Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modeled accurately using the distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or underparameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10 000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42 337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these three sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modeled by a combination of eight edge-specific rate matrices (four for V1 and four for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the seven species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.

Implementation mechanism: Protection against harassment of women at workplace

Pakistan is widely known and appreciated in the world for its history, Islamic culture and norms. Since the creation of Pakistan, it inherited poverty in its roots. There are many reasons for poverty but one lies on the shoulder of women who are 50% of the total population of Pakistan. On the apex of it, women do not take part in the development of Pakistan because when they step out of their homes, they suffer a lot of problems. These problems are a hurdle in their active participation in development .Government has tried to create an environment for those women, who suffer different problems. Harassment of women at work place is one of those problems which discourage women in taking active part in economic and social development of society. Women Activists, from the last decade, were working for the protection of woman’s right at workplace and they succeeded in formulation of Harassment Act 2010. Since law is ineffective without its proper mechanism of implementation, steps should be taken for its proper implementation mechanism. This article aims to provide information about the provisions of law, related to the harassment of women at workplace with an attempt to explore the effectiveness of its implementation. The study was conducted in twin cities of Pakistan, Islamabad and Rawalpindi. Interviews were conducted with the employees and employers of organizations, educational institutions, women activists, NGOs workers, lawyers, judges and some law enforcement officers. Group discussions were also held with teachers, students of Human rights and religious personalities. This report focuses on the implementation mechanism of new legislation in Pakistan. It also highlights some important facts related to its enforcement.

Romantic terrorism? Survivor narratives of psychological and emotional tactics of domestic violence

This paper draws on the theoretical arguments outlined in Hayes (2014) to frame critical analyses of two real life domestic violence narratives. The authors are both academic criminologists and victims/survivors of domestic violence, but within differing contexts – one a conventional heterosexual relationship, the other a female same-sex relationship. Their experiences are intertwined in an extensive collaborative auto-ethnographic analysis that spans seven years of working and socialising together, in which each provided a sounding board and support for the other. The analysis therefore documents two personal journeys. The academic and theoretical are intertwined with the personal and subjective to elicit an evocative and yet empirically validated study. The theoretical underpinnings of romantic love distortion, misogyny and sexism are used to frame these experiences of domestic violence and the differing sexualities of the authors provide a rich context for exploring the ways in which domestic violence victimisation experiences are impacted by gender, sexuality, and heteronormative discourses of love, sex and relationships.

Creating healthy food environments in NSW: A knowledge and evidence synthesis to inform advocacy and action. Seven separate documents across the domains: Overview

Summaries evidence across seven domains of potential food policy action to improve food environments and food supply to prevent obesity for NSW Health

Attrition and success rates of accelerated students in nursing courses: A systematic review

Background There is a comprehensive literature on the academic outcomes (attrition and success) of students in traditional/baccalaureate nursing programs, but much less is known about the academic outcomes of students in accelerated nursing programs. The aim of this systematic review is to report on the attrition and success rates (either internal examination or NCLEX-RN) of accelerated students, compared to traditional students. Methods For the systematic review, the databases (Pubmed, Cinahl and PsychINFO) and Google Scholar were searched using the search terms ‘accelerated’ or ‘accreditation for prior learning’, ‘fast-track’ or ‘top up’ and ‘nursing’ with ‘attrition’ or ‘retention’ or ‘withdrawal’ or ‘success’ from 1994 to January 2016. All relevant articles were included, regardless of quality. Results The findings of 19 studies of attrition rates and/or success rates for accelerated students are reported. For international accelerated students, there were only three studies, which are heterogeneous, and have major limitations. One of three studies has lower attrition rates, and one has shown higher success rates, than traditional students. In contrast, another study has shown high attrition and low success for international accelerated students. For graduate accelerated students, most of the studies are high quality, and showed that they have rates similar or better than traditional students. Thus, five of six studies have shown similar or lower attrition rates. Four of these studies with graduate accelerated students and an additional seven studies of success rates only, have shown similar or better success rates, than traditional students. There are only three studies of non-university graduate accelerated students, and these had weaknesses, but were consistent in reporting higher attrition rates than traditional students. Conclusions The paucity and weakness of information available makes it unclear as to the attrition and/or success of international accelerated students in nursing programs. The good information available suggests that accelerated programs may be working reasonably well for the graduate students. However, the limited information available for non-university graduate students is weak, but consistent, in suggesting they may struggle in accelerated courses. Further studies are needed to determine the attrition and success rates of accelerated students, particularly for international and non-university graduate students.

Prags Boulevard in Copenhagen : from run-down strip to boulevard

Prags Boulevard will form a 2km long pedestrian spine running east-west between the historic cities of Copenhagen and Amager. It is located on a some-what run down site, which accommodated illicit functions such as casual drug use and drinking, as well as sheds for squatters. The renovation of this site by the city of Copenhagen forms part of the Holmbladsgade renovation project, and a two-phase competition was held in 2001 to develop a green area and meeting place, transforming it into a place that residents would want to visit rather than avoid. The designer, local landscape architect Kristine Jensens recognises that though the site is linear it ‘has no traffic importance’, though as she notes ‘we like the project because it runs straight east west from the city pulse to the water of Oresund’. In developing the project, she has attempted to allow it to ‘run parallel’ to its existing illicit uses, using a ‘light touch’ of insertions. While it would be hard to describe the project as truly light in its touch (graphically, it is a very bold scheme), there is no doubt that it is parallel: in terms of use it runs alongside rather than against existing uses; in terms of its type it’s all about length, like a boulevard, although it clearly differs from a boulevard in other respects.

An indexing model for stormwater quality in the Gold Coast

In the era of climate change sustainable urban development and in particular provision of sustainable urban infrastructure has become a key concept in dealing with environmental challenges. This paper discusses issues affecting stormwater quality and introduces a new indexing model that is to be used in evaluation of the stormwater quality in urban areas. The model has recently been developed and will be tested in a number of pilot projects in the Gold Coast, one of the fastest growing and environmentally challenged cities of Australia.

Signs, symptoms and comorbidities in contact lens-related microbial keratitis

Purpose: The aim of this study was to characterize the clinical signs, symptoms, and ocular and systemic comorbidities in a large case series of contact lens-related microbial keratitis. Methods: Two hundred ninety-seven cases of contact lens-related microbial keratitis, aged between 15 and 64 years were detected through surveillance of hospital and community based ophthalmic practitioners in Australia and New Zealand. Full clinical data were available for 190 cases and 90 were interviewed by telephone. Clinical data included the size, location, and degree of anterior chamber response. Symptom data were available from the practitioner and from participant self-report. Associations between symptoms and disease severity were evaluated. Data on ocular and systemic disease were collected from participants and practitioners. The frequency of comorbidities was compared between the different severities of disease and to population norms. Results: More severe disease was associated with greater symptom severity and pain was the most prevalent symptom reported. Ninety-one percent of cases showed progression of ocular symptoms after lens removal, and symptom progression was associated with all severities of disease. Twenty-five percent of cases reported prior episodes requiring emergency attention. Thyroid disease (p 0.05) and self-reported poor health (p 0.001) were more common in cases compared with age-matched population norms. Discussion: Information on the signs, symptoms, and comorbidities associated with contact lens-related microbial keratitis may be useful in patient education and for practitioners involved in the fitting of lenses and management of complications. Although pain was the most common symptom experienced, progression of symptoms despite lens removal was close to universal. Poor general health, particularly respiratory disease and thyroid disease was more common in cases than in the general population, which may prompt practitioners to recommend flexibility in wear schedules when in poor health or the selection of a lower risk wear schedule in at risk patients

In Interaction

The field was the design of cross-cultural media art exhibition outcomes for the Japanese marketplace. The context was improved understandings of spatial, temporal and contextual exhibition design procedures as they ultimately impact upon the augmentation of cross-cultural understanding. The research investigated cross-cultural new media exhibition practices suited to the specific sensitivies of Japanese exhibition practices. The methodology was principally practice-led. The research drew upon seven years of prior exhibition design practices in order to generate new Japanese exhibition design methodologies. It also empowered Zaim Artpsace’s Japanese curators to later present a range of substantial new media shows. The project also succeeded in developing new cross-cultural alliances that led to significant IDA projects in Beijing, Australia and Europe in the years 2008-10. Through invitations from external curators the new versions of the exhibition work subsequently travelled to 4 other major venues including the prestigious Songzhang Art Museum, Beijing in 07/08, the Block, QUT, Brisbane and the Tokyo International Film festival. Inspiration Art Press printed a major catalogue for the event extensively featuring this exhibition. This project also led to the Sudamalis (2007) paper, ‘Building Capacity: Literacy And Creative Workforce Development Through International Digital Arts Projects’ (IDAprojects) Exhibition Programs And Partnerships’.

Globalization, suburbanization, and the creative workforce : Findings from Australian suburban communities

This paper considers the changing relationship between economic prosperity and Australian suburbs, noting that what has been termed “the first suburban nation” in experiencing an intensification of suburban growth in the 2000s, in the context of economic globalization. The paper reports on a three-year Australian Research Council funded project into “Creative Suburbia”, identifying the significant percentage of the creative industries workforce who live in suburban areas. Drawing on case studies from suburbs in the Australian cities of Brisbane and Melbourne, it notes the contrasts between the experience of these workers, who are generally positive towards suburban life, and the underlying assumptions of “creative cities” policy discourse that such workers prefer to be concentrated in high density inner urban creative clusters.

Simple Serological Assays for Detecting Rice Tungro Viruses

An attempt was made to produce sensitive and specific polyclonal antisera against the viruses causing rice tungro disease, and to assess their potential for use in simple diagnostic tests. Using a multiple, sequential injection procedure, seven batches of polyclonal antisera against rice tungro bacilliform virus (RTBV) and rice tungro spherical virus (RTSV) were produced. These were characterized for their sensitivity and specificity using ring-interface precipitin test and double antibody sandwich (DAS) ELISA. Thirty-one weeks after the first immunization, antiserum batch B6b for RTBV showed the highest ring interface titer (DEP = 1:1920). For RTSV, batches S3, S4b and S5b all had similar titres (DEP = 1:640). In DAS-ELISA, however, significant differences among purified antisera (IgG) batches were observed only at IgG dilution of 10-3. At that dilution, IgGB4b showed the greatest sensitivity, while IgGS3 showed greatest sensitivity for RTSV. When all IgG batches were tested against 11 tungro field isolates (dual RTBV-RTSV infections) at sample dilution of 1:10, IgGB4b and IgGB6b for RTBV and IgGS3 and IgGS6b for RTSV performed equally well. However, after cross adsorption with healthy plant extracts in a specially prepared healthy plant-Sepharose affinity column, only IgGB6b could be used specifically to detect RTBV in a simple tissue-print assay.

Report on capacity-building workshops for road safety in Indonesia

In addition to the established problem of road safety in developing countries such as Indonesia, the agencies responsible for road safety often lack personnel with professional training in road safety. In Indonesia this is compounded by a need for more effective collaboration between agencies. In 2009, CARRS-Q was commissioned under the Indonesia Transport Safety Assistance Package to provide professional training in road safety for middle level officers in Jakarta, the province of Jawa Barat, and the cities of Bandung, Bogor and Sukabumi, aimed at developing action plans and fostering collaboration between agencies. This was achieved through a workshop, which followed up by a second workshop with the same participants. The course was very well received, action plans were successfully prepared during the first workshop, and most had progressed well by the time of the second workshop. Good cooperation between agencies was also evident. There would be considerable benefits in extending modified workshops more widely in Indonesia.

Economic prosperity, suburbanization, and the creative workforce : findings from Australian suburban communities

This paper considers the changing relationship between economic prosperity and Australian suburbs, noting that what has been termed “the first suburban nation” in experiencing an intensification of suburban growth in the 2000s, in the context of economic globalization. The paper reports on a three-year Australian Research Council funded project into “Creative Suburbia”, identifying the significant percentage of the creative industries workforce who live in suburban areas. Drawing on case studies from suburbs in the Australian cities of Brisbane and Melbourne, it notes the contrasts between the experience of these workers, who are generally positive towards suburban life, and the underlying assumptions of “creative cities” policy discourse that such workers prefer to be concentrated in high density inner urban creative clusters.

Culture and creative industries in Australia

It has been argued that the origins of modern creative industries policies can be found in Australia. The Creative Nation national cultural policy statement released by the Labor government headed by the Prime Minister Paul Keating in 1994 sought an original synthesis of arts and media policies that was outwardly looking, identifying the opportunities presented by what were then new digital media technologies, and clearly stated the economic opportunities presented by promotion of what were referred to at the time as the cultural industries. Several commentators have identified the influence that Creative Nation had on the Blair Labour government when it came to power in the United Kingdom in 1997. Faced with the question of how to revitalise the once-mighty industrial cities of the U.K. after the Conservative government, the Department of Culture, Media and Sport drew upon policy documents such as Australia’s Creative Nation, as well as the experience of local governments in these cities, in looking to the cultural sectors to spearhead new jobs growth, as well as re-branding the cities as cultural or creative cities in a post-industrial economic landscape. This growing alignment of culture and economics, that has been a characteristic of creative industries policies as they have developed in Australia, Britain, East Asia and Europe, marks an interesting shift in the traditional focus of arts and cultural policy as compensatory to the economic domain. The first Chair of what would become the Arts Council of Great Britain (now the Arts Council of England) was the famous economist John Maynard Keynes. In the First Annual Report of the Arts Council for 1945-1946, prepared in the latter stages of the Second World War, Keynes proposed that “the day is not far off when the economic problem will take the back seat where it belongs, and the arena of the heart and the head will be occupied or reoccupied, by our real problems — the problems of life and of human relations, of creation and behaviour and religion”. 中文摘要 1994年工黨執政時期澳洲總理基挺（Paul Keating）發表創意的國家（The Creative Nation）的文化政策聲明堪稱是澳洲現代創意產業的起源，該聲明試圖將藝術與媒體政策結合在一起，其目的在面向海外，為新數位媒體技術尋找機會。聲明中明確指出要推動文化產業為經濟帶來機會。「文化政策也是經濟政策。文化創造財富與附加價值，對創新、行銷與設計有重要貢獻，是我們工業的標誌（badge）。我們創意的層次實際上決定了我們適應新經濟imperatives的能力。文化本身就是項重要出口，是其他產品出口的主要附件（essential accompaniment）。文化吸引觀光與學生，也是我們經濟成功之關鍵。」 創意產業的策略是構建藝術、媒體與資訊電信科技的網絡以利文化產業在國家創新政策策略中擁有一席之地。此一策略最早是由1990年代末英國布萊爾（Tony Blair）的新工黨政府所採行，其後歐洲聯盟、澳洲、紐西蘭、新加坡、台灣、南韓與中國。

The exchange: an experiment in environmentally sustainable urban practice for a subtropical climate

The exchange pavilion offers a dialogue between two Expositions: 1998 in Brisbane and 2010 in Shanghai; and a chance to examine the impact that climate change will have on urban best practice outcomes in cities of the future. The Exchange exhibits the proposition that environmentally sustainable buildings need to interact responsively with a range of technical innovations to enable communities (and hence cities) to control and better manage their immediate environment. The 'Exchange' pavilion is a design experiment that integrates 3 key research elements: * An interactive digital exchange * A living green system wall (vertical and temporal) * A public urban star (horizontal and spatial) The proposition argues that the environmentally sustainability of any city is reliant on harnessing the full spectrum of intellectual and creative capital of the winder community (from universities to Government bodies to citizens) - a true knowledge city.