VictorJuiz/thesis huggingface dataset:
Factors impacting learners’ proficiency in the Heritage Language Shanghainese

This study aims to better understand the current status of Shanghainese, a Chinese Heritage Language (CHL), and to help its preservation. It explores learners’ usage patterns and their proficiency level in Shanghainese. It also investigates what factors impact the learners’ Shanghainese competence by looking into the relationship between learners’ HL proficiency and their attitudes and beliefs towards the dialect, engagement in dialect-related cultural activities, demographic backgrounds, as well as their home and community language environment. Most previous studies did not specify a regional dialect when researching CHLs, only employed relatively simple statistical analysis, relied on participants’ self-report and focused on a very narrow range of variables that could impact the CHL proficiency. This study designed a questionnaire and a Shanghainese proficiency test to collect speaker information among 187 Shanghainese teenagers between Year 10 (16 years old) and Year 12 (18 years old) from five different high schools in Shanghai. The results showed that the participants generally preferred speaking Mandarin Chinese to Shanghainese in varied scenarios. Their self-perceived and tested Shanghainese proficiency were significantly positively correlated. The participants with a more positive attitude towards Shanghainese, more frequent attendance to dialect-related cultural activities, a more local demographic background, as well as a more dialect-oriented home language environment would have a higher competence level in the dialect Shanghainese. Implications for future research are also provided in this study.

Keywords: Chinese heritage language
Heritage language
HL
language proficiency
Shanghainese
Shanghai dialect
Advisor: Wonnacott, E
A longitudinal study of the effects of teaching motivational strategies to adolescents from a self-determination theory perspective

This study investigated the effects of an intervention program on motivation and English language proficiency amongst English language learners at a middle school in China. Twenty-three grade 7 (11-13-year-olds) were randomly assigned to either the treatment or the control group. The treatment group were explicitly taught the motivated learning strategy of goal setting (goal setting group), while the control (or normal teaching group) received English instruction as usual. The intervention lasted for 18 weeks, wherein students were taught about goal setting, set goals and actions to achieve them, and reflected on them weekly. The evaluation of the effectiveness of the intervention included data from pre and posttest motivation questionnaires, and standard test results for reading and language use, as per the school’s requirement, from two data points (pre and posttest). The results of the immediate training effects of goal setting on motivation and English proficiency were promising, despite being statistically non-significant. The feature of the current study design allowed for an exploration of the possibility of manipulating motivation through goal setting and the possible effect on language achievement.

Keywords: second language acquisition
English proficiency
motivation
ESL
EFL
middle school
self-determination theory
China
LLOS-IEA
EAL
Advisor: Chalmers, H
X-ray Thomson scattering as dynamic temperature and microstructure diagnostic

Whilst the field of High Energy Density physics spans a history of more than a century, it lacks a reliable dynamic temperature diagnostic. This work presents computational and experimental work on developing such technique based on the principle of detailed balance.
In molecular dynamics simulations, monocrystalline copper is shocked along [001] to pressures ranging between ambient and 70 GPa, and its synthetic elastic and inelastic diffraction signal is computed via the spatial and temporal Fourier transforms of the atomic coordinates. In the plastic regime beyond the Hugoniot elastic limit, the crystals slip faults and stacking faults arise, which cause certain Bragg spots to link up in reciprocal space. The compression facilitates the detection of the inelastic phonon modes through pressure hardening by increasing their spacing in energy space, yet the quasi-elastic signal linked to the stacking faults can dominate the spectra outside of the first Brillouin zone. Whilst these temperature measurements highly benefit from increased resolution, it is proposed that the shock compression setups can also determine a Doppler-induced energy shift on the order of meV, which could be used as a direct particle velocity diagnostic.
As part of a collaboration in the European XFEL experiment p2191, the ambient and resistively elevated temperatures of monocrystalline diamond are determined. In order to expand this technique into the field of dynamic compression, more results of experiment p2191 and work of p2656 presented here recorded spectra for polycrystalline copper, cobalt, and nickel samples. Whilst no temperature could be determined, the photon levels for a seeded XFEL sufficed to generate high-resolution spectra of inelastic scattering that exhibit varying asymmetry, indicating the presence of microstructure-related quasi-elastic scattering. Whilst predictions about the inelastic signal strength through a photometrics code could be verified, diffraction data remained inconclusive due to poor grain statistics in the polycrystalline targets.

Keywords: diffraction
nuclear fusion
European XFEL
HED
special relativity
XFEL
LCLS
single photon counting
doppler shift
x-ray
cobalt
CMA-ES
Markow Chain Monte Carlo
phonon
molecular dynamics
shock physics
machine learning
copper
nickel
crystal
Advisor: Wark, J
Gregori, G
Freud's Britain: Family, followers and the dissemination of ideas before and after the Great War


Existing histories of psychoanalysis have by and large paid scant attention to the role the Freud family played in Freud’s mental economy, this neglect being most conspicuous with respect to the British branch of the family. Various family members are glimpsed in Freud’s published correspondence and some – notably his nephew John – appear as key characters in the Interpretation of Dreams and other works. This latter observation points to the importance of Freud’s Britain: Freud’s reflections on his own life experiences, with his close-knit family, became indispensable building blocks in his theorising, both for Freud and subsequent psychoanalytic generations. Through a fine-grained study of Emanuel and Philipp Freud (and their families), the variegated influence of these British Freuds on their younger brother is here revealed for the first time. These relationships shaped Freud’s thinking, attitudes, and theorising. They strengthened, if not created, his Anglophilia. Freud’s Britain thus allows for a better contextualised understanding of the actual sibling and familial ties that went into forming the tapestry of psychoanalysis.
Building on the template of this relational base, Freud’s Britain considers key sites and events through which psychoanalysis was disseminated into British culture up to, through, and immediately following the Great War. Thus, the London Psycho-Analytic Society, the Brunswick Square Clinic, and Craiglockhart War Hospital are explored in detail, each with varying and often contested psychoanalytic credentials and sequelae. In this context, the publication and transmission of ideas, particularly through the trade in psychoanalytic books, was crucial and this is here explored in terms of censorship and the politics of translation. Further contextualised here, these processes, while aiding a type of institutionalisation, contributed at the same time to a rather conservative, elitist psychoanalysis, which shifted away from the demotic, and failed to do full justice to the radical message of Freud.

Keywords: Dissemination of ideas
Freud's family
British Psychoanalytical Society
Sigmund Freud
Psychoanalysis
Publishing
Censorship
Brunswick Square Clinic
Craiglockhart War Hospital
London Psychoanalytic Society
Advisor: Ross, A
Deep learning algorithms for predicting association between antibody sequence, structure, and antibody properties

Antibodies are one of the most important classes of pharmaceuticals, with over 100 antibody therapeutics approved against a wide variety of diseases and many more in active development. However, the development of antibody therapeutics remains a time- and cost-intensive process. While computational screening methods have been used to improve the efficiency of this process, they are limited by a lack of accuracy, lack of generalisability or low-throughput nature. In this thesis, I detail the development of deep learning approaches for the prediction of antibody-antigen binding, harnessing state-of-the-art approaches for the analysis of protein structures.
To this end, I start by outlining improvements to the Structural Antibody Database (SAbDab). I then describe several high-throughput deep learning tools for a structure-based antibody virtual screening pipeline using computationally generated antibody structures (DLAB). I demonstrate that convolutional neural network (CNN) models can improve the prediction of antibody-antigen complex structures through the development of the pose rescoring and docking quality assessment tool DLAB-Re. Further, by developing and evaluating the virtual screening tool DLAB-VS, I show that CNNs enable structure-based antibody-antigen binding prediction. Motivated by recent advances in protein structure analysis and equivariant graph neural network (GNN) models, I extend the DLAB framework to GNNs, developing DLAB-EG and showing that these models can offer significant advantages over existing CNN approaches.
This thesis demonstrates the applicability of state-of-the-art machine learning approaches to the antibody-antigen virtual screening task. I provide a proof-of-principle for a structure-based virtual screening pipeline for antibody model libraries as well as a promising avenue for further improvement of antibody screening capabilities using machine learning approaches.

Keywords: Structural biology
Machine learning
Immunoinformatics
Advisor: Deane, C
The fauna of tree-holes in relation to environmental factors

Water-filled tree-holes are one of a group of similar aquatic habitats found in or upon plants of various kinds. A study has been made of the holes found in the roots and branches of beech trees in Wycham Woods, Berkshire. The habitat has been described in terms of physical, chemical and biological characteristics, the numbers of the species of animal found in it have been recorded over a period of time and some attempt has been made top relate the numbers of animals present to the environmental factors measured.
An integrative approach to profiling the central nervous system

With the current increase in life expectancy comes a higher prevalence of age-associated neurological conditions, thus increasing social and economic pressure to improve maintenance of neurological health. Limited sample accessibility and availability place a technological demand on methods compatible with profiling central nervous system tissue which maximise sample utility. Here we present a label-free multi-modal molecular profiling approach which yields spatially resolved transcriptomic, proteomic and biochemical profiles of brain and spinal cord tissue sections, thus addressing this technological demand. This approach was used to profile samples from individuals without neurological condition (n=19) and individuals with secondary progressive multiple sclerosis (SPMS) (n=18), which is characterised by significant architectural alterations to central nervous system identifiable by histological characterisation. Using machine learning and cluster correlation, we have identified two tissue profiles associated with controls which corresponded to white and grey matter regions based on macromolecular, compositional, transcriptomic and proteomic features. By combining the unsupervised clustering across modalities, we identified and profiled a total of 6 degrees of pathology severity.
Apart from overall tissue classification, this approach has also generated valuable mechanistic biological insight: we have been able to not only recapitulate previously reported SPMS pathological biochemical features, but have also linked these processes to specific cell types and tissue-specific processes. This includes evidence of oxidation and alterations to protein processing/folding in oligodendrocytes and neurons. The protein alterations we report include increased β-sheet content and decreased α-helix content in SPMS, a feature normally associated with neurodegenerative conditions with protein folding alterations, and which had never been, to our knowledge, reported in SPMS and adds to its neurodegenerative-like pathological features. We have also outlined processes in SPMS analogous to injury-associated central nervous system scarring, and pathology-associated deviations from typical responses. In particular, we observed niches with high expression of S100β, a protein which has variable cellular function highly dependent on its concentration within tissue: the highly localised profile of spatial gene expression we observe provides insight into a previously unappreciated mechanism by which gene expression can have a deleterious impact attributable to its spatial expression concentration. We believe these findings support the utility of this technological approach not only for disease characterisation and hypothesis generation, but also generating mechanistic and clinical insight for diseases with limited tissue availability, thus enabling the development of treatments to promote healthy ageing of the CNS.

Keywords: Multiple sclerosis
single nuclear RNA-sequencing
Spatial transcriptomics
Proteomics
Multiomics
Fourier transform infrared microspectroscopy
Advisor: Dendrou, C
Tan, JC
Cinque, G
The role of retinoic acid in cartilage mechanoflammation

Osteoarthritis (OA) is a highly prevalent condition that affects more than 40% of individuals over the course of their lifetime. There are currently no disease-modifying OA drug (DMOAD) licensed for the treatment of this disease. An Icelandic genome wide association study (GWAS) study identified common polymorphic variants in ALDH1A2, the gene which encodes the enzyme involved in the synthesis of all-trans retinoic acid (atRA), with severe hand OA. Subsequent data from our lab showed that atRA-responsive genes are downregulated on cartilage injury. Mechanical injury is one of the principal risk factors in the development of OA. Cartilage injury is known to activate downstream inflammatory signalling that is driven in a transforming growth factor activated-beta 1 (TAK1) dependent manner and thereby increase inflammatory gene regulation, in a process known as mechanoflammation. Talarozole (TLZ), a CYP26 inhibitor, which prevents the breakdown of atRA, suppresses the upregulation of inflammatory genes on cartilage injury. My project sought to identify the mechanism by which atRA-responsive genes were downregulated and determine how atRA suppressed mechanoflammation on cartilage injury. The downregulation of atRA-responsive genes on cartilage injury was mediated in both cytosolic phospholipase A2 (cPLA2) - and reactive oxygen species (ROS)-sensitive manner. TAK1 phosphorylation on cartilage injury was partially mediated in a nicotinamide adenine dinucleotide phosphate oxidase (NOX)-sensitive manner, whereas TAK1 was responsible for the partial phosphorylation of cPLA2 on cartilage injury. Apoptosis signal regulating kinase 1 (ASK1) was the key driver of mitogen activated protein kinases (MAPKs) (Jun N terminal kinase (JNK) and extracellular signal regulated kinase (ERK)) on cartilage injury and downstream inflammatory gene regulation. atRA suppressed mechanoflammation in a peroxisome proliferator activated receptor gamma (PPARG)-sensitive manner. These findings suggest that both boosting atRA level and ASK1 inhibition can suppress mechanoflammation in articular cartilage and identifies each pathway as targets for potential disease modifying drugs in the treatment of OA.

Keywords: inflammation
cartilage
osteoarthritis
retinoic acid
Advisor: Vincent, T
Furniss, D
A systematic review of research on adult L2 language learning strategies and strategy instruction

This systematic review of research on adult L2 language learning strategies and strategy instruction investigated empirical research from 2011-2021 that included delayed posttests and/or longitudinal methodologies. Strategies and pedagogical implications involving language areas such as grammar, speaking, writing, listening, learner autonomy, and orthography were all explored and discussed. The systematic review found the area of adult L2 language learning strategies and strategy instruction to be one developing into a field of research with high quality methodology and actionable implications. However, the field is not mature and more research still needs to be conducted.

Keywords: pedagogy
adult L2 language learning strategies
strategy instruction
Advisor: Rose, H
Examining teachers’ perceptions and attitudes of Japanese use in the English classroom

In Japan, English has been a compulsory school subject from Year 5 of elementary school since 2011 (Japanese Ministry of Education, Science and Culture, 2008). English conversation schools and after school programs have also become increasingly popular. To help bolster Japan’s English education, many public and private schools alike have marketed English-only instruction or “No Japanese” environments as the best way to facilitate learning to children. However, in Japan and across the world, teachers may not always be willing or able to carry out such curricula or policies.
Using a mixed methods approach, this paper aimed to uncover how teachers at various teaching establishments in Japan feel about banning the use of Japanese in the English classroom. Through an online questionnaire, in-class observations, and teacher interviews, participants were asked if and when they use their students’ first language (Japanese) and how they view their current teaching situation as well as their ideal situation.
Correlation analysis of the questionnaires showed that the age of students taught was related to how much teachers use Japanese in the classroom. It also uncovered that the teachers’ school’s policy showed some relationship to how the teacher viewed using Japanese. In other words, teachers with more liberal views of first language use in the classroom tended to work for schools that shared those views or supported first language use in the curriculum.
Qualitative analysis of the observations and interviews showed that a teacher’s education and experience may influence their opinions as well. Although the data collected was limited due to the restraints of the COVID-19 pandemic, this paper highlights the trend that English-only may not be favored by all teachers and may not be entirely realistic within the contexts of English education in Japan.

Keywords: interview
teaching in Japan
first language instruction
questionnaire
English education
target language instruction
A multi-omics approach to understand mesenchymal stem cell ageing

Mesenchymal stem cell (MSC) ageing is characterised by impaired proliferation and osteoblast differentiation, leading to a reduction in bone mass and bone strength. Recent evidence indicates that transcriptional and epigenetic changes may underlie the impaired MSC functions with age. This thesis aims to systematically characterise the transcriptional and epigenetic changes associated with MSC ageing and to identify candidates for restoring MSC functions.
RNA-seq, DNA methylation-array and ATAC-seq were carried out on undifferentiated bone marrow-derived MSCs from young (20 - 29 years) and old (62 – 87 years) donors. The RNA-seq data showed that an increased donor age was associated with significant changes in the expression of lineage determining genes. Moreover, the DNA methylation array and ATAC-seq analysis revealed a less permissible epigenetic state for osteogenesis in the old donors, indicating that a shift in lineage preference was already evident in MSCs prior to differentiation.
In order to compare transcriptional changes during osteogenesis between MSCs from young and old donors, RNA-seq time-course experiments consisting of 16 time points were carried out. The expression profiles of a panel of tri-lineage differentiation markers indicated that the old donor MSCs were unable to fully commit towards osteoblast differentiation upon osteogenic induction and were diverted towards an adipogenic fate. The top 3 enriched gene networks amongst the 91 differentially expressed genes were associated with the canonical WNT, JAK/STAT and PPARG pathways. Canonical WNT activation via GSK3B inhibition significantly increased the ALP activity and matrix mineralisation of the old donors. Interestingly, WNT activation shifted the transcriptomic profiles of the old donors towards the young donors, thus further supporting the thesis that the canonical WNT pathway could be a potential target for restoring the osteogenic potential of ageing MSCs. More importantly, this study demonstrates the validity of the concept that a multi-omics approach has a promising potential for identifying therapeutic candidates to restore MSC functions in the elderly.

Advisor: Roberts, S
Tiny probabilities of vast value

The topic of this thesis is how we should treat tiny probabilities of vast value. This thesis consists of six independent papers. Chapter 1 discusses the idea that utilities are bounded. It shows that bounded decision theories prescribe prospects that are better for no one and worse for some if combined with an additive axiology. Chapter 2, in turn, points out that standard axiomatizations of Expected Utility Theory violate dominance in cases that involve possible states of zero probability. Chapters 3–6 discuss the idea that we should ignore tiny probabilities in practical decision-making. Chapter 3 argues that discounting small probabilities solves the ‘Intrapersonal Addition Paradox’ and thus helps avoid the Repugnant Conclusion. Chapter 4 explores what the most plausible version of this view might look like and what problems the different versions have. Chapter 5 focuses on one type of problem, namely, money pumps. The Independence Money Pump, in particular, presents a difficult challenge for those who wish to discount small probabilities. Finally, Chapter 6 discusses the implications of discounting small probabilities for the value of the far future.

Keywords: population ethics
global priorities research
fanaticism
decision theory
Advisor: Mogensen, A
Thomas, T