VictorJuiz/thesis huggingface dataset:
Investigating the cellular role of the deubiquitylating enzyme ZUP1, a novel player in the DNA damage response
Keywords: Interstrand crosslink repair
DNA damage response
Deubiquitylase
DNA repair
Genome-wide CRISPR screen

The DNA damage response (DDR) is a network of interrelated signal transduction pathways that identify and repair DNA lesions to maintain genome integrity. To coordinate the DDR, cells use post-translational modifications (PTMs) such as ubiquitin to modify and control protein fate and function. Importantly, ubiquitin signalling is a dynamic modification that can be edited or removed from substrates by deubiquitylating enzymes (DUBs). ZUP1 was recently discovered as the founding member of a new DUB class with selectivity against long K63-linked ubiquitin chains and a putative, but poorly defined, role in the DDR. This thesis aimed to improve our understanding of the cellular role of ZUP1 and define which DDR pathway(s) it functions in. To this end, I generated monoclonal ZUP1 knockout (KO) cell lines using CRISPR-Cas9 gene editing and found that these cells were sensitive to genotoxins that induce replication-coupled DNA damage, with hypersensitivity to the interstrand crosslinking agent mitomycin C (MMC), and the PARP inhibitors olaparib and talazoparib. Using the high-content immunofluorescence microscopy technique of quantitative image-based cytometry (QIBC), I then analysed the dynamics of key factors at stressed DNA replication forks and demonstrated that excess generation of ssDNA and persistence of RPA and RAD51 foci underlie the sensitivity of ZUP1 KO cells to MMC. Lastly, I investigated the chemogenetic interactors of ZUP1 in response to MMC in an unbiased manner using genome-wide CRISPR-Cas9 screening and identified potential synergistic interactions between ZUP1 and the factors BRCA2 and HELQ. Collectively, my results suggest that ZUP1 is a novel player in the response to replication-coupled DNA damage and provides new insight into its cellular roles.
The use of subwavelength structures to control and enhance the photoacoustic effect
Keywords: photoacoustics
subwavelength structures
transfer-matrix method

The photoacoustic effect describes the conversion of light to sound, via thermoelastic expansion, and is used extensively in cross-media applications as it combines the favourable properties of light in one medium with the favourable properties of sound in the other. Photoacoustic composites are used for efficient photoacoustic conversion and can be made from planar multilayered structures, comprised of thin layers of optically absorbing media, separated by layers of a thermally-responsive medium. The aim of this project was to formulate a one-dimensional model capable of simulating the acoustic signal generated from a multilayered structure with several absorbing layers. Then, using the model, the effect of subwavelength structures on the generated acoustic signal was investigated for weakly- and strongly-absorbing layers. The transfer-matrix method was used to solve the governing photoacoustic wave equation in the frequency domain and the source function of the second-order differential equation was kept as general as possible so that the user could choose any function to describe the optical absorption profile of the structure. The model was verified by comparing its results with those from previous studies. It was found that acoustic resonant effects could be induced in structures with optically-thin or optically-thick absorbers but that the effect was more pronounced in the spectra of optically-thick absorbers. Furthermore, the features of the frequency spectrum could be explained by considering the poles and zeros of the transfer-matrix when source terms were included. Thus, these observations stimulated the design of a photoacoustic structure with enhanced directivity by using an acoustic high-reflectance coating. The simulated structure was capable of increasing the amplitude of the generated acoustic signal by about 15% at a target frequency, compared to previous methods. These findings indicate that as new photoacoustic composites have reduced dimensions (<10nm), the resonant properties of both light and sound could be utilised to enhance the conversion from optical to acoustic energy.
Understanding loss of consciousness under general anaesthesia using multimodal neuroimaging
Keywords: loss of consciousness
slow wave activity saturation
neuroimaging
electroencephalography
anaesthesia
consciousness
magnetic resonance imaging
general anaesthesia
neuroscience

Despite major advancements in consciousness science over the past few decades, how anaesthesia causes loss of consciousness remains incompletely understood and the translation from basic science to clinical practice has been limited. Recent concurrent electroencephalography (EEG) and functional magnetic resonance imaging (FMRI) evidence indicates that a state of complete perception loss is achieved under general anaesthesia when slow wave activity in the brain reaches saturation. Slow wave activity saturation (SWAS) is therefore a potentially clinically relevant end point for titration of anaesthesia.
We have developed a prototype system for titrating anaesthesia to SWAS within an individual. The system features EEG and anaesthesia data input, modelling of slow wave power and detection of SWAS, and visualisation of the model output in a graphical user interface. The prototype system was applied in a patient pre-surgery study (Study 1) which focused on clinical translation of SWAS, and a healthy volunteer EEG-MRI study (Study 2) which focused on experimental validation of SWAS.
We successfully applied the prototype SWAS system in twelve patients (Study 1) and twenty-three healthy volunteers (Study 2). No subjects in either Study 1 or Study 2 were behaviourally responsive when held at SWAS and none had recall of events from when they were held at SWAS.
In Study 2, we also acquired measures of cerebral blood flow (CBF), and resting and task-related FMRI data during wakefulness and when held at SWAS. When held at the SWAS state, CBF was significantly elevated compared to wakefulness. Furthermore, we found that the brain was unresponsive to external stimulation when held at SWAS even when controlling for the observed CBF changes. Finally, we found that this was accompanied by disruption of functional connectivity in the thalamocortical system and in known resting state networks. Our findings provide further evidence that SWAS is a state of perception loss and a clinically relevant target for surgical anaesthesia.
Branching and fragmenting particle systems in biology
Keywords: fragmentation processes
branching particle system
cell-free DNA
superprocess
lookdown construction

We introduce and study two new classes of branching and fragmenting particle systems in biology. The first class of branching particle systems with interactions model spatially-structured populations with density-dependent birth and death mechanisms. Our spatial model describes spatially heterogeneous populations using point measures, considering birth and death rates based on spatial position and local population density. Notably, our model includes a juvenile phase, where offspring mature with a density-dependent probability. This results in novel scaling limits: an interacting superprocess, a nonlocal partial differential equation (PDE), and a classical PDE (in which the diffusion term is nonlinear). Furthermore, using a lookdown representation, we retain information about genealogies and, in the case of deterministic limiting models, use this to deduce the backwards in time motion of the ancestral lineage of a sampled individual. We observe that knowing the history of the population density is not enough to determine the motion of ancestral lineages in our model.
In our second class of models, motivated by using cell-free DNA (cfDNA) as a biomarker, we capture three mechanisms governing cfDNA fragmentation in the bloodstream. Our Markovian model, FRIME (Fragmentation, Immigration, and Exit), allows the simulation of cfDNA fragment profiles by sampling from its stationary distribution. We validate the model by comparing simulated profiles with mitochondrial and genomic cfDNA fragments, finding consistency with experimental observations. We employ probabilistic tools and the theory of fragmentation processes to establish the first moments of FRIME processes mathematically. This simulation framework improves our computational understanding of DNA fragmentation dynamics in the bloodstream and has the potential to underpin tools for the analysis of liquid biopsy data.
Analysis of Navier--Stokes--Fokker--Planck systems for incompressible dilute polymeric fluids
Keywords: Fokker--Planck equations
Galerkin method
Nonlinear PDEs
Kinetic polymer models
Incompressible Navier--Stokes equations

We show the existence of large-data global-in-time weak solutions to various classes of coupled bead-spring chain models with finitely extensible nonlinear elastic (FENE) type spring potentials for incompressible dilute polymeric fluids in a bounded domain in Rd, d = 2 or 3. The governing system consists of the transport equation and the Navier--Stokes equation coupled to the Fokker--Planck equation through the elastic extra-stress tensor which is defined by the Kramers expression. The proofs are based on truncating the probability density function and approximating with Galerkin semi-discretizations on the spatial domains. We derive uniform bounds independent of the Galerkin and truncation parameters; then with weak compactness and compensated compactness techniques, we pass to the limits in the sequences of Galerkin approximations and in the truncation level. The technical tools involve using Nikolski\u{\i} norm estimates to derive uniform estimates for fractional time derivatives and using various generalizations of the Aubin--Lions Lemma to deduce strong convergence of approximating sequences. We also apply the Div-Curl Lemma and Vitali's Convergence Theorem to deduce the strong convergence of the sequence of approximations of the probability density function in L1
. We first focus on homogeneous dilute polymeric fluids. The key feature is the polymer-number-density-dependent viscosity coefficient appearing in the Navier--Stokes equation. Then we move on to nonhomogeneous dilute polymeric fluids, featuring the presence of a density-dependent and polymer-number-density-dependent viscosity coefficient in the Navier--Stokes equation and a density-dependent drag coefficient in the Fokker--Planck equation. Finally, we consider nonisothermal homogeneous dilute polymeric fluids. To complete the nonisothermal Navier--Stokes--Fokker--Planck system, the temperature evolution equation is also introduced to form a thermodynamically consistent model. To simplify the nonisothermal model, we present the existence proof in the case of a corotational Fokker--Planck equation.
P450–Mediated azepane natural product synthesis
Keywords: Natural Product - Total Synthesis - Biocatalysis - P450 - C-H Activation - Balanol - Cephalotaxine

Chapter 1 introduces methods and applications for C–H activation, cytochrome P450 enzymes and their uses in synthesis, and the relevant families of compounds in which the present work takes place.
Chapter 2 describes the strategy and the attempts of building the natural product balanol and analogues via C–H amination from enzymatically made substrate, along with new bicyclic lactones synthesised via C–H activation.
Chapter 3 presents progress in the synthesis of the carbon skeleton of the natural product cephalotaxine via an intramolecular Schmidt reaction, along with a significantly improved literature method for assembling the cephalotaxine core.
Chapter 4 explores the P450-catalysed oxidations of the previously made cephalotaxine core structure, to access new analogues of this natural product and to draw a P450-reactivity profile of this molecule.
Soil-lubricant-structure interface mechanics for microtunnelling
Keywords: pipejacking
friction
tunnelling

Pipe-jacking is a trenchless underground construction technique commonly used to create conduits for conveying services such as electrical cables, gas, sewerage, or water pipes whilst keeping surface disruption to a minimum. The installation process consists of a tunnel boring machine (TBM) undertaking controlled excavation at the front of a string of pipes, whilst thrust is applied from a jacking frame located at the rear of the string. As the jacking frame advances the machine and pipe string, lubricant (typically comprising Bentonite clay) is simultaneously injected into an overcut between the pipes and soil formed by the TBM . This process is periodically paused whilst pipes are added and for planned or unplanned stoppages. Currently, there is no commonly accepted model for the behaviour of the soil-lubricant-structure (SLS) interface around these tunnel pipes during advances and stoppages, which results in excessive conservatism in the design stage.
This thesis explores the behaviour of the SLS interface using a combination of field and laboratory study. Two custom instrumented jacking pipes have been developed and deployed during two instrumented tunnel drives. Strain gauges, pore pressure sensors and contact stress sensors were used to identify the location and magnitude of stresses at the interface. These field studies are supplemented by analysis of 12 industry case histories, which provide insight into the SLS interface response in different ground conditions.
The field study program is complemented by a suite of laboratory scale testing of tunnelling lubricants and SLS interface behaviour. To facilitate this, a novel scale interface test apparatus has been developed. The plane strain apparatus has been designed to faithfully recreate the conditions at the SLS interface during tunnelling by incorporating such key features as: discrete lubricant injection, large uni-directional shear strains, variable normal stress, and the creation of an overcut at the interface. The apparatus has been used to complete a test program examining the influence of these factors on the SLS interface conditions during tunnelling in sand. To guide this experimentation, an elemental study has been completed to examine the salient properties of common tunnelling lubricants and explore their interaction with sand in isolation.
The findings from the laboratory experimentation and SLS interface behaviours observed during field monitoring are then applied in the development of a new conceptual model of the SLS interface during tunnelling, from which an empirical model of friction prediction is derived that predicts interface friction in different ground conditions during tunnelling. Using this new understanding of the mechanics of the SLS interface, methods to minimise interface friction are also proposed.
Responsive hybrid nanoparticles for MR imaging
Keywords: pH-responsive
K+-responsive
T2 contrast agents
contrast agents
MRI
stimuli-responsive
T1 contrast agents
polymer micelles
nanoparticles
high field imaging
mesoporous silica nanoparticles

The design of nanoparticulate contrast agents that possess an improved relaxometric capacity, stimuli-responsive or otherwise, is a necessity for improved reporting of disease pathology by MRI. To achieve this, much work has focused on engineering the supporting nanoparticle scaffold to introduce functional chemical moieties that can engender a disease-specific reporting capability or augment the generated image contrast. The work included in this thesis emphasises how both can be achieved.
Contrast agents that can enable effective enhancements in image contrast at ultrahigh magnetic fields (≥ 7 T) are desirable, but rare. In Chapter 2 it is shown that by varying the Dy3+-loading density within a mesoporous silica nanoparticle (MSN) scaffold, the dominant Curie-promoted relaxation pathway can be progressively tuned to optimise T2 contrast at fields as high as 11.7 T. This constitutes the first example detailing the influence of paramagnet-loading on Curie-promoted T2 outer-sphere relaxation.
Current clinically employed contrast agents suffer from low longitudinal relaxivity values at commonly used field strengths, with none possessing an environmentally-responsive imaging capability. In Chapter 3, the modification of MSNs with potent hydrogen bond acceptors (HBAs) is shown to dramatically influence the mobility of internalised water to enhance T1 image contrast at clinically relevant fields. The chemical principles derived in this work were applied to generate a potassium-responsive contrast agent by modulating the HBA strength of immobilised K+-specific crown ethers on K+-binding. Notably, this work is the first report of a nanoparticle-based K+-responsive contrast agent.
Polymer-based contrast agents are desirable due to their high biocompatibility, as well as tuneable size/length, shape, and composition at the point of synthesis. Additionally, pH-responsive reporting is aspired in the goal of achieving disease-specific reporting where pathologies deviate from the norm. Chapter 4 illustrates the design of pH-responsive MRI contrast agents, where a reversible switch in polymer strand conformation directly impacts the rotational correlation times of immobilised Gd-chelates, generating a significant switch (~ 50%) in positive image contrast. This constitutes the first reversible pH-responsive polymeric MRI contrast agent, possessing one of the highest r1 values for any micelle contrast agent at both 1.5 T and 3 T.
Design of a 3D-printed soft robotic hand with distributed tactile sensing for multi-grasp object identification
Keywords: object identification
3D printing
soft robotics
tactile sensing
robotic hands

Tactile object identification is essential in environments where vision is occluded or when intrinsic object properties such as weight or stiffness need to be discriminated between. The robotic approach to this task has traditionally been to use rigid-bodied robots equipped with complex control schemes to explore different objects. However, whilst varying degrees of success have been demonstrated, these approaches are limited in their generalisability due to the complexity of the control schemes required to facilitate safe interactions with diverse objects. In this regard, Soft Robotics has garnered increased attention in the past decade due to the ability to exploit Morphological Computation through the agent's body to simplify the task by conforming naturally to the geometry of objects being explored. This exists as a paradigm shift in the design of robots since Soft Robotics seeks to take inspiration from biological solutions and embody adaptability in order to interact with the environment rather than relying on centralised computation.
In this thesis, we formulate, simplify, and solve an object identification task using Soft Robotic principles. We design an anthropomorphic hand that has human-like range of motion and compliance in the actuation and sensing. The range of motion is validated through the Feix GRASP taxonomy and the Kapandji Thumb Opposition test. The hand is monolithically fabricated using multi-material 3D printing to enable the exploitation of different material properties within the same body and limit variability between samples. The hand's compliance facilitates adaptable grasping of a wide range of objects and features integrated distributed tactile sensing. We emulate the human approach of integrating information from multiple contacts and grasps of objects to discriminate between them. Two bespoke neural networks are designed to extract patterns from both the tactile data and the relationships between grasps to facilitate high classification accuracy.
Body composition and heart failure in the UK Biobank: a prospective study of 500,000 adults
Keywords: UK Biobank
obesity
fat mass
heart failure
body mass index
body composition
fat-free mass
mendelian randomisation

Background: Although obesity is an established risk factor for heart failure (HF), the independent relevance of body fat distribution and fat-free mass (body composition measures) to risk of HF and its subtypes remains unclear.
Methods: UK Biobank is a prospective study of 0.5 million participants enrolled between 2006 and 2010 across the UK. Cox regression analyses were used to determine the prospective associations of long-term average (‘usual’) levels of body composition measures (BMI, WC, WHR, body fat mass [BFM], trunk fat mass [TFM] and body fat-free mass [BFFM] with incident HF (and its subtypes); hazard ratios (HR) were expressed as per 5 kg/m2 usual BMI, or equivalent. The potential underlying mechanisms were investigated by determining the associations between mutually adjusted imaging-derived body composition measures and left ventricular ejection fraction (LVEF) using multivariable linear regression. Mendelian randomisation was then used to assess further, the causality of the associations between BMI and WHR with incident HF.
Results: Among 428,087 participants (mean age 56 years, 44% male, mean BMI 27.2 kg/m2) without prior cardiovascular disease, 10,455 first-ever HF events occurred over a median follow-up period of 13.8 years. Overall, HF risk was more strongly associated with central adiposity (WC adjusted for BMI; HR 1.38, 95% CI 1.32-1.45) than general adiposity (BMI adjusted for WC; HR 1.22, 1.16-1.27); although BFM remained directly related to HF after adjustment for BFFM, the association of BFFM with HF was almost completely attenuated when adjusted for BFM. In analyses of HF subtypes, risk of HF with preserved ejection fraction (HFpEF) was strongly and independently associated with BMI (HR adjusted for WC, 1.66, 1.37-2.00) but not with WC (HR adjusted for BMI, 0.90, 0.73-1.12), while HF with reduced ejection fraction (HFrEF) was independently associated with WC (HR 1.38, 1.16-1.63) but not with BMI (HR 1.13, 0.97-1.32). In imaging analyses of body composition measures with LVEF, only visceral adipose tissue (VAT) was independently associated with lower LVEF (β=-0.45; 95% CI: -0.60, -0.31 per SD). Genetically elevated adiposity measures were directly and log-linearly associated with HF risk (BMI: HR 1.93; 1.77-2.11 and WHR: 1.35; 1.19-1.52).
Conclusion: This large-scale study quantifies the conventional and genetic associations between body composition measures and HF. In addition, it describes the independent relevance of different body fat distribution measures to HF subtypes, suggesting different mechanisms may be driving their aetiopathogenesis.