VictorJuiz/thesis huggingface dataset:
Inhibitory superagonistic antibodies as novel therapeutics

Immune cells express many different receptors capable of modulating their behaviour, with inhibitory immunoreceptors being especially important for maintaining immune tolerance by suppressing autoreactivity. Therapeutic antibodies capable of inducing inhibitory immunoreceptor signalling could, in principle, be useful tools for the treatment of autoimmune diseases. The mechanistic basis of signalling by so-called “superagonist” antibodies reactive with immunoreceptor family receptors are becoming increasingly well understood, with the simultaneous binding of a membrane proximal epitope on the immunoreceptor, and Fc receptor engagement, both appearing to be critical requirements. We sought to examine whether the superagonistic activity of an inhibitory antibody against hBTLA could be directed to specific tissues, by making it engage a tissue cell surface antigen in lieu of the Fc receptor in vivo. For this, murine bispecific antibodies were generated, and the approach showed early promise, although further experiments are needed to confirm and extend the initial findings. It is also unknown whether the requirements of immunoreceptor superagonists apply to other receptor families such as the cytokine receptors. To investigate this, we sought to generate murine bispecific IL-10R agonist antibodies capable of dimerising IL-10R and IL-10R. However, none of the anti-IL-10R bispecific antibodies exhibited agonistic activity in vitro or in vivo, indicating that merely co-localising the two receptor chains is insufficient to trigger signalling and that there are likely to be additional strict geometric requirements for signalling. Both sets of experiments relied on the generation of murine bispecific antibodies and two different methods described in the literature were tried. Only one of these was found to produce high quality bispecific antibody. Finally, this thesis describes the use of new surface plasmon resonance (SPR)-based techniques for assessing the functional bispecificity of such molecules. Both a sandwich SPR-based assay and an Rmax comparison SPR-based assay were each developed, with the two complementary approaches producing similar results. Overall, the thesis strengthens the idea that there is considerable scope for generating a large variety of potentially useful therapeutic agonists.

Keywords: receptor agonism
bispecific antibodies
immunology
surface plasmon resonance (spr)
Advisor: Davis, S
Cornall, R
Active tectonics and palaeoseismicity of the Northern Tien Shan and Dzhungaria

This thesis focuses on the active tectonics and the palaeoseismicity around the Dzhungarian Basin. The study of surface ruptures is crucial to comprehending the earthquake occurrences of faults. I investigate geomorphic displacements along the boundary strike-slip Dzhungarian Fault using high-resolution drone and Pléiades satellite imagery. The results reveal possible single-event fault slip along the Dzhungarian Fault in the most recent earthquake. I suggest this earthquake is likely linked with a previously identified palaeo-earthquake rupture on the Lepsy Fault. With a joint rupture of the two faults, it could generate an earthquake with a magnitude up to Mw 8.4, which would be amongst the largest magnitude inferred for a continental earthquake. I further use Quaternary dating techniques and InSAR time-series analysis to determine the geological and geodetic slip rates of the Dzhungarian Fault. The results show that the northern Dzhungarian Fault has a long-term uplift rate of 0.6 ± 0.2 mm/yr, whilst the southern Dzhungarian Fault has geological and geodetic strike-slip rates consistent with a range of 2.1 – 4.7 mm/yr. I also re-investigate three historical earthquakes with magnitudes greater than Mw 7.0: the 1812 Nilke, the 1906 Manas and the 1944 Xinyuan Earthquakes in the Borohoro Shan. By re-analysing source parameters and integrating published data, seismological analysis results, and remote-sensing mapping, the study demonstrates the significance of both reverse and strike-slip faulting in the regional seismotectonics, which also indicates the deformation kinematics of the Borohoro Shan as being in a transpressional zone. I collate my results with those from the literature to propose updated earthquake scaling relationships of intra-continental earthquakes. Finally, this study suggests that the Dzhungarian Basin and its surrounding tectonic units are rotating anticlockwise to accommodate both the N-S crustal shortening and the left-lateral shearing within a large-scale zone from the SW Tien Shan to the Altay Mountains.

Keywords: Palaeoseismicity
Tien Shan
Dzhungaria
strike-slip fault
intra-continental earthquakes
InSAR
quaternary dating
Advisor: Walker, R
Grützner, C
Daout, S
The role of ADAM10 and mucin-like molecules in modulating cell-cell interactions

To preserve the non-inflammatory nature of apoptotic cell death, a rapid removal of apoptotic cells, known as efferocytosis, is required to maintain tissue homeostasis. Uptake of apoptotic corpses by phagocytes is facilitated by the molecular expression and secretion of find-me and eat-me signals by apoptotic cells, balanced with negative efferocytic don’t eat-me sig- nals and don’t-come-close-to-me barriers. Transmembrane mucins, which are traditionally associated with mucosal tissues, are heavily glycosylated proteins and major components of the cell glycocalyx. Their extensive ectodomains protrude far from the cell surface, thereby influencing adhesion and forming a protective barrier. Several mucins are excluded from the immunological synapse, and some have been reported to undergo removal from the cell surface of activated or apoptotic cells. This suggests that the mucin shield necessitates ac- tive regulation to permit cell-cell interactions. The mechanism underlying mucin regulation during efferocytic clearance and T cell activation remain unclear. The main theme of this study explores a novel efferocytic pathway centered around the cleavage of specific mucins on apoptotic T cells, which otherwise function as a don’t eat-me barrier for macrophages. Data presented in this thesis show that the mucins CD43, MUC1 and PSGL-1 are selectively cleaved off the membrane of apoptotic T cells by the metalloprotease ADAM10, and further analysis into the pathway revealed that this process requires activity of the apoptosis-induced phosphatidylserine (PS) scramblase XKR8. When mucin cleavage is prevented, efferocytic uptake by macrophages is reduced in an in vitro assay, and if mucins are removed by a pan- mucinase enzyme, uptake is increased. A related theme of my work is the regulation of mucin expression on activated T cells. In summary, transmembrane mucins have broad impacts on modulating immune cell interactions, and my thesis contributes to our understanding of mucin expression and regulation on T cells under steady-state conditions, activation, and apoptosis.

Advisor: Sattentau, Q
DNA sequence driven machine learning for modelling replication timing

All human somatic cells copy their entire genome during mitotic replication, in the S-phase of the cell cycle. Replication timing (RT) is the temporal order of genome replication in S-phase and has been shown to have consistent global “profiles” across a wide range of tissues and diseases. We demonstrate that while there are many factors that influence the specific RT characteristics of individual cell types, there is a strong link between the DNA sequence composition and the overall RT behaviour. This is achieved by accurately modelling the aggregate profiles from 131 RT experiments constituting 56 unique human cell types, using only engineered features of the DNA sequences as input. We then derive insight into how the composition of DNA sequences impacts RT values, by observing the impact of in silico sequence modifications on model predictions. We further extend our modelling towards cell-type specific predictions with a single model by incorporating a minimal source of extra information, ATAC-seq, which provides context for chromatin organisation. The obtained machine learning models, along with the underlying exploratory data analyses and feature engineering, are both useful for prediction of RT and shed light on the underlying DNA sequence basis of the replication phenomenon.

Keywords: replication
replication timing
machine learning
genetics
Advisor: Sahakyan, A
DeBruijn, M
Antibodies, B cells, and immune tolerance in immunotherapy treated oesophageal cancer

Oesophageal cancer (OC) is a leading cause of cancer mortality that is rapidly rising in prevalence in many parts of the world. Immune checkpoint inhibitors (ICI) have revolutionised treatment of many cancer types and were recently approved by the FDA to treat advanced OC. However, there are still many patients who do not exhibit an improved outcome in response to ICI therapy, and predictive biomarkers are lacking. Studies of multiple cancer types have shown that development of immune related adverse events (irAEs) during ICI treatment is associated with good clinical outcome, suggesting that the baseline immune activation of an individual may influence their response. Similarly, the presence of tertiary lymphoid structures, which are sites in which B cells differentiate into antibody secreting cells, in tumours hasrecently been shown to predict improved clinical outcome to ICI treatment, suggesting that production of tumour-reactive antibodies by intra-tumour B cells may contribute to an effective anti-tumour immune response. Despite this, there is a lack of studies of ICI treated OC which either evaluate markers of baseline immune activation, such as autoantibodies (AAbs), as predictive biomarkers of clinical outcome, or characterise antibodies produced by intratumour B cells. In this thesis, I extensively profile the circulating AAbs and peripheral blood mononuclear cells (PBMCs) of ICI treated OC patients from the LUD2015-005 clinical trial to identify novel and distinct signatures predictive of good clinical outcome and development of irAEs during ICI treatment. Further, through transcriptional profiling of OC tumours I show evidence of fully mature B cell responses and identify B cells expressing tumour-reactive antibodies. In summary, this work characterises the role of baseline immune activation in ICI patient clinical outcomes, and expands our understanding of mechanisms that predispose to good clinical outcome or irAE development during ICI treatment. The validation of these results in larger independent cohorts could inform patient treatment decisions based on biomarkers predictive of clinical outcome.

Keywords: immunotherapy
autoantibodies
immune related adverse events
cancer
immune tolerance
B cells
oesophageal cancer
clinical trial
Advisor: Lu, X
Dustin, L
Description of a novel MHC class II restricted allogeneic TCR T cell therapy for acute myeloid leukaemia

Acute myeloid leukaemia (AML) is an aggressive blood cancer that can be treated with allogeneic haematopoietic stem cell transplantation (allo-HSCT). Although allo-HSCT reduces the chance of relapse because of the Graft-versus-leukaemia (GvL) effect, it is also associated with the Graft-versus-Host Disease (GvHD). This and other treatment or disease related complications mean that only around half of transplanted AML patients survive at 3-years[1]. To harness the GvL effect, on-going research is trying to identify novel GvL-specific allogeneic peptide antigens presented by the major histocompatability complex (MHC), called minor histocompatability antigens (miHA). However, it remains unclear which miHAs mediate a successful GvL effect and what GvL-specific T cell functions are associated with it. This work describes a novel HLA-DP-restricted PADI4 miHA response identified as part of a previous allogeneic antigen screen in a cohort of AML patients with long-term remission post-transplant. Antigen-specific allogeneic T cells were successfully isolated and their T cell receptor (TCR) transferred to third-party primary T cells. PADI4 TCR T cell activation was seen to cancer cell lines, where it could also exert a growth inhibitory effect. Although this work did not show evidence of direct T cell activation to primary leukaemia samples, leukaemia-derived antigen was successfully presented by primary monocyte-derived dendritic cells. PADI4 miHA expression is haematopoietically restricted, suggesting no reactivity to the GvHD target tissues. However, PADI4 TCR T cell activation, without target cell killing, was seen to healthy monocytes. Overall, this data supports the idea that the PADI4 miHA response could exert an anti-leukaemic or a broader anti-haematopoietic effect. This work provides an important starting point to further investigate the PADI4 TCR for its anti-leukaemic effect and the importance of the PADI4 miHA response in other AML patients. It also highlights the role of CD4+ MHC class II-restricted T cell responses in GvL.

Keywords: bone marrow transplantation
acute myeloid leukaemia
immunotherapy
Advisor: Vyas, P
Borrow, P
Chakraverty, R
McMichael, A
Novel pneumatic circuit for the computational control of soft robots

Soft robots are of significant research interest in recent decades due to their adaptability to unstructured environments and safe interaction with humans. Soft pneumatic robots, one of the most dominant subsets of soft robots, utilize the interaction between soft elastomeric materials and pressurized air to achieve desired functions. However, the systems currently used for signal computation and pneumatic regulation often make use of rigid valves, pumps, syringe drivers, microcontrollers et al. These bulky and non-integrable devices limit the performance of pneumatically-driven soft robots, carrying challenges for the robot to be miniaturized, untethered, and agile. This DPhil aims to develop pneumatic circuits that can be integrated into the soft robot bodies while performing both onboard computation and control.
This thesis presents our contributions towards the aforementioned objective step by step. Firstly, we designed a 3D-printable bistable valve with tunable behaviours for controlling soft pneumatic robots. As an integrable control device, the valve stores one bit of binary information without requiring a constant energy supply and correspondingly controls a pneumatic chamber. Secondly, in order to reduce the number of valves required to control multi-chamber soft robots, we introduced a modular approach to design multi-channel bistable valves based on the previous work. Thirdly, in order to achieve continuous pressure modulation with integrable devices, we designed a soft proportional valve, utilizing the continuous deformation of Magnetorheological Elastomer (MRE) under magnetic flux. Apart from the analogue activation manner, this design also ensures a fast response time, operating at a time scale of tens of milliseconds, much shorter than the mechanical response time of most soft pneumatic actuators. Fourthly, to achieve onboard proportional control of multi-chamber soft robots, we developed an MRE valve array with an embedded cooling chamber. Physical experiments showed that our MRE valve array ensured the independence and accuracy of each valve unit within it, with a significantly lowered temperature of 73.9 o
C under 5 minutes of operation. Lastly, we developed an open-source software toolbox supporting the design of integrable pneumatic logic circuits to enhance their accessibility and performance. The toolbox comes with a graphical user interface (GUI) to take users' desired logic functions in the form of a truth table and a set of 2D space constraints related to the available space onboard the robot. It then schedules the pneumatic circuit which performs the desired computation within the space constraints and produces a 3D-printable CAD file that can be fabricated and used directly.
The work presented in this thesis enables the community to simplify the process of integrating control devices into soft pneumatic robots, thereby paving the way for a new generation of fully untethered and autonomous soft robots.

Keywords: soft robotics
pneumatic circuit
computation
magnetorheological elastomer
Advisor: Maiolino, P
Random convex hulls and kernel quadrature

Discretization of probability measures is ubiquitous in the field of applied mathematics, from classical numerical integration to data compression and algorithmic acceleration in machine learning. In this thesis, starting from generalized Tchakaloff-type cubature, we investigate random convex hulls and kernel quadrature.
In the first two chapters after the introduction, we investigate the probability that a given vector θ is contained in the convex hull of independent copies of a random vector X. After deriving a sharp inequality that describes the relationship between the said probability and Tukey’s halfspace depth, we explore the case θ = E[X] by using moments of X and further the case when X enjoys some additional structure, which are of primary interest from the context of cubature.
In the subsequent two chapters, we study kernel quadrature, which is numerical integration where integrands live in a reproducing kernel Hilbert space. By explicitly exploiting the spectral properties of the associated integral operator, we derive convex kernel quadrature with theoretical guarantees described by its eigenvalue decay. We further derive practical variants of the proposed algorithm and discuss their theoretical and computational aspects.
Finally, we briefly discuss the applications and future work of the thesis, including Bayesian numerical methods, in the concluding chapter.

Keywords: hypercontractivity
nyström approximation
random convex hulls
kernel quadrature
cubature
Advisor: Lyons, T
Oberhauser, H
Identification and characterisation of chloroplast 3C and 4C monocarboxylate and dicarboxylate transporters involved in the C4 cycle

C4 photosynthesis is a highly efficient form of photosynthesis that utilises a biochemical pump to concentrate CO2 around rubisco. This biochemical pump is dependent on multiple transport steps to move metabolites between organelles and between cells. However, the transporters that carry out several of these transport steps have evaded identification or characterisation. This lack of molecular characterisation is a major gap in our understanding of terrestrial photosynthetic biology, and also represents a significant barrier to attempts to engineer C4 photosynthesis into C3 crop species to improve yield. This thesis aims to address this problem and identify and characterise some of the missing transporters of the C4 pathway. The first half of this thesis is focussed on the characterisation of the HATCH1 transporter, demonstrating its function in E. coli and assessing the impact of the loss of this transporter (and its paralog) on C4 photosynthesis in Setaria viridis. Ultimately, I demonstrate that HATCH1 is involved in, but not necessary for, C4 photosynthesis and likely acts redundantly with other unknown transporter(s). The second half of this thesis concerns the identification and molecular characterisation of putative metabolite transporters of the C4 cycle in Zea mays. Whilst HATCH1 and HATCH3.1 were identified as candidate C4 cycle transporters, in planta data does not support this. In vitro and in planta data suggest a potential role for another candidate transporter in transport of C4 cycle metabolites at the chloroplast envelope of the bundle sheath cell. Together the results from this thesis increase our understanding of intracellular metabolite transport in C4 plants, and bring us closer to being able to engineer this trait into C3 plants.

Keywords: Photosynthesis
C4 photosynthesis
Chloroplast transporters
Advisor: Kelly, S
Development of functional group tolerant and room temperature hydrogen borrowing enolate alkylation reactions

This thesis describes work completed to expand the scope of hydrogen borrowing enolate alkylation reactions. It was hypothesised that the development of a room temperature reaction would allow utility of a breadth of chemical space previously undemonstrated in these reactions at high temperatures (80–180°C). The first strategy to achieve this was via the generation of excited state intermediates of the hydrogen borrowing cycle using visible light energy and a designed catalyst. A room temperature visible light driven reaction was realised and detailed mechanistic studies unveiled the role of visible light.
Later a light independent room temperature reaction was discovered and further developed to vastly expand the usable chemical space in hydrogen borrowing enolate alkylation reactions. A diverse range of nitrogen rich heterocycles were also demonstrated at higher temperatures (85°C) and mechanistic studies explained the need for anaerobic conditions in the reaction at room temperature.

Keywords: iridium
methodology
borrowing hydrogen
ketone alkylation
hydride
organic chemistry
organometallic
mechanistic studies
general
complexes
photochemistry
enolate alkylation
functioal group diverse
alcohols
catalysis
room temperature
hydrogen borrowing
mild
Advisor: Smith, M
Donohoe, T
Tailored nanocrystal catalysts

The thesis explores the synthesis, characterization, and simulation of the heteroepitaxial monometallic (Ni, Ag, Pd) and bimetallic (Ni@Ag) systems on SrTiO3 substrates.
In monometallic systems, the morphology of nanocrystals is shaped by the combined influence of thermodynamics and kinetics. Factors like crystal volume, metal species, substrate terminations, deposition temperature, post-annealing temperature, and duration collectively influence the nanocrystal’s shape. Extended post-annealing shows a strain relaxation characterized by increased crystal height.
In some monometallic systems, a transition is observed from multi-twinned nanoparticles to single crystals. Comparisons across these systems reveal that factors such as surface/interface energy, elastic constants, surface stress effect, and twin boundary energy collectively influence the critical size at which this transition happens.
The synthesis of Ni@Ag core-shell nanoparticles on SrTiO3(001) is achieved via sequential deposition and annealing at 500◦C. Scanning tunneling microscopy (STM) images highlight a transition from mixed shapes to uniform truncated pyramidal shapes with increased annealing temperature. The h/l ratio analysis, based on STM images, further suggests a core-shell structure. X-ray photoelectron spectroscopy (XPS) results display a pure Ni peak only in the annealed sample, and the selective Ag removal by sputtering rules out the possibility of Ni-Ag alloy formation.
The strain energy in the Ni and Ni@Ag systems was simulated using the finite-element method. The strain energy displays a layered distribution. A simulation for the observed heightening effect for strain energy relaxation is provided. In the Ni@Ag-SrTiO3(001) system, the Ag shell consistently exhibits compressive strain, while the Ni core shows tensile strain. The simulations further reveal that the smaller height-to-length ratio in Ni@Ag, in comparison to the pure Ni core, results from the compressive strain in the shell, corroborating previous experimental findings.
These findings broaden our understanding of heteroepitaxial systems on SrTiO3 substrates and the influence of epitaxial strain on morphologies. This knowledge serves as a stepping-stone towards enhanced synthesis of tailored nanomaterials for a broad range of applications.

Keywords: epitaxial strain relaxation
scanning tunneling microscopy
strontium titanate
heteroepitaxy
finite-element method
x-ray photoelectron spectroscopy
Advisor: Castell, M