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Background: Data cleaning is an important quality assurance in data linkage research studies. This paper presents the data cleaning and preparation process for a large-scale cross-jurisdictional Australian study (the Smoking MUMS Study) to evaluate the utilisation and safety of smoking cessation pharmacotherapies during pregnancy.Methods: Perinatal records for all deliveries (2003-2012) in the States of New South Wales (NSW) and Western Australia were linked to State-based data collections including hospital separation, emergency department and death data (mothers and babies) and congenital defect notifications (babies in NSW) by State-based data linkage units. A national data linkage unit linked pharmaceutical dispensing data for the mothers. All linkages were probabilistic. Twenty two steps assessed the uniqueness of records and consistency of items within and across data sources, resolved discrepancies in the linkages between units, and identified women having records in both States.Results: State-based linkages yielded a cohort of 783,471 mothers and 1,232,440 babies. Likely false positive links relating to 3703 mothers were identified. Corrections of baby's date of birth and age, and parity were made for 43,578 records while 1996 records were flagged as duplicates. Checks for the uniqueness of the matches between State and national linkages detected 3404 ID clusters, suggestive of missed links in the State linkages, and identified 1986 women who had records in both States.Conclusions: Analysis of content data can identify inaccurate links that cannot be detected by data linkage units that have access to personal identifiers only. Perinatal researchers are encouraged to adopt the methods presented to ensure quality and consistency among studies using linked administrative data. [ABSTRACT FROM AUTHOR]

Background: Asthma is among the commonest noncommunicable diseases of childhood and often occurs with other atopic comorbidities. A previous case-control study found evidence that compared to children who received acellular pertussis (aP) vaccines in early infancy, children who received one or more doses of whole-cell pertussis (wP) vaccine had lower risk of developing IgE-mediated food allergy. We hypothesized that wP vaccination in early infancy might protect against atopic asthma in childhood. Methods: Retrospective record-linkage cohort study of children between 5 and < 15 years old and born between January 1997, and December 1999, in the Australian states of Western Australia (WA) and New South Wales (NSW), receiving wP versus aP vaccine as the first pertussis vaccine dose. The main outcome and measures were first and recurrent hospitalizations for asthma; hazard ratios (HRs) and 95% confidence intervals (CIs) were computed by means of Cox and Andersen and Gill models. Results: 274,405 children aged between 5 and < 15 years old (78.4% NSW-born) received a first dose of either wP (67.8%) or aP vaccine before 4 months old. During the follow-up period, there were 5,905 hospitalizations for asthma among 3,955 children. The incidence rate for first hospitalization was 1.5 (95% CI 1.4–1.5) per 1,000 child-years among children receiving wP vaccine as a first dose, and 1.5 (95% CI 1.4–1.6) among those vaccinated with aP vaccine as a first dose. The adjusted HRs for those who received wP vaccine versus aP vaccine as the first dose were 1.02 (95% CI 0.94–1.12) for first hospitalizations and 1.07 (95% CI 0.95–1.2) for recurrent hospitalizations for asthma. Conclusions: We found no convincing evidence of a clinically relevant association between receipt of wP versus aP vaccines in early infancy and hospital presentations for asthma in childhood. [ABSTRACT FROM AUTHOR]

Background: Lucilia cuprina and L. sericata (family Calliphoridae) are globally significant ectoparasites of sheep. Current literature suggests that only one of these blowfly subspecies, L. cuprina dorsalis, is a primary parasite causing myiasis (flystrike) in sheep in Australia. These species and subspecies are difficult to distinguish using morphological features. Hence, being able to accurately identify blowflies is critical for diagnosis and for understanding their relationships with their hosts and environment. Methods: In this study, adult blowflies (5 pools of 17 flies; n = 85) were collected from five locations in different states [New South Wales (NSW), Queensland (QLD), Tasmania (TAS), Victoria (VIC) and Western Australia (WA)] of Australia and their mitochondrial (mt) genomes were assembled. Results: Each mt genome assembled was ~ 15 kb in size and encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The Lucilia species mt genomes were conserved in structure, and the genes retained the same order and direction. The overall nucleotide composition was heavily biased towards As and Ts—77.7% of the whole genomes. Pairwise nucleotide diversity suggested divergence between Lucilia cuprina cuprina, L. c. dorsalis and L. sericata. Comparative analyses of these mt genomes with published data demonstrated that the blowflies collected from sheep farm in TAS clustered within a clade with L. sericata. The flies collected from an urban location in QLD were more closely related to L. sericata and represented the subspecies L. c. cuprina, whereas the flies collected from sheep farms in NSW, VIC and WA represented the subspecies L. c. dorsalis. Conclusions: Phylogenetic analyses of the mt genomes representing Lucilia from the five geographic locations in Australia supported the previously demonstrated paraphyly of L. cuprina with respect to L. sericata and revealed that L. c. cuprina is distinct from L. c. dorsalis and that L. c. cuprina is more closely related to L. sericata than L. c. dorsalis. The mt genomes reported here provide an important molecular resource to develop tools for species- and subspecies-level identification of Lucilia from different geographical regions across Australia. [ABSTRACT FROM AUTHOR]

Detecting animals to estimate abundance can be difficult, particularly when the habitat is dense or the target animals are fossorial. The recent surge in the use of thermal imagers in ecology and their use in animal detections can increase the accuracy of population estimates and improve the subsequent implementation of management programs. However, the use of thermal imagers results in many hours of captured flight videos which require manual review for confirmation of species detection and identification. Therefore, the perceived cost and efficiency trade-off often restricts the use of these systems. Additionally, for many off-the-shelf systems, the exported imagery can be quite low resolution (<9 Hz), increasing the difficulty of using automated detections algorithms to streamline the review process. This paper presents an animal species detection system that utilises the cost-effectiveness of these lower resolution thermal imagers while harnessing the power of transfer learning and an enhanced small object detection algorithm. We have proposed a distant object detection algorithm named Distant-YOLO (D-YOLO) that utilises YOLO (You Only Look Once) and improves its training and structure for the automated detection of target objects in thermal imagery. We trained our system on thermal imaging data of rabbits, their active warrens, feral pigs, and kangaroos collected by thermal imaging researchers in New South Wales and Western Australia. This work will enhance the visual analysis of animal species while performing well on low, medium and high-resolution thermal imagery. [ABSTRACT FROM AUTHOR]

Introduction: The COVID-19 pandemic resulted in a rapid transformation of health services. This study aimed to understand the experiences of healthcare by people with interstitial lung disease (ILD), to inform future service delivery. Methods: Four specialist clinics in tertiary centres in Australia (Victoria:2 sites; New South Wales: 1 site; Western Australia: 1 site) recruited patients with ILD during an 8-week period from March 2021. Participants completed a COVID-specific questionnaire focused on health-related experiences during 2020. Results: Ninety nine (65% of 153) participants completed the questionnaire. 47% had idiopathic pulmonary fibrosis or connective tissue disease-associated ILD, 62% were female and the average age was 66 years. Whilst 56% rated their overall health in 2020 as the same as months prior, 38% indicated a worsening in health attributed to reduced physical activity and fear of contracting the virus. Access to healthcare professionals was 'good' in 61%, and 'fair-to-poor' for 37% due to missed respiratory assessments, with telehealth (mainly telephone) being perceived as less effective. 89% had contact with respiratory physicians, 68% with general practitioners, predominantly via telephone, with few video consultations. High satisfaction with care was reported by 78%, with lower satisfaction attributed to delays in assessments, disruption to usual services such as pulmonary rehabilitation, and dissatisfaction with telehealth. Conclusion: People with ILD were generally satisfied with their care during 2020, however reduced access to healthcare professionals was challenging for those experiencing a deterioration in health. Telehealth was largely well received but did not always meet the needs of people with ILD particularly when unwell. [ABSTRACT FROM AUTHOR]

This study examines differentiated financial risk tolerance attitudes between three listing branches within the Australian Securities Exchange's (ASX) standardised listing environment. Western Australia's (WA) concentration of earlier‐stage IPOs (51% of all ASX small, (predominately mining) initial public offerings (IPOs)) appears to reflect a localised 'entrepreneurial' risk attitude towards smaller, higher‐risk transactions, comparative to New South Wales and Victoria. Our mixed method approach identifies that the concentration of small‐cap, capital raising experiences that are (in)/formally shared through key 'gatekeepers', shape locally adopted funding capabilities, business processes, and risk attitudes. Underlying risk attitudes were influenced by the shared confidence in the recognition and management of risk, thereby increasing the propensity to participate in more speculative opportunities, and WA's presumptive higher risk tolerance. [ABSTRACT FROM AUTHOR]

Introduction: The burden of IgE-mediated food allergy in Australian born children is reported to be among the highest globally. This illness shares risk factors and frequently coexists with asthma, one of the most common noncommunicable diseases of childhood. Findings from a case-control study suggest that compared to immunisation with acellular pertussis vaccine, early priming of infants with whole-cell pertussis vaccine may be associated with a lower risk of subsequent IgE-mediated food allergy. If whole-cell vaccination is protective of food allergy and other atopic diseases, especially if protective against childhood asthma, the population-level effects could justify its preferential recommendation. However, the potential beneficial effects of whole-cell pertussis vaccination for the prevention of atopic diseases at a population-scale are yet to be investigated. Methods and analysis: Analyses of population-based record linkage data will be undertaken to compare the rates of admissions to hospital for asthma in children aged between 5 and 15 years old, who were born in Western Australia (WA) or New South Wales (NSW) between 1997 and 1999 (329,831) when pertussis immunisation in Australia transitioned from whole-cell to acellular only schedules. In the primary analysis we will estimate hazard ratios and 95% confidence intervals for the time-to-first-event (hospital admissions as above) using Cox proportional hazard models in recipients of a first dose of whole-cell versus acellular pertussis-containing vaccine before 112 days old (~4 months of age). Similarly, we will also fit time-to-recurrent events analyses using Andersen-Gill models, and robust variance estimates to account for potential within-child dependence. Hospitalisations for all-cause anaphylaxis, food anaphylaxis, venom, all-cause urticaria and atopic dermatitis will also be examined in children who received at least one dose of pertussis-containing vaccine by the time of the cohort entry, using analogous statistical methods. Presentations to the emergency departments will be assessed separately using the same statistical approach. [ABSTRACT FROM AUTHOR]

Background: This study describes trends in social inequities in first dose measles-mumps-rubella (MMR1) vaccination coverage in Western Australia (WA) and New South Wales (NSW). Using probabilistically-linked administrative data for 1.2 million children born between 2002 and 2011, we compared levels and trends in MMR1 vaccination coverage measured at age 24 months by maternal country of birth, Aboriginal status, maternal age at delivery, socio-economic status, and remoteness in two states.Results: Vaccination coverage was 3-4% points lower among children of mothers who gave birth before the age of 20 years, mothers born overseas, mothers with an Aboriginal background, and parents with a low socio-economic status compared to children that did not belong to these social groups. In both states, between 2007 and 2011 there was a decline of 2.1% points in MMR1 vaccination coverage for children whose mothers were born overseas. In 2011, WA had lower coverage among the Aboriginal population (89.5%) and children of young mothers (89.3%) compared to NSW (92.2 and 92.1% respectively).Conclusion: Despite overall high coverage of MMR1 vaccination, coverage inequalities increased especially for children of mothers born overseas. Strategic immunisation plans and policy interventions are important for equitable vaccination levels. Future policy should target children of mothers born overseas and Aboriginal children. [ABSTRACT FROM AUTHOR]

Two main strategies, home and hotel isolation, have been used to isolate COVID-19 cases in most countries. Both have proven to be somewhat medically effective, but the costs to produce the desired outcome remain unclear. We used a decision tree model to compare alternatives and a simulation model to determine the household structure and provide recommendations for the most cost-effective way to isolate a COVID-19 patient in two Australian States, New South Wales (NSW) andWestern Australia (WA). The results show that although the average cost of isolating a confirmed case at home is lower than that of a hotel quarantine, it is demonstrable that the decision depends on household size and the ages of household members. If the household members' ages are old or the household size is large, the expected mean cost of home quarantine might be higher than hotel quarantine. Our study, therefore, provides the government with a cost-effective insight into making quarantine policies. [ABSTRACT FROM AUTHOR]

Flesh-footed shearwater (Ardenna carneipes) is recognized as vulnerable seabird species in Western Australia and New South Wales, Australia, and its genetic variability and a well-resolved phylogeny is imperative for the species' conservation. Here, we report the first sequenced mitogenome of the Australian A. carneipes. The mitogenome of A. carneipes was 16,370 bp in total length and encompassed 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one non-coding region (D-loop). All of the genes were encoded on the H-strand with the exception of ND6 and eight tRNAs, which is a conserved pattern of the mitogenome for other vertebrates. The mitogenome of A. carneipes was dominated by higher AT (56.5%) than GC (43.5%) content. In the resulting phylogenetic tree using complete mitogenome sequences, flesh-footed shearwater and gray petrel (Procellaria cinerea) grouped together despite the high genetic distance (11.0%) between them, belonging to family Procellariidae. However, the phylogenetic tree was consistent with a previous study using partial nucleotide sequences of the cytochrome b gene. These results highlight that further mitogenome sequences will be required from the closely related species under the genus Ardenna to delineate well-resolved phylogenetic classification at the genus and or species level. The present study provides a reference mitochondrial genome of flesh-footed shearwater for further molecular studies. [ABSTRACT FROM AUTHOR]

Recreational fishing is popular in Australia and is managed by individual states in consultation with the Commonwealth for those fisheries that they regulate and also for Australian Marine Parks (AMPs). Fishers regularly access both state and offshore Commonwealth waters but this offshore component of the recreational fishery is poorly understood. Our study tested the functionality of existing state-based surveys in Western Australia (WA) and New South Wales (NSW) to better inform Commonwealth fisheries and AMP managers about recreational fishing in their jurisdictions. Catch estimates for nine species of interest to the Commonwealth were developed and two case study AMPs [Ningaloo (WA) and The Hunter (NSW)] were also chosen to test the ability of the state survey data to be disaggregated to the park scale. As each state's fishery survey designs were contextual to their own management needs, the application of the data to Commonwealth jurisdictions were limited by their statistical power, however aspects of each states surveys still provided useful information. Continued evolution of state-wide survey methods, including collection of precise spatial data, and regional over-sampling would be beneficial, particularly where there are multiple stakeholder and jurisdictional interests. National coordination, to temporally align state surveys, would also add value to the existing approaches. [ABSTRACT FROM AUTHOR]

Background: Varenicline, bupropion and nicotine replacement therapy (NRT) are three effective pharmacotherapies for smoking cessation, but data about their safety in pregnancy are limited. We assessed the risk of adverse perinatal outcomes and major congenital anomalies associated with the use of these therapies in pregnancy in Australia.Methods: Perinatal data for 1,017,731 deliveries (2004 to 2012) in New South Wales and Western Australia were linked to pharmaceutical dispensing, hospital admission and death records. We identified 97,875 women who smoked during pregnancy; of those, 233, 330 and 1057 were exposed to bupropion, NRT and varenicline in pregnancy, respectively. Propensity scores were used to match exposed women to those who were unexposed to any smoking therapy (1:10 ratio). Propensity scores and gestational age at exposure were used to match varenicline-exposed to NRT-exposed women (1:1 ratio). Time-dependent Cox proportional hazards models estimated hazard ratios (HR) with 95% confidence intervals (95% CI) for any adverse perinatal event (a composite of 10 unfavourable maternal and neonatal outcomes) and any major congenital anomaly.Results: The risk of any adverse perinatal event was not significantly different between bupropion-exposed and unexposed women (39.2% versus 39.3%, HR 0.93, 95% CI 0.73-1.19) and between NRT-exposed and unexposed women (44.8% vs 46.3%, HR 1.02, 95% CI 0.84-1.23), but it was significantly lower in women exposed to varenicline (36.9% vs 40.1%, HR 0.86, 95% CI 0.77-0.97). Varenicline-exposed infants were less likely than unexposed infants to be born premature (6.5% vs 8.9%, HR 0.72, 95% CI 0.56-0.92), be small for gestational age (11.4% vs 15.4%, HR 0.68, 95% CI 0.56-0.83) and have severe neonatal complications (6.6% vs 8.2%, HR 0.74, 95% CI 0.57-0.96). Among infants exposed to varenicline in the first trimester, 2.9% had a major congenital anomaly (3.5% in unexposed infants, HR 0.91, 95% CI 0.72-1.15). Varenicline-exposed women were less likely than NRT-exposed women to have an adverse perinatal event (38.7% vs 51.4%, HR 0.58, 95% CI 0.33-1.05).Conclusions: Pregnancy exposure to smoking cessation pharmacotherapies does not appear to be associated with an increased risk of adverse birth outcomes. Lower risk of adverse birth outcomes in varenicline-exposed pregnancies is inconsistent with recommendations that NRT be used in preference to varenicline. [ABSTRACT FROM AUTHOR]

Belonging to the order Atheriniformes, Craterocephalus is one of the most widespread genera of freshwater fishes in Australia, spanning along the northern coast from central Western Australia to central New South Wales and across the Murray-Darling and Lake Eyre basins. In this study, both conventional cytogenetic techniques (Giemsa, C-banding, CMA3/DAPI staining), and fluorescence in situ hybridization (FISH) with telomeric DNA and rDNA probes were used to examine the karyotypes and other chromosomal characteristics of Darling hardyhead (Craterocephalus amniculus) from New South Wales, Australia. We identified a diploid chromosome number 2n = 48 (NF = 58) in all studied individuals. FISH with rDNA probes showed a nonsyntenic pattern, with signals on one pair of subtelocentric chromosomes for 5S rDNA and one pair of submetacentric chromosomes for 28S rDNA. C-banding displayed the accumulation of constitutive heterochromatin in the centromeric regions of approximately 40 chromosomes. CMA3/DAPI fluorescence staining revealed extremely GC-rich signals in the pericentromeric region of one submetacentric chromosomal pair with size polymorphism. We detected telomeric signals at the end of all chromosomes and no interstitial signals. [ABSTRACT FROM AUTHOR]

Background: The prevalence and impact of musculoskeletal conditions are predicted to rapidly escalate in the coming decades. Effective strategies are required to minimise 'evidence-practice', 'burden-policy' and 'burden-service' gaps and optimise health system responsiveness for sustainable, best-practice healthcare. One mechanism by which evidence can be translated into practice and policy is through Models of Care (MoCs), which provide a blueprint for health services planning and delivery. While evidence supports the effectiveness of musculoskeletal MoCs for improving health outcomes and system efficiencies, no standardised national approach to evaluation in terms of their 'readiness' for implementation and 'success' after implementation, is yet available. Further, the value assigned to MoCs by end users is uncertain. This qualitative study aimed to explore end users' views on the relevance of musculoskeletal MoCs to their work and value of a standardised evaluation approach.Methods: A cross-sectional qualitative study was undertaken. Subject matter experts (SMEs) with health, policy and administration and consumer backgrounds were drawn from three Australian states. A semi-structured interview schedule was developed and piloted to explore perceptions about musculoskeletal MoCs including: i) aspects important to their work (or life, for consumers) ii) usefulness of standardised evaluation frameworks to judge 'readiness' and 'success' and iii) challenges associated with standardised evaluation. Verbatim transcripts were analysed by two researchers using a grounded theory approach to derive key themes.Results: Twenty-seven SMEs (n = 19; 70.4 % female) including five (18.5 %) consumers participated in the study. MoCs were perceived as critical for influencing and initiating changes to best-practice healthcare planning and delivery and providing practical guidance on how to implement and evaluate services. A 'readiness' evaluation framework assessing whether critical components across the health system had been considered prior to implementation was strongly supported, while 'success' was perceived as an already familiar evaluation concept. Perceived challenges associated with standardised evaluation included identifying, defining and measuring key 'readiness' and 'success' indicators; impacts of systems and context changes; cost; meaningful stakeholder consultation and developing a widely applicable framework.Conclusions: A standardised evaluation framework that includes a strong focus on 'readiness' is important to ensure successful and sustainable implementation of musculoskeletal MoCs. [ABSTRACT FROM AUTHOR]

In recent years, many droughts have happened over mainland Australia, especially the two severe prolonged droughts, from 2006 to 2009 and 2018 to 2020, resulting in serious water scarcity. Therefore, using the Total Storage Deficit Index (TSDI) from the Gravity Recovery and Climate Experiment (GRACE), we analyzed the two severe prolonged droughts from the perspective of the affected area, spatial evolution, frequency, severity and drought driving factors. The results show that the affected area of Drought 2006–2009 ranged from 57% to 95%, and that of Drought 2018–2020 ranged from 45% to 95%. Drought 2006–2009 took its rise in southeastern Australia and gradually spread to the central part. Drought 2018–2020 originated in the southwest corner of the Northern Territory and northern New South Wales, and gradually expanded to Western Australia and the whole New South Wales respectively. During Drought 2006–2009, Victoria suffered drought all months, including 59% mild drought and 41% moderate drought, North Territory had the highest drought severity of 44.26 and Victoria ranked the second high with the severity of 35.51 (cm months). For Drought 2018–2020, Northern Territory was also dominated by drought all months, including 92% mild drought and 8% moderate drought, the drought severities were in North Territory and Western Australia with 52.19 and 31.44 (cm months), respectively. Finally, the correlation coefficients between the two droughts and Indo-Pacific climate variability including El Niño-Southern Oscillation and Indian Ocean Dipole (IOD) are computed. By comparing the correlation coefficients of Drought 2018–2020 with Drought 2006–2009, we find that the impact of the El Niño on the hydrological drought becomes weaker while IOD is stronger, and the role of Southern Oscillation on droughts is diverse with the quite different spatial patterns. The results from Fourier analysis confirm that the two hydrological droughts are all related to Indo-Pacific climate variability but with slightly different driving mechanisms. [ABSTRACT FROM AUTHOR]