VictorJuiz/thesis huggingface dataset:
Reverse engineering gene regulatory circuitries in neural crest development and evolution

The neural crest (NC) is an emblematic population of embryonic, stem-like cells characterised by their unique multipotency, migratory behaviour and broad developmental potential. Acquisition of these cells represents one major evolutionary transition in the tree of life, endowing vertebrates with their unique body plan.
A gene regulatory network (GRN) has been proposed to orchestrate NC development. To interrogate the NC-GRN at unprecedented resolution in a genome-wide fashion, we employed single cell transcriptomics and epigenomics at multiple stages of avian NC development. Development of a new pipeline allowed us to reverse engineer the NC-GRN in an unbiased manner. This approach enabled us to identify the cis-regulatory architecture embedding the logic of NC ontogeny. We identified regulatory circuitries involved in the pre-patterning of the early NC. Interrogation of the combinatorial cis-regulatory codes encoded in these enhancers revealed opposing circuitries controlling NC fate decisions.
We next compared the transcriptional heterogeneity of NC cells at single cell resolution across three-species: mouse, chicken and zebrafish. Our results indicate conservation of transcriptional states despite extensive divergence of genomic sequences across these species. Moreover, we also pioneered single-cell transcriptomics in the marine lamprey, enabling us to identify novel genes likely involved in lamprey NC development.
Finally, we interrogated the cis-regulatory landscape of zebrafish and lamprey NC cells, revealing conserved properties between chicken, zebrafish and lampreys, such as motif content, enhancer-promoter communications and dynamics of chromatin accessibility during development. We identified a group of pleiotropic enhancers involved in NC-dependent neurogenesis. We propose these elements have played a pivotal role in the early elaboration of multipotent NC in the stem vertebrate lineage via pleiotropic changes in ancestral enhancer elements. Taken together, this thesis provides important insights into the cis-regulatory basis of NC development and evolution.

Keywords: evolution
neural crest
genomics
gene regulatory networks
transcription
enhancers
Advisor: Davalgiene, T
De bruijn, M
Developing a personalized heterologous prime boost vaccination strategy for tumor therapy

The limited success of therapeutic cancer vaccines to date is likely due to sub-optimal generation of anti-tumor CD8 T cells and insufficient tumor microenvironment (TME) modulation. In this study, a novel intravenous (IV) heterologous prime-boost vaccination strategy with a self-assembling neoantigen-peptide nanoparticle TLR-7/8 agonist (SNP) vaccine platform and a chimp adenovirus (ChAdOx1) was used to elicit high magnitude neoantigen-specific CD8 T cells and modulate the TME. Mice primed with SNP encoding the neoantigen Reps1 for a colon carcinoma (MC38) and boosted with ChAdOx1 IV encoding Reps1 elicited on average ~40% Reps1-specific CD8 T cell responses, which were ~4x higher than mice boosted by the conventional IM route. These CD8 T cells were capable of mediating protection from tumor challenge in a prophylactic setting experiment. Therapeutically, heterologous prime-boost with ChAdOx1 given IV or IM enhanced protection compared to the use of ChAdOx1 alone. Remarkably, IV administration of ‘empty’ ChAdOx1 (not encoding Reps1) after Reps1-SNP prime also improved protection compared to Reps1-SNP prime or ChAdOx1 prime alone. Subsequently, IV vaccination with ChAdOx1 or SNP was found to induce production of IFNα and activation of cDC1s in the spleen, tumor and tumor-draining lymph node (td-LN). The activation of cDC1s was found to be dependent on functional IFNα signaling and blockade of IFNα signaling at the time of boost completely abrogated tumor regression in the therapeutic setting. Together, these data suggest that IV ChAdOx1 boosting not only increases the magnitude of antigen-specific CD8 T cells, but also modulates the TME to promote tumor regression, representing a readily translatable therapeutic paradigm to drive the Cancer Immunity Cycle.

Keywords: neoantigen
intravenous vaccination
heterologous prime boost
personalized cancer vaccine
Advisor: van den Eynde, B
Leung, C
On the reproducibility and interpretability of group-level task-fMRI results

In this thesis, we aim to address two topical issues at the forefront of task-based functional magnetic resonance imaging (fMRI). The first of these is a growing apprehension within the field about the reproducibility of findings that make up the neuroimaging literature. To confront this, we assess how the choice of software package for analyzing fMRI data can impact the final group-level results of a neuroimaging study. We reanalyze data from three published task-fMRI studies within the three most widely-used neuroimaging software packages - AFNI, FSL, and SPM - and then apply a range of comparison methods to gauge the scale of variability across the results. While qualitatively we find similarities, our quantitative assessment methods discover considerable differences between the final statistical images obtained with each package. Ultimately, we conclude that exceedingly weak effects may not generalize across fMRI analysis software.
In the second part of this work we shift our attention to the analytical methods applied for fMRI inference. Here, we seek to overcome limitations with the traditional statistical approach, where for sufficiently large data sizes current methods determine universal activation across the brain, rendering the results as uninterpretable. We extend on a method proposed by Sommerfeld, Sain, and Schwartzman (2018) (SSS) to develop spatial Confidence Sets (CSs) on clusters found in thresholded raw blood-oxygen-level-dependent (BOLD) effect size maps. The CSs give statements on the locations where raw effect sizes exceed, and fall short of, a purposeful non-zero threshold. We propose several theoretical and practical implementation advancements to the original method formulated in SSS, delivering a procedure with superior performance in sample sizes as low as N = 60. We validate the method with 3D Monte Carlo simulations that resemble fMRI data. We then compute CSs for the Human Connectome Project (HCP) working memory task contrast images, illustrating the brain regions that show a reliable %BOLD for a given %BOLD threshold.
In the final part of this thesis, we develop the CSs to operate on standardized Cohen's d effect size images. We derive the statistical properties of the Cohen's d estimator to motivate three algorithms for computing Cohen's d CSs, including a novel method based on normalizing the distribution of Cohen's d. With intensive 3D Monte Carlo simulations, we find that two of these methods can be effectively applied to fMRI data. We compute Cohen's d CSs on the HCP data, and by comparing the CSs with results obtained from a standard testing procedure, exemplify the improved localization of effects that can be gained by using the Confidence Sets.

Keywords: fMRI
Statistical Inference
Reproducibility
Task-fMRI
Advisor: Nichols, T
Maumet, C
Schwartzman, A
The role of microRNA-31 in cardiac fibrosis associated with atrial fibrillation

Cardiac fibrosis is a histological hallmark of atrial arrhythmogenic structural remodelling characterised by increased deposition and accumulation of fibrillar collagen. Despite recent advances in understanding cardiac fibrogenesis, there is a paucity of effective anti-fibrotic therapies. Given the robust effect that single microRNAs can have on gene transcript abundance, these small oligonucleotides have been recognised as potential targets for therapeutic manipulation in a wide range of disease states. Our group has recently shown that increased miR31 expression in cardiomyocytes contributes to electrical remodelling begetting atrial fibrillation and our more recent unpublished data show that miR31 is also upregulated in human atrial fibroblasts derived from patients with chronic AF compared to sinus rhythm controls. Given that miR31 has been shown to drive pro-fibrotic phenotype changes in fibroblasts in other disease models, including ischaemic heart disease, we hypothesised that the observed increase in atrial fibroblast miR31 expression in chronic AF was contributing to fibrotic changes seen in this disease state. Consequently, I conducted experiments whereby miR31 abundance was either enriched or depleted in primary human atrial fibroblasts obtained from healthy patient donors to observe whether manipulation of miR31 in vitro would cause pro-fibrotic gene expression- and phenotype-changes. Results did show significant changes in mRNA of key pro-fibrotic signalling genes however inter-donor variability made it difficult to draw robust conclusions on the role of miR31 in fibroblast phenotype. Additional in vitro experiments in human atrial fibroblasts were conducted to investigate whether the transcription factor ETS1 is involved in regulating miR31 expression and results did show increased miR31abundance following ETS1 depletion. Further, the consequence of miR31 up-regulation on fibrogenesis in vivo was explored in a novel, tamoxifen inducible, global fibroblast-specific miR31 transgenic mouse strain. Results of these mouse experiments demonstrated that increased fibroblast production of miR31 in vivo leads to similar pro-fibrotic gene expression and protein changes observed in human atrial fibroblasts thereby corroborating the separate experimental systems used. Overall, the results of this project are the preliminary evidence that miR31 is involved in the pro-fibrotic response in human atrial fibroblasts, as well as in the intact mouse, and provide the foundation upon which further experiments can be performed and justified.

Keywords: Micro-RNA-31 in cardiac fibrosis and atrial fibrillation
Advisor: Reilly, S
Lygate, C
Remnants of a Roman past: the reuse of Roman objects in early Anglo-Saxon graves, c. AD 5th—7th centuries 

The widespread curation and deposition of Roman material culture in the graves of the Anglo-Saxon dead has long been acknowledged in archaeological study. These reused artefacts have been interpreted in myriad ways: as found curiosities, scrap materials, protective amulets, replacements for contemporary objects, heirlooms, and biographical objects. The first large-scale examination of the typology and use of Roman material was conducted by Roger White in 1988. This thesis builds off the platform set by White to create a wholly new assessment and understanding of the available data.
This methodology is the first to investigate the occurrence of Roman objects in the Anglo-Saxon furnished burial rite throughout space and time by means of a systematic analysis of 5th—7th century burial data. A dataset of 671 objects from 117 cemetery sites is assessed. In four primary veins of multivariate analysis, reused Roman materials are investigated for typological factors and uses, regional distributions, demographic associations, and chronological patterning. Though a wide array of object types is recorded, coins and items which could be used in display are the most numerous. Regionally, the funerary use of Roman artefacts is established to have been most prevalent in the culturally Saxon territories of the Upper Thames Valley and modern-day Wiltshire and Hampshire. Statistical analysis further reveals a disproportionate association between these items and the graves of women and juveniles.
The results of this analysis demonstrate that Roman objects were deposited in different ways and imbued with different social meanings over time, ultimately challenging the ways in which we think about the interactions of 5th—7th century communities and cultures in Britain. These artefacts are interpreted to have played a role in the formation and maintenance of a new cultural identity in late antique Britain through the construction of a shared ‘memory’ of the Roman past.

Keywords: Anglo-Saxon
object reuse
Roman
furnished burial
late antique Britain
Advisor: Hamerow, H
Aspects of Q-ball theory

Q-balls are an example of non-topological soliton that can appear in the spectrum of scalar field theories. They are semi-classical states that minimise the energy for a given Noether charge. If isolated from other sectors, these spherically symmetric objects are kept absolutely stable by energy and Noether charge conservation. Though the properties of Q-balls cannot be determined analytically in general, progress can be made in two opposite limits: the thin-wall (large charge) limit; and the thick-wall (small charge) limit. Q-balls are both interesting phenomenologically and as formal objects in their own right, as evidenced by the large body of work on this subject.
This thesis represents a study on the formal properties of field theories, with the aim to determine the subclass of models that admit Q-ball solutions. To that end, its goals are two-fold. Firstly, to constrain the theories that possess stable Q-ball states by: (i) determining the differential equations that govern the VEV of the constituent scalar in the thin-wall limit, together with the physical properties of the resulting Q- ball; (ii) constraining the small-field expansions that lead to stable thick-wall Q-balls by demanding that the minimum of energy be classically stable against decay to the underlying quanta of the scalar field. Secondly, to determine whether stable Q-balls, in both the thick- and thin-wall limit, can form from scalar mesons, arising from the breaking of an approximate chiral symmetry, in the SM and in a specific BSM theory. We will not discuss the phenomenology of these theories in this thesis.
The content of this thesis is laid out in three parts. Part I is concerned with Q-balls in theories possessing only one scalar field, and comprises Chapters 2 and 3, whereas Part II is concerned with theories with multiple scalar fields, and comprises Chapters 4-6. In these parts, we perform an analysis to determine the existence of Q-ball states, and any constraints required by the theories that possess them. In particular, in Part I, the thick-wall analysis presents us with necessary conditions, whereas in Part II, the thick-wall analysis presents us with sufficient conditions. Fi- nally, Part III analyses theories when the underlying scalars of the theory are pseudo- Nambu-Goldstone bosons arising from the breaking of an approximate chiral sym- metry, as in the Standard Model – this final part comprises Chapters 7 and 8. We show that stable Q-balls are not part of the spectrum of the leading-order Chiral lagrangian, but that they can arise in the class of BSM models we study.
The bulk of the original work of this thesis can be found in Refs. [18,19,100–102], with the remaining work unpublished.

Keywords: Beyond-the-Standard Model
Field Theory
Q-balls
Advisor: March-Russell, J
States of the union: federalism and the origins of American intergovernmental relations, c. 1789-1820

This dissertation explores how American state governments adapted to governing in a new kind of federal union in the three decades following the ratification of the U.S. Constitution. Although existing political histories generally pay only anecdotal attention to the activities of state governments in the early national period, this thesis demonstrates that the creation and implementation of national policy was significantly shaped by interactions between state and federal officials. Minimal manpower and vast distances limited the capacity of the federal government to enforce its own laws across the nation, leaving the federal executive and Congress reliant on the support of state officials and institutions in the implementation of federal policies within the states. The line between state and federal areas of responsibility under the Constitution was often unclear, and the question of which government had the right to legislate in which policy area arose frequently. While state and federal officials regularly disagreed with one another about the interpretation of federal laws and of the Constitution, they learned to resolve these conflicts through negotiation, in most cases avoiding formal litigation. I denominate this pattern of interactions ‘co-ordinated federalism.’
On the basis of archival research in five states, this dissertation builds an administrative history of early American federalism, investigating the impact of intergovernmental interactions on the making and execution of national policies concerning trade and finance, national defence, Indian affairs, and slavery. An introductory chapter summarizes the principal mechanisms by which the state and federal governments conducted their ongoing negotiations, and explores the roles of state governors and legislators in producing regulations, resolutions, and remonstrances designed to influence federal policy. While state governments generally co-operated in the enforcement of federal law, even where it was highly controversial, their considerable capacity for independent action could also pose a threat to the success of federal policies.

Keywords: history
Native Americans
constitutional law
American founding
Slavery
federalism
early American republic
politics
constitutional studies
eighteenth century
United States Constitution
nineteenth century
Advisor: Cole, N
Impact of land-use change on bird communities of a Rwandan biodiversity hotspot

Although land-use change is increasingly flagged as the top driver of biodiversity loss in the tropics, there are important information gaps on its effects on particular facets of biodiversity, particularly in the Afrotropics. To contribute to this research agenda, and with a focus on birds, this study explores how the varying degrees of anthropogenic habitat transformations have affected the patterns of species composition, species diversity, functional and phylogenetic diversity. The study employed a range of methods, however, the core results are based on avian point-count sampling and habitat assessment conducted within major land-use types in the Nyungwe landscape, a tropical montane rainforest and adjacent croplands in Rwanda. Further data on avian functional traits were obtained from museum specimens. The study shows the following in relation to relatively undisturbed forest habitats of the Nyungwe landscape. 1) Species composition was altered and species diversity levels declined in all alternative land-uses. 2) Restored and cultivated areas experienced loss of functional diversity, with steeper falls for the trophic-related traits in the former land-use. 3) Phylogenetic diversity was stable across land-uses, except for cultivated areas, which registered marked declines, particularly in monoculture farms of tea. 4) At the landscape scale, avian diversity was influenced by elevation, soil moisture and the lower vegetation height, however, within cultivated areas and regenerating forests, vegetation composition, and tree cover extent were of high importance. 5) There was no evident superiority of the assisted natural regeneration approach over the passive restoration approach with respect to supported avian diversity, reflecting the long time needed for a full recovery. This study provides evidence of the irreplaceability of primary forests in the tropics, and the crucial roles habitat heterogeneity plays in maintaining avian diversity. The thesis also considers how these findings may inform the conservation planning of multiple-use landscapes in Rwanda, and similar landscapes in the tropics, with attention also to the use of birds as flagships for conservation.

Keywords: Agrobiodiversity
Tropical montane forest
Birds
land-use change
Taxonomic, functional and phylogenetic diversity
Forest restoration
Avian ecology
Nyungwe National Park, Rwanda
The impact of DNA damage repair inhibitors on the therapeutic window of thoracic radiation

Background: Lung cancer is the leading cause of cancer death worldwide. A mainstay of treatment is radiotherapy, although its efficacy is limited by toxicity to surrounding normal tissue. New combination treatments are being proposed to increase the radiotherapy anti-tumour effect, but there has been a lack of preclinical studies looking at normal tissue effects simultaneously.
Aim: To address the need for a mouse model of anti-tumour and normal tissue responses concurrently over an appropriate time-course for early and late tissue effects, we evaluated the A/J model of chemically-induced lung carcinoma.
Methods: Autochthonous lung tumours were induced by urethane treatment of A/J mice. Tumour bearing animals were treated with whole thorax, hemithorax, or CT- guided left lung ionising radiation (IR, 10 Gy, 13 Gy, or 15 Gy single dose or 5 x 5 Gy fractionated dose) alone or in combination with DNA damage response (DDR) inhibitors (AZD6738, AZD7648, AZD1390) at different time points during tumour development. Tumour and normal tissue responses were followed for up to 26 weeks. Lungs were collected and processed for histology, and Masson’s trichrome staining was performed to evaluate collagen deposition in irradiated lungs. Magnetic resonance images of lung and tumours were obtained during the course of the experiments.
Results: Whole thorax IR combined with DDR inhibitors resulted in oesophageal inflammation and immune cell infiltration, so hemithorax fractionated and single dose IR protocols were developed. Hemithorax IR combined with an ATR inhibitor (AZD6738) had limited anti-tumour effects but also few normal tissue responses. In contrast, hemithorax IR combined with a DNA-PK inhibitor (AZD7648) led to significant anti-tumour effects but also was associated with increased skin and lung normal tissue damage. Furthermore, hemithorax IR combined with an ATM inhibitor (AZD1390) resulted in limited anti-tumour effects and also skin and lung normal tissue damage. Early oesophageal modelling of fractionated whole thorax IR with AZD7648 revealed subclinical histological changes.
Conclusions: A/J mice provide a model for the concurrent evaluation of anti-tumour and normal tissue effects and may be useful in assessing the therapeutic window of novel therapies in combination with IR. The value of the model in assessing therapeutic window will need to be confirmed by clinical studies.

Advisor: Ryan, A