VictorJuiz/thesis huggingface dataset:
Exploration of time-warped cortical spike time patterns

The thesis explores the nature of information representation by patterns of action potentials in the cortex. The thesis combines analysis of sensory-evoked in vivo cortical spiking activity, large scale biophysical cortical network simulations, phenomenological modelling of representation learning through spike-time-dependent plasticity and the development of a spiking neural network simulator. Together, these approaches engendered novel findings and hypotheses regarding the nature of cortical processing.
The thesis focuses on patterns of spikes in which each neuron spikes once (`multi-neuron single spike patterns') as a possible fundamental form of cortical information encoding. The thesis characterises the temporal structure of stimulus-evoked multi-neuron single spike patterns in response to single whisker deflections in the barrel cortex of the anaesthetised rat. Spike time patterns are found to be stretched and compressed in time (i.e. time-warped) depending on the excitability of the barrel cortex on a single trial. This partly explains why precise spike time patterns are rarely reported in vivo. It is proposed that downstream neurons may decode such representations in an excitability-dependent manner, thus increasing spike time coding capacity.
The characterised form of spike time variability is tested for in a detailed biophysical model of a column of rat somatosensory cortex. It was hoped that the model could be used to understand the phenomena's underlying mechanisms and to make further predictions. A framework was developed for comparing in vivo and in silico spiking activity. Key differences between in vivo and in silico spiking activity were found, however. These differences have been used to guide further model refinement.
Hypotheses of how time-warped multi-neuron patterns of single spikes may facilitate the brain's solution to the Feature Binding Problem are presented, as well as attempts to test these hypotheses in a phenomenological spiking neural network. The latter made up the initial work of the DPhil, which aimed to explore the emergence of spike time continua. Towards this a GPU spiking neural network simulator was co-created, and was demonstrated (by collaborators) to be the fastest of its class.

Keywords: Time-warp
Precise spike timing
Neural population dynamics
State-dependent coding
Neural coding
Neuroscience
Cortex
Time-warp spike timing
Noise correlations
Advisor: Stringer, SM
Towards the detection of anisotropic magnetic field effects in flavin-based systems

Many animals, and in particular migratory birds, have the ability to use the geomagnetic field to navigate. The leading hypothesis to explain the origin of their compass sense is based on magnetosensitive radical pairs (RPs) formed in cryptochrome flavoproteins.
Numerous studies have demonstrated that the reactivity of light-induced RPs within flavin-based model systems and cryptochromes could be influenced by the magnitude of a magnetic field, giving rise to magnetic field effects (MFEs). Yet, many questions remain unanswered, especially regarding the ability of these systems to detect the direction of the field, which has been shown to provide critical information for navigation.
This work examines different chemical and spectroscopic approaches for their poten- tial to yield or elucidate directionally sensitive magnetic field responses in flavin-based RPs. Chapter 1 explores whether selectively manipulating the magnetic properties of cryptochromes in vivo could disturb the bird’s migratory behaviour. If it did, it would demonstrate that cryptochromes are i) sensitive to the field direction and ii) the primary magnetic sensor for avian magnetoreception. The potential of this ambitious experiment is assessed by examining the impact of isotopic substitution (which changes the hyperfine interaction driving the RPs’ magnetosensitivity) on the MFE of model systems.
In vitro, the directionally dependent response of RPs to a field (anisotropic MFEs) can only be detected if the radicals are immobilised and oriented. In Chapters 2-3, several matrices are investigated as potential immobilisation media and the unexpected behaviour of flavins in glycerol solutions is further examined. Chapter 4 explores direct molecular alignment via protein crystallisation and introduces confocal microscopy as a powerful technique for the study of MFEs in crystals. By exploiting the capabilities of this technique, the MFEs of several cryptochromes, including avian cryptochromes, are investigated and contrasted, leading up to the examination of anisotropic MFEs in cryptochrome crystals (Chapter 5).

Keywords: radical pairs
microscopy
cryptochromes
fluorescence
magnetoreception
Advisor: Timmel, C
Asymptotic behaviour of some measure-valued diffusions

Branching diffusions are introduced as a simple model of the growth of a population of rare mutant genes or of the spread of a small epidemic. Measure-valued critical branching diffusion processes are then constructed as the weak limits of the discrete particle branching diffusions when the scales of mass and lifetime are changed in an appropriate way. The distribution of such a measure-valued process is characterized as the unique solution to a martingale problem and this leads to an expression for its Laplace transform in terms of a deterministic dual process.
The dual process is given as the solution to a non-linear second order partial differential equation —the evolution equation of the measure-valued process. It is immediate that those measure-valued processes whose total mass is initially finite suffer extinction. The solution to the evolution equation is written in the form of a series whose coefficients are expressed in terms of the linear semigroup associated with the spatial diffusion part of the process. Estimates on these coefficients lead to a simple proof that if the spatial diffusion part of the measure-valued process is a recurrent (resp. transient) diffusion on Rd and the initial value of the process is a non-trivial invariant measure of this spatial diffusion then the process has no (resp. has a unique) non-trivial limiting distribution.
In order to overcome the tendency to extinction, a Poisson process of mass creation is introduced into the discrete particle branching diffusion. The resulting processes are rescaled in a way compatible with the previous rescaling to produce a measure-valued process with immigration. This process is also characterized via a deterministic dual, obtained by integrating the solution of the usual evolution equation with respect to time. The series solution to the evolution equation enables the moments to be calculated. It is shown that if the spatial diffusion is positive recurrent then the effect on the limit law of X(t)/t of immigrating at a constant rate is the same as that of conditioning the process without immigration on non-extinction. However, for a null recurrent diffusion it is shown that in the first case the limit is non-trivial (non-random) whereas in the second the limit is zero on any compact region.

Advisor: Edwards, D
Study of catecholaminergic cells in murine heart

Cardiac conduction system (CCS) morphogenesis is essential for correct heart function yet is incompletely understood. During my D.Phil, I established the transcriptional landscape of cell types populating the developing heart by integrating single-cell RNA sequencing and high-resolution spatially resolved transcriptomics (SrT) analyses. This led to the identification of a previously unrecognized cardiomyocyte population expressing dopamine beta-hydroxylase (Dbhh+ -CMs), which is closely associated with the CCS. To further comfirm, genetic fate mapping using DbhCre/Rosa26-tdTomato reporters combined with SrT revealed that Dbh+-CM lineage is Hcn4-independent, first emerged in the sinoatrial node at E12.5, then to atrial and ventricular CCS components at E14.5 and became prominent within CCS at perinatal stages. Dbhh+ -CM populating CCS occurred concurrently with sympathetic innervation. Electrophysiological optogenetic mapping revealed a fast conduction in DbhCre/ChR2-tdTomato hearts by selectively stimulating Dbh+ -CMs. Furthermore, catecholaminergic-type vesicles were identified in adult cardiomyocytes. Thus, by utilising advanced transcriptomic, genetic and functional analyses, my study provides new insights into mammalian CCS development and heterogeneity. Besides, by combining an improved heart tissueclearing technique with high resolution light sheet fluorescence microscopy (LSFM), I conducted three-dimensional and multi-scale volumetric imaging of ultra-thin planes of murine hearts to visualize the specific cardiomyocyte subpopulations. This method provides a tool for further geometrical and topological analysis of these cell types and the correlation with their physiological function in specific region of the murine heart.

Advisor: Leim M
How elite professional service firms recruit graduates in China

China has been experiencing a series of socio-economic transitions since the market reform was explicitly accentuated in the 1990s. On the one hand, China has grown to be the second largest economy and is now producing one of the largest groups of university-educated workers in the world. On the other hand, as a newly emergent player, the professional service sector has contributed to assimilating highly-educated graduates and accelerating the trends of financialisaton, internationalisation and knowledge-based expansion of Chinese society and economy. However, how the growing professional service sector intersects with Chinese transitions is underexplored. In particular, regardless of its theoretical and empirical significance, how professional service firms recruit graduates has long been neglected by existing literature. In this sense, this thesis aims to remedy this gap through a qualitative investigation into the campus recruitment of professional service firms in China. In Chapter 1, I begin by describing key background and context of this thesis as well as its theoretical framework and methodology. In light of a theoretical framework of symbolic boundaries and positional conflict, it attempts to provide the insights into a site of elite hiring and explore its theoretical potential. Drawing on 73 semi-structured interviews with recruiters in elite financial and consulting firms, contents of job advertisements and an array of on-site observations to campus fairs and a day of job interviews, this study is structured as four empirical chapters that chronologically analyse the process of graduate recruitment. Chapter 2 surveys what kinds of talents recruiters were looking for before the formal selection started. Chapter 3 and 4 focus on how recruiters screened and selected résumés. Chapter 5 probs into how recruiters assessed interview performances. Overall, this thesis argues that graduate hiring was a culturally ‘scripted’ project of elite professional service firms in China and shaped by recruiters’ cultural belief and wider organisational and institutional circumstances. In this context, recruiters tended to use various information in order to select graduates akin to or preferred by them or resonant to their ideals for the purpose of maintaining the order of professional workplaces.

Keywords: Higher education
Professional service firms
Elites
China
Hiring
Advisor: Kariya, T
'Women in an extraordinary time': the transnational network and educational spaces of the Canadian Eiwa Girls' mission schools in 1920s and 1930s Japan

The Tōyō Eiwa Jogakkō, Shizuoka Eiwa Jogakkō, and Yamanashi Eiwa Jogakkō girls’ mission schools were founded by the Woman’s Missionary Society of the Methodist Church of Canada (from 1925 the United Church of Canada) in the 1880s in Tokyo, Shizuoka, and Kōfu, Japan respectively. The students, graduates, missionaries, and Japanese educators of these three institutions were physically and intellectually part of a transnational network of Christian women and organizations in 1920s and 1930s Japan. The community these inter-generational and non-diplomatic Eiwa actors built, the communication and exchange students undertook, and the mobility of graduates transcended state boundaries of Japan, Canada, and beyond. By exploring individuals and activities of these three girls’ schools and the network they constructed in the pre-WWII period, this thesis expands our understanding of educational and intellectual life in 1930s Japan. Through network development, physical and intellectual spatial construction, and curriculum and activity design, these historical actors reached outside their institutions to actively connect themselves and their peers with the wider world. In the 1930s, this appears to have been conducted with a sense of urgency. Ultimately, these schools survived a tense and nationalistic period of world history to operate into the present day. By shifting the lens from male educators to little-known women including students, and from missionaries to include Japanese actors, this study shows within these spaces mutual exchange and communication across national borders, international education, and discussions on and activities related to world peace took place throughout the 1930s. These actors envisioned Christianity, women, youth, education, and mutual exchange across state and East-West divides as able to foster understanding between individuals of different nations. This thesis thus looks to Eiwa women and youth in their roles as graduates, educators, and students to demonstrate a dynamic understanding of 1930s Japanese educational and intellectual life.

Keywords: mission schools
Japanese history
women's history
Japan
transnational history
history of education
Advisor: Konishi, S
Graphene nanogaps and nanoelectric devices

Electronic devices based on single-molecules or single-nanoparticles offer the potential for highly energy-efficient devices with chemically tunable properties for applications in computing, sensing and memory storage. However, numerous challenges pose barriers to the realisation of robust, reproducible and scalable single particle devices: in particular, the fabrication of electrodes of suitable dimensions to contact these particles and the challenge of manipulating the target particles into desired positions. This thesis explores the creation of graphene nanogap electrodes as a platform for single-particle devices and some of the unique properties associated with single-molecule devices. It then goes on to detail efforts to improve the yield of nanogap fabrication and to develop a method based on the phenomenon of dielectrophoresis to manipulate nanoscale particles. Finally, it examines the low-temperature transport physics of hybrid graphene-nanoparticle devices created using the dielectrophoretic method. This thesis highlights key challenges in the creation of single-molecule devices, examines methods to better control the formation of such devices and demonstrates a route towards the creation of a plethora of novel, hybrid devices formed from unique nanomaterials coupled to graphene electrodes with diverse potential applications.

Advisor: Mol, J
Briggs, G
Tissue scale electrophysiological-mechanical continuum modelling for white matter transcranial ultrasound neuromodulation

Neurological disorders are a substantial health and economic burden worldwide. Low-intensity transcranial ultrasound stimulation (TUS) is now considered as one of the most promising treatments for neurological disorders due to its high spatial resolution compared to other non-invasive neuromodulation methods. While for many decades now, ultrasound has been known to be able to influence or modulate neuronal activities in the brain, its underlying mechanisms are still poorly understood. Maybe not fully unrelated, while nerve impulses have traditionally been considered to be a purely electrical phenomenon, a growing body of evidence is now pointing towards additional thermodynamic changes occurring alongside the action potential. Numerous models have been proposed to study this electromechanical coupling phenomenon. Among these, the flexoelectric theory is postulating that a temporal variation of strain gradient in the membrane leads to current creation. Whether or not this hypothesis is fully accurate microscopically in the context of TUS, it offers a phenomenological framework that could be used at the organ scale to quantify electrical induction in the presence of minute mechanical vibrations. However, the flexoelectric theory relies on formulations directly built on the microstructural description of the underlying dielectric polarisation. In membranes, this constrains the flexoelectricity modelling to simple membrane morphologies and prevents the simulation of flexoelectricity in large scale assemblies of multiple biological cells. To this end, this work proposes a homogenised bulk flexoelectric model focussing on the continuum level formulations of bundles of flexoelectric cylinders. This model was calibrated against a microscale formulation to ensure multiscale compatibility, but it can be directly used at the macroscale for the description of strain-gradient induced electromechanical coupling without the need to account for the microstructural polarisation. A 1D proof of concept is first proposed, followed by 2D and 3D formulations of the homogenised bulk flexoelectric model. The homogenised model is used for brain white matter tracts in the context of TUS, where ultrasound induced electrical activity arising within the tracts is simulated in a human head model in 2D and a monkey head model in 3D. In the latter case, a direct comparison against experimental models is proposed. In particular, this study proposes a way to predict the loss of brain region correlation during TUS. To conclude, the framework proposed here has the potential to fully capture multiphysics phenomena such as in TUS. The results from this study provide a theoretical building block to identify the desirable ultrasound parameters for clinical and/or experimental applications that can be used for the successful treatment of neurological disorders.

Keywords: homogenised continuum flexoelectricity
ultrasound neuromodulation
electromechanical coupling
Advisor: Jerusalem, A
A signal through the noise: accurate determination of hydrogen atom positions in crystal structures and optimisation of Laue neutron diffraction methods

In this thesis, Laue neutron diffraction methods are applied to determine the positions of hydrogen atoms in crystal structures accurately and with confidence, as well as informing the optimisation and development of these methods. This has allowed a variety of chemically and crystallographically interesting studies to be performed, specifically:
Determining the novel geometry around transition-metal hydride centers, where the signal due to the hydrides can be more confidently distinguished than in an X-ray diffraction experiment; using Laue neutron derived difference Fourier maps to demonstrate that proton disorder can be mistakenly assigned in X-ray derived crystallographic models; performing variable temperature Laue neutron diffraction to identify proton migratory behaviour across short-strong hydrogen bonds; reassigning the space group of a previously reported cobalt(III) coordination complex, in which the lack of inversion symmetry becomes apparent upon accurate determination of the hydrogen atom positions; using Laue neutron diffraction data to more confidently classify systems as co-crystals or salts.
Following this, the optimisation and development of the Laue neutron diffraction methods used is described. This focuses on:
Recommendations for the efficient collection of Laue neutron data, in order to optimise the data set completeness and awarded beam-time; strategic considerations for how to best answer the scientific question(s) at hand in a Laue neutron experiment, whilst planning against future contingencies; improving methods for crystal packing and shipping, particularly for air and moisture sensitive materials; discussing issues arising from ice forming on the crystal during a Laue neutron diffraction experiment, and methods for minimising this problem; more effectively modelling disorder using ring shapes, in the crystallographic refinement package CRYSTALS; providing rationale for Laue neutron specific checkCIF comments.
Alongside the aforementioned research projects, the relevant history and theory contextualising the crystallographic methods used is presented.

Keywords: neutron diffraction
crystallographic modelling
Advisor: Cooper, R
Edwards, A
Translation in context: a descriptive account of Romeo and Juliet in versions by Konstantin Bal’mont and Anna Radlova

This thesis will analyse two translations of Romeo and Juliet completed in the early years of the Soviet Union: one produced by Konstantin Bal’mont in 1919, the other by Anna Radlova in 1934. The research will use the Descriptive Translation Studies framework, particularly Gideon Toury’s idea of translation norms, in order to try to account for some of the choices made in both translations, as well as for the reception of these translations.

Keywords: Translation
Konstantin Balmont
Anna Radlova
Theatre
English
Romeo and Juliet
Shakespeare
Sergei Radlov
Russian
Tairov
Advisor: Bullock, P
Property in criminal law and private law

A proposition of law about the allocation of proprietary rights or about the objects of a proprietary right which is true at private law is, usually, also true at criminal law. In the ordinary course of things, whatever private law takes to be property owned by X, criminal law would take to be property owned by X. To illustrate, it is true to say that things like balloons, balustrades and ballparks count as the sort of object over which a person can have a proprietary interest, as a matter of both private law and criminal law. It is also true to say that if private law allocates to me a certain balloon, balustrade or ballpark then so will criminal law – on the whole. This is what we expect in the ordinary case.
However, there are a number of instances in English & Welsh law in which this expectation does not hold. The aim of the thesis is to explain why the ordinary case occurs most of the time. A derivative aim is to explain why the ordinary case does not obtain all of the time. Certain vivid occasions on which criminal and private law have come apart, cases such as R v Hinks [2001] 2 AC 241, have received attention. However, there has never yet been a sustained exploration of the influence that both criminal and private law, together, bring to bear on the reasoning and outcomes of cases that involve property and wrongdoing.
My proposal is that the ordinary case is explained by the influence which four features of the legal system exert over the reasoning and outcomes in case-law. The four features are: the laws which constitute ownership, the technical lexicon used to state property laws, concurrent civil and criminal jurisdiction over property, and the maxim that wrongdoers should not benefit from their wrongdoing. These are necessary conditions but they are not necessary and sufficient conditions – whether individually or jointly – because, as we have seen, there is case-law which bucks the trend. That latter case-law is, in turn, explained by two things. The first is value pluralism. The second is a contest between two of law’s claims: law’s claim to moral authority and law’s claim to have comprehensive practical authority.

Advisor: Rostill, L
Endicott, T