VictorJuiz/thesis huggingface dataset:
Inference and machine learning across the spatial scales in geophysics

The Anthropocene and the concomitant Great Acceleration – defined by super-exponential growth rates in a collection of measures of human activity – are having a tremendous impact on Earth and its ecosystems. To better understand the consequences of our activity, we must increase our knowledge of all the elements in the Geosystem, loosely defined as Earth, the oceans, atmosphere, and the Sun, and in constant evolution as human activity ties in new elements, e.g. the Moon or Mars. In this thesis, I am focusing on improving our knowledge of elements pertaining to geophysics, while also showcasing the diversity of thematics in the Geosystem. I also emphasize the common grounds and cross-cutting themes in our sundry of projects, in particular the importance of a data-centric approach, including the creation of new sensors, and the necessity of both methodological improvements to our numerical tools, and the adoption of novel methods from machine learning to help us exploit the newly available vast amount of data.
I begin with wildlife conservation, where, with collaborators, we prototype an elephant monitoring system based on the classification of animal generated seismic signals with deep learning. We achieve promising results, with high accuracies in classification of elephants and their behaviour, and with further research I believe our method will bring about a seismic shift to wildlife monitoring. Next, I present a novel method for the computation of Frechet sensitivity kernels for full waveform inversion based on the discrete adjoint approach, resulting in a more advantageous frequency scaling of the computational cost than traditional methods. This discount is crucial to enable us to image the interior of the Earth at higher resolutions, which is necessary to unlock the answers to some of the biggest questions in Earth science, e.g. related to the mechanisms of mantle convection and plate tectonics. Finally, I introduce how, with my teammates, we developed a deep learning replacement to a now defunct Sun-monitoring spectrograph onboard a NASA satellite. The best performing model, a combined linear-CNN architecture, achieves 1.6% median error, virtually reviving the spectrograph and restoring a vital data source, for instance for satellite operators to model atmospheric dynamics and avoid catastrophic collisions.

Keywords: Geophysics
Machine learning
Advisor: Nissen-Meyer, T
The selective partitioning of mRNA in biomolecular condensates

Biomolecular condensates (BMCs) are complex assemblies of RNA and protein that form via the process of liquid-liquid phase separation. They have a diverse range of functionalities, often centered around RNA metabolism, and are found throughout the cell. However, how they selectively partition certain molecules whilst excluding others remains a poorly understood, yet pertinent question in biology. Here we addressed this from an mRNA perspective by developing a simplified, in vitro approach, utilising cytoplasmic RNA in combination with a panel of model BMCs. We identified that the length, GC %, and G-quadruplex frequency of an mRNA were critical in defining how it partitioned in these models. Remarkably, very similar rules persist in defining mRNA selection in cellular P-bodies (PBs) and stress granules (SGs). Supporting this notion, we demonstrated that the transcriptome captured by our in vitro model, DDX4N, was highly comparable to that of PBs. These results strongly suggest that the properties of the mRNA are the fundamental driving force behind how it partitions in BMCs. Moreover, we provide evidence for a novel role of 3’ untranslated region alternative cleavage and polyadenylation (3’UTR-APA), in manipulating the length, GC %, and G-quadruplex content of mRNA in order to selectively distribute mRNA isoforms to BMCs, with profound implications for mRNA metabolism. In addition, we demonstrated that SG and PB proteome components were significantly more likely to exhibit selective isoform partitioning within their respective condensate than the rest of the transcriptome. This raises the intriguing prospect that 3’UTR-APA may also be essential in BMC formation and maintenance.

Keywords: Biomolecular Condensates
Liquid-liquid Phase Separation
Membraneless Organelles
mRNA
Advisor: Furger, A
The effect of plant domestication on the seed microbiome

There is a growing body of literature demonstrating the role of microbial communities in plant growth, health, and resilience. It is becoming increasingly clear that advances in our understanding of plant-microbe interactions could make a significant difference in sustainable agricultural production.
In my thesis, we approach this ever-evolving topic to try to advance our understanding of plant-microbe interactions within the agricultural ecosystem. One key question that has attracted recent research efforts is whether plant domestication has influenced hostmicrobiome assembly and composition.
In Chapter 2, we develop an evolutionary framework explaining that domesticated plants could showcase a reduction in positive microbe-to-host effects as a result of plant phenotypic traits selected by the domesticator through artificial selection. In Chapter 3, we provide evidence of the effect of domesticated plant traits on seed microbiome composition and assembly, partially validating the framework developed in Chapter 2. In Chapter 4, we approach the plant and its microbiome from a broader perspective and reflect on the consequences of plant domestication from a community evolution point of view. In Chapter 5, we develop a tool that will allow researchers to study bacterial plant colonization and how bacteria could eventually be transmitted to the seed compartment. Overall, we show that domesticated plant traits have consistent effects on seed microbiome composition and assembly, independently of the domestication event. We also demonstrate that monitoring bacterial localization in plants can be effectively achieved by combining bacterial bioluminescence with fluorescence.

Keywords: Plant-microbe interactions
Domestication
Advisor: Preston, GM
The effect of context on human decision-making during information integration

Perceiving and interacting with our world is an amazingly complicated computational problem. Our brains need to infer the best cause of action from a long chain of ambiguous and noisy signals reflecting properties from the environment. To solve this problem, our brains make use of multiple pieces of information available in a given context. In these thesis, we explore the influence of context on decision-making. First, we focus on decisions made in the context were three options are available to be chosen. Second, we focus on decisions made in the context of variable prior information about the probability of occurrence of a given event. A particular emphasis is placed on distinguishing mechanisms that optimize the accuracy of decisions from those that comply with axiomatic prescriptions of rational behaviour. We show that even as simple an assumption as having Gaussian noise distorting the representation of value is enough to drive irrational behaviour, calling into question the validity of the axioms of rationality as a yardstick for measuring human behaviour. We also show that uncertainty arising at different stages of the long chain of information processing, can drastically impact the nature of the inference problem that humans have to solve in different contexts. We show two mechanisms present when humans construct their value preferences between three available options. These mechanisms prioritize what information gets further processed in a way that minimizes the effects of noise arising at later stages of processing. Finally, we provide a novel computational explanation for the mismatch typically observed between near-optimal perceptual choices and suboptimal cognitive judgments. Namely, that people are metacognitive blind to noise arising when integrating of multiple pieces of evidence. Together, we show that the brain tends to make excellent use of contextual information to guide it decisions. Perhaps so much so, that we often trust our judgments blindly.

Keywords: human perception
decision-making
optimality
uncertainty
value construction
Advisor: Summerfield, C
Husain, M
Physics for particle detectors and particle detectors for physics: Timing performance of semiconductor detectors with internal gain and constraints on high-scale interactions of the Higgs boson

Experimental particle physics is a science of many scales. A large number of physical processes spanning energies from meV to TeV must be understood for modern collider experiments to be designed, built, and conducted successfully. This thesis contributes to the understanding of phenomena across this entire dynamic range.
Low-energy physics governs the operation of particle detectors, limits their performance, and guides the development of novel instrumentation. To formalise these aspects, classical electrodynamics is used to derive a general description of the formation of electrical signals in detectors, and ideas from quantum mechanics are applied to the study of charge avalanche amplification in semiconductors. These results lead to a comprehensive analytical characterisation of the time resolution and the efficiency of single-photon avalanche diodes, and isolate the most important design variables. They also reveal the applicability of these devices in precision timing detectors for charged particles, which is experimentally verified in a high-energy hadron beam.
Large detector systems at hadron colliders probe fundamental physics at the energy frontier. Data collected with the ATLAS detector during Run 2 of the Large Hadron Collider are used to measure the cross-section for the production of a Higgs boson together with an electroweak boson as a function of the kinematic scale of the process. This measurement provides the finest granularity available to date for this process. It is highly informative of the structure of interactions beyond the direct kinematic reach of the experiment, and new limits are set on the couplings of such interactions within an effective field theory.

Keywords: Single-photon avalanche diode
Higgs
SPAD
Timing
SiPM
Particle physics
Effective field theory
ATLAS
LHC
Advisor: Bortoletto, D
Materialisation and data partitioning algorithms for distributed RDF systems

Many RDF systems support reasoning with Datalog rules via materialisation, where all conclusions of RDF data and the rules are precomputed and explicitly stored in a preprocessing step. As the amount of RDF data used in applications keeps increasing, processing large datasets often requires distributing the data in a cluster of shared-nothing servers. Whereas numerous distributed query answering techniques are known, distributed materialisation is less well understood. In this paper, we present several techniques that facilitate scalable materialisation in distributed RDF systems. First, we present a new distributed materialisation algorithm that aims to minimise communication and synchronisation in the cluster. Second, we present two new algorithms for partitioning RDF data, both of which aim to produce tightly connected partitions, but without loading complete datasets into memory. We evaluate our materialisation algorithm against two state-of-the- art distributed Datalog systems and show that our technique offers competitive performance, particularly when the rules are complex. Moreover, we analyse in depth the effects of data partitioning on reasoning performance and show that our techniques offer performance comparable or superior to the state of the art min-cut partitioning, but computing the partitions requires considerably fewer resources.

Keywords: datalog
distributed systems
materialisation
automated reasoning
data partitioning
Advisor: Motik, B
Horrocks, I
The biology of ADGRL4/ELTD1 in angiogenesis and tumour development

ADGRL4/ELTD1 is an orphan adhesion G protein-coupled receptor that is expressed in both endothelial cells and vascular smooth muscle cells. ELTD1 expression was significantly upregulated in the tumour vasculature and previous studies in our laboratories identified ELTD1 as a novel regulator of tumour angiogenesis. The aims of this project were to further investigate ELTD1’s in vivo role in the normal and tumour vasculature. In this project, both constitutive and inducible endothelial cell-specific Eltd1 knockout mouse models were generated using Tie2-Cre and Pdgfb-Cre lines respectively. Both models exhibited no significant differences in body and organ weights, or other welfare parameters such as behaviour and movement. There were no observed immunohistochemical differences (CD31 and H&E) in the vital organs namely, brain, heart, lung, liver, kidney and spleen. Interestingly, inducible endothelial cell-specific Eltd1 knockout aortic rings showed inhibition in endothelial cell sprouting that was not observed in the constitutive knockout, suggesting a functional compensatory mechanism in the constitutive model. In both E0771 and MC38 syngeneic tumour models, despite no significant differences in tumour growth curves and survival outcomes, there were observed immunohistochemical differences with generally higher necrosis and hypoxia, and reduction in microvessel density and pericyte coverage in the Eltd1 knockout tumours. Both genetic and drug induced endothelial-Eltd1 deletion gave similar results which affirmed the effects of endothelial-Eltd1 on the tumour vasculature in vivo. Single cell sequencing of acute Eltd1-depleted lung endothelial cells revealed heterogeneity in Eltd1-expressing endothelial cells and showed that lung capillary endothelial cells had higher Eltd1 expression compared to lung arterial endothelial cells. Interestingly, their differential gene expression profiles were distinct. But in both endothelial cell subsets, there were differentially regulated genes whose functions have been associated with endothelial biology, angiogenesis, tumour development and immunology. In summary, endothelial-Eltd1 depletion did not cause toxicity but altered the tumour microenvironment. Therefore, ELTD1 could be considered as a potential target for cancer therapy in combination with other therapies targeting hypoxia and angiogenesis.

Keywords: ADGRL4/ELTD1
cancer
angiogenesis
Advisor: Harris, A
Banham, A
Primate archaeology: comparative models for the evolution of primate technical cognition through tool-use

The field of Primate Archaeology is concerned with (A) understanding the origins and development of tool use in non-human primates, and (B) the implications of a general primate model for understanding human technical and cognitive development. Cross-species comparisons, however, remain distinctly anthropocentric in nature. The metaphysical commitments of Neo-Darwinist frameworks reinforce an inherent assumption that cognition is something which takes place in the head, influenced but apart from the body and environment. Assuming psychological discontinuity of this kind, comes at the expense of taking phylogenetic, bodily and environmental differences seriously – a considerable problem when we consider the diversity of primate tool using species which a comparative model must include. In an attempt to overcome issues of heterogeneity and anthropocentrism, this thesis explores the potential of the Material Engagement Theory as a means of re-conceptualizing complexity and causal cognition in Primate tool use, and as the basis of a methodological framework suitable for cross-species comparison. Case-studies of the three living lithic-using non-human primates are compiled and compared, demonstrating the emergent, processual nature of technical cognition as a fundamentally non-individualistic phenomenon co-constituted by the environment and others. General patterns are discussed with reference to theories of technical evolution. The findings of this thesis suggest current hypotheses of primate human and non-human technical evolution, as long as they maintain a separation between mind and matter, cannot accurately account for the role of tool using in cognitive development. To better integrate mind with materials, future research must shift its focus away from the brain, body, and environment, and towards the diachronically shifting, dynamic spaces between.

Keywords: material engagement theory
primate archaeology
animal tool use
cognition
Advisor: Malafouris, L
Observations of dry wear and the development of an improved wear law


Unlubricated wear of metal components is a significant factor in the deterioration of various metal structures and assemblies and has been the focus of intensive research for several decades. Despite this, accurately predicting the quantity and development of wear from information about the geometry, material and loading of the wearing contact appears to be beyond the reach of engineering science at present. The development of more generally applicable, reliable wear prediction method (“wear law”) would be of great benefit in terms of industrial practice and would also close a significant gap in the current state of tribological knowledge.
The research presented in this thesis establishes both the limitations of traditional wear prediction approaches based on two-body contact mechanics and/or Archard’s wear law as well as a possible alternative in the tribological circuit approach, which was initially proposed by Berthier and then refined into a wear model for a closed contact geometry by Fillot, Iordanoff & Berthier. Through experimental research, a number of assumptions and questions put forward by these authors were examined; in particular the interaction between the debris ejection path length, surface profile and debris particle size was found to govern the ejection of wear debris and thus wear. The model was also found to predict a strongly non-linear dependence on normal force for an annular contact geometry, the same geometry in which exactly such dependence has been observed experimentally, but not yet explained. Additional experimental work revealed a tendency for the contact to eject debris along the shortest available path. With this knowledge, a mathematical expression for debris ejection in multiple directions was formulated. With it, the approach proposed by Fillot, Iordanoff & Berthier was expanded to an open contact geometry, successfully achieving a transition of a wear model between geometries. This would also indicate, that the approach studied could be a generally applicable wear model.
To aid the experimental work, a method for observing wear without disturbing it has been developed, using X-ray computed tomography. This is the first such application of X-ray CT to wearing contacts, the first instance of wear being extensively quantified entirely non-destructively (i.e. without dismantling the wearing contact for studies) and has been proven to be very successful as a tool for observing and quantifying wear. The success obtained can also serve as a powerful justification for further development of this approach and progress towards the observations of wear in-situ using penetrating radiation.

Keywords: Tribology
Wear
In-situ experiments
X-ray CT
X-ray diffraction
Wear modelling
Advisor: Huber, J
Hills, D
The use of reduced doses of the yellow fever vaccine in a sub-Saharan African population: safety, immunogenicity and policy

Yellow Fever (YF) is a potentially lethal haemorrhagic fever of significant public and global health importance. The 17-D YF vaccines have been used successfully for several decades with excellent immunogenicity and safety profile. A recent rise in outbreaks in endemic regions has been characterised by a repeated vaccine stock shortage that has led the World Health Organisation (WHO) to recommend the use of fractional doses as a dose sparing strategy. The recommendation was made with limited data from the African region.
A review of literature of the virus, epidemiology, vaccines and the current policies of use the vaccines explored the challenges with an upsurge in disease outbreak in endemic regions and the causes of the recurrent vaccine stock shortage. The literature identified the gaps in evidence on the use of fractional doses as a dose sparing strategy as recommended by the WHO.
Randomised, controlled, non-inferiority clinical trials comparing standard dose and fractional doses were conducted in Kenya and Uganda. In one study, a pragmatic fifth of the standard dose of the 17D-213 vaccine manufactured by the Institute of Poliomyelitis and Viral Encephalitidis, Russian Federation was tested against the standard in HIV-infected individuals. The second study was a dose-response study testing de-escalated doses of the 17D 204 vaccine manufactured by the Institut Pasteur de Dakar against a standard dose in a general population in Kenya and Uganda. The studies assessed safety and immunogenicity, as measured by neutralising antibody assays (PRNT). The studies found the fractional doses to be safe and sufficiently immunogenic with doses as low as 500 IU/dose immunogenically non-inferior to standard doses.
A systematised review of vaccine policy identified actors, mapped out policy processes and elements that influence the direction of vaccines when introducing new vaccine policies and changing existing vaccine policies. A stakeholder analysis with actors involved with YF vaccines explored their perceptions, positions, vaccine policy processes and factors that are vital to consider for wider use of fractional doses beyond the current recommendations by WHO.
In these policy analysis studies, I found that there are systematised processes for introducing and changing vaccine policies at the global and regional levels and that each vaccine policy is unique. There was general support for use of fractional doses of the YF vaccines. However, more evidence is needed for firmer recommendations. Additionally, vaccine policy processes are heavily political with advocacy, lobbying, actor coordination and communication playing important roles.

Keywords: yellow fever
vaccine policy
non-inferiority
fractional doses
clinical trial
safety
immunogenicity
Advisor: Warimwe, G
Molyneux, S
Bejon , P