Diacritic Restoration and the Development of a Part-of-Speech Tagset for the Māori Language

This thesis investigates two fundamental problems in natural language processing: diacritic restoration and part-of-speech tagging. Over the past three decades, statistical approaches to diacritic restoration and part-of-speech tagging have grown in interest as a consequence of the increasing availability of manually annotated training data in major languages such as English and French. However, these approaches are not practical for most minority languages, where appropriate training data is either non-existent or not publically available. Furthermore, before developing a part-of-speech tagging system, a suitable tagset is required for that language. In this thesis, we make the following contributions to bridge this gap: Firstly, we propose a method for diacritic restoration based on naive Bayes classifiers that act at word-level. Classifications are based on a rich set of features, extracted automatically from training data in the form of diacritically marked text. This method requires no additional resources, which makes it language independent. The algorithm was evaluated on one language, namely Māori, and an accuracy exceeding 99% was observed. Secondly, we present our work on creating one of the necessary resources for the development of a part-of-speech tagging system in Māori, that of a suitable tagset. The tagset described was developed in accordance with the EAGLES guidelines for morphosyntactic annotation of corpora, and was the result of in-depth analysis of the Māori grammar

Evaluating the PRASE patient safety intervention - a multi-centre, cluster trial with a qualitative process evaluation: study protocol for a randomised controlled trial

Background: Estimates show that as many as one in 10 patients are harmed while receiving hospital care. Previous strategies to improve safety have focused on developing incident reporting systems and changing systems of care and professional behaviour, with little involvement of patients. The need to engage with patients about the quality and safety of their care has never been more evident with recent high profile reviews of poor hospital care all emphasising the need to develop and support better systems for capturing and responding to the patient perspective on their care. Over the past 3 years, our research team have developed, tested and refined the PRASE (Patient Reporting and Action for a Safe Environment) intervention, which gains patient feedback about quality and safety on hospital wards. Methods/design: A multi-centre, cluster, wait list design, randomised controlled trial with an embedded qualitative process evaluation. The aim is to assess the efficacy of the PRASE intervention, in achieving patient safety improvements over a 12-month period. The trial will take place across 32 hospital wards in three NHS Hospital Trusts in the North of England. The PRASE intervention comprises two tools: (1) a 44-item questionnaire which asks patients about safety concerns and issues; and (2) a proforma for patients to report (a) any specific patient safety incidents they have been involved in or witnessed and (b) any positive experiences. These two tools then provide data which are fed back to wards in a structured feedback report. Using this report, ward staff are asked to hold action planning meetings (APMs) in order to action plan, then implement their plans in line with the issues raised by patients in order to improve patient safety and the patient experience. The trial will be subjected to a rigorous qualitative process evaluation which will enable interpretation of the trial results. Methods: fieldworker diaries, ethnographic observation of APMs, structured interviews with APM lead and collection of key data about intervention wards. Intervention fidelity will be assessed primarily by adherence to the intervention via scoring based on an adapted framework. Discussion: This study will be one of the largest patient safety trials ever conducted, involving 32 hospital wards. The results will further understanding about how patient feedback on the safety of care can be used to improve safety at a ward level. Incorporating the ‘patient voice’ is critical if patient feedback is to be situated as an integral part of patient safety improvements

Sheep Updates 2006 -Part 1

This session covers seven papers from different authors: PLENARY 1. Making Dollars from Merinos, David Sackett, Holmes Sackett & Associates Pty Limited, Wagga Wagga, NSW 2. A new variety of sulla (Hedysarun coronarium)for forage production in southern Australia, Kevin Foster, Ron Yates, Phil Nichols, Department of Agriculture and Food, WA and Centre for Legumes in Mediterranean Agriculture, UWA 3. Mating - Short and fast is better, Graeme Martin, John Milton, Faculty of Natural & Agricultural Sciences, The University of Western Australia 4. Breech strike protection in sheep post 2010, Scott Williams, Program Manager Animal Health and Welfare, Australian Wool Innovation Limited 5. How the West can win!, Garry McAlister, Meat & Livestock Australia Limited, New South Wales. 6. The Merino Company (TMC) - Active Marketing and supply chain management, Mark Suttie, General Manager Marketing – The Merino Company (TMC) 7. Driving on-farm productivity: the next 20 years, Peter Fennessy, Jack Cocks, AbacusBio Limited, Dunedin, New Zealan

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution

Methods for specifying the target difference in a randomised controlled trial : the Difference ELicitation in TriAls (DELTA) systematic review

Peer reviewedPublisher PD

The patient reporting and action for a safe environment (PRASE) intervention: a feasibility study

Background: There is growing interest in the role of patients in improving patient safety. One such role is providing feedback on the safety of their care. Here we describe the development and feasibility testing of an intervention that collects patient feedback on patient safety, brings together staff to consider this feedback and to plan improvement strategies. We address two research questions: i) to explore the feasibility of the process of systematically collecting feedback from patients about the safety of care as part of the PRASE intervention; and, ii) to explore the feasibility and acceptability of the PRASE intervention for staff, and to understand more about how staff use the patient feedback for service improvement. Method: We conducted a feasibility study using a wait-list controlled design across six wards within an acute teaching hospital. Intervention wards were asked to participate in two cycles of the PRASE (Patient Reporting & Action for a Safe Environment) intervention across a six-month period. Participants were patients on participating wards. To explore the acceptability of the intervention for staff, observations of action planning meetings, interviews with a lead person for the intervention on each ward and recorded researcher reflections were analysed thematically and synthesised. Results: Recruitment of patients using computer tablets at their bedside was straightforward, with the majority of patients willing and able to provide feedback. Randomisation of the intervention was acceptable to staff, with no evidence of differential response rates between intervention and control groups. In general, ward staff were positive about the use of patient feedback for service improvement and were able to use the feedback as a basis for action planning, although engagement with the process was variable. Gathering a multidisciplinary team together for action planning was found to be challenging, and implementing action plans was sometimes hindered by the need to co-ordinate action across multiple services. Discussion: The PRASE intervention was found to be acceptable to staff and patients. However, before proceeding to a full cluster randomised controlled trial, the intervention requires adaptation to account for the difficulties in implementing action plans within three months, the need for a facilitator to support the action planning meetings, and the provision of training and senior management support for participating ward teams. Conclusions: The PRASE intervention represents a promising method for the systematic collection of patient feedback about the safety of hospital care

Palliative radiotherapy in addition to self-expanding metal stent for improving dysphagia and survival in advanced oesophageal cancer (ROCS: Radiotherapy after Oesophageal Cancer Stenting):study protocol for a randomized controlled trial

Background: The single most distressing symptom for patients with advanced esophageal cancer is dysphagia. Amongst the more effective treatments for relief of dysphagia is insertion of a self-expanding metal stent (SEMS). It is possible that the addition of a palliative dose of external beam radiotherapy may prolong the relief of dysphagia and provide additional survival benefit. The ROCS trial will assess the effect of adding palliative radiotherapy after esophageal stent insertion. Methods/Design: The study is a randomized multicenter phase III trial, with an internal pilot phase, comparing stent alone versus stent plus palliative radiotherapy in patients with incurable esophageal cancer. Eligible participants are those with advanced esophageal cancer who are in need of stent insertion for primary management of dysphagia. Radiotherapy will be administered as 20 Gray (Gy) in five fractions over one week or 30 Gy in 10 fractions over two weeks, within four weeks of stent insertion. The internal pilot will assess rates and methods of recruitment; pre-agreed criteria will determine progression to the main trial. In total, 496 patients will be randomized in a 1:1 ratio with follow up until death. The primary outcome is time to progression of patient-reported dysphagia. Secondary outcomes include survival, toxicity, health resource utilization, and quality of life. An embedded qualitative study will explore the feasibility of patient recruitment by examining patients’ motivations for involvement and their experiences of consent and recruitment, including reasons for not consenting. It will also explore patients’ experiences of each trial arm. Discussion: The ROCS study will be a challenging trial studying palliation in patients with a poor prognosis. The internal pilot design will optimize methods for recruitment and data collection to ensure that the main trial is completed on time. As a pragmatic trial, study strengths include collection of all follow-up data in the usual place of care, and a focus on patient-reported, rather than disease-orientated, outcomes. Exploration of patient experience and health economic analyses will be integral to the assessment of benefit for patients and the NHS