VictorJuiz/thesis huggingface dataset:
Exploiting stable isotope imaging with high resolution secondary ion mass spectrometry for applications in biology
Keywords: stable isotope
correlative analysis
antimicrobial peptide
NanoSIMS
lipid imaging
glutamine metabolism

This thesis presents applications of high resolution secondary ion mass spectrometry (NanoSIMS) analysis for stable isotope imaging in biological samples. These projects were designed to explore the potential applications of NanoSIMS analysis, and to develop protocols and novel methodologies to visualize and quantify biological processes. Working with collaborators in the UK and USA, I have applied NanoSIMS analysis to study 3 research areas, including molecule interactions, single cell metabolisms and lipid imaging in tissues. Antimicrobial peptides (AMPs) play important role in the immune system, and understanding how AMPs interact with cell membranes can provide useful information to design new therapies to control infection. The pore structures and dynamics of the interaction of AMPs with membranes has been visualized for the first time and confirmed with combined AFM and NanoSIMS analysis. A correlative backscattered electron (BSE) imaging and NanoSIMS analysis methodology has been developed to study glutamine metabolism in single cancer cells. This method enables us to measure the chemical information in specific organelles in these cells and can be widely applied to study metabolisms and to trace the uptake of labelled molecules in biological matrices. Quantitative analysis on the effects of hypoxic conditions and the PYGL gene were studied. Applying correlative BSE and NanoSIMS analysis, I also studied lipid uptake mechanisms in various mouse tissues, including brown adipose tissue, heart, intestines, liver and skeletal muscle, mainly focused on a recently discovered protein, GPIHBP1, and its function in the lipid uptake process. TRL margination was proved to depend on the GPIBP1-LPL complex, and 3 stages of lipid transport from capillary lumen to lipid droplets was also visualized by combined BSE and NanoSIMS analysis.
Kinks in a model for two-phase lipid bilayer membranes
Keywords: 49Q10
82B26
92C10
49J45

In the spontaneous curvature model for two-phase lipid bilayer membranes the shape of vesicles is governed by a combination of an elastic bending energy and an interface energy that penalises the size of phase boundaries. Each lipid phase induces a preferred curvature to the membrane surface, and these curvatures as well as phase boundaries may lead to the development of kinks.
In a rotationally symmetric setting we introduce a family of energies for smooth surfaces and phase fields for the lipid components and study convergence to a sharp-interface limit, which depends on the choice of the bending parameters of the phase field model. We prove that, if kinks are excluded, our energies Gamma
-converge to the commonly used sharp-interface spontaneous curvature energy with the additional assumption of C1
-regularity across interfaces. For a choice of parameters such that kinks may appear, we obtain a limit that coincides with the Gamma
-limit on all reasonable membranes and extends the classical model by assigning a bending energy also to kinks.
We illustrate the theoretical result by some numerical examples.
Measurements of the Higgs Boson in the H - τ τ decay channel
Keywords: vector boson
computing
tau
associated production
higgs boson
GPU

The generation of vector boson mass via the Higgs mechanism in the Standard Model has been confirmed by the 2012 discovery of a candidate Higgs boson in the H→WW, H→ZZ, and H→γγ decay channels. In contrast, the Yukawa couplings hypothesized to provide the mass of fermions in the Standard Model have yet to be observed. The H→ττ decay channel currently provides the best opportunity for observing these couplings.
This thesis describes two separate but related searches for Higgs boson decays in the H→ττ decay channel using proton-proton collisions recorded by the ATLAS detector. The first analysis is a general search for all Higgs boson production mechanisms leading to a H→ττ decay using 4.5 fb−1 of 7 TeV and 20.3 fb−1 of 8 TeV proton-proton collision data. A deviation from the background-only hypothesis is observed with a significance of 4.5σ for a hypothetical Higgs boson mass of mH = 125 GeV — a strong indication of a H→ττ signal. For the same mass point, the best fit value for the signal strength is found to be 1.43 &plus;0.43−0.37 × the Standard Model expectation. The second analysis is a search for Higgs boson production in association with a vector boson using 20.3 fb−1 of 8 TeV proton-proton collision data. Results in the ZllH→τlτh channel indicate limits of 9.14 × the Standard Model expectation for VH signal production at mH = 125 GeV. In addition, two studies on enhancement of computing performance in the ATLAS trigger and data analysis pipeline are presented.
Was Byzantine Egypt a legal anomaly? Looking at testamentary documents for evidence using modern tools
Keywords: Egypt
Late Antiquity
Testamentary Documents
Byzantine

Modern scholars are deeply divided over whether Byzantine Egypt (350 to 650 CE) followed Roman law, with some saying that the effect of Roman law on Egypt was significant and others saying that it was superficial at best. There are a number of reasons for this schism, including the very general references to law in the surviving documents and the differences between Egyptian legal practice and some fundamental elements of Roman legal practice. This thesis seeks to provide additional evidence about the Egyptian adoption of Roman law by using a more systematic approach that looks at testamentary documents and donations mortis causa over a period of time, focusing on whether changes in the law are reflected in changes in the documents. It also uses the newly available word search capability of the papyri databases to look at when Roman legal terms are introduced into Egypt and how they are used.
The conclusion of this thesis is that lawyers and notaries in Byzantine Egypt understood and used elements of Roman law in their testamentary practices that were useful in accomplishing the goals of their clients. They were generally very careful to ensure compliance with procedural requirements. They regularly used concepts such as waivers of the requirement for guardians for women based on 'the right of children,' the confirmation of codicils, and et cetera disinheritance clauses. They did use stipulation clauses in ways that Roman legal practitioners would not, and donations mortis causa developed into a simpler alternative to a will. Cultural practices, such as the inclination to leave property to a surviving spouse with inheritance by the children after the death of the surviving spouse, remained. The impact of Roman law on Egyptian legal practice appears to have accelerated in the sixth and seventh centuries. This information is important to historians because of the light it sheds on the success of the early Byzantine emperors to create one Roman world with shared values and norms.
Endothelial activation in experimental metastasis models
Keywords: pulmonary metastasis
endothelial activation
coagulation
metastasis
VAP-1
VCAM-1

The majority of cancer related deaths occur due to the invasive growth of metastatic lesions. In the early stages of metastasis, circulating cell interact with the endothelial cells to establish at a distant site. In inflammation endothelial activation results in induction of adhesion molecules on the endothelium that participate in the homing of leukocytes. Because of the interactions of metastatic cells with the endothelium, the question was whether some of the characteristic molecules of endothelial activation were induced during metastasis.
In vivo pulmonary metastatic models were used to characterize the expression profile of endothelial activation. Immunohistochemistry identified VCAM-1 to be induced on the pulmonary endothelium following tumour cell arrest. VCAM-1 upregulation was not observed prior to tumour cells arrest or within the first hours. In contrast, tumour cell arrest appeared to be required for endothelial activation, arguing against a mechanism analogous to leukocyte homing. The upregulation of VCAM-1 upon tumour cell arrest corresponded with the initiation of platelet clot formation around the tumour cell and recruitment of leukocytes to the site, both previously shown to be essential for metastasis. Disruption of both phenomena, either through genetic or pharmacological manipulation, demonstrated that in contrast to the recruited leukocytes, platelets were involved in inducing endothelial activation.
Another protein investigated was VAP-1. In contrast to VCAM-1, central to VAP-1 adhesive function is its enzymatic activity. Blocking the functions of either molecule highlighted their role in facilitating the recruitment of the leukocyte population to the tumour cell. Disruption of which led to a significant attenuation of metastasis. While VCAM-1 and VAP-1 function appears critical in the early steps of metastasis, their inhibition had no effect at later stages of pulmonary colonization.
Frustrated magnetism in the extended kagome lattice
Keywords: frustrated magnetism
condensed matter physics
frustration

The extended kagome lattice, composed of alternating kagome and triangular layers, provides a novel geometry for frustrated magnetism. In this thesis, we study the properties of Heisenberg spins with nearest-neighbour antiferromagnetic interactions on this lattice. In common with many other models of frustrated magnets, this system has highly degenerate classical ground states. It is set apart from other examples, however, by the strong interlayer correlations between triangular layer spins. We study the implications of such correlations in both the statics and dynamics.
We characterise classical ground states using a flux picture for a single layer of kagome spins, a theoretical description that sets geometrical bounds on correlations. We quantify the divergent but sub-extensive ground state degeneracy by a Maxwellian counting argument, and verify this calculation by analysing the energy eigenvalues of numerical ground states. We explore the ground state connectedness but do not reach firm conclusions on this issue. We use the self-consistent Gaussian approximation (SCGA) to calculate static spin correlations at finite temperature. The results of these calculations agree well with elastic neutron scattering experiments. We derive an expression for the effective interlayer interaction between kagome spins by integrating out the triangular lattice spins.
We use linear spinwave theory to compute the spin excitation spectrum numerically. This shows encouraging similarity with inelastic neutron scattering data on a single-crystal YBaCo4
O7
sample, for a wide range of wavevector and frequency. This agreement shows that our spin model is a reasonable description of the physics, and suggests that this numerical technique might be useful for other geometrically frustrated magnets.
We study the dynamics analytically using the stochastic SCGA recently developed for the pyrochlore lattice. For technical reasons, we apply this technique on a related model, the stacked kagome lattice, rather than on the extended kagome lattice itself. From this we find slow relaxation at low temperature, with a rate Γ ∼ T2 compared to the faster Γ ∼ T scaling for the pyrochlore. Strikingly, in simulations of the dynamics on the extended kagome lattice by numerical integration of the semiclassical equations of motion, we find two different relaxation rates. Kagome layer spins relax more quickly than the triangular layer spins, having Γ ∼ T.
Developing relations between heritage conservation and urban revitalization: lessons from China
Keywords: Heritage Conservation
World Heritage
The Grand Canal
Urban Development

The overall aim of this thesis is to further understanding of the developing relations between heritage conservation and urban revitalization, by following the on-going World Heritage List nomination process for the Grand Canal in China. A review of the history and current situation of heritage conservation and urban revitalization establishes several key gaps in knowledge, for example, the field of systematic heritage conservation is still left blank. Taking advantage of the opportunity to work with this on-going nomination, the project examines the nature and challenges of heritage conservation research and practice for a heritage property of large scale and complexity, in the form of four linked studies. A critique of the national level nomination process to date illustrates the complexity of the task, and concludes that systematic heritage conservation has not been established as a concentrated and nation-wide heritage conservation activity in China. Focusing on the municipal level nomination process to date through a case study of the city of Zhenjiang (and Yangzhou as a comparator) establishes key reasons why one city has been more successful than the other in its participation in the World Heritage List nomination. A second case study, of the Xi Jin Ferry area in Zhenjiang (Jiangsu Province), provides a fuller account of the ways in which heritage conservation can contribute to, and work with, urban revitalization. Drawing on the case of Xi Jin Ferry, a theoretically-informed, but practically-viable approach to linking heritage conservation and urban revitalization is developed which learns from the past and looks to the future. Building on the empirical research projects, a critique of existing approaches to heritage conservation of large, complex sites leads to a proposal for a 'Heritage System' framework which would facilitate future evaluations and improve the prospects for on-going management of the Grand Canal.
Transnationalism and the Ghanaian diaspora in the UK: regional inequalities and the developmental effects of remittances at the sub-national level
Keywords: remittances
diaspora
transnationalism
development
inequality
sub-national

This thesis presents a sub-national comparative analysis of the nexus between migration and development using the case of two disparate migrant communities (from the Upper East and Eastern regions of Ghana) in the UK.
The aim is to examine how inherent socio-economic inequalities prior to emigration impact on emigrants’ migration patterns, experiences, transnational activities and, ultimately, development outcomes at the micro and meso levels in the sending country. I argue, in this thesis, that the focus by development economists and most migration researchers on national-level macro analysis, as well as ‘location specific’ or single-site sub-national analysis, of the centrality of remittances to the enhancement of development at ‘home’ masks important nuances that are revealed by a comparative sub-national analysis.
This study uses a case study approach, whereby two migrant communities are investigated in detail within their pre-migration contexts. This allows for a deeper understanding of how transnational migration practices and/or processes are influenced by, and influence their context. It examines regional socio-economic inequalities and the interconnections between migration stage, spatial scales and local development.
This is achieved through a fifteen-month fieldwork using multiple research methods (key-informant interviews, in-depth structured and semi-structured interviews, surveys, participant observation and library research) in order to corroborate and triangulate findings from different sources. The thesis takes a spatiotemporal perspective in the migration-development nexus debate. Respondents for this research include economic migrants and refugees/forced migrants.
Among others, I conclude that globalisation and access to effective, yet relatively cheap, technological and communications facilities have bolstered individualistic migratory decision making thus reducing the centrality of the family or household as the unit of analysis in the causes and consequences of migration discourses.
Overall, the thesis aims to contribute a new, broader, and more inclusive perspective to migration research by arguing that migration-development phenomena are better appreciated through a comprehensive approach that encompasses migrants and sending communities and underlines the relationship between the two within a sub-national context.
Mechanisms of induction and modulation of the pro-inflammatory cytokine interleukin-1beta
Keywords: Influenza
iNKT cells
IL-1beta
Inflammasome
Serum Amyloid A

Interleukin (IL)-1beta is a powerful pro-inflammatory cytokine with important roles in directing both innate and adaptive immunity. As a result, its production is tightly controlled, with the synthesis of an inactive form (pro-IL-1beta) and the requirement of a second signal. This induces the formation of the inflammasome, a macromolecular complex which mediates the maturation of IL-1beta into the bioactive cytokine. Given its significance, it is important to identify mechanisms of IL-1beta induction and modulation.
Firstly, we describe serum amyloid A (SAA), an acute phase protein with immunomodulatory properties, as a novel inducer of IL-1beta. Using cells from genetically modified mice, the molecular mechanisms responsible were dissected, demonstrating the receptors TLR2 and NLRP3 as required for this effect. By instilling SAA into mice, we also show that SAA is able to induce IL-1beta production in vivo.
Invariant natural killer T (iNKT) cells have also been shown to be important modulators of immunity, mediating both pro- and anti-inflammatory responses. iNKT cells are non-conventional T lymphocytes which recognise glycolipid in the context of CD1d, with the ability to interact with immature antigen presenting cells in an autoreactive manner. We link the regulatory ability of iNKT cells with IL-1beta production, showing that a low activation signal leads to the induction of an IL-13-dominated cytokine profile, as well as weak engagement of the CD40-CD40L pathway. We show for the first time that through these mechanisms, iNKT cells are able to dampen the secretion of IL-1beta upon subsequent stimulation of dendritic cells.
We hypothesise that this effect of iNKT cells is important in controlling inflammatory responses in vivo, and demonstrate exacerbated IL-1beta production and inflammation during influenza virus infection of iNKT cell-deficient animals. This novel anti-inflammatory property of iNKT cells may be harnessed in the therapeutic intervention of inflammatory disorders.
Proteomics-aided search for extracellular matrix signatures of colorectal hepatic metastases ex vivo
Keywords: extracellular matrix
matrisome
cancer
proteomics

Hepatic metastases are one of the most dangerous consequences of colorectal cancer, and their occurrence often results in poor prognosis and death. There is a need to improve survival and quality of life for patients with colorectal liver metastases.
In this work, we utilised mass-spectrometry method to identify proteins characteristic of mouse colorectal liver metastasis matrisome and further confirmed the expression of some of them in liver metastasis by immunohistochemistry.
We showed ex vivo that S100-A11 and annexin A1 are significantly overexpressed in hepatic metastases according to two different mass-spectrometry approaches. Further, we demonstrated that both S100-A11 and annexin A1 are expressed by cancer cell lines MC38, Pan02, HCT116, HT29, and LoVo in culture. Also, using human xenografts in mice, we were able to identify the source of these proteins by mass-spectrometry. Obtained immunohistochemistry images suggest that S100-A11 and annexin A1 may for a complex within the tumour, which is in agreement with literature data. We next confirmed by immunohistochemistry that annexin A1 is markedly overexpressed in colorectal hepatic metastases, as well as in human liver metastases, as compared to adjacent healthy tissue. Finally, we found that CD45+ but not Ly6G+ or CD11b+ cells express annexin A1 in colorectal hepatic metastases.
Our findings indicate that S100-A11 and annexin A1 may play a role in colorectal liver metastases development. Further in-depth research is necessary to elucidate their impact on tumour biology.
A protocol-based study of L2 problem-solving processes in Korean university students'  L2 English writing
Keywords: L2 English writing
L2 problem-solving processes

Writing has increasingly been emphasised in EFL classrooms in recent years, and Korea is no exception to this trend. The literature indicates that L2 writers experience language problems and attempt to solve them while converting their thoughts into another language. At the moment when learners struggle with a linguistic feature, they become aware of their lack of linguistic knowledge, and try to resolve the problem either by employing their own previously acquired knowledge sources, or by trying to access external knowledge sources. This problem-solving process may occur repeatedly during the L2 writing process.
The aims of the current research are threefold: first, it investigates what Korean university learners of English notice while they are writing in L2; second, it attempts to examine what variables are related to and affect learners' noticing during the L2 problem-solving process and; third, the knowledge sources employed by learners when they face language problems are analysed. In order to achieve these aims, 108 English major students were recruited from three high ranked universities in Korea; think-aloud protocols and stimulated-recall interviews comprised the primary means of data collection. All participants were asked to do a writing task in L2 and to verbalise their thoughts while producing written text. Building on the data gathered from the writing task, stimulated recall interviews were carried out in order to identify the sources of knowledge employed to resolve language problems.
The results of quantitative data analysis showed that the 108 participants in this study noticed approximately five language problems while writing an L2 text for 20 minutes, and verbally expressed many more lexical episodes than grammatical episodes. Regarding the relations between learner-related variables and noticing during the L2 writing process, previous study abroad experience and L2 proficiency affected learners' noticing. It was also found that L2-based verbal working memory had an effect when learners notice language problems in L2 text production, while L1-based verbal working memory had no effect. Moreover, qualitative data analysis indicated that the participants employed various types of knowledge sources in order to solve lexical or grammatical problems. It was found that both explicit linguistic knowledge sources, such as previously acquired L1-L2 translation word pairs, aspects of word knowledge (i.e., form, meaning, or use), episodic memory or analogy, and implicit knowledge sources, such as intuition, were used during the L2 problem-solving process.
Based on these findings, possible implications for L2 writing teaching are discussed, stressing the importance of providing many writing opportunities for students, and suggestions for future research are presented.