VictorJuiz/thesis huggingface dataset:
Local limit theorem in random graphs and graphs on non-constant surfaces
Keywords: growth constant
non-constant surfaces
graph classes
graphs on surfaces
random graphs

The thesis is split into two parts. In the first part we prove a local limit theorem for the number of appearances of the complete graph on four vertices, K4, in the Erdös-Rényi Random graph G(n, p) for p in (0, 1) a fixed constant. The proof of this is based on bounding the characteristic function of the number of K4 in G(n, p) by using different conditioning arguments for different ranges of t. The second part treats classes of graphs embeddable in either an orientable surface of Euler genus at most g(n), denoted by G^(g(n)), or non-orientable surface of Euler genus at most g(n), denoted by H^(g(n)), for different non-constant functions g(n). We first find bounds on the sizes of these classes and prove that as long as g(n) = o(n/log^3(n)), the classes G^(g(n)) and H^(g(n)) both have a growth constant equal to the planar graph growth constant. As long as g(n) = O(n/log(n)) it is further shown that the classes G^g(n) and H^(g(n)) are both small. We then go on to show which properties graphs in these graph classes commonly display, such as giving bounds on the number of edges, faces, pendant vertices, the maximum degree and the probability of connectedness.
Theological exploration of the recognition of another
Keywords: narrative theory
vulnerability studies
Christian praxis
recognition theory
disability studies and theology

Recognition of the ‘other’ is a struggle for many people in Western political, social, cultural, and ecclesial communities. In this study, I take the current challenges of the ‘political recognition’ of the other as a departure point to offer a theological model of recognition that is marked by interrelationality. I argue that a comprehensive recognition of the other requires a broader perspective than the political. Moreover, this study suggests that any acts of recognition which emerge from a religious perspective need to engage with the social and political world—through mutual accompaniment—for the development of persons within communities.
This study is interdisciplinary, utilizing narrative theory, cultural studies, and disability studies. It uses a constructive and hermeneutical method, rather than historical analysis. Thus, I explore contexts—narrative, vulnerability, and difference—that support dispositions and acts of theologically inspired religious recognition. Many critical theorists, such as Charles Taylor and Judith Butler, expound on the value of ‘political recognition’, and more religiously orientated academics, such as Risto Saarinen, communicate the need for religious recognition that begins with the conversion of the recognizer. Building on these points of view, I argue for a more theologically infused praxis of religious recognition in the formation of personhood within communities that is achieved through ecclesial conversion. I call this ‘recognitional accompaniment’.
My study responds to Charles Taylor’s suggestion that religion may be one context that supports the wider recognition of individuals and minority groups. There have been recent advances within critical theory, which have sought to create a more comprehensive account of recognition, and some theologians and scholars of religion have tackled the absence of religion in recognition theory. While this growing interest in recognition acknowledges the relational aspect of personhood, it overly rests on a ‘turn to the subject’ or existentialist turn at the cost of delimiting the authority of the other. This study offers an alternative, theological exploration of recognized mutuality through interpersonal accompaniment.
Signatures in machine learning and finance
Keywords: signatures
finance
derivatives hedging
machine learning
rough path theory
neural networks
optimal execution
high-frequency trading
derivatives pricing

Developed to give meaning to differential equations driven by rough signals, rough path theory has opened in recent years a new approach to tackle certain problems in other fields such as mathematical finance and machine learning. This is due to certain algebraic and analytical properties of an object called the rough path signature. This thesis aims to make a contribution in this direction by introducing signature-based methods to study various problems arising in finance and machine learning.
In the context of finance, we consider two problems: the pricing and hedging of financial derivatives, and the optimal execution of financial securities. We propose numerical methods based on signatures to solve both problems.
Finally, in the context of machine learning we begin by introducing a new neural network architecture called the deep signature model, based on the deep signature transform. The thesis concludes with a practical application of the signature transform on a real-world problem, where we aim to make predictions from psychiatric data using signatures.
Optical spectroscopy of single non-polar InGaN quantum dots
Keywords: quantum optics
non-polar
nitride
quantum dot
single-photon generation

Experimental investigations of single InGaN/GaN quantum dots grown on the non-polar (11-20) plane are presented.
The electrical driving of non-polar nitride quantum dots is demonstrated. Correlation measurements on a single dot prove single-photon emission with a second order correlation value of g2(0) = 0.18(18), taking into account the detector time response. The dot’s emission exhibits a high degree of linear polarisation, in agreement with a study on 76 randomly chosen quantum dots. Current-dependent measurements reveal three biexciton-exciton pairs with a small binding energy of 3meV, indicating dot heights below 5 nm. Electroluminescence of a single dot is demonstrated up to 130 K.
A lateral electric field is applied to quantum dots with the aim of estimating their lateral size and confining potential from linewidth broadening. A measurement on a single dot yields 6(1) nm and 28(3) meV. However, 60 other emission lines do not show a broadening, but their energy shifts allow to determine the magnitude of the in-built dipoles. As expected, these are small compared to those of polar InGaN dots, ranging between -0.4eÅ and +0.3eÅ. The existence of both parallel and anti-parallel dipoles is attributed to competition between the first and second order piezo-electric component. A mean in-built field of -3 kV/cm with a standard deviation of 11 kV/cm is deduced, demonstrating a reduction by more than two orders of magnitude compared to polar InGaN dots. Further observations are unexpected non-parabolic energy shifts, attributed to device fabrication issues, and similar shift behaviour of some emission lines in the same spectrum, attributed to multi-excitonic complexes and excited states.
A correlation method is used along with continuous laser excitation to measure the fast timescale of spectral diffusion of several dots. Only a part of a dot’s linewidth is selected. One randomly chosen dot exhibits a spectral diffusion time of 860(160) ns at low excitation power. The inverse of the spectral diffusion time increases with increasing excitation power, in line with previous reports. Other quantum dots exhibit shorter, but also longer spectral diffusion times, up to 1170(50) ns. This is at least 3.5 times longer than for any previous measurement on a nitride dot.
Integrative structural biology of viruses
Keywords: foot-and-mouth disease
cryo-electron microscopy
FMDV
enterovirus
picornavirus
BEV
EV-F3
poliovirus
X-ray crystallography
virology
structural biology

Picornaviruses include significant infectious agents and are challenging structural targets owing to their pathogenicity. They share a common architecture, but subtle differences in their structure mediate tissue tropism, receptor binding and uncoating cues. This thesis focuses on members of the Enterovirus and Aphthovirus genera, and aims to contribute structural understanding of their lifecycle and the forces that underpin and modulate capsid stability to ultimately inspire novel therapeutics and vaccines. I take advantage of improvements in cryoEM which enable structural biologists to routinely solve complex structures at close to atomic resolution and resolve sample heterogeneity.
EV-F3 is a non-pathogenic enterovirus. Presented crystallographic structures or EV-F3 highlight a potentially druggable site, and soaks with siallactose suggest a cellular receptor. Cryo-EM investigations show intermediate states, confirming that heating can cause transitions to altered particle states seen in other enteroviruses. Long-wavelength X-ray data indicate the presence of K+, but not Ca2+ ions within the capsid.
I present structural characterisation of recombinant VLP vaccine candidates for poliovirus (PV) and foot-and-mouth disease virus (FMDV). For FMDV, I show a continuum of cryo-EM structures with a potential S-S bridge at the 2-fold interface and varied 2-fold structures. A pentamer subassembly is characterised and analysis of metal ion composition in FMDV VLPs gives no evidence for bound Ca2+ ions.
Single-particle cryo-EM experiments of yeast-derived thermostabilised PV-1 and PV-3 VLPs show both C and D antigenic states to be present for PV-1 and demonstrate a predominance of D-antigenic states for PV-3.
Finally, preliminary investigations into aphthovirus uncoating include attempts to express full length αvβ6 integrin receptor and a preliminary structure of FMDV bound to αvβ3 head-group, demonstrating VLP affinity for virus receptors. I demonstrate the potential of caged protons for time-resolved structural studies of FMDV uncoating and present a novel expanded particle structure of an aphthovirus.
Numerical optimization with applications to machine learning
Keywords: linear algebra
machine learning
optimization

The aim of this thesis is to develop scalable numerical optimization methods that can be used to address large problems of practical interest in the Machine Learning (ML) community.

We begin with a motivating application, Bayesian Optimization (BO), which is a popular ML method employed for hyperparameter tuning of expensive, black-box functions. We show that significant improvements can be brought to the scaling and the computational resources required by batch BO by adopting a distributionally ambiguous framework which replaces expensive integrations with Semidefinite Programming problems (SDPs). Typically, thousands of semidefinite problems are solved when performing BO, which makes their efficient solution essential.

Driven by the above application, we adapt the popular Alternating Method of Multipliers (ADMM) to allow for faster solution of general semidefinite problems. In semidefinite programming, ADMM spends most of its time in projecting matrices into the semidefinite cone. We suggest using state-of-the-art eigensolvers for this task, which brings a significant, up to 20x, speedup to ADMM in standard problems and up to 10x for SDPs arising from our BO algorithm. We show that useful bounds for the projection errors can be computed efficiently. This considerably improves standard eigenvalue perturbation theory bounds (e.g. Davis-Kahan bounds) that suggest the projection accuracy to be inversely proportional to the spectral gap. Our results allow to tightly control the projection errors, so that convergence of ADMM either to a solution, or (for the first time in an approximate ADMM framework) to a certificate of infeasibility is guaranteed. Unlike SDP, in quadratic programming ADMM spends most of its time in solving linear systems. We show how these linear systems can be solved efficiently in the quadratic problem of doubly stochastic matrix approximation. Our analysis reveals a surprising structure in the doubly stochastic approximation problem which allows the scaling of very large, sparse matrices, arising, for example, from the 3D structure of the human genome, or spectral clustering.

Finally, we devise an active set algorithm for the solution of nonconvex quadratic problems that include a norm constraint. Our approach is based on repeated solutions of the famous Trust-Region Subproblem, for which we derive novel results regarding the existence and the computation of its local-nonglobal minimizer. The resulting algorithm was demonstrated to be useful in sparse PCA and sequential quadratic programming.
Epiphany in the modernist short story: Italian and English perspectives
Keywords: English literature
James Joyce
Federigo Tozzi
literary epiphanies
short stories
mysticism
Luigi Pirandello
phenomenology
Italian literature
20th century
Katherine Mansfield
psychology

This thesis reconsiders the phenomenon of literary epiphany in the early twentieth-century short story by comparing its occurrence in the work of four Italian and Anglophone authors: Luigi Pirandello (1867-1936), James Joyce (1882-1941), Federigo Tozzi (1883-1920), and Katherine Mansfield (1888-1923). The decentred perspective allowed by this transnational comparison illuminates epiphanies as complex phenomena connected to multiple aspects of modernist culture. ‘Epiphany’ is considered here as a ‘blurred’ category of literary criticism, based on a family resemblance between independent artistic experiences developed in the same decades. Each author’s idea and use of epiphanies is considered separately, but within a common theoretical frame that brings out peculiarities and recurring themes. At least three common threads emerge, as a result, as general characteristics of modernist epiphanies. First, they participate in a phenomenological attempt to rediscover lived experience as a source of partial but reliable knowledge. Second, they are a result of the ‘inward turn’ and of the curiosity for the psyche’s deeper regions that are manifested through the logic of emotions. Third, they re-actualise mystical experiences as conduits to an authoritative insight that relies on unconscious structures to achieve a comprehensive view of life. The main appeal of these moments of enlightenment is precisely their lack of specificity. Far from revealing a truth, they establish an atmosphere of ambiguity where multiple and even contradictory interpretations are possible. By so doing, they succeed in evoking the undifferentiated creative potential that, according to the widespread vitalist philosophies of the age, constitutes the ultimate essence of life. In reframing ambiguity and indeterminacy as spaces of creation and choice, epiphanies thus bring out a lesser known, life-affirming but not naïve vein of modernist inspiration.
Synthesis and reactivity of group 13 phosphaethynolate complexes
Keywords: main group chemistry
low-valent
boron
phosphorus

This thesis describes the synthesis and reactivity of group 13 coordination complexes of the 2-phosphaethynolate anion (PCO–). The synthesis and characterization of a stable phosphaethynolatoborane, [B]OCP ([B] = N,N′-bis(2,6-diisopropylphenyl)-2,3-dihydro-1H-1,3,2-diazaboryl), is described. This compound represents the first main-group, oxygen-bound isomer of the 2-phosphaethynolate anion to be structurally authenticated. The subsequent cyclisation chemistry of this compound was explored.
The reactivity of [B]OCP with a number of neutral and anionic nucleophiles was explored, the reaction outcome was found to be dependent on the properties of the nucleophile employed. Addition of catalytic amounts of tbutyl-isocyanide induced isomerisation to yield the linkage isomer, [B]PCO. The mechanism of this conversion was explored experimentally and computationally.
The nucleophilicity of [B]OCP was also explored, its steric properties allow access to a series of tungsten trisphosphaalkyne carbonyl complexes. The reaction of [B]OCP with tris(pentafluorophenyl)borane demonstrated an increase in nucleophilicity with respect to the alkyl-substituted tert-butyl phosphaalkyne. In an attempt to access the cyaphide anion, CP–, the reduction chemistry of [B]OCP was explored with the aim to selectively cleave the O–C bond. The reaction outcome is dependent on the reducing agent employed, however selectivity for the desired bond was poor, giving rise to complex product mixtures. It was possible to isolate and partially characterise a magnesium cyaphide complex.
Next, a series of gallium phosphaketenes were synthesised. Both photolytic and chemical decarbonylation processes were explored, allowing access to base stabilised phosphinidenes. The ligand displacement methodology was expanded on to allow access to a compound with a gallium phosphorus double bond.
TDP-43 based biomarker development in amyotrophic lateral sclerosis
Keywords: neurodegeneration
biomarker
interactome
amyotrophic lateral sclerosis
motor neurone disease
proteomics
TDP-43

Amyotrophic lateral sclerosis is a devastating neurodegenerative disease which is clinically and aetiologically heterogenous. However, TDP-43 neuropathology is a unifying hallmark found in 97% of ALS cases. Understanding the common pathological pathways downstream of TDP-43 dysregulation is essential for the development of novel drug targets, and the development of a TDP-43 based biomarker for clinical translation would have profound implications for early diagnosis and monitoring of disease progression.

The work presented in the first part of this thesis addresses the need to develop TDP-43 as a unifying disease-specific biomarker. Mass spectrometry was used to detect TDP-43 from insoluble protein fractions extracted from ALS post mortem tissue with TDP-43 pathology which led to the discovery of ALS disease-specific TDP-43 peptides. These peptides were then validated in an independent targeted proteomic experiment which, for the first time, allowed the quantification of disease-relevant peptides. This enabled the measurement of an ALS-specific TDP-43 peptide signal that reflects sites of pathological truncation and an increased C-terminal TDP-43 protein ratio. This now provides a platform with which to investigate ALS biofluids with the aim to ultimately develop a disease-specific TDP-43 in vivo assay for patient stratification.

In the second part of the thesis I describe the use of affinity-enrichment mass spectrometry to investigate the human wild-type and M337V mutant TDP-43 interactome in a low expression (BAC)-transgenic mouse motor neuron model. I demonstrate that the C-terminal mutation of TDP-43 disrupts specific protein-protein interactions associated with human wild-type TDP-43. In response to oxidative stress, wild-type TDP-43 interactions shift towards proteins that are relevant to cellular stress pathways, while mutant TDP-43 is bound to proteins that are independently linked to pathways known to drive ALS pathogenesis. The key interactions that were disrupted by the M337V mutation involve proteins that are important for stress granule formation and extracellular vesicle secretion. Furthermore, I was able to demonstrate correlative phenotypic abnormalities in stress granule assembly and exosome secretion in motor neurons from the human TDP-43 (BAC)-transgenic mouse model and also in human iPSC-derived motor neurons with the same TDP-43 M337V mutation.

In conclusion, work in this thesis provides significant novel data to support the further development of TDP-43 as an in vivo biomarker in ALS. Analysis of the TDP-43 interactome in a physiologically relevant mouse model has defined core cellular pathways matched to relevant phenotypes which will be important for the identification of pathways relevant for drug target development.
Maritime infrastructure in the eastern Mediterranean: a context-based approach to continuity and innovation in nautical technology (c. 1400-700 B.C.)
Keywords: maritime infrastructure
Aegean
Eastern Mediterranean
nautical technology
Early Iron Age
maritime archaeology
Cyprus
ship iconography
Late Bronze Age transition
Late Bronze Age
Levant

The present thesis offers a comprehensive study of ships and nautical technology in the Eastern Mediterranean of the Late Bronze and Early Iron Age periods (c.1400-700 B.C.). Previous synoptic works on the subject typically cover either a single region or period all the while focusing exclusively on the technical aspect of ship depictions. The aim of this thesis seeks to address these limitations in a twofold manner. First, by charting trans-regional trends and patterns from a longue durée perspective, integrating all available representational, textual and shipwreck evidence for Cyprus, the Levant and the Aegean as well as the scatter of additional sources from elsewhere in the broader Eastern Mediterranean region. Second, by approaching ship representations as cultural artefacts, providing a historically situated, context-based analysis that integrates the technical aspects with socioeconomic practices, cultural significance and attitudes. The work includes a detailed catalogue of over 350 ship representations, a third of which consist of new finds which do not feature in previous compilations. In addition to technical description, each individual entry provides detailed information on the medium, archaeological context, visual impact and use of the artefact. Roughly 40% of the corpus was furthermore either drawn or re-drawn to offer high resolution images. An important aim of this structuring was to provide readers with a means to consult, examine and assess individual representations independently of my own analysis and conclusions. The thesis identifies distinct Levantine, Aegean and Cypriot nautical traditions, each comprised of a set of technical, artistic and consumption habits peculiar to the region while also exhibiting a unique pattern in terms of external influences. An effort is made to identify specific vessel types and post terminals as well as to provide a historical trajectory for landmark technological improvements, their potential source of origin, chronology, and long-term historical impact.