VictorJuiz/thesis huggingface dataset:
Temporal orienting in the human brain: neural mechanisms of control and modulation
Keywords: Temporal Expectations
neural oscillations
fMRI
Attention
EEG

The main aim of the experiments reported in this thesis was to explore the neural mechanisms underlying the temporal orienting of attention. In Chapter 3, I explored the possible dissociation between exogenous and endogenous temporal orienting by comparing reaction times to targets appearing after rhythmic or symbolic cues. Behavioural results provided evidence for the existence of dissociable exogenous and endogenous types of temporal orienting of attention. The experiment in Chapter 4 combined spatiotemporal expectations using rhythmic moving cues to test the modulatory effect of exogenous temporal orienting in the brain. Specifically, I used EEG to test the effect of temporal orienting on perceptual and motor stages of target analysis, as well as on anticipatory oscillatory brain activity. The time-frequency analysis revealed that rhythmic cues can entrain slow brains oscillations, providing a putative mechanism for enhancing the perceptual processing of expected events. Spatiotemporal expectations also modulated the amplitude of visual responses and the timing and amount of preparatory motor activity. In Chapter 5, I used a novel task to explore the neural modulatory effects of spatial and temporal expectations acting in isolation or in coordination. For the first time, the analysis of early visual responses demonstrated that temporal expectations alone, independently of spatial orienting, can enhance early visual perceptual processes. The time-frequency analysis in this experiment showed a desynchronisation of alpha oscillations focused over central-parietal electrodes induced by rhythmic cues that were independent of spatial expectations. When rhythmic cues carried spatiotemporal information, the alpha desynchronisation also spread over contralateral occipital electrodes. In Chapter 6, fMRI was used to test the possible neural dissociation between motor and temporal orienting. The results confirmed the large overlap between these two processes, but also indicated independent behavioural and neural effects of temporal orienting. Temporal orienting activated the left IPS across motor conditions, further implicating the left IPS in temporal orienting. Based on the results of these experiments, directions for future studies are discussed.
Cycles in edge-coloured graphs and subgraphs of random graphs
Keywords: edge-colouring
random graphs
Ramsey theory

This thesis will study a variety of problems in graph theory. Initially, the focus will be on finding minimal degree conditions which guarantee the existence of various subgraphs. These subgraphs will all be formed of cycles, and this area of work will fall broadly into two main categories.
First to be considered are cycles in edge-coloured graphs and, in particular, two questions of Li, Nikiforov and Schelp. It will be shown that a 2-edge-coloured graph with minimal degree at least 3n/4 either is isomorphic to the complete 4-partite graph with classes of order n/4, or contains monochromatic cycles of all lengths between 4 and n/2 (rounded up). This answers a conjecture of Li, Nikiforov and Schelp. Attention will then turn to the length of the longest monochromatic cycle in a 2-edge-coloured graph with minimal degree at least cn. In particular, a lower bound for this quantity will be proved which is asymptotically best possible.
The next chapter of the thesis then shows that a hamiltonian graph with minimal degree at least (5-sqrt7)n/6 contains a 2-factor with two components.
The thesis then concludes with a chapter about X_H, which is the number of copies of a graph H in the random graph G(n,p). In particular, it will be shown that, for a connected graph H, the value of X_H modulo k is approximately uniformly distributed, provided that k is not too large a function of n.
Searches with the ATLAS detector for new coloured particles in the Jets + Missing Energy channel in early LHC data
Keywords: Supersymmetry
LHC
SUSY
ATLAS
Physics
Particle Physics

The switching on of the Large Hadron Collider (LHC) in March 2010 and its successful operation thereafter has opened doors in the search for new physics beyond the Standard Model. Supersymmetry (SUSY) is one of the leading theories that extends the Standard Model of particle physics. A search for new SUSY particles is presented requiring large numbers of hadronic jets and missing transverse momentum. Novel background estimation techniques were developed specifically for this final state, allowing the control of the backgrounds where the missing transverse momentum is dominated by jet miss-measurement. Other backgrounds are estimated from Monte-Carlo simulations validated and normalised in dedicated control regions. No significant excess was observed in the search. Model independent upper limits on the number of signal events passing the selection are given and the results are also interpreted in two planes of the parameter space. This is the most recent and sensitive incarnation of several searches developed by the author in this channel.
Efficient approaches to simulating individual-based cell population models
Keywords: scientific computing
individual-based
agent-based
cell population
parallel

Computational modelling of populations of cells has been applied to further understanding in a range of biological fields, from cell sorting to tumour development. The ability to analyse the emergent population-level effects of variation at the cellular and subcellular level makes it a powerful approach. As more detailed models have been proposed, the demand for computational power has increased. While developments in microchip technology continue to increase the power of individual compute units available to the research community, the use of parallel computing offers an immediate increase in available computing power.
To make full use of parallel computing technology it is necessary to develop specialised algorithms. To that end, this thesis is concerned with the development, implementation and application of a novel parallel algorithm for the simulation of an off-lattice individual-based model of a population of cells.
We first use the Message Passing Interface to develop a parallel algorithm for the overlapping spheres model which we implement in the Chaste software library. We draw on approaches for parallelising molecular dynamics simulations to develop a spatial decomposition approach to dividing data between processors. By using functions designed for saving and loading the state of simulations, our implementation allows for the parallel simulation of all subcellular models implemented in Chaste, as well as cell-cell interactions that depend on any of the cell state variables. Our implementation allows for faithful replication of model cells that migrate between processors during a simulation. We validate our parallel implementation by comparing results with the extensively tested serial implementation in Chaste.
While the use of the Message Passing Interface means that our algorithm may be used on shared- and distributed-memory systems, we find that parallel performance is limited due to high communication costs. To address this we apply a series of optimisations that improve the scaling of our algorithm both in terms of compute time and memory consumption for given benchmark problems.
To demonstrate an example application of our work to a biological problem, we extend our algorithm to enable parallel simulation of the Subcellular Element Model (S.A. Sandersius and T.J. Newman. Phys. Biol., 5:015002, 2008). By considering subcellular biomechanical heterogeneity we study the impact of a stiffer nuclear region within cells on the initiation of buckling of a compressed epithelial layer. The optimised parallel algorithm decreases computation time for a single simulation in this study by an order of magnitude, reducing computation time from over a week to a single day.
Definable henselian valuations and absolute Galois groups
Keywords: Valuations
Definability
Henselian
Model Theory of Fields
Absolute Galois Theory

This thesis investigates the connections between henselian valuations and absolute Galois groups. There are fundamental links between these: On one hand, the absolute Galois group of a field often encodes information about (henselian) valuations on that field. On the other, in many cases a henselian valuation imposes a certain structure on an absolute Galois group which makes it easier to study.
We are particularly interested in the question of when a field admits a non-trivial parameter-free definable henselian valuation. By a result of Prestel and Ziegler, this does not hold for every henselian valued field. However, improving a result by Koenigsmann, we show that there is a non-trivial parameter-free definable valuation on every henselian valued field. This allows us to give a range of conditions under which a henselian field does indeed admit a non-trivial parameter-free definable henselian valuation. Most of these conditions are in fact of a Galois-theoretic nature. Since the existence of a parameter-free definable henselian valuation on a field ensures that henselianity is elementary in calLring
, we also study henselianity as an calLring
-property.
Throughout the thesis, we discuss a number of applications of our results. These include fields elementarily characterized by their absolute Galois group, model complete henselian fields and henselian NIP fields of positive characteristic, as well as PAC and hilbertian fields.
Kant, constructivism, and 'Kantian Constructivism'
Keywords: Kant
Kantian constructivism
constructivism
meta-ethics

In recent years a ‘constructivist’ interpretation of Kant’s views on the foundations of morality has become very popular. This thesis argues that Kant did not hold a constructivist view, and that constructivism is not in a broader sense ‘Kantian’ nor a sympathetic revision of Kant’s views. I begin by clarifying what makes a moral theory distinctively ‘constructivist’. Then I argue that the textual evidence does not support a constructivist reading of Kant, and explain some of the passages which suggest constructivism. Finally, I offer a critique of constructivism as a substantive meta-ethical view.
Using uranium- and thorium-series isotopes as tracers for trace-metal inputs to the oceans
Keywords: uranium
geochemistry
thorium
iron
dust
ocean mixing
radium
isotope
nutrient

This thesis explores the use of U-Th series isotopes as tracers to study ocean mixing and chemical inputs to the open ocean from atmospheric dust, rivers, continental shelves and ocean sediments.
The use of Th isotopes as an improved tracer of dust input has been tested by measuring 232Th and 230Th concentrations of upper-ocean seawater at six stations along a meridional Atlantic section that spans the Saharan dust plume. The results of 232Th-derived dust fluxes show good agreements with dust model depositions, and suggest that thorium may be a more accurate tracer of dust input than Aluminium, which is frequently used for this purpose.
A new technique has been developed for the precise measurement of 228Ra/226Ra ratios and 228Ra and 226Ra concentrations in seawater by multi-collector ICP mass spectrometry (MC-ICP-MS). This methods offers improved analytical precision and detection limits relative to previous decay-counting approaches, though is more labour intensive. The accuracy of this method has been proved in the GEOTRACES Ra intercalibration, and shows consistent results with decay counting measurements from other labs. This technique has been applied to water samples in Loch Etive, a Scottish fjord, and in the Cape Basin during the UK-GEOTRACES cruise (GA10E) to investigate ocean mixing and trace-metal fluxes in the oceans.
In Loch Etive, Ra data provide an estimation of sedimentary 228Ra flux of 5.5 ± 0.3 (× 109 atoms m-2 yr-1) in the inner loch deep basin. Short-lived Ra isotope (223Raex) has also been used to estimate surface water transport rate, which is ~ 2.4 ±0.2 cm s-1 from the mouth to the head of the loch. In the Cape Basin, seawater 228Ra and 226Ra activities have been used to estimate vertical and horizontal mixing in the surface ocean. The horizontal mixing (Kx) from the continental shelf to the open ocean is 3.8 ± 0.8 (× 107 cm² s-1) and the vertical mixing (Kz) in the upper 400 m layer is 0.9 – 2.1 cm² s-1. These mixing rates enable the calculation of nutrient flux in the surface ocean. The calculated vertical nitrate fluxes in the Cape Basin are 0.4 – 0.5 mmol N m-2 d-1. This finding shed light on the nutrient inputs to the South Atlantic Subtropical Gyre.
Teachers' understanding of the purposes of group work and their relationship with practice
Keywords: teacher agency
cultural-historical theory
pedagogy
group work

Group work is commonly recommended as a student-centred instructional strategy which may enhance learning. Research in this area has predominantly used controlled interventions focusing on unproductive teacher assistance or specific strategies of doing group work to be applied by teachers. On the other hand, teachers’ own understanding and uses of group work in classrooms have been under-researched. Drawing on cultural-historical theory, this study scrutinises how and why teachers use group work, and how their enacted understanding is related to the broader contexts of teaching.
The present study consists of four teachers of English in two secondary schools in Hong Kong to discern their rationales for and implementation of group work. The analysis delves into the dynamics within the activity of teaching, which comprise the interrelations between teachers' biographies, their purposes for group work in classrooms and what was expected from these teachers within the school practices.
The Vygotskian perspective taken by this study entailed an inquiry into the teachers' intentional actions in everyday teaching. Each teacher was interviewed at the outset and end of the school-based fieldwork for their learning backgrounds and beliefs about teaching. In between these interviews each of them was observed in 15 lessons involving group work and undertook five to six stimulated recall (SR) interviews. These lesson video-recordings provided the stimuli for the SR interviews for probing the teacher’s pedagogic decisions while orchestrating students in small groups.
The data was analysed by deploying concepts from cultural-historical theory, particularly two organising frameworks developed within the approach. One is a pedagogic sequence proposed by Edwards (1995; in press) as a descriptor to categorise the teachers’ purposes for and actions in group work. The other is an adaptation of Hedegaard's (2012) planes of analysis for identifying the various motives and demands in the multi-layered setting of teaching where group work was located.
Group work as a pedagogic tool displayed the intra- and interpersonal dynamics in the activity of teaching. The findings indicate that the teachers' historically-constructed identities as learners of English oriented their intentions for group work and beliefs about teaching the subject. How the schools mediated societal expectations on teaching and learning had a considerable bearing on the teachers enacting their understanding. These institutional objectives and demands in practices created sets of opportunities for group work in the classrooms. The analysis thence was sited at the interface between the teachers' personal pedagogies and the multi-faceted social structure reflected in how education policy was mediated differently in different school contexts. The implications for teacher development are discussed.
Automated image-based recognition and targeted laser transfection techniques for drug development and stem cell research
Keywords: image recognition
transfection
laser
histone demethylase inhibitor
optoporation
automation
JMJD3
stem cell colony

Advances in several areas of scientific research is currently hampered by the slow progress in developing a non-viral, high precision technique capable of safely and efficiently injecting targeted single cells with impermeable molecules. To date, one of the most promising techniques employs the laser to temporarily create a pore in the cell membrane to allow the entry of exogenous molecules. This technique has potentially wide applications.
In this thesis, I utilised the precision of laser transfection, also known as optoporation, to deliver two histone demethylase inhibitors (8-hydroxyquinoline and FMF1293) of the JmjC-domain protein JMJD3 into vital cells. The enzyme, JMJD3, demethylates histone H3 lysine K27, the methylation state of which has been shown in previous studies to regulate genes in such a way as to play a key role in the formation of tumours and even maintenance of stem cell pluripotency. The research here shows proof of principle that optoporation can be employed to quickly screen and test the efficacy of novel drugs by delivering them into cells at significantly low concentrations while still maintaining inhibition activity. I also used optoporation to deliver relatively large proteins such as bovine serum albumin (BSA), phalloidin and novel synthetic antibodies into living cells without fixatives. This offers the possibility of using reporter systems to monitor living cells over time. Finally, an attempt was made to generate iPS colonies by optoporating plasmid DNA into somatic cells, however, I find that this technique was unable to efficiently transfect and reprogram primary cells.
Two automated image-based systems that can be integrated into existing microscopes are presented here. First, an image processing algorithm that can quickly identify stem cell colonies non-invasively was implemented. When tested, the algorithm’s resulting specificity was excellent (95 – 98.5%). Second, because optoporation is a manual and time consuming procedure, an algorithm to automate optoporation by using image processing to locate the position of cells was developed. To my knowledge, this is the first publication of a system which automates optoporation of human fibroblasts in this way.
Robust quantum phenomena for quantum information processing
Keywords: surface codes
spin amplification
single photon source

This thesis is concerned with finding technologically useful quantum phenomena that are robust against real world imperfections. We examine three different areas covering techniques for spin measurement, photon preparation and error correction.
The first research chapter presents a robust spin-measurement procedure, using an amplification approach: the state of the spin is propagated over a two-dimensional array to a point where it can be measured using standard macroscopic state mea- surement techniques. Even in the presence of decoherence, our two-dimensional scheme allows a linear growth in the total spin polarisation - an important increase over the √t obtainable in one-dimension. The work is an example of how simple propagation rules can lead to predictable macroscopic behaviour and the techniques should be applicable in other state propagation schemes.
The next chapter is concerned with strategies for obtaining a robust and reliable single photon source. Using a microscopic model of electron-phonon interactions and a quantum master equation, we examine phonon-induced decoherence and assess its impact on the rate of production, and indistinguishability, of single photons emitted from an optically driven quantum dot system. We find that, above a certain threshold of desired indistinguishability, it is possible to mitigate the deleterious effects of phonons by exploiting a three-level Raman process for photon production. We introduce a master equation technique for quantum jump situations that should have wide application in other situations.
The final chapter focusses on toric error correcting codes. Toric codes form part of the class of surface codes that have attracted a lot of attention due to their ability to tolerate a high level of errors, using only local operations. We investigate the power of small scale toric codes and determine the minimum size of code necessary for a first experimental demonstration of toric coding power.
Digital holographic microscopy for three-dimensional studies of bacteria
Keywords: three-dimensional microscopy
3D imaging
microscopy
micro-organism motility
digital holographic microscopy
optics
holography
bacterial motility

Holography has the ability to render three-dimensional information of a recorded scene by capturing both the amplitude and phase of light incident on the recording medium. The application of digital camera technology and high-speed computing means digital holograms can be analysed numerically and novel applications can be found for this technology. This thesis explores the potential for both inline and off-axis digital holographic microscopy to study the three-dimensional swimming behaviour of bacteria.
A high-magnification (225x) digital holographic microscope was designed and constructed with the ability to switch easily between inline and off-axis imaging modalities. Hardware aspects, in particular the illumination source, the choice of camera and data transfer rates, were considered. Novel strategies for off-axis holography combining dark field microscopy were designed and implemented.
The localisation accuracy of the inline imaging modality was assessed by studying samples of polystyrene microspheres. The microscope is sensitive to stage drift on the order of angstroms per second and can successfully localise microspheres in dilute suspensions at least 100μm from the objective specimen plane. As a simple test of the capabilities of the microscope, the diffusion coefficient of a 0.5μm microsphere was found to be isotropic and consistent with the theoretical value.
Amplitude and phase image reconstructions from the off-axis modality are demonstrated. High-magnification dark field off-axis holographic microscopy is shown to be superior to inline microscopy in localising 100nm gold nanoparticles. An artifact from our method of dark-field imaging, however, restricts the depth range to 15μm.
A lower-magnification (45x) configuration of the microscope was used to study the 3D swimming behaviour of wild type Escherichia coli as a qualitative demonstration of the potential for this instrument in microbiological applications.
An analytical and experimental study of large strain soil consolidation
Keywords: large strain
consolidation
soil

This thesis is concerned with large strain soil consolidation and a large portion of the work is devoted to the theoretical development in modelling this phenomenon. An experimental programme based on a specially designed oedometer is also included. The governing equations are formulated in Chapter 2, where both the material and the space coordinates are considered. In space coordinate the problem is a moving boundary problem, and special numerical techniques for the idealized case of a thin soil layer are developed in Chapter 3. In Chapter 4 the consolidation of a normally consolidated stratum and a dredged fill are considered with a linear soil model, and the consolidation of a deposit undergoing continuous sedimentation is considered in Chapter 5. The material coordinate is used in the analysis which also includes the effect of self weight of soil. These problems are again considered in Chapter 6 and Chapter 7 with a nonlinear soil model. A specially designed oedometer for testing very soft soil is described in Chapter 8, and the experimental results are discussed in Chapter 9. These are compared with the theoretical solutions developed in Chapter 3, and good agreement has been obtained.