VictorJuiz/thesis huggingface dataset:
High capacity materials for next generation Li-ion batteries

With the staggering growth in the recent years of the Lithium Ion Batteries market and the large number of different applications, in which these devices are currently employed, a change of paradigm in terms of the active materials composing the electrodes in these batteries is required. To meet the market needs in terms of performance (energy density and power), safety and respect of the environment, non-toxic light materials with high capacities are highly sought after.
The main goal of this work was to provide an insight into the mechanisms which limit the application of the Li-Rich based cathodes and hard carbon and silicon anodes. These high capacity materials would be ideal candidates to combine into a full cell for next generation batteries with enhanced energy densities.
The mechanisms underpinning the electrochemical behaviour of a family of cobalt-free lithium-rich layered oxide cathodes, with general formula Li(4/3-2/3x)NixMn(2/3-1/3x)O2 (0 ≤ x ≤ 0.3), has been unravelled. Initially, Li1.2Ni0.2Mn0.6O2 was synthesized via a one-pot synthetic route and studied to understand the origin of the high potential plateau appearing over the first charge. Thanks to a careful structural and electrochemical characterization and powerful spectroscopic techniques (XANES, SXAS, RIXS) the presence of reversible anionic redox activity has been demonstrated. Subsequently the focus of the work has moved on to unravelling the role of the nickel substitution in favouring the oxygen redox activity over the oxygen loss phenomenon for this family of materials.
In parallel, a study on the improvement of the cyclability and efficiency of high capacity silicon-based anodes has been carried out using new polymeric binders, some of which, have been shown to guarantee more stable cycling and higher capacities with respect to the established binder sodium carboxymethylcellulose (Na-CMC). Additionally, in the attempt to address the issue concerning the First cycle Irreversible Capacity (FIC) of the silicon anodes, a highly reducing pre-treatment has been performed on the electrodes. As well, the treatment has been tested on hard carbon anodes that, despite being promising materials for Lithium and also Sodium Ion Batteries, are usually plagued by large FIC. An important improvement in terms of coulombic efficiency at the beginning of cycling has been observed in all the tested materials without any sign of detrimental effects on the electrodes overall performance.

Advisor: Bruce, P
Learning to Extract Tumour Vasculature: Techniques in Machine Learning for Medical Image Analysis

Cancer is a leading cause of death worldwide with an estimated 14 million new cases occurring yearly and approximately 8 million deaths. Although much progress has been made in the understanding and treatment of cancer, there are still many mechanisms that remain poorly understood. The development of vasculature is known to be a key element in facilitating the growth of a tumour. Modern imaging modalities such as multi-photon fluorescence microscopy allow unprecedented opportunities to examine and quantify this vasculature in vivo. However, the appearance of vascular networks, imaged at these scales, can be extremely complex and the automatic delineation of such large, tortuous and chaotic vascular networks is a non-trivial task. In this thesis we develop a number of methods for the automatic delineation of tumour vasculature, imaged using in vivo microscopy. Recent developments in machine learning have provided a powerful set of techniques for the automated analysis of complex structures in images. Leveraging these, it is possible to develop algorithms, capable of learning from human annotations, which are able to analyse extremely large images quickly and with a high degree of accuracy. The key contributions of this thesis are as follows: we present a novel supervoxel algorithm for use in a lightweight machine learning framework for segmentation. We adapt the current state-of-the-art in segmentation using 2D deep fully convolutional neural networks for use in 3D vascular segmentation. We further demonstrate the use of hybrid convolutional-recurrent networks for extracting 3D vessel centrelines. We propose the use of Conditional Adversarial Networks for refining the extraction of vessel centrelines directly. Finally, we demonstrate the ability of the developed methods to make quantitative observations on longitudinal changes to in vivo tumour vasculature development.

Advisor: Schnabel, J
Kersemans, V
Grau, V
Essays on expectation formation

This thesis is composed of three independent papers that model patterns of heterogeneity in inflation expectations and price-setting.
In the first paper, I present stylized facts from the Survey of Professional Forecasters that suggest the inflation expectation formation process changes over the term of the forecast. I develop a model to capture these features: forecasters have (1) a cost for inacccuracy, for which they pay the penalty when the variable is realized and (2) a cost for inconsistency (changing a forecast from quarter to quarter), for which they pay the penalty when the adjustment is reported. Due to heterogeneous time discounting, the inconsistency cost is more highly but differentially weighted at long horizons, which induces the observed stylized facts.
In the second paper, I estimate a sector-level Rational Inattention (RI) price-setting model. I estimate the model separately on two regimes (pre-Volcker and Great Moderation) to investigate predictions from RI theory about price-setting reactions to a change in volatility. I find that the model is not capable of reproducing price level dynamics, and that the attention capacity has low predictive power across regimes. Given these caveats, there is some evidence that attention capacity increased across the sample.
In the third paper, I consider two kinds of uncertainty: the mean and the variance of the prior distribution of a stochastic variance. I build a model with strategic complementarity and provide comparative statics welfare results. Higher mean-uncertainty in the private signal always decreases welfare, and higher mean-uncertainty in the public signal sometimes decreases welfare. However, higher variance-uncertainty in the private signal always increases welfare, and higher variance-uncertainty in the public signal sometimes increases welfare. This finding contributes to the debate as to whether this class of model supports limited transparency among policy makers.

Advisor: Mavroeidis, S
Genetic and Phenotypic characterisation of a novel Efl1 mouse mutant of shwachman diamond syndrome

A novel mouse mutant was identified through an ENU (N-ethyl-N-nitrosourea) mutagenesis screen due to an abnormal gait. Next generation sequencing revealed the causative mutation to be in the gene Efl1 (K983R). The protein EFL1 is involved in ribosome maturation, a cellular process that is defective in diseases collectively known as ribosomopathies. More specifically, EFL1 is critical for the release of anti-association factor eIF6 from the 60S subunit, which allows subsequent joining with the 40S subunit to form a translationally active particle. ShwachmanDiamond syndrome (SDS) is a ribosomopathy in which this process is known to be defective.
SDS is an autosomal recessive disorder typified by bone marrow failure, pancreatic insufficiency and various anaemias. 90% of patients with SDS have missense mutations in the gene SBDS. The protein SBDS, together with EFL1, binds to the 60S subunit and causes the release of the anti-association factor eIF6. Both SBDS and EFL1 are needed for this process to occur correctly. In patients with SDS, eIF6 release is impaired due to a deficiency of functional SBDS, thus causing a ribosomal joining defect. Current research into SDS focuses on yeast models or conditional knockout/embryonic mouse models. However, this gives a limited view of the disorder as it does not reflect the multi-system nature or temporal aspects of SDS.
In depth phenotypic characterisation of the Efl1-K983R mouse-line has revealed many phenotypes that reflect human SDS symptoms, such as small size, various haematological abnormalities, reduced bone mass density, deafness secondary to otitis media and behavioural deviations. At the molecular level, impaired eIF6 release has been demonstrated in mouse embryonic fibroblasts and liver. Multiple tissues from mutant mice show severe EFL-1 deficiency, suggesting that these symptoms may be reflective of the SBDS deficiency seen in SDS patients. Approximately 10% of SDS patients do not have SBDS mutations, and these patients are referred to as having ‘genetically undefined’ SDS. The cause of patients symptoms in these cases are unclear, and no causative gene has been found.
Here we present data that suggests that Efl1 may be a candidate gene for ‘genetically undefined’ SDS. The data presented here also suggests that this mouse represents an opportunity to study SDS-like processes in a long lived, multi-system mammalian model, which is otherwise unavailable for Sbds mutants.

Advisor: Acevedo, A
Remotely detecting submarine volcanic activity at Monowai: insights from International Monitoring System hydroacoustic data

Monowai is an active submarine volcanic center in the Kermadec Arc, Southwest Pacific Ocean. We show, using cross-correlation and time-difference-of-arrival techniques, that low-frequency underwater sound waves from the volcano travel in the Sound Fixing and Ranging (SOFAR) channel and can be detected by bottom-moored hydrophone arrays of the International Monitoring System (IMS), a global sensor network maintained by the Comprehensive Nuclear-Test-Ban Treaty Organization. Hydroacoustic phases associated with the May 2011 eruption at Monowai are identified in the record of the IMS station at Ascension Island, Equatorial Atlantic Ocean. The source-receiver distance of ~15,800 km is the furthest documented range of any naturally occurring underwater signal ever observed. Our observations are consistent with results from transmission loss modeling, which suggest that acoustic propagation at southern latitudes is facilitated by the anomalous temperature regime of the Antarctic Circumpolar Current. Subsequently, we examine the 3.5-year record of the IMS hydrophone station near Juan Fernández Islands, Southeast Pacific Ocean, for volcanic activity at Monowai. Density-based clustering of arrivals during the time periods when data is available, i.e. from July 2003 to March 2004, and between April 2014 and January 2017, reveals 82 discrete episodes that are spaced days to weeks apart, typically ranging from a few hours to days in length. The resolution of the hydrophone data for seismic events at the volcano is estimated at 2.2 mb and exceeds regional broadband networks by one order of magnitude. Considering the results and techniques developed in the study of Monowai, we investigate the 2014 submarine eruption of Ahyi volcano in the Northern Mariana Islands. Acoustic phases of the 15-day episode are identified in the record of an IMS hydrophone array located at Wake Island in the northwestern Pacific Ocean. Explosive volcanic activity occurred in two bursts, accompanied by a decrease in low-frequency arrivals that is interpreted as a shift in signal source parameters. Acoustic energy released during the event is on the order of 9.7 1013 J.

Keywords: CTBTO
Submarine volcanism
Monowai
IMS
Advisor: Watts, AB
Of sounds, photons and maps: in vivo optical characterisation of the auditory thalamocortical system

As information ascends up the sensory streams, the maps of receptor surface might be faithfully relayed from one brain structure to another, degraded or lost altogether. Such transformations can inform about the type of circuit computation carried out in each region. In vivo high-resolution imaging methods, like two-photon microscopy, are useful for characterising the functional architecture of neuronal circuits down to the micro-scale. To better understand the rules governing thalamocortical connectivity and the origin of cortical maps, I used in vivo two-photon calcium imaging to characterise the properties of thalamic axons innervating different layers and subfields of mouse auditory cortex. Although topographically organised at a global level, I found the frequency selectivity of individual thalamocortical axons to be surprisingly heterogeneous, even in the middle layers (L3b/4) of the primary cortical areas where the thalamic input is dominated by the lemniscal projection. Subsequently, I employed a dual-colour imaging approach to explore the spectral transformations taking place between the thalamocortical projection and granular and supragranular layers of auditory cortex. Some differences in local spectral properties between neurons in L4 and L2/3 were observed in awake, passively listening mice, confirming previous observations on the anaesthetised preparation. Finally, I present a demonstration of a novel fibre-based high-resolution fluorescence imaging method to optically investigate neuronal circuits in deep brain regions, with minimal invasiveness. In short, my work provides some new insights on the functional micro-organisation of the auditory thalamocortical system and constitutes a classical example of the power of optical methods for the study of neuronal circuits in vivo.

Advisor: Dahmen, J
King, AJ
Emptage, N
The integration of Spanish and Portuguese organ music within the liturgy from the latter half of the sixteenth to the eighteenth century

Spanish and Portuguese organ music still remains a relatively unchartered area escaping the attention of most general assessments of European musical history. The work which has been done in this field has tended towards stylistic appreciations of the published large-scale compositions and the compilation of short biographies of prominent musicians. No extensive investigation has yet been undertaken which deals with such fundamental issues as the role of the organist and the origins and function of the extant organ repertory, of which a large proportion lies dormant in manuscripts, within the liturgy. Indeed, there is no monograph about organists and organ music in the Iberian peninsula as a whole.
The overall aim of this thesis is to provide a musical background and liturgical context for short organ pieces called versos which were thoroughly integrated within a musical celebration of the Offices. For this end, a variety of musical and documentary material has been examined: practical sources of organ music; plainchant manuals; ceremonials and musical treatises. To an enormous extent this organ music was subject to long-standing liturgical customs and legislation, as well as to strongly defined traditions of musical composition.
The prescriptions to the organist given in the ecclesiastical constitutions and how these may have been realized in the Canonical Hours and in the Mass constitutes the essence of part two of this thesis. This interpretation of musico-liturgical practices has entailed an examination of the relationship between plainchant and the organ verset and the technicalities of mode and tranposition which were involved when alternating the organ with choral plainchant. An analysis is also made of the musical development of versets based on the psalm-tones, organ hymns (the Pange lingua in particular) and the 'organ mass'. An anthology of transcriptions complementing this discussion is contained in a separate volume.
As a counterbalance to the analytical discussion in part two, part one provides an historical and cultural background to the subject. An assessment is made of the contribution made by individual organists and organ 'schools' and some consideration is made of the extent to which both royal and ecclesiastical patronage was responsible for the livelihood of music and the arts.

Keywords: sixteenth
liturgy
music
organ
Portuguese
18th
eighteenth
Spanish
seventeenth
16th
17th
Inflammasome regulation and activation in the intestinal epithelium

Microbiota colonisation of the intestinal tract makes it difficult for pattern recognition receptors (PRR) to discriminate between beneficial microbes and harmful pathogens. We aim to define the roles of cytosolic Nod-like receptors (NLR) in intestinal immunity and homeostasis. Upon activation, some NLR form inflammasomes that mediate the release of inflammatory cytokines and pyroptosis, an inflammatory form of cell death. NLR activation in the non-hematopoietic compartment was shown to be protective during acute intestinal infection. To identify the cell type responsible for this protection, we generated transgenic mice in which the key inflammasome adaptor molecule Asc is selectively ablated in intestinal epithelial cells (IEC) (AscΔVC) and observed that inflammasomes are important for controlling Citrobacter rodentium clearance in these mice. To further dissect the importance of pathogen clearance by IEC inflammasome, ex vivo cultures of primary IEC organoids were established. Thus far this system has revealed profound differences in inflammasome regulation between IEC organoids and bone marrow-derived macrophages (BMDM). This research will inform our understanding of cell type-specific regulation of inflammasomes.

Keywords: Citrobacter rodentium
Pattern recognition receptors
Organoids
Intestinal epithelium
Inflammasome
Pyroptosis
Advisor: Maloy, K
Micro- and macro-mechanical testing of grain boundary sliding in a Sn-Bi alloy

This project explores the fundamental mechanisms of grain boundary sliding (GBS) with an emphasis on its role in superplasticity, using both micro- and macro-mechanical testing methods. GBS plays an important role in the deformation of polycrystalline materials, especially at high homologous temperatures (above half of the melting point). Classical models for GBS (Rachinger sliding and Lifshitz sliding) assume that all grains and grain boundaries undergo the same process, but recent research has shown this is not true. Individual grain boundaries differ in their ability to participate in sliding and diffusion. Therefore, it is important to investigate the response of individual grain boundaries to stress. This project uses microcantilevers, loaded using a nanoindenter, to investigate the response to stress of individual grain boundaries in Sn-1%Bi, which is expected to exhibit GBS at room temperature. The response of individual grain boundaries are correlated with grain boundary characters determined using electron backscattered diffraction (EBSD). On the macroscopic scale, both in-situ and ex-situ shear tests are conducted to investigate the superplastic behaviour of this material. The strain rate sensitivity index of the material with a grain size of 8.5 μm is found to be around 0.45. Surface marker lines have quantitatively revealed grain boundary sliding. The investigation from surface studies is expanded to the interior of bulk material in 3D by conducting an in-situ tensile test coupled with diffraction contrast tomography (DCT) at a synchrotron facility.
The microcantilever tests enable grain boundary sliding and diffusion creep to be investigated separately by varying the normal and shear stresses on the grain boundary plane. GBS is dependent on grain boundary structure (misorientation angle, rotation axis and grain boundary plane orientation). The microcantilever size is similar to the grain size used in the macro-mechanical tests. It is demonstrated that the shear stress for steady-state GBS is comparable in micro- and macro-tests. Grain neighbour switching events have been identified in the interior of bulk material in 3D for the first time.

Keywords: Superplasticity
Grain boundary sliding
Micromechanics
Advisor: Wilkinson, A
Todd, R
Auditory cuing of visual attention: spatial and sound parameters

The experiments reported in this thesis investigate whether the current understanding of crossmodal spatial attention can be applied to rear space, and how sound parameters can modulate crossmodal spatial cuing effects. It is generally accepted that the presentation of a brief auditory cue can exogenously orient spatial attention to the cued region of space so that reaction times (RTs) to visual targets presented there are faster than those presented elsewhere. Unlike the conventional belief in such crossmodal spatial cuing effects, RTs to visual targets were equally facilitated from the presentation of an auditory cue in the front or in the rear, as long as the stimuli were presented ipsilaterally. Moreover, when an auditory cue and a visual target were presented from one of two lateral positions on each side in front, the spatial co-location of the two stimuli did not always lead to the fastest target RTs. Although contrasting with the traditional view on the importance of cue-target spatial co-location in exogenous crossmodal cuing effects, such findings are consistent with the evidence concerning multisensory integration in the superior colliculus (SC). Further investigation revealed that the presentation of an auditory cue with an exponential intensity change might be able to exogenously orient crossmodal spatial attention narrowly to the cued region of space. Taken together, the findings reported in this thesis suggest that not only the location but also sound parameters (e.g., intensity change) of auditory cues can modulate the crossmodal exogenous orienting of spatial attention.

Keywords: Looming sounds
Exogenous
Spatial cuing
Rear space
Attention
Crossmodal
Advisor: Spence, C
Uncertainty characterisation in action potential modelling for cardiac drug safety

Drugs can interact with cardiac cells to produce dangerous effects on the heart's natural rhythm. Pharmaceutical companies and regulators are interested in predicting these unintended side effects during the drug development and safety testing process. One clinical trial is the Thorough QT (TQT) study, where a drug is administered to healthy patients and particular changes in their cardiac electrical behaviour are monitored. Clinical trials such as the TQT study are expensive and time-consuming. Following a workshop in July, 2013 at the US Food and Drug Administration (FDA), the Comprehensive in-vitro Proarrhythmia Assay (CiPA) initiative was proposed to improve safety testing, led by a number of drug safety and regulatory bodies around the world. The CiPA initiative aims to replace the TQT study with a combination of in-vitro ion channel screening and mathematical mechanistic models of single-cell cardiac electrophysiology to predict a drug's proarrhythmic risk. Typically, mathematical models of ion channel screening and of single-cell electrophysiology are published with single best-fit parameter values. These point estimates do not account for any uncertainty in the models, which can come from many different sources. Therefore, predictions from these models will provide single point estimates. While such a prediction may suggest that the 'most likely' outcome given the available data is safe, it will not describe the other likely outcomes which may be dangerous. We adopt a Bayesian statistical framework to characterise some of the uncertainty in both ion channel screening data and in action potential model parameters. We then propagate this uncertainty into predictions of how a drug will affect a cardiac cell's electrical behaviour. We obtain a probability distribution describing possible effects of a particular concentration of a drug, instead of a point estimate. Such probability distributions contain more information than single point estimates: for example, the probability of crossing some dangerous threshold, which may be omitted from the point estimate if the most likely output is evaluated as safe. This process of uncertainty characterisation and propagation allows for more-informed decision-making when assessing a pharmaceutical compound's potential proarrhythmic risk.

Advisor: Mirams, G
Gavaghan, D
Bardenet, R
Polonchuk, L
Davies, M