An insight into adolescent transition from rural to urban centres

[Abstract]: A cooperative research project between the Health Promotion Unit of the Health Department and the university is tracking the adjustment of adolescents leaving country towns to seek educational or employment opportunities in urban centres. Over 400 Queensland families willingly participated in the project, their enthusiasm reflecting the widespread concern in Australian country towns about the out-migration of their youth, their apparent failure to return and a sense of hopelessness about how to stem the flow. The project collects data on three occasions over a twelve month period during which time a proportion of the adolescents move to the city. Additional data are contributed by the family or caregiver and the school teacher. Only Time 1 data are available for this study which investigates how parent and child expectations and preferences are implicated in one of the key adolescent transitions, that of leaving a rural home and school to enrol in an urban boarding school. Data show some unexpected discrepancies and the discussion reviews some key features that could be important components for future health promotion intervention programs designed to prepare and support adolescents in transition

Predictive Modeling of Cholera Outbreaks in Bangladesh

Despite seasonal cholera outbreaks in Bangladesh, little is known about the relationship between environmental conditions and cholera cases. We seek to develop a predictive model for cholera outbreaks in Bangladesh based on environmental predictors. To do this, we estimate the contribution of environmental variables, such as water depth and water temperature, to cholera outbreaks in the context of a disease transmission model. We implement a method which simultaneously accounts for disease dynamics and environmental variables in a Susceptible-Infected-Recovered-Susceptible (SIRS) model. The entire system is treated as a continuous-time hidden Markov model, where the hidden Markov states are the numbers of people who are susceptible, infected, or recovered at each time point, and the observed states are the numbers of cholera cases reported. We use a Bayesian framework to fit this hidden SIRS model, implementing particle Markov chain Monte Carlo methods to sample from the posterior distribution of the environmental and transmission parameters given the observed data. We test this method using both simulation and data from Mathbaria, Bangladesh. Parameter estimates are used to make short-term predictions that capture the formation and decline of epidemic peaks. We demonstrate that our model can successfully predict an increase in the number of infected individuals in the population weeks before the observed number of cholera cases increases, which could allow for early notification of an epidemic and timely allocation of resources.Comment: 43 pages, including appendices, 5 figures, 1 table in the main tex

Computational method development for drug discovery

Protein-small molecule interactions play a central role in various aspects of the structural and functional organization of the cell and are therefore integral for drug discovery. The most comprehensive structural characterization of small molecule binding sites is provided by X-ray crystallography. However, it is often time-consuming and challenging to perform direct experimental analysis. Therefore, it is necessary to have computational methods that can predict binding site locations on unbound structures with accuracy close to that provided by X-ray crystallography. This thesis details four projects which involve the development of a fragment benchmark set, evaluation of allosteric sites in G Protein-Coupled Receptors (GPCRs), computational modeling of binding pocket dynamics, and the development of an Application Program Interface (API) framework for High-Performance Computing (HPC) centers. The first project provides a benchmark set for testing hot spot identification methods, emphasizing application to fragment-based drug discovery. Using the solvent mapping server, FTMap, which finds small molecule binding hot spots on proteins, we compared our benchmark set to an existing benchmark set that with a different method of construction. The second project details the effort to identify allosteric binding sites on GPCRs. We demonstrate that FTMap successfully identifies structurally determined allosteric sites in bound crystal structures and unbound structures. The project was further expanded to evaluate the conservation of allosteric sites across different classes, families, and types of GPCRs. The third project provides a structure-based analysis of cryptic site openings. Cryptic sites are pockets formed in ligand-bound proteins but not observed in unbound protein structures. Through analysis of crystal structures supplemented by molecular dynamics (MD) with enhanced sampling techniques, it was shown that cryptic sites can be grouped into three types: 1) “genuine” cryptic sites, which do not form without ligand binding, 2) spontaneously forming cryptic sites, and 3) cryptic sites impacted by mutations or off-site ligand binding. The fourth project presents an API framework for increasing the accessibility of HPC resources

Geogenomic segregation and temporal trends of human pathogenic Escherichia coli o157:H7, Washington, USA, 2005-2014

The often-noted and persistent increased incidence of Escherichia coli O157:H7 infections in rural areas is not well understood. We used a cohort of E. coli O157:H7 cases reported in Washington, USA, during 2005–2014, along with phylogenomic characterization of the infecting isolates, to identify geographic segregation of and temporal trends in specific phylogenetic lineages of E. coli O157:H7. Kernel estimation and generalized additive models demonstrated that pathogen lineages were spatially segregated during the period of analysis and identified a focus of segregation spanning multiple, predominantly rural, counties for each of the main clinical lineages, Ib, IIa, and IIb. These results suggest the existence of local reservoirs from which humans are infected. We also noted a secular increase in the proportion of lineage IIa and IIb isolates. Spatial segregation by phylogenetic lineage offers the potential to identify local reservoirs and intervene to prevent continued transmission

Breast education for schoolgirls; why, what, when and how?

Schools are fundamental settings for health education and adolescent females are an important group for promoting positive breast habits. We surveyed 2089 schoolgirls (11-18 years) to provide evidence for, and guidance on, breast education for schoolgirls. 26% reported negative feelings about their breasts and 87% reported ≥ one breast concern. 72% wanted to know more about breast cancer (69% rating this extremely important). >50% wanted to know more about breast sag and breast pain. Preferred delivery format was age eleven (50%), girls only taught sessions (41%) with female teachers (43%). A need for breast education and delivery preferences was identified

Habitat preferences, foraging behaviour and bycatch risk among breeding sooty shearwaters Ardenna grisea in the Southwest Atlantic.

Pelagic seabirds are important components of many marine ecosystems. The most abundant species are medium/small sized petrels (<1100 g), yet the sub-mesoscale (<10 km) distribution, habitat use and foraging behaviour of this group are not well understood. Sooty shearwaters Ardenna grisea are among the world’s most numerous pelagic seabirds. The majority inhabit the Pacific, where they have declined, partly due to bycatch and other anthropogenic impacts, but they are increasing in the Atlantic. To evaluate the sub-mesoscale habitat preferences (i.e. the disproportionality between habitat use and availability), diving behaviour and bycatch risk of Atlantic breeders, we tracked sooty shearwaters from the Falkland Islands during late incubation and early chick-rearing with GPS loggers (n = 20), geolocators (n = 10) and time-depth recorders (n = 10). These birds foraged exclusively in neritic and shelf-break waters, principally over the Burdwood Bank, ~350 km from their colony. Like New Zealand breeders, they dived mostly during daylight, especially at dawn and dusk, consistent with the exploitation of vertically migrating prey. However, Falkland birds made shorter foraging trips, shallower dives, and did not forage in oceanic waters. Their overlap with fisheries was low, and they foraged at shallower depths than those targeted by trawlers, the most frequent fishing vessels encountered, indicating that bycatch risk was low during late incubation/early chick-rearing. Although our results should be treated with caution, they indicate that Atlantic and Pacific sooty shearwaters may experience markedly differing pressures at sea. Comparative study between these populations, e.g. combining biologging and demography, is therefore warranted

e-Consent in UK academic-led clinical trials : current practice, challenges, and the need for more evidence

Peer reviewe

PyCogent: a toolkit for making sense from sequence

The COmparative GENomic Toolkit, a framework for probabilistic analyses of biological sequences, devising workflows and generating publication quality graphics, has been implemented in Python

"They're thinking, well it's not as bad, I probably won't get addicted to that. But it's still got the nicotine in it, so…":Maturity, control and socialising: Negotiating identities in relation to smoking and vaping. A qualitative study of young adults in Scotland

Objective: To explore the understandings of and engagement with e-cigarettes, of young adults from disadvantaged backgrounds, and how these may be impacting upon existing smoking identities. Methods: Twenty-two small group and 11 individual qualitative interviews conducted in Central Scotland with 72 16-24 year olds between September 2015 and April 2016. Participants were mostly smokers and ex-smokers from socio-economically disadvantaged backgrounds. Results: While most participants had tried e-cigarettes, they generally held ambivalent views about e-cigarettes and vaping. Two overarching themes were identified which helped understand this. Firstly, e-cigarettes were understood by the participants in relation to their existing smoking identities. Vaping was viewed as less controllable and more addictive than smoking, which did not fit with their self-identity as controlled smokers. Secondly, they felt that vaping could not replace the social and cultural importance that smoking had in their lives. Conclusion: This study suggests that while young adults from disadvantaged areas are trying e-cigarettes for various reasons, vaping is rarely sustained. Through their own experiences of vaping and their observations of others vaping, the participants perceive the behaviour as endangering an existing acceptable and controlled smoking identity. Additionally, e-cigarettes were considered to be a jarring presence in existing social situations were smoking was valued. This study therefore provides insights into how young adults may be rationalising their continued smoking in the face of potentially less harmful alternatives. Implications: As new and novel nicotine delivery devices, and due to their similarity to smoking, e-cigarettes have the potential to help smokers in their quit attempts. However, the findings from this study raise questions about whether e-cigarettes are regarded as having this potential by young adult smokers from disadvantaged socio-economic environments where smoking is more commonplace and acceptable