VictorJuiz/thesis huggingface dataset:
Processes of change in cognitive therapy for posttraumatic stress disorder

Although trauma-focused cognitive therapy for PTSD is effective and recommended in international treatment guidelines as a first-line intervention for PTSD, the psychological processes through which this treatment drives clinical improvement have rarely been investigated. The aim of this thesis is to improve our understanding of how cognitive therapy for PTSD works by testing predictions made by Ehlers and Clark’s (2000) cognitive model of PTSD in two large datasets of patients receiving cognitive therapy in routine care (N1 = 330; N2 = 343). To increase the transparency and reproducibility of my work, I developed research software tools that help implement the methods used in this thesis in a transparent and reproducible way.
I used bivariate latent change score models to test whether changes in the PTSD symptoms are preceded by changes in theory-derived cognitive processes and coping strategies during treatment. The results show that changes in PTSD symptoms were preceded by changes in negative appraisals, flashback quality of unwanted memories, and unhelpful responses to intrusions, but not vice versa. The relationship between changes in trauma memory disorganisation and changes in PTSD symptoms was bidirectional.
To investigate sudden symptom improvements during cognitive therapy for PTSD I developed the R package suddengains. First, I examined how cognitive factors change before, during, and after sudden gains in PTSD symptom severity. The results indicate that sudden gains were accompanied, and to a smaller degree preceded, by improvements in negative appraisals and flashback quality of unwanted memories. A second study extended these results by exploring improvement in individual PTSD, depression, and anxiety symptoms during sudden gains in total PTSD symptoms. The results suggest that patients experience different patterns of sudden symptom improvements, while showing similar overall treatment outcomes.
The studies presented in this thesis contribute further evidence supporting predictions about maintenance factors and clinical recovery during treatment by Ehlers and Clark’s (2000) cognitive model of PTSD. This thesis also contributed to clinical research methodology by developing research software that facilitates reproducible analyses as well as a collaborative evaluation and further development of methods evaluating processes of change in psychological therapies. Overall, this thesis supports interventions targeting the identification and modification of cognitive and behavioural processes in PTSD.

Keywords: Cognitive therapy
Posttraumatic stress disorder
Processes of change
Advisor: Clark, DM
Ehlers, A
Explanation through functionalism

The notion of explanation has been widely used to determine and single out dependencies within the Philosophy of Science. In particular, it is often believed that symmetries have a certain priority over laws on the basis of their explanatory role [E.g. Wigner 1964] or that one of the criteria that are employed to discriminate between laws and accidental generalisations is that laws are supposed to "explain" their instances (E.g. Bird 1998). These stances can lead to different hierarchical proposals, sometimes merely methodological but often with strong metaphysical outcomes.
In this work, I am proposing a functional account of explanation, which refrains from a hierarchical commitment, although recognising the different roles that symmetries, laws and phenomena play within the physical theories. In particular, the form of functionalism I am endorsing is the one first introduced in Cassirer 1910 and Cassirer 1937. Addressing the fact that this form of functionalism has been considered a predecessor of structural realism (French 2014), I shall deal with contemporary issues in the Philosophy of Science (E.g. French and Saatsi 2018, Weatherall 2011) as well as recent versions of Kantianism (Massimi 2011a).

Keywords: Physics
Science
Scientific Theories
Functionalism
Structuralism
Explanation
Kantianism
Philosophy of Phyiscs
Philosophy of Science
Advisor: Read, J
In silico characterisation of antigen receptor binding site structures

The adaptive immune system defends the host against the invasion of foreign molecules known as the "antigens". These antigens are recognised by two main types of antigen receptors: T-cell receptors (TCRs) and antibodies. While both proteins share a globally similar β-sandwich architecture and are encoded by similar genetic mechanisms, TCRs are polyspecific and have medium affinity to their peptide antigens, while antibodies are highly specific and have high affinity to their targets. Their different behaviours are thought to be at least partially dictated by their binding site features. In this thesis, we aim to analyse their binding site structures and develop tools that can leverage the greater breadth of binding site diversity unveiled by repertoire sequencing.
In both types of proteins, the majority of the binding site is constituted by the complementarity-determining region (CDR) loops. In this thesis we first describe the development of a rapid sequence-based canonical form prediction tool (SCALOP) for antibody CDRs and for TCR CDRs. Based on this initial structural annotation, we then explored the structural differences between antibody and TCR CDRs and found that TCR CDRs tend to adopt multiple conformations, more often than their antibody counterparts. To capture the potential ensemble of binding site conformations, we built a TCR modelling tool, TCRBuilder.
Moving on from the structure of CDR alone, we then developed Ab-Ligity, a structure-based method that identifies sequence-dissimilar antibodies against the same epitope. This method incorporates the predicted antibody structure and the physicochemical properties of the binding site. Finally, as Ab-Ligity is dependent upon prediction of the paratope, we evaluated the leading paratope prediction method, Parapred. We attempt to highlight possible features that could portray paratopes with interpretable statistical models. The thesis concludes with the potential future directions of the work on binding site analysis for antibodies and TCRs.

Keywords: structural bioinformatics
antibody
paratope
binding site
T-cell receptor
Advisor: Deane, CM
Implementing effective verbal feedback in primary classrooms

Although feedback in teaching and learning has the potential to impact positively, in the reality of classroom practice - feedback is differentially effective. It is therefore important for schools to consider the relevant research recommendations, alongside their collective experience, to develop effective feedback practice which maximises these potential learning gains. This is particularly important when schools are making substantial changes to their feedback practice.
Recently, many primary schools in England have been reforming their feedback practice as a result of national educational changes. The school in which I work is one of these schools. The primary school is a voluntary academy, serving approximately 200 children ages 5-11 in the north west of England. The school had moved away from written feedback and trailed verbal feedback approaches. The following practitioner research outlines this context in more detail, and reviews the relevant literature, before exploring the overarching research question: How can teachers work together to implement more effective verbal feedback?
In doing so it documents and evaluates the process of collaborating to improve the effectiveness of the school’s feedback practice.

Keywords: MLT
MLT2020
Cinemas in the classroom: increasing student motivation and listening skills in L2 through the use of film

Motivation is key to learning and using a foreign language (Ellis: 1997) Low levels of motivation towards language learning are remarkably well hidden in the Irish secondary school system. This is due to the fact that, although foreign language learning is optional, it is a prerequisite for most 3rd level institutions. Previous research I conducted in collaboration with the Irish Film Institute demonstrated an increase in motivation towards French learning when film was used as a language learning tool with students deemed at risk of leaving school early.
But what about students in high achieving schools? Despite diligent work and A grades, student motivation level in French may still be low. In this study I will attempt to increase motivation levels and enhance listening skills in students from a very high achieving, all-girl, secondary school by using film as a classroom language learning tool and hopefully demonstrate an increase in motivation and interest towards language learning, along with improved listening skills.

Keywords: MLT
MLT2014
The rise of ‘Republican fever’ in the PRC: China’s pre-communist legacies and post-Mao national identity

The Chinese Communist Party bases much of its legitimacy on its ‘liberation’ of China from the Nationalist government, and its official historiography describes the Republican era as a dark, chaotic and oppressive period and a part of the ‘Century of Humiliation’. However, during the reform era, while the orthodoxy has persisted, a new image of Republican China has emerged. In books, newspaper articles, documentaries and dramas, pre-communist China has sometimes been portrayed as a vibrant society making remarkable progress in modernization in the face of severe external challenges. In the mid-2000s, the growing fascination with the Republican era became known as ‘Republican fever’. This dissertation seeks to find out why positive reassessments of the Republican era, which deviates from the orthodox historiography, have been allowed to emerge in a country where the media remain under strict state control. Using data gathered mainly from China’s official media. I found that the ‘Republican fever’ has been allowed to emerge and even thrive because, in the reform era, China’s official identity narrative has been gradually evolving from that of a revolutionary socialist state into that of a modernizing nationalist state. While the regime has continued to use the negative view of China’s pre-communist history to maintain its historical legitimacy, it has also been promoting a positive view of aspects of the same period in order to support its post-1978 priorities of modernisation and nationalism. The official reassessment meant that some previously off-limits discursive elements, i.e. Republican legacies, became allowable topics of public discussion. Though the regime imposed its own official framings on these topics, ‘authoritarian fragmentation’ meant that media professionals could act as ‘policy entrepreneurs’ and push for alternative framings of the historical legacies. Collectively, the unofficial framings of Republican legacies led to ‘Republican fever’, which has caused damage to the CCP’s official national identity narrative.

Keywords: Republican fever
Chinese historiography
Chinese nationalism
modern Chinese history
national identity
Advisor: Mitter, R
Indigenous women leading the defence of human rights from the abuses by mega-projects in Latin America, in the face of extreme violence

In the face of extreme violence, some Indigenous women-led social movement organisations defending human rights from the abuses related to mega-projects have achieved favourable changes in corporate practices. In the predominantly patriarchal, capitalist and racist context of Latin America, what explains the success (or not) of Indigenous women-led mobilisations regarding the most politically and economically powerful actors? Although there is a well-established literature on social movements, some dedicated to the influence on corporate practices, there is a lacuna concerning the agency, leadership and impact of Indigenous women-led movements in the context of mega-projects.
This thesis uses a multi-level qualitative research methodology to develop a theoretical framework to explain their outcomes. It involves three main comparisons of cases of success and non-success: (1) within-country variation comparing Lenca women-led organisations contesting abuses related to hydroelectric dam projects in Honduras; (2) within-case variation over time of a Binni’za women-led mobilisation against violations connected to wind farm projects in Mexico; and (3) a small-N cross-national comparison of mobilisations in Ecuador, Peru and Colombia led by Sarayaku, Asháninka and Wayuu women challenging the abuses related to oil extractives, hydroelectric dam projects, and coal mining respectively. Also, I develop a qualitative comparative analysis of all these cases, which includes a Boolean minimisation process.
The thesis finds that in a minimally favourable context the following four factors operating together in a braid of action lead to success (i.e., a favourable change in corporate behaviour): (1) transforming the territory into power; (2) Indigenous women’s effective leadership; (3) human rights framing; and, (4) reacting to a grave violation overtly involving corporations. These four strands interweaved in a tough braid of action are capable of harnessing mobilisation power, achieving success over much materially powerful corporate forces. If some of the strands are weak or frayed, the braid cannot achieve this success.

Keywords: mega-projects
social movements
women human rights defenders
mobilisation
Latin America
leaders
change in corporate practice
human rights defenders
indigenous people
indigenous women
corporate responsibility
human rights
Advisor: Payne, L
The (im)possibility of feminist critique in authoritarianism: Revisiting Western knowledge-transfer in Russia and Serbia

This thesis proposes a critique of the critique of transnational feminism in post-communist Europe. The critique of transnational feminism asserts that the process is, in essence, a unilateral knowledge-transfer, and as such functions as one among many exercises of Othering the West has employed vis-à-vis its Semi-Other since the fall of communism. Using case studies of Russia and Serbia, this research challenges this argument from three angles.
First, it shows that it is ahistorical. Transnational feminist encounters occurred in the communist period, and were characterised by Soviet Russian and Yugoslav feminists’ independence and assertiveness. Second, by applying the critical theory framework to over sixty interviews with feminists in Russia and Serbia that were conducted by the author, an empirical examination demonstrates that a critique of knowledge-transfer is marginal in both cases. This acts as a springboard for the third and central claim.
Based on a computer-aided, post-Marxist discourse analysis of the interviews, the thesis argues that feminists’ priorities undergo a fundamental shift under authoritarianism. In settings where authoritarian regimes propagate an anti-Western discourse, that relies on anti-gender discourse in attempts at Othering back, the subversion of this hegemonic discourse becomes the priority for feminists on the ground. From this perspective, the argument proposed by critical theory – that transnational feminism is a form of Western domination expressed through knowledge-transfer – resonates with the authoritarian discourse. This is why critique of knowledge-transfer is not only marginal, but rejected in an effort not to become complicit in the authoritarian discourse. As a result, Russian and Serbian feminists focus on formulating alternative signifiers for knowledge-transfer in order to subvert the authoritarian regime. First, they endorse knowledge-transfer but attach positive meanings of agency and empowerment to it. Second, they reframe it as an exchange between equals. Finally, they reject the dichotomous boundaries of West/East associated with it.

Keywords: Discourse Analysis
Transnational feminism
Othering
Knowledge-transfer
Russia
Post-communist Europe
Serbia
Authoritarianism
Interpretivism
Anti-gender backlash
Advisor: Sasse, G
Frazer, E
Crisis and convergence: how the combination of a weak economy and mainstream party ideological depolarisation fuels anti-system party success

When do radical parties gain support?
Previous studies cite the importance of economic hardship and mainstream party ideological convergence. Responding to earlier inconsistent findings regarding these two factors, I provide evidence for an interactive approach to understanding the growth of ‘anti-system parties’. These radical outsiders are most likely to succeed when mainstream parties are simultaneously presiding over an ailing economy and failing to provide the diversity of political opinion necessary for the electorate to meaningfully challenge the policies associated with this malaise, through which dissatisfaction with the status quo could otherwise be channelled. The mainstream party establishment is most vulnerable when it is no longer supplying valued outputs or inputs to the political process.
This thesis presents four empirical studies designed to test this ‘crisis and convergence’ model. First, drawing on data from over 350 elections in 22 advanced Western democracies across an extended time period, I demonstrate that the anti-system vote is greatest during times of negative economic growth and widespread mainstream party ideological depolarisation. Second, using a combined individual-level dataset of over 70 national election surveys, I show that personal perceptions of mainstream party convergence are themselves more closely related to anti-system voting when the macroeconomy is sickly. Mainstream party homogeneity radicalises the economic vote and strengthens anti-system challengers. The final two studies corroborate these findings by explicitly testing the crucial underlying assumption that individuals’ perceptions of the uniqueness of mainstream parties are not mere products of partisan rationalisation. Evidence from a multiyear panel dataset in Britain and an original survey experiment conducted in Germany suggests that perceptions of mainstream party similarities are as, if not more, likely to cause a reduction in one’s strength of feeling towards mainstream parties than be caused by this dealignment.
This thesis concludes with a thorough summary of these results, as well as a discussion of potential caveats and grounds for future research. The ‘crisis and convergence’ model is judged to be worthy of consideration in future conversations about the factors that have led to our current political climate of volatile voters and stuttering centrist parties.

Keywords: Elections and Public Opinion
Economic Voting
Comparative Politics
Radical Political Parties
Advisor: Tilley, J
Protein unfolding and refolding by single-molecule nanopore analysis

Nanoscale pores, nanopores, offer single molecule analytical capability that is achieved by electrophoretically driving the analytes in solution through them. The translocation of biological polymers through the nanopores has been investigated over three decades with particular focus on nucleic acids and, later on, peptides and proteins.
Chapter 1 presents the principles and technical aspects of nanopore stochastic sensing with an emphasis on a biological pore, α-hemolysin. It serves as a versatile model for sensing the translocation of nucleic acid polymers and discriminating stationary oligonucleotides at single-base resolution. With the development of the enzymatic ratcheting of polynucleotides through the pore, base-by-base, nanopore-based DNA strand-sequencing has proven achievable. Protein information can also be read upon the protein analyte unfolding and translocating through the pore. This was achieved by either using a molecular motor or an electric potential acting on an oligonucleotide attached to the protein terminus.
Taking advantage of the ability of nanopores to discriminate stationary oligonucleotides, the potential-driven method for protein translocation can be advanced to determine the directionality of entry (N or C terminus-first). To achieve the discrimination, the protein is expected to attach a different oligonucleotide to each terminus. In Chapter 2, we used a site-specific N-terminal cysteine condensation reaction, followed by a disulfide bond forming reaction, to conjugate two different oligonucleotides to a model protein (thioredoxin), one to the N terminus and the other to the C terminus.
Chapter 3 presents the nanopore analysis of protein translocation direction. The oligonucleotide-attached protein bearing a single streptavidin bound at one of the two biotinylated oligonucleotide ends became unfolded as the unoccupied end was pulled through the pore under an applied potential. The different extent to which N- and C-terminal oligonucleotides block the pore indicated the direction of protein translocation through the pore.
Interrogation of the reversal process, protein refolding, is described in Chapter 4. Upon binding the two biotinylated oligonucleotides to streptavidin at both ends, a single molecule of thioredoxin was captured within the pore. The protein could be subjected to repeated cycles of translocation and retro-translocation. After each unfolding and retro-translocation back, it was allowed to refold for various delay times before translocation again. Therefore, this system allows the characterization of protein folding at the single-molecule level. Thioredoxin collapses to a stable native-like structure rapidly, but the full refolding to its native state is approximately four orders of magnitude slower, possibly due to a rate-limiting step of cis prolyl peptide bond formation.
The full details of methods are listed in Chapter 5.

Advisor: Bayley, H
Widening access to higher education in Brazil: A document analysis of assessment policy, purpose and practice

To what extent did the changes in purposes of the Brazilian National Upper-Secondary Exam (ENEM) in 2009 affect the social equality gap and widened the access to higher education? Policy making can be a process where social inequalities are maintained, produced or tackled, affecting or being affected by a large-scale and high-stakes assessment as is the case of the ENEM. From 1998 to 2015, the assessment underwent major reformulations with the explicit intent to widen the access to higher education, especially to the socially underprivileged. With that context in mind, I perform a policy cycle analysis of the ENEM purposes in relation to its practical uses when connected to other related policies. My theoretical framework was informed by a literature review on assessment purposes, as discussed by Pellegrino, Chudowsky, and Glaser (2001) and Newton (2007); specific literature on equality of opportunities in the access to education, with a focus on the Maximally Maintained Inequality hypothesis (Raftery & Hout, 1993) and on the Effectively Maintained Inequality conjecture (Lucas, 2001); and Ball’s Policy Cycle (Ball, 1994; Bowe, Ball, & Gold, 1992). The data collected consisted of policy, legislation, technical, report, institutional and academic texts, searched in specialised databases. My results uncover patterns that indicate that the uses proposed to the ENEM, in connection with a broader network of educational and social reforms, can indeed tackle the inequality of opportunities in the access to higher education. This could add to the international literature on the subject not only for the focus on the ENEM, which presents a rare case in the international assessment literature; but also as a counter-example to the reasonably consensual Maximally Maintained Inequality; and by providing a more comprehensive understanding of assessment not only as a policy in isolation of context, but as part of a larger policy framework.

Keywords: MEA 2020
MEA