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Deep learning with simulated data for medical imaging
Get PDFThis thesis addresses critical challenges in the application of deep learning to medical imaging, particularly focusing on brain vasculature. Deep learning, a specialized branch of machine learning, has shown remarkable potential in tasks such as object classification, detection, and image segmentation. However, its effectiveness is often limited by the scarcity of large, diverse, and labeled datasets in the medical domain. This scarcity stems from the time-consuming and expertise-dependent nature of medical image annotation, making it impractical to manually create extensive datasets for training deep learning models. The research tackles three primary challenges: the disparity in data availability across different imaging modalities, the
underrepresentation of certain phenotypes in medical imaging datasets, and the limited availability of data for rare conditions. To address these issues, the thesis explores innovative approaches to data generation and synthesis, aiming to augment existing datasets and create new ones.
The work employs advanced techniques such as cross-modality synthesis using learned local attention masks to generate MRA images from T2-weighted brain MR images, addressing the data availability discrepancy between modalities. Furthermore, the thesis investigates the use of diffusion models for synthetic generation of brain vasculature, particularly focusing on the intricate Circle of Willis to address phenotype underrepresentation.
The research also introduces few-shot learning with diffusion models to enable conditional generation of brain vessels with aneurysms, tackling the
challenge of limited training data for rare conditions.
By systematically addressing these challenges, this thesis contributes to advancing the field of medical imaging and enhancing the training of deep
learning models in healthcare applications
Enhanced Oil Recovery using Functionalised and Shape-Modified Silica Nanoparticles: Mechanisms, Efficiency, and Applications in Sandstone Reservoirs
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Development of a liver tissue organoid
Get PDFDespite the ability of liver to regenerate from one third its size, little is known about the cellular mechanisms that underpin such an almost limitless potential for regeneration. In vitro culture of cells is often plagued with reductions in cell viability and function, providing limited understanding of regenerative capability outside of in vivo environments. Even in vivo, once sufficient tissue is lost, native regenerative response limits further regeneration capability. Studies using decellularised liver grafts have potential for understanding the mechanisms behind wound healing and repair as well as providing long term evaluation of drug toxicity after seeding due to the native like biological, biochemical and architectural characteristics.
This study aimed to develop a decellularised porcine liver scaffold with native histoarchitecture and biochemical composition, based on the Leeds method, that can support and develop current knowledge of cell seeding methods. Combination of hypo-and hyper-tonic buffers, low concentration SDS (0.1%) and nucleases resulted in effective decellularisation of tissue and maintenance of ECM histoarchitecture. One cycle of SDS (0.1%) showed sufficient cellular and nuclear removal from native porcine liver tissue, creating a biocompatible scaffold that retained overall histoarchitecture. Subsequent investigation of seeding methods identified key areas for development including volume of cell suspension for better cell coverage, analysis of seeding time to increase cell attachment, modification of cell density to alter cell attachment and use of dynamic and static culture conditions to maximise cell penetration. HepaRG and Huh7 cells supported cell attachment for up to 28 days culture, and proliferation for up to 14 and 28 days respectively. Furthermore, functional HepaRG were identified even after 28 day culture. Results indicate the potential benefits of HepaRG and/or Huh7 seeded discs in developing understanding of cell repair, regeneration and wound healing, as well as the dysregulation of matrix remodelling after injury
Towards institutional innovations for Phosphorus circularity: an analysis of governance arrangements in the European Union
No full textPhosphorus is an exhaustible resource essential for food security that is increasingly important for technological sectors. However, its governance is largely missing. Although it is a complex, wicked and system-wide problem that has attracted significant scholarly attention, phosphorus has by far been investigated through siloed perspectives. This reproduces institutional fragmentation and limits the possibility of it becoming an element of the political agenda of institutions. To overcome this the thesis explores phosphorus governance in the EU and seeks to answer the reasons for this fragmentation, what are the dominant and emergent perspectives that can inform its governance and how can the external dimension of phosphorus governance be steered. To do so, the thesis adopts framing as an analytical heuristic that can delineate, collate and potentially converge institutional and stakeholder views. It consists of a scoping review, a frame-critical analysis of intersectoral framings of relevance to phosphorus, as well as participatory scenario building. Although investigated through various scholarly perspectives, adopting a framing heuristic allows to borrow and incorporate framings from other sectors and instruments, as well as to generate innovative policies and design features. Additionally, it can improve intersectoral coherence and connect Phosphorus to salient objectives that are higher on the institutional agenda
Witnessing the text: a critical empathetic approach to Ecclesiastes with affect, trauma and bystander perspectives
Get PDFThis thesis explores the significance and effectiveness of a three-pronged reading strategy that is aimed at facilitating critical empathy and focuses particularly on the biblical wisdom book of Ecclesiastes. The three components of this strategy draw on affect studies, trauma studies, and the bystander approach, with the latter adapted from Holocaust studies. Following examination of biblical Hebrew affect vocabulary as a means to better understand the emotional force and multiple impacts of the phenomenon of trauma, the bystander approach extends analysis of the trauma response beyond its usual focus on the direct victim to consider bystanders of traumatic situations or events. This method focuses both on Qoheleth, the narrator of Ecclesiastes, as a bystander and on the reader of Ecclesiastes as a participatory and affected reader. As such, this research examines how readers’ experiences and emotional engagements with the text can illuminate and deepen biblical interpretation. The study also argues that the three approaches foster critical empathy—that is, the co-emphasis on emotional engagement alongside intellectual analysis. This, in turn, it is proposed, brings relevance, meaning, and transformation to both text and reader. Critical empathy is relatively new in terms of its explicit inclusion in biblical criticism. Also innovative is the application of the bystander approach to the book of Ecclesiastes. The thesis, therefore, contributes in original ways to a deepened encounter with the ancient book of Ecclesiastes; the proposed reading method also offers opportunities beyond this text
Evaluating the transition towards a circular economy in agri-food supply chains: Examining the role of supply chain integration in the adoption of circular economy practices through the arcs of integration
No full textThe circular economy (CE) has emerged as a transformative concept, replacing the traditional take- make-dispose model with a system of sustained regeneration and cyclical flows of materials and energy. Acknowledging its potential to address resource inefficiencies, the CE holds particular significance for agri-food supply chains, given their reliance on finite resources and the pervasive issue of food waste across all supply chain stages. Existing research has highlighted that collaboration and coordination are essential to achieving a systemic shift towards circular supply chains, with enhanced capacity for information and knowledge exchange among supply chain actors being crucial to minimise uncertainty and reduce resource dependence. Although previous studies have underscored the importance of supply chain integration (SCI) in supporting the implementation of CE practices, this concept has largely been explored within the context of conventional linear supply chains. Therefore, this thesis aims to address this limitation by assessing the role of SCI in the transition to a CE within agri-food supply chains. To this end, a multi-case study approach involving six companies in the agri-food sector is employed to highlight the potential of Frohlich and Westbrook’s (2001) arcs of integration as a tool for simultaneously examining the levels of forward and reverse SCI. By identifying the SCI and CE practices implemented by each company, the findings are analysed through the lens of resource orchestration theory (ROT) to evaluate the role of forward and reverse SCI configurations in supporting CE- related activities. Based on the results, three propositions are developed, reflecting the type and degree of SCI. The findings reveal that companies with higher levels of both forward and reverse integration are better positioned to develop and implement CE-related capabilities with suppliers and customers. The thesis concludes with research implications, policy recommendations, contributions to theory and practice, and directions for future research
Exploring the Landscape of σ-hole Interactions
No full textσ-hole interactions are a class of noncovalent interactions involving p-block elements. Comparable in strength and directionality to hydrogen bonds, σ-hole interactions present a useful tool for a wide range of applications.
The σ-hole arises when a polarisable p-block element is covalently bonded to an electron withdrawing group (EWG). The σ-bond to the EWG creates a charge anisotropy, resulting in a depletion of electron density along the extension of the σ-bond, the electropositive σ-hole.
Detailed searches of the CSD were constructed to investigate the geometric characteristics of σ-hole interactions to various nitrogen and oxygen lone-pair-possessing Lewis bases. Trends in the identity of the σ-hole donor atom and EWG were explored. The σ-hole acceptors also play a key role in the interactions and so were investigated on a functional group basis. Nitrogen Lewis bases are generally better σ-hole acceptors than oxygen Lewis bases, but oxygen Lewis bases show greater variety.
To predict the interaction energies for -hole interactions, the σ-Hole Approximation Tool (σHAT) was constructed. Based on a XGBoost regression machine learning model, and trained on geometric measurements and adapted molecular fingerprints of σ-hole complexes from a data set of high accuracy calculated σ-hole interactions. This model performs comparably to density functional theory (DFT) on the test set, with an RMSD of 1.03 kcal/mol, which is very close to the 1 kcal/mol "chemical accuracy" threshold.
This model was validated using cutouts derived from crystal structures in the CSD, which possess halogen bonds (a subset of σ-hole interactions). DFT calculated interaction energies for these cutouts were used to compare against the σHAT predicted interaction energies. The performance on this validation set showed an RMSD of 2.02 kcal/mol, but differed depending on the halogen bond donor atom, suggesting different character of the interactions
Formalizing, Analyzing and Improving Aerospace Security Protocols
Get PDFSecure networking protocols for domains such as the internet and the internet-of-things are regularly scrutinized and discussed by the research community. This status quo can be attributed to their pervasiveness in the modern technological landscape and the heavy dependence on the security of these protocols to reliably fulfill myriad everyday tasks. In contrast, the security of aerospace protocols has not received a proportionate level of investigation despite the fact that an attack on these protocols may result in catastrophic consequences. The reason for this can be twofold; the digitization of avionic communication is an experimental and ongoing process with legacy analogue components still in use; and most non-terrestrial communication protocols are closed-source which limits their public scrutiny. This work endeavors to address this gap in three parallels; we propose a formalism that captures the security of the integral handover phase of aviation communication; we analyze the security of non-terrestrial protocol Bundle Protocol Security (BPSec) and propose security improvements; finally, we propose quantum-secure protocol constructions for aviation communication, supported by empirical results of their performance on resource-constrained devices.
We begin by introducing a universal formalized framework that captures handover schemes as a unique primitive. Moreover, we construct security experiments that cap- ture distinct security properties for handovers, and propose a generic protocol construction that captures all identified security properties. We then shift our focus to the analysis of the non-terrestrial BPSec protocol, which we analyze as a flexible secure channel and propose a stronger construction with additional integrity guarantees. Finally, we return to the aviation domain and propose quantum-secure protocol constructions for air-to-ground communication as well as handovers. We implement our secure avionic constructions and evaluate their performance on resource-constrained devices to account for resource limitations of on-board avionic components. We design our avionic handover construction
integrating our formalism for handovers, focusing on reducing the computational overhead of complex cryptographic operations. We formally prove the cryptographic security of our avionic protocol constructions within appropriate models capable of capturing their post- quantum security
Exploring the Lived Experiences of Educational Psychologists in Using Reflection and Ethics as Virtues
Get PDFThis research explores lived experiences of five Educational Psychologists (EP) with varying experiences, length of practice and job roles, working within one Local Authority. Using semi-structured phenomenological interviews, participants reflected upon a work dilemma in which themes of reflection and ethics were commonly raised. This study aims to consider these concepts as ‘virtues’: an acquired human quality which can be strengthened. This research aims to understand EP’s experiences of manifesting and enacting the virtues of reflection and ethics. The exploration into current literature highlights the necessity of this research. Virtues are seldom considered within the world of Educational Psychology. This research aims to address this noticeable gap and develop the theoretical and practical development within Educational Psychology.
Five interviews with EPs were analysed using Interpretive Phenomenological Analysis (IPA), as denoted by Smith et al, (2022). Findings revealed seven Group Experimental Themes (GETS): Using virtuous reflection, virtuous ethicality, the dynamic relationship between the virtues; manifestations of virtues in supporting the job, emotional evocation manifestation, experiences that impact virtues, and barrier to engaging in virtues. These GETs then have associated subthemes which explore the lived experience in more depth. The findings suggest both ethical and reflective virtues are present within Educational Psychology practice and are a crucial part of being an Educational Psychologist. However, there are significant experiences and barriers to engaging in virtues that can be a result of personal, professional or systemic aspects. Additionally, this research highlights a bi-directional relationship between virtuous reflection and virtuous ethics. The deeply complex, nuanced and interwoven nature of virtues is explored. This study calls for additional research into virtues’ place within Educational Psychology, whether this be in the Doctoral training programme, EP practice, or systemic awareness. In essence, this research merely touches on the expanse of how virtues can, and should, be used
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