VictorJuiz/thesis huggingface dataset:
Investigating the tonal system of Plastic Mandarin: a cross-varietal comparison
Keywords: Mandarin variation
Plastic Mandarin
prosody
mixed models
phonetics
neutral tone

The city of Changsha, Hunan Province, China has seen an increase in the use of Mandarin in the past decade, overshadowing the local non-Mandarin variety, Changsha. A new variety “Plastic Mandarin”, mostly spoken by millennials and younger generations, has emerged. It is defined in this thesis as a non-standard Mandarin accent that features the speech of young urban residents in Changsha and that has crystallised over the past few decades.
This thesis presents a detailed phonetic investigation of the tonal system of Plastic Mandarin through a cross-varietal comparative approach, mainly divided into two streams: citation tones and neutral tones in contexts. The defining characteristic of the citation tone system for Plastic Mandarin is established first: a mid-level tone, a low to mid rising tone, a low falling tone, and a high rising tone. By comparing the citation tones of the three varieties that coexist in the city of Changsha, the thesis provides acoustic evidence that Plastic Mandarin may arise when Mandarin tones adapt the pitch pattern of some corresponding Changsha tones.
In addition to citation tones, this thesis disentangles the sources of variability in the syllable duration and f0 contour of speech sequences containing neutral tone syllables, i.e. those do not have any of the four canonical lexical tones and often overlooked in prior studies of tones. The data show that f0 contours converge at the end of two consecutive neutral tone syllables at a low pitch in both Mandarin varieties. It suggests that a neutral tone or a sequence of consecutive neutral tones tends to be associated with a low pitch target, despite the varying f0 shapes largely predicted by the preceding lexical tone. The thesis proposes a probabilistic target-approaching model for Mandarin tones in connected speech, in which pitch targets may be fewer than the number of syllables. While the phonetic realisation of the four lexical tones in Plastic Mandarin is consistently different from that in Standard Mandarin, the pitch target of neutral tone syllables tends to remain constant in this process of Mandarin variation and change, which may be attributed to the stable transfer of prosodic structure.
Plasma proteomic landscape and patient stratification in response to severe infection
Keywords: precision medicine
critical illness
mass spectrometry
plasma
sepsis
sub-phenotyping
proteomics
transcriptomics
COVID-19

Rationale: A dysregulated host response to infection can cause life-threatening organ dysfunction, presenting as the clinical syndrome of sepsis. Sepsis is an unmet global health challenge, with substantial clinical and molecular heterogeneity hindering the development of targeted therapies. Subphenotypes in sepsis have been identified at the clinical and molecular levels, especially using the leukocyte transcriptome. Due to the limited throughput of proteome profiling, there has not been a comprehensive analysis of the sepsis plasma proteome that enables understanding of the individual response. In severe COVID-19, a maladaptive immune response to SARS-CoV-2 infection can also lead to organ failure and adverse outcome. This thesis characterises the proteomic landscape in sepsis and COVID-19 to investigate disease mechanisms and inter-individual variation in the response.
Methods: The plasma proteome was profiled using high-throughput mass spectrometry for 2622 samples from 1612 individuals, including ICU sepsis patients with community acquired pneumonia or faecal peritonitis and non-septic controls. Higher-depth proteomics and cytokine data were also generated for subsets of the sepsis patients to complement the analysis. For understanding the COVID-19 blood proteome, 395 plasma and serum samples from patients and controls were analysed.
Results: Various aspects of the immune response distinguished sepsis from control conditions, highlighting alterations in innate immunity, acute-phase response, neutrophil function and extracellular matrix organisation, with sepsis-specific proteins identified. Three sepsis patient subgroups based on the plasma proteome were identified and validated in independent samples. The subgroups were associated with differential clinical severity and distinct molecular characteristics, including one subgroup showing greater activity in immune pathways and predictive of higher mortality. The proteomic and previously defined leukocyte transcriptomic patient subgroups exhibited significant interaction, shared and distinct molecular mechanisms, and improved risk stratification when combined. Proteomic features of COVID-19 severity were identified, including acute-phase response, complement cascade, tissue necrosis and shifted lipoprotein metabolism.
Conclusion: This thesis has identified key biological processes of the sepsis response and clinically informative patient subgroups at the plasma proteome level, highlighting opportunities for patient stratification and development of a precision medicine approach.
On-surface synthesis of two-dimensional conducting metal-organic frameworks
Keywords: on-surface synthesis
metal-organic frameworks
STM

This thesis focuses on the synthesis of two-dimensional metal-organic frameworks (MOFs) using on-surface methods on metal substrates. Scanning tunnelling microscopy (STM) and density-functional theory (DFT) calculations are used as the experimental and theoretical tools to study the structural and electronic properties of the frameworks.
The thesis starts with the study of hexahydroxytriphenylene (HHTP) molecules on a Au(111) substrate. Following vapour deposition from a Knudsen cell, HHTP molecules self-assemble into a near close-packed phase with two alternating molecular rows. After reacting with transition metals (Ni/Co), HHTP forms a dense structure on the surface. The metal centres adopt a three-fold coordination geometry, connecting all the molecules into a network.
Changing the ligand to hexaaminotriphenylene (HATP), single-layer MOFs with a honeycomb structure can be synthesised when metals (Ni/Co) are evaporated onto the surface containing HATP molecules. The Ni-HATP MOF has a shape of large islands, while the Co-HATP domains are long ribbons. A bimetallic MOF can also be obtained by co-depositing Ni and Co atoms. Different metal centres can be separately visualised in STM images and identified with the aid of DFT modelling.
Using a smaller ligand, hexahydroxybenzene (HHB), nonporous metal-organic coordination polymers are synthesised on the Au(111) substrate. Ni- and Co-HHB polymers have an identical structure in which each molecule is bonded with six metal atoms. The only difference is that Ni atoms are visible in STM images, while Co atoms are not evident because of their lower height.
When mixing HHTP and HHB, two phases of self-assemblies are found on the Au(111) surface. The α-phase has an HHTP : HHB ratio of 2 : 1, and the β-phase has a ratio of 6 : 1. Depositing Ni onto the α-phase mixture can create a dual-ligand MOF, where each Ni atom coordinates with one HHTP and one HHB. Besides, HHB has a stronger coordination ability than HHTP and HATP, causing ligand substitution reactions on the Au(111) surface.
Characterising the iron dependence of T-cells
Keywords: T-cell
Immunology
TCA cycle
Iron
Mitochondria
Aspartate
Demethylation
Immunity
Metabolism

Iron is an essential micronutrient which interacts with ~400 different protein types in human cells. Meanwhile, iron deficiency remains globally prevalent affecting >1.2 billion people. Pre-clinical studies demonstrate that iron restriction impairs T-cell proliferation, activation and effector function in models of vaccination, autoimmunity and infection. However, the biochemical mechanisms underlying these effects remain undefined. In this thesis, in silico, in vitro and in vivo methods were used to examine Tcell iron usage and dependence. Initial mathematical modelling predicted T-cells dramatically increase iron demands post-activation. Further transcriptomic and proteomic profiling of in vitro activated iron deficient CD8+ T-cells revealed induction of the P53 cell cycle arrest pathway and suppression of mTORC1 and MYC signalling, together indicative of aberrant metabolic rewiring. Iron deprived CD8+ T-cells show increased mROS generation suggestive of electron transport chain dysfunction, and impaired tricarboxylic acid (TCA) cycle progression through the iron dependent enzymes aconitase 2 and succinate dehydrogenase, such that downstream metabolites α- ketoglutarate, fumarate and malate are depleted. The repressive histone mark H3K27me3 is normally removed by the iron and α-ketoglutarate dependent enzymes, KDM6A/B, but accumulates in iron deprived T-cells. Despite TCA cycle dysfunction, aspartate, which is produced downstream of the TCA cycle, was unexpectedly increased in iron restriction. Higher aspartate is proposed to be partly driven by suppressed aspartate usage by downstream iron-dependent pathways including translation and nucleotide synthesis. Interestingly, exogenous aspartate substantially rescues the proliferation of iron deprived CD8+ T-cells suggesting that endogenous aspartate sources are unusable, possibly due to trapping of aspartate within the mitochondria. Overall, this thesis demonstrates that iron deprivation impairs T-cell biochemistry at multiple nodes providing insight as to how metabolic and iron modulatory interventions could be coupled to augment or suppress immunity.
3d printed cortical tissue and implantation
Keywords: 3D Bioprinting
Brain Repair
Neuroscience
hiPSCs

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.
Museological approaches to pre-Christian funerals and the representation of the past in Old Norse literature
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

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.
Multiscale modelling of the action of low salinity
Keywords: fluid dynamics
multi-phase flow
oil recovery
flow through porous media
homogenisation

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.
Searches for rare nuclear decays in the LUX-ZEPLIN experiment
Keywords: dark matter
particle physics
LZ
LUX-ZEPLIN
double electron capture

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.
Non-people in the People’s Republic: ‘Landlords’ and ‘rich peasants’ under Maoist state socialism
Keywords: class enemies
landlords and rich peasants
friend-enemy binary
Maoist China

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.
An ethics account of global health security
Keywords: health security
infectious disease
pandemics
epidemics
empirical ethics
bioethics
global health security
global health

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.