VictorJuiz/thesis huggingface dataset:
3d printed cortical tissue and implantation

It is a considerable challenge to engineer human tissue with multiple cell types and a defined cellular structure and function. The outer layer of the brain, the cerebral cortex, is composed of a layered architecture, which consists of multiple types of layer-specific neurons arranged into vertical columns. The layered structures enable higher cognition via intricately wired neuronal circuits; however, the present tissue engineering technique cannot generate these structures. In the current DPhil project, we used a droplet-based bioprinting technique to assemble living tissues mimicking simplified cerebral cortical columns. Upper- and deep-layer cortical neural progenitors were differentiated from human-induced pluripotent stem cells (hiPSCs) and were then droplet printed into two-layered cerebral cortical tissues. In the subsequent characterization, we found that the tissues demonstrated layer-specific biomarker expression and produced an integrated axon network. The printed cerebral cortical tissues were implanted into mouse brain explants, which revealed a considerable host–implant connection across the boundaries via axon projection, neuron migration, and the establishment of correlated calcium ion signals. Implanted brain explants can be applied in the evaluation of compounds and nutrients that facilitate tissue integration. Moreover, our technique might be used in personalized implantation therapy by 3D-printed tissues generated from patients’ own iPSCs.

Keywords: 3D Bioprinting
Brain Repair
Neuroscience
hiPSCs
Advisor: Bayley, H
Museological approaches to pre-Christian funerals and the representation of the past in Old Norse literature

Death and the disposition of the body are essential to all cultures. These events are of particular significance for medieval Scandinavia, however, as dealing with the dead was a key issue in the transition from heathen religions to Christianity. Depictions of pre-Christian funerals in Old Norse sources are thus key sites for understanding medieval attitudes towards the pagan past. This thesis examines depictions of pre-Christian funerals in Old Norse literature as representations of the past through a unique theoretical framework derived from museology and heritage studies. It is built around three core concepts: the process of musealization; the idea of the ‘curatorial present’; and the production and promotion of ‘Authorised Heritage Discourses’ (AHDs). This theoretical framework is used to analyse depictions of cremation and mound inhumation in both prose and poetry from museological and heritage studies perspectives.
The beliefs and practices concerning death and funerals at the time in which the Old Norse corpus was produced are examined through religious texts, legal codices, and sagas. Cremation funerals are only ever depicted in the remote past of myth and legend, and the custom is characterised as an imported practice performed primarily by non-Scandinavian elites. Mound inhumation is depicted as a Scandinavian innovation that is practised up until the conversion to Christianity. The relegation of cremation to the most remote past, the emphasis placed on its foreignness, and the taboo nature of cremation within medieval Christianity and its association with exorcising the undead evidences a desire to distance this aspect of the past. This is examined through the museological concept of ‘difficult heritage’ and its application to the depiction of the funeral of Brynhildr and Sigurðr in Sigurðarkviða in skamma, Helreið Brynhildar, Vǫlsunga saga, and Norna-Gests þáttr. The widespread geographical and temporal depiction of mound inhumation, and its characterization as a Scandinavian practice, suggests the construction of cultural heritage, as it can be aligned more readily with the burial practices of the Christian curatorial present. It is examined as a heritage practice that links past and present funerary rites in Heimskringla, Landnámabók, and the Íslendingasögur through the shared practice of inhumation, creating a community of the pre-Christian dead. In the Íslendingasögur, the practice of burying the ‘bad’ dead in dysjar (stone cairns) can catalyse their transformation into malevolent draugar (revenants), reflecting medieval anxieties about life after death, the potency of the dead body, and improper burial.

Keywords: Iceland
cremation
draugar
heritage studies
haugr
death studies
Medieval Christianity
burial mounds
Old Nordic religion
Old Norse literature
cultural memory
burial archaeology
Norway
museology
inhumation
Viking funeral
revenants
Viking age archaeology
commemoration
Advisor: O'Donoghue, H
Examining medical doctors’ internship training experience and labour market transition in Kenya

Kenya has a severe shortage of doctors. Despite medical schools increasing the numbers of medical officers (MO) in training, less than half of newly qualified/registered MOs were absorbed by the public sector between 2015 and 2018. It seems timely to understand the labour market for this profession in system terms and in personal terms for doctors, especially during their labour market entry. I used a multiple-method approach including literature reviews, quantitative survey and qualitative interviews to examine doctors’ internship training experiences and labour market transition in Kenya.
I found that the resources available in hospitals overall was often inadequate to support medical internship training in Kenya, especially for Level 4/district or smaller hospitals. Over half reported that their hospitals did not have enough consultants, physical resources and supplies of diagnostics, equipment and medications required for their study and work. Over half of the interns experienced burnout and anxiety, some did not have good supervision at all times and had to perform inappropriate tasks, especially in smaller hospitals. Such poor internship experiences influenced MOs’ career intentions. Some preferred to leave the public sector, however the majority still preferred to work in the public sector or continue with specialist training immediately after internship. Nonetheless, as decentralisation in 2013 led to county governments being responsible for local workforce recruitment, they are not absorbing these MOs into the public sector. This is for reasons including limited health system financing, a willingness to rely on interns to provide hospital care, and preference for recruiting other cheaper health worker cadres. These findings suggest that Kenya needs to take a strategic approach to match the demand and supply of physicians, especially at labour market entry (i.e. internship) as well as improve the internship training resources and capacity. Poor planning and management not only wastes resources and undermines healthcare delivery, but can also be detrimental to individual physicians.

Advisor: English, M
Nicodemo, C
Gathara, D
Multiscale modelling of the action of low salinity

Experimental evidence shows that injecting low salinity water into an oil reservoir can lead to an increase in the amount of oil recovered. However, due to the complexity of the chemical interactions involved in this pro- cess, there has been much debate over the dominant mechanism causing this effect. Numerous mechanisms have been proposed, and, in recent years, one which has gained notable support is the multicomponent ionic exchange (MIE) mechanism.
The aim of this thesis is to understand how the microscale reactions de- scribed by the MIE mechanism affect the oil recovery on the macroscopic scale. We first consider a simple two-dimensional model for the motion of an oil slug through a clay pore throat in order to determine the effect of the ion-exchange reactions on the fluid dynamics at the pore scale. We further this investigation by studying two-phase flow through a three-dimensional channel with varying elliptic cross section in the limit in which the water phase is restricted to a thin film between the oil and the surface of the throat. We then investigate the effect of salinity on the permeability of a periodic porous structure for the case in which the water phase is confined to a thin film coating the solid surface, and derive a method for estimating the permeability using a network model. We develop this approach fur- ther by presenting a network model for two-phase flow through a porous structure. Finally, we use a discrete form of the method of multiple scales to homogenise our network model and derive a set of continuum equa- tions for the saturation and ion concentrations which are applicable on the macroscopic scale.

Keywords: fluid dynamics
multi-phase flow
oil recovery
flow through porous media
homogenisation
Advisor: Breward, C
Chapman, J
Searches for rare nuclear decays in the LUX-ZEPLIN experiment

The fundamental nature of dark matter stands as one of the greatest mysteries in physics. A compelling body of evidence indicates that dark matter accounts for 84% of the total matter density of the universe, and yet the detection of its constituent particles remains elusive. Stationed deep underground, the LUX-ZEPLIN (LZ) experiment utilises several tonnes of xenon in a dual-phase time projection chamber to conduct direct searches for particle dark matter. A world-leading limit was recently set by the LZ experiment for interactions between nucleons and weakly interacting massive particles, the most promising dark matter candidate. The work of this thesis leverages the unprecedented sensitivity and versatility of the LZ detector to expand the scientific programme to searches for rare phenomena beyond dark matter.
A comprehensive background model of detector materials is constructed in this work, using a combination of real data and simulations within a novel approach, as informed by expectations from an extensive radioassay campaign. This result is primarily applicable to searches for hypothesised neutrinoless double beta decays, the observation of which would shed light on the underlying properties of massive neutrinos, and is tied to the matter-antimatter asymmetry of the universe. With a large quantity of xenon, an ultra-low background environment, and excellent energy resolution, LZ is projected to achieve a sensitivity that is competitive with dedicated experiments.
The first LZ measurement of Xe-124 decay through the process of two-neutrino double electron capture is also presented here. This is the rarest nuclear decay observed to date, with a half-life that significantly exceeds the age of the universe. The dominant I-125 background is constrained with a detailed neutron activation model, and the exposure is maximised with an optimised fiducial volume. A half-life of (1.09 ± 0.18 stat ± 0.03 sys) × 10^22 years is observed with a statistical significance of 7σ. In future runs, the discovery of even rarer Xe-124 decay modes, namely two-neutrino electron capture with associated positron emission, will be within the physics reach of LZ.

Keywords: dark matter
particle physics
LZ
LUX-ZEPLIN
double electron capture
Advisor: Kraus, H
Non-people in the People’s Republic: ‘Landlords’ and ‘rich peasants’ under Maoist state socialism

For some thirty years, a substantial minority of the Chinese population was excluded from the political and moral community of the People. The largest number of non-People were the only literal ‘class’ enemies in the People’s Republic: those labelled ‘landlords’ and ‘rich peasants’ during land reform by reference to their socioeconomic position in rural society before the revolution. This thesis is a political, cultural, and social history of this group. It approaches the ‘landlord-rich peasant question’ as a single subject, one which originated in the 1920s, was central to politics, culture, and social life in the Mao era, and which, in a number of sometimes unexpected ways, continued well into the Reform era.
Existing scholarship is unanimous that class labels were a hugely important feature of political and social life in the Mao era. This thesis argues that the categories of landlord and rich peasant were more central among ‘bad’ labels than most scholarship has appreciated, and that those identified as landlords and rich peasants by the CCP bore much of the human cost of the three-decade long centrality of the divide between the People and their enemies in Chinese political and social life. It also shows, however, that the permanence and heredity of these labels observed under late Maoism was not part of a consciously designed system: during the early People’s Republic, a significant minority of class enemy labels were removed, and many young people from such families were able to find a place in the new society.
The eventual permanence and heredity of class enemy labels was instead the outcome of a contingent historical process, with major turning points in 1957 and especially 1962. These features always remained in tension with ideological and policy commitments to reform and non-heritability, which the Party maintained even as it carried out a systematic campaign to re-stigmatize class enemies after 1962. In post-1962 China, where the narrative of ‘class struggle’ permeated political and social life, ‘reform’ tended to become little more than a justification for a series of coercive and demeaning practices, and non-heritability the grounds for forcing those from class enemy families to demonstrate that they had come to hate their own parents. But when Chinese political life was redirected away from class struggle after 1978, the Party could proclaim that it had completed its mission of reforming class enemies, and that the mistreatment of their children and grandchildren had been a violation of policies that the Party had been committed to all along.

Keywords: class enemies
landlords and rich peasants
friend-enemy binary
Maoist China
Advisor: Harrison, H
Smith , SA
An ethics account of global health security

Global health security is defined by World Health Organization as “the activities required…to minimize vulnerability to acute public health events that endanger the collective health of populations” (2007). Despite this definition, global health security is a contested area because of concerns about the focus and beneficiaries of the enterprise. The aim of this thesis is to explore the scope, limits, and ethical issues within the global health security enterprise, in the context of infectious disease outbreaks.
The first stage of the thesis examined ethics in the global health security literature both before and during the COVID-19 pandemic. The findings from the critical interpretive review undertaken show that although ethical terms are frequently called for in global health security, there is little ethics analysis of what they mean, nor perspectives from those that work in this area.
To address this gap, a study utilising symbiotic empirical bioethics methods was undertaken. Thirty-eight qualitative interviews with professionals working in global health security, or in related areas, were completed. The thematic analysis of this data illustrates that those working in global health security operate in a complex moral landscape. This landscape involves everyday ethical considerations in the work of global health security, as well as wider concerns that can be understood as moral boundaries and borders. These moral boundaries include definitional boundaries about what global health security means; boundaries about dividing resources, roles and responsibilities by whether an outbreak is natural in origin, as opposed to accidental or deliberate; and geopolitical boundaries concerning the nature and limits of nationalism.
The final stage of the thesis brings together the findings from the qualitative analysis and compares it to relevant concepts in the ethics literature. I conclude that 1) current arguments for expanding the scope of global health security may not be the solution to moral concerns in the enterprise, 2) there needs to be care around the use and implications of ‘natural’ outbreaks, and 3) there is room for reclaiming a globally just nationalism as a moderate framework for how global health security should operate. I then situate these findings within the practice and policy context of global health security.
This thesis presents one of, if not, the first, empirical ethics studies on global health security, and argues that global health security must be acknowledged as a moral enterprise in order to fulfil its potential to protect persons globally.

Keywords: health security
infectious disease
pandemics
epidemics
empirical ethics
bioethics
global health security
global health
Advisor: Parker, M
Kingori, P
'This cloud had been written upon': Investigating digital editing methods for Anne Bathurst's visionary writing

This dissertation will feature a digital asset, a complete digital edition of Anne Bathurst’s ‘Rhapsodical Mediations’, in addition to an essay detailing the theories behind the digital methods employed in creating this edition as well as an assessment of their results.
This will hone in on the specifics of Anne Bathurst’s manuscript – a historically-significant religious diary which has thus far not been digitised in full – as well as zooming out to the wider implications of what it means to digitise a manuscript which not only contains interesting material features, but, also intensely spiritual content.
The questions at the heart of this dissertation are whether the physical or the mystical can be captured by any pre-existing digital methodology, whether creating a bespoke methodology is worthwhile to this field and whether mystical objects should be digitised at all. After all, how can an interoperable, standardised digital edition be imbued with the mystical essence of visionary writing? – and, how can it meaningfully present the physicality of a manuscript? The mission statement for this project is that an object’s physical existence and digital existence should be intimately interlinked in a creative way, and that this interlinking is a valuable scholarly exercise.
The digital tools involved in this discussion are TEI, IIIF, html, and some AI. In the main, this study will focus on evaluating TEI and other elements which can be interoperable with this widely adopted language. This will be integrated with more traditional humanities scholarship surrounding the physical volume, providence research, the transmission of ‘female knowledge’ in this source material and an exploration of its religious language. This study anticipates that the aforementioned digital methods will further investigations in these areas of study.

Keywords: Editorial Theory
Dissenting Christianity
TEI
Manuscript Studies
Textual Innovation
Digital Editions
Feminism
Religion
Philadelphian Society
Mysticism
Anne Bathurst
Radical Theology
Bibliography
17th Century
Literature
IIIF
Advisor: Williams, A
Higher-order inference in conditional random fields using submodular functions

Higher-order and dense conditional random fields (CRFs) are expressive graphical models which have been very successful in low-level computer vision applications such as semantic segmentation, and stereo matching. These models are able to capture long-range interactions and higher-order image statistics much better than pairwise CRFs. This expressive power comes at a price though - inference problems in these models are computationally very demanding. This is a particular challenge in computer vision, where fast inference is important and the problem involves millions of pixels. In this thesis, we look at how submodular functions can help us designing efficient inference methods for higher-order and dense CRFs. Submodular functions are special discrete functions that have important properties from an optimisation perspective, and are closely related to convex functions. We use submodularity in a two-fold manner: (a) to design efficient MAP inference algorithm for a robust higher-order model that generalises the widely-used truncated convex models, and (b) to glean insights into a recently proposed variational inference algorithm which give us a principled approach for applying it efficiently to higher-order and dense CRFs.

Advisor: Mudigonda, P
The search for CP violation in neutrino oscillations at T2K

T2K is a long-baseline neutrino oscillation experiment, designed to study the oscillation of a high-intensity muon neutrino beam produced by the J-PARC ac- celerator facility. Neutrinos are detected 295 km downstream of the production point at Super-Kamiokande, a 50 kt water Cherenkov detector capable of differ- entiating between muon neutrino and electron neutrino events. Two beam configurations are possible at T2K, each used to create neutrino beams composed of predominantly neutrinos or anti-neutrinos. Comparisons of the disappearance of muon neutrinos and the appearance of electron neutrinos in the neutrino and anti-neutrino beams are used to measure the neutrino oscillation parameters.
Presented in this thesis are the results of many analyses designed to study various combinations of the Super-Kamiokande oscillation data sets. Analyses considering the antineutrino beam data sets found no substantial evidence for ν ̄e appearance in a ν ̄μ beam or ν ̄μ oscillation inconsistent with observed νμ oscillation. A combined study of all available Super-K oscillation samples measured the CP violating phase δCP and the sine square of the mixing angle θ(13).
This analysis excluded δCP = 0 at the 2σ confidence level under both normal and inverted ordering hypotheses and produced a constraint of -2.978 rad < δCP < -0.467 rad in the normal ordering hypothesis.

Keywords: neutrino oscillation
charge parity violation
CP symmetry
mixing angle
Mathematical modelling and transcriptional characterisation of intratumoral regulatory T cell sub-populations

Regulatory T cells (Tregs) suppress harmful immune responses and help prevent autoimmune reactions. However, high densities of Tregs accumulate in solid tumours and contribute to the suppression of anti-tumor responses. The targeting of intratumoral Tregs via antibody-mediated blockade/depletion is a promising cancer treatment strategy but remains ineffective and induces adverse events. Some of these challenges can be addressed by conducting extensive transcriptional profiling of intratumoral Tregs and quantitatively assessing Treg migration dynamics to identify appropriate therapeutic targets and guide the development of safe and effective Treg-targeting therapeutics.
We hypothesised that tumours harbour resident and transient Tregs with distinct transcriptional and migratory profiles. To test our hypothesis, we used photoconvertible Kaede mice to label and quantify Tregs in MC38 and CT26 tumours. We developed a mathematical model to investigate whether the presence of resident and transient tumour Tregs aligns with the observed data and applied Bayesian parameter estimation to infer the rates of intratumoral Treg migration. In both tumours, we confirmed the presence of resident and transient Tregs and found that Tregs egressed from CT26 tumours to lymphoid tissue to a larger extent than MC38 tumours. Single cell analysis of intratumoral Tregs revealed that resident Tregs upregulate Lag3, Tnfrsf18 and Tnfrsf9. To investigate similarities between murine and human intratumoral Tregs, we constructed Treg meta-atlases using public single cell datasets. In mice, we observed that Lag3 and Ccr8 are unique to tumour Tregs and exhausted CD8 T cells. In humans, CCR8 expression was confined to tumour Tregs whereas LAG3 was mainly expressed on exhausted CD8 T cells.
Collectively, our findings outlined the presence of kinetically and transcriptionally distinct intratumoral Treg subpopulations. Furthermore, our Treg meta-atlases exposed key differences in CCR8 and LAG3 expression between mouse models and humans and supported the potential of CCR8 as a target for depleting human intratumoral Tregs.

Keywords: mathematical modelling
single cell meta-atlas
LAG3
immunotherapy
CCR8
tumour Tregs
Advisor: Coles, M
Gaffney, E