Integrating genealogical and dynamical modelling to infer escape and reversion rates in HIV epitopes

The rates of escape and reversion in response to selection pressure arising from the host immune system, notably the cytotoxic T-lymphocyte (CTL) response, are key factors determining the evolution of HIV. Existing methods for estimating these parameters from cross-sectional population data using ordinary differential equations (ODE) ignore information about the genealogy of sampled HIV sequences, which has the potential to cause systematic bias and over-estimate certainty. Here, we describe an integrated approach, validated through extensive simulations, which combines genealogical inference and epidemiological modelling, to estimate rates of CTL escape and reversion in HIV epitopes. We show that there is substantial uncertainty about rates of viral escape and reversion from cross-sectional data, which arises from the inherent stochasticity in the evolutionary process. By application to empirical data, we find that point estimates of rates from a previously published ODE model and the integrated approach presented here are often similar, but can also differ several-fold depending on the structure of the genealogy. The model-based approach we apply provides a framework for the statistical analysis of escape and reversion in population data and highlights the need for longitudinal and denser cross-sectional sampling to enable accurate estimate of these key parameters

Cockatoo Sands in the Victoria Highway and Carlton Hill areas, East Kimberley: baseline surface water quality

Cockatoo Sands are recognised as potentially suitable for irrigated agriculture because they are generally well drained and not subject to waterlogging and inundation. These characteristics allow them to be cultivated and prepared for planting of various crops during the wet and dry seasons of northern Australia

Role Of Digital Health Wearables In The Wellbeing And Quality Of Life Of Older People And Carers

The number of adults aged 65 and over has increased by 2% across Europe in the past 15 years, and in Northern Ireland by 22% between 2003-2013. The proportion of the population in this age group is projected to increase by 63% to just under 0.5 million by 2033 – which will be a quarter of the population in Northern Ireland. Given Northern Ireland’s Active Ageing Strategy (2015-2021), there is an increasing focus on encouraging physical activity as we get older to preserve mobility and motor skills, and to enjoy the benefits of living longer and to minimise health problems associated with ageing. Over the last two years, we have been investigating the role of wearable activity tracking technologies in self-monitoring of activity by people aged over 55. Example technologies include activity trackers from Fitbit, Garmin and Samsung, and smart watches. Typically, these devices record steps walked, sleep patterns, calories expended and heart rate. Based on empirical investigations, this policy paper describes the benefits of activity monitors for people aged over 55 for self-monitoring of physical activity, for adopting healthy lifestyles, and for increasing or maintaining physical activity as a way to avoid high blood pressure, obesity, diabetes, and other medical conditions associated with weight or lower physical activity. It outlines the role of activity trackers in post-operative monitoring of mobility during rehabilitation, in caring, and for possible use of the data for diagnosis and medical interventions. It then discusses the challenges for adoption of these technologies, given currently, off-the-shelf devices are designed and calibrated for use by physically fit (typically young active people) with unrealistic fitness targets for the older generation

Investigating the influence of wearable activity - tracking technologies on behaviour change in people aged 55 and over

Our research project (http://www.shaileyminocha.info/digital-health-wearables/) at UK’s Open University and in collaboration with Age UK Milton Keynes aims to investigate whether behaviour changes in people aged over 55 years through the use of wearable activity-tracking technologies. Example technologies include those from Fitbit, Jawbone, or smart watches from Apple or Samsung. Typically, these devices record steps walked, sleep patterns, or calories expended.    The benefits of regular physical activity for older adults and those with chronic disease and/or mobility limitations are indisputable. Regular physical activity attenuates many of the health risks associated with obesity, cardiovascular disease, diabetes, depression and anxiety, and cognitive decline. As physical activity levels among older adults (both with and without chronic disease) are low, facilitating an increase in activity levels is an important public health issue. Walking has been identified as an ideal means of low-impact, low-risk physical activity that can boost physical and mental wellbeing. An author of a recent study said: “Physical activity may create a ‘reserve’ that protects motor abilities against the effects of age-related brain damage”. Walking has been shown to improve cognitive performance in older people. Our previous research has shown that walking with others can help reduce social isolation and loneliness among people aged 55 and over. In our year-long project (May 2016 – April 2017) and funded by the Sir Halley Stewart Trust, we have given activity-trackers to 17 participants in the age range from 55 – 80. Through monthly workshops, diaries that the participants are maintaining and sharing with us on a weekly basis, and through one-to-one interviews with them, we are investigating how the behaviours of our participants is changing – whether there is an increase in their activity such as walking or gardening, lifestyle changes, attitudes towards food/diet, and so on. There is already some evidence emerging such as: increase in activity levels in all the participants; increased awareness of food intake; and sharing of data with the GPs to diagnose the non-optimal sleep patterns (one of them now has a treatment plan in place for poor sleep). A couple of participants have joined the gym when they realised that their desk-based work-life doesn’t give them the opportunity to stay active during the week. In addition, we have conducted two surveys: the first survey is aimed at people aged 55 years and over who are already using these devices - to investigate their experiences and the changes in their behaviours that they perceive; and the second survey is aimed at medical professionals to explore whether they use the data from these devices for diagnosis and intervention. Most importantly, do medical professionals use data from these devices to determine the behaviour or lifestyle changes in people aged over 55 years? The Open University's Human Research Ethics Committee has approved the research design of this project (HREC/2016/2191/Minocha/1)

Seasonal and interannual variability of North American isoprene emissions as determined by formaldehyde column measurements from space

Formaldehyde (HCHO) columns measured from space by solar UV backscatter allow mapping of reactive hydrocarbon emissions. The principal contributor to these emissions during the growing season is the biogenic hydrocarbon isoprene, which is of great importance for driving regional and global tropospheric chemistry. We present seven years (1995-2001) of HCHO column data for North America from the Global Ozone Monitoring Experiment (GOME), and show that the general seasonal and interannual variability of these data is consistent with knowledge of isoprene emission. There are some significant regional discrepancies with the seasonal patterns predicted from current isoprene emission models, and we suggest that these may reflect flaws in the models. The interannual variability of HCHO columns observed by GOME appears to follow the interannual variability of surface temperature, as expected from current isoprene emission models

Position estimation using the Digital Audio Broadcast (DAB) signal

Over the past decades, there have been a number of trends that have driven the desire to improve the ability to navigate in all environments. While the Global Positioning System has been the driving factor behind most of these trends, there are limitations to this system that have become more evident over time as the world has increasingly come to rely on navigation. These limitations are mostly due to the low transmission power of the satellites, where navigation signals broadcast from space are comparatively weak, especially by the time they have travelled to receivers on the ground. This makes the signals particularly vulnerable to fading in difficult environments such as "urban jungles" and other built up areas. The low signal-to-noise ratio (SNR) also means, that the signals are susceptible to jamming, both hostile and accidental. This motivates the need for alternatives technologies to satellite navigation and consider terrestrial based alternatives such as LORAN-C and eLORAN, but there is also significant interest in the exploitation of other non-navigation signals for positioning and navigation purposes. These so-called 'Signals of Opportunity' do not generally require any alterations to existing communications transmission infrastructure and utilise alternative multi-carrier modulation techniques to those used by navigation systems. This project examines the use of such a signal, the Digital Audio Broadcast (DAB) signal, as a positioning source. This thesis contains complete research from initial coverage simulations in the UK, through to extensive static testing, and the use of the signal in a dynamic environment and it has been shown that the Digital Audio Broadcast signal has potential as a terrestrial based positioning signal

Designing an institutional network for improving farm animal welfare in the EU

Improvements in the welfare of farmed animals in the EU have been achieved by legislation, increased welfare capacity in the food chain, greater public awareness, welfare measurement tools and dissemination of best practice. However, pressure for improvement grows. The EC recognises that delivering improved welfare would best be achieved by increasing welfare capacity, including establishing a Network of Welfare Reference Centres to provide support for welfare research, knowledge transfer and policy design. Designing a structure for this Network presents a challenge, as it would have multiple functions, interact with diverse stakeholders and operate in a complex environment. Here, we describe the use of a novel strategic planning approach to design an optimal structure for this Network. Our evaluation found that no existing structure was ideal, but that by taking functional units from several existing models, an optimal model could be identified

The influence of incorporating a forecutter on the performance of offshore pipeline ploughs

AbstractInstallation of offshore pipelines in the seabed can be efficiently achieved using pipeline ploughs. Increased efficiency may be achievable through incorporating a smaller forecutter in advance of the main plough share. Currently guidance is limited and conflicting as to the advantages or disadvantages of incorporating a forecutter. To investigate the effect of forecutter inclusion model tests were undertaken at 1/50th scale under laboratory conditions in sand beds prepared at different relative densities in both dry and saturated conditions. Dry sand tests were used to determine the effect of the forecutter on the static or passive components of plough tow force. The currently adopted passive pressure coefficient (Cs) did not appear to vary with relative density to the same degree as previously suggested and the forecutter increased the magnitude of the passive or static resistance to ploughing. Saturated tests were used to determine the effects of the forecutter on the rate dependant component of ploughing resistance and allow verification of a dimensionless form of rate effect representation. The forecutter acts to reduce the rate effect component of plough tow force in both fine sand (low permeability) and to a lesser extent in medium sand (higher permeability). In fine and silty sands, however, incorporating a forecutter would seem highly beneficial at all ploughing depths and soil densities but in medium sand (higher permeability) the benefits of incorporation are limited to an operating window at shallower trench depths and lower relative density

Social isolation and loneliness in people aged 55 and over in the UK

In association with Age UK Milton Keynes, we have conducted research to investigate the conditions that lead to social isolation and loneliness among older people (55 years and above) in Milton Keynes, and to recommend possible strategies and solutions to prevent and mitigate isolation. The project was funded by the Milton Keynes Council and commissioned by the Senior Joint Commissioner, Adult Community Services. The research has involved a review of academic and policy literature on social isolation and loneliness, and an information gathering exercise that included expert workshops, individual and group interviews, and site visits. This talk will be based on the project's report (http://oro.open.ac.uk/43925/) and will discuss several case studies of older people and interventions for social isolation and loneliness within Milton Keynes. We hope that the recommendations and the resources from our report and in this talk would be useful for other communities, towns and cities, who may also be facing the challenges of supporting an ageing population. Taking the example of an online photo journal which encourages users to document their life with just one photo each day, we will discuss how online social interactions influence the lives of older people, the challenges that they face, and the concerns that they have about being online

Social isolation and loneliness in people aged 55 and over in Milton Keynes: the way forward

The Ageing Well and Living Well Scoping Workshop was organised by Gail Addison, Head of Public Health – Delivery, People Directorate, Milton Keynes Council in collaboration with Age UK Milton Keynes. The aims of the workshop were to: • Explore the connectivity between the Health and Wellbeing Board (HWB) and existing Partnership and Programme Boards across Milton Keynes • Explore the remit of the Partnership and Programme Boards in order to identify commonalities and fit with the HWB Board’s Strategic Implementation Plan and Priorities, including; • Social Isolation (Priority focus for Ageing Well partnership) • Reducing Obesity (Priority focus for Living Well partnership) • Identify next steps and commitment to action At this workshop, Professor Shailey Minocha of The Open University along with Jane Palmer, CEO, Age UK Milton Keynes led the track on social isolation and loneliness in people aged over 55 years in Milton Keynes. We highlighted the effects of social isolation and loneliness on the well-being and quality of life of people. For example, individuals lacking social contact carry a health risk equivalent to smoking up to 15 cigarettes in a day. We discussed the societal impacts of social isolation such as increased use of health and social care services, higher number of emergency admissions and GP consultations, slower discharge from hospitals which causes pressure on financial resources and health services. We outlined the risk factors of social isolation and particularly in the context of Milton Keynes. Drawing on from our report (http://oro.open.ac.uk/43925/), we emphasised the challenges for the community and for older people due to the increasing population of older people in Milton Keynes. We presented possible solutions for addressing the problem of social isolation and loneliness in Milton Keynes in three categories: one-to-one interventions (e.g. visits by community home visitors, regular phone conversations, visits by neighbours); group interventions (e.g. Men in sheds, lunch clubs, coffee mornings, inter-generational initiatives – for example, learning to get online, walking groups, local history society) and wider community and neighbourhood interventions such as encouraging older people to be volunteers; co-designing the programmes with older people - e.g. neighbouhood watch programmes and design of age-friendly design of spaces – local neighbourhoods and city centre in Milton Keynes