VictorJuiz/thesis huggingface dataset:
Reconstruction of cardiac magnetic resonance images using short and long axis slices

Cardiac Magnetic Resonance Imaging (MRI) provides high resolution images of the heart, facilitating its functional and anatomical analysis, and is often regarded as the gold standard for diagnosis. Slow imaging times as well as patient and heart motion constraints are making it impractical to image volumes at isotropic high resolution in cardiac MRI. As a result, multi-slice studies, composed of highly anisotropic slices acquired at different orientations, are usually acquired. Most clinical imaging protocols consist in a stack of short axis slices and a few (typically two or three) long axis slices orthogonal to the short axis stack. Post processing methods may be used to reconstruct an isotropic volume. Most of the methods presented in the literature, however, use imaging protocols which are not commonly followed in clinical practice.
In this thesis, we developed three reconstruction methods for cardiac MRI reconstructions using long and short axis images as acquired in clinical practice. First, we showcase our work on a method which does not rely on machine learning or the use of a large database. Our method handles short and long axis data in a contrast independent manner, and is based on regularised least squares and the novel three dimensional directional total variation. We validated the algorithm using pre-clinical data, and showed improvements in reconstructions of in vivo data. We also explored hypothetical protocols for reconstructions, while keeping the number of slices constant. The best results came from balancing short and long axis slices.
We subsequently shifted the research focus to deep learning, allowing a comparison of different methodologies. We used a large publicly available dataset of clinical acquisitions and separated methods into static and dynamic approaches. For the static approach, we present several architectures and show that our networks are able to recover high resolution long axis slices from synthetic data, as well as interpolated short axis stacks. We show that using a conditional Generative Adversarial Network gives the best qualitative and quantitative results, while other models show improved results that are overly smooth. For the dynamic data, we use Long Short-Term Memory. Including temporal context from adjacent frames present in cine data results in enhancement of results compared to the static method. For both methods, we see qualitative as well as quantitative improvements in peak signal-to-noise ratio and structural similarity over interpolations. Our methods could impact cardiac MRI acquisition and analysis in two ways. In the short term, they could be used to reconstruct missing or additional slices in current acquisitions. In the medium term, they could be used in combination with a fast, optimised acquisition protocol from which slices in any orientation could be obtained at post-processing.

Advisor: Grau, V
Why are statements unable to receive contraries over time?

In Categories chapter 5 [4a10-4b19], Aristotle sets out to defend the claim that primary substances are the only individual existents which admit of receiving contrary attributes over time. To perform this task, he considers whether a statement may also admit of receiving contraries. It is the contention of this study that Aristotle disqualifies simple present-tensed statements from admitting of receiving contraries in their own right, by only allowing for the same statement to admit of receiving contrary attributes over time in an incidental sense. Aristotle’s chosen strategy for defending this stance consists in a progressive refinement of the realist account of truth-making which he lays out in Cat.12. This leads up to his endorsement of a deflationary version of this account, which accommodates temporalist assumptions. Upon the interpretation of this deflationary account of truth-making which is here proposed, a statement which admits of being true and false at different times may not enjoy the attribute true or its contrary, false, in itself, but only in relation to an actual entity other than itself and, thus, incidentally. As a result, a statement may only incidentally come and cease to be true and false over time. Since a statement cannot change from being-true to being-false (or vice-versa) in a genuine sense, but an individual existent only admits of receiving contraries by being able to change, a statement may not receive contrary attributes over time in a genuine sense. Thus, a statement which admits of being true and false at different times is not, strictly speaking, able to receive contraries.

Keywords: Contraries
Substance
Categories
Statements
Aristotle
Time
Advisor: Peramatzis, M
Unsymmetrical group 4 permethylindenyl ansa-metallocenes as polymerisation catalysts

The primary aims of the thesis were to: (i) discover catalyst systems that maintained high α-olefin polymerisation activities in the presence of hydrogen while producing polymers with low molecular weights (Mw <10 kg mol−1) and (ii) find new single-site initiators for the ring-opening polymerisation (ROP) of lactide monomers.
The thesis begins by offering a brief introduction to α-olefin and lactide polymerisation, including discussions on known polymerisation catalysts. The synthesis and characterisation of a series of well-defined group 4 ansa-bridged permethylindenyl complexes based on the Me2SB(CpR,I*)ZrX(Y) ({(η5-C9Me6)Me2Si(η5-C5H3R)}ZrX(Y) where R = H, Me and nBu) motif is then discussed. The application of these complexes as α-olefin polymerisation catalysts, both in solution-phase and when immobilised on a range of inorganic solid supports (MAO modified silica, MAO modified layered double hydroxide and solid MAO) is then detailed. It was found that solid MAO supported catalytic systems exhibited some of the highest slurry-phase polymerisation activities reported in the literature. The systems produced HDPE with minimal branching, uniform polymer morphology and low polymer molecular weights (Mw <100 kg mol–1 at 80 °C). A variety of polymerisation conditions were studied, including the effects of temperature, scale, pressure, scavenger, catalyst loading and time.
The slurry-phase ethylene/1-hexene copolymerisation ability of the catalysts is then demonstrated. The effects of hydrogen on ethylene polymerisation activity and polymer properties are also discussed. The overall effect of 1-hexene was found to depend on the identity of the catalyst and the amount of co-monomer in the system. All catalysts demonstrated remarkable stability in the presence of hydrogen, which was accompanied by a significant decrease in polymer molecular weights to produce commercially viable polyethylene waxes.
Finally, four unsymmetrical permethylindenyl zirconocenes are presented as initiators for the ROP of L-, D- and rac-lactide. The kinetics of polymerisation, overall rate equations and the effects of temperature, initiator concentration, scale and co-initiator concentration are discussed. A variety of techniques were used to characterise the polymers in order to deduce tacticity, molecular weights and chain end groups.

Keywords: Metallocene
Lactide
Catalysis
Ethylene
Polymerisation
Advisor: O'Hare, D
Nano-electronic devices using two-dimensional and phase change materials

This thesis describes nanoscale devices utilizing phase change and two-dimensional materials. The fundamentals, modeling, chip design, nano-fabrication process, measurement setups and experimental results of such devices are discussed.
In the first example, a graphene-nano-gap phase change memory device concept is proposed, in which a phase change material bridges graphene electrodes that are spaced sub-1 nm apart. These devices are fabricated using a lithography-free self-alignment technique. The manufacture and metrology of such devices are studied, with a demonstration of a Kelvin Probe Microscopy based approach for in-situ imaging. Such devices enable ultra-scaled memory cells for energy efficient operation. Scaling limit of such devices are studied and an intrinsic gap length is found below which carbon filamentation overwhelms resistive switching in the phase change material.
The second example features the study of electronic properties of two-dimensional materials under external perturbation, such as strain. A new approach based on Kelvin Probe Microscopy is demonstrated to overcome the limitations (materials, resolution and substrate effects) of commonly used optical spectroscopy tools, and reveals strain-driven changes in the work functions, including junction potentials in ultrathin heterostructures. A device concept termed strain-effect transistor is proposed wherein two-dimensional materials can be strained cyclically by the reversible amorphous-crystalline phase transition in the underlying phase change material. Crucially, a chalcogenide glass with high volume changes is explored for this application. The volume changes in the material are observed to complement changes in optical properties and are further exploited for a demonstration of solid-state reflective displays and tunable photonic resonators.
The third example reveals the light-matter interaction in low dimensional phase change materials using graphene nano-gaps and crossbar nanoscale devices. Contrary to the existing understanding of these interactions, the complex interplay of three independent mechanisms, viz. photoconductive, photo induced-crystallization and photo-induced-thermoelectric effects, are observed to govern the photoresponse of the material. Significant photovoltaic effects are observed in such devices, which might lead to phase change devices for photonic applications being potentially self-powered. The photodetection bandwidth and photo-responsivity are observed to be tunable based on the state of the phase change material, enabling the development of tunable photodetectors. Finally, the concept of a spiking photodetector is introduced that utilizes the strong-light matter coupling in chalcogenide glasses. Such devices could be used in the development of artificial retinas.

Advisor: Bhaskaran, H
Mol, J
Mentality as nonderivative intentionality

I here advance the following deductively valid argument:
P1. For all x, if x is mental, x is intentional.
P2. For all x, if x is mental and intentional, x is nonderivatively intentional.
P3. For all x, if x is nonderivatively intentional, x is mental.
––––––
C. For all x, x is mental if and only if x is nonderivatively intentional.
I thus maintain that all and only mental phenomena are nonderivatively intentional – that nonderivative intentionality is ‘the mark of the mental’. The simplest explanation for this fact is that mentality consists in nonderivative intentionality.

Keywords: Mental
Phenomenal
Tim Crane
Intentionality
Mentality
Intentionalism
Nonderivative
Intentional
Mental representation
Qualia
Advisor: Schear, J
The dynamical foundations of physical geometry

This thesis is in two related parts. The first part presents arguments against the claim that the metric of general relativity is invariably spatiotemporal. This is done by discussing plausible criteria for spatiotemporality and demonstrat- ing violations of those criteria. This leads to a question about the so-called chronometric significance of the metric, a central component of Brown and Pooley’s dynamical approach to spacetime theories. The dynamical approach is scrutinised and, in the second part of the thesis, expressed, in opposition to the geometrical approach in a mathemtically novel way. This re-formulation of the position is then used to counter an ostensibly robust argument against the dynamical approach. This thesis is composed of five chapters.

Advisor: Wallace, D
Saunders, S
Caulton, A
Development of MKID Instrumentation for exoplanet direct imaging

Microwave Kinetic Inductance Detectors (MKIDs) are a highly sensitive cryogenic photodetector. These devices operate by measuring the increase in the surface impedance of a superconducting film when Cooper Pairs are broken by incident photons. This technique allows MKIDs inherent spectral resolution and instantaneous read out with essentially no false counts. In contrast to other cryogenic detectors, the intrinsic multiplexing of the pixels in frequency domain means that arrays of several tens of thousand of pixels can be readout with just a few feed-lines using room temperature radio electronics. These unique properties make MKIDs potentially transformative for exoplanet direct imaging, where residual speckle noise currently limits the minimum mass of the discernible exoplanets to several Jupiter masses. In this thesis I describe some of the developments of MKID instruments required for exoplanet imaging, and I investigate the potential of MKIDs to provide new discoveries in this field.
One of the required developments was the automation of the tuning of pixel biasing prior to taking a set of observations. Previously this required inspecting the transmission profile of each pixel by eye and then selecting the optimal power. For the large format arrays necessary for exoplanet direct imaging (on the order of tens of thousand pixels) this process can take approximately 24 human hours to complete. I show that a machine learning-based algorithm can replicate this process in a matter of minutes with equivalent accuracy to that of humans when compared to a control dataset. I then discuss an extension to this algorithm that should enhance the phase measurement performance of MKIDs, ultimately improving the limiting mass of detected exoplanets.
Simulation software was developed to make pragmatic predictions on the capabilities of MKIDs for exoplanet direct imaging. This software demonstrates the utility of Dark-Speckle Imaging discrimination technique for a realistic MKID device with appropriate limitations such as maximum count and reduced pixel yield. Possible extensions to this technique that exploit the wavelength dependence of speckles are also explored, which are found to yield superior performance to standard differential imaging methods. I also make predictions on the performance of a next generation MKID-based instrument systems. Preliminary results show that this system can achieve the contrast performance necessary for Neptune sized exoplanets and below.
Finally, I present on-sky results of planetary nebula NGC 6751 taken with the ARCONS MKID instrument at Palomar. The inherent spectral resolution of the device meant that a low resolution spectrum of the central star could be created that provided further evidence to clarify its spectral type. The central star was also explored in the time domain at the fine resolution of MKIDs. No periodic feature was found on the time scale of the observation.

Keywords: Exoplanets
Instrumentation
Advisor: Thatte, N
O'Brien, K
Moving Muslims: the great northwestern rebellion and the transformation of Chinese Islam, 1860-1896

This thesis explores the history of an empire’s attempt to remake its Muslim subjects. The reconstruction process that followed the Great Northwestern Muslim Rebellion (1860-1874) was a highly ambitious project of social engineering that strove not to resurrect the antebellum order, but to transform the entire northwest. Governor-General Zuo Zongtang proposed the resettlement of thousands of Chinese Muslims (Hui) away from their Han Chinese neighbours, on the grounds that separating the two groups was the only way to ensure that violence would not reoccur.
Based on extensive archival research using a local Qing county archive combined with gazetteers, Muslim histories, interviews and stele from local areas, this thesis opens with a revisionist history of the role Sufi paths played in the 18th century extension of Qing empire into Gansu’s Sino-Tibetan fringes. Whilst the Sufi paths were politically dominant in He-Huang prior to the Great Northwestern Rebellion, the reconstruction period fundamentally changed the structures of everyday life and governance. The new clusters of Muslim settlement and rise of generation of military elites in the postbellum period produced the conditions for a religious revival which ultimately ended the political role of Sufi lineages in borderland life and created the conditions for the arrival of currents of Islamic reformism in China. This outcome is the product of the complex interplay of a new nationalism with older Qing ideas of empire and ethnicity, and of the local, half-implemented reconstruction project that remade the Gansu-Qinghai social world in unanticipated ways. The legacy of the resettlements, however, lives on in the process of minoritization it catalysed: Muslims in China today are considered an entirely separate ethnicity from the Han. Overall, this thesis describes two parallel arcs: the rise and fall of China’s Sufi paths and the rise of the Muslim nationalist military lineages, who would become the Republican-era ‘Muslim warlords’.

Keywords: Qing
Sufism
Zuo Zongtang
Islam in China
Linxia
Empire
Hui
Great Northwestern Muslim Rebellion
Advisor: Harrison, H
Erie, M
Structural studies of the human GABAB receptor using cryo-electron microscopy

The metabotropic gamma-aminobutyric acid type-B receptor (GABABR) mediates slow and prolonged inhibitory neurotransmission in the mammalian nervous system. GABABR belongs to the Class C GPCR family and is the first GPCR reported to function as an obligate heterodimer. Structurally, GABABR displays distinctive features for its lack of the cysteine-rich domain found conserved among other Class C receptors. GABABR’s extracellular Venus flytrap (VFT) domain is directly connected to the transmembrane domain (TMD), followed by a small cytoplasmic domain. To date, structures of an isolated extracellular VFT domain and an intracellular coiled-coil domain have been solved using X-ray crystallography. No structure of the transmembrane domain (TMD) or the full-length receptor has been reported.
This project focused on the recombinant production and structural analysis of the full-length human GABABR using single-particle cryo-Electron Microcopy (cryo-EM). It was determined that the HEK293 GnTI- cells were a suitable host cell system for production of the integral human GABABR. Following extensive optimisation of constructs and expression conditions, stable cell lines were generated which yielded sufficient material for structural work. GABABR was isolated from the membranes using a combination of detergents that maintained the receptor’s ligand binding activity. The high purity heterodimeric GABABR samples obtained were used to screen various reconstitution systems compatible with cryo-EM, including amphipols, salipro particles and MSP nanodiscs. The MSP2N2 lipid nanodisc was found to be optimal for reconstituting GABABR, yielding intact receptor capable of binding to G protein. Thus far, medium resolution ( 10 ~ 15Å) models have been reconstructed for the full-length GABABR. These models provided new insights regarding GABABR domain organisations and receptor dynamics. In addition, a ~4Å reconstruction was obtained for the extracellular VFT domain alone and showed density for regions missing in the published crystal structures. The work presented in this thesis provides the foundation for solving higher-resolution GABABR structures and for their detailed mechanistic investigation.

Advisor: Aricescu, R
Huiskonen, J
Repositioning the gender gap in UK biology and physics: behind the numbers

Whilst there is an internationally acknowledged chronic gender gap in science, most of the literature offering evidence for and explanations why gender inequality endures focusses on why women choose not to participate in science fields, or why female academics leave academic science. This mixed-methods study investigated the pathways navigated by some of the most successful and elite female biologists and physicists in the UK, in order to uncover best practices and common experiences. The main original contribution to knowledge of this thesis is an empirically based analysis of how women in these fields have negotiated their gendered identities in order to ‘fit in’ and progress to an elite status, which had not been investigated previously.
Secondary statistical analysis of university data were investigated for frequencies, proportions, and trends of female participation in biology and physics over the last 40 years. British female biologists and physicists meeting the study parameters of ‘elite’ were recruited to participate in semi-structured guided life-history interviews: 10 biologists and 6 physicists participated. Theoretical tools from gender performativity theory formed the overarching framework for the analysis, enhanced and reinforced by perspectives from sociological research, third wave feminist theory, and postcolonialism.
Statistical analysis showed that female participation in biology has increased, making females the majority of biology undergraduates. At the academic level, however, attrition is equivalent in both fields, suggesting that retention needs improvement. Analysis of the interview data revealed key coping mechanisms and experiences that have been crucial in helping respondents to choose to participate in biology or physics and to persist to their current elite status. Comparing findings for the biologists with those for the physicists, there were similarities and differences: similarities were found in mindsets towards embracing challenges, and in choosing subfields, but the ways in which the biologists constructed their gendered identities were different to the physicists. These identity constructs provide insight into how women can achieve success in these fields, but also reveal the inherent and ongoing challenges women face in each field. The implications of these findings impact educationalists and policy makers at every level of education and academia, and carefully implemented programmes based on the findings would increase both recruitment and retention for UK women in biology and physics.

Advisor: Hillier, J
Childs, A
Essays on the emotions

In these essays, I hope to shed light on a range of basic philosophical issues concerning the emotions. To this end, I engage with many of the central ideas and questions found in philosophy of emotion over recent decades; Including, notably, the perceptual model of emotion, cognitivist theories of emotion, and questions concerning their intentional nature and epistemic role. This thesis is comprised of an introductory chapter which details the theoretical architecture that unifies this body of work, followed by four closely related essays within the philosophy of the emotions—each relating in some way to their intentional structure and epistemic significance. Among the salient influences are Timothy Williamson’s recent work in epistemology and Paul Grice’s work on the nature of reasons.

Advisor: Magidor, O