VictorJuiz/thesis huggingface dataset:
The effects of interlocutor backchannels and L1 backchannel norms on the speech of L2 English learners

Verbal backchannels – short responses such as 'uh-huh' and 'mhm' given by an interlocutor to the main speaker – have been studied extensively for several decades. The great majority of the research has been descriptive or based on backchannel uses. In contrast, little has been reported of their effects on spoken interaction and almost no research has examined their effects on second language (L2) speech. Given that first language (L1) backchannel norms vary, L2 speakers unaccustomed to different norms could be affected when exposed to such variation. This thesis investigated such effects through the use a quasi-experimental repeated measures design that compared the effects of two backchannel frequencies – one approximately a third of the other – on L2 English speech. The 37 L1 Japanese and 34 L1 Mandarin Chinese participants spoke in English to an interlocutor who varied the frequency of backchannels that they were given in different dyadic interactions. The resultant audio recordings were transcribed and analysed using common measures of speech complexity, accuracy and fluency. Multivariate analyses of variance and t-tests helped show that the fluency of each group was increased when the higher of the two frequencies was given and that, while the accuracy of the Japanese group did not alter, the Chinese group was less accurate in one set of interactions when receiving the higher frequency of backchannels. Effect sizes for these changes (d = 0.19–0.87) were comparable with other studies that used the same measures of fluency and accuracy. There were no statistically significant differences for measures of complexity. The findings show that the contribution of L1 norms to the effects of backchannels on L2 interactions is not as clear-cut as assumed by previous research. The implications of the findings extend into language testing, teaching, theory and research methods.

Advisor: Macaro, E
Organization matters: the causes and consequences of organizational choices in the private and public sectors

This thesis explores organizational choices of establishments in the public and private sectors. Chapter 1 introduces the topic and details the motivating stylized facts from the main dataset used in this work: theWorld Management Survey (WMS). Chapter 2 focuses on family firms, the most prevalent type of firm in the world, and investigates the relationship between family control and quality of management in manufacturing firms as well the link to firm performance using two new datasets: the Ownership Survey and the WMS. The results suggest that family owned-and-controlled firms are worse managed, with coefficients being over twice larger under 2SLS than OLS. The negative link seems to stem from the family vs non-family control rather than simply family or non-family ownership. Chapter 3 develops a theoretical framework to understand one possible mechanism behind the low adoption of management practices at family firms. The model suggests that industry-specific parameters such as higher cost of laying off workers (ie. unionized environments), higher cost of firm reputation for family CEOs (ie. eponymous firms) and higher shares of low ability workers all contribute to lower adoption of management. Simple stylized facts are presented and testable implications requiring more rigorous tests are suggested. Chapter 4 details the development of an expanded evaluation tool for measuring quality of management in schools mirrored in the tool used in Chapter 2, the Development WMS (D-WMS), and presents the first stylized facts with new data from Mexico, India and Colombia. One of the stylized facts is that there is a large difference in management practices between private and public schools in India. Chapter 5 explores this further and results suggest that what drives the private school management premium is the better people management. Using additional detailed student- and teacher level panel data, I show that the combination of performance-driven teacher selection and pay practices may be behind the parallel private school student achievement premium as well.

Advisor: Stevens, M
Quinn, S
Bond, S
Impact of S. aureus colonisation in human &amp; mouse populations and relationship to vaccination

Staphylococcus aureus (S. aureus) is both a commensal and a pathogenic Gram-positive bacterium. Approximately one third of the adult population are asymptomatic nasal carriers of S. aureus. Clinical staphylococcal disease can range from skin and soft tissue infections to bacteraemia, often caused by the carriage strain. For this reason, interventions which reduce colonisation should reduce the mortality and morbidity of disease, something which has been proved using antimicrobial decolonisation. An alternative approach to doing this is through vaccination. However, to date, vaccines against S. aureus in clinical trials have been unsuccessful, their failure highlighting our lack of understanding of the interactions between the bacterium and the host in both carriage and infection situations. While human carriage studies and animal experimental models are both useful for dissecting out such interactions, the latter represent a platform in which to test pre-clinical vaccine candidates against colonisation.
In this thesis I have investigated the relationship between S. aureus colonisation and immune responses against the organism. I have done this both in a human cohort study in a unique confined population, and in a murine model. I present evidence that interactions between S. aureus and other species within the microbiome can influence magnitude of immune responses in humans in a confined environment. I have established a novel, long-term murine S. aureus gastrointestinal (GI) tract model which is needle-free and does not require antibiotics. I used this model to investigate immune phenotype of colonisation and to assess efficacy of S. aureus vaccine candidates in reducing colonisation. I identified a vaccine candidate which, when administered prophylactically, can reduce subsequent experimental S. aureus colonisation in mice.
Through studies of both human and murine colonisation, this thesis increases our understanding of the host-bacterium relationship during colonisation. A new colonisation model is now available for testing vaccines and one vaccine candidate deserves further investigation.

Advisor: Wyllie, D
Klenerman, P
Molecular dynamics simulations of lipase-surface interactions

Lipases are enzymes that play fundamental roles in fat digestion and metabolism, and function at the interface formed between hydrophobic molecules and the surrounding aqueous environment. These interfacial interactions are thought to induce conformational changes in a "lid" region of the lipase, leading to a dramatic increase in activity. This thesis aims to provide insight into the interactions that govern lipase association with interfaces of di erent structural characteristics, and the possible conformational changes that arise as a function of these interactions. A multi-scale molecular simulation approach (combining atomistic and coarse-grained methods) was applied to study two different lipases with a range of interfaces, including "soft" biological surfaces and "hard" non-biological surfaces.
Three major insights were gained from these studies. First, interactions of a small bacterial lipase (M37) with lipid interfaces resulted in substantial structural changes in a lid region, uncovering of the underlying active site. A mechanism of interfacial ac- tivation is proposed for this lipase. Second, the interaction of M37 with non-biological interfaces di er from lipid interfaces, leading to altered interfacial orientations with possible functional consequences. Third, the amino acid composition of the lid region of a yeast lipase (TLL) is shown to play crucial roles in lipase activation and structural stability.

Keywords: Surface Interactions
Molecular Dynamics
Membranes
Enzymes
Lipases
Advisor: Sansom, M
Molecular mechanisms of hedgehog signal transduction by the G-protein coupled receptor smoothened

The Hedgehog signalling pathway is an essential developmental pathway present in all bilaterians that is involved in embryogenesis, body patterning and stem cell homeostasis. Dysregulation of the Hh pathway leads to various kinds of cancer, such as basal cell carcinoma and medulloblastoma. Smoothened (SMO), a Frizzled-type G-protein coupled receptor (GPCR), is the essential transmembrane signal transducer within the Hh pathway, conveying the signal from the upstream transmembrane protein, Patched1 (Ptc1), to the downstream intracellular proteins. The mechanisms by which SMO transmits the Hh signal from the extracellular environment, through the plasma membrane and to the intracellular proteins are not known. In this thesis, I present my work into the structural and functional characterisation of the extracellular and transmembrane domains (TMD) of human SMO in order to better understand the molecular mechanisms of its signal transduction. The extracellular region of SMO contains a highly conserved cysteine-rich domain (CRD) and a linker domain (LD). I present the first crystal structure of the CRD, LD and TMD of SMO, which is also the first crystal structure of a GPCR with a large functional extracellular domain. This structure revealed a domain architecture for SMO that enables regulation of its transmembrane domain by its extracellular domains. It also revealed a cholesterol molecule bound to the CRD, which we subsequently determined to be a new endogenous small-molecule agonist for SMO. I present five further structures of SMO bound to different small molecule agonists and antagonists. Together, these structures demonstrate that the position of the CRD relative to the TMD reflects the activation state of SMO. We also generated nanobodies against the extracellular region of SMO in order to stabilise its conformation. These studies not only improve our understanding of the workings of a key transmembrane protein within a fundamental signalling pathway but will also aid efforts to develop better therapeutics for an important cancer target.

Keywords: x-ray crystallography
GPCR
Advisor: Siebold, C
Mixed discrete-continuous fragmentation equations

The work contained in this thesis concerns the development, and the mathematical and numerical analysis, of a new class of hybrid discrete-continuous fragmentation model. The framework is introduced as a potential answer to the occurrence of 'shattering' mass loss, commonly observed in purely continuous fragmentation models.
Initially, the study begins by introducing the model, which takes the form of an integro-differential equation, coupled with a system of ordinary differential equations. Once the model has been established, it is subjected to a rigorous mathematical analysis, using the theory and methods of operator semigroups and their generators. Most notably, by applying the theory relating to the Kato-Voigt perturbation theorem, honest substochastic semigroups and operator matrices, the existence of a unique, differentiable solution to the model is established. This solution is also shown to preserve non-negativity and conserve mass.
Having determined the existence of a solution, the work continues with the development of a numerical scheme for the approximate solution of the modelling equations. Considering a truncated version of the equations, rewritten in an alternative conservative form, the scheme is built around a finite volume discretisation. Using a standard weak compactness argument, the approximations generated by the numerical scheme are shown to converge (weakly) to a weak solution of the truncated equations.
By relating this weak solution to the strong solutions provided by the earlier semigroup analysis, the weak solution is found to be unique and as a consequence, differentiable, non-negative and mass-conserving. The theoretical study is completed with an examination of the effect of varying the truncation point. In particular, establishing that as the length of the truncated interval is increased, in the limit, the original solution to the full model is obtained.
Finally, the thesis is completed with a numerical investigation, seeking to experimentally confirm the assertions of the earlier theoretical work and assess the performance of the numerical scheme for a suite of test models.

Advisor: Suli, E
Residual stress evaluation and modelling at the micron scale

The presence of residual stresses in engineering components may significantly affect damage evolution and progression towards failure. Correct evaluation of residual stress is of crucial importance for assessing mechanical components, predicting response and ensuring reliability. For example, when failure occurs due to cyclic loading, the underlying damage begins at the nano-, and then micro-scale. It is clear that improving engineering reliability at the micro-scale requires the ability to evaluate residual stress and mechanical properties at the appropriate scale.
The key objective of the thesis is to advance the understanding and practice of residual stress evaluation at the micro-scale, and to examine the implications and applications that follow. Significant effort was devoted to the evaluation of two aspects of the relatively novel FIB-DIC micro-ring-core experimental technique: assessing the effects of Ga-ion damage and the quantification of uncertainty in stress evaluation due to unknown crystal orientation.
FIB-DIC micro-ring-core milling was then used alongside with synchrotron XRD to study residual stress effects on fatigue crack growth propagation rate following the occurrence of overload or underload. The effects of the two principal mechanisms of crack retardation following an overload, residual stress and crack closure, were separated by testing samples at different loading ratios. Whilst, the acceleration after an underload was studied using validated non-linear FEM analyses.
Conceptual focus was placed on the macro-micro-nano residual stress decomposition into Type I, II & III according to scale and, detailed examination was conducted experimentally and numerically. In the context of shot-peening surface treatment, residual stresses were modelled using a novel eigenstrain-based modelling procedure for arbitrarily shaped components. Furthermore, a fine scale characterisation was performed of the recast layer produced by EDM, with particular attention paid to the residual stress.
The investigations presented in this thesis open new perspectives for the assessment of material reliability. Improved failure prediction models will be elaborated based on the insights obtained in the present study.

Keywords: FEM
microscopy
synchrotron
fracture mechanics
structural integrity
residual stress
polycrystalline materials
modeling
FIB-DIC
Advisor: Korsunsky, A
Dynamical circulation regimes in planetary (and exo-planetary) atmospheres

In this thesis, we study the effect of diurnally- and seasonally-varying forcing on the global circulation of planetary atmospheres explored within a large parameter space. This work focusses on studying the spacial and spectral energy budgets across a large range of planetary parameters as well as the momentum transfer as a response to diurnal and seasonal effects.
We simulate planetary atmospheres using PUMA-GT, a simple GCM co-developed for this work, that is forced by a semi-grey two-band radiative-convective scheme, dissipated by Rayleigh friction and allows for temporally varying insolation. Our parameter regime includes the variation of the planetary rotation rate, frictional timescale in the boundary layer, the thermal inertia of the surface and the atmosphere, as well as the short-wave optical thickness.
We calculate the energy transfer in Martian atmosphere to have a reference case of an atmosphere that is subject to very strong seasonal and diurnal variation. For this we present the first Lorenz energy budget calculated from reanalysis data of a non-Earth planet. A comparison between Martian and Earth atmosphere reveals a fundamentally different behaviour of the barotropic conversion term in the global mean. A significant impact of the thermal tide can be discerned in the generation of eddy kinetic energy, especially during global dust storms.
Our study of seasonal variation reaffirms previous work that the equatorial super-rotating jet in the slow-rotating regime is arrested for strong seasonal variation. We find a novel explanation as to why the Titan atmosphere is able to maintain super-rotation despite strong surface seasonality; for non-zero short-wave absorption in the atmosphere the mechanism that hinders equatorial super-rotation is weakened.
Diurnally-varying forcing can significantly enhance the equatorial super-rotation in cases with non-zero short-wave absorption. In our simulations this enhancement is maintained by a convergence of vertical momentum flux at the equator. Efforts to identify the atmospheric waves involved in this enhancement point towards thermally-excited gravity waves.

Keywords: super-rotation
macroturbulence
diurnal forcing
planetary atmospheres
seasonal forcing
Advisor: Read, P
An investigation of Korean learners' difficulties in using English intonation to express emotion: perception and production

The present study investigated whether Korean English as a Foreign Language learners experience difficulties in using English intonation particularly to perceive and express emotion. The difficulties are examined in both perception and production of emotional intonations by comparing the differences in the emotional responses of Korean English as Foreign Language learners and native speakers to the presented emotional declarative sentences. Based on Core Affect theory, the construct of emotion was operationalised on a two-dimensional matrix: valence (positive vs. negative) and intensity (strong vs. weak). A combination of the Autosegmental Matrix Model and Halliday’s tone models were adapted to analyse intonation patterns. The study conducted a three-phase data collection process: (a) Phase 1: conducting an emotion word rating survey, (b) Phase 2: conducting a production task, a brief stimulated interview, and a perception task for American undergraduate participants (c) Phase 3: conducting the same production task, stimulated recall task, and perception task for Korean students. The results of the current study provided empirical evidence that Korean English as Foreign language learners experience difficulties in using English intonation to express emotions. The results of this study showed that on the word perception level, Korean participants experienced a lesser degree of emotional valence when reading emotion words compared to the American group. Korean students also were less likely to recognise English prosodic cues as semantic components when they listen to emotional utterances. On the production level, Koreans also used a different parsing pattern and utilised a narrower range of pitch variations, which can contribute to diminishing the pragmatic force of their spoken messages. Korean students also tended to recall contexts that were less personal and specific when producing emotional utterances. All these aspects led to Korean students' pragmatic difficulties in communicating emotion in English.
The study, therefore, calls attention to the need for the teaching of intonation patterns to express emotions, which in turn may help learners to take more ownership of using English for internal and emotional use.

Advisor: Macaro, E
Numerical modelling and experimental characterisation of mechanical performance of ceramic materials at multiple scales

Among countless engineering applications of ceramic materials, the design of reliable ceramic armour remains one of the most challenging. The complexity of deformation and failure mechanisms amplified by the rate-dependent behaviour, observable in service and corresponding experiments, still hinders the development of novel materials capable of demonstrating a significantly improved performance.
The main aim of the research discussed in this thesis is to increase the understanding of the physical phenomena surrounding the response of ceramic materials to rapidly applied loading, such as that arising from explosion and collision, by combining experimental and numerical methodologies at different length scales.
Multiple experimental techniques have been adopted to characterise the materials considered. At the micro-scale, the mechanical properties of single grains, single grain boundaries, and polycrystalline structures have been measured with micro-cantilever beam tests, and the results. At me macro-scale, instead, the quasi-static characterisation tests have been combined with the outcome of high strain-rate tests (i.e. impact) to provide an overview of the macroscopic behaviour of the ceramic materials considered at multiple rates, thus increasing the understating of the rate dependent deformation and failure processes in ceramic materials.
The numerical approach also focused on two distinct scales, aiming to reproduce the geometrical features of the microstructures of polycrystalline ceramic materials, as well as the mechanical response at both the micro- and the macro-scales.
At the micro-scale an innovative method to model the grain structure of polycrystalline materials has been developed. Experimentally obtained results were used both in the generation of the models to guarantee their representativeness, as well as to validate the developed numerical simulation methodologies. This provided the required confidence in the algorithms developed to simulate the response of realistic, statistically representative micro-structures which would be extremely difficult to investigate experimentally. This offered the unique opportunities to explore the physical phenomena which would otherwise be very difficult to generate, let alone observe and measure in reality (i.e. in-situ dynamic crack propagation and branching within three-dimensional domains).
At the macro-scale a constitutive model for simulation of deformation and failure of ceramic materials has been developed, overtaking some limitations of the state-of-the-art material models. An analytical model of the crack growth has been implemented, based on the study of the behaviour of a single sharp crack randomly oriented within an elastic continuum medium, and embedded into an ad-hoc modified constitutive model to lay the fundaments for the future development of methodology for concurrent multi-scale modelling of ceramic materials subjected to impact loading.

Advisor: Petrinic, N
Todd, R