VictorJuiz/thesis huggingface dataset:
Plantiness: Re-evaluating plant human relationships across temporal landscapes in Britain
Keywords: more-than-human
plants
archaeobotany
theory
prehistory

‘Plantiness’ explores the notion that plants are lively, active beings with the ability to shape and change us as we have also done to them. This theory of reciprocity considers plant intelligence and plant materiality, while incorporating ideas of making-in-growing, aesthetics, labour, and edibility. This provides a framework for approaching plant-human relationships in a way that is accessible to those outside of plant studies/sciences. With the help of a range of disciplines — including plant biology, ethnobotany, critical plant studies, and archaeobotany — plantiness can expand the vegetal world and encourage us to consider the ‘planty’ perspective within archaeology.
In order to explore such planty perspectives, archaeological work is set within the highly dynamic landscapes of the Fens of eastern England. Moving chronologically and temporally, sites including Etton, Haddenham, Barleycroft/Over, and Holme I/II, will be discussed, providing unique examples of the reciprocal relationships that are negotiated between humans and plants. Further sites from within the Flag Fen Basin, including Flag Fen, Bradley Fen, and Must Farm demonstrate different studies of how we can understand plant-human relationships within geographically linked places. The plants discussed within these case studies are both trees and cereals, two significantly different types of plants within the plant kingdom, but the two most likely to be preserved by charring (carbonisation) in archaeological contexts. These trees and cereals negotiated relationships with humans in unique ways, which can be explored via a number of different theoretical approaches. Engaging with plantiness provides insight into human inter-relationships of the past, considering notions of what it means to be human while also adding to larger ideas of human becoming.
Structural studies of prokaryotic surface layer proteins
Keywords: S-layer
cryo-ET
cryo-EM
Caulobacter crescentus
Deinococcus radiodurans
subtomogram averaging
Nitrosopumilus maritimus
Haloferax volcanii
prokaryotic cell surfaces

Many prokaryotic organisms are encapsulated by a flexible two-dimensional proteinaceous surface layer (S-layer) consisting of repeating units of surface layer proteins (SLPs). SLPs are often the highest copy-number macromolecules in these cells, playing key roles in essential cellular functions including cell-shape maintenance, protection against predators and interaction with the environment. Using recently developed electron cryomicroscopy (cryo-EM) and electron cryotomography (cryo-ET) techniques, I have determined the structures of several S-layers across domains of life, from archaeal and bacterial model organisms and investigated their molecular function.
In the Gram-negative bacteria model organism Caulobacter crescentus, the S-layer is anchored to the cell envelope via lipopolysaccharide (LPS). Using cellular cryo-ET coupled with subtomogram averaging (STA) I resolved a 3.5 Å resolution in-situ structure of the complete S-layer, showing how the native S-layer is anchored at the tip of the lipopolysaccharide.
Combining structural studies with deep-homology bioinformatics (in collaboration) for Haloferax volcanii archaeal and Deinococcus radiodurans bacterial SLPs, I showed that immunoglobulin containing S-layers are widespread in prokaryotes. Additionally, I structurally characterised an abundant outer membrane β-barrel protein from D. radiodurans, elucidating its multidomain architecture and how it tethers the outer membrane to the underlying peptidoglycan layer and thereby shapes and maintains the cell envelope.
Finally, I elucidated the in-situ structure of the S-layer of the ammonia-oxidising archaeon Nitrosopumilus maritimus. Using whole cell isothermal titration calorimetry and molecular dynamics simulations (in collaboration), I showed that this S-layer is required for ammonium enrichment from a dilute marine environment, facilitating the conversion of ammonium oxidation to nitrite.
Taken together, these findings revealed common principles of S-layer arrangement and assembly, advancing our understanding of this important and widespread cellular organelle.
A longitudinal study of child mental health in the UK: the role of income and other risk factors
Keywords: health inequality
child mental health
income gradient

Background
Previous evidence suggests child mental health is associated with family income, with poorer mental health amongst those in less affluent families. This DPhil research investigates the relationship between family income and child mental health from early childhood to adolescence, potential variation with age, and the factors that may explain the relationship.
Methods
Three complementary analytical approaches were employed to analyse data for a consistent cohort of children when they were aged 3, 5, 7, 11, 14 and 17 years, using data from the UK Millennium Cohort Study. Cross-sectional analyses were used to examine the association between family income and child mental health while exploring the role of child, family, and peer-related factors in elucidating the association. Panel data analyses were used to investigate the variation of the longitudinal association over time. Finally, the concentration index approach, coupled with its decomposition method, was used to quantify the degree of income inequalities in child mental health and analyse underlying factors contributing to the inequalities.
Results
Higher family income was associated with fewer child mental health problems; the magnitude of this gradient varied with age, being larger in adolescence than in childhood. The strength of the association was reduced after adjustment for factors reflecting Parental Stress and Investment theories, with the larger attenuation driven by Parental Stress factors. Accounting for peer-related factors during adolescence did not markedly attenuate the association further. The presence of income-related inequalities in child mental health was observed in childhood and adolescence, affirming the reported link between income and child mental health. Maternal depression and parent-child relationship emerged as the key contributors to inequalities across all ages.
Conclusions
The income gradient and income inequalities in child mental health observed in this research, along with the factors that underpin the relationship, suggest that income-support interventions may be a way to reduce child mental health problems, while also benefiting the wider family. Adolescence emerges as an important stage for implementing income interventions, offering a greater potential for reducing child mental health problems compared to other periods.
Systemic fates of non-classically restricted, commensal specific T cells 
Keywords: inflammatory bowel disease
mucosal immunology
h2-m3 restricted t cells
colitis
immmunology
microbiota specific t cells
non-classical immunity
microbiota

Inflammatory Bowel Diseases (IBD), encompassing both Crohn’s disease and ulcerative colitis, are characterized by destruction of the gut epithelial barrier, dysbiosis and aberrant immune reactivity to the microbiota. Although multiple studies have revealed CD8+ T cell signatures in the tissues and circulating PBMC of patients with IBD, the role of CD8+ T cells in the initiation or perpetuation of disease has remained understudied.
Work investigating the contribution of immunity to the commensal microbiota in the skin identified a population of innate like CD8+ T cells restricted by the MHC-Ib molecule H2-M3, that play critical roles in wound healing and barrier repair. However, these commensal reactive CD8+ T cells have not yet been described in the gut. Thus, the aim of this DPhil project was to describe commensal specific, innate-like CD8+ T cells in this tissue. To achieve this, we leveraged established H2-M3 tetramer tools to track commensal specific CD8+ T cell responses during homeostasis and a model of colitis wherein colonization with the pathobiont Helicobacter hepaticus and treatment with αIL-10R antibody mimics genetic susceptibility and aberrant reactivity to the microbiota found in some patients with IBD.
Using a range of histological and flowcytometry measurements, we describe the architecture of the colon with and without H2-M3 restricted and MHC-Ia restricted CD8+ T cells in homeostasis and colitis, illustrating that MHC-Ib restricted CD8+ T cells can dominantly contribute to the CD8+ T cell response during inflammation. Further, we confirm the residence of H2-M3 restricted commensal reactive CD8+ T cells in the large intestine where they adopt a primarily Tc1 phenotype, differing from their Tc17 signature in the skin. During inflammation, we also report an upregulation of H2M3 gene expression in whole colon tissue and colon organoids as well as an expansion of commensal reactive CD8+ T cells secreting pro-inflammatory cytokines. We also observed expansion of commensal reactive CD8+ T cells to the colon during colitis after skin association, where they again exhibit a pro-inflammatory Tc1 phenotype. Finally, subsequent computational identification of predicted H2-M3 binding peptides produced by Helicobacter hepaticus, we developed novel tetramer tools which illustrate the high relative frequency of H2-M3 restricted CD8+ T cells in naïve animals.
Taken together, these findings lay the groundwork for further investigation into the impact of commensal reactive CD8+ T cells on the etiology or perpetuation of IBD.
On the processing of vowels in the mammalian auditory system
Keywords: sound categorization
auditory objects
rats
auditory cortex
sound perception

The mammalian auditory system generates representations of the physical world in terms of auditory objects. To decide which object class a particular sound belongs to, the auditory system must recognise the patterns of acoustic components that form the acoustic “fingerprint” of the sound’s auditory class. Where in the central auditory system such patterns are detected and what form the neural processing takes that underlies their detection are unanswered questions in sensory neurophysiology.
In the research conducted for this thesis I used artificial vowel sounds to explore the neural and perceptual characteristics of auditory object recognition in rats. I recorded cortical responses from the primary auditory cortex (A1) in anaesthetised rats and determined how well the spiking responses, evoked by artificial vowels, resolve the spectral components that define vowel classes in human perception. The recognition of an auditory class rests on the ability to detect the combination of spectral components that all member sounds of the class share. I generated and evaluated models of the integration by A1 responses of the acoustic components that define human vowels classes. The hippocampus is a candidate area for neural responses that are specific to particular object classes. In this thesis I also report the results of a collaboration during which we investigated how the hippocampus responds to vowels in awake behaving animals. Finally, I explored the processing of vowels behaviourally, testing the perceptual ability of rats to discriminate and classify vowels and in particular whether rats use combinations of spectral components to recognise members of vowel classes. For the behavioural training I built a novel integrated housing and training cage that allows rats to train themselves in auditory recognition tasks. Combining the results and methods presented in this thesis will help reveal how the mammalian auditory system recognises auditory objects.
Wild animal suffering and human responsibility: Essays on the ethics of beneficent intervention in nature
Keywords: population ethics
wild animal suffering
non-identity problem
animal ethics
longtermism

Over the past five decades, animal ethicists have made tremendous progress in articulating the moral importance of the wellbeing of non-human animals. Their work has naturally focused on those domesticated animals we use for food, research, etc. Comparatively little has been written about the moral importance of the wellbeing of wild animals. This is unfortunate, as wild animals far outnumber human beings and their domestic animals, and they suffer from a great number of harms such as predation, parasitism, starvation, and disease. In fact, because most animals reproduce in vast numbers while their populations remain relatively stable, we can infer that the vast majority of them die before reaching reproductive age (Ng, 1995; Horta, 2010; Faria 2023a). The typical life of a wild animal is to be born alongside dozens, hundreds, or thousands of siblings, to receive no parental care, and to struggle for survival in a hostile world, before succumbing to predation or starvation only a few hours or days after birth.
This is the problem of wild animal suffering (WAS). The central question is whether humans should try to intervene in nature to reduce the suffering of wild animals, and, if so, what interventions should be performed. Positions on the intervention question range from complete prohibition (Regan, 2004; Palmer, 2010; Korsgaard, 2018) right up to massive genetic modifications of wild animals (Pearce, 1995; Johannsen, 2021), deliberately making certain animals go extinct (McMahan, 2010, 2015; Bramble, 2021), and the deliberate destruction of wild animal habitats (Tomasik, 2016).
In this integrated thesis, I assume an interventionist position. I explore the implications of recognizing the scale and severity of WAS, and the moral complexities that arise once we begin to systematically intervene in nature on a large scale. In paper one I critique Milburn’s (2022) version of the relational objection to intervention in nature, and I argue that human beings have been morally entangled with wild animals since prehistory. In paper two I argue that the non-identity problem affects the strength and kind of our moral reasons to intervene in nature. In paper three, I argue that WAS is a predictable outcome of the evolutionary process, and this gives us a strong reason not to spread animal life to other planets. In paper four I argue that the basic argument for longtermism applies to animals just as much as it does to human beings, that longtermists ought to take animals much more seriously than they do, and that animal advocates ought to be concerned about the long-term future. In the fifth paper I argue that Totalism has deeply counterintuitive implications when we include animals in the populations to be evaluated.
Engineering the ceramic-polymer interface for advanced ballistic protection
Keywords: polyurethane
J-integral
dynamic
FEA
polymer
DIC
stress relaxation
ballistics

Ballistic impact on body armour is a complex phenomenon involving sophisticated materials and multiple interactions. The armours of interest to this study are polymer-backed ceramic plate composites, which are standard amongst military personnel. The composite nature adds complexity to the armour because of the interaction between the ceramic and polymer, which is thought to play a significant role in the armour performance; however, despite this importance, this interplay is relatively poorly understood. The research in this thesis aims to explore the effect of the interface and polymer backing on armour performance. A methodical study into the fundamental behaviour of armour using simplified materials and interactions has been performed. Two commercially available polyurethanes (PUs) were selected, and these were first characterised to find the effect of loading rate and temperature on the mechanical response. Interfaces between these polymers and the chosen ceramic (alumina) were also characterised with respect to rate and temperature using a variety of surface modifications. These characterisation experiments were used to model behaviour of simplified armours, which were also impacted over a range of speeds in a series of experiments in which the influence of the backing and interfacial properties on overall armour response was recorded. The model armour was designed to be quasi-1D to allow the fracture pathways and failure, which would otherwise be obscured by the geometry of the material, to be visually investigated. The polymer and interfacial characteristics influenced the observed fracture pathways of the model armour under quasi-static and impact loading which affected the energy absorptive capabilities of the armour. This behaviour was further predicted from independently calibrated FEA simulations.
Mechanisms of transcription regulation by full-length CREB
Keywords: protein disorder
basic leucine zippers
bZIP
DNA-binding interactions
cAMP response element binding protein
DNA-binding domains
transcription
CREB
gene expression
transactivation domains

CREB (cAMP response element binding-protein) is a disordered essential mammalian transcription factor, activated by the cAMP signalling cascade. It is involved in a myriad of biological processes including memory and the circadian clock. Moreover, CREB is overexpressed in many cancers, such as leukaemia, sarcomas, melanoma. Thus, to understand both mammalian and cancer biology, it is important to characterise it well.
The C-terminal end of CREB contains a bZIP DNA-binding domain (DBD), and the N-terminal end of CREB contains three domains - two glutamine-rich domains surround its acidic activation domain KID (kinase inducible domain). Previous biophysical (and structural) studies have focused on understanding CREB’s behaviour using isolated KID and bZIP domains, but few have used full-length CREB or looked at the influence of the other domains on its biophysical properties. Recent work has challenged simplistic modular architectural understandings of transcription factors, for example: there is increasing evidence that these disordered sequences are essential for efficient target search. This Thesis aims to directly address this issue through comparative studies with full-length CREB and its isolated domains.
In this Thesis I developed a high yield methodology for production of highly pure full-length CREB protein and used the material to conduct thorough biophysical characterisation of CREB and its binding to DNA in-vitro. I found CREB’s non-DBDs lower DNA affinity around 5-fold compared to the isolated bZIP, but the homodimerization and target DNA affinity remain in the nanomolar range whereas affinity to non-target is in the micromolar range. Altogether, this makes the full-length CREB target search more efficient and less likely to be sequestered away by non-target DNA in a cellular context. Moreover, each of CREB’s non-bZIP domains impedes binding to DNA to a similar extent. Finally, current literature suggests bZIP transcription factors dimerise following target binding through a monomer search pathway. However, I find a high CREB homodimer stability which, together with unquantifiable binding of CREB monomers to DNA, favours a dimeric pathway instead.
Libertas regimine crescit – developing a working theory of improvising in the course of composing music for improvised performance
Keywords: pro-improvisatory composition
libertas regimine crescit

This essay approaches the field of improvisation studies from the perspective of a composer. A broad ‘Working Theory of Improvising’ is offered, summarised in the symbiotic relationship between Freedom and Governance, under the term ‘Libertas Regimine Crescit’ (Freedom [which] grows out of Governance). This theoretical framework, being developed in abstract, is presented as a departure from much existing scholarship of a ‘micro-to-macro’ order which uses specific improvisatory contexts to derive broader theory.
This ‘macro-to-micro’ Working Theory is then overlaid onto some existing scholarship, highlighting its similarities and differences. In doing so, certain flaws inherent within ‘micro-to-macro’ thinking are exposed, particularly with regard to the use of Free Improvisation as a catalyst for the production of improvisation theory of a pronounced leaning towards concepts of the ‘uninhibited’ and ‘non-idiomatic’. The work of Benjamin Libet et al. (1983) is cited as a basis on which to build an understanding of the corporeal ‘habitus’ that acts as a foundational Governance in the performance of any music. This evidence invites an appreciation of the subconscious (involuntary) nature of improvising; it is presented in opposition to existing theory that promotes the idea of ‘spontaneous’ decision-making ‘in the moment’.
Emphasising process over product (Small, 1998), this essay references Deleuze and Guattari’s ‘rhizomatic’ theory (1987) as a metaphor within which to consider the development of musical products as they are arbitrary ‘surface’ markers of ongoing improvisatory processes. Following Nicholas Cook’s notion of ‘symbolic poverty’ inherent in musical notation, ‘Pro-improvisatory composing’ (or ‘PIC’) is proposed as an opportunity for the marriage of improvisation theory and the Work Concept (Goehr, 1992). Lastly, the application of this theory is revealed both in the compositions within the accompanying portfolio, and in case studies that provide direct comparisons between specific fully-notated and ‘pro-improvisatory’ compositions.
Antibody structure prediction using deep learning
Keywords: ka-search
structure
deep learning
antibody
immunebuilder
plabdab
bioinformatics
ablooper

The aim of this doctoral project was to improve the prediction of antibody structures and optimise the use of existing antibody data. As a starting point, we developed ABlooper, a tool that predicts the position of backbone atoms for CDR loops in antibodies. In Chapter 2, we present the methods and results for ABlooper. This tool has enabled the modelling of antibody structures at previously unprecedented speeds, predicting the CDR loops for one hundred structures in less than five seconds. However, ABlooper has some limitations: it cannot model side-chain atoms and sometimes generates unphysical structures, which need to be corrected using computationally expensive methods.
To overcome these limitations, we developed ImmuneBuilder, a novel method based on the recently released AlphaFold2 models. ImmuneBuilder is a set of deep learning-based tools for modelling antibodies, nanobodies, and TCRs. In contrast to ABlooper, this method can accurately predict the position of both backbone and side-chain atoms. Moreover, it predicts the structure of the entire variable domain, not just that of the CDRs. Chapter 3 describes the ImmuneBuilder method in detail.
With next-generation sequencing studies routinely generating millions of antibody sequences, effectively searching this data has become a challenge. In Chapter 4, we present KA-Search a tool that allows for the rapid search of billions of antibody sequences by sequence identity across either the whole chain, the complementarity-determining regions, or a user defined antibody region. We show KA-Search in operation on the 2.4 billion antibody sequences available in the OAS database.
In addition to next-generation sequencing data, there is a vast amount of literature that focuses on a small number of antibodies. For these smaller scale experiments, the amount of available information for each individual antibody is much greater. To facilitate the retrieval of this information, we developed the Patent and Literature Antibody Database (PLAbDab), an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures. Chapter 5 describes how this database was generated and gives examples of how it could be used.
The final chapter draws conclusions and proposes future avenues of research.