VictorJuiz/thesis huggingface dataset:
Pelagiaria (Teleostei: Acanthomorpha) as a non-analogue adaptive radiation
Keywords: landanichthys
fossil fishes
morphology
pelagiaria
evolution
phylogenetics
eocoelopoma
trichiuridae
scombridae
gempylidae

Pelagiaria is an anatomically disparate clade of open-ocean fishes identified through molecular studies, comprising 16 families not previously united on the basis of morphology. It has been postulated that ecologically distinct lineages of Pelagiaria diverged rapidly early in the Paleogene. This differs from ‘model’ adaptive radiations like cichlid fishes and Anolis lizards in age and geographic scale, but corresponds closely to patterns in Cenozoic mammals, the group where the concept was first defined. Well-preserved material from the UK, Angola and other sites provides an opportunity to investigate the evolutionary history of Pelagiaria and test these hypotheses of adaptive radiation. I use micro computed tomography (μCT) to investigate key three-dimensionally preserved fossils belonging to groups now assigned to Pelagiaria, focussing on scombrids (tunas, mackerels) and trichiuroids (snake mackerels). I develop character sets for trichiuroids and scombrids, allowing placement of key fossils associated with these groups. I also use μCT to collect three-dimensional cranial landmark data from 68 extant species of Pelagiaria, representing 15/16 extant families and a quarter of living species. These phenotypic data are studied in combination with a time-calibrated molecular phylogeny, which I apply using multiple comparative approaches. Results indicate that Pelagiaria showed an initial, diffusive phase of phenotypic evolution in the early Paleogene, followed by constrained patterns of cranial change from the Eocene onward. This adds quantitative support to previous hypotheses of adaptive radiation in the group, and suggest Pelagiaria might represent a useful a new study system for investigating this key macroevolutionary concept.
New anion receptors for molecular recognition and organocatalysis
Keywords: chalcogen bonding
transesterification
anion sensing
molecular recognition
anion binding
anion recognition
halogen bonding

This thesis describes the investigation of anion binding molecules in application to molecular recognition and organocatalysis. A focus is made on exploring the properties of σ-hole interactions: halogen and chalcogen bonding which are scarcely studied in the context of anion sensing, especially in an aqueous environment.
Chapter 2 describes the preliminary design of a tetradentate XB anion receptor. This system is shown to be effective for anion complexation in organic solvent media, more so than the isostructural HB analogues. Fluorescent sensing and chiral discrimination capabilities are also demonstrated.
Chapter 3 discusses the water-soluble, preorganised XB and ChB anion receptors. This provides the first examples of charge-neutral, all-XB and all-ChB host molecules to be used for anion binding in water. In addition to the fundamental studies of anion coordination, applications in fluorescent and electrochemical anion sensing are shown.
Chapter 4 details the development of biomimetic transesterification catalysts that include an oxyanion hole function. The series of compounds is iterated towards high reactivity, arriving at highly effective catalysts with a modular, easily customised structure.
Singly and co-doping of ZnO thin films by spray pyrolysis
Keywords: ZnO
Semiconductor
Thin Film
Materials
Grain Boundary
Spray Pyrolysis
Chemistry
Zinc Oxide
Transparent Conductive Oxide
Doping
TCO

Indium-based transparent conducting oxides (TCOs) are widely used in optoelectronic devices. An important goal of this project is to search for TCOs that have reduced In content or indeed no In. The cheap zinc-based TCOs are good candidates to replace expensive indium-based TCOs in applications. A co-doping protocol has been established using both Si and In to obtain films with both good optical and electrical properties. This co-doping strategy can dramatically reduce the cost of the expensive element In while maintaining better optoelectronic performances compared to singly doped ZnO thin films.
The spray pyrolysis technique is used to deposit TCO thin films, which is famous for its lower cost compared with physical deposition methods such as sputtering. I have studied the detailed properties of singly doped (Si or In) ZnO together with co-doped (Si and In together) ZnO thin films. I have also related their optoelectronic performances with structures, elemental compositions, and chemical environment to understand their properties in depth.
It is the first time co-doped ZnO thin films based on Si and In have been successfully synthesised with high optoelectronic performances. Therefore, it is a basis for further development in co-doping and material design. The total chemical composition of elements in the bulk of a TCO material has not been measured previously. Nevertheless, I have studied these to see the limitations or restrictions in doping, thus understanding how doping affects optoelectronic properties including metal-insulator transition. Our ultimate goal is to develop an applicable deposition method and find suitable TCO materials to meet application requirements on both the optoelectronic performance and cost.
Optimising statistical methodologies for estimating antimalarial efficacy for uncomplicated Plasmodium falciparum malaria
Keywords: Malaria
Efficacy

Plasmodium falciparum malaria remains one of the greatest causes of mortality and morbidity globally. Estimates of treatment efficacy provide critical information for optimising treatment guidelines. The aim of this thesis was to quantify the magnitude of variation in the derived estimates attributable to study design and analytical approaches in uncomplicated P. falciparum in patients treated with artemisinin combination therapies (ACTs). This thesis utilised individual patient data collated from 92 clinical trials, including 31,507 patients treated with ACTs extracted from WorldWide Antimalarial Resistance Network (WWARN) repository.
This thesis presents a number of novel findings relevant to clinical researchers and policy makers. The current recommended follow-up period of 28 days with artemether-lumefantrine regimen missed an estimated 58% [95% Confidence Interval (CI): 47% – 74%] of treatment failures in Africa and 32% [95% CI: 15% – 45%] in Asia. For dihydroartemisinin-piperaquine (DP) regimen, a study with 42 day follow-up was estimated to miss 47% [95% CI: 19 – 90%] of the treatment failures in those who were adequately dosed. These results confirmed that studies adhering to the current follow-up recommendations provide an overestimate of the drug efficacy and longer follow-up is warranted for these regimens to adequately capture treatment failures.
The derived estimates were further vulnerable to analytical approaches adopted. Kaplan-Meier (K-M) approach, the currently recommended method, overestimated treatment failure by up to 3.6% compared to a competing risk survival analysis approach. Simulation studies demonstrated that the magnitude of this overestimation increased with declining drug efficacy in high transmission areas, where a substantial fraction of patients develop new infections. Similarly, excluding patients with indeterminant outcomes (i.e. whether parasite recurrence is a treatment failure or new infection cannot be determined) was associated with an upwards bias in the derived estimate of efficacy by up to 1.7% compared to using the sophisticated methods of multiple imputation and inverse probability weighting for dealing with the indeterminant outcomes.
This thesis highlighted that the choice of analytical approaches led to variability around the derived estimates of drug efficacy. The findings of this thesis are discussed with regards to current World Health Organization guidance to change treatment policy.
Hume's problem, Kant's solution
Keywords: Induction
Nonconceptualism
Causation
Hume
Kant
Scepticism

These essays are four independent contributions to scholarship on David Hume’s and Immanuel Kant’s metaphysics, epistemologies, and philosophies of mind. They converge on Kant’s response to Hume’s causal scepticism. By ‘Hume’s causal scepticism’, I mean: first, Hume’s doubt that we can cognise causation a priori (what Kant called ‘the Humean doubt’); second, Hume’s doubt that the justification of induction is rational (Hume’s so-called ‘problem of induction’).
Essay 1, ‘Hume’s Alleged Lapse on the Causal Maxim’, argues that Hume was prima facie justified in doubting the ‘absolute’ necessity for the impression of any event to be preceded by the impression of a cause. Essay 2, ‘Kant’s Humean Problem’, argues that Kant, recognising the coherence of Hume’s doubt that we can cognise causation a priori and not just empirically, took his own Transcendental Analytic to directly refute Hume’s doubt. Essay 3, ‘Kantian Objectivistic Nonconceptualism’, argues that the ‘nonconceptualist’ reading of Kant’s Transcendental Deduction—on which intuiting objects does not require applying a priori concepts—is incorrect because it does not directly refute Hume’s doubt that we can cognise causation a priori. Essay 4, ‘Did Kant Solve Hume’s Problem of Induction?’, argues that Kant offered resources for a limited solution to Hume’s ‘problem of induction’, i.e., the demand to rationally justify our presupposition that any object or event resembling those perceived as conjoined with a specific quality is also conjoined with that quality.
Order, motion and relaxation in radical pair compass magnetoreception
Keywords: Spin Chemistry
Redfield Theory
Magnetoreception
Spin Relaxation
Radical Pair Mechanism

Traditionally, biological systems are thought to be governed by classical, rather than quantum behaviour. In the warm, aqueous environment of a cell, the thermal energy kBT is much larger than the spacing of quantum energy levels and there are many processes, such as molecular motion, that can rapidly destroy delicate quantum coherences. An exception may be the remarkable ability of birds to navigate using the Earth's pervasive but extremely weak magnetic field; an ability that is thought to depend on the spin-selective reactions of photochemically-generated radical pair species.
Despite substantial (although inconclusive) evidence pointing towards a radical pair mechanism of avian magnetoreception, whether, and how, spin coherence can be maintained long enough to produce a field-dependent compass signal remains a key question. It becomes even more critical in light of recent work, presented in this thesis, showing that coherence lifetimes > 10 microseconds reveal `spiky' features in the compass signal that could explain the astonishing precision of the avian compass and its sensitivity to radiofrequency noise. In the first half of this thesis, two different models are used to explore the resilience of the compass to restricted rotational motion of individual radicals, with a focus on the flavin and tryptophan radicals in the proposed magnetoreceptor, cryptochrome. Fast, highly constrained motion is found to be crucial for the flavin radical, whilst the tryptophan radical can be allowed greater motional freedom, in keeping with its position near the surface of the protein. However, even in an optimised system, very little compass information is likely to survive in the presence of realistic relaxation, suggesting that our current understanding of the radical-pair mechanism may be incomplete.
Chapter 7 investigates how relaxation effects could be exploited to probe the function of cryptochrome. An experiment in which relaxation rates are locally enhanced by the presence of the biomimetic, superparamagnetic nanoparticle magnetoferritin is proposed and assessed. This experiment could provide much-needed evidence for the identity of the magnetoreceptor, allowing for more focused investigation of the compass mechanism.
Finally, the requirements for highly restricted motion and long-range ordering of the magnetoreceptors make the radical pair compass inherently sensitive to polarized light. This is potentially problematic because natural variations in skylight polarization could compromise detection of the magnetic field. A combination of algebraic and biological arguments are used to demonstrate how unwanted information can be filtered out of the compass signal by taking the ratio of signals from two neighbouring cells related by a 180° rotation about their line-of-sight. The combination of magnetic field patterns from the two cells additionally helps to pinpoint a precise heading.
How can a peer mentoring programme be developed in order to help meet a school's pastoral care development priorities?
Keywords: MLT2018
MLT

This research project explores the development of a peer mentoring programme in my school during the academic year 2017-18. The main focus of the project is how the peer mentoring programme can be aligned to help fulfil my school’s pastoral care priorities. The importance of encouraging a whole-school approach to well-being is also considered. There is currently a growing awareness of pastoral issues such as mental health in schools, and the research regarding peer mentoring is developing concurrently. For instance, recent governmental guidelines (2017) encourage peer support as a proactive tool to tackle mental health issues, and studies demonstrate that peer mentoring can develop resilience in young people. However, the research regarding peer mentoring is limited.
Action research was employed for this project in order to ensure a continued focus on the development of the peer mentoring programme and to ensure regular collaboration with both pupils and staff, allowing for both feedback on interventions and suggestions for the future. Three cycles were undertaken, with a key focus on pastoral priorities for each cycle. Mixed methods surveys were employed in order to allow for both quantitative and qualitative data. This provided a broad range of responses from the pupils and staff which the programme engages with.
This project resulted in significant changes to the peer mentoring programme in my school setting. Working in collaboration with a range of pupils and staff has allowed me to re-structure the peer mentoring programme for the next academic year, focussing on the quality rather than quantity of peer mentoring available, and employing participatory action research has encouraged a more meaningful engagement with the development of the programme. A whole-school approach to well-being is, over time, being developed in my school setting, and the peer mentoring programme will play a proactive part in that.
What is the impact of collaborative working between teachers on their classroom practice?
Keywords: MLT2018
MLT

Socio-cultural theorists and empirical studies suggest teachers increase their expertise through collaborative learning in environments with specific modi operandi and ways of thinking. However, few of these studies examine the classroom impact of this collaboration. In this inquiry, the factors which enable and constrain collaborative task design between teachers in a large modern languages faculty are explored. The classroom impact of this collaboration and the reasons for differences between colleagues are then examined. Classroom impact appeared most significant when colleagues had the autonomy to choose their area for development, based on an immediate gap identified in their pupils’ knowledge and when a menu of research-informed classroom tasks to bridge that gap was provided. Factors such as trust between participants, teacher agency and beliefs, the extent to which managers relinquished their power and competing demands on teachers’ time also explained differences in classroom outcomes. An additional finding, often neglected in the write-ups of action research, are the challenges faced in data-collection and interpretation, when the researcher and the participants’ line manager are one and the same person.
Intrinsic motivation: exploring the effect of praise and reward on pupil engagement
Keywords: MLT
MLT2018

Motivating pupils to learn in the classroom has been on the agenda in schools and academic research for decades. This case study takes a look at school where pupils are not fully engaging in their education and implements an intervention with a view to increase the pupil motivation, and more specifically the pupils’ intrinsic motivation. Findings from the intervention show that there is a strong causal link between pupil motivation in the classroom and praise and reward.
Phenotypic and genotypic characterisation of juvenile myelomonocytic leukaemia
Keywords: Targeted sequencing
Single cell genotyping
Leukaemia stem cell
Stem cell assays

Paediatric myelodysplastic syndromes and Juvenile Myelomonocytic Leukaemia (JMML) are very rare haematological diseases of childhood, with an estimated incidence of 1 case per million. Due to their rarity there is relatively little known about their natural history and disease biology. As a result, there are often significant challenges in establishing a diagnosis and there are very few treatment options available for these children. The only curative treatment is bone marrow transplantation but even this is associated with a high risk of disease relapse, particularly in JMML where relapse rates are approaching 35%.
In the work described here, I first set up a national observational study to prospectively collect serial patient samples in order to phenotypically and molecularly characterise these patients at diagnosis and to establish the basis for a prospective natural history study. The clinical and molecular characterisation of these diseases allowed me to devise new diagnostic and management algorithms for paediatric MDS and JMML.
In order to understand more about the biology of this group of disorders I decided to focus on JMML as this was the largest distinct group of patients enrolled in the study. My specific aim has been to identify and characterise the disease-propagating population in JMML (the JMML 'leukaemic stem cells, LSC); which is a crucial step in understanding the disease evolution and dynamics of relapse. Prior to this work, there was almost nothing known about the haematopoietic hierarchy in JMML and the impact of JMML-associated mutations on haematopoiesis. With this study I analysed the JMML haematopoietic stem cell and progenitor cell (HSPC) compartments gaining new insights into the architecture of the JMML HSPC and their lineage potential. Using a single cell genotyping approach I was able to map the JMML mutations onto the haematopoietic hierarchy identifying for the first time the cellular compartment in which the JMML-associated mutations originate. The stem cell capacity of candidate JMML LSC was assessed with in vitro and in vivo stem cell assays establishing the identification of the disease propagating population(s). Molecular techniques, including RNA sequencing, then allowed me to molecularly characterise the JMML LSC and identify putative disease-specific targets and biomarkers that might be utilised in the future for disease burden monitoring and more effective treatments.
The language of covenant
Keywords: covenant
semantics
biblical
semantic
Genesis
berit
Hebrew
Bible

The centrality of covenant in the Hebrew scriptures has made it a theme of enduring significance. Accordingly, the language of covenant has acquired a corresponding importance. Whereas study of the language of covenant has not been neglected by scholars. the combination of impetus from ”Biblical Theology,” together with the tenets of traditional philology, has resulted in word-studies, which regard words as convenient labels for concepts. Some of the dangers of this approach have been exposed by Dr. James Barr, and, in the realm of New Testament Greek research, Dr. Nigel Turner has sought to explore the value of syntax and style. The present dissertation constitutes a determined attempt to discover the values of a similar approach to Biblical Hebrew semantics, in the restricted field of covenant language. If this approach has an appearance of being somewhat pedestrian, then that is due, in large part, to the absence of the kind of literature that facilitates the task of lexicography; the spadework of structural semantics is yet to be done, and the ground is fallow. The aim, therefore, is an articulation of the semantic structures of language associated with ברית. If any justification for this be required, then this writer's apology will be the same as Dr. Turner's: “my apology must be that the mechanics of speech provide a delicate and flexible means of communication which is worth scientific study.”
Continued in theses ...
Algebraic quantum structures for reference frame-independent quantum teleportation and pseudo-telepathy
Keywords: quantum algebra
pseudo-telepathy
linear constraint system games
projective representation theory
noncommutative mathematics
groups of central type
nonlocal games
quantum graph isomorphisms
Teleportation
noncommutative graphs

Part I: We present two new schemes for teleportation of a quantum state between parties whose local reference frames are misaligned by the action of a compact Lie group G. These schemes require no prior alignment of reference frames and are unaffected by arbitrary changes in reference frame alignment during execution, suiting them to situations of rapid reference frame drift. Our tight scheme yields improved purity compared to standard teleportation, in some cases substantially ---including the case of qubit teleportation under arbitrary SU(2) reference frame uncertainty--- while communicating no information about either party's reference frame alignment at any time. Our perfect scheme performs perfect teleportation, but does communicate some reference frame information. The mathematical foundation of these schemes is a unitary error basis permuted up to a phase by the conjugation action of a finite subgroup of G; we completely classify such unitary error bases for qubits, exhibit constructions in higher dimension, and provide a method for proving nonexistence in some cases.
Part II: Quantum pseudo-telepathy is a phenomenon whereby two non-communicating parties can use the non-signalling correlations from shared quantum entanglement to perform a task that would ordinarily be impossible without communication. Here we consider the graph isomorphism game: an instance of the game is defined by a pair of graphs, and a perfect deterministic classical strategy precisely corresponds to an isomorphism of those graphs. We call a pair of graphs for which a perfect strategy using shared entanglement (a quantum strategy) exists pseudo-telepathic, and call a quantum strategy a quantum isomorphism between the graphs. Using a deep connection between noncommutative mathematics and nonlocal games, we classify all graphs quantum isomorphic to a given graph in terms of the quantum automorphism group of the graph. This implies a construction of quantum isomorphisms from central type subgroups of the ordinary automorphism group; we give an explicit description of the resulting quantum strategy and the new graph. We consider generation of new examples of quantum contextuality from central type groups. For abelian central type groups we show that this reduces to construction of quantum solutions of a binary linear constraint system from the abelianisation of its homogeneous solution group.