Volcanic architecture and chemostratigraphy within the Kalkarindji Continental Flood Basalt Province, Northern Territory : implications for eruption style from multiple fissure eruptions

This thesis was the first to define individual lava flow chemical variation and a detailed definition of the Kalkarindji Continental Flood Basalt Province, a lesser known province of the Phanerozoic eon. This thesis conducted an intensive field study that yielded numerous samples for petrography and chemical analyses as well as the generation of a detailed map of a portion of the Kalkarindji province.

An evaluation of medication review reports across different settings

Background There is a growing body of evidence which supports that a pharmacist conducted medication review increases the health outcomes for patients. A pharmacist integrated into a primary care medical centre may offer many potential advantages in conducting medication reviews in this setting however research describing this is presently limited. Objective To compare medication review reports conducted by pharmacists practicing externally to a medical centre to those medication review reports conducted by an integrated practice pharmacist. The secondary objective was to compare medication review reports conducted by pharmacists in the patient’s home to those conducted in the medical centre. Setting A primary care medical centre, Brisbane, Australia Method A retrospective analysis of pharmacist conducted medication reviews prior to and after the integration of a pharmacist into a medical centre. Main outcome measures Types of drug related problems identified by the Pharma cists, recommended intervention for drug related problems made by the pharmacist, and the extent of implementation of pharmacist recommendations by the general practitioner. Results The primary drug related problem reported in the practice pharmacist phase was Additional therapy required as compared to Precautions in the external pharmacist phase. The practice pharmacist most frequently recommended to add drug with Additional monitoring recommended most often in the external pharmacists. During the practice pharmacist phase 71 % of recommendations were implemented and was significantly higher than the external pharmacist phase with 53 % of recommendations implemented (p\0.0001). Two of the 23 drug related problem domains differed significantly when comparing medication reviews conducted in the patient’s home to those conducted in the medical centre.

Levels of social trust among men from refugee backgrounds after the 2011 Queensland floods

Purpose This paper examines the relationship between flood exposure and levels of social trust among a cohort of adult men from refugee backgrounds who were affected by the 2011 Queensland floods in Australia. Design/methodology/approach A quantitative questionnaire was administered to 141 men from refugee backgrounds almost two years after the 2011 Queensland floods. The survey was administered in person by trained peer in-terviewers, and included a number of standardised instruments assessing respondents’ so-cio-demographic characteristics, levels of social trust towards and from neighbours, the police, the wider Australian community, and the media, and exposure to and impact of the floods. Multiple logistic regression analyses were used to assess the relationship between flood exposure and social trust adjusting for pre-disaster levels of trust and other potentially confounding variables. Findings Participants with higher levels of flood exposure were significantly more likely to report greater levels of trust both towards and from their neighbours, the wider Australian community, and the media, and they were also more likely to believe that most people can be trusted. Research limitations/implications Although the study reports on data collected two years after the floods, the analysis has adjusted for pre-disaster measures of social trust and other socio-demographic variables. Originality/value Our paper has highlighted the important place of social trust and social capital for refugee communities in a post-disaster setting. Disaster responses that support social capital among marginalised populations are critical to increasing community resilience and supporting recovery.

Why disaster survivors speak to reporters

Practice-led journalism research techniques were used in this study to produce a ‘first draft of history’ recording the human experience of survivors and rescuers during the January 2011 flash flood disaster in Toowoomba and the Lockyer Valley in Queensland, Australia. The study aimed to discover what can be learnt from engaging in journalistic reporting of natural disasters, using journalism as both a creative practice and a research methodology. (Lindgren and Phillips, 2011, 75). The willingness of a very high proportion of severely traumatised flood survivors to participate in the flood research was unexpected but made it possible to document a relatively unstudied question within the literature about journalism and trauma – when and why disaster survivors will want to speak to journalists. The study reports six categories of reasons interviewees gave for their willingness to speak to the media: for their own personal recovery; their desire for the public to know what had happened; that lessons need to be learned from the disaster; their sense of duty to make sure warning systems and disaster responses are improved in future; the financial disinterest of reporters in listening to survivors; and the timing of the request for an interview. In addition, traumatised flood survivors found both the opportunity to speak to the media and the journalistic outputs of the research cathartic in their recovery.

Animal stories : flash flood 2011

Flash flood disasters happen suddenly. The Toowoomba Lockyer Valley flash flood in January 2011 was not forecast by the Bureau of Meteorology until after it had occurred. Domestic and wild animals gave the first warning of the disaster in the days leading up to the event and large animals gave warnings on the morning of the disaster. Twenty-three people, including 5 children in the disaster zone died. More than 500 people were listed as missing. Some of those who died, perished because they stayed in the disaster zone to look after their animals while other members of their family escaped to safety. Some people who were in danger refused to be rescued because they could not take their pets with them. During a year spent recording accounts of the survivors of the disaster, animals were often mentioned by survivors. Despite the obvious perils, people risked their lives to save their animals; people saw animals try to save each other; animals rescued people; people rescued animals; animals survived where people died; animals were used to find human victims in the weeks after the disaster; and animals died. The stories of the flood present challenges for pet owners, farmers, counter disaster planners, weather forecasters and emergency responders in preparing for disasters, responding to them and recovering after them.

The impact of OCR accuracy on automated cancer classification of pathology reports

Objective To evaluate the effects of Optical Character Recognition (OCR) on the automatic cancer classification of pathology reports. Method Scanned images of pathology reports were converted to electronic free-text using a commercial OCR system. A state-of-the-art cancer classification system, the Medical Text Extraction (MEDTEX) system, was used to automatically classify the OCR reports. Classifications produced by MEDTEX on the OCR versions of the reports were compared with the classification from a human amended version of the OCR reports. Results The employed OCR system was found to recognise scanned pathology reports with up to 99.12% character accuracy and up to 98.95% word accuracy. Errors in the OCR processing were found to minimally impact on the automatic classification of scanned pathology reports into notifiable groups. However, the impact of OCR errors is not negligible when considering the extraction of cancer notification items, such as primary site, histological type, etc. Conclusions The automatic cancer classification system used in this work, MEDTEX, has proven to be robust to errors produced by the acquisition of freetext pathology reports from scanned images through OCR software. However, issues emerge when considering the extraction of cancer notification items.

Classification of pathology reports for cancer registry notifications

Objective: To develop a system for the automatic classification of pathology reports for Cancer Registry notifications. Method: A two pass approach is proposed to classify whether pathology reports are cancer notifiable or not. The first pass queries pathology HL7 messages for known report types that are received by the Queensland Cancer Registry (QCR), while the second pass aims to analyse the free text reports and identify those that are cancer notifiable. Cancer Registry business rules, natural language processing and symbolic reasoning using the SNOMED CT ontology were adopted in the system. Results: The system was developed on a corpus of 500 histology and cytology reports (with 47% notifiable reports) and evaluated on an independent set of 479 reports (with 52% notifiable reports). Results show that the system can reliably classify cancer notifiable reports with a sensitivity, specificity, and positive predicted value (PPV) of 0.99, 0.95, and 0.95, respectively for the development set, and 0.98, 0.96, and 0.96 for the evaluation set. High sensitivity can be achieved at a slight expense in specificity and PPV. Conclusion: The system demonstrates how medical free-text processing enables the classification of cancer notifiable pathology reports with high reliability for potential use by Cancer Registries and pathology laboratories.

Clinician-driven automated classification of limb fractures from free-text radiology reports

The aim of this research is to report initial experimental results and evaluation of a clinician-driven automated method that can address the issue of misdiagnosis from unstructured radiology reports. Timely diagnosis and reporting of patient symptoms in hospital emergency departments (ED) is a critical component of health services delivery. However, due to disperse information resources and vast amounts of manual processing of unstructured information, a point-of-care accurate diagnosis is often difficult. A rule-based method that considers the occurrence of clinician specified keywords related to radiological findings was developed to identify limb abnormalities, such as fractures. A dataset containing 99 narrative reports of radiological findings was sourced from a tertiary hospital. The rule-based method achieved an F-measure of 0.80 and an accuracy of 0.80. While our method achieves promising performance, a number of avenues for improvement were identified using advanced natural language processing (NLP) techniques.

Automatic classification of free-text radiology reports to identify limb fractures using machine learning and the SNOMED CT ontology

Objective To develop and evaluate machine learning techniques that identify limb fractures and other abnormalities (e.g. dislocations) from radiology reports. Materials and Methods 99 free-text reports of limb radiology examinations were acquired from an Australian public hospital. Two clinicians were employed to identify fractures and abnormalities from the reports; a third senior clinician resolved disagreements. These assessors found that, of the 99 reports, 48 referred to fractures or abnormalities of limb structures. Automated methods were then used to extract features from these reports that could be useful for their automatic classification. The Naive Bayes classification algorithm and two implementations of the support vector machine algorithm were formally evaluated using cross-fold validation over the 99 reports. Result Results show that the Naive Bayes classifier accurately identifies fractures and other abnormalities from the radiology reports. These results were achieved when extracting stemmed token bigram and negation features, as well as using these features in combination with SNOMED CT concepts related to abnormalities and disorders. The latter feature has not been used in previous works that attempted classifying free-text radiology reports. Discussion Automated classification methods have proven effective at identifying fractures and other abnormalities from radiology reports (F-Measure up to 92.31%). Key to the success of these techniques are features such as stemmed token bigrams, negations, and SNOMED CT concepts associated with morphologic abnormalities and disorders. Conclusion This investigation shows early promising results and future work will further validate and strengthen the proposed approaches.

ShARe/CLEF eHealth Evaluation Lab 2013, Task 3: Information retrieval to address patients' questions when reading clinical reports

This paper presents the results of task 3 of the ShARe/CLEF eHealth Evaluation Lab 2013. This evaluation lab focuses on improving access to medical information on the web. The task objective was to investigate the effect of using additional information such as the discharge summaries and external resources such as medical ontologies on the IR effectiveness. The participants were allowed to submit up to seven runs, one mandatory run using no additional information or external resources, and three each using or not using discharge summaries.

Automated classification of limb fractures from free-text radiology reports using a clinician-informed gazetteer methodology

Background Timely diagnosis and reporting of patient symptoms in hospital emergency departments (ED) is a critical component of health services delivery. However, due to dispersed information resources and a vast amount of manual processing of unstructured information, accurate point-of-care diagnosis is often difficult. Aims The aim of this research is to report initial experimental evaluation of a clinician-informed automated method for the issue of initial misdiagnoses associated with delayed receipt of unstructured radiology reports. Method A method was developed that resembles clinical reasoning for identifying limb abnormalities. The method consists of a gazetteer of keywords related to radiological findings; the method classifies an X-ray report as abnormal if it contains evidence contained in the gazetteer. A set of 99 narrative reports of radiological findings was sourced from a tertiary hospital. Reports were manually assessed by two clinicians and discrepancies were validated by a third expert ED clinician; the final manual classification generated by the expert ED clinician was used as ground truth to empirically evaluate the approach. Results The automated method that attempts to individuate limb abnormalities by searching for keywords expressed by clinicians achieved an F-measure of 0.80 and an accuracy of 0.80. Conclusion While the automated clinician-driven method achieved promising performances, a number of avenues for improvement were identified using advanced natural language processing (NLP) and machine learning techniques.

Turbulence in an inundated urban environment during a major flood : implications in terms of people evacuation and sediment deposition

Floods through inundated urban environments constitute a hazard to the population and infrastructure. A series of field measurements were performed in an inundated section of the City of Brisbane (Australia) during a major flood in January 2011. Using an acoustic Doppler velocimeter (ADV), detailed velocity and suspended sediment concentration measurements were conducted about the peak of the flood. The results are discussed with a focus on the safety of individuals in floodwaters and the sediment deposition during the flood recession. The force of the floodwaters in Gardens Point Road was deemed unsafe for individual evacuation. A comparison with past laboratory results suggested that previous recommendations could be inappropriate and unsafe in real flood flows.

Validity of family child care providers' proxy reports on children's physical activity

Background Interventions to promote physical activity (PA) in children attending family child care homes (FCCHs) require valid, yet practical, measurement tools. The aim of this study was to assess the validity of two proxy report instruments designed to measure PA in children attending FCCHs. Methods A sample of 37 FCCH providers completed the Burdette parent proxy report, modified for the family child care setting for 107 children 3.4±1.2 years of age. A second sample of 42 FCCH providers completed the Harro parent and teacher proxy report, modified for the family child care setting, for 131 children 3.8±1.3 years of age. Both proxy reports were assessed for validity using accelerometry as a criterion measure. Results Significant positive correlations were observed between provider-reported PA scores from the modified Burdette proxy report and objectively measured total PA (r=0.30; p<0.01) and moderate-to-vigorous PA (MVPA; r=0.34; p<0.01). Across levels of provider-reported PA, both total PA and MVPA increased significantly in a linear dose-response fashion. The modified Harro proxy report was not associated with objectively measured PA. Conclusion Proxy PA reports completed by family child care providers may be a valid assessment option in studies where more burdensome objective measures are not feasible.