental benefits. More generally, it aims to facilitate awareness in young people, of the role of design in society and the value of design thinking skills in generating strategies to solve basic to complex systemic challenges, as well as to inspire post-secondary pathways and idea generation for education. The toolkit encourages students and teachers to develop sketching, making, communication, presentation and collaboration skills to improve their design process, as well as explore further inquiry (background research) to enhance the ideation exercises. Exercise 1 focuses on the ‘Inquire’ phase, Exercise 2 the ‘Inquire’ and ‘Ideate’ phases, and Exercise 3 concentrates on the ‘Implement’ phase. Depending on the intensity of the focus, the unit of work could be developed over a 4-5 week program (approximately 4-6 x 60 minute lessons/workshops) or as smaller workshops treated as discrete learning experiences. The toolkit is available for public download from http://designminds.org.au/the-big-picture/ on the Design Minds website.

Design Minds Tomorrow's Classroom Toolkit

The Design Minds Tomorrow’s Classroom Toolkit was one of six K7-12 secondary school design toolkits commissioned by the State Library of Queensland (SLQ) Asia Pacific Design Library (APDL), to facilitate the delivery of the Stage 1 launch of its Design Minds online platform (www.designminds.org.au) partnership initiative with Queensland Government Arts Queensland and the Smithsonian Cooper-Hewitt National Design Museum, on June 29, 2012. Design Minds toolkits are practical guides, underpinned by a combination of one to three of the Design Minds model phases of ‘Inquire’, ‘Ideate’ and ‘Implement’ (supported by at each stage with structured reflection), to enhance existing school curriculum and empower students with real life design exercises, within the classroom environment. Toolkits directly identify links to Naplan, National Curriculum, C2C and Professional Standards benchmarks, as well as the student capabilities of successful and creative 21st century citizens they seek to engender through design thinking. This toolkit explores, through four distinct exercises, different design tools and ways to approach the future design of environments (classrooms/schools) to facilitate the Reggio Emilia philosophy of learning, while addressing diverse and changing social, cultural, technological and environmental challenges. The Design Minds Tomorrow’s Classroom Toolkit encourages students to explore architecture and interior design, and to think about their (life-long) learning as a product of inspiring interactions with people and the environments around them, and that their potential role in contributing to both delightful and functional design solutions requires a deep understanding of the user experience. More generally, it aims to facilitate awareness in young people, of the role of design in society and the value of design thinking skills in generating strategies to solve basic to complex systemic challenges, as well as to inspire post-secondary pathways and idea generation for education. The toolkit encourages students and teachers to develop sketching, making, communication, presentation and collaboration skills to improve their design process, as well as explore further inquiry (background research) to enhance the ideation exercises. Exercise 1 focuses on the ‘Inquire’ and ‘Ideate’ phases, Exercise 2 on the ‘Inquire’, Exercise 3 builds on ideation skills, and Exercise 4 concentrates on the ‘Implement’ phase. Depending on the intensity of the focus, the unit of work could be developed over a 2-5 week program (approximately 4-10 x 60 minute lessons/workshops) or as smaller workshops treated as discrete learning experiences. The toolkit is available for public download from http://designminds.org.au/tomorrows-classroom/ on the Design Minds website. This toolkit inspired the authorship and facilitation of a 2-day design workshop entitled Learning Environment 2050 at John Paul College, Daisy Hill, Brisbane on the 15-16 August 2013. 120 Grade 7 students and their teachers, under the mentorship of two design academics, 3 QUT design students and a professional architect, as part of a QUT School of Design Project Week community engagement activity, explored the formulation of a participatory design brief for the redesign of the school’s Wesley Precinct (including classrooms, a sustainable farm and recreation areas).

Instability of the cellular lipidome with age

The human lens nucleus is formed in utero, and from birth onwards, there appears to be no significant turnover of intracellular proteins or membrane components. Since, in adults, this region also lacks active enzymes, it offers the opportunity to examine the intrinsic stability of macromolecules under physiological conditions. Fifty seven human lenses, ranging in age from 12 to 82 years, were dissected into nucleus and cortex, and the nuclear lipids analyzed by electrospray ionization tandem mass spectrometry. In the first four decades of life, glycerophospholipids (with the exception of lysophosphatidylethanolamines) declined rapidly, such that by age 40, their content became negligible. In contrast the level of ceramides and dihydroceramides, which were undetectable prior to age 30, increased approximately 100-fold. The concentration of sphingomyelins and dihydrosphingomyelins remained unchanged over the whole life span. As a consequence of this marked alteration in composition, the properties of fiber cell membranes in the centre of young lenses are likely to be very different from those in older lenses. Interestingly, the identification of age 40 years as a time of transition in the lipid composition of the nucleus coincides with previously reported macroscopic changes in lens properties (e.g., a massive age-related increase in lens stiffness) and related pathologies such as presbyopia. The underlying reasons for the dramatic change in the lipid profile of the human lens with age are not known, but are most likely linked to the stability of some membrane lipids in a physiological environment.

A molecular phylogeny of the checkered beetles and a description of Epiclininae a new subfamily (Coleoptera: Cleroidea: Cleridae)

We provide the first molecular phylogeny of the clerid lineage (Coleoptera: Cleridae, Thanerocleridae) within the superfamily Cleroidea to examine the two most recently-proposed hypotheses of higher-level classification. Phylogenetic relationships of checkered beetles were inferred from approximately ~5,000nt of both nuclear and mitochondrial rDNA (28S, 16S, and 12S) and the mitochondrial protein-coding gene COI. A worldwide sample of ~70 genera representing almost a quarter of generic diversity of the clerid lineage was included and phylogenies were reconstructed using Bayesian and Maximum Likelihood approaches. Results support the monophyly of many proposed subfamilies but were not entirely congruent with either current classification system. The subfamilial relationships within the Cleridae are resolved with support for three main lineages. Tillinae are supported as the sister group to all other subfamilies within the Cleridae, whereas Thaneroclerinae, Korynetinae and a new subfamily formally described here, Epiclininae subf. n, form a sister group to Clerinae + Hydnocerinae.