VictorJuiz/thesis huggingface dataset:
Molecular architecture of SAS-5 enables construction of a daughter centriole
Keywords: protein structure
biophysics
X-ray crystallography
structural biology
biochemistry
centrioles

In dividing cells, centrioles are duplicated once per cell cycle in a semi-conservative manner. A daughter centriole forms perpendicularly to the mother in a process templated by cartwheel-like structures. Cartwheels are found in centrioles of most eukaryotes, and are regarded as the key factor in establishing the nine-fold symmetry of centrioles. Cartwheels comprise the self-oligomerising protein SAS-6, recruitment of which to the mother centriole is mediated by direct binding to protein SAS-5 (also known as Ana2 or STIL). Although SAS-5 is an essential protein for centriole duplication, depletion of which completely terminates centrosome-dependent cell division, its exact role in this process has remained obscure. Using X-ray crystallography and a range of biophysical techniques, we have determined the molecular architecture of SAS-5. We show that SAS-5 forms a complex oligomeric structure, mediated by two self-associating domains: a trimeric coiled coil and a novel globular dimeric Implico domain. Disruption of either domain leads to centriole duplication failure in worm embryos, indicating that large SAS-5 assemblies are necessary for function. We propose that SAS-5 provides multivalent attachment sites that are critical for promoting assembly of SAS-6 into a cartwheel, and thus centriole formation.
States' prescriptive jurisdiction and the 'police powers doctrine'
Keywords: customary international law
jurisdiction
sources
public interest
regulation
police power

States' ability to promote the 'public interest', and to pursue their social, environmental, economic and fiscal objectives in light of widening and deepening international economic regulation has generated significant discussion. This dissertation critically examines the 'police powers doctrine' developed in arbitral practice and academic discussion concerning international law on investment protection. It considers whether police powers can be reconciled with the 'traditional' approach to States' regulatory authority in general international law, the rules governing prescriptive jurisdiction.
Three main issues are considered: (i) how general international law governs States' ability to create and apply laws within their territory; (ii) the origins of the police powers doctrine and how it has featured in arbitral practice on investment protection; and (iii) whether police powers can be doctrinally and conceptually reconciled with the general international law governing States’ prescriptive jurisdiction.
It is demonstrated that police powers suffers from critical flaws when considered from both legal validity and coherence perspectives. The dissertation’s central argument however is that police powers is more broadly irreconcilable with the general international law governing States’ prescriptive jurisdiction. It is shown that police powers represents a significant departure from the extant law on States' prescriptive jurisdiction in three respects: (i) it changes the nature of States' authority to create and apply laws within their territory from one of residual plenary freedom to one based on conditional authorisation; (ii) it shifts from an approach based on legality to one based on 'legitimacy'; and (iii) it shifts the focus away from the legal content and consequences of States' assumed obligations, with corresponding consequences for auto-limitation as the basis of obligation in the protection of foreign investment.
Nitrogen-status sensing in Arabidopsis
Keywords: plant science nitroge metabolism nitrogen-status sensing

Plant nitrogen use efficiency (NUE) is important in agriculture because it significantly influences yield and fertiliser requirements. Many factors influence NUE; these include nitrogen availability, internal nitrogen-status, nitrogen uptake and assimilation rates as well as carbon status. Previous attempts to improve NUE by targeting the main nitrogen uptake or assimilation machinery (e.g. over-expression of nitrate reductase or glutamine synthetase) have had mixed results. This is because these enzymes are strictly controlled by multiple feedback mechanisms relating to internal and external nitrogen-status. Arguably, a better approach to manipulating NUE would be to identify and supress these feedback signals either alone, or in conjunction with over-expression of the uptake and assimilation machinery. This could enhance exploitation of nitrogen resources leading to increased growth.
Internal nitrogen-status signalling is poorly understood. However, it is known that amino acids, when exogenously supplied, inhibit the uptake of nitrate. The mechanism for this inhibition has not been identified, but it is likely the result of sensing of internal nitrogen status, the amino acids representing a signal of nitrogen sufficiency, in turn leading to reduced expression and activity of the nitrogen uptake and assimilation machinery. In this thesis I conducted a reverse-genetic screen based on the response of candidate amino acid transporter knock-out mutants to exogenous alanine. In wild-type Arabidopsis, exogenous alanine caused inhibition of vegetative growth, which is accompanied by a reduction in nitrate uptake and transcripts encoding nitrate transporters. In the reverse-genetic growth screen, I identified four mutants with vegetative growth that was insensitive to exogenous alanine. Further characterisation of these mutants revealed that nitrogen uptake was not inhibited and this was accompanied by a lack of repression of nitrate transporter transcripts. Based on this evidence, I concluded that these amino acid transporter mutants were perturbed in nitrogen-status signalling. However, the origin of this signalling perturbation remains unclear. I formulated two hypotheses to explain how four amino acid transporter mutants could have the same signalling phenotype. The first suggested that the four alanine-insensitive transporters could form a functional complex, which is part of the nitrogen-status signalling pathway. The second suggested that the loss-of-function of the amino acid transporter perturbs metabolite levels, in a common way in each mutant, producing a metabolic signature which is sensed downstream of the transporter by an unknown mechanism. The latter hypothesis was tested by extensive metabolite profiling and I could find no evidence in support of the hypothesis. Preliminary investigations were made of the functional-complex hypothesis but technical problems prevented significant progress.
Up-down asymmetric tokamaks
Keywords: Gyrokinetics
Intrinsic rotation

Bulk toroidal rotation has proven capable of stabilising both dangerous MHD modes and turbulence. This has allowed existing tokamaks to generate extra fusion power at a fixed size and magnetic field. However, most methods of inducing the plasma to spin do not appear to scale well to larger devices such as ITER or a future power plant. In this thesis, we explore a notable exception: up-down asymmetry in the tokamak magnetic equilibrium. When tokamak flux surfaces are not mirror symmetric about the midplane, turbulence can transport momentum from one surface to the next, creating spontaneous rotation that is "intrinsic" to the geometry. We seek to maximise this intrinsic rotation by finding optimal up-down asymmetric flux surface shapes.
First, we use the ideal MHD model to show that low order external shaping (e.g. elongation) is best for creating up-down asymmetric flux surfaces throughout the device. Then, we calculate realistic up-down asymmetric equilibria for input into nonlinear gyrokinetic turbulence analysis. Analytic gyrokinetics shows that, in the limit of fast shaping effects, a poloidal tilt of the flux surface shaping has little effect on turbulent transport. Since up-down symmetric surfaces do not transport momentum, this invariance to tilt implies that devices with mirror symmetry about any line in the poloidal plane will drive minimal rotation. Accordingly, further analytic investigation suggests that non-mirror symmetric flux surfaces with envelopes created by the beating of fast shaping effects may create significantly stronger momentum transport.
Guided by these analytic results, we carry out local nonlinear gyrokinetic simulations of non-mirror symmetric flux surfaces created with the lowest possible shaping effects. First, we consider tilted elliptical flux surfaces with a Shafranov shift and find little increase in the momentum transport when the effect of the pressure profile on the equilibrium is included. We then simulate flux surfaces with independently-tilted elongation and triangularity. These two-mode configurations show a 60% increase over configurations with just elongation or triangularity. A rough analytic estimate indicates that the optimal two-mode configuration can drive rotation with an on-axis Alfven Mach number of 1.5% in an ITER-like machine.
Molecular mechanisms of immune regulation by the receptors CD5 and CD6
Keywords: CD6
TCR signalling
CD5

T cells are adaptive immune cells that are essential for initiating and regulating immune responses. T cell activation is triggered by stimulation of the T cell receptor. However, sustained T cell activation requires the function of a variety of coreceptors, among them CD5 and CD6. Both receptors have been shown to have activating and inhibitory functions and modulation of CD6 function is dependent on engagement by its ligand CD166. Costimulatory signalling by CD6 involves a phosphorylation-dependent interaction between the C-terminal Y662 residue and the adaptor protein SLP-76. However, the CD6 cytoplasmic region is one of the longest in the immune system and contains phosphorylated residues which suggests that additional signalling molecules can be recruited.
I identified an interaction of CD5 and CD6 with the cytoskeleton via ezrin, radixin and moesin. This interaction has an activating function on Jurkat cell activation and may play a role in receptor localisation.
I also identified the adapter protein GADS as a binding partner of the CD6 Y629 residue and found evidence for bivalent binding of the GADS/SLP-76 complex to the CD6 C terminus. Costimulation by CD6 is dependent on the recruitment of this complex and mutant CD6 that cannot recruit it does not provide costimulation and may even be inhibitory in the absence of its ligand. These results suggest a model in which costimulation by CD6 depends on cooperative binding of the GADS/SLP-76 complex to two C-terminal phosphotyrosine residues in the CD6 cytoplasmic region. Binding of this complex to CD6 may enhance long-term signalling by keeping GADS/SLP-76 at the membrane or it may provide an alternative signalling pathway that enhances TCR signalling.
Models for prebiotically-relevant self-reproducing systems
Keywords: interferometric scattering microscopy
physical autocatalysis

Autocatalysis is central to the propagation of living systems and is widely agreed to have played a central role in the emergence of life on earth. Chemical systems which self-reproduce like living cells can offer insight into the transition from chemistry to biology. Self-reproducing micelles and vesicles, or physical autocatalysts, are an important class of autocatalytic chemical systems that have used to model the first living systems for several decades.
The study of physical autocatalysis has been restricted to a limited set of reactions, and hindered by experimental difficulties precluding full characterisation. Together these limitations pose both conceptual and technical barriers to a deeper understanding of this important class of prebiotic system. This thesis addresses both limitations in turn.
Chapter 1 introduces the concept of physical autocatalysis and argues for its importance in the field of prebiotic chemistry. A survey of chemical models of physical autocatalysis is presented and the present work is placed into context.
Chapter 2 describes the development of the first examples of physical autocatalysis driven by irreversible bond-forming reactions. Steps towards the development of asymmetric variations and systems of self-reproducing vesicles are discussed.
Chapter 3 describes the application of interferometric scattering microscopy to physical autocatalysis, allowing for the first time the observation of micellar self-reproduction on the single particle level.
Chapter 4 discusses the limitations of this work and argues that the results described in Chapters 2 and 3 respectively address major conceptual and technical barriers to the study of physical autocatalysis, with recommendations for future work.
Lipschitz geometry and rough paths
Keywords: Rough Paths

Motivated by building a Lipschitz structure on the reachability set of a set of rough differential equations, we study first Lipschitz maps in full detail and in many aspects: we show embedding properties of Lipschitz spaces, study algebraic properties, local versus global behaviour of Lipschitz maps, give a version of the inverse function and the constant rank theorems and analyse flows of Lipschitz vector fields. Along the way, we give quantitative estimates, which is, after all, one of the main strengths of the Lipschitz geometry. Second, we combine our observations on the local properties of rough paths and Lipschitz maps to give a rather flexible structure on manifolds that allow the definition of rough paths on them and explain how the same process can be used to define a notion of coloured paths on manifolds, assuming that one can build a suitable functorial rule. Finally, we make use of those remarks to derive a quantitative condition that endow orbits of vector fields with the structure of a Lipschitz manifold and show, that under this condition, the space of solutions of rough differential equations driven by rough paths is the same as the one we obtain by driving the RDEs with smooth paths.
Multi-parametric MRI techniques for the non-invasive assessment of patients with liver disease
Keywords: liver related end points
collagen proportionate area
MRI
liver fibrosis
non-alcoholic fatty liver disease
portal hypertension

Liver disease is a major worldwide health problem with high prevalence and poor patient outcomes. In the last decade, efforts to improve liver disease severity assessment have led to the development of many non-invasive methods, including magnetic resonance (MR) techniques.
The overarching aim of this thesis was to examine a multi-parametric MR technique in the evaluation of different aspects of liver disease. The MR protocol included T1 and T2&ast; mapping techniques which were used to compute the iron corrected T1 (cT1) and the liver inflammation and fibrosis (LIF) score as measures of liver inflammation and fibrosis.
In healthy volunteers, it was found that premenopausal women had a higher median liver cT1 (784ms) compared to postmenopausal women (741ms; p=0.038) or age matched men (742ms; p=0.005). Furthermore, blood volume was identified as the most significant physiological determinant of liver cT1 and a correction algorithm was developed to compute the "volume adjusted and iron corrected T1" (vacT1), which removes the confounding effect of liver congestion and improves the performance of the test as a biomarker of liver fibrosis.
Against histology, liver cT1 was strongly associated with liver collagen proportionate area, particularly in patients with viral hepatitis (r=0.80; p&LT;0.0001). Furthermore, liver cT1 / LIF had an excellent diagnostic accuracy for the assessment of multiple aspects of non-alcoholic fatty liver disease (NAFLD) with an area under the receiver operating curve of 0.89 for the identification of significant NAFLD.
In the evaluation of portal hypertension, liver cT1 (r=0.49; p=0.038) was associated with the hepatic vein pressure gradient (HVPG), and spleen cT1 was identified as a new biomarker of portal pressure (r=0.66; p&LT;0.0001 vs HVPG). Furthermore, liver cT1 / LIF was shown to be useful in predicting clinical outcomes, with a negative predictive value of 100% for a LIF&LT;2.
Overall, this thesis demonstrated multi-parametric MR to be a robust technique that can assess the whole spectrum of liver disease.
Peeping in, peering out: monocularity and early modern vision
Keywords: anamorphosis
optical illusion
monocular vision
linear perspective

One of the central theoretical tenets of linear perspective is that it is based upon the idea of a monocular observer. Our lived perception, also referred to in the Renaissance as perspectiva naturalis, is always rooted in binocular vision, however, the guidelines for perspectiva artificialis often imply a single peeping eye as a starting point. In the early modern period, a number of rare art forms and instruments follow the prescriptive character of linear perspective to ludic ends. By focusing on this special class of what I would call 'monocular art forms', I will analyse the extent to which the perspectival method has been successfully applied in material form beyond the classic two-dimensional paintings. This special class of objects include: anamorphosis, peep-boxes, catoptrics, dioptric perspective tubes, and perspective instruments. It is my intention to draw attention to the different ways traditional perspectival paintings, exceptional cases such as perspective boxes and anamorphoses, and optical devices were encountered in the early modern period. In this thesis I will be examining the specific sites of each case study in depth so as to describe the various contexts—aristocratic, intellectual, religious—in which these items circulated. In Chapter 1 I illustrate a special class of perspective and anamorphic designs that confined their illusions to a peepshow. Chapter 2 examines one of the most consummate applications of the monocular principle of perspective: seventeenth-century Dutch perspective boxes. In Chapter 3, monocular catoptric designs are studied in light of the vogue for mirror cabinets in the seventeenth century. Chapter 4 examines the innovative techniques of drawing machines and their collection in early modern courts through close study of the 'perspectograph.'
Intestinal tissue engineering
Keywords: Tissue Engineering
Transplantation
Intestine

Tissue engineering (TE) principles have been successfully clinically applied to treat disease affecting specific organs (e.g. trachea) but developments in some organs has lagged behind. The inability to repair or replace significantly damaged intestinal tissue remains a barrier to improving patient outcomes and the promise of Tissue Engineered Intestine (TEI) that was first made more than 20 years ago, is yet to be realised.
This work explored the potential of TEI and literature review formed a basis for developing a clinically transferrable experimental model. It was hypothesised that, porcine large intestine could be retrieved from pigs and decellularized to create a biological scaffold that demonstrated favourable properties for TE, including potential for vascular perfusion and cell engraftment. Novel experiments were performed in intestinal retrieval and decellularization, resulting in scaffolds characterised by a number of methods (e.g. histology, immunohistochemistry). Assessment of the scaffold’s ability to support cell engraftment required development of protocols for isolation and culture of appropriate progenitors, including adipose/ bone marrow derived mesenchymal stromal cells and intestinal organoid units. Finally, in-vitro cultures combining scaffolds and cells were used to assess the ability of scaffolds to promote tissue regeneration.
Perfusion decellularization methods proved effective in creating biological scaffolds that retained radiologically demonstrated vascular perfusion networks, permitting a future route for recellularization and/or transplantation. Scaffolds demonstrated retention of essential extracellular matrix components (e.g. glycosaminoglycans, collagen) and an absence of cell nuclei. Mesenchymal stem cells were isolated, cultured and combined in-vitro with scaffolds in an attempted scaled-down seeding model. Control of culture conditions was challenging and results inconclusive with respect to the scaffold’s regenerative potential. The work demonstrates an exciting prospect for biological scaffold development for a clinically transferrable, semi-xenogeneic transplant or drug delivery model but further experiments in scaffold seeding are required to assess the full potential.
Clinical translation of a simple cognitive task to reduce the occurrence of intrusive memories after a psychological trauma
Keywords: Trauma
Behavioural intervention
Computerized treatment
Cognitive intervention
Intrusive memories
Preventive intervention
Post-traumatic stress disorder

Preventive interventions after psychological trauma are lacking. Intrusive memories in the first few weeks after a traumatic event can be highly distressing, and also predict later post-traumatic stress disorder (PTSD). Laboratory studies with healthy volunteers have found that engaging in a visuospatial cognitive task soon after an experimental trauma film can reduce the frequency of intrusive memories over the following week. The aims of this research were to a) develop the a simple cognitive task intervention (a memory reactivation cue followed by playing the computer game "Tetris") for use in a hospital emergency department (ED) with patients who had experienced a road traffic accident, and b) provide a preliminary test of the efficacy of the intervention using a randomised controlled trial design.
First, the current evidence base for preventive interventions after trauma was reviewed, and theory was drawn from experimental psychology and clinical psychology to propose that delivering a simple cognitive task involving playing Tetris in the immediate aftermath of trauma may offer a novel preventive intervention for PTSD symptoms (Chapter 1). Next, the laboratory procedure was adapted for use in a hospital ED, based on direct observation in the ED, and existing literature (Chapter 2).
An initial pilot study (n = 10) tested key procedures in the ED, namely recruitment of road traffic accident patients, practical delivery of the intervention and completion of an intrusion diary over the first week (Chapter 3). A second pilot study (n = 23) was conducted to improve the study procedures, test both the intervention and control conditions, and assess participant experience (Chapter 4). The recruitment rate, eligibility criteria, drop-out rate and completion rate of the intrusion diary were all improved. Participant feedback was used to refine the intervention and control procedures.
Finally, a main randomised controlled study (n = 71) was conducted, comparing the simple cognitive task intervention with usual care in the emergency department (with a simple activity diary). As predicted, participants in the intervention group had fewer intrusive memories in the first week, and less severe clinical intrusion symptom scores, than those in the control group. Further, participant feedback highlighted the value of being offered an intervention in the emergency department. This research was the first to successfully translate laboratory findings to a clinical emergency department setting. Findings provide a first step towards developing an accessible, low intensity preventive intervention to target intrusive memories after trauma. Further trials and mechanism studies are warranted.