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    Low Energy, Passive Acoustic Sensing for Wireless Underwater Monitoring Networks

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    Ph. D. ThesisThis thesis presents the research conducted to develop low energy passive acoustic monitoring (PAM) algorithms. There are many signal processing techniques and machine learning systems which are capable of detecting and classifying target signals. However, this project aims to produce PAM detection and classification results using a low energy budget. The benefit of using this approach is that physical devices can be developed and deployed in open sea for several months using only battery power. This opens up the deployment area to very deep water where power sources are not readily available. Using passive acoustic communication to relay the detection data produced by the algorithm, it is expected that these systems could form an underwater network of sensor nodes. There are three targets for passive acoustic detection/classification included in this thesis, which are motorised surface vessels, cetacean clicks and cetacean whistles. The surface vessel detection method is based on a low energy implementation of Detection of Envelope Modulation On Noise (DEMON). Vessels produce high frequency modulated noise during propeller cavitation which the DEMON method aims to extract for the purposes of automated detection. The vessel detector design has different approaches with mixtures of analogue and digital processing, continuous and duty-cycled sampling/processing. The detector has been integrated with a low cost/power acoustic modem platform to provide acoustic communication of data in near real time. The vessel detector has been deployed at 20m depth for a total of 84 days in the North Sea providing a large data set, which the results are based on. Open sea field trial results have shown the detection of single and multiple vessels with a 94% corroboration rate with local Automatic Identification System (AIS) data. Results have shown additional information about the detected vessel, such as the number of propeller blades, can been extracted solely based on the detection data. The attention to energy efficiency has led to an average power consumption of 11.4mW enabling long term deployments of up to 6 months using only four alkaline C cells. Additional battery packs and a modified enclosure could enable a longer deployment duration. As the detector was still deployed during the first UK lockdown, the impact of Covid-19 on North Sea fishing activity has been captured in the results. Cetacean click detection is based on identifying and classifying the high frequency impulsive click trains created by cetaceans during navigation and foraging. A low energy method of detecting these vocalisations is proposed alongside a statistical based method of classification. The algorithm developed was tested using real recordings of cetacean activity and comparisons have been conducted against a commercially available cetacean monitoring system. The results show that the energy efficient algorithm produces comparable results to the commercial system when real recordings are processed. The cetacean whistle detection algorithm is based on a low energy phase locked loop (PLL) technique. PLL methodology has been adapted for this project to aid in developing a low energy approach to detecting cetacean whistles by tracking the sweeps in frequency they produce. Results are based on offline processing using real recordings of these animals. The results have shown a 75% success rate when comparing against human analysis of the recording. Future work includes the further development of the cetacean related algorithms into fully deployable, battery-powered, nodes for open sea field trails. The future work related to vessel detection includes adding a tracking feature to the passive acoustic monitoring technology.Engineering and Physical Sciences Research Council (EPSRC

    Induction of plasticity in subcortical structures and its application in spinal cord injury

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    Ph. D. ThesisMost current non-invasive plasticity protocols target the motor cortex and its corticospinal projections. Approaches for inducing plasticity in sub-cortical circuits and alternative descending pathways such as the reticulospinal tract (RST) are less well developed. The overall aim of this thesis was to gain a better understanding of the extent to which corticospinal transmissions are altered after spinal cord injury (SCI) and to explore the mechanisms of non-invasive stimulation protocols at the cortical and subcortical level. In the first study, transcranial magnetic stimulation was used to elicit motor-evoked potentials (MEPs) in the biceps brachii using different coil orientations, which allows for preferential activation of different neural elements. Analysis of MEP latencies suggests that differences between MEPs elicited by specific coil orientations may not be fully preserved in humans with cervical SCI, both in the biceps and in more distal muscle groups. In a second study, we developed a novel associative stimulation paradigm, which paired loud acoustic stimuli with transcranial magnetic stimulation over the motor cortex in healthy participants and observed enhanced motor output after stimulus pairing ended. Electrophysiological measurements in humans and direct measurements in monkeys undergoing a similar protocol implicate corticoreticular connections as the most likely substrate for the plastic changes. Finally, we used a custom built device to deliver precisely paired auditory clicks with electric stimulation to the muscle. We observed changes in electrophysiological measurements consistent with the induction of sub-cortical plasticity in the biceps muscle. We then used the same protocol to target the triceps muscle in individuals with SCI over the course of 4 weeks. Notably, we did not observe the same changes as in the biceps muscle, suggesting that elbow flexors and extensors have a different potential for plasticity, perhaps due to a differential control of flexor and extensor motoneurons by corticospinal and reticulospinal pathways.International Spinal Research Trus

    Using audit and feedback to improve colonic polyp detection, qualitative studies within the national endoscopy database automated performance reports to improve quality outcomes trial (NED APRIQOT)

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    M.D ThesisColorectal cancer (CRC) arises from polyps, and polyp detection and resection at colonoscopy is pivotal in preventing CRC. Colonoscopists with a low polyp detection rate have a higher rate of CRC after colonoscopy. The National Endoscopy Database Automated Performance Reports to Improve Quality Outcomes Trial (NED-APRIQOT) is a randomised cluster control trial of electronic audit and feedback (A&F) in English endoscopy centres. This MD aimed to (1) assess the acceptability of colonoscopy key performance indicators (KPIs); (2) develop an evidence-based and theoretically informed behaviour change intervention (BCI), an A&F endoscopist performance report, for implementation in the trial; and (3) explore pre-trial experiences of endoscopy A&F. A narrative review of A&F and KPIs in the colonoscopy literature was undertaken. This informed selection of KPIs for a Delphi consensus, to determine the clinical acceptability of KPIs available through the NED. A panel of UK experts in colonoscopy, reflecting the varied professional backgrounds performing endoscopy, undertook three rounds rating statements and provided free-text comments. A case-mix adjusted mean number of polyps (MNP) was chosen for the trial. An A&F behavioural theory review informed the design of a draft BCI. Interviews were undertaken with 19 endoscopists from six English NHS endoscopy centres, purposively sampled for clinical background and professional experience. The BCI was iteratively refined through rounds of cognitive interviews in which participants interacted with and ‘talked aloud’ about the BCI. The finalised BCI was implemented in the NED-APRIQOT. These participants also undertook semi-structured interviews exploring current colonoscopy A&F practices. A framework thematic analysis mapped themes to Feedback Intervention Theory (FIT) and the Theory of Planned Behaviour. A FIT-based model described A&F’s intended and paradoxical effects on endoscopist behaviour. Detection and patient safety were dependent on coaching, team behaviours and unit-leads managing underperformance. Future endoscopy A&F interventions should consider targeting behaviours using theoretical models

    The potential for carbon capture and utilization (CCU) for the state of Kuwait

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    PhD ThesisCarbon Capture and Utilization (CCU) is a crucial enabling technology that supports delivery of the dual challenges of maintaining fossil fuels as a key energy source, whilst simultaneously dramatically reducing the associated CO2 emissions. This thesis aims to develop a realistic database of CO2 emission sources in the state of Kuwait. The research then investigates the potential of deploying CCU in Kuwait, currently one of the highest carbon emitting countries in the world. After identifying the major sectors responsible for CO2 emissions, both 'top-down' and 'bottom-up' approaches were used to aggregate data from these sectors. The Emission Factors (EFs) were acquired from open literature such as the Intergovernmental Panel on Climate Change (IPCC). The analysis then explored the stakeholders’ inclinations towards CCU. Both qualitative and quantitative surveys methods were conducted in the form of focus group discussions and the Information- Choice Questionnaire (ICQ), respectively. The Kuwaiti power sector proved to be the predominant stationary source of carbon dioxide (CO2) emissions (42%) due to high regional demand for electricity and water. The chemical industry ranked second in this analysis with a significant share of CO2 emissions (26%) which was attributed to heavy and energy intensive industries, and this was followed by road transportation (16%). The total process emissions were covered in this analysis for the first time which explains the variation between the real carbon footprint of Kuwait 98 Mt CO2/y and both the World Bank 91.03 Mt CO2/ y (WBR, 2006) and International Energy Agency 69.82 Mt CO2/ y (IEA, 2010b) with differences of 7.7% and 40%, respectively. The geographical distribution of CO2 emissions was analysed, showing that high emission facilities are clustered mainly in the southeast which is the predominant industrial area in the state. This distribution could potentially be favourable for the formation of a ‘capture cluster’ which could reduce the overall cost of carbon capture deployment as a route for a sustainable carbon mitigation practice. If the Kuwait government diversify its economy towards non-oil bases, the carbon footprint of the state will increase from 118 to 126 Mt/y. Overall, there was a positive attitude among all stakeholders, across a number of different sectors, regarding the potential of deploying CCU technology. However, some technical and economic barriers should first be addressed in each of the sector facilities since they are not designed to be retrofitted with carbon capture units. iii In general, limited flexibility in Kuwaiti facilities with regard to being retrofitted with CCU technologies, and the impact of this process on their efficiencies, represent the main technical obstacles in the State. In addition to the technical barriers of reusing the existing high-pressure natural gas infrastructure for CO2 transportation and managing the injecting process of CO2 into a deep saline aquifer. From an economic aspect, the economic burden of introducing this technology to various institutions in the country will vary significantly depending on the lifetime and operating conditions of the current facilities. Oxy-fuel combustion appears to be the most economically attractive technology with its cumulative cost equivalent to approximately one third of the cost of post-combustion. The key actions required to fully understand the potential of CCU in the state of Kuwait include developing new environmental regulations, extending the scope of the analysis to include techno-economic analyses, deployment of more pilot plants for CO2-EOR in the north of Kuwait, and carrying out field optimization studies for the saline aquifer reservoirs

    A flat extension theorem for truncated matrix-valued multisequences

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    PhD ThesisGiven a truncated multisequence of p × p Hermitian matrices S := (Sγ1,...,γd ) (γ1,...,γd)∈Nd 0 0≤γ1+···+γd≤m , the truncated matrix-valued moment problem on R d asks whether or not there exists a p×p positive semidefinite matrix-valued measure T, with convergent moments of all orders, such that Sγ1,...,γd = Z · · · Z Rd x γ1 1 · · · x γd d dT(x1, . . . , xd) for all (γ1, . . . , γd) ∈ N d 0 which satisfy 0 ≤ Pd j=1 γj ≤ m. When such a measure exists we say that T is a representing measure for S. We shall see that if m is even, then S has a minimal representing measure (that is, Pκ a=1 rank Qa is as small as possible) if and only if a block matrix determined entirely by S has a rank-preserving positive extension. In this case, the support of the representing measure has a connection with zeros (suitably interpreted) of a system of matrix-valued polynomials which describe the rank-preserving extension. The proof of this result relies on operator theory and certain results for ideals of multivariate matrix-valued polynomials. Our result subsumes the celebrated flat extension theorem of Curto and Fialkow. We shall pay particularly close attention to the bivariate quadratic matrix-valued moment problem (that is, where d = 2 and m = 2)

    Software-in-the-Loop combined Artificial Intelligence for Optimised Design and Dynamic Performance Prediction of Floating Offshore Wind Turbines

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    PhD ThesisFloating Offshore Wind Turbines (FOWTs) have shown a promising future due to the goal of Net Zero emissions by 2050. However, the highly coupled nonlinear performances of FOWTs bring many challenges to the implementation of numerical and basin experimental methods in design and optimisation. This PhD project proposes an innovative method, named SADA (Software-in-the-Loop combined Artificial Intelligence Method for Dynamic Analysis of Floating Wind Turbines), to optimise the design and predict dynamic performances of FOWTs. SADA is built based on a coupled aero-hydro-servo-elastic programme DARwind and Machine Learning Algorithms. Firstly, the concept of Key Disciplinary Parameters (KDPs) is inspired by FOWT-related disciplinary theories. Secondly, DARwind will take continuous action through the Software-in-the-Loop (SIL) model to obtain more accurate prediction results. Thirdly, SADA can build data sets and analyse deep-seated physical laws of FOWTs. Then, case studies were conducted to prove the feasibility of the SADA method on the basin experiment data. The results show that the mean values of some physical quantities can be predicted by SADA with higher accuracy than the original DARwind simulation results. In addition, full-scale case studies were conducted by extending SADA to engineering applications, though some design parameters are not accessible. Furthermore, other physical quantities that cannot be obtained directly in full-scale measurement easily but are of great concern to industry can also be obtained from a more credible perspective. The proposed SADA method could benefit the wind industry by taking advantage of the numerical analysis method and AI technology. This brings a new and promising solution for overcoming the handicap impeding direct use of traditional basin experimental technology or full-scale measurement. Therefore, designers in the wind industry can optimise FOWTs designs to a higher level, thereby achieving a better method of and maintaining safe operation of FOWTs in a complex sea state

    Novel features in accelerometer-based gait analysis for long-term monitoring of Parkinson’s disease : a signature of gait.

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    PhD ThesisParkinson’s Disease (PD) is a neurodegenerative disease that can lead to restricted or slowed movement, gait impairments and increased risk of falling. Over recent decades, instrumented gait analysis (IGA) has contributed much to the understanding of gait impairments in PD. Due to the complexity of gait and high clinical interest a plethora of features have been suggested for gait analysis in the literature pertaining to several groups such as: traditional spatio-temporal (e.g. gait speed), frequency domain, etc. A subset of these traditional gait features has been proposed and validated in PD and older adults as a comprehensive model of gait comprising five factors: pace, rhythm, asymmetry, variability, and postural control. Analysis of gait may be grouped into the assessment of two types of variability, namely, within-subject variability which is needed for personal disease management and inter-subject variability which is useful in quantifying the overall impact of PD on gait. Advances in wearable technology have led to much smaller devices (e.g. accelerometers) being commercially available in conjunction with greatly increased battery lives to the degree that not only lab-based but also continuous recordings over 7 days (real-world) are possible. Wearable technology-based gait analysis is indeed emerging as a powerful tool to detect early disease and monitor progression. Data recorded as part of the ICICLE-GAIT 1 study provides acceleration data for over 100 people with PD and age-matched control subjects in both lab and realworld conditions. These datasets form the basis for the development of a new Phase plot methodology for gait analysis in PD. In this thesis I present a novel methodology for both assessing PD and tracking individual disease progression over multiple timescales. To accomplish this, I introduce a new feature domain, the Phase domain, based on a particular type of recurrence plot known as a Poincar´e plot. Poincar´e plots are sometimes referred to in the literature as return maps, self-similarity plots or Phase plots. Phase plots were being used in the early 1990s in ECG studies to produce self-similarity plots of beat-to-beat intervals. This technique proved to be reliable in detecting atrial fibrillation. The rare instances of its application to other fields are very limited and do not demonstrate any modification or development beyond that which has been used in ECG studies for decades. I develop methodology for application to gait analysis and, indeed, any cyclical biosignals. In this thesis I used the data from the ICICLE-GAIT study to demonstrate that with specific modifications and newly identified features (comprising the Phase domain), this novel Phase plot methodology is highly applicable to gait analysis within PD and provides a framework for: (i) identifying and characterising PD and (ii) individual disease tracking over the years following diagnosis. Throughout these analyses, traditional gait features serve as an established reference and benchmark. I employ statistical methods, such as non-linear mixed effects models and Statistical Parametric Mapping, to model PD progression and assess the clinical utility of Phase plots. I also used Discrete-Time Markov chain modelling, longitudinal analyses, and functional principal components analysis to demonstrate that Phase plots provide an objective, personalised, and clinically relevant signature of gait. In the case of PD patients (and controls to a lesser extent) four distinct Phase plot Types emerge and occur with high within-subject reproducibility, hence the signature interpretation. Many features within the Phase domain proved to be highly sensitive to the disease (people with PD versus controls). Using lab-based data, the Phase domain features outperformed traditional spatio-temporal features in classifying PD. Each domain of features performed similarly well in the prediction of MDS-UPDRS 2 (a useful proxy for PD progression). Specifically, part III of the UPDRS scale was used as this relates to motor function. In real-world conditions Phase plot features showed sensitivity to disease state and physical capability across multiple timescales e.g., daily fluctuations, and also across 18-month follow up time points. The Phase plot-based signature of gait is validated under lab-based conditions to reflect participants’ capacity for gait as well as under real-world conditions as a compact means of monitoring PD and walking performance through gait

    Advanced adaptive modelling approaches in the evolution of vector/cell manufacturing processes

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    PhD ThesisThe field of cell gene therapy has seen significant progress in recent years. The last decade has seen the licensing of the first Cell Gene Therapy (CGT) treatments in Europe and clinical trials have demonstrated safety and efficacy in the treatment of numerous severe inherited diseases of the blood, immune and nervous systems. Specifically, autologous viral vector-based CGT treatments have been the most successful to date. However, the manufacturing processes for these CGT treatments are at an early stage of development, and high levels of complexity, process variability and a lack of advanced process and product understanding in vector/cell manufacturing are hindering the development of new processes and treatments. Here, Multivariate Data Analysis (MVDA) and Machine Learning (ML) techniques, which have not yet been widely exploited for the development of CGT processes, were leveraged to address some of the main hurdles in the development and optimisation of CGT processes. Principal component analysis (PCA) was primarily used for feature extraction to understand the main correlations and sources of variability within the process data, and to evaluate the similarities and differences between batches. Additionally, a sparse PCA algorithm was developed to ease the interpretation of the principal components with a large number of variables present in the dataset. Predictive modelling techniques were utilized to model the relationships between process variables and critical quality attributes (CQAs) of the viral vector and cell drug products. The infectious titres of lentiviral vector (LV) products from both adherent cell cultures and suspension cell cultures were modelled and predicted successfully and critical process variables were identified with statistically significant correlations to this CQA. In cell drug product manufacturing, the LV copy number in the patient’s transduced cells was also modelled and process parameters in LV manufacturing and cell drug product manufacturing were linked to this CQA. Overall, the modelling process recovered valuable information from historical process data from the early stages of process development. This data frequently remains unexploited, due to its commonly truncated and unstructured nature; however, this work showed that MVDA/ML techniques can yield beneficial insights despite less than ideal data structure and features.GlaxoSmithKline and the Engineering and Physical Sciences Research Counci

    Spatial optimisation for resilient infrastructure services

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    Ph. D. Thesis.Infrastructure networks provide crucial services to the functioning of human settlements. Extreme weather events, especially flooding, can lead to disruption or complete loss of these crucial infrastructure services, which can have significant impacts on people’s health and wellbeing, as well as being costly to repair. Urban areas concentrate infrastructure and people, and are consequently particularly sensitive to disruptions due to natural (and human-made) disasters. Flooding alone constituted 47% of all weather-related disasters between 1995 and 2015, causing enormous loss of lives and economic damages. Climate change is projected to further exacerbate the impacts that natural disasters have on cities. Choices about where to site infrastructure have a significant impact on the impacts of extreme weather events. For example, investments in flood risk management have typically focussed on prioritising interventions to protect people, houses and businesses. Protection of infrastructure services has either been a bonus benefit of flood defence protection of property, or been implemented by individual infrastructure operators. Spatial planning is a key process to influence the distribution of people and activities over broad spatial scales. However, decision-making processes to locate infrastructure services does not typically consider resilience issues at broad spatial scales which can lead to inefficient use of resources. Moreover, spatial planning typically requires consideration of multiple, sometimes competing, objectives with solutions that are not readily tractable. Balancing multiple trade-offs in spatial planning with multiple variables at high spatial resolution is computationally demanding. This research has developed a new framework for multi-objective Pareto-optimal location-allocation problems solving. The RAO (Resource Allocation Optimisation) framework developed here is a heuristic approach that makes use of a Genetic Algorithm (GA) to produce Pareto-optimal spatial plans that balance a typical tradeoff in spatial planning: the maximisation of accessibility of a given infrastructure service vs the minimisation of the costs of providing that service. The method is applied to two case studies: (i) Storage of temporary flood defences, and (ii) Location of healthcare facilities. The RAO is first applied to a flood risk management case study in the Humber Estuary, UK, to optimise the strategic allocation of storing space for emergency resources (like temporary flood barriers, portable generators, pumps etc.) by maximising the accessibility of warehouses (i.e. minimising travel times from storing locations to deployment sites) and minimising costs. The evaluation of costs involves both capital and operational costs such as the length of temporary defences needed, storage site locations, number of lorries and personnel to enable their deployment, and maintenance costs. A baseline is tested against a number of scenarios, including a flood disrupting road network and thereby deployment operations, as well as variable infrastructure and land use costs, different transportation and deployment strategies and changing the priority of protecting different critical infrastructures. Key findings show investment in strategically located warehouses decreases deployment time across the whole region by several hours, while prioritising the protection of the infrastructure assets serving larger shares of population can cut costs by 30%. Moreover, the analysis of the ensemble of all scenarios provides crucial insights for spatial planners. For example, storage sites in Hull or Hedon, and in the areas of Withernsea and Drax are robust choices under all scenarios. Meanwhile, the Humber Bridge is shown to play a crucial role in enabling regional coverage of temporary barriers. The second case study shows how emergency response strategies can be enhanced by optimal allocation of healthcare facilities at a regional scale. The RAO framework allocates healthcare facilities in Northland (New Zealand) balancing the trade-off between maximisation of accessibility (i.e. minimisation of travel times between households and GP clinics) and minimisation of costs (i.e. number of clinics and doctors). Results show how c.80% of Northland’s population lives within a 20 minutes drive from the closest GP, but this can be increased to 90% with strategic investment and relocation of doctors and clinics. By accounting for flood and landslide risk, the RAO is used to identify strategies that improve accessibility to healthcare services by up to 5% even during extreme events (when compared to the current business as usual service accessibility). Application to these two problems demonstrates that the RAO framework can identify optimal strategies to deploy finite resources to maximise the resilience of infrastructure services. Moreover, it provides an analytical appreciation of the sensitivity between planning tradeoffs and therefore the overall robustness of a strategy to uncertainty. The method is consequently of benefit to local authorities, infrastructure operators and agencies responsible for disaster management. Following successful application to regional scale case studies, it is recommended that future work scale the analysis to consider resource allocation to protect infrastructure at a national scaleEngineering and Physical Sciences Research Counci

    Socio-ecological indicators for sustainable management of global marine biodiversity conservation using sharks as a model species

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    Ph. D. ThesisGlobal biodiversity is disappearing at an unprecedented rate; sharks are currently among the most threatened vertebrate groups with widespread overexploitation leaving 31% of all species at risk of extinction. Since 2009, 17 coastal nations have adopted a precautionary approach banning all commercial shark fishing. However, evaluating effectiveness of these ‘shark sanctuaries’ is impeded by a lack of robust data. Evidence-based conservation urgently requires data against which socio-ecological change can be measured to assess efficacy of policy and management interventions. This thesis takes an interdisciplinary approach to advance understanding of the complexities of shark conservation within one of the world’s principal shark sanctuaries - the Maldives. Historical abundance trends derived from fisher Local Ecological Knowledge (LEK, 87 interviews) showed substantial declines in shark population abundance (>65%) and distribution (>60%) between 1970-2019. Validation of contemporary spatial LEK using Baited Remote Underwater Videos (BRUVs, 50 hours of footage) highlighted the potential of LEK to provide fine-scale distribution data for shark populations in data poor regions. Analysis of BRUVs (464 hours of footage) and citizen science data (2,024 dives) over a 5-year period (2016-2020) revealed historical population declines have now been halted and suggests species abundances are stable following sanctuary implementation. However, positive correlations between prey and reef shark abundance raises uncertainty over the long-term efficacy of sanctuaries, which still permit exploitation of prey species. Interviews with fishers (n = 103) identified correlations between fisher characteristics, perceptions, and support for the Maldives shark sanctuary. Findings identified several management actions that could increase support: increasing stakeholder participation and representation (voice to capture local knowledge); mitigation of the costs associated with fisher-shark interactions and increasing transparency in management decision making. The potential severity and inequity in livelihood costs associated with shark sanctuaries was also highlighted revealing that small-scale reef fishers were disproportionally impacted compared to pelagic tuna fishers. This thesis highlights the importance of integrating human and ecological dimensions into shark conservation to tailor measures more likely to be effective in specific contexts and suggests that low support for sanctuary regulations, fisher-shark conflict and overexploitation of reef resources, could hinder long-term population recovery. Findings outline rapid, cost-effective approaches towards generating priority data to provide a basis for evidence-based management that will help define future efforts to enhance shark conservation in the context of achieving the UN Sustainable Development Goal (SDG) 14.Newcastle University’s Institute for Sustainabilit

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