Automated categorisation of patent claims that reference human genome sequences

Debates on gene patents have necessitated the analysis of patents that disclose and reference human sequences. In this study, we built an automated classifier that assigns sequences to one of nine predefined categories according to their functional roles in patent claims by applying natural language processing and supervised learning techniques. To improve its correctness, we experimented with various feature mappings, resulting in the maximal accuracy of 79%.

Performance enhancement: A whole of person approach to first year dance students’ transition into tertiary training

The transition into university presents very particular challenges for students. The First Year Experience (FYE) is a transitional liminal phase, fraught with uncertainty, ripe with potential. The complexity inherent in this initial phase of tertiary education is well documented and continues to be interrogated. Providing timely and effective support and interventions for potentially at-risk first year students as they transition into tertiary study is a key priority for universities across the globe (Gale et al., 2015). This article outlines the evolution of an established and highly successful Transitional Training Program (TTP) for first year tertiary dance students, with particular reference to the 2015 iteration of the program. TTP design embraces three dimensions: physical training in transition, learning in transition, and teaching for transition, with an emphasis on developing and encouraging a mindset that enables information to be transferred into alternative settings for practice and learning throughout life. The aim of the 2015 TTP was to drive substantial change in first year Dance students’ satisfaction, connectedness, and overall performance within the Bachelor of Fine Arts (BFA) Dance course, through the development and delivery of innovative curriculum and pedagogical practices that promote the successful transition of dance students into their first year of university. The program targeted first year BFA Dance students through the integration of specific career guidance; performance psychology; academic skills support; practical dance skills support; and specialized curricula and pedagogy.

MicroRNA regulation of epithelial-to-mesenchymal transition during re-epithelialisation: Assessing an open wound

It is becoming increasing clear that microRNAs contribute to the regulation of many biological processes, including wound healing. After injury, keratinocytes need to undergo what is known as an epithelial-to-mesenchymal transition (EMT) to initiate re-epithelialisation. During this process, keratinocytes reduce their attachment to the underlying matrix, extend membrane protrusions, become motile and migrate over the wound bed, affecting wound closure. MicroRNAs that regulate EMT are aberrantly upregulated in keratinocytes at the edge of non-healing wounds and potentially play a role in the chronicity of these wounds. In vitro and in vivo, downregulation of these microRNAs promotes EMT and migration, facilitating re-epithelialisation in wound models. This review will focus on the role of microRNAs that regulate or have potential to regulate EMT and re-epithelialisation during wound healing

Mapping the regulatory sequences controlling 93 breast cancer-associated miRNA genes leads to the identification of two functional promoters of the Hsa-mir-200b cluster, methylation of which is associated with metastasis or hormone receptor status in advanced breast cancer

MicroRNAs (miRNAs) are small non-coding RNAs of 20 nt in length that are capable of modulating gene expression post-transcriptionally. Although miRNAs have been implicated in cancer, including breast cancer, the regulation of miRNA transcription and the role of defects in this process in cancer is not well understood. In this study we have mapped the promoters of 93 breast cancer-associated miRNAs, and then looked for associations between DNA methylation of 15 of these promoters and miRNA expression in breast cancer cells. The miRNA promoters with clearest association between DNA methylation and expression included a previously described and a novel promoter of the Hsa-mir-200b cluster. The novel promoter of the Hsa-mir-200b cluster, denoted P2, is located 2 kb upstream of the 5′ stemloop and maps within a CpG island. P2 has comparable promoter activity to the previously reported promoter (P1), and is able to drive the expression of miR-200b in its endogenous genomic context. DNA methylation of both P1 and P2 was inversely associated with miR-200b expression in eight out of nine breast cancer cell lines, and in vitro methylation of both promoters repressed their activity in reporter assays. In clinical samples, P1 and P2 were differentially methylated with methylation inversely associated with miR-200b expression. P1 was hypermethylated in metastatic lymph nodes compared with matched primary breast tumours whereas P2 hypermethylation was associated with loss of either oestrogen receptor or progesterone receptor. Hypomethylation of P2 was associated with gain of HER2 and androgen receptor expression. These data suggest an association between miR-200b regulation and breast cancer subtype and a potential use of DNA methylation of miRNA promoters as a component of a suite of breast cancer biomarkers.

Submission to the draft Migration Assurance Policy - Improving the transition to the fixed-line national broadband network review

The rights of individuals to self-determination and participation in social, political and economic life are recognised and supported by Articles 1, 3 and 25 of the International Covenant on Civil and Political Rights 1966.4 Article 1 of the United Nations’ Human Rights Council’s Resolution on the Promotion and Protection of Human Rights on the Internet of July 2012 confirms individuals have the same rights online as offline. Access to the internet is essential and as such the UN: Calls upon all States to promote and facilitate access to the Internet and international cooperation aimed at the development of media and information and communications facilities in all countries (Article 3) Accordingly, access to the internet per se is a fundamental human right, which requires direct State recognition and support.5 The obligations of the State to ensure its citizens are able, and are enabled, to access the internet, are not matters that should be delegated to commercial parties. Quite simply – access to the internet, and high-speed broadband, by whatever means are “essential services” and therefore “should be treated as any other utility service”...

Global, regional, and national disability-adjusted life years (DALYs) for 306 diseases and injuries and healthy life expectancy (HALE) for 188 countries, 1990–2013: Quantifying the epidemiological transition

Background The Global Burden of Disease Study 2013 (GBD 2013) aims to bring together all available epidemiological data using a coherent measurement framework, standardised estimation methods, and transparent data sources to enable comparisons of health loss over time and across causes, age–sex groups, and countries. The GBD can be used to generate summary measures such as disability-adjusted life-years (DALYs) and healthy life expectancy (HALE) that make possible comparative assessments of broad epidemiological patterns across countries and time. These summary measures can also be used to quantify the component of variation in epidemiology that is related to sociodemographic development. Methods We used the published GBD 2013 data for age-specific mortality, years of life lost due to premature mortality (YLLs), and years lived with disability (YLDs) to calculate DALYs and HALE for 1990, 1995, 2000, 2005, 2010, and 2013 for 188 countries. We calculated HALE using the Sullivan method; 95% uncertainty intervals (UIs) represent uncertainty in age-specific death rates and YLDs per person for each country, age, sex, and year. We estimated DALYs for 306 causes for each country as the sum of YLLs and YLDs; 95% UIs represent uncertainty in YLL and YLD rates. We quantified patterns of the epidemiological transition with a composite indicator of sociodemographic status, which we constructed from income per person, average years of schooling after age 15 years, and the total fertility rate and mean age of the population. We applied hierarchical regression to DALY rates by cause across countries to decompose variance related to the sociodemographic status variable, country, and time. Findings Worldwide, from 1990 to 2013, life expectancy at birth rose by 6·2 years (95% UI 5·6–6·6), from 65·3 years (65·0–65·6) in 1990 to 71·5 years (71·0–71·9) in 2013, HALE at birth rose by 5·4 years (4·9–5·8), from 56·9 years (54·5–59·1) to 62·3 years (59·7–64·8), total DALYs fell by 3·6% (0·3–7·4), and age-standardised DALY rates per 100 000 people fell by 26·7% (24·6–29·1). For communicable, maternal, neonatal, and nutritional disorders, global DALY numbers, crude rates, and age-standardised rates have all declined between 1990 and 2013, whereas for non–communicable diseases, global DALYs have been increasing, DALY rates have remained nearly constant, and age-standardised DALY rates declined during the same period. From 2005 to 2013, the number of DALYs increased for most specific non-communicable diseases, including cardiovascular diseases and neoplasms, in addition to dengue, food-borne trematodes, and leishmaniasis; DALYs decreased for nearly all other causes. By 2013, the five leading causes of DALYs were ischaemic heart disease, lower respiratory infections, cerebrovascular disease, low back and neck pain, and road injuries. Sociodemographic status explained more than 50% of the variance between countries and over time for diarrhoea, lower respiratory infections, and other common infectious diseases; maternal disorders; neonatal disorders; nutritional deficiencies; other communicable, maternal, neonatal, and nutritional diseases; musculoskeletal disorders; and other non-communicable diseases. However, sociodemographic status explained less than 10% of the variance in DALY rates for cardiovascular diseases; chronic respiratory diseases; cirrhosis; diabetes, urogenital, blood, and endocrine diseases; unintentional injuries; and self-harm and interpersonal violence. Predictably, increased sociodemographic status was associated with a shift in burden from YLLs to YLDs, driven by declines in YLLs and increases in YLDs from musculoskeletal disorders, neurological disorders, and mental and substance use disorders. In most country-specific estimates, the increase in life expectancy was greater than that in HALE. Leading causes of DALYs are highly variable across countries. Interpretation Global health is improving. Population growth and ageing have driven up numbers of DALYs, but crude rates have remained relatively constant, showing that progress in health does not mean fewer demands on health systems. The notion of an epidemiological transition—in which increasing sociodemographic status brings structured change in disease burden—is useful, but there is tremendous variation in burden of disease that is not associated with sociodemographic status. This further underscores the need for country-specific assessments of DALYs and HALE to appropriately inform health policy decisions and attendant actions.

Draft genome and plasmid sequences of Chlamydia pneumoniae strain B21 from an Australian endangered marsupial, the western barred bandicoot

Chlamydia pneumoniae is a ubiquitous intracellular pathogen, first associated with human respiratory disease and subsequently detected in a range of mammals, amphibians, and reptiles. Here we report the draft genome sequence for strain B21 of C. pneumoniae, isolated from the endangered Australian marsupial the western barred bandicoot.

Transition: Exchange establishing a visual arts practice based on personal pedagogy

There is a perceived tension in the relationship between the roles of art teacher and artist that led to the question: can an art teacher use their professional training and experience to establish an authentic artistic identity? This self-study tracked and analysed how the process of making her own art enabled an art teacher to also identify as an artist. Drawing on Lamina, the public exhibition of her multimedia artworks, the final exegesis proposes five conditions for art teachers in developing their own art practice: developing an identity as artist, using time and space mindfully, tolerating uncertainty, mentoring, and privileging the process.

Shape transition in very large germanium islands on Si(111)

Ge islands with areas up to hundreds of μm2 were grown on Si(111). These islands, grown above 750 °C and at a deposition rate of 1 monolayer/min, become decreasingly compact with increasing size and can have nonuniform cross sections with heights reaching over 500 nm. The largest islands are ramified, often comprising multiple discrete parts. X-rayphotoemission electron microscopy absorption maps show that the islands have a higher concentration of Ge at their centers, with more Si near the edges. We propose that the shape transformation is driven by strain relief at the island perimeters.

Public disclosure of biological sequences in global patent practice

Biological sequences are an important part of global patenting, with unique challenges for their effective and equitable use in practice and in policy. Because their function can only be determined with computer-aided technology, the form in which sequences are disclosed matters greatly. Similarly, the scope of patent rights sought and granted requires computer readable data and tools for comparison. Critically, the primary data provided to the national patent offices and thence to the public, must be comprehensive, standardized, timely and meaningful. It is not yet. The proposed global Patent Sequence (PatSeq) Data platform can enable national and regional jurisdictions meet the desired standards.

Transition of self: Repositioning the celebrity brand through social media—The case of Elizabeth Gilbert

Transitioning the personal brand from one representation to another is sometimes necessary, particularly within the public eye. Marketing literature regarding celebrities focuses on brand endorsement (see for example Till, 1998 or Erdogan, 1999), rather than the positioning of a celebrity brand. Furthermore, the role of social media in strengthening the celebrity brand has received limited attention in the literature outside of political marketing (see for example Crawford, 2009 and Grant, Moon and Grant, 2010). This study focuses on the brand of “Elizabeth Gilbert,” author of the bestseller memoir, Eat, Pray, Love (2006). Through critical discourse analysis, the way the author has used social media to reposition her celebrity brand at the time of the launch of her new novel, ‘The Signature of All Things’ (2013) is examined. This study focuses on the use of social media by celebrities to strengthen the celebrity brand.

Improved estimation of size-transition matrices using tag-recapture data

We derive a new method for determining size-transition matrices (STMs) that eliminates probabilities of negative growth and accounts for individual variability. STMs are an important part of size-structured models, which are used in the stock assessment of aquatic species. The elements of STMs represent the probability of growth from one size class to another, given a time step. The growth increment over this time step can be modelled with a variety of methods, but when a population construct is assumed for the underlying growth model, the resulting STM may contain entries that predict negative growth. To solve this problem, we use a maximum likelihood method that incorporates individual variability in the asymptotic length, relative age at tagging, and measurement error to obtain von Bertalanffy growth model parameter estimates. The statistical moments for the future length given an individual's previous length measurement and time at liberty are then derived. We moment match the true conditional distributions with skewed-normal distributions and use these to accurately estimate the elements of the STMs. The method is investigated with simulated tag-recapture data and tag-recapture data gathered from the Australian eastern king prawn (Melicertus plebejus).

Transition to fatherhood: A cross-cultural comparison

A prospective study was conducted of fathers' transition to parenthood from mid-pregnancy to 6 weeks postpartum. The subjects were 198 fathers from Greece (Athens) and 142 from Britain (Bristol). Social class, age and parity distributions were similar between the two populations. The culture and social structure experienced by each varied widely, however, and was a focus of interest. Two major themes in fatherhood across the two populations were explored: first, the father's instrumental role in provision of emotional and practical support to his partner and care for his child; and second the father's emotional reaction to his partner's pregnancy, the birth of his child and early parenthood. In both cultures fathers reported that they took an active instrumental role in supporting their partner and in participating in childcare. Markedly more British fathers attended the delivery. There were no overall differences in the degree to which fathers participated in childcare though the nature of this participation varied. British fathers more commonly took on housework duties. During their partner's pregnancy Greek fathers experienced significantly higher malaise than their British counterparts and also reported feeling that they had less social support. Common to many fathers in both cultures during this time were fears that their partner might change or be damaged by the pregnancy. After the birth, there was no difference in emotional well-being between the Greek and British fathers. Reactions to fatherhood and enjoyment of the child were similar for the two cultures also. Patterns of correlation between variables both within and across the antenatal and postnatal time periods were, for the most part, similar for the two cultures. Social support, however, was found to relate to father's emotional and instrumental reaction to parenthood only in the case of the British sample. Findings are discussed in terms of each culture's point on the continuum of social change.

Predicting a new phase (T′′) of two-dimensional transition metal di-chalcogenides and strain-controlled topological phase transition

Single layered transition metal dichalcogenides have attracted tremendous research interest due to their structural phase diversities. By using a global optimization approach, we have discovered a new phase of transition metal dichalcogenides (labelled as T′′), which is confirmed to be energetically, dynamically and kinetically stable by our first-principles calculations. The new T′′ MoS2 phase exhibits an intrinsic quantum spin Hall (QSH) effect with a nontrivial gap as large as 0.42 eV, suggesting that a two-dimensional (2D) topological insulator can be achieved at room temperature. Most interestingly, there is a topological phase transition simply driven by a small tensile strain of up to 2%. Furthermore, all the known MX2 (M = Mo or W; X = S, Se or Te) monolayers in the new T′′ phase unambiguously display similar band topologies and strain controlled topological phase transitions. Our findings greatly enrich the 2D families of transition metal dichalcogenides and offer a feasible way to control the electronic states of 2D topological insulators for the fabrication of high-speed spintronics devices.

Promoting and maintaining physical activity in the transition to retirement: A systematic review of interventions for adults around retirement age

It has been argued that transition points in life, such as the approach towards, and early years of retirement present key opportunities for interventions to improve the health of the population. Research has also highlighted inequalities in health status in the retired population and in response to interventions which should be addressed. We aimed to conduct a systematic review to synthesise international evidence on the types and effectiveness of interventions to increase physical activity among people around the time of retirement. A systematic review of literature was carried out between February 2014 and April 2015. Searches were not limited by language or location, but were restricted by date to studies published from 1990 onwards. Methods for identification of relevant studies included electronic database searching, reference list checking, and citation searching. Systematic search of the literature identified 104 papers which described study populations as being older adults. However, we found only one paper which specifically referred to their participants as being around the time of retirement. The intervention approaches for older adults encompassed: training of health care professionals; counselling and advice giving; group sessions; individual training sessions; in-home exercise programmes; in-home computer-delivered programmes; in-home telephone support; in-home diet and exercise programmes; and community-wide initiatives. The majority of papers reported some intervention effect, with evidence of positive outcomes for all types of programmes. A wide range of different measures were used to evaluate effectiveness, many were self-reported and few studies included evaluation of sedentary time. While the retirement transition is considered a significant point of life change, little research has been conducted to assess whether physical activity interventions at this time may be effective in promoting or maintaining activity, or reducing health inequalities. We were unable to find any evidence that the transition to retirement period was, or was not a significant point for intervention. Studies in older adults more generally indicated that a range of interventions might be effective for people around retirement age.