VictorJuiz/thesis huggingface dataset:
Investigations into the regulation of sister chromatid cohesion
Keywords: sister chromatid cohesion
protein purification
cohesin
sororin
yeast

Cohesin, a ring-shaped complex composed of four subunits, is an essential player involved in timely and accurate segregation of genetic material at mitosis and meiosis. Cohesin performs a highly conserved role by topologically embracing sister chromatids until their concerted disjunction at anaphase, when the α-kleisin subunit of the ring is irreversibly cleaved by separase. A central part of the cohesin cycle is its cleavage-independent removal from chromatin through the action of the releasing complex.
In more complex eukaryotes, stabilisation of cohesin on DNA depends on the presence of sororin, a small functionally conserved protein whose association with cohesin is thought to counteract the releasing reaction. The first part of this thesis aimed to address the discrepancy of a sororin orthologue never having been identified in S. cerevisiae. This was undertaken using an imaging-based approach to screen a subset of the yeast genome for proteins with cohesin-like localisation. The screen was streamlined such that candidate genes had periodically cycling mRNA transcripts, similarly to cohesin subunits. No novel cohesin-associated proteins could be identified, although this could be in part due to technical limitations of the screen.
The precise molecular details of cohesin’s function and regulation remain poorly understood. A conclusive way to address many questions about cohesion as a whole would be to set up an in vitro assay capable of reconstructing cohesin loading, cohesion establishment, and the releasing reaction. The second part of this thesis aimed to establish a reliable purification protocol for the S. cerevisiae cohesin complex using a bacterial expression system for use in such biochemical assays. While purification of all components of the cohesin trimer (Smc1, Smc3, Scc1) was achieved successfully, the complex could not be confirmed to assemble functionally, as determined by chemical crosslinking of the Smc3/Scc1 interface.
Integrating and querying semantic annotations
Keywords: machine learning
information extraction

Semantic annotations are crucial components in turning unstructured text into more meaningful and machine-understandable information. The acquisition of the mass of semantically-enriched information would allow applications that consume the information to gain wide benefits.
At present there are a plethora of commercial and open-source services or tools for enriching documents with semantic annotations. Since there has been limited effort to compare such annotators, this study first surveys and compares them in multiple dimensions, including the techniques, the coverage and the quality of annotations.
The overlap and the diversity in capabilities of annotators motivate the need of semantic annotation integration: middleware that produces a unified annotation with improved quality on top of diverse semantic annotators. The integration of semantic annotations leads to new challenges, both compared to usual data integration scenarios and to standard aggregation of machine learning tools. A set of approaches to these challenges are proposed that perform ontology-aware aggregation, adapting Maximum Entropy Markov models to the setting of ontology-based annotations. These approaches are further compared with the existing ontology-unaware supervised approaches, ontology-aware unsupervised methods and individual annotators, demonstrating their effectiveness by an overall improvement in all the testing scenarios. A middleware system – ROSeAnn and its corresponding APIs have been developed.
In addition, this study also concerns the availability and usability of semantic-rich data. Thus the second focus of this thesis aims to allow users to query text annotated with different annotators by using both explicit and implicit knowledge. We describe our first step towards this, a query language and a prototype system – QUASAR that provides a uniform way to query multiple facets of annotated documents. We will show how integrating semantic annotations and utilizing external knowledge help in increasing the quality of query answers over annotated documents.
Ethical issues in the bioprediction of brain-based disorder
Keywords: Biomarkers
neuroscience
epilepsy
omics
ethics
psychosis
bioprediction
psychiatry
neuroethics
predictive biomarkers
DSM
distributive justice
MAOA
disorder
neurology
risk
applied philosophy
public health
alzheimers disease

The development of predictive biomarkers in neuroscience is increasingly enabling bioprediction of adverse behavioural events, from psychosis to impulsive violent reaction. Because many brain-based disorders can be thought of as end-states of a long development, bioprediction carries immense therapeutic potential.
In this thesis, I analyse issues raised by the development of bioprediction of brain-based disorder. I argue that ethical analysis of probabilities and risk information bioprediction provides is confounded by philosophical and social structures that have, until recently, functioned nominally well by assuming categorical (binary) concepts of disorder, especially regarding brain-disorder. Through an analysis of the philosophical concept of disorder, I argue that we can and ought to reorient disorder around probability of future harm and stratify disorder based on the magnitude of risk. Rejection of binary concepts in favour of this non-binary (probability-based) one enables synergy with bioprediction and circumnavigation of ethical concerns raised about proposed disorders of risk in psychiatry and neurology; I specifically consider psychosis and dementia risk.
I then show how probabilistic thinking enables consideration of the implications of bioprediction for two areas salient in mental health: moral responsibility and justice. Using the example of epilepsy and driving as a model of obligations to protect others against risk of harm, I discuss how the development of bioprediction is poised to enhance moral responsibility. I then engage with legal cases and science surrounding a predictive biomarker of impulsive violent reaction to propose that bioprediction can sometimes rightly diminish responsibility.
Finally, I show the relevance of bioprediction to theories of distributive justice that assign priority to the worse off. Because bioprediction enables the identification of those who are worse off in a way of which we have previously been ignorant, a commitment to assign priority to the worse off requires development of and equal access to biopredictive technologies.
Bank credit and legal status in Moroccan manufacturing
Keywords: Moroccan manufacturing
information asymmetry
company law
development economics

Moroccan manufacturing firms generally choose to incorporate under one of two legal forms: ‘Société Anonyme’ (SA) and ‘Société À Responsibilité Limitée’ (SARL). This thesis is about that choice and its consequence for firms’ access to bank overdraft facilities. In 2001, Morocco made a radical change to its company law regime: it replaced a company law dating from 19th-century France with modern standards of corporate governance and accountability. In Chapter One, I use the two-period FACS/ICA panel to analyse that reform and to evaluate its impact upon manufacturing firms’ access to bank credit. I find that the reform induced a substantial share of SA firms to switch to SARL, and that — relative to firms remaining in the SA status — this caused a significant and substantial withdrawal of bank overdraft facilities. In Chapter Two, I develop a theoretical model in which an agent signals its continuous type by using a variable that may take one of only two values (a ‘binary signal’); this is intended to represent a firm’s choice of legal status. I show that this binary signal provides only ‘coarse information’, and I consider the consequences of this coarseness; I solve for equilibrium conditions and I consider both the role of a principal’s risk aversion and the role of other observable agent characteristics (‘indices’). Chapter Three uses the results of Chapter Two to develop a new structural methodology for the separate identification of information and incentive effects. I apply the method to the data used in Chapter One, on the subset of firms having an overdraft facility in both survey periods (approximately two-thirds of the total sample). I find that, among that limited sample, there is no relevant information asymmetry. I estimate the potential welfare loss and conclude that, in the 95% confidence region of potential information effects and incentive effects, the maximum median welfare loss from information asymmetry is equivalent to approximately only 3% of the median bank overdraft limit. For the sample of firms having an overdraft facility in both survey periods, this challenges the common narrative that information asymmetry is an important reason for bank credit market failure.
Mechanistic studies on 2-oxoglutarate dependent oxygenases
Keywords: DAOCS
NMR
uncoupled turnover
enzyme mechanism
2OG oxygenases
mass spectrometry

The first identfied 2-oxoglutarate (2OG) dependent oxygenase was a collagen modifying enzyme in the work by Hutton et al. in 1967. Subsequent work has revealed that 2OG dependent oxygenases are a large family with diverse biological roles. With small molecule substrates, these enzymes catalyse a wide range of oxidative reactions, including those that form part of antibiotic biosynthetic pathways. The currently accepted consensus mechanism for catalysis by 2OG-dependent oxygenases is based on crystallographic data, kinetics and on quantum chemical calculations. The consensus mechanism involves oxidative decarboxylation of 2OG by reaction with an oxygen molecule producing CO2, succinate and a reactive oxidising species that reacts with the `prime' substrate.
Deacetoxycephalosporin C synthase (DAOCS) is a 2OG-dependent oxygenase involved in cephalosporin biosynthesis. The mechanism of DAOCS is of particular interest because it has recently been proposed to be different from the consensus mechanism. The new mechanism proposal from Valeg ard et al. is primarily based on high-resolution crystallographic data with support from steady-state kinetic experiments and quantum-chemical calculations.
The work in discussed in this thesis aimed to test the proposal of Valegård et al. by using a combination of spectroscopic and spectrometric methods analysing enzyme-substrate interactions. Substrate binding was investigated using both protein-observe (Chapter 3) and ligand-observe (Chapter 4.1 and 4.2) methods. Preliminary UV-visible data on enzyme-substrates complex formation was also obtained. The strength of substrate and cosubstrate binding was characterised through dissociation constant measurement. An activity assay (Chapter 2) that allows for direct and simultaneous monitoring of 2OG decarboxylation and penicillin ring expansion was optimised.
Both the ligand-observe and protein-observe binding experiments as well as the preliminary UV-visible data indicate that the formation of a ternary complex between DAOCS, 2OG and the penicillin substrate is viable. The activity assay conclusively showed that in the presence of unnatural substrates, such as penicillin G, 2OG oxidation is significantly uncoupled from penicillin oxidation. Uncoupled turnover does not occur in the presence of the natural substrate, penicillin N, which is an aspect that should be considered in the analysis of the steady-state kinetic data.
Overall, the results provide evidence that, the consensus mechanism for 2OG-dependent oxygenases is viable for DAOCS, at least in the presence of the natural substrate, penicillin N. It is possible that in the presence of an unnatural substrate, the catalytic process undergoes a more complex mechanism, possibly with the direct involvement of reducing agents in the system.
From Jew to Gentile: Jewish converts and conversion to Christianity in medieval England, 1066-1290
Keywords: Great Britain -- Church history -- 1066-1485
conversion
Christianity and other religions
Church history -- Middle Ages
Christianity
Christian converts from Judaism -- England -- History
Judaism -- History
Judaism -- Relations -- Christianity -- History
600-1500

The subject of this thesis is Jewish conversion to Christianity in medieval England. The majority of the material covered dates between 1066 and c.1290. The overall argument of the thesis contends that converts to Christianity in England remained essentially Jews. Following a discussion of the relevant secondary literature, which examines the existing discussion of converts and conversion, the principal arguments contained in the chapters of the thesis include the assertion that the increasing restrictiveness of the laws and rules regulating the Jewish community in England created a push factor towards conversion, and that converts to Christianity inhabited a legal grey area, neither under the jurisdiction of the Exchequer of the Jews, nor completely outside of it. Numerous questions are asked (and answered) about the variety of convert experience, in order to argue that there was a distinction between leaving Judaism and joining Christianity. Two convert biographies are presented. The first shows how the liminality that was a part of the conversion process affected the post-conversion life of a convert, and the second shows how a convert might successfully integrate into Christian society.
The analysis of converts and conversion focusses on answering a number of questions. These relate to, among other things, pre-conversion relationships with royal family members, the reaction to corrody requests for converts, motives for conversion, forced or coerced conversions, the idea that a convert could be neither Christian nor Jew, converts re-joining Judaism, converts who carried the names of royal functionaries, the domus conversorum, convert instruction, and converting minors. The appendix to the thesis contains a complete catalogue of Jewish converts in medieval England. Among other things noted therein are inter-convert relationships, and extant source material. Each convert also has a biography.
Completely iterative monads in semantics of coinductive programs
Keywords: coinduction
coalgebra
monad
semantics

Some programs are not merely sets of batch instructions performed in isolation. They interact, either directly with the user, or with other threads and resources. This dissertation tackles the problem of mathematical description (denotational semantics) of the observable behaviour of such programs.
In the tradition of denotational semantics and functional programming, one can distinguish between pure computations, which are regarded as mathematical functions, and effectful ones, like those generating behaviour. Both effects in general and behaviour of interactive systems have been thoroughly studied, and they both have elegant category-theoretic explanations: the frameworks of, respectively, monads and coalgebra. The point of this dissertation is to explore the area where the two meet.
The thesis of this dissertation is that the right kind of monads to describe the observable behaviour of programs are completely iterative monads (cims), introduced by Elgot and more recently studied by Adamek and others. They are monads equipped with a certain corecursion scheme that allows us to describe the computation in a coinductive, step-wise manner.
To support this, we introduce a formal coinductive semantics parametrised with a cim. We study its properties and show that it instantiates to a number of known approaches, based on metric spaces and final coalgebras.
Then, we focus on studying properties of cims, especially those important in semantics and programming, like composability. We show that a number of constructions used in denotational semantics to model different aspects of behaviour are instances of the constructions that we introduce. The most important structure that we study are coinductive resumptions, generalising previous results by Moggi or Hyland, Plotkin, and Power.
The language of our development is category-theoretic, and so are the properties that we investigate. We are interested in universal properties, distributive laws, algebras, and monadicity. Thus, the results apply not only to semantics and programming, but can be construed as a general investigation of algebraic structures with iteration.
Craftsmanship, teleology, and politics in Plato's 'Statesman'
Keywords: Plato
'Statesman' (dialogue)
Ancient philosophy

In this thesis I attempt to bring out some interesting implications of Plato’s political thought as it is presented in the Politicus. In particular, I will show how this dialogue provides a new picture of the relation between ruler and ruled; a picture that stresses the importance and responsibility of every citizen, not just of the statesman himself. This is achieved by an analysis of the notion of political craftsmanship envisaged by the main speaker of the dialogue, the Eleatic Stranger. However, before I turn to consider the Politicus itself, I provide a brief presentation of another Platonic craftsman, the demiurge of the Timaeus. As will be clear, the teleological structure, and the accompanying terminology, of his craftsmanship will mirror that of the true statesman and thus help us understand the latter’s political rule. My choice to focus on this aspect of the Politicus is motivated by the text itself. For the question of the kind of craftsmanship involved in political rule is picturesquely, yet effectively, brought to the fore by the myth in the early parts of the dialogue, which distinguishes between two rival conceptions and associates the statesman with one of them.
I conclude by reflecting on the significance of my findings for Plato’s political thought as a whole.
Measuring treatment effects in poverty alleviation programs: three essays using data from Turkish household surveys 
Keywords: Turkey
health insurance for the poor
poverty
crisis
rural development
health policy
impact evaluation
social networks
social protection

The dissertation is a compilation of three essays on Turkey's poverty alleviation programs. The first paper focuses on the welfare impact of the global financial Crisis on Turkish households. The second paper considers the protective impact of the Green Card non-contributory health insurance program in Turkey during the Crisis in 2008-2009. The third paper uses experimental data from the field in eastern Turkey, to look at patterns of agricultural technology diffusion in a rural development program implemented in a post-conflict setting.
Inclusion and exclusion: NGOs and politics in Zimbabwe
Keywords: NGOs
elections
Zimbabwe
constitution
churches

The thesis explores the changing relations between the Zimbabwean state and local nongovernmental organizations (NGOs) after independence. It focuses on debates over the role of NGOs in democratization in developing countries, using Zimbabwe as an example. The thesis argues that the study of democratization is best accomplished through detailed empirical case studies, relying on historical narratives and participant-observation research. Such research reinforces our understanding of democratization as a complex and dynamic process.
The thesis proposes a framework for understanding state and society relations in Zimbabwe, emphasizing the ruling party’s use of coercive and consent-generating mechanisms to establish hegemony over the new nation. It examines the changing relationship between NGOs and the state after independence, when the ruling party’s efforts to include most groups within its nationalist coalition extend to NGOs. Case studies of NGO coalitions show how activist NGOs fail to mobilize others owing to the unwillingness of many NGOs to challenge the ruling party’s control over policy-making.
The establishment of the National Constitutional Assembly by some NGOs, churches and trade unionists set the stage for an increasingly tense engagement between NGOs and the state after 1997. The constitutional debate opened up the public sphere in new ways. As the ruling party attempted to retain control over the political sphere and the constitutional debate, NGO politics became increasingly polarized. The emergence of the opposition Movement for Democratic Change, and the prominence of NGO activists within its leadership, led to further conflict. After losing the February 2000 constitutional referendum, the regime sanctioned violent attacks on white farmers, businesspeople, and NGOs. While the ruling party attempted to shore up its support through nationalist rhetoric and financial incentives, groups perceived to oppose the state were excluded and vilified.
Sea change: a sensemaking perspective on competing institutional logics
Keywords: dialogical change
sensemaking
institutional theory
deinstitutionalization
institutional change
sensegiving
institutional logic
institutional complexity

In recent years, institutional theorists have been increasingly interested in institutional change, seeking to understand the contextual factors and agents responsible for alterations to existing institutional arrangements. Institutional theory’s historical focus on isomorphism has made it challenging to account for actors’ motivations to pursue change projects. It is generally believed, though, that agents are mobilized through exposure to multiple institutional logics. Recently, scholars have begun to recognize that competition among multiple logics may not quickly produce a ‘winning logic’; rather, such logics may co-exist for prolonged periods in a context of ‘institutional complexity’. The turn toward institutional complexity reveals that preoccupation with the ‘paradox of embedded agency’ has left the development of change projects themselves under-theorized: What happens when organizational actors must interpret puzzling institutional contexts and generate alternatives?
In seeking to understand organizational actors’ efforts to cope with conflicting logics in a context of scientific uncertainty, this study aligns with this growing interest in institutional complexity. Drawing on concepts from sensemaking theory, this research illuminates how actors with divergent interests, enacting their organizational roles, cope with competing logics and interact around a change project that emerges as a result of their efforts at coping. It thus contributes to institutionalist understandings of institutional complexity and change and adds to an emerging body of research linking institutional theory and sensemaking.
The empirical setting for this single-case study is the ‘sustainable seafood’ discourse that began in the early 1990s when the cod collapsed off North America’s eastern seaboard. Prolonged scientific uncertainty regarding the collapse made generation of preferred alternatives problematic; this resulted in lengthy sensemaking efforts by multiple stakeholder groups, drawing on different institutional logics to produce divergent and competing interpretations and action scripts. Tracing the evolution of this discourse through documents, observations, and interviews empirically reveals processes of interrelated sensemaking, and further, exposes sensegivers as bricoleurs who use institutional elements creatively to affect the sensemaking of others.