VictorJuiz/thesis huggingface dataset:
C-infinity algebraic geometry with corners
Keywords: Derived Geometry
Schemes
Manifolds with corners
Manifolds

C∞-schemes are a generalisation of manifolds that have nice properties such as the existence of fibre products. C∞-schemes have been used as a model for synthetic differential geometry, as in Dubuc, Kock, and Moerdijk and Reyes, and for defining derived differential geometry as in Lurie, and Spivak.
Manifolds with corners are a generalisation of manifolds locally modelled on [0,∞)k × Rn-k, and their smooth maps behave well with respect to the corners as in Melrose. In particular, Joyce describes a corner functor from the category of manifolds with corners to the category of 'interior' manifolds with corners with mixed dimension.
C∞-algebraic geometry with corners is the study of C∞-rings and C∞-schemes with corners, which we define in this thesis. We define (local/interior/firm) C∞-rings with corners, and study categorical properties such as the existence of limits and colimits using various adjoint functors. We describe a spectrum functor from C∞-rings with corners to local C∞-ringed spaces with corners, and show this a right adjoint to a global sections functor. We define C∞-schemes with corners using this spectrum functor.
We show there is a full and faithful embedding of the category of manifolds with corners into the category of firm C∞-schemes with corners, and that fibre products of firm C∞-schemes with corners exist. We show that manifolds with corners are affine under geometric conditions. We define (b-)cotangent sheaves of C∞-schemes with corners and show they correspond to the (b-)cotangent bundles of manifolds with corners of Joyce.
We describe the categories of interior local C∞-ringed spaces with corners and interior firm C∞-schemes with corners. We construct corner functors for both of these categories, which are right adjoint to the inclusion of these interior spaces/schemes into the non-interior ones. We show that these corner functors correspond to the corner functor for manifolds with corners.
We expect applications of this work in defining derived spaces with corners in derived differential geometry, and we explore the connections of this work to log geometry and the positive log differentiable spaces of Gillam and Molcho.
Christian angelology in pseudo-Dionysius and Sergius Bulgakov
Keywords: Hierarchy
Bulgakov
Sophia
Personhood
Angelology
Pseudo-Dionysius

This thesis aims to explore the different theological languages employed by Pseudo-Dionysius and Sergius Bulgakov to express their respective ideas about angels. Although Bulgakov provides a number of references to Pseudo-Dionysius and draws on his ideas extensively, no single study exists dedicated to Bulgakov’s appropriation of Pseudo-Dionysius.
We argue that in order to engage fully with Bulgakov’s ideas there is a need to approach his texts not as sui generis theological or philosophical system but as an interpretation of traditional Christian theology as found in scriptural, liturgical and patristic sources. The main difference between these two approaches is that, while the former envisages only one logical level – the logic of the whole system (otherwise the system would disintegrate), the latter presupposes a parallel existence in the same text (or body of texts) of two distinct logical levels – the logic of that which is being interpreted, and the logic of the interpreter (the ‘metalanguage’). We also argue that the same approach can be applied to the analysis of the Corpus Dionysiacum.
Thus, we distinguish three different theological languages in the writings on angels by Pseudo-Dionysius and Bulgakov. In Part 1 of the thesis we begin the reconstruction of their angelologies by analysing their respective metalanguages of hierarchy and Sophia. In Part 2, we proceed by engaging with the philosophical language of nature and hypostasis in both authors. In the final chapters of the thesis, in Part 3, we turn to the most fundamental level, which is referred to as the language of anthropology. This language is based on the immediate human experience of angels – the manner in which angels are depicted in the Bible, in visions and accounts of mystic experiences. We demonstrate that the anthropological and philosophical languages are continually reinterpreted by Pseudo-Dionysius in his metalanguage of hierarchy, and by Bulgakov in his metalanguage of Sophiology.
Analysis of the roles of the plastidic E3 ligases SP1 and SPL2 in tomato and wheat
Keywords: Chloroplast
Plastid biogenesis
Plastid
Plastid protein import
Chromoplast
SPL2
SP1

Plastids are an important group of plant organelles, and depending on their morphology and functions, plastids exist in different forms and have the ability to convert between these forms. Development of plastids depends on the import of preproteins from the cytosol through outer and inner envelope chloroplast membranes, TOC and TIC complexes. The TOC complex incorporates different client-specific receptors and these contact preproteins with differing specificity, controlling the proteomic composition, development fate, and functions of the plastid. The first identified chloroplast-localized E3 ligase of the plastid outer membrane, SP1, is a regulator of the TOC translocon. In Arabidopsis, SP1 functions to attach ubiquitin to TOC proteins for ubiquitin-proteasome system (UPS)-mediated degradation, controlling the proteomic composition of plastids.
In this thesis, detail analyses of the role of SP1 were conducted in tomato and wheat plants with altered SP1 expression (both overexpression [OEX] and RNA interference-based knockdown, in each case), to further assess the extent to which its functions are conserved in different species, and to elucidate possible practical applications in crops.
In accordance with previous findings in Arabidopsis, SP1 OEX promoted abiotic stress tolerance and leaf senescence in both tomato and wheat. SP1 was found to influence the abiotic stress tolerance where its particular effect on the plants’ responses to stress conditions was dependent on the developmental stage at which the exposure to stress occurred. SP1 RNAi delayed senescence under dark-induced and natural senescence conditions, and influenced yield in ‘stay-green’ SP1 RNAi wheat plants. SP1-mediated changes in tomato were found to alter the duration of fruit ripening, without affecting the size and firmness of the fully ripened fruit. Specifically, SP1 OEX fruit showed accelerated ripening, and SP1 RNAi fruit showed delayed ripening.
Finally, the role of SPL2, a homologue of SP1, in tomato was investigated. The RNAi-mediated knockdown of SPL2 expression in tomato plants had similar effects on fruit ripening, leaf senescence, and abiotic stress tolerance to SP1 RNAi, even though the transcript abundance of tomato SPL2 in various plant tissues was much less than that of tomato SP1.
Kant on citizenship
Keywords: political philosophy
Kant
rights
history of philosophy
citizenship

This thesis argues that Kant has a systematic account of citizenship. Kant claims that citizens possess three attributes: (i) freedom, (ii) equality, and (iii) independence. Each of these attributes specifies a relation between the state and its members. Freedom is the institutionalised version of the innate right to freedom. Citizens possess freedom when the state only permits its members to perform those actions that are compatible with the innate right. Equality is possessed by citizens when each member of a state bears the same relationship to the law as every other member. Finally, independence is the attribute possessed by members of a state who are not under the authority of any other member and who contribute to the state.
There are three kinds of rights in Kant's political philosophy: the innate right to freedom, acquired rights, and public rights. Each of the attributes of citizenship provides us with additional resources for thinking about one of these rights. Freedom sheds light on the innate right by specifying the requirements of that right in the only condition in which it imposes constraints on the actions of others (i.e., the state). Equality sheds light on acquired rights. This is because the implications of Kant's account of the equality of citizens primarily concern those rights. Kant's account of equality tells us both that privileges associated with a certain status cannot be hereditary, and that great material inequality is permissible. Independence sheds light on public rights. Those who are independent are active citizens. Active citizens are free and equal members of a state who contribute to the existence and the laws of that state. In doing so, they also contribute to a necessary condition for the validity of the rights of each.
Influences of environmental change on the eco-evolutionary dynamics of an insular bird Zosterops lateralis
Keywords: zosterops lateralis
life history traits
integral projection models
survival rates
island syndrome
growth rates

The colonisation of islands exposes species to novel biotic and abiotic conditions, that can produce convergent adaptations in morphological and life history traits. One phenotypic pattern, the “island rule”, states that initially large bodied species evolve smaller body sizes on islands and smaller species become larger. The underlying mechanisms for this pattern are likely to be complex, and depend on demographic variables and interactions among different phenotypic traits. In this thesis I evaluate mechanisms that may explain evolution of larger body sizes in insular birds by examining the influence of intrinsic and extrinsic factors on morphological and life history traits, and population dynamics of an insular passerine bird, using empirical and modelling approaches. Examining growth, a key determinant of body size, I found that altricial birds tend to grow slower on islands. Intriguingly, a simple integral projection model I analysed showed that the optimal pathway to larger body size was to grow faster. However, the model did not account for more subtle processes, such as within-individual optimisation of resource allocation. This is possibly occurring, as nestling growth variation was not proportional to parental care expenditure. Additionally, larger nestlings and juveniles had higher survival, while survival for all age classes was density-dependent. My findings suggest that island birds may achieve large body sizes by prioritizing offspring quality through slower growth and that size advantages are particularly important at early life stages.
Targeting the VLA-4/VCAM-1 interaction for the diagnosis and prevention of brain metastases
Keywords: Cell adhesion molecules
Brain metastasis
Magnetic resonance imaging

Background: Brain metastasis is a major cause of cancer patient morbidity and mortality. The late stage of diagnosis and the difficulty in defining the tumour boundary both contribute to the lethality of brain metastases. Cell adhesion molecules (CAMs), such as very late antigen-4 (VLA-4) and its ligand vascular cell adhesion molecule-1 (VCAM-1), have been implicated in the metastatic process. By targeting the VLA-4/VCAM-1 interaction, I applied different methods to improve the diagnosis of brain metastases and to prevent their formation.
Aims: (i) To determine if VCAM-1 targeted MRI is able to detect brain micrometastases from different tumour types in mouse models; (ii) to determine if VCAM-1 targeted MRI is able to detect the brain metastasis invasive margin in rat models; and (iii) to determine if tumour cell VLA-4 knockdown inhibits metastatic spread of cancer to the brain in mouse models.
Findings: VCAM-MPIO MRI could detect brain metastases of different tumour types before gadolinium enhanced T1-weighted MRI. Furthermore, the imaging contrast improved delineation of the invasive margin of brain macrometastases on T2*-weighted MRI, when used in conjunction with conventional techniques. Whilst knockdown of VLA-4 does not entirely prevent brain metastasis formation, the trend to benefit suggests testing in combination with knockdown of other CAMs may yield a significant reduction in metastatic potential.
Discussion: I present a multi-faceted approach, exploiting the roles of VLA-4 and VCAM-1 in brain metastatic formation and progression, for improved diagnosis of brain micro/macrometastases and possible inhibition of metastatic seeding in the brain. Future studies will focus on improving the preventative capacity of anti-CAM therapy and the clinical translation of VCAM-MPIO MRI to human applications.
No strings attached: the expanding frontiers of low-cost transnational surrogacy
Keywords: transnational
Surrogacy
Global markets
India
Facilitation
Assisted Reproduction

This thesis is about global low-cost surrogacy markets in India and beyond. It explores the so far largely unexamined role of intermediaries, mostly fertility doctors and international facilitators, in efforts to turn surrogacy into a streamlined industry and avoid regulation. In Part I, I analyse how industry practice and discourse is aimed at reducing surrogate women to their reproductive capacity as wombs and cutting them off from potential relationships with the babies or the intended parents. This discussion incorporates a critical examination of surrogacy as a part of the category of bioeconomies. I argue that while attempts to reduce the surrogate to a reproductive body make commercial surrogacy appear as a union of biology, technology and capitalism, the efforts needed to contain the potential for emotion, intimacy and relationships in surrogacy show its embeddedness also within economies of care. Part II traces the low-cost surrogacy industry’s transformation after it’s ban in India. It underlines the way the depersonalisation and control of surrogate women that I describe in Part I allows the industry to set up quickly in new destinations, and even move pregnant surrogates across national borders to avoid becoming subject to regulation. In the final chapter I identify in the representations of surrogacy doctors and international facilitators a discourse of entitlement to carry on providing surrogacy service despite criticism and regulation. Within this discourse, professionals see their work not as problematic but as reproductive activism of helping discriminated groups achieve parenthood while providing low-income women with the choice to lift themselves out of poverty. Overall, the thesis argues that attempts to curb low-cost surrogacy only through criminalisation are unlikely to succeed due to the ability of the industry to control surrogate women, move quickly between countries and perpetuate a discourse of surrogacy as a mutually beneficial arrangement.
The importance of the active site canopy in [NiFe]-hydrogenases from Escherichia coli
Keywords: Hydrogen
Active Site Canopy
Nanoclusters

Hydrogenase-2 from E. coli is a multi-faceted [NiFe]-hydrogenase that is important because of its dual role as a model enzyme capable of reversible proton reduction and its prominence in microbe metabolism, yet previous investigations of Hyd-2 have been limited by low yield. In this investigation, a novel overexpression system for the catalytic core of Hyd-2 (termed Hyd-2 NOP) was designed and used to increase the yield of Hyd-2. Hyd-2 NOP was thoroughly characterized to ensure it remained nearly identical to Hyd-2 purified by previous strategies. The increased yield enabled structural characterization of the enzyme, and the structure allowed for a more accurate prediction of the full quaternary structure of Hyd-2. The structure also confirmed the positioning of three amino acid residues that are theorized to play an important, yet ambiguous, role in catalysis.
These residues were mutated, and the resulting protein variants were electrochemically and structurally characterized to better understand the role of these amino acid residues. Two of these residues, Asp103 and Arg479, are located directly above the bimetallic cofactor in the active site, and when mutated, confirmed the significance of the secondary coordination sphere in H2 activation. Fortunately, the R479K mutation trapped intermediates in the inactivation pathway that have never been isolated. The third residue, Glu14, has been shown to be important for the proton pathway in [NiFe]-hydrogenase, yet recent evidence from Hyd-1 challenged that finding. Comparative studies between the Hyd-1 and Hyd-2 variants with a Glu14 mutation showed the unique role of the proximal Fe-S cluster in Hyd-1 of repairing the proton pathway.
Collaborations with Guangyu Liu (Sir William Dunn School of Pathology, University of Oxford) and Dr. Liyun Zhang (Armstrong Group, Inorganic Chemistry Laboratory, University of Oxford) also explored the role of Hyd-2 in pathology and as a crucial component of biotechnology, respectively.
On the circulation response to climatic forcing
Keywords: Extreme event
Sensitivity study
Jet stream
Atmospheric dynamics
Eddy-driven jet
North Atlantic Oscillation
Climate change

Climate change is expected to cause changes in the general atmospheric circulation. Particularly important to the global population is an understanding of how weather and climate will change. North Atlantic jet stream changes will drive weather and climate changes, primarily over North-Western Europe, but also over North America, Asia and other parts of the globe. This makes it vital to understand how climate change will affect the jets to determine how the weather and climate will respond. However, the exact nature of the climate change forcings affecting the jet are uncertain.
Here, sensitivity studies using a hierarchy of models to determine possible circulation changes due to the thermal forcing of the atmosphere are performed. It is found that the location of forcing, both its latitude-longitude position and its height, has a profound effect on how the circulation responds. A simple mechanistic understanding for shifts and strengthening of the jet through changes in the mean meridional temperature gradients is presented, along with mechanisms for how Hadley circulation changes can affect the jet, and for how tropically forced waves affect the Northern Hemisphere circulation. Important differences between the responses in winter and summer are observed, which can lead to seasonally dependent extreme temperature and precipitation responses.
Key forcing locations that force the atmospheric circulation effectively are highlighted. In these locations, the uncertainties in how the forcing due to climate change will manifest must be reduced so that the circulation response can be better quantified. An important uncertainty is how the atmosphere heats up compared to how sea surface temperatures change and connected to this, how the land-sea temperature contrast will respond. As these uncertainties are reduced, the results from these sensitivity studies will provide a guide to understanding how the circulation will change and the associated impacts of the changes.
Modulation of visual-motor responses by the perception of object affordance, automatic imitation  and action agency
Keywords: social cognition
action agency
automatic imitation
object affordance

When we interact with the environment in our everyday life the relationship between what we see and what we do is under continuous coupling, i.e., our perceptions and actions are built through a continuous reciprocal flow of information between sensory and motor processes. This thesis reports a series of experiments investigating perception-action coupling in terms of modulation of response selection and execution processes by the perception of object affordances, automatic imitation and action agency.
In Chapter 2, I focused on demonstrating the automaticity of the action priming effect directing attention and its relationship with awareness of object affordances. Different from the classical studies on object affordances, I addressed this relationship through attentional effects to avoid SRC effects as a confound. The result suggested that, at least for error rates, when the relationship between an object and its action-related stimulus is explicit, affordances can elicit an attentional bias towards a representation of the action that a recently seen object affords.
In Chapter 3, I investigated the temporal aspects of automatic imitation focusing on the discussion regarding the stage of information processing where the interfering effects of observing an incongruent action takes place. The results demonstrated that the automatic imitation effect interferes not only with response selection but also with response execution, therefore providing new evidence of the reach of perception-action coupling effects.
In Chapter 4, I investigated the role of a prominent self-stimulus and the sense of agency in the automatic imitation effect. The results clearly demonstrated that automatic imitation effects can be modulated as a function of self-related information, reducing sensitivity to observed movements as a consequence of self-focus.
Overall, this thesis demonstrated a strong relationship between perception and action affecting the response process. Actions can be primed by the perception of either object affordance properties or by the perception of actions performed by others.
Attentional control of goal directed behaviour
Keywords: Functional Status
Stroke
Lesion Mapping

The ability to modulate behaviour in a goal directed manner, is fundamental to all aspects of life. To become goal directed, attention must be configured to bias perception and action in favour of the current directive. This competitive process allows expansive possibilities to be moulded into coherent purposeful behaviour. It allows intention to become action.
The following thesis can be broken down into two parts. The first part is comprised of three empirical chapters that examine the functional consequences and neural underpinnings of impaired attentional control following stroke.
The second part is comprised of two empirical chapters aimed at more specific experimental questions. These chapters propose novel paradigms aimed at answering finer grained questions regarding the structure of attentional control.
Part I: Chapter 2 examines the functional consequences for patients with impaired attentional control. Chapter 3 takes a subset of patients from the previous chapter and uses a voxel-based lesion-symptom mapping approach to examine damage associated with impaired attentional control. Chapter 4 utilises a BiFactor model to examine whether executive dysfunction manifests differentially after frontal and posterior damage.
Part II: Chapter 5 proposes a novel paradigm that allows better dissociation of errors associated with the breakdown of goal directed behaviour. Chapter 6 examines how attention is distributed during concurrent processing and maintenance activities.