VictorJuiz/thesis huggingface dataset:
Inferring brain network dynamics of MEG and EEG in healthy aging and Alzheimer’s disease
Keywords: electroencephalography
aging
magnetoencephalography
Alzheimer's disease
brain network dynamics

Alzheimer’s disease (AD) has long been encumbered by a lack of clinically effective biomarkers, which has impeded its early-stage detection and relegated diagnostic practices to symptom-based observations. Amidst the ongoing quest to discover novel biomarkers with enhanced clinical utility, this thesis aims to elucidate the prospect of static and dynamic changes in brain network features, derived from electroencephalography (EEG) and magnetoencephalography (MEG), to explicate the earliest changes in the brain caused by AD.
The first component of the thesis contrasts MEG and EEG in capturing age-related effects within the healthy aging datasets and validates the methodologies initially designed for MEG for their application to EEG. We demonstrate that while both modalities reveal analogous age effects in static power spectra and narrow-band power, MEG exhibits higher sensitivity to age effects in various brain network features within source space. The adopted analysis techniques successfully replicated previously documented healthy aging effects, substantiating their credibility in inferring transient resting-state network (RSN) dynamics from M/EEG data.
Leveraging the findings above, the second component of the thesis focuses on identifying modality-specific biomarkers for mild cognitive impairment (MCI) and early-stage AD from resting-state M/EEG. The reproducibility of known biomarkers --- evident in static RSN features and the posterior default mode network --- is confirmed in our dataset. Furthermore, we show that the dynamic effects of MCI and early-stage AD in the wide-band power and temporal dynamics of RSNs can be recognized as potential AD biomarkers. These results are among the first to demonstrate the statistically significant effects of prodromal AD in resting-state M/EEG.
Together, our findings provide a concrete case that M/EEG-derived static and dynamic RSN features can potentially be reliable and clinically meaningful biomarkers. This research propels the field towards refining early detection mechanisms for AD, laying a foundation for ensuing research to build upon, and steering future diagnostic practices towards enhanced efficacy.
Assessing the stability of mineralogical collections in museums
Keywords: state survey
damage
mineral susceptibility
preventive conservation
collection surveying
pyrite
pyrite decay
mineral collections
condition
collection assessment

At least 10% of currently identified mineral species are susceptible to deterioration within the museum setting. The significance of this, however, is largely unknown, as there is a substantial lack of quantitative information pertaining to mineral susceptibility within the heritage literature. Findings from other scientific fields—such as the geosciences and materials science—rarely enter the heritage sector, as relevant research outputs are not easily accessible or transferable. The doctoral research outlined in this thesis was designed as a response to these challenges, with the aim of developing of an efficacious methodology for facilitating the determination of mineral susceptibility. This was achieved via database, survey, and colorimetric methods. The Mineral Susceptibility Database (MSD) was produced as a single, openly accessible repository of currently published research relevant for mineral preservation, and contains 957 entries for 596 mineral species. The Deterioration Phenomena (DP) State Survey Method was designed to mitigate current shortcomings of collection surveying and provide quantitative data pertaining to the state of mineral specimens. The DP Method was used to survey 13,716 specimens from Oxford University Museum of Natural History’s (OUMNH) systematic mineral collection, and to characterise the types of deterioration prevalent within similar collections. The survey results corroborate that the types of reactions recorded in the MSD are indeed found within museum collections. Experiments validating the use of colorimetry on mineral specimens were performed and confirmed application to opaque and metallic species. Colorimetry was then used in conjunction with the DP Method to survey 1,273 pyrite specimens held at OUMNH, National Museum Cardiff, National Museums Liverpool, and the Sedgwick Museum of Earth Sciences. The results of this cross-museum survey elucidated the nature of pyrite deterioration within the museum environment, as summarised by the impurity hypothesis: the concentration of impurities within pyrite is the primary factor influencing the pyrite decay reaction. The formulation of this hypothesis demonstrates that the aim of this thesis was achieved, and that the aforementioned methods can produce robust data from which the deterioration of other mineral species can be characterised.
The artefacts of intelligence: governing scientists' contribution to AI proliferation
Keywords: language models
AI governance
artificial intelligence

This DPhil dissertation is about attempts to govern how artificial intelligence (AI) researchers share their work. There is growing concern that the software artefacts built by AI researchers will have adverse impacts on society if made freely available online. AI research is a scientific field, and openly sharing these artefacts is routine and expected, as part of the functioning of the scientific field. Recently, there have been a number of occasions where members of the AI research community have trialled new ways of sharing their work, in response to their concerns that it poses risks to society. The case study follows: the ‘staged release’ of the GPT-2 language model, where more capable models were gradually released; the platform through which researchers and developers could access GPT-3, the successor to GPT-2; and a wave of new ethics regimes for AI conference publications. The study relies on 42 qualitative interviews with members of the AI research community, conducted between 2019 and 2021, as well as many other publicly available sources such as blog posts and Twitter. The aim is to understand how concerns about risk can become a feature of the way AI research is shared. Major themes are: the relationship between science and society; the relationship between industry AI labs and academia; the interplay between AI risks and AI governance regimes; and how the existing scientific field provides an insecure footing for new governance regimes.
Late medieval Marian lyric in urban spaces: puy poetry and Meistergesang, 1388-1525
Keywords: medieval
Meistergesang
Virgin Mary
lyric
medieval german
urban spaces
medieval french
puys

Although it is often noted that there are striking similarities between the puys, Marian poetry competitions in Northern France, and institutionalised Meistergesang, very little comparative work has been undertaken investigating these similarities. This thesis aims to explore Marian lyric composed in urban spaces in the late Middle Ages, both to gain a greater understanding of the individual poetic traditions, and to assess the significance of urban Marian lyric. I argue that the figure of Mary appealed to those living in towns and cities because she reflected the boundedness and privilege of the ideal, imagined city. Moreover, Marian lyric is an ideal method of communicating religious knowledge, both catechetical and experiential. The form of poetry helps audiences to engage with knowledge doctrinally and affectively, with Mary acting both as inspiration for poets and as a teacher. In examining the interplay between the playful and devotional ends of Marian lyric produced in a competitive context, I show that play and piety are mutually enriching and suggest play is a helpful lens for understanding engagement with poetic traditions and the poetic community. Religious lyric is often neglected in discussions of late-medieval poetics in continental French and German Studies, and this demonstrates the need to take religious lyric into consideration as a significant element of poetic production. The comparative study enables us to understand late-medieval Marian lyric in its context, and is significant as the first such Anglophone study. This thesis shows that urban Marian lyric warrants further critical attention, and signals new directions for research into the puys and Marian Meistergesang. Furthermore, it has implications beyond the field of Marian lyric, opening up new avenues for research into the late-medieval lyric, lay piety and urban history.
Theory and simulation of DNA damage and supercoiling
Keywords: functional determinants
plectonemes
DNA
supercoiling
DNA damage
wlc
polymer physics
path integrals
thermal fluctuations
thymine dimer

We employ an array of methods including statistical mechanics and computer simulation to better understand how both damaged and undamaged DNA respond to linear and torsional mechanical stress and the effect of damage on supercoiled phenomena.
Via the use of an all-atom thymine dimer residue, damaged linear and circular DNA were simulated atomistically for various biologically relevant systems using the AmberTools molecular dynamics package. Local structural parameters and global properties are characterised and shown to agree well with experimental data.
Using oxDNA, a nucleotide level coarse-grained model of DNA, we make use of another model for a thymine dimer to probe larger systems and for longer times, investigating a 336-bp minicircles and its negatively supercoiled topoisomers as well as a 160-bp minicircle. We show that the presence of a thymine dimer causes a sharp local increase in curvature as well as increase in negative writhe for the under-twisted systems - potentially helping to suppress bubble formation.
A planar model for damaged DNA via a piecewise construction of worm-like chains with different bending moduli is developed. This model is then applied to curls, plectonemes and minicircles. A more general twist-storing model of plectonemes is also developed and shown to reproduce phase diagrams in accordance with experiments and simulations.
The theory of thermal fluctuations through a polymeric path integral is developed for a ribbon-like model of DNA in the fixed linking number ensemble. This theory is then applied to several systems such as straight chains and solenoids, successfully reproducing some well-known results. Finally we apply the theory to a previously intractable system of non-trivial saddle points, with the general systematic methodology elucidated.
Between company and state: Anglo-Ottoman diplomacy and ottoman political culture, 1565-1607
Keywords: sublime porte
sixteenth century
political culture
trade
new diplomatic history
anglo-ottoman diplomacy
actor networks
istanbul
correspondence
trading companies
cosmocracy
embassies
ambassadorial roles
anglo-ottoman relations
east india company
trans-imperial subjects
state papers foreign
seventeenth century
cultures of diplomacy
practices of diplomacy
embassy households
diplomatic letters
cultural history
elizabethan
microhistory
c17th
tudor england
c16th
ottoman empire
early modern
ambassadors
tudor
diplomacy
levant company

This thesis focuses on the diplomatic relationship between England and the Ottoman Empire between roughly 1565 and 1607, using an actor-centric approach to provide case studies of the first three English embassies in Istanbul. These studies engage with wider historiographical debates in the ‘New Diplomatic History’, early modern English commercial expansion and the roots of its later evolution into colonialism, and the form and exercise of political power within the Ottoman Empire at the turn of the sixteenth to the seventeenth century. Drawing heavily on archival material from England, Venice, France, and the Ottoman Empire, the thesis argues that the success of these earliest English ambassadors to the Ottomans reflected the growing self-confidence of the merchant class driving England’s switch to an import economy. Successful import of luxury goods from Asia built the financial and social basis for the political significance of merchants to rise at home, while the diplomatic role of the company in Istanbul gave leading members plenty of practice in engaging in high politics abroad. With the Ottoman Empire being a vast, diverse, and decentralised territory, and politics in the capital becoming increasingly fractious and factional as the sixteenth century drew to a close and the seventeenth began, English merchant-diplomats had to develop their political reach and standing through building networks of alliances amongst the Ottoman political elite in Istanbul and participating in disputes and intrigues surrounding foreign (and, occasionally, domestic) affairs within the Ottoman government. The thesis reveals successive embassy households straddling the uncertain boundaries between being English state actors, developing a pioneering trading company invested with some state-like powers, and performing as players in Ottoman high politics alongside state representatives of France, Spain, Venice, and the Holy Roman Empire.
Regulation of the carotid body type-1 cell by lipid signalling pathways
Keywords: hypoxia
TASK channels
carotid body
respiratory physiology

Despite several proposed theories, the precise mechanism underlying acute oxygen sensing in type-1 cells of the carotid body remains elusive. This thesis investigates the role of Gq- coupled receptors and PLC signalling molecules in the regulation of carotid body type-1 cells by utilizing Ca2+ measurements and single channel electrophysiology. This thesis investigates the involvement of these signalling molecules in hypoxia-induced [Ca2+]i rise and TASK channel inhibition in type-1 cells. In addition, this thesis examines the role of PLC signalling molecules in mediating the effects of metabolic poisons and volatile anaesthetics on TASK channels in type-1 cells. This thesis seeks to address the question as to whether there might be a common signalling pathway mediating all these effects. Specifically, it proposes that lipid signalling may ultimately be central to all these forms of TASK channel regulation.
Following the general introduction and methods chapters, chapter 3 examines the effects of Gq- coupled receptors and PLC signalling molecules on the hypoxia-induced [Ca2+]i rise in type-1 cell. The results show that hypoxia-induced [Ca2+]i rise was sensitive to alterations in Gq-coupled receptors and PLC-signalling molecules, suggesting that these signalling molecules are involved in mediating the hypoxia-induced [Ca2+]i rise in type-1 cells.
Chapter 4, further examines the role of these signalling molecules by looking at their effects on the activity of TASK channels in type-1 cells. This chapter presents novel findings demonstrating the involvement of PLC signalling molecules in mediating the hypoxic inhibition of TASK channels in type 1 cells. It proposes a model for acute oxygen sensing in these cells, incorporating findings from chapters 3 and 4.
Chapter 5 examines the role of PLC signalling molecules in mediating the effects of metabolic inhibitors on TASK channels. Metabolic inhibitors are known to inhibit TASK channels in type-1 cells and other cell types. We further confirmed this and showed that these effects are not likely to be mediated by PLC-produced DAG.
Chapter 6 examines the interactions between DAG and halothane on TASK channels in type-1 cells. We demonstrated that DiC8, a DAG analogue, induced a strong, reversible, and dose-dependent inhibition of TASK channels and inhibited the halothane-induced activation of these channels. These novel findings support the hypothesis that anaesthetics and endogenous ligands may compete for binding sites in sensitive proteins.
In conclusion, this thesis presents novel findings on the role of Gq-coupled receptors and PLC signalling molecules in the regulation of carotid body type-1 cells and suggests that these signalling molecules are involved in mediating the responses of type-1 cells to various endogenous and exogenous stimuli. Additionally, it posits that PLC signalling molecules establish a connection between metabolic function and the modulation of TASK channels by hypoxia in type-1 cells.
The toucan in early modern French culture (1526-1650)
Keywords: cabinet de curiosités
semiosis
monsters
early modern France
natural history
craft
travel literature
confessional discourses
idolatry
toucan
ingenuity
material history
colour
agency

This is a thesis about the life of a strange little bird in early modern European culture. Bright and colourful in feather yet bizarre in physical form, bearing a seemingly impossible bill, the Toucan inspired wonder in many a traveller to the New World. Transcribed into text, it soon appeared in books of several genres, in the drawings of artists and, as a material sample, in the cabinets de curiosités of collectors and dignitaries. The sheer breadth of source material available indicates the cultural significance of the Toucan; our discussion sets out to assess the bird's impact on early modern thought and culture.
To fully understand the shape and nature of the bird's influence -- or what I refer to as its several 'lives' in European culture -- we develop an analytical framework based on the methodological cores of semiosis and agency. Our analysis shows how the 'lives' of the Toucan disrupted and reshaped a number of cultural frames, both in discursive formations and in cultural practices. These disruptions, in turn, transformed some major European cultural frames of reference regarding scientific and artistic mimesis and their didactic as well as theological stakes: idolatry, eschatology, deformity and hybridity, ingenuity and craft are all in play in these.
The thesis is organised into three principal chapters, each one following the Toucan in a distinct area of early modern culture -- that is, natural-historical writing, confessional discourses and material cultures of collecting and making. Reading familiar material in the new lights of semiosis and agency and drawing several new conclusions, the discussion also broaches little-known texts and reaches the borders between languages and genres. By focusing on European interactions with a challenging New World creature, this thesis tells a story of broader European re-imaginings of the natural world in a time of social and cultural transformation.
Medical image analysis for simplified ultrasound protocols
Keywords: Machine learning
Medical image analysis
Obstetrics
Ultrasound video sweeps
Fetal imaging
Simplified ultrasound protocols
Deep learning
Video analysis
Ultrasound
Global health
Placenta

Ultrasound is an imaging tool used in obstetrics to identify high-risk pregnancies. However, ultrasound (US) requires a trained operator, who guides a transducer in response to real-time interpretation of video content. In low- and middle-income countries (LMICs), there is a shortage of trained sonographers. In this thesis, we address this key challenge by combining simple US video sweeps with computational algorithms to provide clinical benefit. The sweeps can be taken by an US novice. First, we design an algorithm that automatically creates an assistive video overlay from a simple video sweep. The overlay assists interpretation of US video to assess placenta location. We describe the design and evaluation of a deep learning-based automatic segmentation model and a statistical data visualisation of 2-D placenta shapes. The data visualisation reveals the spectrum of placenta shapes in this problem space. A probabilistic graphical model is used to improve segmentations with regards to the highly variable placenta shape. From the automatic segmentations, image guidance is created, translating the clinical criteria into assistive visual information. Second, we explore analysis of multiple video sweeps using graphs. A three-node graph models three video sweeps, where the nodes encode binary sequences representing the fetal head frame-level detection across all video frames in a sweep. To better characterise the sweeps, we perform a statistical analysis of large-scale manual annotations of video sweeps in our dataset. This reveals common patterns of frame-level anatomy occurrence for different video sweep trajectories. Particular insight is gained for patterns that correspond to fetal pose. In this regard, we build a graph convolutional network to automatically classify fetal presentation, using graphs that combine complementary video sweep information relating to fetal pose. Finally, we demonstrate the feasibility of placenta 3-D reconstruction using multiple video sweeps. We pose this challenging problem as spatio-temporal alignment of US video. We first temporally align video sweeps to represent video content at the same temporal scale. Then, we use affine transformations to spatially align images in temporally aligned video. The results in this chapter are exciting as they show the feasibility of placenta 3-D reconstruction in a simple US sweep system.
Automated quality control by application of machine learning techniques for quantitative liver MRI
Keywords: liver
MRI
deep learning
quality control

Quantitative magnetic resonance imaging (qMRI) and multi-parametric MRI are being increasingly used to diagnose and monitor liver diseases such as non-alcoholic fatty liver disease (NAFLD). These acquisitions are comparably more complicated than traditional T1-weighted and T2-weighted MRI scans and are also more prone to image quality is- sues and artefacts. In order for the output of the qMRI scans to be useable, they must undergo a rigorous and often lengthy quality control (QC). This manual QC is prone to human error and subjective. Additionally, with the development of new qMRI tech- niques, this leads to the manifestation of new quality issues. This thesis focuses on the development and implementation of automated QC processes for liver qMRI scans, that is where possible tag-free such that the process can be adapted to different imag- ing techniques. These automated QC processes were implemented using a variety of machine learning (ML) and deep learning (DL) approaches. These methods, developed on T1 mapping in UKBiobank, were designed to output metrics from the MRI scans that could be used to identify a specific quality issue, such as in chapter 3, or give a more general indication of the image quality in chapter 4. Furthermore, it was hypothe- sised that the introduction of associated meta-data, such as patient factors and scanning parameters, into these deep learning models would increase overall performance. This was explored in chapter 5. Finally, in order to assess the utility of our developed al- gorithms in a wider setting except for T1 mapping in UKBiobank, we tested it in two settings. Pilot study one assessed the utility of the model in T1 mapping in a separate study (CoverScan). Pilot study two assessed the utility of the model in a different qMRI acquisition; proton density fat fraction (PDFF) acquisitions from UKBiobank.