Melbourne School of Population and Global Health - Research Publications
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ItemThree Certificates are not enough: Rover Thomas and Art Centre Archives(UWA Publishing, 2017-11-01)
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ItemAn Uncertainty-Accuracy-Based Score Function for Wrapper Methods in Feature Selection(IEEE, 2023-08-13)Feature Selection (FS) is an effective preprocessing method to deal with the curse of dimensionality in machine learning. Redundant features in datasets decrease the classification performance and increase the computational complexity. Wrapper methods are an important category of FS methods that evaluate various feature subsets and select the best one using performance measures related to a classifier. In these methods, the accuracy of classifiers is the most common performance measure for FS. Although the performance of classifiers depends on their uncertainty, this important criterion is neglected in these methods. In this paper, we present a new performance measure called Uncertainty-Accuracy-based Performance Measure for Feature Selection (UAPMFS) that uses an ensemble approach to measure both the accuracy and uncertainty of classifiers. UAPMFS uses bagging and uncertainty confusion matrix. This performance measure can be used in all wrapper methods to improve FS performance. We design two experiments to evaluate the performance of UAPMFS in wrapper methods. In experiments, we use the leave-one-variable-out strategy as the common strategy in wrapper methods to evaluate features. We also define a feature score function based on UAPMFS to rank and select features. In the first experiment, we investigate the importance of considering uncertainty in the FS process and show how neglecting uncertainty affects FS performance. In the second experiment, we compare the performance of the UAPMFS-based feature score function with the most common feature score functions for FS. Experimental results show the effectiveness of the proposed performance measure on different datasets.
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ItemModelling mass drug administration strategies for reducing scabies burden in Monrovia, Liberia(CAMBRIDGE UNIV PRESS, 2023-08-18)Scabies is a parasitic infestation with high global burden. Mass drug administrations (MDAs) are recommended for communities with a scabies prevalence of >10%. Quantitative analyses are needed to demonstrate the likely effectiveness of MDA recommendations. In this study, we developed an agent-based model of scabies transmission calibrated to demographic and epidemiological data from Monrovia. We used this model to compare the effectiveness of MDA scenarios for achieving scabies elimination and reducing scabies burden, as measured by time until recrudescence following delivery of an MDA and disability-adjusted-life-years (DALYs) averted. Our model showed that three rounds of MDA delivered at six-month intervals and reaching 80% of the population could reduce prevalence below 2% for three years following the final round, before recrudescence. When MDAs were followed by increased treatment uptake, prevalence was maintained below 2% indefinitely. Increasing the number of and coverage of MDA rounds increased the probability of achieving elimination and the number of DALYs averted. Our results suggest that acute reduction of scabies prevalence by MDA can support a transition to improved treatment access. This study demonstrates how modelling can be used to estimate the expected impact of MDAs by projecting future epidemiological dynamics and health gains under alternative scenarios.
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ItemNo Preview AvailableThe Colorectal cancer RISk Prediction (CRISP) trial(ROYAL COLL GENERAL PRACTITIONERS, 2023-08)BACKGROUND: A risk-stratified approach to colorectal cancer (CRC) screening could result in a more acceptable balance of benefits and harms, and be more cost-effective. AIM: To determine the effect of a consultation in general practice using a computerised risk assessment and decision support tool (Colorectal cancer RISk Prediction, CRISP) on risk-appropriate CRC screening. DESIGN AND SETTING: Randomised controlled trial in 10 general practices in Melbourne, Australia, from May 2017 to May 2018. METHOD: Participants were recruited from a consecutive sample of patients aged 50-74 years attending their GP. Intervention consultations included CRC risk assessment using the CRISP tool and discussion of CRC screening recommendations. Control group consultations focused on lifestyle CRC risk factors. The primary outcome was risk-appropriate CRC screening at 12 months. RESULTS: A total of 734 participants (65.1% of eligible patients) were randomised (369 intervention, 365 control); the primary outcome was determined for 722 (362 intervention, 360 control). There was a 6.5% absolute increase (95% confidence interval [CI] = -0.28 to 13.2) in risk-appropriate screening in the intervention compared with the control group (71.5% versus 65.0%; odds ratio [OR] 1.36, 95% CI = 0.99 to 1.86, P = 0.057). In those due CRC screening during follow-up, there was a 20.3% (95% CI = 10.3 to 30.4) increase (intervention 59.8% versus control 38.9%; OR 2.31, 95% CI = 1.51 to 3.53, P<0.001) principally by increasing faecal occult blood testing in those at average risk. CONCLUSION: A risk assessment and decision support tool increases risk-appropriate CRC screening in those due screening. The CRISP intervention could commence in people in their fifth decade to ensure people start CRC screening at the optimal age with the most cost-effective test.
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ItemNo Preview AvailableSpectrum and Frequency of Germline FANCM Protein-Truncating Variants in 44,803 European Female Breast Cancer Cases.(MDPI AG, 2023-06-23)FANCM germline protein truncating variants (PTVs) are moderate-risk factors for ER-negative breast cancer. We previously described the spectrum of FANCM PTVs in 114 European breast cancer cases. In the present, larger cohort, we report the spectrum and frequency of four common and 62 rare FANCM PTVs found in 274 carriers detected among 44,803 breast cancer cases. We confirmed that p.Gln1701* was the most common PTV in Northern Europe with lower frequencies in Southern Europe. In contrast, p.Gly1906Alafs*12 was the most common PTV in Southern Europe with decreasing frequencies in Central and Northern Europe. We verified that p.Arg658* was prevalent in Central Europe and had highest frequencies in Eastern Europe. We also confirmed that the fourth most common PTV, p.Gln498Thrfs*7, might be a founder variant from Lithuania. Based on the frequency distribution of the carriers of rare PTVs, we showed that the FANCM PTVs spectra in Southwestern and Central Europe were much more heterogeneous than those from Northeastern Europe. These findings will inform the development of more efficient FANCM genetic testing strategies for breast cancer cases from specific European populations.
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ItemNo Preview AvailableDNA Mismatch Repair Gene Variant Classification: Evaluating the Utility of Somatic Mutations and Mismatch Repair Deficient Colonic Crypts and Endometrial Glands(MDPI, 2023-10)Germline pathogenic variants in the DNA mismatch repair (MMR) genes (Lynch syndrome) predispose to colorectal (CRC) and endometrial (EC) cancer. Lynch syndrome specific tumor features were evaluated for their ability to support the ACMG/InSiGHT framework in classifying variants of uncertain clinical significance (VUS) in the MMR genes. Twenty-eight CRC or EC tumors from 25 VUS carriers (6xMLH1, 9xMSH2, 6xMSH6, 4xPMS2), underwent targeted tumor sequencing for the presence of microsatellite instability/MMR-deficiency (MSI-H/dMMR) status and identification of a somatic MMR mutation (second hit). Immunohistochemical testing for the presence of dMMR crypts/glands in normal tissue was also performed. The ACMG/InSiGHT framework reclassified 7/25 (28%) VUS to likely pathogenic (LP), three (12%) to benign/likely benign, and 15 (60%) VUS remained unchanged. For the seven re-classified LP variants comprising nine tumors, tumor sequencing confirmed MSI-H/dMMR (8/9, 88.9%) and a second hit (7/9, 77.8%). Of these LP reclassified variants where normal tissue was available, the presence of a dMMR crypt/gland was found in 2/4 (50%). Furthermore, a dMMR endometrial gland in a carrier of an MSH2 exon 1-6 duplication provides further support for an upgrade of this VUS to LP. Our study confirmed that identifying these Lynch syndrome features can improve MMR variant classification, enabling optimal clinical care.
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ItemNo Preview AvailableIdentifying and responding to family adversity in Australian community and primary health settings: a multi-site cross sectional study(FRONTIERS MEDIA SA, 2023-09-13)BACKGROUND: Unaddressed family adversity has potentially modifiable, negative biopsychosocial impacts across the life course. Little is known about how Australian health and social practitioners identify and respond to family adversity in community and primary health settings. OBJECTIVE: To describe, in two Australian community health services: (1) the number of adversities experienced by caregivers, (2) practitioner identification of caregivers experiencing adversity, (3) practitioner response to caregivers experiencing adversity, and (4) caregiver uptake of referrals. METHODS: Survey of caregivers of children aged 0-8 years attending community health services in Victoria and New South Wales (NSW). Analysis described frequencies of caregiver self-reported: (1) experiences of adversity, (2) practitioner identification of adversity, (3) practitioner response to adversity, and (4) referral uptake. Analyses were sub-grouped by three adversity domains and site. RESULTS: 349 caregivers (Victoria: n = 234; NSW: n = 115) completed the survey of whom 88% reported experiencing one or more family adversities. The median number of adversities was 4 (2-6). Only 43% of participants were directly asked about or discussed an adversity with a practitioner in the previous 6 months (Victoria: 30%; NSW: 68%). Among caregivers experiencing adversity, 30% received direct support (Victoria: 23%; NSW: 43%), and 14% received a referral (Victoria: 10%; NSW: 22%) for at least one adversity. Overall, 74% of caregivers accepted referrals when extended. CONCLUSION: The needs of Australian families experiencing high rates of adversity are not systematically identified nor responded to in community health services. This leaves significant scope for reform and enhancement of service responses to families experiencing adversity.
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ItemNo Preview AvailableAdvancing cross-sectoral data linkage to understand and address the health impacts of social exclusion: Challenges and potential solutions.(Swansea University, 2023)The use of administrative health data for research, monitoring, and quality improvement has proliferated in recent decades, leading to improvements in health across many disease areas and across the life course. However, not all populations are equally visible in administrative health data, and those that are less visible may be excluded from the benefits of associated research. Socially excluded populations - including the homeless, people with substance dependence, people involved in sex work, migrants or asylum seekers, and people with a history of incarceration - are typically characterised by health inequity. Yet people who experience social exclusion are often invisible within routinely collected administrative health data because information on their markers of social exclusion are not routinely recorded by healthcare providers. These circumstances make it difficult to understand the often complex health needs of socially excluded populations, evaluate and improve the quality of health services that they interact with, provide more accessible and appropriate health services, and develop effective and integrated responses to reduce health inequity. In this commentary we discuss how linking data from multiple sectors with administrative health data, often called cross-sectoral data linkage, is a key method for systematically identifying socially excluded populations in administrative health data and addressing other issues related to data quality and representativeness. We discuss how cross-sectoral data linkage can improve the representation of socially excluded populations in research, monitoring, and quality improvement initiatives, which can in turn inform coordinated responses across multiple sectors of service delivery. Finally, we articulate key challenges and potential solutions for advancing the use of cross-sectoral data linkage to improve the health of socially excluded populations, using international examples.
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ItemNo Preview AvailableWeb-Based STI/HIV Testing Services Available for Access in Australia: Systematic Search and Analysis(JMIR PUBLICATIONS, INC, 2023-09-22)BACKGROUND: Sexually transmitted infection (STI) rates continue to rise in Australia, and timely access to testing and treatment is crucial to reduce transmission. Web-based services have been viewed as a way to improve timely access to STI/HIV testing and have proliferated in recent years. However, the regulation of these services in Australia is minimal, leading to concerns about their quality. The purpose of this review was to systematically identify web-based STI/HIV testing services available in Australia and assess them on aspects of quality, reliability, and accessibility. OBJECTIVE: We aim to systematically identify and assess web-based STI/HIV testing services available in Australia. METHODS: A Google search of Australian web-based services was conducted in March 2022 and repeated in September 2022 using Boolean operators and search terms related to test services (eg, on the internet or home), STIs (eg, chlamydia or gonorrhea), and test type (eg, self-test). The first 10 pages were assessed, and services were categorized as self-testing (ST; test at home), self-sampling (SS; sample at home and return to laboratory), or self-navigated pathology (SNP; specimens collected at pathology center). Website reliability was assessed against the Health on the Net Foundation code of conduct, and service quality was assessed using a scorecard that was developed based on similar reviews, Australian guidelines for in-person services, and UK standards. Additionally, we looked at measures of accessibility including cost, rural access, and time to test results. RESULTS: Seventeen services were identified (8 ST, 2 SS, and 7 SNP). Only 4 services offered recommended testing for all 4 infections (chlamydia, gonorrhea, syphilis, and HIV) including genital, anorectal, and oropharyngeal sites, and 5 offered tests other than those recommended by Australian testing guidelines (eg, Ureaplasma). Nine services (1 SNP, 8 self-test) had no minimum age requirements for access. Reliability scores (scale 0-8) were similar between all services (range 4.75-8.0). Quality weighted scores (scale 0-58) were similar between SNP and SS services (average 44.89, SD 5.56 and 44.75, SD 1.77, respectively) but lower for ST services (22.66, SD 8.93; P=.002). Government-funded services were of higher quality than private services (43.54, SD 6.71 vs 29.43, SD 13.55; P=.03). The cost for services varied between SNP (Aus $0-$595; ie, US $0-$381.96), self-sample (Aus $0; ie, US $0), and ST (Aus $0-$135; ie, US $0-$86.66). The time to test results was much shorter for SNP services (~4 days) than for SS (~12 days) and ST (~14 days). CONCLUSIONS: This review identified considerable variability in the quality and reliability of the web-based STI/HIV testing services in Australia. Given the proliferation and use of these services will likely increase, it is imperative that Australia develops national standards to ensure the standard-of-care offered by web-based STI/HIV testing services is appropriate to protect Australian users from the impact of poorly performing and inappropriate tests.
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ItemNo Preview AvailableRemoving Pathoanatomical Content From Information Pamphlets About Knee Osteoarthritis Did Not Affect Beliefs About Imaging or Surgery, but Led to Lower Perceptions That Exercise Is Damaging and Better Osteoarthritis Knowledge: An Online Randomised Controlled Trial(J O S P T, 2023-04)OBJECTIVE: Compare the effects of osteoarthritis information, with or without pathoanatomical content, on people's beliefs about managing osteoarthritis. DESIGN: Online randomized controlled trial involving 556 participants. METHODS: Participants considered a hypothetical scenario where their doctor informed them that they had knee osteoarthritis. Participants were randomized to a control condition, where they received currently available osteoarthritis information with pathoanatomical content or an experimental condition, where they received the same osteoarthritis information but without pathoanatomical content. Primary outcomes were participants' beliefs about the need for x-ray to confirm diagnosis and joint replacement surgery in the future. RESULTS: There were no between-group differences in primary outcomes for x-ray (mean difference [MD], -0.3; 95% confidence interval [CI]: -0.9, 0.4) and surgery (MD, -0.2; 95% CI: -0.7, 0.2), each rated on an 11-point numeric rating scale. Participants in the experimental group had lower perceptions that exercise would damage the knee (MD, -0.4; 95% CI: -0.8, 0.0; rated on an 11-point numeric rating scale) and better osteoarthritis knowledge (MD, 0.9; 95% CI: 0.0, 1.9; rated on a scale ranging from 11 to 55). Among those without tertiary education, participants in the experimental group had lower perceptions that x-ray was necessary than control (MD, -0.8; 95% CI: -1.5, -0.1). Among those who had never sought care for knee pain, participants in the experimental group had lower perceptions about the need for surgery (MD, -0.7; 95% CI: -1.2, -0.2). CONCLUSIONS: Removing pathoanatomical content may not change beliefs about imaging and surgery but may lead to lower perceptions that exercise is damaging and may improve osteoarthritis knowledge. However, effects were small and of unclear clinical relevance. Tertiary education or a history of care seeking for knee pain may moderate effects on primary outcomes. J Orthop Sports Phys Ther 2023;53(4):1-15. Epub: 12 December 2022. doi:10.2519/jospt.2022.11618.