Variational inference for stochastic processes

PhD ThesisStochastic process models such as stochastic differential equations (SDEs), state-space models (SSMs), Gaussian processes (GPs) and latent force models (LFMs), provide a powerful collection of modelling techniques to better our understanding of many physical systems. In treating these models within the Bayesian paradigm, we further yield a rich expression of our uncertainty, and gain the ability to incorporate our prior beliefs. However, performing Bayesian posterior inference is not without significant challenge. Exact likelihood calculations can often be intractable, take an infeasibly long time to compute, or be challenging to approximate in the presence of missing data. Therefore, designing new approaches to perform Bayesian inference for this family of stochastic process models is of great scientific interest. Variational inference (VI) has had great success is scaling Bayesian inference across a range of problem domains. Historically, however, its successful application to stochastic process models has been limited. The reason is two-fold. Firstly, mini-batch likelihood estimation techniques often employed by VI have only previously been applicable to models of independent data. Secondly, approximating distributions have often imposed unrealistic assumptions over the posterior. Fortunately, however, recent advances in generative modelling have provided the framework with which to solve these problems. Here, artificial neural networks can be used to flexibly construct powerful density approximations, which are then amenable to fast computation using modern GPUs. This is otherwise known as black-box-variational inference. This thesis presents a collection of black-box variational methods for the purposes of approximate inference in SDEs, SSMs, GPs and LFMs. Here we leverage artificial neural networks to parametrise our approximate posterior distributions, permitting accurate inference in a short time. We begin by presenting two methods for SDE inference. The first, inspired by the Euler-Maruyama discretisation, approximates the discrete-time solution to a conditioned diffusion process using recurrent neural networks. The second, which extends the first, eschews a discretisation scheme and approximates the continuous-time process directly. Finally we consider the use of normalising flows for inference using SSMs (including discrete-time SDEs), GPs and LFMs. Here we design a generative architecture that permits mini-batch optimization, allowing approximate inference for big dat

The Impact of Bioactive Collagen Peptides on Promoting Cutaneous Wound Healing

Ph. D. Thesis.Chronic wounds continue to be a major clinical and financial burden to healthcare providers worldwide with increased prevalence associated with an ageing population and systemic diseases such as diabetes. An acute unmet need for innovative therapies for effective wound repair thus remains. Recent studies using bioactive collagen peptides report their ability to promote cellular differentiation, proliferation and migration in animal models of cutaneous wound healing, leading to the present study aimed at defining the potential for and the mechanistic action of porcine-derived collagen peptides (Peptan P) to increase cutaneous healing in primary human keratinocytes and dermal fibroblasts in vitro and in wounded full thickness ex vivo skin equivalents, in an age dependent context. Results demonstrated Peptan P significantly promoted wound closure of both dermal fibroblasts and keratinocytes derived from young or aged individuals by enhancing cellular proliferation, with additional studies demonstrating the ability for Peptan P to also promote keratinocyte and dermal fibroblast wound closure in a hyperglycaemic environment. Mechanistic studies revealed Peptan P induced significant increase of both integrin α2 and β1 subunit expression by both keratinocytes and dermal fibroblasts, promoting activation of an ERK-FAK signalling cascade during keratinocyte wound closure, whilst integrin ligation most likely activates other downstream signalling pathways to promote dermal fibroblast wound closure. These observations were further supported by studies showing diminished Peptan P-induced wound closure of keratinocytes and fibroblasts following siRNAmediated knockdown of the integrin β1 subunit. Studies in optimised 3D human skin equivalent models subjected to punch biopsy-induced wounding further revealed Peptan P promoted wound closure through enhanced re-epithelialisation. Collectively, these data highlight the translational and clinical potential for Peptan P as a viable topical therapeutic to promote re-epithelialisation of superficial cutaneous wounds

Critical transport across a finite temperature bosonic Josephson junction : resistive superflow dynamics, vortex ring generation and thermal damping

PhD ThesisA Josephson junction consists of two-weakly coupled quantum fluids through a barrier and is an ideal environment for studying coherent quantum transport and its breakdown due to dissipation, depending on whether or not the superfluid velocity exceeds a critical value. Motivated by a recent experiment with 6Li (in the Bose-Einstein condensation limit) at LENS (Florence), in this thesis we firstly characterised the dynamical regimes observed experimentally for an elongated three-dimensional bosonic Josephson junction: the coherent dynamics Josephson ‘plasma’ oscillations regime and the dissipative one. Our analysis is based on both zero-temperature mean-field theory (Gross-Pitaevskii equation), and its finite temperature kinetic theory generalisation, in which the condensate is coupled to a dynamical thermal cloud, described by a quantum Boltzmann equation (Zaremba Nikuni-Griffin method), and reveals excellent agreement with experimental findings. Secondly, we showed a direct connection between resistive superfluid current and vortex ring (VR) nucleation, through the mechanism of phase slips, thus demonstrating a close analogy with the phase-slippage phenomenon in superfluid helium. Specifically, we identify the origin of dissipation as the transfer of the incompressible kinetic energy from the axial flow to the VR swirling flow, and the phonon emission during vortex propagation. Performing a detailed study of the VR dynamics in our three-dimensional inhomogeneous superfluid, we highlighted the role of trap asymmetry on the emergence of elliptical VRs exhibiting Kelvin wave excitations. The dissipation due to relative condensate-thermal motion (at fixed condensate number, well below the transition temperature) was found to have no effect at early times but it becomes relevant at longer timescales, affecting both the oscillatory relative population dynamics and the VR dynamics. Exploring a wider range of barrier heights/widths beyond the experimental parame ters, we constructed an extended phase diagram for the elongated trap, including –beyond Josephson ‘plasma’ and dissipative regimes discussed above – also the expected Macro scopic Quantum Self-Trapping regime. Confirmation of the emergence of an analogous phase diagram in a spherical trap, demonstrates unequivocally that all three regimes should be observable in carefully-tailored ultracold experiments. Studying the role of finite temperature, we distinguished two regimes: at relatively low temperatures, where condensate mean field dynamics dominates, the relative population imbalance oscillates with two main frequencies: in this regime, the thermal cloud is driven by the condensate, with its presence damping the condensate motion and decreasing its frequency. However, when the temperature becomes such that the thermal cloud mean ki netic energy exceeds the barrier height, the thermal cloud oscillates with its own frequency, and begins to drive the condensate, significantly affecting its observable dynamics

Developing tools to investigate initiating events of mitochondrial translation

PhD ThesisMitochondria are the predominant source of adenosine triphosphate (ATP) in nucleated human cells. ATP is required as cellular energy source and mitochondria synthesise ATP by coupling the oxidative phosphorylation (OXPHOS) system. Mitochondria contain their own circular DNA (mtDNA) which encodes 11 messenger RNA (mt-mRNA), 2 ribosomal RNA (mtrRNA), and 22 tRNA (mt-tRNA) molecules which are all utilized for the synthesis of 13 proteins, all key components of the multi-subunit OXPHOS complexes, by the mitochondrial ribosome (mitoribosome). Much of the life cycle of mt-RNA and the process of translation is still unclear, in particular a full understanding of mt-mRNA stability, delivery, and loading onto the mt-SSU (or mitoribosomes) is lacking. The aim of this research was to investigate these processes using super resolution imaging of mt-rRNA and proximity-dependent proteomic analysis. I have visualised mt-rRNA molecules beyond the diffraction limit by the development and application of RNA Fluorescent In Situ Hybridisation (FISH) compatible with STimulated Emission Depletion (STED) microscopy. This technique was used to validate the loss of the 16S mt-rRNA upon induction of the mitochondrially-targeted VapC20 endonuclease and has contributed to a model wherein the formation of the monosome is an important factor in mtmRNA transcript stability. To further understand the process of mt-mRNA loading onto the mitoribosome, I employed proximity-dependent biotin identification (BioID) to uncover proteins which may be enriched at the mitoribosome mt-mRNA entry site. Multiple mitoribosomal proteins were fused to the BioID moiety, expressed in human cells, and screened for their ability to assemble into the mitoribosome. Mass spectrometry was used to characterise the proximal interaction network of MRPS39 and MRPS27 which uncovered the heterodimeric proteins PHB and PHB2. These proteins were then investigated to further understand their roles in mitochondrial translation. This thesis presents a thorough investigation into mt-RNA and mitochondrial translation and provides tools and techniques that complement the current literature

Optical MEMS sensors for wall-shear stress measurements

Ph. D. Thesis.This research reports on the development and experimental characterisation of optical sensors based on Micro-Electro-Mechanical-Systems (MEMS) technologies for walls hear stress quantification in turbulent boundary-layer flows. The MEMS sensors are developed to measure the instantaneous wall-shear stress directly via a miniature flush-mounted floating element, which is on the order of hundreds of microns square. The floating element is suspended flush to the wall by up to four specially designed micro-springs. As the flow passes over the wall, the sensor’s floating element moves, allowing direct measurement of the local forces exerted by the flow on the wall. A new optical transduction scheme based on the Moiré fringe pattern is developed alongside with an optical pathway to measure the instantaneous wall-shear stress using a single photodetector. Using this new optical technique consists of a lens array and fibre optics that provides the ability to detect the wall-shear stress using different sensing element sizes, leads to miniaturisation of sensors. Utilising the lens array, the focused light spot size is controlled, providing the opportunity of scanning the Moiré fringe pattern area on the sensors with different sensing element sizes. The microfabrication process of the devices are carried out by using a four mask bulk Silicon-on-Insulator (SOI) process and a BF33 wafer, where each device is placed at the center of a 5 mm × 5mm chip. Two generations of sensor packaging are developed to accommodate the sensors’ dies as well as the sensors’ optoelectronics, whilst the floating element is flush-mounted to the surface. The MEMS sensors calibration is carried out in a laminar flow rig over a wall-shear stress range of 0 to 5.32 Pa, where the results indicate a sensitivity range of 38 to 740 nm/Pa, an accuracy range of 1.4 to 2.36% and a repeatability range of 0.68 to 1.96%. The value of the of minimum detectable wall-shear stress for the developed MEMS wall-shear stress sensors varies in a range of 17 to 593 µPa, resulting in a minimum and maximum dynamic range value of 79 dB and 109 dB, respectively. The results from the dynamic characterisation indicate a resonant frequency range of 1 to 8.3 kHz. In a series of wind tunnel experiments over a range of Reτ = 560 to 1320, the instantaneous wall-shear stress within the turbulent boundary-layer flow is measured simultaneously by the MEMS sensors and an by either hot-wire anemometry or laser Doppler velocimetry using the near-wall velocity gradient technique. Excellent agreement is observed in the time series and statistics across these three independant measurement techniques.Faculty of Science, Agriculture and Engineering (SAgE), Newcastle Universit

Role of retrotransposons in hepatocellular carcinoma origin and progression – potential biomarker and therapeutic target?

PhD ThesisIntroduction Hepatocellular carcinoma (HCC) has the fourth highest cancer-related mortality worldwide and is associated with a poor 5-year survival. Current therapies are limited and provide short median survival. Thus, there is an urgent need to develop novel therapies. Long interspersed class elements1 (LINE1 or L1) activation has been demonstrated in several cancers including HCC and can inhibit tumour suppressor genes or activate oncogenes. However, the role of L1 in hepatocarcinogenesis is still unknown. Methods L1 expression was evaluated in the RNAseq data of HCC (n=372) from the cancer genome atlas liver hepatocellular carcinoma (TCGA LIHC) study and formalin-fixed paraffin-embedded (FFPE) patient biopsies (n=48) from our own biobank. RNAseq data was analysed for L1 counts and their distribution was assessed in different HCC subclasses based on previously known molecular classifications and associations with clinical parameters were explored. Likewise, FFPE samples were stained for L1orf1p using an automated immunohistochemistry machine and were scored by a pathologist; associations between L1orf1p expression in HCC and clinical parameters like cirrhosis, tumour stage, albumin, bilirubin, alpha fetoprotein (AFP) and survival were explored. The role of L1 was further characterised in different liver cancer cell lines utilising L1 knockdown and overexpression systems. L1 knockdown was achieved using a lentivirus-based shRNA expression vector targeting L1orf1 in Huh-7 cells. The influence of L1-knockdown on functional properties such as proliferation, migration and invasion of the cells were investigated by comparing L1-knockdown cells with wild type and non-targeted controls. RNAseq evaluated the influence of L1-knockdown on whole transcriptome. Transient L1 full-length overexpression and conditional L1orf1p overexpression were used to further validate the influence of L1 on cell signalling pathways. Results L1 expression was elevated in HCC both at transcript and protein level compared to adjacent nontumour tissues. L1 transcripts correlated with high AFP, TP53 mutation, macrovascular invasion and activated TGF-β signalling. Likewise, L1orf1p expression correlated with AFP, activated TGFβ signalling and poorly differentiated tumours. A positive association between L1orf1p and pSMAD3 confirmed the relationship between L1 expression and TGF-β signalling in HCC. L1 knockdown in Huh-7 cells led to decrease in migratory and invasion capacity of the cells compared to control cell lines. Furthermore, gene set enrichment analysis (GSEA) of the RNAseq data demonstrated downregulation of TGF-β pathway in Huh7-L1knockdown cells compared to non- targeting control cells, which was confirmed by Pai1-lucifease reporter assay. Conversely, L1 overexpression (full-length and L1orf1 alone) increased TGF-β signalling as confirmed by Pai1- lucifease reporter assay, RT-qPCR and FACS analysis in HepG2, PLC/PRF-5 and HHL5 cell lines. Conclusion L1 is upregulated in human HCC and associated with high AFP, TP53 mutation and activated TGFβ signalling. Further in vitro studies demonstrated a crosstalk between L1orf1p and TGFβsignalling. Overall, our data demonstrates a causal link between L1orf1p and TGFβ signalling, which presents a novel therapeutic avenue and potential treatment stratification biomarker for HCC

The transformative potential of philosophical dialogue: space for children and young people to explore their multi-storied lives

DAppEdPsy ThesisThis thesis explores experiences of philosophical dialogic inquiry as a pedagogical approach with children and young people (CYP), for example, the use of Philosophy for Children (P4C). It contains four chapters: a systematic literature review, a critique of ethical and methodological choices, an empirical research project and a reflexive chapter, which considers personal and professional implications of the thesis. Chapter 1: How do children and young people experience the process of philosophical dialogic inquiry and the wider implications of this pedagogical approach? This systematic literature review explores children and young people’s (CYP’s) experiences of philosophical dialogic inquiry, a pedagogical approach that invites CYP to engage in critical thought and discuss a philosophical topic together. A metaethnography was used as a process to search and synthesise qualitative literature. Five papers were selected and reviewed. The key themes identified were features of a dialogic process, experiences of learning as a sociocultural experience and, reconstructed perceptions of the self, others, and learning. The influence of the context on the experiences of CYP was also identified as a critical theme. A line of argument was expressed in a visual form to illustrate the relationship of these themes to one and other. The review highlights the momentary experience of engaging in a dialogic process and wider implications for CYP, such as, engagement in dialogue outside of the school context and shifts in perceptions. Teacher accounts in the synthesised research also illustrated how philosophical dialogic inquiry can challenge adults’ perceptions of CYP and what they are capable of. This may illustrate the potential for transformative change for CYP and adults. Chapter 2: An ethical and methodological critique This chapter explores ethical and methodological considerations during the development of the research project outlined in Chapter Three. The philosophical orientation of the research was social constructionism; therefore, the construction of language and power were critically considered throughout. The research was informed by participatory principles and narrative inquiry. Due to the COVID-19 pandemic, the research was facilitated virtually. Thus, virtual methodologies, and the associated implications of this, were continually reflected upon. iv Relational ethicality guided the process of the research as there was ongoing attunement to interpersonal dynamics. This is arguably an aspect of quality and rigour in qualitative research (Groundwater‐Smith & Mockler, 2007). Chapter 3: A narrative inquiry with autistic young people and teachers in their school: how are the narratives they have constructed about themselves and their experiences woven and explored during philosophical dialogue? The purpose of this empirical research is to understand how stories can be constructed and enacted in P4C. The project was undertaken in a specialist school / sixth form in the North East of England and adopted a qualitative approach. Autistic CYP, and teaching staff participated in the construction of the research approach, analysis, and dissemination decisions. Virtual semi-structured interviews were carried out to explore biographical stories and experiential stories. The interviews were constructed and analysed using Narrative Orientated Inquiry, Collocation Analysis and Critical Narrative Analysis. Findings are discussed with regards to the connections in the rich life stories and experiential stories shared by an individual, this aims to address how narratives can be woven and explored during a P4C process. By developing an understanding of the transformative potential of philosophical dialogue, I hope this will inform holistic understandings of CYP, and creative pedagogical practice. Chapter 4: How did I shape the research and how did the research shape me? Personal and professional implications. This chapter explores personal and professional implications of the research project outlined in Chapter Three. Engaging in participatory processes had implications on how I negotiated a relational dynamic when working alongside CYP and teachers. The use of narrative psychology was therapeutic and transformational, this consolidated narrative ways of ‘being’ as a key aspect of my professional practice. The stories shared in the research also prompted me to rethink pedagogy and how I could construct space for shared reflection on pedagogical approaches, and the underpinning philosophical principles, in education. Unpicking and understanding moments of reflexivity during the research has highlighted my key values as a person, researcher, and Educational Psychologist (EP)

An evaluation of the therapeutic potential of human amniotic epithelial cells during ex-vivo donor lung perfusion

Ph. D. Thesis.Introduction: Ex Vivo Lung Perfusion (EVLP) provides a normothermic isolated environment for the evaluation and reconditioning of donor lungs deemed unsuitable for immediate transplantation and offers a unique opportunity to administer advanced therapeutics, such as cell-based therapies. Human Amniotic Epithelial Cells (hAECs) have been shown to have immunomodulatory properties that could reduce injury in donor lungs. Our aim was to assess the anti-inflammatory actions of hAECs when administered during EVLP to lungs declined for transplant due to poor organ function. Methods: hAECs were isolated from term placenta through enzymatic digestion. In in vitro studies, THP-1 derived macrophage phagocytosis and activation was determined after treatment with hAECs for 6 hours. Neutrophils were migrated through an IL-1b activated Human Microvascular Endothelial Cells (HMEC)-1 monolayer, after treatment of hAECs. In ex vivo perfusion studies; human lungs declined for transplant were split, with 150 x 106 hAECs or the HTR-8/SVneo cell line administered to each single lung and perfused concurrently for up to 4 hours (n=3). Serial samples of perfusate and tissue biopsies were collected for ELISA, qPCR and immunofluorescence (IF). Results: hAECs were isolated with 94 ± 4% purity, with an average isolation yielding 134.2 x 106 with viability >90%. hAECs reduced neutrophil transendothelial migration (p=0.0128). hAEC treatment of macrophages led to an increase in phagocytosis observed in vitro and a decrease in CXCL8 (p=0.0465) and TNFa (p=0.0158) expression. hAEC-treated lungs had significantly reduced TNFa expression in the tissue (p=0.0415). IF staining demonstrated reduced expression of CXCL8 and 3- nitrotyrosine in the hAEC-treated lungs compared to the HTR cell treated lungs. Conclusion: In vitro assays demonstrated the potential of hAECs to minimise proinflammatory macrophage activation and neutrophil migration. hAEC-treated lungs led to a reduction in pro-inflammatory cytokine production and oxidative stress. hAECs may offer a therapeutic approach to reduce inflammation in donor lungs during EVLP.NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation (BTRU-ODT

Professional learning re-constructed through narrative inquiry in the United Arab Emirates

PhD ThesisResearch on teacher educators’ professional learning within the United Arab Emirates is an emerging field. My roles as a senior educational professional have inspired my interest in the professional learning of teacher educators and specifically in reflecting on my own professional learning. This study adopts a narrative inquiry approach to my personal and professional learning in the United Arab Emirates. As a teacher educator, I operate within a complex cultural and economic environment that is underpinned by Emirati culture, Islamic values and a neo-liberal, market-based approach to education. As a result, I have worked in various professional roles with a high degree of uncertainty, and I have navigated unfamiliar professional boundaries to achieve personal agency. There are three main phases of this study which has taken place over a six year period; the first phase captures my thinking as an early career teacher, before progressing to a teacher educator role working across schools, and then working in a senior role, juggling a range of commercial and educational responsibilities. In order to make empowering decisions about my professional learning, I have needed to develop a set of researcherly dispositions, which has emerged from my awareness of the contextual challenges and opportunities within the UAE education sector. My narrative as a teacher educator is illustrated with cameos of two teacher educators and a teacher with whom I have worked, each with unique profiles and development needs that have informed my approach to the design of professional learning opportunities. Through my work with these educators I explore the conditions that have supported my professional growth and outline the impact this has had on me. This narrative study, which draws on European models, namely the Dutch Standards (VELON) and the Flemish Teacher Educator Development Profile (VELOV) and also Kelchtermans ‘Dynamics of Learning’ model (2018), demonstrates that I have been required to exhibit certain dispositions that are relevant to the UAE education context in order to perform in a variety of professional roles. The findings of this study reveal that I have examined my professional contexts in pursuit of personal agency, and attempted to capture the nuances of my professional learning, and the professional learning o

Co-destruction & Co-creation of Value: The Influence of Basic Values, Traits, Motives and Benefits on Consumer Behaviour and Choice

Ph. D. Thesis.Co-destruction and co-creation are both likely outcomes of interactions between firms and consumers. Whilst co-creation has been studied within the literature, co-destruction has not been studied as extensively. This work attempts to bridge this gap by highlighting factors innate to consumers which increase their likelihood to co-destroy value during interactions with firms. Whilst the focus of this work is co-destruction, the study utilises co-creation to put co-destruction into context. Data were collected through an online sample and a variety of methods were used to determine the effect of basic human values, motivation and personality traits on consumer co-destruction and co-creation behaviour and consumer co-destruction and co-creation choice. This work also determined the benefits sought by consumers who co-destroy or co-create value during interactions with firms. With regards to basic human values, this work finds that personal values which express self-enhancement and openness-to-change facilitate co-destruction behaviour, while personal values which express self-transcendence and conservation facilitate co-creation behaviour. The results also suggest that the basic human values circumplex structure can be divided beyond the current division to reflect co-creation and co-destruction values. For personality traits, this work finds neurotic consumers are most likely to exhibit behaviours which will co-destroy value for the firm while conscientious and agreeable consumers are consumers least likely to co-destroy value. Neurotic consumers are consumers least likely to co-create value while extroverted and open consumers are most likely to co-create value during interactions. Findings from this work also show that both values and traits predict consumer co-destruction and co-creation choices during interactions. Basic human values show a stronger prediction of co-destruction choices in comparison to co-creation choices, highlighting the more cognitive nature of co-destruction. The study has also found that whilst traits contribute to the variance in choice, traits do not necessarily show better classification of choice in comparison to values. Finally, this study finds that a range of intrinsic and extrinsic motives drive consumers to exhibit co-destructive behaviours. These include revenge motives, egoistic motives and hedonic motives. Whilst consumers co-destroy value for both utilitarian and hedonic benefits, consumers are more likely to co-destroy value for hedonic benefits as opposed to co-destroying value for utilitarian benefits