General Practice - Research Publications
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ItemRuns of homozygosity in killer whale genomes provide a global record of demographic histories.(Wiley, 2021-12)Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.
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ItemHandling uncertainty using features from pathology: Opportunities in primary care data for developing high risk cancer survival methods(ACM, 2021)More than 144 000 Australians were diagnosed with cancer in 2019. Diagnosing cancer in primary care is challenging due to the non-specific nature of cancer symptoms and its low prevalence. Understanding the epidemiology of cancer symptoms and patterns of presentation in patient's medical history from primary care data could be important to improve earlier detection and cancer outcomes. As past medical data about a patient can be incomplete, irregular or missing, this creates additional challenges when attempting to use the patient's history for any new diagnosis. Our research aims to investigate the opportunities in a patient's pathology history available to a GP, initially focused on the results within the frequently ordered full blood count to determine relevance to a future high-risk cancer prognosis, and treatment outcome. We investigated how past pathology test results can lead to deriving features that can be used to predict cancer outcomes, with emphasis on patients at risk of not surviving the cancer within 2-year period. This initial work focuses on patients with lung cancer, although the methodology can be applied to other types of cancer and other data within the medical record. Our findings indicate that even in cases of incomplete or obscure patient history, hematological measures can be useful in generating features relevant for predicting cancer risk and survival. The results strongly indicate to add the use of pathology test data for potential high-risk cancer diagnosis, and utilize additional pathology metrics or other primary care datasets even more for similar purposes.
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ItemDetection of a soil moisture and groundwater signal in ground-based gravity observations(Conference Organising Committee for the 40th Australian Conference of Economists, 2006)Gravity observations have the potential to provide an exciting new source of remotely sensed data to constrain the water balance in land surface models. This would result in more accurate soil moisture and flux predictions and correspondingly improved numerical weather prediction and global climate forecasts. However before existing or future (GRACE or GOCE) dedicated gravity satellites can be utilised in an operational setting it must be shown that a soil moisture signal is detectable in gravity observations. This is extremely difficult to show directly for the satellite observations due to the massive spatial scale involved (1000 km2or larger depending on accuracy requirements), so a ground-based field study of soil moisture, groundwater and gravity changes is essential in verifying the magnitude of the hydrological signal in gravity observations. This paper presents results from two field sites in the Kyeamba Creek catchment in NSW where soil moisture, groundwater and gravity have been monitored for one year. One is a hillslope site with no groundwater whereas the other is a valley site with a shallow water table. After correcting for earth tides and gravity meter drift, a gravity network adjustment is performed for two time periods chosen to capture the full range of subsurface water storage (autumn and spring). The adjustment improves the precision of the gravity estimates at each site relative to a hydrologically stable bedrock reference site. A t-test is performed on the gravity changes at the two sites and the valley site is found to have a significant change in gravity that corresponds extremely well to the predicted hydrologically induced gravity change. There are many complicating factors in a ground-based study, but nevertheless a hydrological signal (predominantly soil moisture) has been detected in the gravity observations of a valley site with a shallow groundwater table.
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ItemBYOD in Hospitals-Security Issues and Mitigation Strategies.(ACM Press, 2019)The demand for using personal devices in hospitals (BYOD) has increased rapidly over the years. However, BYOD also means that healthcare organisations are at great risk of leaking sensitive information assets like Personal Health Information (PHI) of patients, given that personal devices are outside the control of hospital IT management and may lack important security measures. Hence, the aim of this research is to develop a mitigation strategy which can cater to such security issues. A comprehensive literature review was conducted to identify BYOD security issues and mitigation solutions. This was followed by using two existing security frameworks, the BYOD security framework and People Policy Technology (PPT) model to shape a stepwise mitigation strategy. Technical, managerial and social issues were identified which include unsecure user behaviour by hospital employees, lack of security awareness, usability issues, legal requirements and lost devices. The mitigation strategy elucidates that while information and communication technologies allow better enforcement of security measures; policies and training provide the desired guidance to influence positive user behaviour among employees. The paper also discusses the need for a balance between usability and security in the success of BYOD in hospitals and hence provides systematic guidelines to curb BYOD security risks in hospitals.