VictorJuiz/thesis huggingface dataset:
Respiratory quality indices for automated monitoring of respiration from sensor data

Abnormal respiratory rate (RR) is known to be one of the most clinically effective predictors of catastrophic decline. Despite this, RR is often the least monitored and most inaccurately measured vital sign. This is primarily because of the lack of a non-invasive, robust, automated method for estimating RR. It has previously been shown that the amplitude modulation (AM), frequency modulation (FM), and baseline wander (BW) of both the electrocardiogram (ECG) and photoplethysmogram (PPG) contain respiratory waveform information. However, these respiratory modulations are driven by the physiologic interrelationship between the cardiovascular and respiratory systems and may or may not be present based on a patient's characteristics and condition. Despite this, current methods for RR estimation from ECG and PPG do not account for this physiologic variability. The investigations in this thesis describe the development and evaluation of respiratory quality indices (RQIs), a novel method for evaluating the presence or absence of physiologically important respiratory information from the AM, FM, and BW extracted from the ECG and PPG. This work is conducted in three unique data sets, CapnoBase, MIMIC-III, and Dialysis III, all of which represent important, different patient populations. Five initial RQIs are described based on five signal processing techniques: fast Fourier transform (FFT), autocorrelation, cosine correlation, autoregression, and Hjorth parameters. Of these, the individual RQIs based on the FFT, autocorrelation, and autoregression are deemed to be good predictors of the presence of respiratory waveform data. The three individual RQIs are used to derive three fusion RQIs based on two supervised learning algorithms: linear regression and support vector regression (SVR) and one unsupervised learning algorithm: principal component analysis (PCA). Both the linear regression and PCA fusion RQIs are accurate and robust. The linear regression fusion RQI is used in the development of an RR estimation algorithm, termed RQIFusion, which achieves highly accurate and more complete RR estimates than existing methods. In the Dialysis III data set, implementation of RQIFusion improved RR estimation error by between 1.35 to 2.29 breaths per minute (brpm) to achieve RR estimation errors between 2.18 to 3.46 brpm, depending on the RR estimation algorithm employed. These results represent a marked improvement in RR estimation and indicate the importance of conducting respiratory quality analysis using RQIs on respiratory modulations extracted from ECG and PPG prior to RR estimation.

Keywords: Signal quality
Electrocardiography (ECG)
Photoplethysmography (PPG)
Signal fusion
Respiratory Quality Index (RQI)
Respiratory rate (RR)
Advisor: Clifton, D
Integration and segregation in whole-brain networks: implications for altered states of consciousness

To survive in an ever-changing environment, the brain must seamlessly integrate a rich stream of incoming information into coherent internal representations that can then be used to efficiently plan for action. The brain must also balance its ability to integrate information with a complementary capacity to segregate information into modules which perform specialized computations in local circuits.
The central focus of this Thesis is to investigate the dynamical properties of the integration/segregation balance in functional MRI data collected in two distinct altered states of consciousness: slow-wave sleep, and a psychedelic experience induced by intravenously administering psilocybin; the psychoactive compound in “magic mushrooms”.
In Chapter 2, I implement a novel method for identifying highly integrative nodes in human brain networks from the persistent homology of fMRI data, as a complement to standard graph theoretical methods. I report that topologically central nodes in the ‘persistence homological scaffold’ have a combination of high betweenness-centrality and high participation coefficient, whilst simultaneously avoiding densely connected neighborhood clusters.
In Chapter 3, I investigate dynamical changes in global measures of functional integration and segregation derived from fMRI data. Synchrony, metastability and chimeraness metrics are computed separately in slow-wave sleep and in the psychedelic state. It is found that global synchrony and metastability are reduced in slow-wave sleep relative to a wakeful rest baseline, whilst chimeraness is increased. Diametrically opposite effects on each measure are observed in the psychedelic state.
Chapter 4 characterizes the brain’s dynamical landscape from a system-level perspective under psilocybin by computing the fractional occupancy and transition probabilities of specific functional network states over time. An increase in the probability of occurrence of a globally coherent functional connectivity state is observed, alongside a strong decrease in the fractional occupancy of a fronto-parietal control network.
In Chapter 5, I further characterize the capacity of brain areas to dynamically broadcast regional activity signals locally or globally in both deep sleep and the psychedelic state. The results notably show that intrinsic activity perturbations in a given brain area are more likely to propagate strictly locally in slow-wave sleep than during wakeful rest. In the psychedelic state, the size of integration cascades elicited by local perturbations over time is significantly more variable than during the baseline scan.
The experimental findings presented in this Thesis indicate that alterations in consciousness level and/or contents are accompanied by temporally-dependent changes in the brain’s integration and segregation balance, promoting cross-modular integration in the psychedelic state, and functionally segregated brain dynamics in slow-wave sleep.

Advisor: Kringelbach, M
Lambiotte, R
Evaluating voters' appearance-based strategies in congressional elections

In this era of candidate-centered politics a wealth of research has shown that candidate appearance can predict electoral success. Many of these studies attribute this link to voters incorporating candidate image into their electoral decision making. Specifically, several studies have asserted that candidates who are viewed as more attractive or competent gain an electoral advantage because they draw voters who lack partisan affiliations or lack the political sophistication necessary to utilize more complex cues – such as candidate ideology.
Utilizing survey data of voters and data from the U.S. House of Representatives, this project combines theories from electoral studies, cognitive psychology, and evolutionary leadership research to investigate the degree to which candidate appearance influences vote-choice. Evidence from this thesis suggests that while unaffiliated and unsophisticated voters are the most likely to change their vote choice on the basis of candidate appearance, they are also the least likely to convert that preference into meaningful political action.
This thesis adds to the literature on candidate appearance by suggesting a new mechanism through which positive candidate image leads to electoral success – by increasing the enthusiasm of all voters for a candidate, and thus bolstering mobilization efforts and voter turnout.

Advisor: Johnson, D
Homogeneous Model Theory as a Framework for Algebraic Stability Theory

In this thesis we aim to persuade the readers to reconsider homogeneous model theory as a framework in which to study Algebraic Stability Theory. We argue that the tight link between homogeneous model theory and categorical amalgamation constructions gives it a flexibility beyond what the ordinary first-order context can offer while simultaneously it allows the development of a stability-theoretic machinery very close to classical first-order stability. Thus we first introduce homogeneous model theory and categorical amalgamation theory separately (Chapters 1 and 2), laying out our own contributions alongside the known theory, before we utilise their interactions to prove related results pertinent to several different questions in algebraic stability theory. In Chapter 3 we give a very general result on omitting (possibly isolated) types from homogeneous models, generalising an analogous theorem by Hrushovski and Itai [18] regarding differential fields. Our method makes it possible to omit any family of types of trivial geometry from a superstable (and simple) homogeneous model without impacting the dividing structure and thus the stability class of the model. In Chapter 4 we apply homogeneous model theory to the study of Hrushovski constructions, enabling us to give a general treatment of the fundamental stabilitytheoretic properties beyond the combinatorial case to which such general accounts are usually confined. We obtain a general characterisation of dividing and by extension of U-Rank in the amalgamation limits of those constructions, and since we are not limited to finitary cases we can use our results for studying pseudo-exponentiation in the next two chapters. In Chapters 5 and 6 we thus narrow our focus even more and apply the tools developed above to the single class of exponential fields, illustrating the power of our general results through application to a topic which has been under close investigation ever since Boris Zilber proposed pseudo-exponentiation as a model-theoretic approach to complex exponentiation in the 2000s [42]. In passing we will also construct a non-almost-exponentially-algebraically closed quasiminimal exponential field, answering a question asked by Bays and Kirby in their recent [7].

Advisor: Zilber, B
Hrushovski, E
Cognitive and neural foundations of perceptual biases for the self and social groups

The notion of the self as distinct from other people is fundamental to the study of human psychology. Closely tied to this sense of self is the profound importance of belonging to social groups. The cognitive prioritisation of self- and ingroup-related information, known as self-bias and ingroup-bias, occurs across a multitude of cognitive domains. Although adaptively beneficial, biases arising from social categorisation are the source of prejudiced attitudes, discriminatory behaviours and intergroup conflict.
Several studies have demonstrated enhanced response times and accuracy performance in perceptual matching for self and ingroup stimuli compared to others and outgroups. However, the cognitive and neural mechanisms underlying these effects are relatively unexplored. The present thesis examines five core outstanding research questions: 1. What is the relationship between perceptual prioritisation for the self and social ingroups? 2. How does social context modulate ingroup-bias? 3. How quickly does group affiliation affect early perceptual processing? 4. Do trait differences underlie the strength of perceptual prioritisation for the self and social groups? 5. What are the commonalities and distinctions in the neural regions that underpin biases for the self and social ingroups?
Broadly, the findings of this thesis suggest that: 1. There is an overlap in the representation of stimuli associated with the self and ingroups but the performance advantages are likely to be driven by partly distinct processes. 2. Perceptual biases for ingroups are robust across differing social contexts. 3. Social categorisation quickly enhances low-level perceptual processing even when this categorisation is novel and random. 4. There is no evidence to suggest that individual trait differences in group identification or self-concept underpin the perceptual biases. 5. Cognitive prioritisation for the self and ingroups are supported at least in part by distinct neural mechanisms. Together, these findings provide a novel perspective on the relations between self and ingroup representation in brain and behaviour.

Keywords: Social neuroscience
Social cognition
In-group bias
Self bias
Social identity
Advisor: Hewstone, M
Lockwood, P
Sui, J
Joshua and Judges: a sociological analysis of Hebrew biblical war narrative in its ancient Near Eastern context

Descriptions of warfare persist throughout the Hebrew Bible as well in the extra- biblical texts from the ancient Near East. This thesis seeks to discern what is common among ancient Near Eastern warfare accounts, and what is distinctive about the accounts of warfare in the books of Joshua and Judges. This research aims to address the question: What purposes within the context of warfare in the ancient Near East do warfare accounts fulfill, and might the accounts of warfare in Joshua and Judges serve a similar function?While others have examined the Hebrew texts concerning conquest and warfare the purpose of such scholarship has often been to gain an ethical understanding of the texts by answering the question: How could God (whether as a literary figure in the text, or as an actual being) command or allow the violence described in the Hebrew Bible? This thesis argues, however, that the texts ought first to be understood for what they are, that is war narrative, and within their wider purpose qua war narrative. While others have sought to understand biblical accounts of warfare in their ancient Near Eastern context, these studies lacked the benefit of current sociological theory concerning the emergence of warfare. This thesis brings current sociological insights into the emergence of large-scale organised violence, that is, warfare, to bear on the ancient Near Eastern texts and the books of Joshua and Judges. In doing so, this thesis illustrates that there are persistent themes that run throughout ancient Near Eastern warfare accounts. These themes are equally present in the books of Joshua and Judges and they appear to reflect and contribute to the social, ideological, and military forces necessary for the achievement of ancient Israelite military goals.

Advisor: Southwood, K
A real-world competency framework for evidence-based general practice

BACKGROUND: Evidence-Based Health Care (EBHC) has become established as a cornerstone of modern medicine. Its guiding principle is that decisions should be based upon an integration of the best available evidence from research, the practitioner's expertise and the patient's values. General Practitioners (GPs) describe numerous constraints to EBHC. They lack an EBHC competency framework that acknowledges these constraints. The aim of this thesis was to construct such a framework for use in performance appraisal and routine practice.
METHODS: A multi-source synthesis was conducted in three stages: (1) a synthesis of qualitative and quantitative evidence from the research literature about EBHC competence in general practice resulted in five themes, which formed the basis of a preliminary ‘straw model’ competency framework; (2) a Delphi process among a panel of experts refined the straw model framework and generated a further seven themes; (3) themes from stages 1 and 2 were synthesised, resulting in a final real-world competency framework for general practice. A content analysis was carried out on a sample of GP performance appraisals to determine the content validity of the new framework. It also generated behavioural descriptors for emerging and full competence, and illustrative clinical vignettes to assist GPs in its application.
RESULTS: The real-world framework comprised three competencies: (1) mindfulness in one's approach towards EBHC itself, and to the influences on decision-making; (2) pragmatism in one's approach to finding and evaluating evidence; and (3) knowledge of the patient as the most useful resource in effective communication of evidence. The content validity of the new framework was confirmed.
CONCLUSION: A new real-world EBHC competency framework was developed for use in GPs’ performance appraisals and in their routine practice. Behavioural descriptors and illustrative vignettes accompany the framework to assist its application.

Advisor: Heneghan, C
Ward, A
Virtual play in the Victorian novel

Novelists in the mid-nineteenth century speculated about the specificity and concreteness of their fictions, and reflected on what it meant to engage with imaginary objects and worlds. W. M. Thackeray is troubled by the novelist’s capacity to ‘see visions, hold conversations with, even draw the likeness of, people invisible’. Anthony Trollope has ‘so realized the place, and the people, and the facts,’ of the setting he invented that ‘to me Barset has been a real county, and its city a real city, and the spires and towers have been before my eyes’. Charlotte Brontë’s heroines always live ‘two lives – the life of thought, and that of reality,’ one fed with ‘daily bread’ and the other with ‘the strange necromantic joys of fancy’.
Such contemporary fascinations with the nature of fictional encounters have fared badly under the twentieth century’s disenchantments with subjectivity, especially with the absorptiveness of novels as a form of potential interpolation. More recently, however, literary studies has increasingly called for other modes of critical engagement with literature than those of detachment and suspicion, suggesting instead sympathy and participation as ways to new interpretations. In particular, the work of Brigid Lowe and John Plotz have brought old critical interests back to the fore with a renewed emphasis on the immersive experience of the novel. As Nicholas Dames has argued, this emerging scholarship engages ‘the challenge of exploring the unique specificities of fictional, or virtual, experiences’.
Virtual Play in the Victorian Novel takes up this challenge of recovering a literary criticism of the fictional. Following the work of philosopher J. David Velleman, this project develops a method for exploring the ‘virtual’ experience of the novel through the heuristic of play; in particular, a historical play phenomenon documented by the biographies and juvenilia of Hartley Coleridge, Thomas De Quincey, Anthony Trollope, and the Brontë siblings. What developmental psychologists now term paracosmic play, seemingly emergent in the early nineteenth century, involves the written elaboration of complex imaginary worlds. This research into play’s archives proposes how its make-believe rules, procedures, and assumptions exemplify a virtual practice, and that this practice offers new perspectives on the analogous rules that govern novel fiction.
The project’s chapters on Brontë, Trollope, Thackeray, and Dickens each begins by examining a documented aspect of paracosmic play (omnipotence, improvisation, affective attachment, and sensory imagination) in relation to a literary critical aspect of the novel (authorship, plot, form, and description), and each concludes with a close analysis of this relation at work in an exemplary text.

Keywords: literary theory
virtuality
fictionality
novels
charlotte bronte
charles dickens
anthony trollope
hartley coleridge
play
virtual
paracosms
thomas de quincey
william makepeace thackeray
victorian
Advisor: Russell, D
Analysis of higher order RNA structures in the influenza a virus genome

Influenza viruses are respiratory pathogens, which constitute a major threat to public health. Up to 650,000 deaths and 5 million severe cases caused by seasonal influenza strains are recorded each year and potential pandemic influenza outbreaks pose a constant risk to the human population worldwide. Influenza viruses belong to the family Orthomyxoviridae and contain single stranded negative sense segmented RNA genomes. Each viral genome segment is maintained in a viral ribonucleoprotein complex (vRNP), which consists of the viral polymerase, oligomeric nucleoprotein and the viral RNA (vRNA). Little is known about the conformation of the vRNA in the context of the vRNP, although it has been proposed that secondary RNA structures in the vRNPs are essential for successful packaging of the influenza virus genome. The aim of the work presented in this thesis was to analyse the global secondary RNA structure of the influenza virus genome. To this end selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) method was used to perform secondary RNA structure analysis on naked and vRNP-associated vRNA. The analysis showed that multiple secondary RNA structures are present in the genomes of influenza viruses, each vRNA segment has a unique secondary RNA structure fold, and no clear NP binding footprint was observed in the SHAPE reactivities. The presence of the structured vRNA sites suggested that some secondary RNA structures may be accessible to form interactions between vRNPs, therefore, further analysis using sequencing of psoralen crosslinked, ligated, and selected hybrids (SPLASH) was performed to detect inter-segment RNA-RNA interactions. A redundant network of RNA-RNA interactions was detected to be present inside influenza virions and mutagenesis work was performed to show that disruption of inter-segment RNA interactions can lead to defects in the virus genome packaging and attenuated virus growth. The relevance of this work to the reassortment between different influenza strains and the emergence of new pandemic strains is discussed.

Advisor: Fodor, E
Rehwinkel, J
Bauer, D
Electronic structure of low-valent transition metal oxide phases

Transition metal oxide phases have been studied intensively in recent years due to their flexible chemistry that may potentially lead to novel physical and chemical properties. Low-temperature synthetic strategies allow for the reduction of traditional high-valent transition metal oxides into low-valent ones, where the metaloxide frameworks have lower dimensions and the central metal cations have lower coordination numbers. In particular, for the perovskite family, the reduced phases consist of two-dimensional layers with the metals located in square-planar coordination environments. The structural stability of these apparently two-dimensional systems comes from the strong intrinsic electronic interactions. In this thesis, the electronic structure of layered oxides containing the low-valent metal cations V3+, Ti3+, Ni+ and Ru2+ is discussed in detail.

Advisor: McGrady, J