Read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molec- ular biology, allowing routine clinical sequencing. NGS data consists of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans, with some strains exhibiting antibiotic resistance. Here we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from other pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

"They did not believe me” Responding to child sexual abuse by Church personnel in Australia

Child sexual abuse (CSA) by Church personnel has been subject to study internationally. Such studies have often held a specific focus on the Roman Catholic Church in nations such as Ireland, Belgium and the United States of America (USA). This paper discusses the findings of a study conducted by the author which considers the perspectives of 81 survivors of child sexual abuse by Church personnel in Australia. Participants in this study completed an online survey and then nominated to undertake an in depth interview. The majority of respondents to the survey (66 - 69%) reported experiencing CSA in a Roman Catholic Church, school or children’s home. This paper explores the voices of survivors and recognises the complex and dynamic ways in which they continue to construct and manage their experiences of CSA by Church personnel. In particular, this study considers survivors’ perspectives of the ways in which Churches have responded to their informal disclosures and official complaints of CSA by Church personnel. Similarly to other locations across the world, participants in this study reported feeling re-victimised by Church processes. Participants reported high levels of dissatisfaction with Church policy and procedure in managing child protection issues, as well as high levels of dissatisfaction with the outcome of their complaints.

FRC erection stages dynamic behaviour under wind loads

Buffeting response of a cable-stayed bridge under construction is investigated through wind tunnel tests and numerical simulations. Two configurations of the erection stage have been considered and compared in terms of dynamic response and internal forces using the results of the experimental aeroelastic models. Moreover the results of a numerical model able to simulate the simultaneous effects of vortex shedding from tower and aeroelastic response of the deck are compared to the wind tunnel ones.

Long-term azithromycin for Indigenous children with non-cystic-fibrosis bronchiectasis or chronic suppurative lung disease (Bronchiectasis Intervention Study) : a multicentre, double-blind, randomised controlled trial

Background Indigenous children in high-income countries have a heavy burden of bronchiectasis unrelated to cystic fibrosis. We aimed to establish whether long-term azithromycin reduced pulmonary exacerbations in Indigenous children with non-cystic-fibrosis bronchiectasis or chronic suppurative lung disease. Methods Between Nov 12, 2008, and Dec 23, 2010, we enrolled Indigenous Australian, Maori, and Pacific Island children aged 1—8 years with either bronchiectasis or chronic suppurative lung disease into a multicentre, double-blind, randomised, parallel-group, placebo-controlled trial. Eligible children had had at least one pulmonary exacerbation in the previous 12 months. Children were randomised (1:1 ratio, by computer-generated sequence with permuted block design, stratified by study site and exacerbation frequency [1—2 vs ≥3 episodes in the preceding 12 months]) to receive either azithromycin (30 mg/kg) or placebo once a week for up to 24 months. Allocation concealment was achieved by double-sealed, opaque envelopes; participants, caregivers, and study personnel were masked to assignment until after data analysis. The primary outcome was exacerbation (respiratory episodes treated with antibiotics) rate. Analysis of the primary endpoint was by intention to treat. At enrolment and at their final clinic visits, children had deep nasal swabs collected, which we analysed for antibiotic-resistant bacteria. This study is registered with the Australian New Zealand Clinical Trials Registry; ACTRN12610000383066. Findings 45 children were assigned to azithromycin and 44 to placebo. The study was stopped early for feasibility reasons on Dec 31, 2011, thus children received the intervention for 12—24 months. The mean treatment duration was 20·7 months (SD 5·7), with a total of 902 child-months in the azithromycin group and 875 child-months in the placebo group. Compared with the placebo group, children receiving azithromycin had significantly lower exacerbation rates (incidence rate ratio 0·50; 95% CI 0·35—0·71; p<0·0001). However, children in the azithromycin group developed significantly higher carriage of azithromycin-resistant bacteria (19 of 41, 46%) than those receiving placebo (four of 37, 11%; p=0·002). The most common adverse events were non-pulmonary infections (71 of 112 events in the azithromycin group vs 132 of 209 events in the placebo group) and bronchiectasis-related events (episodes or investigations; 22 of 112 events in the azithromycin group vs 48 of 209 events in the placebo group); however, study drugs were well tolerated with no serious adverse events being attributed to the intervention. Interpretation Once-weekly azithromycin for up to 24 months decreased pulmonary exacerbations in Indigenous children with non-cystic-fibrosis bronchiectasis or chronic suppurative lung disease. However, this strategy was also accompanied by increased carriage of azithromycin-resistant bacteria, the clinical consequences of which are uncertain, and will need careful monitoring and further study.

Medieval knights amid the gum-trees : the experience of European heritage tourism in south-east Queensland, Australia

This paper is interested in the way in which the heritage of another place, time, and culture is repurposed for popular consumption in an experience economy, as well as the way in which the visitors experience their own past and the past of others. We trace the processes of engagement, education and nostalgia that occur when the European heritage is presented in a postcolonial context and an Australian environment. The information presented includes the results of qualitative and quantitative research conducted at the Abbey Museum over the December-Jan. period of 2012-13.

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).

The Australian Nonprofit Sector Legal and Accounting Almanac 2013

INTRODUCTION CASES For a number of years, Professor Myles McGregor-Lowndes, Frances Hannah and Anne Overell have compiled one to two page summaries of cases involving nonprofit organisations and published them on The Australian Centre for Philanthropy and Nonprofit Studies, Developing Your Organisation (DYO) website.1 You can be alerted of new case summaries as they are posted to the DYO website by subscribing to the ACPNS RSS feed or the ACPNS twitter service.2 There were some very significant cases during 2013, such as Commissioner of Taxation v Cancer & Bowel Research Association (see case notes 2.8.2 and 2.8.11), The Hunger Project case which is under appeal, but could change the face of PBI jurisprudence (see case note 2.8.7) while Home Health Pty Ltd retained the PBI status quo but might have been different if appealed (see case note 2.8.8). For sheer interest there is nothing better in my 30 odd years of reading tax and charity judgements than case involving The Study and Prevention of Psychological Diseases Foundation Incorporated (see case note 2.1.1). It even rivals some of the more bizarre cases from the US jurisdiction of which St Joseph Abbey v Castille (case note 2.10.9) is certainly ‘dead centre’. A set of cases which stand out for attention are those involving New Zealand’s Christchurch Cathedral which anyone with responsibility for heritage-listed buildings should study carefully, for implications in relation to their own circumstances. A number of cases summarised in this Almanac are working their way through the appeals process and care should be taken with their application. In addition, some of the cases are from jurisdictions outside Australia, and readers should exercise caution when considering the implications of these cases for Australian law. LEGISLATION The Almanac includes a review of major statutory amendments during 2013, which are relevant to the nonprofit sector in all Australian jurisdictions. Special thanks must go to Nathan MacDonald and the JusticeConnect team for providing legislative updates for Victoria. SPECIAL ISSUES DURING 2013 A number of legal practitioners have contributed articles on significant legal issues facing nonprofit organisations: charitable trusts giving to government entities (Alice Macdougall); workplace bullying (Tim Longwill); and privacy (James Tan and Nina Brewer). WORLD ROUND-UP Major developments from the UK and Ireland (Kerry O’Halloran), Canada (Peter Broder), New Zealand (Michael Gousmett and Susan Barker) and Jamaica (Frances Hannah) are all summarised in a review of a significant part of the common law charity jurisdictions. WHAT DOES 2014 HOLD The final section moves from looking in the rear view mirror to peering out the front windscreen to discern the reform agenda. The view from the windscreen in 2013 was of considerable reform traffic at the Commonwealth level jostling for a place in the parliamentary agenda. This year is quite different with a smaller number of vehicles ahead, but the potential for significant impact.

Part 1 MOO methods for multidisciplinary design using parallel evolutionary algorithms, game theory and hierarchical topology. (Part 1.) Theoretical aspects

Two lecture notes describe recent developments of evolutionary multi objective optimization (MO) techniques in detail and their advantages and drawbacks compared to traditional deterministic optimisers. The role of Game Strategies (GS), such as Pareto, Nash or Stackelberg games as companions or pre-conditioners of Multi objective Optimizers is presented and discussed on simple mathematical functions in Part I , as well as their implementations on simple aeronautical model optimisation problems on the computer using a friendly design framework in Part II. Real life (robust) design applications dealing with UAVs systems or Civil Aircraft and using the EAs and Game Strategies combined material of Part I & Part II are solved and discussed in Part III providing the designer new compromised solutions useful to digital aircraft design and manufacturing. Many details related to Lectures notes Part I, Part II and Part III can be found by the reader in [68].

Analysis of simplified variants of SHA-256

In this paper we analyse the role of some of the building blocks of SHA-256. We show that the disturbance-correction strategy is applicable to the SHA-256 architecture and we prove that functions Σ, σ are vital for the security of SHA-256 by showing that for a variant without them it is possible to find collisions with complexity 2^64 hash operations. As a step towards an analysis of the full function, we present the results of our experiments on Hamming weights of expanded messages for different variants of the message expansion and show that there exist low-weight expanded messages for XOR-linearised variants.

SCRAMSPACE : Radical-Farming Scramjet for access to space

Scramjet-based launch systems offer considerable promise for safe, reliable and economical access to space. A general Scramjets introduction is first provided, followed by the specifics of Australian Scramjet Research and the recent progress in inlet-injection radical-farming scramjets as part of the SCRAMSPACE program. Through both flight and ground tests, leveraging Australias world leadership in scramjet R&D, the SCRAMSPACE project is designed to answer key scientific and technological questions and build an industry-ready talent pool for a future Australian space industry. An extensive descriptions of all phases of the development of the SCRAMSPACE I scramjet-powered free-flight experiment are described in these lecture notes.

Part 2. MOO methods for multidisciplinary design using parallel evolutionary algorithms, game theory and hierarchical topology. (Part 2.) Numerical aspects and implementation of model test cases

These lecture notes describe the use and implementation of a framework in which mathematical as well as engineering optimisation problems can be analysed. The foundations of the framework and algorithms described -Hierarchical Asynchronous Parallel Evolutionary Algorithms (HAPEAs) - lie upon traditional evolution strategies and incorporate the concepts of a multi-objective optimisation, hierarchical topology, asynchronous evaluation of candidate solutions , parallel computing and game strategies. In a step by step approach, the numerical implementation of EAs and HAPEAs for solving multi criteria optimisation problems is conducted providing the reader with the knowledge to reproduce these hand on training in his – her- academic or industrial environment.

Part 3. MOO methods for multidisciplinary design using parallel evolutionary algorithms, game theory and hierarchical topology. (Part 3.) Practical application to the design and optimisation of UAV systems

These lecture notes highlight some of the recent applications of multi-objective and multidisciplinary design optimisation in aeronautical design using the framework and methodology described in References 8, 23, 24 and in Part 1 and 2 of the notes. A summary of the methodology is described and the treatment of uncertainties in flight conditions parameters by the HAPEAs software and game strategies is introduced. Several test cases dealing with detailed design and computed with the software are presented and results discussed in section 4 of these notes.

Telomerase activity : detection and clinical implications in human cancer

Telomerase is an extremely important enzyme required for the immortalisation of tumour cells. Because the gene is activated in the vast majority of tumour tissues and remains unused in most somatic cells, it represents a marker with huge diagnostic, prognostic and treatment implications in cancer. This article summarises the basic structure and functions of telomerase and considers its clinical implications in colorectal and other cancers.

The effect of ß-alanine on buffering capacity and exercise performance during and following high-intensity exercise in healthy males

Introduction Intense exercise induced acidosis occurs from the accumulation of hydrogen ions as by-products of anaerobic metabolism. Oral ingestion of ß-alanine, a limiting precursor of the intracellular physiochemical buffer carnosine in skeletal muscle, may counteract any detrimental effect of acidosis and benefit performance. The aim of this study was to investigate the effect of ß-alanine as an ergogenic aid during high intensity exercise performance in healthy males. Methods Five males ingested either ß-alanine (BAl) (4.8 g.d-1 for 4wk, then 6.4 g.d-1 for 2wk) or placebo (Pl) (CaCO3) in a crossover design with 6 wk washout between. Following supplementation, participants performed two different intense exercise protocols over consecutive days. On the first day a repeated sprint ability (RSA) test of 5 x 6s, with 24s rest periods, was performed. On the second day a cycling capacity test measuring the time to exhaustion (TTE) was performed at 110% of their max workload achieved in a pre supplementation max test (CCT110%). Non-invasive quantification of carnosine, prior to, and following each supplementation, with magnetic resonance spectrometry was performed in the soleus and gastrocnemius. Time to fatigue (CCT110%), peak and mean power (RSA), blood pH, and plasma lactate were measured. Results Muscle carnosine concentration was not different prior to ß-alanine supplementation and increased 18% in the soleus and 26% in the gastrocnemius, respectively with 6 wk supplementation. There was no difference in the measured performance variables during the RSA test (peak and average power output). TTE during the CCT110% was significantly enhanced following the ingestion of BAl (155s ± 19.03) compared to Pl (134s ± 26.16). No changes were observed in blood pH during either exercise protocol and during the recovery from exercise. Plasma lactate in the BAl condition was significantly higher than Pl only from the 15th minute following exercise during the CCT110%. FIG. 1: Changes in carnosine concentration in the gastrocnemius prior and post 6 week chronic supplementation of placebo and β-alanine. Values expressed as mean.* p<0.05 from Pl at 6 weeks, # p<0.05 from pre supplementation. Conclusion/Discussion Greater muscle carnosine content following 6wk supplementation of ß-alanine enhanced the potential for intracellular buffering capacity. However, this only translated into enhanced performance during the CCT110% high intensity cycling exercise protocol, with no change observed during the RSA test. No differences in post exercise and recovery plasma lactates and blood pH, indicates that 6wks ß-alanine supplementation has no effect on anaerobic metabolism during multiple bout high intensity exercise. Changes in plasma lactate during recovery supports that ß-alanine supplementation may affect anaerobic metabolism however during single bout high intensity.

An evidence-based program to improve analgesic practice and pain outcomes in residential aged care facilities

Pain is common in individuals living in residential aged care facilities (RACFs), and a number of obstacles have been identified as recurring barriers to adequate pain management. To address this, the Australian Pain Society developed 27 recommendations for comprehensive good practice in the identification, assessment, and management of pain. This study reviewed preexisting pain management practice at five Australian RACFs and identified changes needed to implement the recommendations and then implemented an evidence-based program that aimed to facilitate better pain management. The program involved staff training and education and revised in-house pain-management procedures. Reviews occurred before and after the program and included the assessment of 282 residents for analgesic use and pain status. Analgesic use improved after the program (P<.001), with a decrease in residents receiving no analgesics (from 15% to 6%) and an increase in residents receiving around-the-clock plus as-needed analgesics (from 24% to 43%). There were improvements in pain relief for residents with scores indicative of pain, with Abbey pain scale (P=.005), Pain Assessment in Advanced Dementia Scale (P=.001), and Non-communicative Patient's Pain Assessment Instrument scale (P<.001) scores all improving. Although physical function declined as expected, Medical Outcomes Study 36-item Short-Form Survey bodily pain scores also showed improvement (P=.001). Better evidence-based practice and outcomes in RACFs can be achieved with appropriate training and education. Investing resources in the aged care workforce using this program improved analgesic practice and pain relief in participating sites. Further attention to the continued targeted pain management training of aged care staff is likely to improve pain-focused care for residents.