VictorJuiz/thesis huggingface dataset:
The Kakimizu complex of a link
Keywords: Seifert surfaces
57M25
knots
links
homogeneous links
Alexander polynomial
Kakimizu complex
alternating links

We study Seifert surfaces for links, and in particular the Kakimizu complex MS(L) of a link L, which is a simplicial complex that records the structure of the set of taut Seifert surfaces for L.
First we study a connection between the reduced Alexander polynomial of a link and the uniqueness of taut Seifert surfaces. Specifically, we reprove and extend a particular case of a result of Juhasz, using very different methods, showing that if a non-split homogeneous link has a reduced Alexander polynomial whose constant term has modulus at most 3 then the link has a unique incompressible Seifert surface. More generally we see that this constant term controls the structure of any non-split homogeneous link.
Next we give a complete proof of results stated by Hirasawa and Sakuma, describing explicitly the Kakimizu complex of any non-split, prime, special alternating link.
We then calculate the form of the Kakimizu complex of a connected sum of two non-fibred links in terms of the Kakimizu complex of each of the two links. This has previously been done by Kakimizu when one of the two links is fibred.
Finally, we address the question of when the Kakimizu complex is locally infinite. We show that if all the taut Seifert surfaces are connected then MS(L) can only be locally infinite when L is a satellite of a torus knot, a cable knot or a connected sum. Additionally we give examples of knots that exhibit this behaviour. We finish by showing that this picture is not complete when disconnected taut Seifert surfaces exist.
Specialisation of political participation in Europe: a comparative analysis
Keywords: immigrants
political engagement
voting
mobilization
political integration
protest
political action
ethnic minorities

This thesis answers the question how and why do individuals specialise in different types of political participation? By examining the degree to which individuals concentrate their political activities within one type of political participation, or spread them out across many. This thesis complements previous research on rates of political participation; and adapts and extends existing theories of political participation to explain differences in the degree of specialisation between different groups in society and between countries.
Using data from the European Social Survey, covering as many as 21 European countries, and applying a range of different statistical methods, I distinguish four types of political participation: voting, conventional and unconventional political participation and consumer politics. I show that in countries with higher levels of socio-economic development, more democratic experience, and an increased presence of mobilising agents, the degree to which individuals concentrate their political activities within one type of political participation is higher, regardless of the accessibility and responsiveness of their political institutions. This is partly due to the fact that these countries have a higher educated population and that higher educated individuals specialise more. Specialisation also varies along the lines of other socio-demographic divisions, such as those based on gender. Moreover, I show that in contexts in which political issues are salient, such as during an election year, individuals are more likely to engage in non-electoral types of political participation if they also vote. This implies that specialisation is reduced during times of country-wide political mobilisation.
The final finding of my thesis is that non-Western immigrants tend to concentrate their political activities less within one type of political participation than the majority population in Western Europe. Western immigrants specialise quite differently, suggesting differences in the way in which they are mobilised.
As well as providing an important contribution to the study of political participation, these findings are relevant to discussions regarding citizen engagement and representation.
The 'crime scene' experiment: improving public knowledge through the provision of factual information on crime and criminal justice
Keywords: mixed-methods research
experiment
public opinion
knowledge

This thesis explores the relationship between crime, media, and public opinion of crime and criminal justice. It sets out current levels of knowledge and contemporary debates in each of the three academic disciplines devoted to these aspects of social life, and discusses how they relate to each other. It focuses on the capacity of information and public education to influence levels of public knowledge of and, as a secondary concern, attitudes towards, crime and criminal justice.
The empirical research at the heart of the thesis employed a mixed methods research study drawing on quantitative – experimental research using a public opinion survey – as well as qualitative research methods – in-depth interviews and contextual data. The experimental research, the Oxford Public Opinion Survey and the publication of the Crime Scene column, was designed to measure the impact of providing factual information about crime and criminal justice to the public in a naturalistic way, i.e. by using a local newspaper column as the conveyor of such information.
The key finding from the research was that readership of the column was low and that the column had no measurable impact on readers. Overall, the research findings suggest that interest in, take-up, and retention of factual information on crime and criminal justice is not as high as previous empirical research has suggested. The Crime Scene study has implications for sociological theories of crime and punishment which rely on simplistic orthodoxies concerning the media’s importance in influencing public opinion on crime and criminal justice and the related assumption that ‘the public’ is straightforwardly punitive.
Mouse models for the investigation of MAPT and its role in neurodegenerative disease
Keywords: tau protein
neurodegeneration
frontotemporal dementia

Microtubule-associated protein tau plays an important role in many neurodegenerative diseases. By using and creating various novel mouse models, the role of tau and its relationship with other amyloidogenic proteins was investigated.
Behavioural and molecular characterization of novel mouse models expressing all six isoforms of human wild-type (H1) or N296H mutant (N51) tau protein was carried out to study the age-related emergence of phenotypes commonly associated with tauopathies. Mutant animals displayed no degenerative cognitive or motor phenotype. However, a possible mood phenotype was observed even at a young age. No formation of intracellular tau inclusions was observed. Using acute slice cultures, I further investigated phosphorylation of N296H mutant tau. Relative tau hypophosphorylation was observed in a N296H mutant compared to the wild-type tau expressing animals. In the hippocampus, exposure to Abeta led to an increase in tau phosphorylation at S202/T205 in H1, but not N51 mice. Electrophysiological studies by M. Vargas-Caballero showed that H1, but not N51 animals are susceptible to Abeta-induced LTP impairment. Taken together, these results suggest that tau phosphorylation could mediate the effects of Abeta on LTP. N51 mice also showed a trend towards increased fyn expression. Fyn relocalization into the soma was not detected either in N51 or tau knockout animals.
The functional relationship between tau and α-synuclein was investigated in several novel models. Neither acute exposure of acute slices to α-synuclein oligomers nor α-synuclein overexpression induced tau hyperphosphorylation. A novel mouse model lacking both tau and α-synuclein was generated, but revealed no remarkable behavioural changes. Finally, a new mouse model was created overexpressing human wild-type α-synuclein on a tau knockout background to investigate whether tau is required for α-synuclein-induced dopamine release deficits previously observed in α-synuclein overexpressors.
Category-theoretic quantitative compositional distributional models of natural language semantics
Keywords: vector space models
category theory
distributional semantics
semantics

This thesis is about the problem of compositionality in distributional semantics. Distributional semantics presupposes that the meanings of words are a function of their occurrences in textual contexts. It models words as distributions over these contexts and represents them as vectors in high dimensional spaces. The problem of compositionality for such models concerns itself with how to produce distributional representations for larger units of text (such as a verb and its arguments) by composing the distributional representations of smaller units of text (such as individual words).
This thesis focuses on a particular approach to this compositionality problem, namely using the categorical framework developed by Coecke, Sadrzadeh, and Clark, which combines syntactic analysis formalisms with distributional semantic representations of meaning to produce syntactically motivated composition operations. This thesis shows how this approach can be theoretically extended and practically implemented to produce concrete compositional distributional models of natural language semantics. It furthermore demonstrates that such models can perform on par with, or better than, other competing approaches in the field of natural language processing.
There are three principal contributions to computational linguistics in this thesis. The first is to extend the DisCoCat framework on the syntactic front and semantic front, incorporating a number of syntactic analysis formalisms and providing learning procedures allowing for the generation of concrete compositional distributional models. The second contribution is to evaluate the models developed from the procedures presented here, showing that they outperform other compositional distributional models present in the literature. The third contribution is to show how using category theory to solve linguistic problems forms a sound basis for research, illustrated by examples of work on this topic, that also suggest directions for future research.
Investigating the ecology, diversity and distribution of cord-forming fungi in Great Britain
Keywords: Phylogenetics
ecology
forest ecology
species distribution modelling
restoration
regeneration
cord-forming fungi

Cord-forming fungi (CFF) are an assemblage of saprotrophic fungi which can use complex foraging organs of longitudinally arranged hyphae to join up disparate substrates in a patchy resource environment. Their importance to woodlands lies, mainly, in their ability to modify nutrient cycling and soil structure. Therefore, in order to enable woodlands to continue to thrive in terms of their health and ecosystem function, it is necessary to understand the factors contributing to the establishment, success and diversity of this group. Whilst work to date on CFF has focussed on their physiology and interactions in laboratory conditions, little work has been carried out on their taxonomy and establishment/presence in the field. The work in this thesis begins to address these crucial unanswered questions in CFF ecology.
By carrying out investigations at a range of scales, from phylogenetic analysis to UK wide Species Distribution Modelling, this thesis reaches a number of surprising results with potentially important implications for woodland management. This is most evident in Chapter 3 where our hypothesis that fungal communities develop over time in plantations of different woodland ages was disproved, illustrating that even 13 years after planting, fungal communities in plantations on ex-agricultural land had not begun to reach those in established ASNW. These unexpected results continue into Chapter 4, where the thesis demonstrates that dominant canopy species has a greater impact on community composition than any other woodland factor. Chapter 5 continues this theme, by showing that removal of invasive species is not always beneficial for the cord-forming fungal communities, especially if it involves removing the woody substrate.
The work described, detailed and analysed in this thesis has initiated further investigations, proposed changes to woodland management practices and laid the foundations for future work relating to CFF and their role and function in British woodlands.
Changes in functional connectivity due to modulation by task and disease
Keywords: functional connectivity
fMRI
stroke
resting state networks
task modulation

Soon after the advent of signal-recording techniques in the brain, functional connectivity (FC), a measure of interregional neural interactions, became an important tool to assess brain function and its relation to structure. It was discovered that certain groups of regions in the brain corresponding to behavioural domains are organized into intrinsic networks of connectivity (ICNs). These networks were shown to exhibit high FC during rest, and also during task. ICNs are not only delineated by areas which correspond to various behaviours, but can be modulated in the long and short-term in their connectivity by disease conditions, learning, and task performance. The significance of changes in FC, permanent and transient, is poorly understood with respect to even the simplest ICNs corresponding to motor and visual regions. A better grasp on how to interpret these changes could elucidate the mechanisms and implications of patterns in FC changes during therapy and basic tasks. The aim of this work is to examine long-term changes in the connectivity of several ICNs as a result of modulation by stroke and rehabilitation, and to assess short term changes due to simple, continuous task performance in healthy volunteers.
To explore long-term changes in ICN connectivity, fifteen hemiparetic stroke patients underwent resting state scanning and behavioural testing before and after a two-week session of Constraint Induced Movement Therapy (CIMT). It was found that therapy led to localized increases in FC within the sensorimotor ICN.
To assess transient changes in FC with task, sixteen healthy volunteers underwent a series of scans during rest, continuous performance of a non-demanding finger-tapping task, viewing of a continuous visual stimulus, and a combined (but uncoupled) visual and motor task. Group Independent Component Analysis (ICA) revealed that canonical ICNs remained robustly connected during task conditions as well as during rest, and dual regression/seed analyses showed that visual and sensorimotor ICNs showed divergent patterns of changes in FC, with the former showing increased intra-network connectivity and the latter decreased intra-network connectivity. Additionally, it was found that task activation within ICNs has a relationship to these changes in FC.
Overall, these results suggest that modulation of functional connectivity is a valuable and informative tool in the study of disease recovery and task performance.
Spatiotemporal dynamics of cytoskeletal and chemosensory proteins in the bacterium Rhodobacter sphaeroides
Keywords: chemotaxis
cytokinesis
spatial organisation
Rhodobacter sphaeroides
prokaryotic cytoskeleton
polar localisation
FtsZ
fluorescence microscopy
bacterial cell division
MreB
chemosensory clusters

The discovery of the prokaryotic cytoskeleton has revolutionized our thinking about spatial organisation in prokaryotes. However, the roles different bacterial cytoskeletal proteins play in the localisations of diverse biomolecules are controversial. Bacterial chemotaxis depends on signalling through large protein clusters and each cell must inherit a cluster on cytokinesis. In Escherichia coli the membrane chemosensory clusters are polar and new static clusters form at pre-cytokinetic sites, ensuring positioning at new poles after cytokinesis and suggesting a role for the bacterial FtsZ and MreB cytoskeletons. Rhodobacter sphaeroides has both polar, membrane-associated and cytoplasmic, chromosome-associated chemosensory clusters. This study sought to investigate the roles of FtsZ and MreB in the partitioning of the two chemosensory clusters in R. sphaeroides. The relative positioning between the two chemosensory systems, FtsZ and MreB in R. sphaeroides cells during the cell cycle was monitored using fluorescence microscopy. FtsZ forms polar spots after cytokinesis, which redistribute to the midcell forming nodes from which gradients of FtsZ extend circumferentially to form the Z-ring. The proposed node-precursor model might represent a common mechanism for the formation of cytokinetic rings. The MreB cytoskeleton continuously reorganizes between patchy and filamentous structures, and colocalises with FtsZ at midcell. Membrane chemosensory proteins form individual dynamic unit-clusters with mature clusters containing about 1000 CheW3 proteins. These unit-clusters diffuse randomly within the membrane but have a higher propensity for curved regions like cell poles. Membrane clusters do not colocalise with FtsZ and MreB and appear excluded from the Z-ring vicinity. The bipolar localisation of membrane clusters is established after cell division via random diffusion and polar trapping of clusters. The cytoplasmic chemosensory clusters colocalise with FtsZ at midcell in new-born cells. Before cytokinesis one cluster moves to a daughter cell, followed by the second moving to the other cell. FtsZ and MreB do not participate in the positioning of cytoplasmic clusters. Therefore the two homologous chemosensory clusters use different mechanisms to ensure partitioning, and neither system utilizes FtsZ or MreB for positioning.
The role of HLA-B27 in the pathogenesis of spondyloarthritis
Keywords: HLA-B27
major histocompatibility complex
spondyloarthropathies
arthritis
ankylosing spondylitis
pathogenesis

The Human Leukocyte Antigen (HLA)-B27 is a Major Histocompability Complex (MHC) class I antigen that is strongly associated with development of a group of closely related arthritic diseases, collectively known as the spondyloarthropathies (SpA). However, the mechanism by which HLA-B27 confers this susceptibility is unclear. Studies have shown that HLA-B27 heavy chains can form classical heterotrimers associated with peptide and β2-microglobulin (B27HT), and also non-classical heavy chain homodimers (B27₂). B27₂ assemble intracellularly during maturation and are also expressed at the cell surface following endosomal recycling of B27HT. A pathogenic role for B27₂ has been proposed in two of the current theories of pathogenesis: the B27 homodimer theory and the B27 misfolding and UPR theory. Yet, determinations of the extent, distribution, and triggers of B27₂ expression, as well as the functional consequences of its receptor interactions in AS pathogenesis, have been hampered by the lack of a specific detection reagent. Therefore, to investigate the role of B27₂ in AS, we generated a novel antibody to B27₂ – HD6 – using phage display technology, which binds to in vitro refolded B27₂ but not B27HT complexes by ELISA. This thesis provides evidence that HD6-reactive molecules, which include B27₂, are expressed at the cell surface in both cell lines and in the context of a disease setting. Recognition is B27-specific and strongly correlated with the magnitude of B27 expression, which could account for the lack of staining in some cell subsets. Moreover, staining was comparable in cell lines expressing the disease-associated B*27:05 and the less disease-associated subtype B*27:09. In addition, I have shown cells expressing physiologic levels of B27, including EBV-transformed BCLs and AS patient PBMCs, are capable of expressing the HD6 epitope upon low pH treatment. Interestingly, these ‘acid-inducible HD6’ molecules were absent from cells lacking a functional PLC. Finally, I have shown that HD6-reactive molecules can derive from pre-existing folding B27 molecules at the cell surface, which may be inhibited by the addition of exogenous B27-binding peptides. These findings are consistent with a mechanism of pathogenesis involving the surface expression and recognition of B27₂ and/or other aberrantly folded forms of B27, as proposed in the homodimer theory. HD6 will be a powerful tool to address the potential pathogenic role of B27₂ in SpA and may additionally have therapeutic potential.
Topics in general and set-theoretic topology: slice sets, rigid subsets of the reals, Toronto spaces, cleavability, and neight
Keywords: rigid
forcing
homogeneity
slice set
real line
cleavage
2-point set
Toronto problem
neight
cleavability
Toronto space

I explore five topics in topology using set-theoretic techniques. The first of these is a generalization of 2-point sets called slice sets. I show that, for any small-in-cardinality subset A of the real line, there is a subset of the plane meeting every line in a topological copy of A. Under Martin's Axiom, I show how to improve this result to any totally disconnected A. Secondly, I show that it is consistent with and independent of ZFC to have a topologically rigid subset of the real line that is smaller than the continuum. Thirdly, I define and examine a new cardinal function related to cleavability. Fourthly, I explore the Toronto Problem and prove that any uncountable, Hausdorff, non-discrete Toronto space that is not regular falls into one of two strictly-defined classes. I also prove that for every infinite cardinality there are precisely 3 non-T1 Toronto spaces up to homeomorphism. Lastly, I examine a notion of dimension called the "neight", and prove several theorems that give a lower bound for this cardinal function.
Pericyclic and related rearrangements for the synthesis of nitrogen heterocyclic ring systems
Keywords: total synthesis
pericyclic reactions
azides
allenes
rearrangement
cycloadditions
azatrimethylenemethane
ene reaction
Radianspene J

The thesis describes synthesis and reactions of allene azides tethered to various functional groups and the application of the discovered cascade transformations towards the synthesis of radianspene J model system.
Chapter 1 covers reactions of simple allene azides containing alkyl and cycloalkyl substituents. Thermal rearrangements of these substrates delivered isocyanides and azadienes via the proposed azatrimethylenemethane (ATMM) intermediates.
On the other hand, vinylidenecyclopropanes (VDCPs) gave dramatically different products, as described in Chapter 2. A phenyl-substituted VDCP was transformed into an unstable polycyclic compound by a divinylcyclopropane rearrangement. Chapter 3 discusses allene azides tethered to furan, N-substituted pyrroles, and E- and Z-dienes. Depending on the structure of the starting material, products of formal (3+4)- or (2+3)-cycloaddition were formed.
Finally, an application of the discovered cyclisation cascade towards total synthesis is described in Chapter 4. A model system of radianspene J was assembled using a key transannular cycloaddition of a macrocyclic allene.