VictorJuiz/thesis huggingface dataset:
Characterising the determinants of hypoxia inducible transcription factors binding to chromatin
Keywords: Transcription
Gene regulation
Hypoxia
Molecular biology

Hypoxia regulates many hundreds of genes that play important roles in numerous physiological and pathophysiological processes. The hypoxia inducible transcription factors (HIFs) are central to the transcriptional activation of these hypoxia-regulated genes. However, to date, little is known about the determinants of HIF-1 and HIF-2 binding site selection. Both HIF-1 and HIF-2 appear to bind as HIF-α/HIF-1β heterodimers, and recognise the same core consensus DNA motif, the hypoxia response element (HRE). However, each has its own distinct but partially overlapping set of binding sites that accounts for only a subset of the total accessible HRE motifs. Here, I have utilised ChIP-seq to systematically compare pan-genomic HIF-1α, HIF-2α and HIF-1β DNA binding in multiple cell lines and have related this to RNA-seq analyses and other publically-accessible next-generation sequencing datasets. I show that endogenous HIF-α subunits exhibit a high-degree of binding site concordance with HIF-1β, consistent with largely canonical binding of intact heterodimers. Despite cell-type specific differences in HIF-1 and HIF-2 binding site occupancy, each isoform exhibits a remarkable rigidity in its preference to bind either promoter-proximal or promoter-distal sites, respectively. These specific distribution patterns are unaffected by the absence of the other HIF-α subunit, suggesting that they do not result from exclusion of one isoform by competition with the other, but rather are discrete properties of each. Furthermore, hypoxia regulated genes neighbouring sites that are shared by both HIF-1 and HIF-2 are more likely to be regulated by HIF-1 when the site is closer to the gene and by HIF-2 when further away, indicating that post-binding mechanisms of transcriptional regulation also follow a similar pattern. Comparison of sites preferentially bound by HIF-1 and HIF-2, respectively, revealed associations with distinct histone environments, distinct accessory transcription factor binding motifs and distinct patterns of transcription factor binding site occupancy, suggesting that each may be influencing specific HIF-1 and HIF-2 binding site selection. In particular, both the AP-1 motif and AP-1 binding site occupancy were enriched within HIF-2 binding sites compared to HIF-1 sites. Intervention on AP-1 DNA-binding using the dominant-negative protein, AFos, attenuated HIF binding, specifically at sites co-occupied by AP-1 and HIF. This indicates that a cooperative relationship exists between the two transcription factors. However, binding of both HIF-1α and HIF-2α were affected suggesting that while AP-1 binding may account for the ability of HIF to bind some HRE motifs but not others, it is not a determinant of differential binding between the two isoforms. Overall, this work reveals remarkably distinct and functionally relevant patterns of HIF-1 and HIF-2 binding across the genome, and provides insight into underlying mechanisms of binding.
Mathematical modelling of tumour evolution and radiation response: The impact of heterogeneity
Keywords: cancer
radiation therapy
mathematical oncology

This thesis seeks to use mathematical and computational models to develop measures of clinically available data to deepen our understanding, and improve our treatments, of cancer. We consider two broad characteristics of cancer: heterogeneity, in the form of differences in cellular phenotype, and the physical microenvironment; and evolution, which has become accepted as a driver of tumour progression. To ensure that the conclusions drawn are as translatable as possible, we will attempt to use data types that are clinically available. Using a hybrid discrete-cell-based model in two spatial dimensions, we focus on these fundamental aspects of cancer, with the hope of generating new understanding and useful hypotheses to benefit current patients and oncologists.
First, we model a tumour growing under the rules of the cancer stem cell hypothesis and a neutral model of evolution, and ask if we can infer the underlying biological proliferative structure. Specifically, we work toward predicting the symmetric division probability of our simulated tumours from clincally relevant observables, as this is a key driving parameter of tumour progression and therapeutic response. We focus on measures of clonal diversity, group size and shape, and a suite of statistical measures of the phylogenetic trees resulting from the tumour's evolution in different regions of parameter space. We find strikingly different patterns in these measures for changing symmetric division probability which hinge on the inclusion of spatial constraints. These results give us insight into differences between solid and liquid tumours, and also generate a number of actionable clinical and biological hypotheses.
Second, we explicitly consider the physical microenvironment of tumours invading into healthy tissue, and model oxygen transport, uptake and cellular competition. We then explore the effect of spatial organisation of blood vessels within the tumour on tumour growth kinetics and cellularity. Finding wide variability in the distribution of oxygen across tumours dependent on both vascular organisation and density, we proceed to explore the utility of spatial measures of vessels on radiation efficacy. Our results offer a novel hypothesis as to the failure of vascular normalisation therapy and radiation, and a possible clinical solution.
Novel and selective small molecule inhibitors and activators for the prolyl hydroxylase domain enzyme
Keywords: HIF
PHD2

Hypoxia Inducible Factors (HIF) functions are master regulators of oxygen homeostasis and have a key role in the physiological responses to hypoxia including angiogenesis and erythropoiesis. Under hypoxia, levels of HIF-α subunits increase, they hetereodimerise with HIF-1β sub unit and promote the initiation of transcription of target genes. Under normoxia, oxygen dependent HIF-α degradation is promoted by hydroxylation of either of two proline residues (Pro402 and Pro564). The interaction of prolylhydroxylated HIF-α with the Von Hippel -Lindau protein (pVHL) promotes hydrolytic degradation of HIFα through an E3 ubiquitin ligase proteasomal pathway. HIF prolyl hydroxylation is catalysed by three 2-oxoglutarate (2OG)-dependent oxygenases known as prolyl hydroxylase domain (PHD 1-3) proteins, through an Fe(II) mediated catalytic process using 2OG, and oxygen. The PHDs are part of the family of Fe(II) bound 2OG dependent oxygenases. There are approximately 70 human 2OG oxygenases many of which have biologically important roles. Small-molecule inhibitors have reached advanced clinical trials; however, many clinical candidates inhibit other structurally similar 2OG oxygenases (OGFOD1 and vCPH) potentially altering the therapeutic effect. This thesis describes the design and synthesis of potent and 2OG oxygenase selective inhibitors for the PHDs.
The 1,3,8-triazaspiro[4.5]decane-2,4-dione and 4-hydroxy-2-(pyrazole)pyrimidine-5-amide series were chosen as initial 'hits' (reported in the patent literature). The main analogues of the series were characterised in vitro and in cells as potent and selective PHD inhibitors over structurally similar 2OG oxygenases (Chapter 2). Broad structure activity relationship (SAR) of both initial series demonstrated the sensitivity for PHD2 inhibition (Chapter 3). Combination of SAR work described in Chapters 2 and 3 lead to the development of the novel 4-hydroxy pyridine series. In-depth SAR resulted in optimised analogues including 1 (IC50 69 nM) and highly selective over structurally similar 2OG oxygenases including OGFOD1. The completed SAR work led to the development of two novel pharmacophores 2 and 3. Both pharmacophores displayed potent PHD inhibition and selectivity over OGFOD1. Analogues including 1 and 3 displayed on target cellular activity stabilising HIF-1α at 20 μM (Chapter 4).
The 4-dimethylamine pyridine analogue displayed an increase in substrate hydroxylation on PHD2 in contrast to the DMSO control (Chapter 3). SAR and cellular characterisation indicated that the effect observed was not an assay artifact (Chapter 5).
Fenofibrate was used as a starting point for the development of novel inhibitors of the oxygen consumption rate (OCR) via mitochondrial inhibition (Chapter 6). Analogues were synthesised in order to conduct broad SAR and on-target cellular activity was observed in a Seahorse XF assay (50% reduction in the OCR at 1 μM). A selection of amino and amide analogues warrant further investigation.
Understanding the constraints on the operation of corporate insolvency law in the economic transition of developing countries: the case of China
Keywords: transition economy
China
insolvency law
law reform

This thesis seeks to contribute to our understanding of why creditors and debtors do not ordinarily use China’s reformed Enterprise Bankruptcy Law ('EBL'), whether the low use of the EBL is problematic, and if so, what can be done to ensure a more efficient resolution of corporate insolvencies and corporate financial distress in China. The EBL has been lauded – domestically and internationally – as a major legislative success. However, despite the rapidly growing number of companies, level of corporate indebtedness and non-performing loans – which should, one might expect, lead to an increase in the use of the EBL – the number of court-run insolvency cases has in fact been decreasing since the law was implemented in 2007. The thesis draws on newly collected insights from a series of interviews in China – to supplement the scarce and often incoherent data that is available – to determine what motivates debtors and creditors not to use the EBL. The findings are presented as four complementary constraints on a more effective and efficient operation of the EBL. First two constraints relate to the low payoffs under the EBL that debtors and creditors expect to receive due to (i) flaws in the EBL itself and (ii) problems in surrounding non-bankruptcy rules and practices that reduce or prevent recoveries under the EBL. A third constraint affects those debtors and creditors who wish to use the EBL despite the low expected payoffs – for example to avoid directors' liability for corporate insolvency – but are prevented from doing so due to (iii) potential enforcers' limitations and biases. A fourth and final constraint on the use of the EBL that reinforces debtors' and creditors' unwillingness to use the EBL is (iv) the parties' (often inaccurate) perception that alternative debt enforcement mechanisms may offer comparatively higher payoffs (v. the EBL).
Building on this discussion, the thesis then considers the desirability of, and options for, reform. It argues that reform and subsequent greater use of court-enforced insolvency law are desirable in China because the (reformed) EBL has the potential to contribute to economic development through more efficient resolution of complex financial distress; better control of bad debt; easier and cheaper corporate financing; more efficient allocation of resources; and more entrepreneurial activity. However, because the necessary changes to deliver this are likely to be slow in coming, it proposes a dual-track reform encompassing (i) substantive reform of the EBL and select non-bankruptcy laws and practices; accompanied by (ii) the introduction of a new speedy, independent and confidential mechanism for insolvency resolution, 'MedArb.'
The molecular epidemiology and ecology of Neisseria species in the African meningitis belt
Keywords: Neisseria
bacterial genomics
African meningitis belt

Neisseria meningitidis (Nm) is one of the major causes of bacterial meningitis in the African meningitis belt (AMB). This organism is part of the genus Neisseria, which includes ten human restricted species, mostly harmless commensals of the nasopharynx; however, Nm is capable of causing invasive meningococcal disease. The transition from carriage to pathogenic state remains perplexing, and strict virulece factors have yet to be identified.
It has been hypothesised that non-pathogenic Neisseria (NPN) carried asymptomatically in the oroopharynx could play a role in modulating carriage of Nm, and therefore, its likelihood of invasion. In chapter 3, the diversity of the genus was characterised within a collection of 46 034 nasopharyngeal samples obtained across the AMB: five different species were identified, with Nm and NPNs displaying inversely related risk factors fo carriage. Chapter 5 presents the whole genome sequence (WGS) analysis of 107 Neisseria isolates unclassified by other methods. This higher genetic resolution, complemented with the use of a novel speciation approach, revealed seven novel Neisseria species, mostly collected in African countries.
The invasive potential may also be due to the presence of particular genetic factors in the meningococcal genome. Chapter 4 presents the WGS comparison of 23 carried and invasive serogroup A Nm collected in Chad during the 2011 meningitis epidemic. Isolates from both phenotypic groups were found to be part of the same bacterial populations; however, discrete clusters were identified, associated with distinct age groups.
These results indicate that genomic analyses are essential to appropriately study Neisseria diversity, and that lower resolution methods have greatly underestimated the diversity of the genus in Africa. The identification of Nm clusters associated with certain niches and of the differences in carriage risk factors suggests that variation in the environment, including the presence of NPNs, may be key in modulating carriage of Nm.
Robust lifelong visual navigation and mapping
Keywords: Localisation
SLAM

The ability to precisely determine one’s location in within the world (localisation) is a key requirement for any robot wishing to navigate through the world. For long-term operation, such a localisation system must be robust to changes in the environment, both short term (eg. traffic, weather) and long term (eg. seasons).
This thesis presents two methods for performing such localisation using cameras — small, cheap, lightweight sensors that are universally available. Whilst many image-based localisation systems have been proposed in the past, they generally rely on either feature matching, which fails under many degradations such as motion blur, or on photometric consistency, which fails under changing illumination.
The methods we propose here directly align images with a dense prior map. The first method uses maps synthesised from a combination of LIDAR scanners to generate geometry and cameras to generate appearance, whilst the second uses vision for both mapping and localisation. Both make use of an information-theoretic metric, Normalised Information Distance (NID), for image alignment, relaxing the appearance constancy assumption inherent in photometric methods. Our methods require significant computational resources, but through the use of commodity GPUs, we are able to run them at a rate of 8-10Hz. Our GPU implementations make use of low level OpenGL, enabling compatibility across almost any GPU hardware.
We also present a method for calibrating multi-sensor systems, enabling the joint use of cameras and LIDAR for mapping.
Through experiments on both synthetic data and real-world data from over 100km of driving outdoors, we demonstrate the robustness of our localisation system to large variations in appearance. Comparisons with state-of-the-art feature-based and direct methods show that ours is significantly more robust, whilst maintaining similar precision.
Identification and characterisation of the genetic determinants of variable response to antigens from infectious agents
Keywords: Antibody
Genome-wide association study
Human leukocyte antigen
Pertussis
Africa

Despite the success of vaccines in routine use worldwide, there are substantial challenges hampering our ability to develop vaccines against extant diseases including malaria and tuberculosis. Novel approaches are urgently required to help us understand immunological correlates of protection against disease and facilitate our understanding of the impact of human genetic variation on the success of diverse vaccines.
To identify host genetic factors responsible for variation in antibody responses against vaccine antigens delivered routinely to infants worldwide I performed a genome-wide association study (GWAS) involving 2,499 infants recruited from three diverse sites across Africa. I identified strong genetic associations between variants in the class II major histocompatibility complex (MHC) locus and responses against five antigens: pertussis toxin (PT), filamentous haemagglutinin (FHA) and pertactin; diphtheria toxin (DT); and hepatitis B surface antigen.
To characterise these associations at the gene and allelic level I developed a large, high-resolution (6-digit ‘G’) population-specific human leukocyte antigen (HLA) imputation reference panel including 697 individuals from the vaccine GWAS typed at 11 genes, highlighting the diversity of HLA across the African continent. Using this panel I imputed HLA into the remaining GWAS dataset to fine-map the associations to specific HLA alleles, amino acid and single nucleotide polymorphism sites; some of which were found to be African specific.
I then used these HLA association findings observed with PT response to correlate, through genetics, this trait with susceptibility to whooping cough in an independently recruited and analysed set of cohorts from the UK. I further used these genetic correlations to demonstrate the relevance of levels of PT-specific circulating follicular helper T-cells and TRBV29-1 T-cell receptor gene expression levels in the development of this protective immune response against PT. By using HLA-peptide binding studies I also demonstrate the diversity of mechanisms that are involved in HLA-disease association, showing that the breadth and affinity of DT-peptide binding are increased with HLA-DRB1 alleles associated with increased DT antibody responses.
Taken together, these data represent the first comprehensive genetic association study of multiple vaccine responses undertaken in African infants. These results highlight the importance of human genetics in modulating protective responses against vaccine antigens and demonstrate how such associations can be harnessed to understand biological mechanisms of protective efficacy in greater detail that may in turn facilitate future vaccine development.
Translational control of autophagy rejuvenates immune responses
Keywords: Ageing
Spermidine
Immunity
TFEB
eIF5A
Translation
Autophagy

As our body's guardian, the immune system maintains systemic health through removal of pathogens, damage and cancer. Ageing of the immune system is associated with compromised immune responses as well as decreased tumour surveillance and is therefore a key risk factor for major diseases in the elderly. Adaptive immune responses are mediated by T and B lymphocytes, and failure in adaptive immunity is a particular hallmark of the ageing organism. Here we show that autophagy is impaired in aged murine B lymphocytes, and loss of autophagy causes severely reduced B cell responses. Our data demonstrate that B cell senescence can be reversed in an autophagy-dependent manner by spermidine, a naturally occurring polyamine metabolite. Mechanistically, our study reveals that the translation factor eIF5A, that requires spermidine for its activation, regulates the expression of the master autophagy/lysosomal transcription factor TFEB. Importantly, we show in humans that spermidine, eIF5A and TFEB levels decrease with age and may serve as ageing biomarkers. Taken together our results indicate that the translational control of autophagy by eIF5A is dysregulated with ageing, and identify a novel pathway with therapeutic implications.
The construction of professional identities in medical writing and fiction, c. 1830s-1910s
Keywords: medicine
Victorian
literature
periodicals

This thesis examines the representation of medical practitioners between the 1830s and 1910s in Britain and its Empire, drawing on the medical press and fiction. Moving away from the notion that practitioners’ identities were determined chiefly by their qualification or professional appointment, it considers how they were constructed in relation to different axes of identity: age, gender, race, and the spaces of practice.
Each chapter concentrates on a different figure or professional identity. I begin by looking at the struggling young medical man, before examining metropolitan practitioners (from elite consultants to slum doctors), and the hard-working country general practitioner. I then consider how gender and professional identities intersected in the figure of the medical woman. The last chapter examines practitioners of colonial medicine in British India.
This thesis considers a range of medical journals, from well-known titles such as the Lancet and British Medical Journal, to overlooked periodicals including the Medical Mirror, Midland Medical Miscellany, and Indian Medical Record. It also examines fiction by medical authors such as Arthur Conan Doyle and W. Somerset Maugham, and lesser-known figures including Margaret Todd and Henry Martineau Greenhow. I read these texts alongside other contemporary writing (from advice guides for medical men to fiction by lay authors) to scrutinise how ideas about practice were shaped in the medical and cultural imagination.
My research demonstrates not only how medical journals fashioned networks among disparate groups of practitioners but also how they facilitated professional rivalries. I reveal the democratising tendency of print culture, highlighting how it enabled a range of medical men and women to write about practice. Ultimately, the thesis develops our understanding of medical history and literary studies by uncovering how the profession engaged with textual practices in the formation of medical identities.