VictorJuiz/thesis huggingface dataset:
Understanding the role of Caspr2 in the developing cerebellum
Keywords: Caspr2
cerebellum
cellular morphology
Inositol 1,4,5-trisphosphate receptor type 1

Despite receiving renewed attention due to the revelation it is involved in higher cognitive functions, we still know little about how the cerebellum develops and operates. Studies suggest Contactin-associated protein-like 2 (Caspr2), a member of the Neurexin superfamily, has a cerebellar function. However, the cellular and molecular bases for this remain unknown.
An initial assessment of the spatio-temporal expression pattern of Caspr2, using immunohistochemistry and biochemical fractionation, suggested that Caspr2 is expressed at specific synapses in the developing cerebellum. Little is known about the function of Caspr2 at synapses and so the Caspr2 domain exposed to the synaptic cleft, the Caspr2 extra-cellular domain (ECD), was focused on. The addition of recombinant Caspr2 ECD to organotypic cerebellar slice cultures prepared from Cntnap2-/- mice rescued a dendritic morphology defect observed in untreated cultures, suggesting Caspr2 affects cellular morphology during cerebellar development. To understand the molecular basis for this effect, a pull down assay was used to identify the synaptic binding partners of Caspr2. Unexpectedly, mass spectrometry analysis of this experiment revealed that the Ca2+ channel Inositol 3,4,5- trisphosphate receptor type I (IP3R1) is a cognate partner of Caspr2 at synapses in the developing cerebellum. Further biochemical assays revealed both that the Caspr2-IP3R1 interaction underlies the regulation of cellular morphology by Caspr2 and that Caspr2 may modulate cytoplasmic Ca2+ levels. Combined with data from co-immunoprecipitation assays suggesting that Caspr2 interacts with the IP3R1 poreforming domain, these data are consistent with Caspr2 acting via IP3R1 to regulate cellular morphology during cerebellar development, most likely by directly affecting the IP3R1 pore region environment.
Together, these experiments therefore reveal novel cellular and molecular roles for Caspr2 in the developing cerebellum. As well as improving our understanding of the nervous system, knowledge such as this will likely be increasingly clinically relevant, given the previously overlooked links between the cerebellum and cognition.
Investigating a role for telomeric transcription in cancer
Keywords: Transcription
Cancer
Telomere

A constitutive hallmark of cancers is the extension of telomeric DNA. Approximately 85% of cancers extend their telomeres through the upregulation of the enzyme telomerase; whereas the remaining proportion use a recombination-based method known as Alternative Lengthening of Telomeres pathway (ALT). Tumours that exhibit the so-called ‘ALT’ pathway include: pancreatic neuroendocrine tumours, astrocytoma and osteosarcoma. The prognosis for many of these tumours is poor and the development of novel therapies is therefore an important unmet need.
Recent work has shown, however, that ALT cancer cells exhibit some characteristic hallmarks which include; a near universal loss of the chromatin remodelling factor ATRX and increases in the transcription of a long non-coding RNA from telomeres, denoted TERRA. This project aims to determine: a) do increases in TERRA transcription facilitate the ALT pathway and b) could targeting of the TERRA transcript be a viable therapeutic approach for the treatment of ALT cancers?
Consistent with a role for TERRA in facilitating ALT we demonstrate that ALT positive cancer cells exhibit changes in the nuclear distribution of TERRA, with clear telomeric foci detectable via RNA-FISH. Furthermore, we demonstrate that the use of LNA GapmeR antisense oligonucleotides can be used as a strategy to deplete TERRA levels. Importantly depletion of TERRA correlated with a loss in C-circles, a major marker of an active ALT pathway. Future work will determine how this affects longterm viability and whether this provides potential for therapeutic intervention in ALTpositive cancers.
X-ray powder diffraction as a non-destructive tool for characterising laser wakefield betatron radiation
Keywords: Electron spectrometer
Powder diffraction
XCERP diffraction
Image analysis
Betatron radiation
Ross filter
Spectral reconstruction
Single photon counting
X-ray diffraction
Geant4

Laser wakefield accelerators provide a relatively simple means of generating bright X-rays beams which are useful across many fields and industries. To achieve this, a sufficiently powerful laser is required and just a few centimetres of gas. In contrast, other bright X-ray sources, such as synchrotrons, require significantly more infrastructure and can span many hundreds of metres.
This thesis looks at a novel diagnostic technique based on X-ray diffraction from a powder in order to characterise X-ray beams with large shot-to-shot variations. The mechanics behind the method, named XCERP diffraction, are presented and the results of simulations are provided as a proof of principle study. XCERP diffraction is shown to be able to retrieve details of the energy spectrum and the beam divergence in a single shot without prior knowledge of the spectral shape.
A campaign at the Centre for Advanced Laser Applications in Munich focused on the first experimental demonstration of XCERP diffraction. The results reveal that an increased level of radiation shielding was required as a source of ionising radiation was found to be present whenever an electron beam was generated. This source of radiation is thought to have obscured potential X-ray diffraction.
An investigation of the unknown radiation source was performed using GEANT4. From simulations of the CALA target chamber, it was found that the CCD of interest would have been subjected to both bremsstrahlung radiation and stray electrons when an electron beam is steered into a steel floor. Further simulations show potential methods of reducing the flux of particles reaching the CCD.
Finally, the designs of an electron spectrometer and filter array are described in detail to measure properties of the electron bunches and betatron radiation produced during an experimental campaign at the Astra Gemini laser facility.
Serial verb constructions in Barayin: Typology, description and lexical-functional grammar
Keywords: Barayin
Lexical-Functional Grammar
Chadic
Typology

Barayin is an East Chadic language spoken by around 5000 people in the Guera region of the Republic of Chad. This dissertation examines a particular type of syntactic construction in the language, serial verb constructions, from the perspectives of typological (or comparative) syntax, descriptive grammar, and the formal syntactic theory of Lexical-Functional Grammar (LFG). Typologically, serial verb constructions are problematic because they represent a heterogeneous set of multiverb constructions that have features that do not fit into traditional syntactic categories like subordination, conjunction and adjunction. Part A of this dissertation describes these problematic features in detail, providing a succinct overview of the literature which can serve as a resource for field linguists describing similar constructions. Part B of the dissertation gives a detailed description of the morphology, syntax and semantics of serial verb constructions in Barayin. These chapters contribute to our knowledge of the world’s languages by documenting a complex syntactic phenomenon in an area of the world where most of the languages are significantly understudied. The most common type of SVC in Barayin involves a deictic motion verb. The motion is normally (but not always) understood to take place prior to the activity or state predicated by the main verb. The formal analysis of Barayin SVCs in Lexical-Functional Grammar in Part C uses recent developments in the theory to show how argument sharing in SVCs can be represented in a connected s-structure that conforms to the standard mechanisms of LFG. The approach is compared to two previous analyses of complex motion predicates in other languages which appeal to a non-standard formal mechanism to model complex predicates.
Critical theories of biography in England 1800 - 1831
Keywords: Letters
Anecdotes
Diaries

An examination, taken from published biographies and periodic reviews, such as the Quarterly, of the emerging consensus of what should be contained in a biography, and how it should be presented.
The years 1800 - 1851 mark the period when ideas about biography were first widely discussed. The critical principles are described as they evolved against the background of the huge proliferation of biography which accompanied the "Age of Personality." The past and present were generously documented with biographies long and short, although reviewers grew increasingly hostile to redundant and extended works. The emergence and acceptance of autobiography and literary biography were the most important innovations.
The complex task of framing an aesthetic for biography is then described. The major findings are the importance and place given to detail, the rejection of life—and-times and the welcoming of life-and-letters forms of biography. The argument that biographers should incorporate abundant original materials is then detailed, as it affected the use of letters, diaries, autobiography, anecdotes, and conversation. The discrediting of these original materials by over-use is traced. Lastly, two moralistic issues are considered; how a biographer might be truthful and yet conform to powerful demands not to speak unduly ill of the dead or to touch on taboo subjects, and the writing of biography for utilitarian purposes.
During the period biography was reviewed extensively for the first time, and reviews and independent assessments provide a large amount of material. Although the findings interestingly reflect the age at many points, nothing like a Romantic theory of biography emerges. Rather, the period established the major areas of biographical discussion, which are little altered 150 years later. The thesis deals also with unfamiliar areas of the work of many of the best known writers of the generation.
Colonisation and infection with antibiotic-resistant organisms in patients in the adult intensive care unit, hospital for tropical diseases, Ho Chi Minh City, Vietnam
Keywords: Antibiotic-Resistant Organisms
Colonisation
Infection

In Vietnam, data about colonisation and subsequent infections with antibiotic-resistant organisms (AROs) are limited, particularly from intensive care units (ICUs). A prospective longitudinal study was conducted in Adult ICU, Hospital for Tropical Diseases, Vietnam from 10th November 2014 to 14th January 2016 to characterize colonisation, identify risk factors for colonisation and understand its relationship with infections by Staphylococcus aureus, Escherichia coli, Klebsiella spp., Pseudomonas aeruginosa, and Acinetobacter spp..
63.1% (529/838) of patients admitted to ICU were colonised with AROs. 61.3% (223/364) of patients with an ICU stay >48 hours acquired AROs colonisation in ICU. Increased Charlson Comorbidity Index score and receipt of antimicrobial therapy on ICU admission were significant risk factors for AROs acquisition. The proportion of patients with hospital-acquired infections (HAIs) was 23.4% (85/364), and AROs accounted for 41.5% (44/106) of pathogens causing HAIs. Vascular catheterization was identified as a risk factor for ICU-acquired bloodstream infection.
Of 67 Staphylococcus aureus isolates identified by conventional microbiology, 6 isolates (9%) were sequenced as Staphylococcus argenteus. Multilocus sequence typing (MLST) analysis indicated matching sequence types of infecting and previously colonizing isolates in 90% (9/10) and 94.4% (17/18) patients with HAIs by Staphylococcus aureus and Klebsiella pneumoniae, respectively. Phylogenetic analysis confirmed that ICU patients became infected with their previously colonizing Staphylococcus aureus ST188 (4 patients) or Klebsiella pneumoniae ST17, ST23 and ST86 (6 patients). Whole-genome sequencing helped to disprove 3 patient-to-patient transmission events (1 Staphylococcus aureus and 2 Klebsiella pneumoniae) that were suggested by MLST, and identified one additional Staphylococcus aureus transmission which was missed by other methods.
This thesis provides evidence of the high burden of antimicrobial resistance in Vietnam along with high rate of colonisation and infections with AROs. Therefore, the implementation of infection control measures and antimicrobial stewardship programs is urgently needed in Vietnam.
Payments, ecosystems and development: Payments for Environmental Services (PES) in the Mexican Lacandona rainforest
Keywords: market-based conservation
Lacandon forest
deforestation
forest conservation policy
Mexico
Payments for Ecosystem Services (PES)

Payments for Environmental Services (PES) emerged as a popular forest conservation policy across the Global South since the 1990s, first in Latin America and then elsewhere. PES aim to reduce deforestation and degradation by providing payments to participants conditional on forest protection. PES attracted much attention among policy-makers as a potentially cost-effective and efficient conservation alternative, and for their poverty-alleviation prospects when operating among ‘poor’ forest-dwellers. This rising agenda has been accompanied by significant scholarly efforts to understand PES and their socioenvironmental effects. However, such understandings have overlooked local stakeholder perspectives, and evaluations have mostly examined short-term effects. Thus, less is known about PES’ long-term effects, their determinants, and how local stakeholders perceive them.
Using a multidisciplinary, multi-level, and dynamic livelihood approach combining geospatial and socioeconomic data collected from 2013-2017, this thesis helps to fill this gap by examining PES’ role in the broader livelihood strategies of six communities in the Mexican Lacandona Rainforest. The thesis makes three main contributions to PES literature. Methodologically, it presents a novel lens to understand PES effects, one that brings to the fore the voice of local stakeholders, while paying attention to evolving context and design aspects. Empirically, it shows that participants think about their livelihoods at broader temporal and spatial scales than short-term policies, which allows them to exert some control on the various policies they encounter. This longer-term thinking is reflected in the three analytical chapters in this thesis that examine how people engage with PES among other land uses, how communities devise payment distribution mechanisms, and how people combine multiple policies to pursue various goals. Conceptually, it shows that unless aspects of ‘context’, ‘design’, and ‘decision-making’ are examined simultaneously, PES’ manifold, multi-level, and evolving effects will not be sufficiently understood. Overall, the thesis shows that there are real implications for conceptualising rural development policy as an integrated ‘policy matrix’, instead of individual and self-contained policies.
New methods for identifying dune system reactivation drivers and responses, Nebraska Sandhills
Keywords: Landscape sensitivity
Drylands
Optically Stimulated Luminescence
Changepoint analysis
Artificial Neural Networks

Two billion people living in drylands are affected by land degradation and the destabilisation of surface sediments. However, a detailed understanding of the combined effects of natural and anthropogenic factors in contributing to sediment remobilisation is absent from the literature. A quantified awareness of vegetation cover sensitivities and resultant land degradation to forcing factors is needed if the vegetation and landscape response to future climatic changes and human pressure are to be better predicted.
Measuring past environmental response in a location with a known disturbance history allows us to identify thresholds and explore the relationship between disturbance forces and sedimentary response within a dryland environment. The Nebraska Sandhills, located in the Central Great Plains, is a semi-arid dune field with a reactivation history spanning the last 10,000 years and a well-documented history of forcing factors over recent decades. Whilst regional reactivations in the Central Great Plains have largely been attributed to palaeoclimatic change, the role of humans (e.g. The Dust Bowl of the 1930s), in particular over grazing, has also been cited as a potential cause of land degradation and sediment reactivation.
Using quartz luminescence dating, secondary datasets of forcing factors and statistical inference methods, this thesis identifies the record of sediment deposition in near-surface aeolian stratigraphies in the northern remits of the Nebraska Sandhills and explores the relationship between environmental sensitivity and external disturbance factors. High-resolution luminescence techniques allow us to construct a detailed chronological history of sedimentary deposition events over the last 900 years, producing a record of the environmental response across a range of aeolian features within the semi-arid setting. Combined with a detailed history of climatic, grazing and wildfire pressures, supervised machine learning techniques explore the relationship between forcing factor and environmental response, highlighting the importance of both regional and localised conditions in contributing to the heterogeneous sedimentary response found in the record.
Investigation of the molecular effects of cooling human burns
Keywords: Complement
Thermal injury
Coagulation
Transcriptomics
Human
Proteomics
Cooling

Cooling of burns is key to acute burn management, and is a widely accepted practice in modern medicine. Cooled burns are less painful, heal more quickly, require fewer skin grafts, and leave less scarring. The vast majority of research in this area has used animal models, and focussed on optimising cooling, rather than investigating its mechanism. Cooling is not without risks and limitations, and understanding the mechanism might lead to pharmacological alternatives.
We aimed to develop a standardised human model for burning and cooling, and used this to investigate the transcriptional and proteomic effects of burning and cooling. This model used redundant skin discarded during surgery, and purpose-built apparatus for burn creation and cooling. Microvascular and other histological changes were demonstrated in response to burning, and modified by cooling. RNA and protein extracts from cooled and uncooled samples of burned and unburned skin were analysed with RNAseq and LC/MS3 techniques, respectively. Findings were validated with immunohistochemistry and qPCR.
We demonstrated that there was a significant change in 22% of the transcriptome of the skin, with gene ontologies related to wounding, angiogenesis, inflammation, haemostasis, innate immune response, degranulation and chemotaxis among those significantly upregulated. Downregulated ontologies included keratinisation, epidermal differentiation, hair follicle development and cornified envelope. Cooling of burns significantly increased the transcription of genes related to hair follicle differentiation while reducing the transcription of heat-shock proteins.
Burning caused significant activation of the complement and coagulation cascades, while cooling reduced the scale of these changes. Immunohistochemistry confirmed complement proteins, including the membrane-attack complex (MAC) localised to the immediate area of the blistered epidermis, as were fibrinogen and platelets, with evidence of early neutrophil migration.
We have demonstrated the role of complement and coagulation activation as a damage-amplifying agent following thermal injury, and the role of cooling in attenuating this effect. The preservation of transcription of follicle-related genes indicates preservation of epidermal appendages as sites of re-epithelialisation.
Complement blockade is already utilised in the management of autoimmune conditions, and transplant rejection, and could modify the complement activation in burns, reducing injury-progression, and the associated systemic effects, and improving patient outcomes.
Investigating the molecular, metabolic, and psychological effects of minocycline
Keywords: NMDA Receptors
Minocycline
Emotional Processing
Metabolomics

An immune component has been suggested to underlie the pathophysiology of psychiatric diseases, and is thought to involve pro-inflammatory cytokines. Thus, there is the potential for drugs with anti-inflammatory properties to act as therapeutic agents for psychiatric illnesses. Minocycline has shown promise in pre-clinical animal models and early phase clinical trials for a variety of psychiatric disorders. Previous studies on minocycline have also shown its ability to suppress microglia activity and reduce inflammatory cytokine levels, and its behavioural effects on depressive-like behaviour in animals and humans. However, the underlying mechanisms that lead to minocycline’s psychotropic effects are not clear.
This dissertation investigated the proposal that the anti-inflammatory mechanisms of minocycline underlie its psychotropic effects, as well as explored the pathways that mediate inflammation-induced behavioural changes. To that end, four studies were conducted. The first study looked at inflammation-induced modulation of GluN2 subunit expression and downstream signalling, effects which were rescued by prior treatment with minocycline (Chapter Two). The second study explored the effects of inflammation and minocycline administration on plasma and brain metabolites in mice (Chapter Three). The third study and fourth study investigated the psychological effects (Chapter Four) and biochemical effects (Chapter 5) of an acute dose of minocycline in healthy volunteers. It was revealed that minocycline administration decreased fear misclassification, increased contextual learning, decreased levels of the inflammatory marker CRP, and increased serum lipoprotein.
Overall, minocycline was able to ameliorate inflammation-induced changes, suggesting that anti-inflammatory mechanisms are linked to glutamatergic signalling and synaptic transmission which lead to downstream psychotropic effects. However, metabolomic analysis also revealed changes in lipid metabolism and energy-related metabolites that could potentially underlie a separate mechanism for minocycline’s actions. Nevertheless, given the association between metabolites, and inflammation, it is possible that these pathways interact.