Supervisors:

Dr David Richards, MRC Career Development Fellow, Senior Lecturer, Physics and Astronomy, University of Exeter.

Dr Melanie White, ARC Future Fellow - GL Institute for Molecular Bioscience, University of Queensland.

Project Summary

How the central nervous system develops from its embryonic precursor, the neural tube, is still only poorly understood. Rectifying this is important since incorrect formation of the neural tube leads to developmental defects that account for some of the most common and severe birth defects in humans. As such, this topic is crucial for healthy living, particularly for ensuring healthy lives of children and improving global life expectancy.  Progress in this area has been hampered by the lack of an animal model that is sufficiently close to human but is still genetically tractable. Avian embryos are a better model of human neural tube development than fish or rodents, but their utility has been hampered by the difficulty of making transgenic birds. However, we have recently been involved in developing an innovative, novel quail model that has the potential to lead to a step change in the field. Importantly, this model has a substantially shorter generation time than the chicken and a number of key transgenic lines have recently been developed. 

To make progress, a purely experimental approach is unlikely to be optimal. Instead a multidisciplinary approach that intimately combines mathematical modelling, computer simulation, live imaging and automatic image analysis is needed. By combining a theoretical group at the University of Exeter with an experimental group at the University of Queensland, this is precisely what this PhD will involve.  This cross-disciplinary PhD will involve the student spending time in both the Richards Group in the Living Systems Institute (Exeter), performing the mathematical modelling, computer simulations and image analysis, and the Dynamics of Morphogenesis Lab (Queensland), capturing time-lapse images of neural tube formation.

The student will also join the new Quantitative Health Network in Exeter in order to obtain a broad understanding of the role of mathematical modelling throughout biology and human health.  The project will investigate the dynamic mechanisms that control neural tube development, focusing on the roles of cell fate determination, the biophysical forces involved, the role of the actin cytoskeleton, and the spatiotemporal coordination across multiple scales.  Public involvement will also play an important part in this studentship. The student will work directly with the MAGPIEs (a group of lay people involved in medical research at the University of Exeter) in order to disseminate results, guide research and ensure that future impact is achieved.

Project Description:

This project will study how the neural tube develops in a quail animal model, with applications to understanding developmental defects that account for some of the most common and severe human birth defects.  The overall aim is to develop a novel mathematical model, driven by time-lapse imaging, of the spatiotemporal dynamics of neural tube development. This model will then be used to suggest potential avenues for tackling related birth defects. Key questions that will be addressed include how biophysical forces and cell fate specification interact to generate the spatiotemporal pattern, the role of the actin cytoskeleton, and how system robustness is achieved.  One of the chief advantages of this project is its multidisciplinary nature, intimately combining wet-lab work and theoretical work. This interdisciplinary combination is increasingly being used in both biological and biomedical research, and will give the student an excellent, highly sought-after skillset that will place them in a strong position with a broad range of future career options. 

The project will involve the following three objectives:  (1) High-resolution long-term time-lapse imaging (based on expertise in Queensland). The student will perform confocal imaging of the developing neural tube in transgenic quail embryos expressing various markers of the nucleus, cell membrane, actin cytoskeleton and cell fate markers. Quail embryos will be cultured on agar-albumin in glass-bottomed imaging dishes for 48 hours from the start of neural tube formation using a protocol optimised in the White group. Cellular dynamics of the developing neural tube will be visualised by capturing confocal images every 7 minutes at 40x magnification for ~16 hours.  (2) Automatic image analysis (based on expertise in Exeter). Building on existing custom-built software within both the Richards and White groups, software will be developed that automatically segments and tracks cells in the developing neural tube. This will involve a combination of blob detection, edge detection, thresholding and Hough transforms. Tracking between frames will use a custom-built Hungarian algorithm. Cell division will be identified as in the recent work by Katie McDole et al. and others.  (3) Mathematical modelling (based on expertise in Exeter). A mathematical model/computer simulation will be designed based on a vertex model that the Richards group have already developed to describe an earlier stage of development. Cells will be described by marker points that move due to vertex-vertex forces. Vertices will be connected by springs with a tension force governed by a viscoelastic extension of Hooke’s law. Other forces will operate, including a curvature force (given by the Helfrich energy), an intracellular actin force and a volume conservation force. Cell-to-cell interaction and signalling will be included at adjacent cells.

How to Apply:

https://www.exeter.ac.uk/study/funding/award/?id=4495

Supervisors:

Dr Bert Bond, Sport and Health Sciences, University of Exeter.

Prof Simon Smith, Professorial Research Fellow, nstitute for Social Science Research, Faculty of Humanities and Social Sciences, University of Queensland.

Project Summary

Just one night of poor sleep is known to impair cognitive function, whilst habitual sleep loss may accelerate cognitive decline with ageing and increase dementia risk. Despite this, approximately 75% of the Great British public fail to achieve 7 hours of sleep per night. Furthermore, only 20% of Australians sleep through the night uninterrupted, which is thought to cost $45.2 billion per year (including direct healthcare costs and productivity losses).
 
The ways in which sleep influences these important outcomes is not well understood, and interdisciplinary research is needed to address this contemporary and pertinent public health concern. Emerging evidence indicates that both sleep quantity and quality may be important, in addition to an individual’s preferred sleep-wake timing (“chronotype”). All three of these dimensions of sleep health have been linked to cognitive and health outcomes, and all three change over the lifespan. Specifically, habitual sleep duration is greatest in young people and declines with age, whilst older adults may experience poorer sleep quality and changes in sleep timing. Adolescents represent the age group with the most extreme propensity towards going to, and rising from, bed later (i.e. a “night owl” rather than “morning lark”). This change is thought to be an intrinsic part of pubertal maturation, and may explain why cognitive function tends to be higher in the afternoon compared to the mornings in this group. Following adolescence, there is a gradual shift towards sleeping and rising earlier, which becomes particularly pronounced in older adults.
 
This PhD studentship intends to scrutinize the influence of sleep loss across the lifespan in order to further our understanding of the importance of sleep quantity, quality and chronotype on outcomes related to learning and cognitive decline. These include both functional, and physiological measures, which will be assessed in a series of interventional studies. The research will pool expertise across a diverse field, including vascular physiology, sleep science and biomedical engineering, in order to provide insight from a powerful, multi- and inter-disciplinary perspective. In so doing, the collaboration will enhance the research capacities of both laboratories (Exeter and Queensland). This knew knowledge and shared expertise will then provide an excellent platform from which to attract future funding from grant bodies concerned with not only ageing and dementia, but also learning and education policy.

Project Description

Sleep is an essential recuperative and restorative process. Just one night of sleep loss has been shown to impair a variety of cognitive abilities. These abilities are essential for learning, work, social participation, and independence throughout life. Habitual sleep loss is also a risk factor for cognitive decline and dementia. Accordingly, understanding how sleep influences these processes is an important research priority.

The brain stores very little energy, which means that increases in cerebral metabolism during a cognitive task must be supported by region-specific brain blood flow. The ability to match increases in brain activation with blood flow (“neurovascular coupling”) is critical for cognitive health. This ability generally declines with age, and is thought to precede cognitive decline and dementia. Alterations in this fundamental process are also observed following sleep loss, and may contribute to the alterations in cognitive ability associated with poor sleep. However, few studies have experimentally addressed this.

There is also a tight coupling between cerebral metabolism and blood flow during sleep, and this is dynamic across sleep stages. For example, brain blood flow increases during rapid eye movement (REM) sleep. Reduced blood flow during REM sleep has been associated with poorer cognitive function and implicated in cognitive decline. Rhythmic neural activity and arterial pulsations in the brain during non-REM sleep are also thought to aid the clearance of ’waste’ compounds from the brain, but the effectiveness of this “pump” may be lost without close neurovascular coupling. Emerging data indicate that these processes are also altered due to sleep loss, and may provide a further mechanism that links poor sleep to poor daytime cognitive outcomes.

The aim of this PhD studentship is to address these research gaps in order to better understand the relationship between sleep, cognitive function and cerebrovascular function. To do so, will require symbiotic collaboration between research groups at Exeter and Queensland.

Adolescents, adults, and older adults will be recruited into a series of experimental trials, utilising existing links (e.g. local schools) and infrastructure (the Exeter 10,000). Sleep will be manipulated via established paradigms including partial or complete sleep restriction, and via manipulation of circadian timing of sleep and wake times. This will only be possible via expertise from Drs Smith and Mann (Queensland). We will observe the influence of these manipulations in sleep on a variety of age-appropriate cognitive outcomes in each age group. These may include measures of reaction time, cognitive throughput, decision making and risk, attention and concentration, and potentially other indices such as wake EEG, heart-rate variability, and pupillometry. We will also quantify any changes in the coupling between cerebral metabolism and brain blood flow across a variety of cognitive challenges by using the minimally obtrusive transcranial Doppler techniques which Dr Bond has extensively used in adolescents and adults (Exeter).

Finally, the adolescents recruited in Year 1 of the PhD will be invited back in Year 3, in order to understand whether the effects of sleep loss change across pubertal maturation, which is a contemporary concern amongst education policy makers.

How to Apply:

https://www.exeter.ac.uk/study/funding/award/?id=4496

Supervisors:

Dr Saffron O'Neil, Associate Professor in Geography, University of Exeter.

Professor Roland Bleiker, Professor of International Relations, Peace Studies and Political Theory University of Queensland.

Project Summary

How the media communicate about climate change both shapes and reflects how society engages with the issue. Whilst social scientists have long sought to understand how the media represent climate change in text form, there has been far less research on how climate change is represented in visual imagery. Yet images are a key part of setting the ‘frame’ of a media story: they are vivid, colourful and memorable - drawing readers in, giving them the essence of a story, what should be done about it, and whose responsibility it is. If particular types of visual frame become dominant, they privilege certain groups in society (and marginalise others), influence public opinion and shape policy options.  Climate stories increasingly use the news hook of migration. Migration is a hugely contentious policy issue, not least in Australia and the UK. The role of climatic changes in impacting migration is increasingly contested, too: from fantastical (albeit contentious) numbers of migrants crossing international borders, to claims migration is one of the most powerful tools for facilitating adaptation. So, which imaginaries are invoked when climate migration is visualised? Which voices do these visual frames privilege (and which are marginalised)? How might a more diverse and equitable visual narrative of climate migration challenge and unsettle these power relations?

This project brings together the following supervisory team:  Lead supervisor A/Prof Saffron O’Neill has held two fellowships on the visual communication of climate change (ESRC Future Leaders, Leverhulme Research Fellow) and works with a diversity of stakeholders on climate communication (including the IPCC, Getty Images, Studio Silverback, Climate Outreach). Second supervisor Professor Roland Bleiker explores the politics of aesthetics, visuality and emotions, which he examines across a range of issues, from humanitarianism, security and peacebuilding to protest movements and conflict. He leads the ARC Linkage Project ‘The Politics and Ethics of Visualising Humanitarian Crises’, with the World Press Photo Foundation, the International Committee of the Red Cross, the Australian Red Cross and Médecins Sans Frontières.   There is a secondary supervisor at both UoE and UQ. Dr Ricardo Safra de Campos (UoE) is a population geographer working on the spatial mobility dimensions of human interaction with environmental change, with a focus on migration. Professor Karen McNamara (UQ) is a development geographer interested in how livelihoods can be enhanced to respond to the triple crises of poverty, disaster risk and climate change. She has extensive experience working throughout the Asia-Pacific.

Project Description

We propose an interdisciplinary, multi-method and sequential design. A suitable research programme could encompass the following (though the student would develop this with the supervisory team, subject to their own interests and expertise): 

Study one could seek to document the current visual discourse of climate and migration, and to place it in socio-political context. It might use a critical visual discourse analysis of climate and migration visuals, sourced from a diversity of outlets including the news media, white papers and policy documents. Additionally, study one could document the sources of these images, to further understand the news production dimensions of climate-migration imagery. This analysis could be carried out as a cross-cultural comparison between Australia and the UK. 

Study two would look to understand the drivers behind the production of dominant visual frames of climate and migration, as well as opportunities and barriers to overcoming dominant visual discourses. Drawing on contacts arising from the PhD advisors as well as the findings from study one, the student would undertake a range of stakeholder interviews (e.g. photojournalists, image library curators, editors, charities, thinktanks, academics). Again, this second study would seek perspectives from both UK and Australian stakeholders (and beyond); recognising that national borders constrain news media less and less in our increasingly internationally-mediated news media ecosystem. Many of the interviews would happen in online fora (zoom, Teams), though provision in the RTSG would allow the student to travel to centres of news production (e.g. London for UK media) in order to undertake interviews in-person as circumstances allow. Study two will benefit from the experience of one of O’Neill’s current PhD students (Hayes), who used a similar methodological approach in UK newsrooms during 2021-22. 

Study three could look to intervene in the visual politics of climate and migration, by opening up the visual discourse through action research. The student could work with a community group impacted by visual discourses of climate and migration in order to co-produce a more equitable and empowered visual discourse. This might be through re-imagining (climate changed) futures in a Small Island State in the South Pacific (to challenge the common and highly disempowering visual narrative of ‘sinking islands’). A potential link is with Kathy Jetn̄il-Kijiner, founder of Marshall Islands charity Jo-Jikum, as they have an ongoing climate-arts programme which seeks external collaborators - but this is a relationship which will be initiated by the student through the PhD.

The student would start their PhD in January 2023. They will spend 12 months at UQ, and the remainder at UoE. It is anticipated that the student would spend three months at UQ in year 1 (Apr-Jun 2023), to consolidate links with Bleiker, and work on their literature review and upgrade document.

The second period at UQ could occur in year 2 (Apr-Jun 2024), to enable data collection with Australian news media organisations.

We anticipate the final period at UQ to occur in year 2-3 (Dec 2024-Jun 2025), to enable the student to undertake fieldwork in the South Pacific.

How to Apply:

https://www.exeter.ac.uk/study/funding/award/?id=4497

Supervisors:

Professor David Tollerton, Associate Professor in Memory Studies, University of Exeter.

Dr Kirril Shields, Atrocity Prevention Grants Program Manager, University of Queensland.

Project Summary:

Within academic genocide studies, recent years have witnessed a significant growth in scholarship
addressing environmental issues. The proposed project will move this research forward by being

- future-oriented – concerned with the potential for climate breakdown to increase the
competition for resources, mass-migration, and socio-political stresses that collectively make
instances of mass violence more likely.

- policy-oriented – concerned with forging better connections between climate policy and
genocide prevention in the work of governments and NGOs.

The project will be centred on addressing three key research questions:

1. How are genocide prevention actors currently engaging with climate change issues, and how
might they more effectively target contexts most vulnerable to the effects of climate
breakdown?

2. How can public memorialisation and education related to past genocides more effectively
sensitise participants to the future interconnections between climate breakdown and mass
atrocity?

3. How can public, organisational, and governmental discourses on climate crisis incorporate
an increased awareness of genocide prevention?

For the studentship holder, there will be broadly three steps required of the research:

1. Establishing the state of scholarship on links between climate stress and genocide.

2. Establish the extent to which public bodies involved with genocide prevention and climate action are conscious of such links. It is anticipated that interviews with key actors will form a substantial part of this work.

3. Establish means by which to improve awareness of the connections between threats of
climate breakdown and mass violence.

Alongside the doctoral thesis, the studentship holder will be expected to work with the supervisory
team and selected external organisations to produce and disseminate two public reports: the first
targeted at participants in genocide prevention and remembrance work; the second addressing
climate policy actors in the UK and Australia. The aim of the project is to thus impactfully drive
forward the development of interconnections between climate action and genocide prevention, in
this way contributing toward the resilience of climate vulnerable communities.

The project will utilise networks already embedded into Exeter’s Green Futures research strand and
Queensland’s Asia Pacific Centre for the Responsibility to Protect, though also forge links with
organisers of the new $3.5 million Brisbane Holocaust Museum & Education Centre as well as the
UK/Rwanda-based Aegis Trust for the Prevention of Crimes Against Humanity.

The proposed studentship uses resources and supervisory expertise unique to the Exeter-
Queensland partnership to impactfully develop a currently underdeveloped connection between
climate research and genocide studies."

How to Apply:

https://www.exeter.ac.uk/study/funding/award/?id=4498

Supervisors:

UQ - Dr Duncan Keenan-Jones, Associate Professor Pauline Pounds

Exeter - Dr Daniel King, Dr Maria Gerolemou

Project Description:

Digital and disruptive technologies are changing all aspects of our modern world, including how we do ancient history and archaeology. Digital textual analysis from the text to the corpus scale is changing our understanding of ancient authors and their work. Geophysics and coring are informing and, often, replacing excavation. Photogrammetry, cloud digital forms and laser scanning are replacing traditional methods of recording. Archaeological science is answering new questions about sites and archaeological materials. 3D computer-aided design (CAD) is one such digital, disruptive technology. It has the potential to revolutionise our understanding of ancient technologies.

Hero claims that he has improved the feasibility and reproducibility of previously described devices. Some of Hero’s texts also purport to be Do-It-Yourself guides to building your own devices. This project aims to investigate the extent to which Hero’s writings were a technical treatise, exaggeration/self-aggrandisement and/or a playful work of imagination. How much prior knowledge was required to follow Hero’s instructions? To what extent was Hero a practical automaton-maker?

We have assembled the perfect supervisory team for this project. UQ provides the expertise in 3D modelling and mathematical simulation (Pounds and Keenan-Jones), and in the history of the Roman Empire and its technology (Keenan-Jones). Duncan Keenan-Jones (Classics and Ancient History, UQ) is pioneering digital experimental archaeology. At the University of Glasgow, he carried out a similar project investigating a different device of Hero’s Assoc. Prof. Pauline Pounds (Engineering, UQ) runs a robotics and SolidWorks design laboratory with undergraduate and postgraduate students that is the ideal community of practice for the PhD student and project.

Exeter provides expertise in the Greek language, literature (King and Gerolemou) and science, especially Hero of Alexandria (Gerolemou). Dr King’s research focuses on the impact that Greek culture has had on the later world. Dr Gerolemeu is an expert on Hero of Alexandria and his texts in particular.

The project will follow this schedule (including approaches and methods):

• Framing and planning of the project (UQ, January – February 2023)
• Literature review and research into Hero, his predecessors, his devices and writings (Exeter, February – July 2023)
• literature review of the Roman Imperial context in which Hero was writing and of relevant ancient technologies, including previous modelling, simulation and experimental archaeological approaches to them (UQ, July – October 2023)
• SolidWorks training and construction of 3D models of Hero’s devices and improvements proposed by later scholars(UQ, October 2023 -July 2024)
• Mathematical simulation of the operation of Hero’s devices (UQ, July – November 2024)
• Detailed interpretation of the results in the context of Hero and his writings and Greek literature (Exeter, November 2024  – April 2025) and the Roman Empire (UQ, April – August 2025)
• Final completion and compilation of drafted sections on each component, completion of thesis (UQ, August – December 2025)

How to Apply:

https://scholarships.uq.edu.au/scholarship/quex-phd-scholarship

Supervisors:

UQ - Dr Mashhuda Glencross, Dr Lisa Bode, Dr Ivano Bongiovanni, Associate Professor Stephen Viller

Exeter - Dr Mathilde Pavis

Project Description:

Background & Context

Advances in computer graphics, use deep generative models to synthesise 3D models and reflectance for visual realism (Seymour 2021). Humans are closely attuned to notice flaws in digital characters, the “uncanny valley” suggests imperfect synthetic characters closely resembling us, provoke an uncomfortable emotional response (Mori 1970). Neural rendering techniques can now create visually realistic digital characters from video surpassing this uncanny valley. While realistic human AI behaviour is lagging, the near future will bring convincingly approaches for driving them algorithmically. The past two years has seen legitimate applications of deepfake technology aimed at corporate communications, digital assistants, digital companions etc. For these to be effective, much like trust in internet technologies (Worthy 2016), trust in legitimate deepfakes is crucial.
 
Governments have introduced a raft of regulations, reforms and invested in detection to contain the harms associated with misuse of deepfakes (Kampf & Kelley 2018; Knight 2018). These include stability of states or organisations (by disrupting elections, sabotage, blackmail) and the autonomy of individuals (through harassment or identity theft). Less attention has been focussed on the benefits and commercial applications of the technology for which trust plays a critical role (Pavis 2021). This project fills an important gap in both the technology and knowledge for policy-making and law.

Aims & Objectives

This interdisciplinary PhD proposes technological interventions for conveying trust in legitimate digital humans created using AI while safeguarding the interests of users. Outputs will include:

1. an interdisciplinary doctoral thesis blending knowledge in Human Computer Interaction and Law
2. up to three academic journal articles
3. appropriate policy briefs;

Methods & Approaches

Adopting a codesign methodology (designing with stakeholders), the student will begin by studying human-digital character interaction in three application contexts. Using opensource deepfake tools (eg. DeepFaceLab), the student will implement these to study trust in each and understand the influences of context and realism.

1. A social conversation
2. An application to alleviate loneliness
3. Online home medical help for the elderly

The legal study will be conducted using a speculative design approach to generate a broad range of scenarios and analyse the extent and likelihood of security threats that interactions with digital humans pose in legitimate applications. These will be classified by risk timeline and analysed in the context of legal frameworks in Australia and the UK to investigate how law and policy will adapt to these.

Finally, technological interventions (overlays that can be added to digital humans), will be co-designed and evaluated to build trust in the information communicated as well as show users where the provenance of the character is questionable.

Expertise of supervisory team

Dr Glencross is a leading scholar in Computer Graphics. Dr Pavis is a leading scholar in Law and human digitisation. Dr Bode brings expertise in histories of perception and illusion, Dr Bongiovani brings expertise in information security and Dr Viller brings expertise in interaction design.

The supervisory team is uniquely placed to supervise this PhD project due to their complementary expertise and experience in bringing PhD students to completion.

How to Apply:

https://scholarships.uq.edu.au/scholarship/quex-phd-scholarship

Supervisors:

UQ - Dr Mashhuda Glencross, Associate Professor Stephen Viller

Exeter - Professor Tim Lenton, Dr Iain Soutar

Project Description:

Background & Context

EV vehicle adoption is only just beginning in Australia and an opportunity exists to develop technology to drive its adoption together with that of related technologies triggering tipping cascades. This interdisciplinary project brings together experts in Information Technology and Complex Systems Science with expertise in energy data visualisation, interaction design and climate change. The strengths of both the UQ and Exeter supervisory teams will be core to the success of the project.

Aims & Objectives

This PhD project proposes technological interventions for driving adoption of EVs (and related technologies) by triggering tipping-cascades for their adoption. Outputs will include:

1. an interdisciplinary doctoral thesis bridging knowledge in Information Technology, Complexity Science, Earth System Science and non-linear economics
2. up to three academic journal articles
3. appropriate software tools;

Methods & Approaches

This project will be carried out in three phases:

Phase 1: Data Gathering and Analysis

This part of the project will focus on studying the adoption pattern of rooftop solar in Australia and identifying the features and policies that led to the tipping point in adoption of this technology. A study of the patterns of adoption of EVs in Australia, the UK and Norway will also be carried out. These will be compared to see where the UK and Australia lie in the pattern of EV adoption versus Norway. The EV pattern of adoption will also be contrasted with that of rooftop solar and batteries in Australia. The PhD student will also analyse these patterns over time and their relationship to policy in each of the countries.

Phase 2: Visualisation Design

The data and analysis from the first phase will form the basis for design of visualisations to communicate patterns of adoption discovered and align them with events triggering a tipping point or tipping cascades. Several different visualisations will be designed to explain patterns in rate of adoption of rooftop solar, batteries and EVs, temporal difference in adoption patterns between countries, location of adoption (e.g. cities vs rural), key trigger events in the adoption timeline and predictive visualisations based on current patterns and triggers.

Phase 3: Digital Applications

The first two phases will be used as input patterns to detect and predict tipping points and events that could trigger tipping cascades. These, together with co-designed applications connecting motivated communities that have already adopted rooftop solar into energy focussed social networks will be prototyped. These prototype applications will be evaluated for how effectively they motivate adoption of EVs, batteries and related low-emissions technologies.

Expertise of supervisory team

Dr Glencross is a leading scholar in Computer Science in Computer Graphics Energy Data Visualisation.

Prof Lenton is a leading researcher in the application of complexity science to the Earth system and tackling climate change

Dr Glencross, Prof Lenton, A/Prof Viller and Dr Soutar are uniquely placed to supervise this PhD project due to their complementary expertise and experience in bringing PhD students to completion.

Dr Glencross, Prof Lenton, A/Prof Viller and Dr Soutar will be able to give the PhD researcher access to an extensive network of industry and academic experts in IT and Climate Change.

How to Apply:

https://scholarships.uq.edu.au/scholarship/quex-phd-scholarship

Supervisors:

UQ - Dr Alejandro Melendez-Calderon, Dr Taylor Dick, Dr Camila Shirota

Exeter - Dr Dominic Farris

Project Description:

Since the early 2000s, robotic gait trainers have become valuable aids for rehabilitation post-stroke. These devices allow adaptation of assistance parameters (e.g. limb guidance) to challenge patients in an ‘optimal’ way. However, these functions are not often used in clinical practice because clear guidelines on the progression of these parameters are lacking and the consequences of the changes to the underlying neurophysiology are not clear.

Here, we propose a framework for personalizing the assistance based on optimizing muscle activations. We aim at promoting recovery at the neurophysiological level, which requires adequate timing of muscle activation patterns, rather than typical kinematic (e.g. gait trajectories) or kinetic (e.g. joint torques) parameters. We hypothesize that adaptive assistance, based on individuals’ ability to activate different muscle groups, can lead to better outcomes and functional recovery. We will use data-driven, personalized neuromechanical models to predict muscle patterns, when interacting with an exoskeleton. We will test whether this can (i) facilitate more targeted muscle activations, as compared with ‘traditional’ robot-assisted or conventional therapy; (ii) help correct abnormal gait patterns, and (iii) promote recovery and decrease the user's reliance on the device over time.

Specific Aim 1

Personalization of exoskeleton assistance based on data-driven personalized neuromechanical modelling and human-in-the-loop optimization (Months M1-M18)

The EXOPS exoskeleton platform, available at UQ, will be used to develop and evaluate an adaptive control framework that maximizes the user’s residual neuromuscular activity, while ensuring safe walking patterns. Adaptive robotic assistance will be derived using Artificial Intelligence in combination with high-fidelity closed-loop simulations that include personalized neuromechanical models of the users. The refinement of control policies will be optimized during use of the exoskeleton by the patient (human-in-the-loop).

Initially (M1-M9, UQ), the student will become proficient with the equipment, and establish a preliminary framework to use neuromechanical models to optimize robotic assistance. Next, derivation and validation of the personalized neuromechanical models will be done (M10-M18, UoE). The student will integrate the developments and prepare experimental validation of the approach (M19-M24, UQ).

Outcomes

(1) human-in-the-loop methodology for personalizing robotic assistance based on data-driven neuromechanical models; (2) experimental protocol and ethics for Aim 2.

Specific Aim 2

Evaluate the effects of novel exoskeleton assistance on post-stroke gait kinematics and neuromuscular function, and its feasibility as a rehabilitative intervention.

We will conduct clinical experiments in collaboration with regional hospitals including PA Hospital and STARS (M25-M33, UQ). In the UK (M34-M36, UoE), the student will establish a replica of experimental methods (in preparation for follow-up study), and conduct the analysis of the neuromechanical data collected in the first study. Back in Australia (M37-M39, UQ), the student will wrap up the findings.

Outcomes

(1) detailed analysis of post-stroke walking function with and without exoskeleton assistance; (2) quantification of usability of technology for rehabilitation of walking function; (3) preliminary data and evidence for a novel approach to robotic assistance for post-stroke rehabilitation, which sets up the basis for power analysis and further clinical trials.

We expect at least 3 top-tier journal publications, and 3 conference papers from Aims 1-2.

How to Apply:

https://scholarships.uq.edu.au/scholarship/quex-phd-scholarship

Supervisors:

UQ - Dr Jake O'Brien, Professor Kevin Thomas

Exeter - Professor William Gaze, Dr Aimee Murray, Dr Anne Leonard

Project Description:

Antimicrobial resistance (AMR) occurs when microorganisms (e.g. bacteria, fungi, parasites and viruses) adapt over time to current treatments (e.g. antibiotics), reducing their effectiveness. Acquired resistance can develop in specific microorganisms, via genetic mutations or by the transfer of resistance genes from one species to another. Human use (including overuse and misuse) of antimicrobials, pharmaceuticals and chemicals are key drivers of AMR leading to rapid global development of multi-drug resistance. Standardised global surveillance strategies are required to monitor this emerging global health problem. The World Health Organisation (WHO) launched the Global Antimicrobial Resistance Surveillance System (GLASS) (WHO 2015), but critical data gaps remain in monitoring pathogens of major public health importance. The CDC estimates that AMR is already responsible for >2.8M infections and 35,000 deaths per year in the US alone, costing over US$35 billion per year in indirect societal costs (e.g. the burden on health care systems and reduced population health and well-being).  The UK Risk Register and previous Chief Medical Officer, Professor Dame Sally Davies, have compared the potential level of harm from AMR to be equivalent to that of climate change and global terrorism.

Most work on AMR to date has focused on a small number of clinical pathogens causing infection, however in many cases AMR evolves independently of pathogen host as resistance genes themselves can be mobilised between bacteria on mobile genetic elements. As such, the development of AMR is not just limited to the clinical setting. Hence surveillance of both the general population and the environment is also warranted to rapidly identify and respond to disease outbreaks. Additionally, the relationship between antibiotic usage and AMR at a human meta-microbiome level is poorly understood and WBE may be key to elucidating population level drivers of AMR.

Wastewater analysis has been proposed as a potentially suitable AMR surveillance strategy in the general population. In fact, our research on the potential for SARS-CoV-2 wastewater surveillance (Ahmed et al, STOTEN, 2020) quickly became pivotal for how governments around the globe rapidly identify and target responses to COVID-19 outbreaks. In terms of AMR wastewater surveillance, The Global Sewage Surveillance project demonstrated the power of the approach across countries. Through our collaboration with Prof Will Gaze’s group at Exeter, we have demonstrated that even within a country, large differences in AMR between geographically close catchment populations exist. As such this project will focus on understanding these differences and whether or not they are linked to differences between the catchment population (e.g. demographics, antibiotic usage profiles, geographic, international transport hubs), or if they are artefacts of methodological or in-sewer/in-sample processes.

To disentangle this phenomenon, this project will systematically evaluate wastewater surveillance for AMR by working through the WBE biomarker suitability workflows as described by Gracia-Lor et al (Env Int 2016). This includes assessing sampling methodology, in-sewer and in-sample stability. We will then model the findings for specific wastewater catchments to reveal associations between AMR endpoints, demographics, pharmaceutical residue and pharmaceutical usage data, as well as associated risks of AMR selection.    

How to Apply:

https://scholarships.uq.edu.au/scholarship/quex-phd-scholarship

Supervisors:

UQ - Dr Adnan Sufian, Professor Alexander Scheuermann

Exeter - Professor Gavin Tabor, Dr Prakash Kripakaran

Project Description:

Resilient infrastructure can adapt to changing conditions whilst maintaining its intended functionality. Improving the resilience of bridges and roads to scouring in major flood events remains a challenge facing governmental departments managing public assets and the industry involved in the design, construction, and maintenance of these public assets. Bridges and roads play a significant social role in connecting communities, as well as an important economic role in the movement of goods and services. Improving their resilience impacts the wider community and directly addresses Goal 9 of the UN Sustainable Development Goals.

Current approaches have investigated the scouring process from a macro-scale perspective with simplified analytical models and empirical relationships. However, scouring is rooted at the particle-scale with the detachment and transport of soil particles, and the limited consideration of the particle-scale mechanisms has led to a challenge in understanding the underlying mechanisms of the scouring process. This project addresses this gap by developing novel computational tools that model fluid-particle systems using CFD-DEM. The key objectives of this project are:

• Enhancing CFD-DEM models to account for hydrodynamics of fast flowing floodwaters, as existing models do not adequately account for turbulence (WP1).
• Investigating the combined influence of hydraulic and geotechnical conditions on the susceptibility and extent of scouring, as current practice predominantly focusing on hydraulic conditions as recognised in the current US Federal Highway Administration NextScour program (WP2).
• Development of micro-mechanically inspired sediment transport models, which can be incorporated into existing design approaches set out in the TMR Bridge Scour Manual and the CIRIA C472 Report (WP3). 

These objectives form the Work Packages (WPs), which are also aligned with the year of study (i.e., WP1 in Year 1). The PhD student will visit the University of Exeter (UoE) towards the end of Year 1 to work on WP1 and WP2, while WP3 will be completed at the University of Queensland (UQ). The primary resource required is HPC facilities which are readily available at UQ (e.g. Tinaroo and NCI Gadi) and UoE (e.g. ISCA and GW4 Isambard), and are extensively used by the advisory team.

The project will be led by Dr Adnan Sufian (UQ) and Professor Gavin Tabor (UoE). The open-source CFD-DEM software developed by Dr Sufian will be used, which couples LAMMPS for modelling particle behaviour, with OpenFOAM for modelling fluid behaviour. Dr Sufian has strong expertise with LAMMPS for a wide range of geotechnical problems, which is complemented by Prof Tabor’s expertise with CFD across a broad range of applications. Prof Tabor has extensive expertise with OpenFOAM, having been part of the original development team, and is an active member of the OpenFOAM Community as well as being the Chair of the Joint Technical Committees for the development of OpenFOAM. The combination of an early-career researcher mentored by an experienced academic will enable this project to develop innovative capabilities to model scour. The project will also be supported by Professor Alexander Scheuermann (UQ), who has strong expertise with geophysical measurements of erosion phenomena, and Dr Prakash Kripakaran (UoE), who has ongoing experimental research exploring scouring. The complementary expertise of the project team provides the platform to successfully deliver the project and develop a long-term collaboration that will explore external funding through EPSRC and ARC.

How to Apply:

https://scholarships.uq.edu.au/scholarship/quex-phd-scholarship

Supervisors:

UQ - Associate Professor Jan Engelstaedter

Exeter - Dr Ben Longdon

Project Description:

Ecosystems are constantly faced with a critical environmental hazard: infectious diseases. This is because many pathogens do not only attack a single species but several species within an ecosystem. A major source of emerging infectious diseases in humans, wildlife and agriculture are host shifts, where pathogens jump between host species. To assess ecosystem resilience to the threat of invading pathogens, an in-depth understanding of the dynamics of host range evolution and its consequences is vital. In this project, we will make important steps towards this goal by investigating the interplay between host shift dynamics and host-pathogen coevolution. Host shifts are often studied as purely ecological or epidemiological processes. Conversely, host-pathogen coevolution is typically studied within a single host species. Our proposed research will combine these two aspects into a single framework. This is important because adaptations and counter-adaptations of hosts and pathogens will be a major determinant of the likelihood of a host shift being successful.

Our project will have a theoretical and an experimental component that mutually benefit each other. In the theoretical part, to be performed at UQ under the supervision of Dr Engelstaedter, the PhD candidate will develop mathematical models of ecosystems consisting of several host and pathogen species. The aim of these models is to make predictions for how host-pathogen coevolution is expected to affect a pathogen’s host range, prevalence and how this feeds into the stability of the ecosystem. In the experimental part of the project, to be performed at the University of Exeter under Dr Ben Longdon’s supervision, the PhD candidate will carry out empirical work with bacteriophages (viruses) and their bacterial hosts. This system has many advantages that make high-throughput experimental evolution studies feasible, and the phage has a broad host range (infecting several Staphylococcus species) that makes it ideally suited to study host shifts. The experiments will be the first to investigate how coevolution with their hosts will affect a pathogen’s ability to infect other hosts. The experiments will also test whether coevolution with a pathogen will affect a host’s susceptibility to new pathogens.

Our project is expected to make major contributions to our understanding of the factors underlying pathogen host shifts between species in an ecosystem. This in turn will help us understand and ultimately predict the emergence of infectious diseases. Staphylococcus species are important pathogens of both humans and livestock. The phage we will use has been isolated for use in phage therapy, and so by carrying out fundamental research into its host range, we will examine what determines it host range and trade-offs in infectivity between host species, which is ever important in a world with drug resistant infections.

How to Apply:

https://scholarships.uq.edu.au/scholarship/quex-phd-scholarship