VictorJuiz/thesis huggingface dataset:
Novel molecular markers for assessment of human embryo competence
Keywords: human embryology
genetics
proteomics

In vitro fertilization treatments are responsible for 1-5% births in industrialized countries. The safest way to generate a pregnancy is to transfer a single embryo to the mother, reducing the likelihood of multiple gestations. Hence, in order to maximize the chance of success, it is extremely important that the embryo prioritised for transfer is the most capable within the cohort of embryos generated by the patient. Along with cytogenetic components, it has been suggested that embryo protein expression patterns may correlate with its ability to implant. However, embryo proteomics strategies have not been easy to harness mainly due to the complexity of the media the embryos are cultured in, and the low concentration of the proteins that are secreted.
In this study, the use of the blastocentesis procedure, which allows the safe retrieval of embryo inner fluid (blastosol), was described. The use of the blasocoel fluid as a source of embryonic DNA for preimplantation genetic assessment was also investigated. From this highly purified embryonic sample, a comprehensive catalogue of proteins present in the human blastosol was generated using standard and custom- made mass spectrometry strategies. The embryonic origin of these proteins was validated by gene expression microarray and RNASeq analysis. These experiments also allowed the identification of differentially expressed genes in the first two cell lineages, the Inner Cell Mass and the Trophectoderm. Finally, a targeted proteomics strategy able to measure part of the previously described protein targets in single blastosol samples was employed. The correlation between the presence and abundance of proteins of interest in single blastosols and several biological characteristics of the embryo, including its chromosomal status, was assessed.
These data are of major interest for the understanding of human embryo development. The validated embryo-derived protein catalogue and blastocyst gene expression profiles generated in this study, provides access to a thorough document for consultation in human embryology proteomics-based experiment design, paving the way to next-generation proteomic-based embryo assessment.
Statistical and Computational Methodology for the Analysis of Forensic DNA Mixtures with Artefacts
Keywords: probabilistic expert system
DNA mixture analysis
probability propagation
forensic genetics
statistics
gamma distribution
Bayesian network

This thesis proposes and discusses a statistical model for interpreting forensic DNA mixtures. We develop methods for estimation of model parameters and assessing the uncertainty of the estimated quantities. Further, we discuss how to interpret the mixture in terms of predicting the set of contributors.
We emphasise the importance of challenging any interpretation of a particular mixture, and for this purpose we develop a set of diagnostic tools that can be used in assessing the adequacy of the model to the data at hand as well as in a systematic validation of the model on experimental data.
An important feature of this work is that all methodology is developed entirely within the framework of the adopted model, ensuring a transparent and consistent analysis.
To overcome the challenge that lies in handling the large state space for DNA profiles, we propose a representation of a genotype that exhibits a Markov structure. Further, we develop methods for efficient and exact computation in a Bayesian network. An implementation of the model and methodology is available through the R package DNAmixtures.
Rule and identity in a diverse Mediterranean society: aspects of the county of Tripoli during the twelfth century
Keywords: Latin East
Tripoli (Lebanon)
crusader states
Outremer
crusades
Syria
Occitania
Lebanon

The county of Tripoli (Lebanon) was one of four “crusader states” established in the Levant after the First Crusade (1095-99). Compared to the other states, the county of Tripoli has suffered from a disproportionate level of historiographical neglect. What has been produced has taken an institutional and Eurocentric approach to the subject and its sources. The present thesis jettisons this in favour of a post-institutional methodology, approaching the county from the perspectives of geography and demographics, which together ensure that it is treated within its proper Syro-Lebanese context. Chapter one looks at the role of local geography in shaping the political frontiers of the county of Tripoli and its neighbours, arguing that topography was more important than the agency of the European settlers. Chapter two continues to challenge traditional assumptions regarding European influence, arguing that the specifically southern French origins of many of the county’s settlers were of little significance. Chapter three analyses the use of Arabic by the Frankish government of the county, informed by an awareness of diglossia. It argues that the Franks were more likely to know spoken Arabic than written, but remained reliant upon local intermediaries when ruling over Arabophones. Chapter four looks at popular religion, arguing that the cross-fertilisation of religious beliefs and practices was widespread but poorly understood by the contemporary intelligentsia, upon whose sources historians rely. As a whole, the thesis argues that the county’s inhabitants lacked a distinctive culture, identity, religion or language. The sole justification for viewing the county as an integrated unit is geographical.
Editors, artists and the changing status of manga in Japanese society, 1986-1995
Keywords: Editors
Japan
Status
Manga
Artists
Magazines
Japanese

The contemporary Japanese manga industry began in 1959 when the first weekly manga magazines were published. Throughout the 1960s publishing companies attracted a large adult readership by incorporating radical political themes and realistic drawing styles in manga magazines. The readership continued to expand throughout the 1970s and 1980s and manga became a mass medium on a similar scale to television or pop-music.
This thesis identifies two distinct trends in the cultural status of manga which were developing from the mid-1980s onwards. On the one hand, what had previously been seen as 'commercial' manga became respected as an 'art' form and highbrow communication medium. On the other, manga was vilified as pornography and as the extreme expression of an increasingly fragmented society. In the former trend, prestigious corporations sponsored a new category of 'information' manga, whilst in the latter, 'girls' and 'otaku' manga genres were censured by a quasi-governmental censorship movement. The amateur manga subculture in particular became the focus of a 'moral panic' where those involved were characterised as isolated and socially dysfunctional.
This thesis, based on ten months' participant observation and intensive interviews in 'Morning' manga magazine editorial office in 1994, examines how this editorial was influenced by the changing status of manga in Japanese society in the formulation of its editorial policy and production methods. Editors felt that in the 1990s social changes presented the manga industry with serious production problems - in particular, a dearth of 'good' artists who could produce social themes, and a shrinking readership. Morning editorial attempted to overcome these problems by pioneering a new form of artistic, high-quality and respectable adult manga, aimed at older and more socially-elite readers. By creating a new proactive intellectual role for manga editors at the same time as sponsoring experimental graphic styles, Morning editorial produced a distinctive new form of conservative, state-supporting social and political adult manga.
The re-definition of specific genres of manga as 'art' by Japanese institutions was paralleled by changes in commercial manga production which privileged the social and intellectual interests of editors over those of readers and artists. This study concludes that editors have become increasingly impo7tant in manga production between 1986 and 1995, and that there is a tight interrelationship between commercial cultural production and broader cultural and social discourses generally.
The normative ethics of immigration detention in liberal states
Keywords: Asylum
Immigration detention
Liberalism
Practical ethics
State power
Immigration

This thesis explores the normative propriety of immigration detention in liberal states. In the first part of the thesis, I explore the development, current practice, and popular justifications for immigration detention in the United Kingdom. I argue that a crucial but unacknowledged role for immigration detention is to function as a political spectacle of the centralisation of power in liberal states. I find that the key motivation for detaining non-citizens is that they could abscond before their removals. I conclude that this basis for detention is normatively acceptable in only very limited cases and, even then, alternatives are often available and ethically preferable. Based on the fact that there is a normatively acceptable rationale, albeit circumscribed, for detention practices, I then propose a framework of minimum standards of treatment in detention that I advise all liberal states to follow.
After outlining my proposal, I turn in the second part of the thesis to an examination of the normative theories of immigration control and how they take account of detention. Normative theorists differ in how they balance their commitments to individual and state rights, yet I find the majority concedes the need for some degree of immigration admissions control. Such theories face a moral dilemma: there can be no immigration control without detention, and so detention becomes an implicit assumption for these normative theories to be coherent. A potential solution for combating the practical problems associated with the growing, worsening detention estates as well as the moral dilemma of incarcerating a non-citizen based on fear of absconding would be to open borders and eliminate immigration control. Given the reality of the sovereign right to control immigration, however, I argue that the more feasible normative answer is lobby liberal states to adopt my framework of minimum standards of treatment while simultaneously pressing for open borders as the long-term ethical goal.
Characterizing the spatial properties of high harmonic generation
Keywords: coherence
x-ray
metrology
ultrafast

This thesis is concerned with describing a novel technique for characterizing the (spectrally resolved) spatial properties of light. The new approach, known as Scanning Interference Method for Integrated Transverse Analysis of Radiation (SCIMITAR), is a specific implementation of a variable-separation two-pinhole interferometer. Evaluation of the series of interference patterns produced by a SCIMITAR measurement allows the transverse profiles of intensity and spatial phase to be retrieved, while at the same time characterizing the spatial coherence of light. Including a diffraction grating in the simple experimental arrangement permits the spectral dependence of the aforementioned quantities to be measured.
The SCIMITAR technique was demonstrated by characterizing the spatial properties of high harmonic generation (HHG). Excellent agreement with an alternate characterization technique known as SWORD was observed. The spectral dependence of the harmonic spatial properties was also investigated. Evidence suggesting absorption may play a role in shaping the harmonic intensity and spatial coherence was presented. Treating the harmonic radiation as either a fully coherent or partially coherent beam allowed the intensity width, spatial phase curvature and coherence width of the harmonic radiation source to be deduced.
Measurement of the fine variation of the harmonic complex coherence factor (CCF) with pinhole separation revealed distinctive modulations. The Van Cittert-Zernike theorem was modified by including a Gerchberg-Saxton inspired improvement, allowing data missing from the SCIMITAR measurement to be inferred. The harmonic equivalent incoherent source intensity profile was found to be asymmetric with low intensity features isolated away from the optical axis. Calculations of the diffraction pattern produced by illumination of a non-redundant array of pinholes showed that the modulated harmonic properties could adversely influence lensless imaging-type experiments.
Deterministic simulation of multi-beaded models of dilute polymer solutions
Keywords: high-dimensional PDE
numerical analysis
Fokker-Planck equations
spectral methods
polymer solutions
greedy algorithms
Mathematics Subject Classification (2000): 65N15,65D15,41A63,41A25
statistical mechanics
nonlinear spproximation

We study the convergence of a nonlinear approximation method introduced in the engineering literature for the numerical solution of a high-dimensional Fokker--Planck equation featuring in Navier--Stokes--Fokker--Planck systems that arise in kinetic models of dilute polymers. To do so, we build on the analysis carried out recently by Le~Bris, Leli\`evre and Maday (Const. Approx. 30: 621--651, 2009) in the case of Poisson's equation on a rectangular domain in R2
, subject to a homogeneous Dirichlet boundary condition, where they exploited the connection of the approximation method with the greedy algorithms from nonlinear approximation theory explored, for example, by DeVore and Temlyakov (Adv. Comput. Math. 5:173--187, 1996). We extend the convergence analysis of the pure greedy and orthogonal greedy algorithms considered by Le~Bris, Leli\`evre and Maday to the technically more complicated situation of the elliptic Fokker--Planck equation, where the role of the Laplace operator is played out by a high-dimensional Ornstein--Uhlenbeck operator with unbounded drift, of the kind that appears in Fokker--Planck equations that arise in bead-spring chain type kinetic polymer models with finitely extensible nonlinear elastic potentials, posed on a high-dimensional Cartesian product configuration space D=D1×⋯×DN
contained in RNd
, where each set Di
, i=1,…,N
, is a bounded open ball in Rd
, d=2,3
. We exploit detailed information on the spectral properties and elliptic regularity of the Ornstein--Uhlenbeck operator to give conditions on the true solution of the Fokker--Planck equation which guarantee certain rates of convergence of the greedy algorithms. We extend the analysis to discretized versions of the greedy algorithms.
Contract enforcement in post-Soviet Ukrainian business
Keywords: post-Soviet transition
dispute resolution
courts
Ukraine
contract enforcement
reputation

Using the findings of a five-year ethnographic study, this thesis examines the contractual relationships that prevail in low-technology moderately competitive industries characteristic of the contemporary Ukrainian economy. The research reports on how contracts are enforced and how the stability of business relationships is ensured in Ukraine.
The established view of many scholars that business efficiency is held back in most post-Soviet economies by frequent contractual violations and dysfunctional courts is not entirely supported by the research underpinning this thesis: in Ukraine, contract enforcement is generally effective enough to allow stability in day-to-day transactions, and the commercial courts do provide adequate backing.
Although the mechanisms used to enforce contracts in Ukraine are generally similar to those found in developed countries, there are distinctive features within the overall pattern. In particular, firms rely extensively on repeated interactions and self-enforcing devices while signing short-term formal contracts and avoiding interdependency between trading partners. They do not rely on their reputation or business association memberships and they make no use of private arbitration. Instead, a few legal institutions dating back to the Soviet period proved adaptable and viable in a market economy.
When transactions involve either state-owned companies or the exercise of administrative resources, contract enforcement becomes problematic. Illegal kickbacks from suppliers and the coercive use of state machinery come into play, and asking a court to enforce a contract is more costly and less effective than in other cases. However, the author shows that in the typical everyday transactions of Ukrainian private firms, the state and its administrative resources are involved in the minority of cases, and that they do not undermine the dominant pattern of orderly contractual dealings.
The thesis concludes that the contractual pattern prevalent in Ukraine effectively serves straightforward traditional buyer-seller transactions but it is ill-suited to meet the requirements of globalized trade, production diversification and technological progress. Adaptations of the existing system to meet these requirements are likely to depend upon changes in the wider business environment, namely upon institutions constraining the coercive power of the state.
Simulation studies of monodisperse self-assembly
Keywords: Self-assembly
monodisperse
virus
Monte Carlo
simulation

The processes by which anisotropic colloidal and nanoscale particles may come together to form ordered monodisperse structures are not well understood. The canonical example of such a system is provided by the assembly of virus capsids, in which tens to thousands of particles of one or a few types assemble efficiently into ordered, highly symmetrical shells. Other examples include a wide variety of protein oligomers, and there is interest in producing analogous systems of synthetic particles.
In this thesis I study the self-assembly of simple model particles, consisting of spheres decorated with attractive patches. I consider in detail the assembly of clusters of particles corresponding to the Platonic solids. For the majority of these structures assembly is found to be efficient over a wide range of parameter space. The optimal conditions represent a compromise between thermodynamic stability and kinetic accessibility.
We consider two versions of the model, with and without constraints on the torsion angle of bound particles. In both cases the structures with triangular faces are found to assemble most easily. In the absence of torsional constraints dodecahedra will not assemble under any set of parameters as a result of the preferential formation of disordered aggregates. With torsional constraints included all of the Platonic solids assemble successfully and the behaviour of the model is considerably changed. In particular disordered aggregates become far less favourable.
I explore possible methods of assembling larger structures, either via “hierarchical” assembly where small clusters are first assembled and then used as building blocks in another stage of assembly, or by a templating method in which an inner cluster acts as a template for a larger outer cluster. These approaches are studied using the “Virtual Move Monte Carlo” cluster move algorithm, the behaviour of which we examine in some detail.
Asymmetric synthesis of heterocycles via cation-directed cyclizations and rearrangements
Keywords: Asymmetric catalysis
phase-transfer catalysis
methodology

The aim of this project was to utilize chiral cation-directed catalysis in the asymmetric synthesis of novel hererocycles. This goal was initially realized by the synthesis of azaindolines in high yields and enantioselectivities (Chapter 2).
Extension of this methodology to substrates bearing two stereogenic centres was successful, although control over both diastereoselectivity and enantioselectivity in this process was modest.
Finally the synthesis of heterocycles utilizing cation-directed rearrangement processes was examined, with proof of concept obtained for a novel asymmetric cyclization to form xanthenes.
The role of two pore channels (TPCs) in pancreatic beta cell stimulus-secretion coupling
Keywords: Calcium Signalling
Stimulus-Secretion Coupling
NAADP
TPC
Pancreatic Beta Cells
Two Pore Channels

This thesis presents an investigation into the role of the recently identified two pore channels (TPCs) in beta-cell stimulus-secretion coupling. TPCs are the receptors for calcium mobilising messenger nicotinic acid adenine dinucleotide phosphate (NAADP) located in the membrane of acidic intracellular calcium stores. It is proposed that they are responsible for the ATP-sensitive potassium channel (KATP channel) independent pathway of stimulus-secretion coupling; and that this pathway is not subordinate to the KATP channel dependent pathway; but an alternative explanation of stimulus-secretion coupling in its own right.
The first section of this thesis presents a characterisation of sub-membrane calcium signals observed in primary mouse beta-cells in response to glucose and the membrane-permeable acetoxymethyl ester form of NAADP (NAADP-AM) using the non-ratiometric fluorescent calcium indicator fluo-4 and total internal reflection (TIRF) microscopy. These are compared to global cytosolic calcium changes observed with epifluorescence microscopy. Factors affecting the shape and time course of responses are investigated, and pharmacological tools used to provide evidence for the role of intracellular calcium release from acidic stores mediated by NAADP.
Having characterised the calcium responses of beta-cells using TIRF; the second part of the thesis examines the effects of knocking out TPC2 (single KO), or both TPC1 and TPC2 (DKO) on these responses; after an initial assessment of pancreatic islet and beta-cell morphology using electron microscopy. Gender differences in beta-cell responses to glucose and NAADP are assessed in both wild type and knockout animals.
Finally, the third section presents the discovery of elementary calcium release events in pancreatic beta-cells. The current project visualises what are likely the triggering events for the global calcium signals examined in sections one and two. They take the form of localised calcium release in response to NAADP-AM and glucose; akin to sparks and puffs observed by stimulation with cADPR and IP3. Optical quantal analysis demonstrates the quantal nature of the events and estimates the size of the unitary calcium release unit (CRU) for NAADP.