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ERA is a digital repository of original research produced at The University of Edinburgh. The archive contains documents written by, or affiliated with, academic authors, or units, based at Edinburgh that have sufficient quality to be collected and preserved by the Library, but which are not controlled by commercial publishers. Holdings include full-text digital doctoral theses, masters dissertations, project reports, briefing papers and out-of-print materials.

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Deer management in the Scottish Highlands: change, conflict and finding common ground
(2026-05-19) Leavey-Wilson, Callum; Fisher, Janet; Staddon, Samantha; Metzger, Marc; Natural Environment Research Council (NERC); E4 Doctoral Training Partnership, University of Edinburgh (Grant Reference Number: NE/S007407/1); NatureScot: CASE studentship
Conflicts over upland deer management in the Scottish Highlands have intensified in recent years, shaped by intersecting concerns relating to biodiversity loss, climate change, rural livelihoods and shifting expectations of land use. This thesis examines these tensions through drawing on data collected through the Finding the Common Ground on Sustainable Upland Deer Management (FtCG) mediation process and its successor, the Common Ground Forum (CGF). Drawing on 52 semi-structured interviews, extensive participant observation, estate visits, stalking experiences and survey data collected between 2022 and 2024, the research explores how land-use conflict, environmental conflict resolution and land-use change unfold within this changing socio-ecological and policy context. The findings indicate that disagreements over deer management cannot be understood solely as a technical dispute over the environmental impacts of deer, as is commonly presented. Instead, conflict in this case operates at multiple, interacting levels. Surface-level debates over cull targets and habitat conditions were underpinned by deeper tensions relating to identity, legitimacy, historical grievances and competing understandings of land stewardship. Stakeholder groups were found to be internally diverse and often divided, challenging simplified depictions of polarised camps. In particular, the study reveals significant heterogeneity among deer stalkers, whose positions reflected varied combinations of professional identity, local attachments, ecological motivations and economic vulnerability. A recurring empirical theme was a perceived loss of control amongst some stalkers and private land managers in the context of increasing state intervention and policy reform. This sense of diminished autonomy shaped responses to land-use change and influenced their engagement with the mediation process. The evaluation of FtCG suggests that whilst the process contributed to improved dialogue, relationship-building and opportunities for recognition, it did not resolve deeper structural disagreements. Rather than eliminating conflict, mediation reshaped the terms of engagement between actors and altered relational dynamics within the sector. Conceptually, the thesis demonstrates how a layered understanding of conflict, combined with a critical realist approach, helps to illuminate the interaction between structure and agency in environmental governance. By analysing how values, rules and knowledge intersected in this setting, the research further shows how collaborative initiatives operate within historically embedded patterns, institutional reform trajectories and asymmetries of authority. Overall, the study contributes empirically grounded insights into contemporary deer management reform in Scotland and offers broader reflections on the possibilities and limits of environmental conflict resolution within rural socio-ecological transitions.
Vascular mobile signals prime plant immune responses through chromatin manipulation
(2026-05-19) Mason, Robert Oskar; Spoel, Steven; Bayne, Elizabeth; Biotechnology and Biological Sciences Research Council (BBSRC); EASTBIO BBSRC Doctoral Training Partnership
Globally, disease is responsible for reducing crop yield by over 20% every year. Mitigating these losses will drastically improve global food security, aiding efforts to feed the growing human population. Traditionally, pesticides and breeding are used to reduce disease in plants, but breeding proves too slow to combat rapidly emerging pathogens, pesticides are increasingly regulated due to toxic side effects, and both are losing efficacy as established pathogens evolve. Initial infection can immunise plants to establish systemic acquired resistance (SAR) against future pathogen attacks. SAR is associated with the priming of immune responses, leading to faster and stronger immune activation against a wide range of pathogens. Vascular mobile signals that travel through the phloem are vital for the establishment of SAR throughout the entire plant. The aim of this study is to investigate the roles of mobile signals in immune priming, as these pose a promising avenue for harnessing the plant’s own immune system to improve disease resistance. Phloem mobile phytohormones have been identified as the signals that establish the primed state, but how they induce priming remains unknown. Here, I focus on the interactions between mobile signals and the immune hormone salicylic acid (SA), a key component of SAR. In Chapter 3, I assessed interplay between the mobile signal azelaic acid (AzA) and SA in terms of SA-responsive gene expression and SA-mediated immunity. Using sequential AzA and SA treatments I show that AzA pre-treatment modulates the expression of 74.1% of SA-dependent transcripts, primarily by reducing their SA-responsiveness. GO term analysis revealed that many of the genes targeted by AzA are involved in hypersensitive cell death and suppression of photosynthesis, suggesting AzA acts to balance investment in growth and hypersensitive defence during activation of a primed immune response. Accordingly, AzA was unable to enhance SA-responsiveness of immune responses against Pseudomonas syringae, suggesting other signals act to boost immunity, while AzA may balance energy investment. N-hydroxy-pipecolic acid (NHP) is a phloem mobile signal that has been shown to directly prime plant immunity. In Chapter 4, I investigated the interaction between NHP and SA in establishing immunity. I discovered that NHP affects 75.2% of SA-responsive transcriptome, primarily by priming or cumulatively increasing their expression. GO term analysis showed that NHP primed immune-responsive genes but not those linked to programmed cell death, showing little overlap with AzA targets. I also show that NHP primed SA-mediated immunity against pathogen infection such that in presence of NHP, previously inert concentrations of SA induced resistance against P. syringae. Thus, NHP-mediated priming of the SA-responsive transcriptome enhances immune responsiveness. In search of an NHP regulator, I found that NHP stabilised the levels of SA-induced NPR1 protein, a master transcription coactivator of SAR, possibly through post-translational modification. Overall, these data show that NHP primes SA-responsiveness to increase the strength of immune responses, possibly through manipulation of transcriptional regulators such as NPR1. To understand how NHP primes SA-responsive genes, I then searched for binding motifs in NHP-primed genes. Strikingly, NHP-primed genes were enriched with WRKY family transcription factor binding sites, and after testing several mutants I found that WRKY38 and WRKY62 are indispensable for priming. Through RNA sequencing (RNA-seq) I demonstrate that in wrky38/62 double mutants the majority of NHP responses are iv dysregulated and immune priming by NHP is lost. Because WRKY38/62 may be involved in chromatin remodelling, I investigated the impact of NHP on chromatin accessibility through Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq). Here, I found that NHP dramatically reorganises chromatin accessibility, but this effect is largely abolished in absence of WRKY38/62. Comparison between NHP-primed genes and NHP-dependent chromatin reorganisation showed that NHP mediates priming primarily through WRKY38/62-dependent chromatin remodelling. In summary, I demonstrate phloem mobile signals have previously unrecognised roles in SAR and suggest that several phytohormones work in tandem to optimise and regulate the process of immune priming. By identifying the key priming regulators WRKY38 and WRKY62, I propose targets for either chemically-induced or gene-edited induction of priming, which could be used to protect a variety of crop species without limiting yield or damaging the environment.
Granular changes in brain networks: multiplex nodal modularity for Alzheimer's disease characterization and simulation
(2026-05-19) Campbell-Cousins, Avalon; Escudero Rodriguez , Javier; Thompson, Jack; Arslan, Tughrul
Neurodegenerative diseases, most prevalently Alzheimer’s disease (AD), cause progressive cognitive and intellectual decline, placing immense emotional and financial strain on families and government services. Primary methods in the diagnosis of AD typically focus on cognitive questionnaires, screening tests, medical history, and neuropsychological examinations. However, early detection of AD remains difficult, with gaps in our understanding of how early stages contribute to the disease’s progression. To this end, a range of neuroimaging methods both structural, such as structural magnetic resonance imaging (sMRI) and diffusion tensor imaging (DTI), and functional, including functional magnetic resonance imaging (fMRI) and electroencephalography (EEG), have been used to study changes in the brain across the AD continuum and uncover biomarkers of disease progression. These advancements in brain imaging have facilitated a network-based model of the brain where brain regions are linked according to anatomical connections or functional associations. This model captures the inter-dependencies and interactions between brain regions that drive complex cognitive processes. These brain regional interactions can be modelled as single-layer networks or as a collection of brain networks (multiplex networks) which evolve across time or other indexed data. Brain networks organize and reorganize themselves in a multitude of ways such as in response to task stimuli or as a result of damage due to disease. Organizational topological structures, captured as modules (groups) composed of a collection of brain regions, can be dynamically explored and are of particular interest for diseases such as AD where progression causes abnormal altering of these modular structures. However, modularity in its current state is limited in its use as a metric describing the total extent to which the brain is segregated into distinct modules. It does not currently describe the individual contributions of individual brain regions to overall brain modularity. To tackle this, we introduce nodal modularity (nQ) as a novel graph measure that extends classical modularity to individual nodes for both single-layer and multiplex networks. We assess the novelty of nQ against other common single-layer and multiplex measures of node influence. Additionally, we explore the hypothesis that nQ would yield novel insights into the progression of amnestic Mild Cognitive Impairment (aMCI, a prodromal stage of AD) given that global changes in modularity have been previously observed along this continuum. This is investigated in single and multiplex networks of a visual short-term memory binding task (VSTMBT – a cognitive biomarker of AD) constructed from DTI and task-fMRI data. The results indicated that nQ could effectively characterize the transition point from MCI to AD (MCI converters, or MCIc). Additionally, results corroborated previously understood progression pathways of AD including the identification of key subnetworks affected by the disease (visual, limbic and paralimbic), along with agreement with amyloid-β and tau deposition for subjects with poor visual short-term memory binding. Following the introduction of nQ, we expand the study to larger multiplex networks with a focus on covering typical constructions in neuroimaging research. We verify that nQ is distinct from other multiplex measures of node influence across a number of multiplex surrogate networks. We find that, as network size and the number of network layers increase, that nQ captures unique information distinct from other multiplex network metrics, reflecting nQ’s ability to capture more wide-reaching changes in network topology than the typical local measures used (multiplex clustering coefficient, multiplex PageRank, and degree). Additionally, we explore specific cases where nQ does not provide a significant advantage as a network measure over the state of the art, largely driven by cases of highly modular networks with high within module connectivity and low between module connectivity. Furthermore, we propose collapsibility as a novel method of simplifying analyses of nQ in larger networks, explored in tandem with multiplex flexibility. We apply these to multiplex frequency-based networks of source-space EEG data during the VSTMBT, and analyse changes along the healthy to MCI progression of AD. We found changes in nQ and collapsibility which agree with known changes in grey matter and with abnormal functional connectivity around the thalamus as a result of MCI and AD. Lastly, we explore how nQ can facilitate the simulation of AD progression by developing novel targeted attack models. Specifically, we investigate the current state of the art in targeted attacks in our task-fMRI data in the modelling of healthy to MCIc progression. We find that prior research in targeted attacks that focus on node degree were not sufficient in describing this progression from healthy to MCIc for task-fMRI. To tackle this, we propose a brain lobebased targeting system informed by prior findings on nQ progression and established hypotheses on network damage in AD. Additionally, we confirm that improvements in simulated progression using the lobe-based method are not explainable solely by preferential attacks on long distance connections, achieved through the introduction of a targeted attack model based on Euclidean distance. We then leverage nQ to improve the lobe-based model and show that both lobe-based and nQ-based targeted attack models improve on the state of the art. In sum, this thesis highlights the importance of considering granular changes in network topology to capture complexities in brain structure and function. Specifically, through the establishment of a novel metric of granular community structure, nQ, providing methodological considerations for the use of this measure in larger networks, and in exploring the simulation of granular changes due to AD through novel targeted attack models. Given modularity’s widespread use as a global measure, nQ represents a significant advancement, providing a granular measure of network organization applicable across disciplines. In regard to AD, this thesis motivates additional study of nQ in characterizing the stages of MCI and particularly in disentangling MCI from MCI converters during the VSTMBT.
Mixed discrete continuum modelling of dense granular flow
(2026-05-19) Mathews, Akhil; Ooi, Jin; Papanicolopulos, Stefanos; Angeloudis, Athanasios; European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 955661
Granular materials are central to many natural and industrial processes, yet faithfully simulating their behaviour at full scale remains challenging. The Discrete Element Method (DEM) resolves grain-scale physics but becomes costly for large assemblies, while the Finite Element Method (FEM) accelerates computation by treating the material as a continuum at the expense of particle level detail. Coupling DEM at the particle scale with FEM at the macro scale offers a practical route for large-scale problems. This thesis introduces a hybrid DEM–FEM framework implemented in the open-source KRATOS MULTIPHYSICS platform, in which the two descriptions overlap in a hybrid zone; displacement compatibility is enforced via a penalty, and smoothly varying weights enable seamless transfer of stress and strain across the interface. Rather than focusing solely on bulk metrics, the verification campaign resolves the mechanics within the overlap and quantifies the influence of coupling parameters. The framework is first exercised on an analytically guided one-dimensional force-transfer problem, then on two benchmarks: uniaxial compression of a monodisperse column and compaction of a polydisperse assembly. A systematic study charts how penalty stiffness, weight-function shape, mesh-to-particle size ratio, and inter-particle friction affect stress/strain transfer and convergence, yielding practical guidelines for robust, resolution-aware coupling across a range of mesh–particle ratios and overlap thicknesses. A compact, dimensionally consistent scaling for the penalty, ε =CE/(d Lc), is proposed, where E is an effective modulus, d a characteristic particle size, Lc the hybrid-zone thickness, and C accounts for nonidealities due to weighting, mapping, and engagement. Choosing C ≈ 10 reliably places the coupling in a high-fidelity regime over diverse mesh/particle ratios and overlap sizes. For the polydisperse system under cyclic loading, a calibrated elasto-plastic Drucker–Prager continuum reproduces DEM responses, capturing friction-dependent stiffening and the evolution of the lateral stress ratio K while maintaining stable overlap behaviour. Industrial relevance is demonstrated through a large silo-discharge simulation in which flowing regions are resolved with DEM and quasi-static zones are represented by an elasto-plastic FEM. Hybrid predictions of vertical stress, lateral stress ratio, and grain-scale kinematics are benchmarked against a high-resolution DEM reference, confirming process-scale fidelity and indicating where continuum constitutive enrichment (e.g., dilatancy-evolving or nonlocal models) can further reduce residuals. By releasing the implementation through Kratos’s CoSimulation module, the work provides a flexible, open-source foundation for adaptive model switching, multi-rate co-simulation, uncertainty quantification, and multiphysics extensions, alongside new insight into the mechanics of DEM–FEM overlap zones.
Listen and learn: examining the role of schools radio broadcasting in Scotland's classrooms
(2026-05-19) Kramber , Adele Liu; Lorimer, Hayden; Hunt, Rachel; Bell, Alistair; Plaine, Vicky; Fitzpatrick, Hannah; Arts and Humanities Research Council (AHRC)
This thesis presents a historical-cultural geography of BBC schools radio broadcasting in Scotland. Through an interpretive engagement with mixed archival sources materials, it considers the ways in which the BBC researched, produced, and transmitted radio broadcasts to classrooms across the nation, positioning the medium centrally in children’s primary and secondary education. When tuning in to radio programmes, children were exposed to different voices and sounds from across the nation, and as such, were encouraged to understand Scotland’s past and present, and its place in the world, through differing subjects on the curriculum. By focusing on four different and interrelated themes for analysis, this thesis examines the regulation, production, transmission, and reception of BBC schools radio programmes across Scotland. First, it examines the new media landscape into which schools radio emerged, and the ways in which broadcasts were shaped and regulated by specialist councils and committees. Second, it explores how diverse lesson content was crafted for radio, and how producers incorporated various methods of audio production to engage listening children by bringing the outside world into the classroom. Third, it traces programme content from geography, and geography-adjacent, radio series to analyse the ways that lessons taught children about their country, thus constructing a unique geographical imagining of Scotland. Fourth, it investigates how classroom teachers and their pupils were intended to receive these lessons, absorb the material, and apply it to activities within and beyond the classroom. As an integrated piece, this thesis highlights the significance of listening and learning from radio as it distinctively engaged children with sound, simultaneously shaping new social imaginaries where radio directed pupils’ understanding of nationhood, citizenship, and geography.