VictorJuiz/thesis huggingface dataset:
Dynamics, formation and segregation of the cytoplasmic chemoreceptor cluster in Rhodobacter sphaeroides

The internal organisation of bacteria is far more complex than originally thought. Many components of the cell have specific localisation patterns. Proteins are localised to many different regions of the cell by numerous mechanisms, and often their function depends on correct localisation.
Bacterial and plasmid DNA are also highly organised and actively positioned. These tightly regulated positioning patterns ensure stable maintenance of genetic material. Members of the ParA/MinD family of ATPases are responsible for the segregation of a large number of bacterial chromosomes and plasmids. Recently members of this family have been shown to position and segregate protein complexes. One such complex is the cytoplasmic chemosensory cluster of Rhodobacter sphaeroides. This large complexes are segregated from a single cluster positioned at the mid-cell to two clusters at 1/4, 3/4 positions by the ParA homologue PpfA using the nucleoid as a scaffold. This ensures that each daughter cell inherits a cluster.
This study sought to investigate this cytoplasmic chemosensory cluster, and its positioning and segregation by PpfA through the cell cycle.
The use of fluorescence recovery after photobleaching revealed that like membrane bound chemoreceptor arrays the cytoplasmic cluster of R. sphaeroides is a highly stable complex. The difference seen between the cytoplasmic cluster and the data reported for the membrane bound cluster of Escherichia coli is probably due to the lack of membrane helping hold the array together.
Investigation of the role of PpfA in segregation of the cytoplasmic cluster, using fluorescence imaging and single molecule tracking with a range of mutants through the cell cycle, suggest that it uses a mechanism unlike any reported for ParA homologues. Single molecule tracking of PpfA molecules shows that the chemoreceptor TlpT stabilises PpfA molecules resulting in slower diffusion of PpfA molecules at the cluster. The use of a ΔppfA mutant shows that PpfA restrains the movement of the cluster, together these results suggest a model in which TlpT stabilises PpfA’s interaction with the nucleoid and PpfA positions the cluster.

Keywords: Chemoreceptors
Chemotaxis
Rhodobacter sphaeroides
Advisor: Judith, A
Essays in labour economics: Thailand’s labour market adjustment during the structural transformation process

I examine the importance of human capital for economic development in Thailand during the period of high economic growth and structural transformation (1985-2000), using labour force survey data. The three main chapters attempt to estimate the effects of education, as a measure of human capital, on three major outcomes in the Thai labour market, namely (i) earnings; (ii) sector of employment; and (iii) earnings inequality. I address the endogeneity problem of education using an education policy shift—the change in the compulsory schooling law—that produces exogenous variation in education. The three main chapters adopt distinct modelling frameworks. The details of each of the main chapters are as follows.
The third chapter investigates how education increases earnings and the probability of being in the non-agricultural sector. As the education policy shift influences educational attainment in a discontinuous way, a regression discontinuity (RD) framework is adopted to identify the average returns to education and the effect of education on the sector of employment. It is important to emphasise that the RD technique constrains the effects of education on the two outcomes to be linear and to be applicable only to sub-populations. My results confirm significant effects of education on both earnings and the sectoral sorting process. In addition, there are heterogeneous effects of education by gender.
The fourth chapter is an extension of the previous chapter. I allow the returns to education to be heterogeneous across education levels and sectors of employment, while attempting to estimate the returns for the entire population. I use a control function (CF) approach and a double selection correction to estimate the sectoral earnings process, while jointly accounting for the choice of education and the selection into sectors and paid employment. I find that the returns to education are non-linear and higher in the non-agricultural sector especially for medium and highly educated workers. This suggests that human capital plays a crucial role in facilitating a structural transformation towards the non-agricultural sector.
In the final chapter, I study how the increased primary education completion rate affects earnings inequality. While there exists a burgeoning literature on the average returns to education, less attention has been devoted to estimating the effects of education on the distribution of earnings. I identify the effects of primary education completion on earnings at different points of the distribution, and thus earnings inequality, using a recently developed approach, called regression discontinuity distributional treatment effects. My results suggest that the increased primary education completion rate reduces earnings inequality as the returns to primary education are larger for the poor than the rich.

Keywords: inequality
human capital
Thailand
labour markets
structural transformation
Advisor: Teal, F
Bhattacharya, D
Synthesis and properties of giant porphyrin nanorings

Fully conjugated porphyrin nanorings combine an end-free π-system with well defined size and shape. They provide models for testing our understanding of light harvesting in natural photosynthetic systems, and may lead to the creation of new functional materials. This thesis describes the template-directed synthesis of novel 10, 16, 18, 20, 24, 30, 40 and 50-porphyrin nanorings using small templates, as well as the investigation of their structure, electronic properties and supramolecular chemistry in solution and on surfaces. This work illustrates the scope of Vernier templating as a tool for the synthesis of monodisperse molecules of unprecedented sizes.
Chapter 1 introduces key properties of porphyrins and π-conjugated linear and cyclic porphyrin oligomers and describes the principle methods of preparing non-conjugated and conjugated cyclic polymers. It also covers recent advances in the synthesis of fully-conjugated porphyrin nanorings, in particular Vernier templating.
Chapter 2 discusses the formation of higher order porphyrin nanorings (18- and 24-porphyrin nanorings) in the classical synthesis of 6-porphyrin nanoring and the Vernier-templated synthesis of 12-porphyrin nanoring.
Chapter 3 describes the Vernier-templated synthesis of 24-porphyrin nanoring and its characterization.
Chapter 4 shows that the flexibility of 24-porphyrin nanoring can be locked by the formation of a “sandwich” complex in the presence of a bidentate ligand or by solvent-induced formation of aggregates.
Chapter 5 demonstrates the use of templates to control the cyclooligomerization of linear porphyrin oligomers. Vernier-templated synthetic routes to 10-, 30- and 40-porphyrin nanorings are investigated.
Chapter 6 reports the electronic properties of porphyrin nanorings as probed by electrochemistry (for 6 porphyrin nanoring) or fluorescence anisotropy measurements (for 24 porphyrin nanoring). Crystal structures of 6 and 12 porphyrin nanoring template complexes are presented.
Chapter 7 contains experimental procedures and characterization data of known and novel compounds synthesized in the course of this thesis.

Keywords: porphyrin chemistry
cyclic polymers
supramolecular chemistry
Advisor: Anderson, H
Development of an aerosol-CVD technique for the production of CNTs with integrated online control

This dissertation summarises the study of different aspects of the aerosol-assisted chemical vapour deposition (AACVD) technique for the production of multi-wall carbon nanotubes (MWCNTs). Upscaling the synthesis while retaining the quality of MWCNTs has been a prime objective throughout the work. A key aspect of this work was the study of different growth parameters and their influence on the homogeneity of the products across the reactor. The effect of the precursor composition on the yield and quality of MWCNTs were also investigated. It was shown that the synthesis rate can be significantly (60 – 80 %) increased by tuning the composition of the precursor. Moreover, by optimising the synthesis recipe and using a larger reactor, the synthesis rate and efficiency of the precursor were increased fivefold (up to 14 g/hr) and twice (up to 88 %) respectively. Large area (up to 90 cm2), mm-thick carpets of MWCNTs which were both free-standing and on substrate were produced. The carpets could withstand normal handlings without tearing apart, making them suitable for macroscopic characterisations and applications. By in-situ qualitative and quantitative gas analysis of the atmosphere of the reactor, the thermocatalytic cracking behaviour of 25 precursors was investigated and a mechanism for successive formation of different hydrocarbon fragments inside the reactor was proposed. A number of dedicated gas analysis methods and apparatuses such as a probe for zone-by-zone gas analysis of reactor and a heated chamber for preparation of standard gas analysis samples were developed to explore some of the least investigated aspects of the thermocatalytic cracking of precursors. Mapping the reactor revealed that some single-wall and double-wall carbon nanotubes (SWCNTs and DWCNTs) were also produced near the exhaust of the reactor. The SWCNTs were partly covered by fullerene-like species and resembled different forms of carbon nanobuds. In addition, the effect of the electron beam on the interaction of the SWCNTs and the fullerene-like species was studied in situ using high-resolution transmission electron microscopy (HRTEM).

Keywords: chemical vapour deposition
carbon nanotubes
aerosol-assisted chemical vapour deposition
carbon nanomaterials
Advisor: Grobert, N
The string axiverse and cosmology

This thesis studies the cosmology of ultra-light scalar fields with masses in the range 10−33 eV ≲ m ≲ 10−18 eV and their effects on cosmology. The existence of such fields is motivated by the theoretical framework of the "String Axiverse". All types of string theory contain multiple axion fields associated with antisymmetric tensor fields compactified on closed cycles in the compact space. Since the masses of these fields scale exponentially with the volume of the cycle, it is possible for them to be naturally light. We study the effects of these fields as a component of the dark matter and show analytically and numerically that they cause a suppression of structure formation on cosmological scales set by the inverse mass. We show that it will be possible with future galaxy redshift and weak lensing surveys to detect an ultra- light field comprising of order a percent of the total dark matter. If such a field is allowed to couple to the geometry that provided its mass via a phenomenological scalar potential for the axion and modulus, then the expansion of the universe can be altered significantly. In particular, we find that it is possible to have multiple epochs of accelerated expansion over a large region of parameter space, and to have a flat universe with a big crunch in the distant future. Finally, we address the issue of isocurvature perturbations in axion cosmologies, and demonstrate that in the ultra-light case the power spectrum is effected. This may have implications for the conclusions made about fine tuning in the axiverse in relation to a potential detection of tensor modes in the CMB that are different to the case of a standard axion.

Keywords: physics
astrophysics
cosmology
string theory
Advisor: Ferreira, PG
March-Russell, J
Aerodynamic and mechanical performance of a high-pressure turbine stage in a transient wind tunnel

Unsteady three-dimensional flow phenomena have major effects on the aerodynamic performance of, and heat transfer to, gas-turbine blading. Investigation of the mechanisms associated with these phenomena requires an experimental facility that is capable of simulating a gas turbine, but at lower levels of temperature and pressure to allow conventional measurement techniques. This thesis reports on the design, development and commissioning of a new experimental facility that models these unsteady three-dimensional flow phenomena. The new facility, which consists of a 62%-size, high-pressure gas-turbine stage mounted in a transient wind tunnel, simulates the turbine design point of a full-stage turbine. The thesis describes the aerodynamic and mechanical design of the new facility, a rigorous stress analysis of the facility’s rotating system and the three-stage commissioning of the facility. The thesis concludes with an assessment of the turbine stage performance.

Keywords: aerodynamics
turbomachinery
transient wind tunnel
mechanical performance of a high pressure turbine stage
Advisor: Schultz, D
Ainsworth, R
Roman diet and nutrition in the Vesuvian region:  a study of the bioarchaeological remains from the Cardo V sewer at Herculaneum

The Roman town of Herculaneum, due to its burial by the eruption of Vesuvius in AD79, provides the rare opportunity to study the diet of middle and lower class Romans living in an urban context in mid-1st century AD Italy. Knowledge concerning Roman diet, prior to the growth of bioarchaeology in the 1960s and 1970s, was derived from the ancient texts and focused primarily on the elite diet. The diets of the poorer classes have often been considered monotonous and unhealthy and consequently, malnutrition is believed to have been widespread in urban centres. Collaboration between the numerous sub-disciplines of bioarchaeology, including archaeobotany and zooarchaeology, has begun to take place amongst scholars working on the Vesuvian sites and diet is currently being studied using a more holistic approach. The ancient sources act as a secondary resource and it is now the physical food remains that play a crucial role in examining Roman diet and associated topics such as trade, health and nutrition.
This thesis investigated the bioarchaeological remains from the Cardo V sewer that ran beneath the shop/apartment complex of Insula Orientalis II in Herculaneum. It is the first large scale study to combine both new and existing bioarchaeological material from Herculaneum in an effort to provide the site with its own bioarchaeological data set, particularly with regards to food and diet. In total, 220L of soil was examined for carbonized and mineralized seeds, seashells, eggshells and fish bones. 194 taxa were identified, included including 94 botanical, 45 fish, 53 shellfish and two bird taxa. 114 of the 194 taxa can be considered edible foodstuffs. The statements of the ancient authors concerning dietary diversity have been examined in light of these findings and found to be comparable. The material displayed little taphonomic bias when compared to Pompeian bioarchaeological assemblages. The excellent preservation of the material, combined with data from modern food sciences, has allowed for much needed interpretation to take place in the areas of health and nutrition. The variety of cereals, fruits and seafood indicate close connections with the nearby land and sea and consequently, the economic implications of such extensive resource exploitation have been considered. A nutritional analysis of the finds have shown that diets were nutrient dense and healthy, enabling the people of Herculaneum to achieve modern day stature as well as survive and recover from illness. Thus it can no longer be assumed that those of moderate means ate an unhealthy and monotonous diet, that malnutrition was widespread in urban centres, and finally, that descriptions of foodstuffs in the ancient sources apply only to the wealthy.

Keywords: Herculaneum
Archaeology
food
Pompeii
Italy
nutrition
diet
Roman
archaeobotany
fish
Advisor: Robinson, M
Dangerous Politics

The thesis constitutes a detailed historical reconstruction of the creation, contestation and subsequent amendment of the Imprisonment for Public Protection sentence, the principal ‘dangerous offender’ measure of the Criminal Justice Act 2003. Underpinned by an interpretive political analysis of penal politics, the thesis draws on a detailed analysis of relevant documents and 53 interviews with national level, policy-oriented actors. The thesis explores how actors’ conceptions of ‘risk’ and ‘the public’ interwove with the political beliefs and political traditions relied upon by the relevant actors. It is argued that while there was general recognition of a ‘real problem’ existing in relation to dangerous offenders, the central actors in the creation of the IPP sentence crucially lacked a detailed understanding of the state of the art of risk assessment and management (Kemshall, 2003) and failed to appreciate the systemic risks posed by the IPP sentence. The creation of the IPP sentence, as with its subsequent amendment, is argued to highlight the extreme vulnerability felt by many government actors. The efforts of interest groups and other pressure participants to have their concerns addressed regarding the systemic and human damage subsequently caused by the under-resourcing of the IPP sentence is explored, and the challenge of stridently arguing for substantial change while maintaining ‘insider’ status is discussed. As regards senior courts’ efforts to rein in the IPP sentence, it is argued that the increasingly conservative nature of the judgments demonstrate that the judiciary are not immune from the creep of a ‘precautionary logic’ into British penal politics. Regarding the amendment of the IPP sentence, the Ministry of Justice’s navigation between the twin dangers of a systemic crisis and a political crisis are explored. In conclusion, the IPP story is argued to demonstrate a troubling ‘thoughtlessness’ by many of the key policymakers, revealing what is termed the ‘banality of punitiveness.’ The potential for a reliance on political beliefs and traditions to slip into this thoughtless state, and possible ways of ensuring that such policy issues are engaged with in a more inclusive and expansive manner, are discussed.

Keywords: risk
New Labour
penal policy
dangerousness
British politics
judiciary
pressure groups
criminal justice
Advisor: Loader, I
"Not to offer himself again and again": an exegetical and theological study of repetition in the letter to the Hebrews

Repetition has received a bad press in certain streams of theological tradition; this reception has in part been caused by, and has in turn affected, readings of the Letter to the Hebrews, which speaks about repetition in ways unique in the New Testament. The present study addresses the insufficient critical attention paid to repetition in Hebrews, challenging the assumption that it functions uniformly and negatively throughout the letter, and exploring the variety of ways in which Hebrews presents repetition. The plurality of prophetic speech displays God’s manifold kindness in the old covenant; such speech is not opposed to but is fulfilled in Christ’s coming, and its ongoing repetition in the new covenant through citation and exposition serves to promote and explicate that event. Repeated mutual encouragement is essential to persevering in the Christian life and avoiding apostasy. And the regular entry of the Levitical priests into the outer sanctuary of the tabernacle in Heb 9.6 foreshadows the continual access to God achieved through Christ. Where repetition has a negative or contrastive role in the author’s argumentation, it does not cause inefficacy but rather indicates a weakness whose source is elsewhere – and which, moreover, is revealed fully only in the light of the Christ event. The uniqueness of Christ and of his death construed as a sacrifice, developed from concepts of singularity in Day of Atonement and early Christian crucifixion traditions, forms a unifying strand in the letter’s Christology. Rather than functioning in simple opposition to repetition, this singularity corresponds to continuity and eternity, and is developed at times in contrast to, and at times in correspondence with, repetition. The study thus offers a reappraisal of repetition in Hebrews, laying the foundations for renewed appreciation of the importance of repetition for theological discourse and religious life.

Keywords: Second Temple Judaism
New Testament
repentance
repetition
epistle to the Hebrews
cult
baptism
sacrifice
early Christianity
Advisor: Bockmuehl, M
Characterisation and targeting of stem cells in myelodysplastic syndromes

Understanding which cells within a cancer are responsible for its initiation and propagation is vital if we are to achieve cure. If cancer stem cells are the only population able to sustain a tumour long term, designing therapeutic strategies to target this population will give medical science the best chance of long-term cure. Significant controversy remains over the existence of cancer stem cells, predominantly due to the lack of a sensitive human cancer stem cell assay. This thesis investigates whether two haematological malignancies, myelodysplastic syndromes (MDS) and chronic myelomonocytic leukaemia (CMML) can only be driven by rare and distinct cancer stem cells. We have demonstrated that low and intermediate-1 risk MDS is driven solely by the stem cell (Lin- CD34+ CD38- CD90+ CD45RA-) by developing a novel genetic approach, tracing all somatic mutations and karyotypic abnormalities back to this population.
Prior to this study, very little was known about the clonal architecture of CMML. By performing detailed phenotypic, functional, molecular and genetic analysis of patients with CMML, we were able to demonstrate that the most likely candidate driver cell in these patients was also the stem cell rather than any of the down-stream progenitors.
Currently, effective therapeutic strategies for MDS or CMML are very limited. Allogeneic stem cell transplantation is the only potential cure and not suitable for most patients. Cancer stem cells, including MDS stem cells are known to be highly quiescent and selectively resistant to therapy. Having demonstrated that both MDS and CMML were driven by stem cells, we developed a novel therapeutic targeting strategy. Using the thrombopoietin receptor agonist, Romiplostim, we were able to activate stem cells and enhance their subsequent sensitivity to chemotherapy dramatically. This approach may facilitate improved remission rates and prevent cancer stem cell driven relapse in many diseases.

Keywords: stem cells
myelodysplastic syndromes
Advisor: Jacobsen, S