VictorJuiz/thesis huggingface dataset:
On the non-compositionality of monads via distributive laws

Monads are a useful tool in both computer science and mathematics: they model computational behaviour, describe data structures, and give access to Kleisli and Eilenberg-Moore categories. To utilise multiple monads simultaneously, monads can sometimes be composed to form composite monads. Distributive laws ensure that such composite monads capture the full behaviour of both their components, creating a lifting of the component monads to the appropriate Kleisli or Eilenberg-Moore categories. However, for a given pair of monads there does not necessarily exist a distributive law to compose them.
This thesis presents a new method to prove so called no-go theorems: theorems that identify cases in which a distributive law cannot exist. The method, which uses an algebraic perspective on monads, has unique advantages over the more usual categorical approaches. The most important advantage is that it produces no-go theorems that identify large classes of monads that do not compose via distributive laws, where previously only a few specific counterexamples were known.
Among the many examples in this thesis, there are several that answer open questions from the literature, and some that identify previously unnoticed mistakes in the literature. Our no-go theorems will hopefully prevent these type of mistakes from happening in future.

Keywords: Boom hierarchy
Monad compositions
Monads
Algebraic theories
Distributive laws
Composite theories
Advisor: Gibbons, J
Coecke, B
Marsden, D
Honest fitness advertisement in European badgers (Meles meles) 

By using European badgers (Meles meles) as a model species, my thesis examines how wild mammalian populations utilise olfactory communication via specialised glandular secretions and metabolic by-products when advertising fitness-related information to conspecifics. This research utilised bomb calorimetry to quantify energetic content within subcaudal gland secretion (a uniquely evolved scent gland), enzyme immunoassays to measure sex-steroid levels within urine, and scent-provisioning experiments which assessed behavioural responses to particular scent marks.
Compared to other communication modalities, olfactory communication allows conspecifics to exchange individual- and group-related information without both parties (signaller and receiver) being present simultaneously. Section I addresses the factors that olfactory signals/cues must possess in order to be effective and common methodologies used within semiochemical research. Section II addresses olfactory advertisement with specialised glandular secretions with a focus on the specially evolved subcaudal gland and the secretion production costs incurred by individuals. By using bomb calorimetry and scent-provisioning experiments, I found that i) the energetic content of subcaudal secretion varies significantly based on individual fitness and season, and ii) conspecific responses vary their behavioural responses based on the perceived energetic costs along with donor-related traits (i.e., age and sex).
Metabolic by-products (e.g., urine) incur minimal production costs compared to specialised glandular secretions. Chemical profiles within urine vary depending on individual parameters, and Section III addresses if/how information encoded within urine influences conspecific responses. My findings indicated that, throughout the year, adult females responded more than adult males to urine marks while urine marks from non-resident badgers – particularly badgers from neighbouring setts – elicited more responses. Additionally, adults and cubs adjusted their behaviour accordingly when presented with urine from different species, suggesting that badgers utilise olfactory cues in risk determination.
Section IV concludes my thesis by comparing the utilisation of subcaudal gland secretions and urine within olfactory fitness advertisement. Overall, subcaudal gland secretions appear to function as a primary source for individual fitness information while urine serves a subsidiary role in fitness advertisement. Avenues for future research – particularly longitudinal studies involving the correlation of behavioural responses to reproductive output – are discussed.

Keywords: Scent secretion
Olfaction
Mustelids
Badger
Urine
Meles meles
Metabolic by-product
Scent marking
Olfactory communication
Advisor: Macdonald, D
Wyatt, T
Buesching, C
Structural insights into the Fanconi Anaemia pathway

The human genome is subject to numerous endogenous and exogenous stresses that cause a variety of DNA damage and has thus evolved a complex DNA damage response (DDR). Within this DDR are a number of DNA repair pathways, which have evolved to repair different types of DNA damage. One such mechanism is the Fanconi Anaemia (FA) pathway, which repairs interstrand crosslinks (ICLs). Crucial to the activation of this pathway is the recognition of the ICL, and the subsequent recruitment and ubiquitination of the FANCD2/FANCI heterodimeric complex. This complex is site-specifically monoubiquitinated on each protomer which is essential for the removal of the ICL and the subsequent repair of DNA. In addition, the deubiquitination of the monoubiquitinated FANCD2/FANCI has been shown to be necessary for the FA pathway to function. The FA pathway is a complex pathway and many open questions remain to be answered, including the mechanism of recognition of the ICL, how the FANCD2/FANCI complex is ubiquitinated, and whether it is ubiquitinated as a heterodimeric complex or sequentially as single substrates, as well as whether ubiquitination and deubiquitination occur on or off DNA in vivo. In addition, it has been postulated that upon ubiquitination of the complex, FANCD2/FANCI undergo a conformational change locking onto DNA, perhaps necessary for the recruitment of downstream repair factors.
Here, in vitro investigation of the key FANCD2/FANCI complex was undertaken, including studies on whether monoubiquitination is stimulated by DNA, and whether deubiquitination of the monoubiquitinated FANCD2/FANCI occurs on or off DNA. Work towards the structures of FANCD2/FANCI and possible ubiquitination intermediates, monoubiquitinated-FANCD2/FANCI and monoubiquitinated-FANCI/FANCD2 via negative staining electron microscopy (EM) and cryo-EM is also described. Furthermore, the investigation of filament formation upon ubiquitination of FANCD2/FANCI was carried out. Additionally, a previously identified ICL sensor protein, UHRF1, was also investigated. Specifically, the effect of UHRF1 on the monoubiquitination of FANCD2/FANCI was explored in vitro as well as progress towards the first full-length UHRF1 structure via negative staining EM and cryo-EM is described.

Advisor: Cohn, M
Protein processing in Nicotiana benthamiana by Vacuolar Processing Enzymes and other proteases

Protein processing by proteases is an irreversible post-translational modification that shapes the proteomes of all organisms. The outcomes of protein processing by proteases have diverse effects on protein function. This thesis describes the investigation of the landscape of protein processing in the model plant Nicotiana benthamiana.
Firstly, this thesis presents a snapshot of processed proteoforms in leaves captured by two degradomic techniques: PROtein TOpography Migration Analysis Platform (PROTOMAP) and Terminal Amine Isotopic Labelling of Substrates (TAILS). In combination these techniques revealed putative processing of 58% of the 4769 identified protein groups. Several case studies of putative processing events are discussed, which illustrate the value of this dataset as a resource to support future studies of plant proteins.
Secondly, this thesis explores the roles of two major vacuolar processing enzymes (VPEs) in leaves, NbVPE1a and NbVPE1b, are explored. VPEs are described as positive regulators of programmed cell death (PCD). Using a CRISPR-Cas9 generated vpe1a/b double mutant in N. benthamiana we demonstrate that NbVPE1a and NbVPE1b are responsible for the major VPE activities in leaves. Despite this, vpe1a/b mutants were not compromised in hypersensitive response PCD, nor in responses to salt, nitrogen, heat or ER stresses.
Finally, to elucidate the contribution of NbVPEs to protein processing, High-Efficiency Undecanal-based N-Termini EnRichment (HUNTER) was used to identify substrates of NbVPE1a/b. The N-terminome captured by HUNTER revealed significant changes in protease activity between the vpe1a/b and WT leaves and a clear preference of overexpressed NbVPE1b for asparaginase activity. Several candidate NbVPE substrates were identified, including the receptor-like protein NbFERONIA and papain-like cysteine proteases NbRD21 and NbALP. These were subject to further investigation.
Together this thesis presents an insight into general protein processing in leaves and the specific contribution of NbVPEs to the protease activities and stress responses of N. benthamiana.

Advisor: van der Hoorn, RAL
Climate change and major plagues in the Roman period

This thesis examines the climate of the ancient Mediterranean from the second century BC to the sixth century AD, as well as major outbreaks of disease, with the principal aim of investigating potential explanations for apparent connections between climate change and the major pandemics of the Roman world. In addition, I consider the influence of the three great Roman “plagues” on society, assessing whether their effects, or lack thereof, are as apparent as scholars suggest.
Incorporating paleoclimatic and paleoenvironmental research into the study of ancient history and classical archaeology has become an important addition to the sphere of classical studies; as has the history of disease through the use of archaeogenetics and phylogenetics. These are the fields of science that I utilise in this thesis to explore possible relationships between climate and environmental change and outbreaks of the Antonine Plague (AD 165-190), the Plague of Cyprian (AD 251/2-270), and the first wave of the Justinianic Plague (AD 541-544). It becomes apparent that significant climatic and environmental variability probably contributed to the diseases of the Antonine and Justinianic pandemics reaching the Empire, while climate change does not appear to be linked with the Plague of Cyprian.
The debates concerning the impact of the three pestilences on Roman society continue to be vigorous. However, both exaggerated and understated interpretations of their effects dominate the histories of these pandemics, in spite of the evidence. This thesis approaches the question of impact with caution, by avoiding generalisations and focusing on case studies that depict local effects. I argue that impact should be assessed regionally, and that in many cases the consequences of the “plagues” are not at all clear.
Ultimately, the thesis provides a method to synthesise evidence from a range of historical and scientific disciplines with the aim of explaining how ecological calamities affected the Roman world.

Keywords: the Antonine Plague
Justinianic Plague
Roman climate
Plague of Cyprian
ancient disease
Advisor: Wilson, A
The affective mind: essays on Nietzsche's philosophical psychology

This thesis comprises three stand-alone papers, each concerning the philosophical psychology that can be drawn from the writings of Friedrich Nietzsche. The thread running throughout the thesis is a focus on affective states.
The first paper (“The Heart of Flesh”) concerns the question of what exactly Nietzsche thinks emotions and moods are. I argue, contra received opinion, that Nietzsche had some rather sophisticated and substantive views about affects, comprising a somatic account of the role of the body and an interpretive account of the process through which we identify our own states. I also demonstrate some of the ways in which these views surface in works such as On the Genealogy of Morality and Twilight of the Idols.
The second paper (“Conscious and Unconscious Thought”) provides the first reconstruction of Nietzsche’s enigmatic claims about thinking. Starting from §354 of The Gay Science, I draw on the view of affects laid out in the preceding paper to explicate Nietzsche’s (broad-brushstroke, but philosophically interesting) account of non-linguistic, unconscious cognition. I then turn to his remarks on conscious thinking, addressing two influential readings of the claim that conscious thought alone “takes place in words” (GS §354). Neither, I argue, is entirely successful. I propose instead an alternative that draws on work on inner speech.
The third paper (“The Social Structure of Drives”) concerns Nietzsche’s suggestion in Beyond Good and Evil that the soul should be understood as a “social structure of drives and affects” (BGE §12). I first examine the only extant treatment of this metaphor in the literature, arguing that it is philosophically and textually problematic. In its place, I suggest a new reading, which draws on Nietzsche’s doctoral notes and his subsequent engagement with physiology. By the time of his remarks on the formation of the state in the Genealogy, I contend, Nietzsche’s view has developed considerably into a precise and interesting view.

Keywords: Philosophy of mind
Philosophy of emotion
19th century German philosophy
Nietzsche
Advisor: Kail, P
Mulhall, S
Stratification of disease severity in patients with liver fibrosis, cirrhosis and portal hypertension using novel multiparametric magnetic resonance imaging techniques

Chronic liver diseases (CLDs) affect millions worldwide and are a major cause of mortality. Recently, multiparametric magnetic resonance (MR) methods have been proposed as a non-invasive, quantitative biomarker for assessment of CLD. CLD traverses a spectrum of severity, and the aim of this thesis was to apply MR methods across this spectrum for a quantitative assessment of disease severity. The primary variable of interest was the iron and field strength corrected T1 (cT1), generated by LiverMultiScanTM software from T1 and T2* mapping techniques. Liver cT1 was found to predict liver-related clinical outcomes in patients with CLD (p<0.0001), including in patients with compensated disease only. Liver cT1 performed especially well in patients with non-alcoholic fatty liver disease (NAFLD), alcohol-related liver disease (ArLD) and viral hepatitis (VH) with a cut-off of liver cT1>825ms having a negative predictive value (NPV) of 100%. Liver cT1 quantitatively assessed changes in fibroinflammation in 15 patients with chronic hepatitis C virus (HCV) undergoing treatment by direct acting antiviral (DAA) therapy. Liver cT1 showed significant decreases from baseline to 24 weeks after end of treatment (EoT) (876 vs 806 ms, p=0.002), from baseline to 48 weeks EoT (876 vs 788 ms, p=0.0002) and from 24 weeks EoT to 48 weeks EoT (806 vs 788ms, p=0.016). Spleen cT1 had good diagnostic accuracy for presence of portal hypertension in both an adult cohort with CLD and a paediatric cohort with autoimmune liver disease (area under the receiver operating curve (AUC) of 0.85 and 0.81 respectively). In another adult cohort, spleen cT1 was predictive of future episodes of variceal bleeding (AUC: 0.74), especially in those on non-selective beta-blocker treatments (AUC: 0.97). A reference range for spleen T1 and cT1 was established using data from the United Kingdom Biobank population health study and healthy volunteers from our centre. Higher spleen T1 /cT1 was observed in women vs men and in children vs adults. This thesis provided further evidence that multiparametric MR methods combining T1 and T2* relaxometry can be used across the spectrum of CLD for stratification of disease severity.

Keywords: MRI
liver cT1
portal hypertension
spleen cT1
chronic liver disease
Advisor: Neubauer, S
Barnes, E
Kelly, M
New Jerusalems : military chaplains and the ideal of redemptive sacrifice in the Great War

In 1914 the language of sacrifice and redemption was everywhere. This thesis compares the responses of English Anglican and German Protestant military chaplains to the Great War (1914-1918). Instead of reconstructing their relationship with combatants, it reconstructs their mental worlds. Examining their diaries, sermons, letters, articles, and meditations, it traces their religious ideals of redemption through blood. It argues that chaplains on both sides of the front shared a moral language of redemptive sacrifice, articulating different permutations of the same idea. That moral language initially comprehended the war as an episode of salvation, correcting a crisis of modernity through sacred violence. War was interpreted as the culmination of the 'social question,' the climax of the churches’ quest for community, social cohesion, the healing of class antagonism, the reclamation of the sacred. They proclaimed the war as a sacrament, a rite of purification that would purge modernity of its disorders, restore morality and renew piety. They commonly presumed a fallen, hedonistic and profane industrialised world, its social cohesion threatened by godless materialism, and its need for redemption. By blood the dead would purchase a cleansed, uplifted and redeemed society. Witnessing catastrophic bloodshed, the central moral problem for most chaplains was not high casualties alone. It was the threat that mass death would not morally and spiritually transform their societies. As the conflict escalated into attrition and stalemate, chaplains' increasingly doubted whether war could be intrinsically redemptive, redefining the ideal as a duty of civilians to repay their blood-debt to the dead and justify the sacrifices of their compatriots. Because chaplains were implicated in mass death by virtue of their office, the ideal of redemption through war became more an obligation than perception, an ideal that must be pursued lest the sacrifices of soldier-martyrs be cheapened. Divergences and nuanced differences emerged that distinguished Anglican and Protestant perceptions of the moral and spiritual impact of the war. Intraconfessional divergences emerged, in England over the relationship with French Catholic iconography and patri-passionism, in Germany over the meaning of defeat and the legitimacy of the new political order that replaced the Wilhelmine constitution. However, the common moral language of redemptive sacrifice outweighs the confessional and national differences in their responses to mechanised slaughter.

Keywords: military
War
Jerusalem
redemptive
sacrifice
chaplain
Jerusalems
chaplains
Multiple zeta values and iterated Eisenstein integrals

The affine ring of the motivic path torsor 0Πmot1:= π mot1 (P1\ {0, 1,∞},~10, −~11) is an ind-object in the Tannakian category MT(Z) of mixed Tate motives over the integers [16]. Its periods are Q[(2πi) ±]-linear combinations of multiple zeta values (MZVs). Brown showed that O(0mot1) generates MT(Z) by exhibiting a specific basis for the Q-vector space of motivic MZVs [5].
Brown also introduced a class of periods of fundamental groups called multiple modular values [7]. They are periods of the relative completion of the fundamental group of the moduli stack M1,1 of elliptic curves [22]. Among such quantities are iterated integrals of Eisenstein series along elements of the topological fundamental group of M1,1 based at the tangential basepoint ∂/∂q at the cusp, which is isomorphic to SL2(Z).
In this thesis we prove that all motivic MZVs may be expressed as certain Q[2πi]- linear combinations of motivic iterated Eisenstein integrals (Theorem 12.0.1). This uses a construction relating the (relative) de Rham fundamental groups of P1\ {0, 1,∞} and M1,1 via the de Rham fundamental group of the fiber E × ∂/∂q of the punctured Tate curve over ∂/∂q. We explain how the coefficients in this linear combination may be partially determined using the Galois coaction on motivic periods.
As a consequence we also obtain a new Tannakian generator for MT(Z) constructed from the universal monodromy representation of the relative fundamental group of M1,1 on the fundamental group of E × ∂/∂q (Theorem 13.1.1).

Keywords: motives
periods
iterated Eisenstein integrals
mixed Tate motives
multiple zeta values
multiple modular values
fundamental group
Galois theory
Advisor: Brown, F
Solvent and additive engineering for low band gap perovskite solar cells

Due to their tuneable band gaps, ease of processing and excellent optoelectronic properties, perovskite-based solar cells have attracted much attention in recent years, with rapidly increasing efficiencies which already match those of the industrially dominant multi-crystalline silicon. This work concerns modification of the perovskite semiconductor layer in low band gap materials containing the mixed metals tin and lead. These materials have promising commercial applications both in theoretically optimal single-junction solar cells and in multi-junction perovskite-perovskite tandem devices as a replacement for silicon.
An improved processing method by modification of the deposition solvent together with an appropriate antisolvent or stream of nitrogen is shown to slow crystallisation, leading to thin films with long diffusion length and high mobility. Use of a formamidinium cation rather than methylammonium is shown to improve efficiency, with further performance enhancement on substitution of a small amount of caesium. An optoelectronically defective region is identified with small amounts of substitution of lead for tin, with a recovery in film quality and lowest band gap values with 40-60% tin content. In collaboration with others, this processing enhancement leads to high efficiency single-junction low band gap perovskite solar cells and multi-junction perovskite- perovskite tandem devices.
The additives tin(II) fluoride and tin(II) chloride are shown to function as reducing agents in precursor solutions, and compensators in thin films for tin vacancies produced by the instability of tin(II). These additives are able to rebalance the stoichiometry of both tin(II) and iodide, allowing formation of perovskite films with less bulk vacancy defects, leading to improved morphology and optoelectronic quality, and less initial p-doping. A secondary phase seen on the surface of the films is identified as excess tin(II) fluoride. Over time in air, competing p-doping and degradation mechanisms are identified, and additives shown to slow the onset of degradation. High efficiency solar cells are fabricated with both additives, with tin(II) fluoride showing less sensitivity to precise processing concentration.
A compositional screening study of methylammonium, formamidinium and caesium cations in low band gap perovskite materials is performed, identifying thin film properties and fabricating solar cells from compositions with different combinations of these cations using a universal deposition protocol. The resulting compositional space is demonstrated to be almost fully accessible using this method, with all three cations substituting into the perovskite crystal lattice, although a compositional instability between formamidinium and caesium is identified. Power is generated from solar cells of all other compositions, laying the foundations for future optimisation work on new low band gap materials within this compositional space.

Keywords: perovskite
solvent
additive
tin fluoride
tin chloride
solar cell
low band gap
Advisor: Snaith, HJ