VictorJuiz/thesis huggingface dataset:
Investigating the role of lipids for membrane protein complexes using native mass spectrometry and molecular dynamics simulations
Keywords: molecular dynamics
BK channel
SemiSWEET
scientific software
membrane proteins
native mass spectrometry
ion channels
K channels
potassium channels
protein-lipid interactions
cardiolipin

The work described in this thesis is a combination native mass spectrometry experiments, molecular dynamics simulations and scientific software development. It consists of three results chapters which each chapter describing a distinct project with a focus on one of the aspects above.
In chapter 3, I employed molecular dynamics simulations in a collaborative project on using surface-induced dissociation to probe the effect of lipid binding on the stability of oligomerisation interfaces. My simulations offer a rationale of lipid bind- ing to different locations to explain these stability differences. In addition, I contributed to experiments to probe the molecular features of these interfaces through site-directed mutagenesis to weaken these interfaces.
Chapter 4 describes my investigation on lipid binding to a bacterial potassium channel, MthK. Native mass spectrometry and molecular dynamics simulations are used to characterise lipid binding after initial experiments indicated endogenous lipids being bound to MthK. Cardiolipin has been revealed to bind specifically to MthK. These results are compared to the eukaryotic homologues through further simula- tions. A part of this chapter outlines different approaches to obtain the in vivo stoichiometry. Among these approaches I employed SoLVe-MS, which leads to very complex mass spectra. The analysis of these spectra sparked the development of the program described in chapter 5.
In the final results chapter, a web-based program for the analysis of native mass spectra, NaViA, is described. This program allows one to analyse native mass spectra through a visual user interface directly in a web browser. In addition, it offers auxiliary tools to facilitate the analysis as well as the ability to save and load sessions for sharing spectra including analysis or depositing them for publication. The ease of use and the instructive auxiliary tools make it a valuable addition to the suite of software available for the analysis of native mass spectrometry.
The role of CD2 in recognition of weak antigens and its implications for adoptive cell transfer
Keywords: Adoptive Cell Therapy
Immunotherapy
T cell immunology
CD2
Adoptive Cell Transfer
Adhesion receptors

Adoptive cell transfer (ACT) of genetically modified T cells expressing engineered T cell receptors (TCRs) holds potential in the treatment of cancer. However, concerns about off-tumour toxicities continue to hinder widespread adoption of TCR-T cells. Current mitigation strategies against off-tumour toxicity such as affinity tuning, kill switches, and logic gates, can sometimes compromise the efficacy of ACT. In this work, we postulate that the human CD2 co-receptor can mediate off-tumour toxicities in ACT, and we propose the targeted manipulation of the CD2/CD58 axis to ameliorate these toxicities. We engineered a Chinese hamster ovary line and used it as a surrogate antigen presenting cell (APC), generating a xenogeneic platform to quantitatively study the role of human CD2 in enabling T cell recognition of low density and/or low affinity ligands (weak antigens). Using Jurkat and primary human CD8+ T cells, we found that, when disrupting the CD2/CD58 axis through CD2 ablation, T cell antigen sensitivity was reduced by 4-15 fold. In co-cultures between Jurkats and the T2 archetypal APC line, transducing the Jurkat effectors with elongated CD2 chimeras generated modest reductions in sensitivity (2-8 fold), a phenomenon that might be attributable to disruption of the CD2/CD58 canonical binding. Moreover, we showed in CD8+ T cells that CD2 knockout appeared to ameliorate the previously reported low affinity, self-pMHC cross-reactivity of the affinity enhanced wt/c51 TCR. Taken together, our results suggest that CD2 might contribute to two types of off-tumour toxicity observed in ACT, namely on-target/off-tumour and off-target/off-tumour cross-reactivity. Therefore, routine manipulation of the CD2/CD58 axis could provide a way of enhancing ACT safety when using engineered TCRs. Our findings could be applicable to other synthetic receptors, provided they exploit the CD2 co-receptor as TCRs do.
Longitudinal modelling of genetic risk for common diseases
Keywords: Low-rank representation
Multi-morbidity
Survival analysis
Genetic subtypes
EHR
Bayesian statistics
longitudinal data
epidemiology
Frailty model
genetics

Recent large cohort studies follow participants for tens of years to collect their medical histories, allowing longitudinal analysis of many complex diseases. These datasets are typically accompanied by genotype data, whose effects on diseases are typically estimated as static values without reference to potential age varying effects. In this work we developed methods to study the relationship between genetic variations and complex diseases as a function of age. In the first step, we developed methods that focus on a single disease at a time, which we applied to infer the age-varying genetic risk profiles for common complex diseases. When applying the methods to 24 common diseases in the UK Biobank, we found a common decreasing pattern of genetic risk effect for several complex diseases, after using a frailty model to adjust for unobserved risk factors such as environmental factors. In the second step, we developed methods that look at many common diseases simultaneously, which we applied to infer age-dependent multi-morbidity profiles under a low-rank representation framework. We analysed the shared genetic variations underlying clusters of diseases as well as the genetic heterogeneity among subtypes of diseases implied by the comorbidity profiles. When jointly modelling 349 Phecodes that have more than 1000 occurrences in the UK Biobank, we identified several disease topics that contain genetically- correlated diseases. When assigning incident diseases in the UK Biobank to these topics, several complex diseases are stratified into subtypes that have different genetic profiles. Our results suggested that genetic risks are modulated by contexts including age and comorbid diseases. To better predict disease incidences and identify biological pathways, genetic information should be modelled jointly with other information available in biobank data sets.
Creation and chaos: myth and ideology in the ancient Near East and the Bible
Keywords: Genesis
Bible
Comparative mythology
Ideological criticism
Minimal Counterintuitiveness
Creation myth

This thesis reframes comparative mythological methodology in the context of recent developments in evolutionary anthropology. In doing so, it applies new insights into the origins and function of supernatural concepts in storytelling to biblical, Mesopotamian, Northwest-Semitic, and Egyptian myths.
Part 1 provides a broad overview of past theories and identifies a lack of methodological attention to ideological aspects of myth. It outlines Pascal Boyer’s minimal counterintuitiveness (MCI) paradigm and builds on it to arrive at an empirical definition of myth. Expanding further on this definition, a context-specific approach is developed, enabling a broad reading of myths as vehicles for group identity signals. Separately, the agency of mythographers and their original audience is reemphasised against universalist readings; myths are explicitly framed as deliberate and actively-composed texts.
Part 2 applies these insights to the well-preserved Mesopotamian mythical corpus, using the well-preserved creation and chaos myths from Sumerian, Assyrian, and Babylonian contexts as examples. A close reading of these texts against the background of MCI theory demonstrates their authors’ (or editors’) concern with contemporary politics, and reveals the in-group-specific nature of supernatural concepts utilised. Furthermore, a diachronic analysis of the key text, Enūma elîš, and its reception demonstrates that the promulgation of, and engagement with, these supernatural concepts was actively shaped by changing ideological concerns in different political contexts.
Part 3 raises a further methodological complication by introducing Hutcheon’s theory of adaptation. Combining MCI theory with this approach, this part considers the effect of adaptation on MCI concepts using several (likely adapted) biblical myths as case studies. Inthis context, the compositional process of the adaptations (Gen 1; Ps 29; Ps 104) must be understood as prescriptive, creating a new theological paradigm for its audience, rather than describing an existing one.
Essays on information, asset bubbles, and economic policy
Keywords: imperfect information
income inequality
overconfidence
asset pricing bubbles
monetary policy
fiscal policy

This work consists of three self-contained essays tackling independent research questions pertaining to information constraints, asset price bubbles, economic policy, or a combination thereof.
The first chapter tackles the problem of growing income inequality by weighing the effectiveness of an array of fiscal policies currently available to policy-makers. To do so, I evaluate the impact of alternative forms of public expenditure in an overlapping generations framework where households' ability to invest in the education of their offspring is constrained by various sources of heterogeneity. I find that the optimal use of public funds consists in a combination of public grants aimed at improving educational quality and an increase in the upper limit of student loans. The subsequent panel data analysis corroborates my results and suggests that parental income remains the largest determinant of earnings and inequality.
In Chapter 2, I turn my attention to the challenges posed by imperfect information about the source of asset price movements. I develop a New Keynesian model where stock prices contain a fundamental and a bubble component, both unobservable to agents and the central bank, who are forced to speculate about their value. I use this model to analyse the implications for investors' behaviour and monetary policy. I find that, under perfect information, a systematic increase in interest rates in response to growing bubbles exacerbates market volatility and welfare losses. For high levels of noise, the central bank should reverse its policy stance. However, due to the continuous underestimation of the size of bubbles, policy responses are perpetually inadequate.
Finally, Chapter 3 explores the extent to which cognitive biases can explain market anomalies such as the formation of large financial bubbles. To this end, I develop a stochastic bubbles framework with imperfect information about the probability of a future market crash, where investors are overconfident about the accuracy of their knowledge. I put forward a number of generalisable propositions about the relationship between overconfidence and bubbles in general equilibrium frameworks. In particular, I find that overconfidence can play a key role in the existence of bubbles and is able to rationalise excessive market movements. I quantify my results and test the validity of the framework in a numerical analysis.
Dynamic buckling instabilities in fluids and solids
Keywords: dynamic buckling
wrinkling
buckling
pattern formation
temporal cascade
coarsening

Many natural phenomena encountered in nature may be understood through the paradigm of buckling instability. Examples include the design of columns in structural engineering, the folding of geological formations, the collapse of blood vessels, and the fragmentation of uncooked spaghetti, to name only a few. The phenomenon of buckling has traditionally been seen only as a nuisance, but more recently it has also proven useful as a potential tool for pattern formation, particularly at small scales. Many studies have focused on the features of static buckling, particularly pattern formation.
This thesis focuses on how dynamic buckling affects the spontaneous selection of patterns in a number of canonical problems.
We first study the effect of curvature on dynamic buckling in circular geometries. We study the pattern observed when a ring made of either a viscous liquid or an elastic solid is subject to a suddenly applied external pressure. We develop numerical schemes to study the evolution of the ring’s profile and compare those results to linear stability analysis. A weakly nonlinear analysis is performed to understand the behaviour of the observed shape beyond the onset of instability, with results that compare well with both numerical and experimental work.
In the late stages of instabilities, buckles merge — the wrinkle pattern coarsens. To understand this coarsening we consider the non inertial problem of a beam sit- ting on a viscous layer. We explain how wrinkle coarsening occurs as the result of wave dispersion and quantify coarsening by presenting an asymptotic analysis of the governing equation. We also study the effect of confinement and show that it has a crucial effect on coarsening at late times. We develop an analytical expression for the effect of confinement, which allows us to better explain previously published experimental data. Finally, our numerical solution reveals a new regime as the wavelength of wrinkles become comparable to the size of the system. In this regime the dynamics is relatively slow with the system remaining for long periods with one particular mode before rapidly switching to another. We study this regime, the so-called temporal cascade, in detail.
The problems we are considering have different geometries and different material constitutive relations, but highlight a number of common themes. Mathematically, those systems are described by a Partial Differential Equation with a global constraint whose numerical solution is found by framing it in the language of Differential Algebraic Equations.
Heteroatom-substituted bicyclo[1.1.1]pentanes
Keywords: Bioisosteres
Sulfonyl halide
Photochemistry
Bicyclo[1.1.1]pentane
Atom transfer radical addition
Nitrogen Radical
[1.1.1]propellane
Giese reaction

The theme of this thesis is to explore novel methodologies to access useful heteroatom-substituted bicyclo[1.1.1]pentane (BCP) scaffolds. BCPs are utilised as non-classical bioisosteres and as a metabolically stable spacer unit in their own right within pharmaceutical and agrochemical industries, they have also found application in materials chemistry.
Firstly, we investigated the addition of nitrogen-centred radicals across the strained central bond of [1.1.1]propellane as an efficient entry to iodo-bicyclo[1.1.1]pentylamines (BCPAs). In an atom-transfer radical addition (ATRA) process, we demonstrated fragmentation of α-iodoaziridines for the formal addition of N,I across [1.1.1]propellane to give BCPAs. The developed methodology demonstrates good functional group tolerance and applicability to pharmaceutical analogues.
Having discovered that BCPA iodides were significantly more challenging to functionalise than carbon-substituted BCPs, due to expulsion of the amine component from anionic BCPA intermediates, the development of a novel C–C bond formation tolerant of heteroatom-substituted BCP halides was required. Through investigation into the use of photocatalysis as a means to generate BCPA radical intermediates, we demonstrated that the resident iodide of BCP(A) iodide compounds could be functionalised through a photocatalysed silyl-mediated Giese reaction. This transformation enables access to challenging and desirable N,C-disubstituted BCPAs, for example α-amino acid analogues. In combination, these two methodologies contribute a significant advancement to the field and provide access to aniline and N-t-butyl bioisosteres.
Following a serendipitous result from the synthesis of BCPA iodides, we discovered that sulfonyl halides, generated in situ from readily accessible sulfinate salts, add rapidly to [1.1.1]propellane under mild conditions and in exceptional yields. This methodology represents the first synthesis of sulfonyl BCP iodides and bromides.
A framework for interpreting the right to freedom of association of workers and trade unions in European human rights law
Keywords: worker empowerment
trade unions
freedom of association
Article 11 ECHR
collective labour rights

The right to freedom of association, as a labour right, has long been protected by Conventions 87 and 98 of the International Labour Organization, and by the European Social Charter. The European Convention on Human Rights and European Union law have more recently emerged as sources of protection of collective labour rights. This thesis identifies a particular concern arising from this development, namely that ECHR and EU norms that diverge from and conflict with ILO and ESC freedom of association guarantees could displace and undermine the authority of the latter, specialist mechanisms, which provide an overall higher level of protection. This thesis proposes that this concern could be addressed to a significant extent through the interpretation of ECHR and EU freedom of association guarantees in closer alignment with ILO and ESC norms. It first argues that there is a normative, moral justification for convergence between ECHR and EU human rights norms, and ILO and ESC specialist labour law norms. On this basis, it proposes that in interpreting ECHR and EU freedom of association guarantees, the respective Courts should look to ILO and ESC norms as key sources of authority; and that a divergent interpretation of these norms should be justified on the basis of appropriate reasons. These could be reasons pertaining to the text or aims of the relevant instruments and legal systems, particular institutional characteristics, or the fact that the ECHR and EU enforcement bodies are courts and not committees. The analysis concludes that the institutional concern cannot be completely resolved through the interpretation of ECHR and EU freedom of association guarantees in line with ILO and ESC norms, since differences between norms are sometimes well-justified. Nevertheless, the proposed interpretive framework could go significant distance towards achieving this goal, and make a substantial contribution to strengthening the protection of collective rights in Europe.
Measuring the masses of planets around young active stars
Keywords: radial velocity
young planets
Exoplanets
exoplanet detection
stars
AU Mic
extrasolar planets
Gaussian process
Astrophysics
stellar activity

A quarter century after the famous discovery of 51 Peg b, the radial velocity (RV) method remains a key exoplanet detection and characterisation method. For transiting planets, RVs allow us to measure mean densities and draw conclusions about the planets’ compositions. This is particularly valuable for young planets, which are sensitive probes of formation and evolution models. Stellar activity is the main factor limiting RV searches for both young planets and small, temperate planets around older stars. In this thesis, I developed and tested novel approaches to extract RVs from spectra using Gaussian process (GP) regression. I then used a multi-dimensional GP framework to model the impact of stellar activity on those RVs and to disentangle activity-induced and planetary signals in the data from a year-long intensive RV monitoring campaign of the bright, young M-dwarf AU Mic using the HARPS spectrograph. This enabled me and my collaborators to measure the masses of two transiting planets, which have previously been discovered by the TESS satellite, finding Mb = 11.7±5.0 M⊕ and Mc = 22.2±6.7 M⊕. As both planets are similar in size to Neptune, their contrasting densities represent a challenge for current planet formation models, and warrant further investigation. Finally, I also present extensions to the standard Generalised Least-squares Periodogram (GLS), which attempt to account for stellar activity explicitly. I used these to search for additional planets in the AU Mic system using both archival and new HARPS data, excluding the presence of any additional planets with RV semi-amplitudes ≥ 50 ms−1 and periods 20 ≤ P ≤ 1000days.
Investigation of sleep homeostasis: a chronic imaging study

Keywords: long-term imaging
neurobehavioural dynamics
sleep homeostasis

Drosophila shows complex behaviours but performs these with relatively few neurons. Genetic tools for mapping brain circuits and perturbing neurons, together with the ability to record neural activity, offer the potential to link behaviours with brain circuits and dynamics. Neurobehavioural dynamics are complex and short experiments do not capture dynamics occurring over multiple days.
To overcome this limitation, I developed a chronic imaging protocol which allows the recording of neurobehavioural dynamics of a fly living for days on a spherical treadmill under a two-photon microscope. To validate this approach, I followed the Ca2+ dynamics in a genetic line (23E10-GAL4) labelling the switch neurons controlling sleep and wake. Sleep was measured as locomotor inactivity lasting for 5 or more minutes.
I explored the relationship between the dendritic Ca2+ dynamics in the switch neurons and sleep. I found that some of the features describing the dendritic Ca2+ dynamics correlate with “future sleep” and the time of day.
To overcome another limitation of current experiments investigating sleep homeostasis, I developed a protocol to sleep deprive flies during imaging experiments. I proved that the protocol is effective in causing sleep rebound after sleep deprivation and does not affect the lifespan of the experimental fly.
Our study paves the way for new experiments investigating sleep homeostasis and the detrimental effects of sleep deprivation over extended periods of time. It is also a validation of the virtues of Drosophila as a model for systems neuroscience.