VictorJuiz/thesis huggingface dataset:
Investigation of motion perception learning in healthy subjects, for application as a rehabilitative therapy for visual field defects following primary visual cortex damage

Perceptual learning is the ability to improve performance of a perceptual task, with repeated practice. The concept of perceptual learning in the adult visual system has been established for many years, however, the neural mechanisms which mediate it have proved complex to unravel. Improved understanding could be used to guide novel rehabilitative strategies for those with damage to the brain which a↵ects the primary visual cortex (V1) in the occipital lobe. Motion perception learning is thought to involve the brain area hMT+, which is located in the parieto-temporo- occipital cortex, distal from V1. It is possible that motion perception training may improve the vision or subjective quality of life for individuals with damage to V1.
This project initially looked at the e↵ect of motion perception training in healthy individuals, in order to establish and quantify the potential behavioural and neural impact of behavioural training.
A five-day motion perception training paradigm applied in these experiments produced robust improvement of motion perception in healthy participants. This learning was found to be partially transferable to untrained regions of the visual field. If the training timecourse was reduced to a single day, the location specificity of learning e↵ects was increased significantly.
Functional MRI analysis indicated that the motion perception training paradigm applied here altered activity at extrastriate visual areas and frontotemporal decision areas.
When motion perception training was combined with brain stimulation, it was shown that 20 minutes of anodal transcranial direct current stimulation (tDCS) over hMT+ had no impact on learning magnitude or timecourse.
Finally, the motion perception training paradigm was applied as a case study in a patient with damage to V1. The results were promising but inconclusive with such a minimal dataset.
Motion perception training produces robust improvements in perception in healthy individuals, which are likely mediated by visual extrastriate and decision-making areas of the brain. As such, motion perception training shows promise, with further development, as an avenue for rehabilitation of the visual system and visual perception following damage to the primary visual cortex.

Keywords: brain injury
perceptual learning
hemianopia
motion perception
magnetic resonance imaging
visual field defects
brain stimulation
psychophysics
Advisor: Kennard, C
Bridge, H
Synthetic glyco-viruses for targeted DNA vaccination vectors

Viruses are powerful vectors for the delivery of nucleic acids, with applications in gene therapy and vaccination. However, major challenges for this technology include mis-targeting of the vector and neutralization by host antibody responses. Here we show that chemical addition of synthetic glycans to adenovirus (Ad) increased resistance to neutralizing antibodies and other critical host clearance mechanisms. Carbohydrate ligands were synthesised and functionalised with a cyanol methyl thiol group, which was subsequently activated to the amine reactive 2-imino- 2-methoxyethyl (IME). Ads were coated with ligand whilst maintaining virus cogency, with up to 58% of total Ad lysine resides glycosylated. The viral tropism of glyco-Ads was switched to target macrophages and dendritic cells (DCs), with high selectivity for the complementary sugar receptors. In vaccination studies, DC targeted glyco-virus enhanced antigen-specific T cell responses. Thus, chemical glycosylation of the Ad capsid allows modulation of tropism and shielding from sequestration and neutralizing antibodies. Since manipulation of this process is facile, it provides a flexible and potentially universal solution to key obstacles facing the utilization of viral vectors in therapeutic and vaccination contexts.

Advisor: Davies, B
Theodore Metochites: Byzantios, or, About the imperial megalopolis

As the title suggests, Byzantios or About the Imperial Megalopolis is the eulogy of Constantinople, one of Theodore Metoehites' many works that still remain unpublished due to the writer's obscure style. My primary aim in this edition has been to establish the text, an oration written by one of the most prominent figures of the Palaeologan Renaissance. In fact, the text constitutes the eulogy of the Capital of the Byzantine Empire and it could provide useful information to historians, archaeologists and Various scholars. However, I must ask for the reader‘s understanding regarding the matters of punctuation. The artificial style and rhetorical presentation in many passages make no wonder if a satisfactory rendering of the Greek can be achieved.
I have added an Introduction where I deal with Metochites' life and works, the genre of Byzantios and a few more issues raised by the oration (missing folios, dating of the oration, etc.).
The text needs to be elucidated from a wide Variety of sources, historical and literary, and this is the main aim of the commentary. In addition. I wished to present reasons for my interventions in the Greek text, to offer some parallels from other - mainly rhetorical - works and to give the quotations of the classical authors to which Metochites refers. Obviously the commentary does not provide exhaustive discussion of the many different topics raised in Byzantios, but I hope to have provided a minimum bibliography for further study.
The appendix at the end shows how much Metochites followed Menander's precepts. I believe that the indexes will also prove useful to the reader.

Keywords: Byzantium
Byzantios
imperial
Constantinople
Metochites
megalopolis
Istanbul
Bayesian fusion of continuous-valued labels in biomedical applications

Expert labelling is the gold standard for diagnosing patient-specific diseases from medical data. However, experts are relatively scarce, their time is expensive, and the task of labelling is time-consuming. While automated algorithms offer advantages of time efficiency, repeatability, and cost-saving benefits compared to manual labelling, there remains a substantial discrepancy in their estimation as well as reliability that limit their use.
Two commonly-encountered and clinically-important examples were considered for the use of concept labels in clinical practice: the QT interval in the electrocardiogram and the respiratory rate estimation from the photoplethysmogram. This thesis sought to combine outputs of automated annotators (i.e., algorithms) to improve estimation of these exemplars in a principled manner.
A series of methods were proposed for inferring a consensus in a scenario when only noisy annotations of some presumed underlying ground truth are provided: (1) the Bayesian Continuous-Valued Label Aggregator (BCLA) with independent annotators was proposed to infer the ground truth while jointly predicting each algorithm's bias and precision. Both maximum-a-posteriori and Gibbs sampling approaches were derived to compute parameters in the BCLA model (denoted as BCLA-MAP and BCLA-Gibbs, respectively); (2) BCLA incorporating the notion of signal quality (i.e., BCLAs) was also proposed to provide a confidence measure relating to the quality of the input recordings; (3) BCLA with correlated annotators (BCLAc) model was further proposed to provide a more generalised framework for BCLA, in particular, two variants of BCLAc were considered to model the correlation of errors among annotators directly and indirectly. Furthermore, the proposed methods were compared to the mean, median, best-performing single annotator with least root-meansquared- error, and two state-of-the-art benchmarking approaches described in the literature, namely "scalar Simultaneous Truth and Performance Level Estimation" and an Expectation- Maximisation label aggregation approach.
This thesis considered two exemplary medical datasets as well as simulated datasets to validate the proposed methods. The results of the proposed BCLA had optimal performance over the other comparison voting strategies in all datasets. Furthermore, BCLA-Gibbs as a fully-Bayesian approach was superior to BCLA-MAP. When incorporating an extension to include signal quality (i.e., the BCLAs model), results of BCLAs-MAP and BCLAs-Gibbs outperformed those of the basic BCLA methods consistently. Finally, we modelled the inclusion of potentially-correlated annotators using BCLAc.
In summary, the results of the methods proposed in this thesis improve accuracy by inferring a consensus in a scenario when only noisy labels of a group of imperfect algorithms are available. The proposed methods operate in an unsupervised Bayesian learning framework, and have the potential for real-time application to produce estimates that are more robust than any of the algorithms independently considered.

Advisor: Clifton, D
Clifford, G
The prevalence, risk factors and behavioural and emotional consequences of acute seizures in a rural Kenyan setting

The incidence of acute seizures (e.g. both febrile seizures and acute symptomatic seizures) is higher in Africa than elsewhere, but most studies are based on hospital admissions. Acute seizures in children are associated with behavioural/emotional problems which may be related to the seizures, underlying aetiology, neurological impairments and/or genetic predisposition. Behavioural/emotional problems occur in up to 26% of older Kenyan children in the community, but there are no large community-based studies in preschool children in Africa to plan interventions.
I screened 7,047 children aged 1-6 years living in Kilifi, Kenya for acute seizures with a proportion of these (N=3,273) examined for behavioural/emotional problems using the Child Behaviour Checklist (CBCL). Factorial structure of the CBCL was examined using structural equation modelling, while associations were determined using several regression analysis techniques. Prevalence of behavioural/emotional problems and acute seizures was computed as a probability of occurrence, by exponentiation of the constant term of a logit model.
The CBCL had between good and excellent psychometric properties and the seven-syndrome structure fitted well with the Kenyan preschool children. The prevalence of total behavioural/emotional problems was high (13% (95%CI, 12%-14%)) and so was that for acute seizures (6.1% (95%CI, 5.5%-6.8%). Behavioural/emotional problems were particularly associated with seizure disorders, which explained the greatest variation in a structural equation model. Risk factors for acute seizures included family history of seizures, previous hospitalisation and snoring at night. The overall crude prevalence of behavioural/emotional problems in those with acute seizures was 27% (95%CI, 21%-34%), being significantly greater than for those without seizures (11% (95%CI, 11%-12%); X2 p≤0.001). Acute seizures remained associated with behavioural/emotional problems (RR=2.40 (95%CI, 1.61-3.58)), externalising problems (RR=2.09 (95%CI, 1.40-3.13)) and internalising problems (RR=1.99 (95%CI, 1.36-2.91)), after accounting for potential confounders.
The prevalence of behavioural/emotional problems and acute seizures is high in preschool children in this rural area, and are associated with preventable risk factors. Behavioural/emotional problems are associated with acute seizures and should be assessed and addressed in preschool children with seizures.

Advisor: Newton, C
Stein, A
Marsh, K
Computational studies on ring-opening and closure: origins of selectivity and catalysis

This thesis describes the application of computational chemistry to understand the origins of the regioselectivity and stereoselectivity in reactions involving the opening and formation of cyclic species. In particular, we have used transition state modeling to gain quantitative insight into an area of organic chemistry where previous understanding has been heavily unfluenced by empirical observations. Our work provides a basis to understand regioselective ring-opening of epoxides in systems controlled by subtrate- or solvent effects. We have also studied enantioselective catalysis using phosphoric acids, which promote enol ether spirocyclizations and the desymmetrization of meso epoxides and aziridines.
In Chapter 2 we investigate the unusual 6-endo-tet selectivity of epoxide-opening cyclizations, which form a tetrahydropyran motif found in several marine natural products. Through DFT calculations we have established the stereoelectronic effect of neighboring groups in weakening the adjacent C-O bond, which directs the nucleophilic attack at this position. We also discover that the role of a template provides a thermodynamic bias towards the pyran product, but that it also influences charge separation in the competing transition state structures. The 5-exo-tet pathway suffers from greater charge separation, and entropically unfavorable solvation effects.
In Chapters 3 and 4 we turn to enantioselective catalysis with chiral phosphoric acids. Here we investigated the origins of enantioselective enol ether spiroketalization. We have established that selectivity arises in a concerted, but asynchronous step in which the enol ether is protonated, and the developing oxonium is quickly intercepted. The computations are able to account for the sense and level of enantioselectivity based on this mechanistic model. We then focus on the desymmetrization of meso epoxide and aziridines using the same class of catalyst: again a bifunctional mechanism emerges from our studies in which ring opening and nucleophilic attack are promoted by the phosporic acid in a single step. A model for enantioselectivity has been developed to account for the sense of selectivity for this synthetic transformation.

Advisor: Paton, R
Halogen and hydrogen bonding host structures for anion recognition and ternary complexes for modulating luminescent output

This thesis describes the synthesis and anion recognition properties of a series of halogen and hydrogen bonding acyclic and interlocked host receptors and the use of the inclusion supramolecular chemistry of cucurbit[n]uril derivatives in switchable luminescent output.
Chapter 1 introduces the field of anion supramolecular chemistry and the properties of cucurbit[n]uril macrocycles which pertain to the research detailed in subsequent chapters.
Chapter 2 describes the synthesis and anion recognition properties of a new class of chelating, halogen and hydrogen bonding host molecules. The halogen bonding enhanced selectivity for the Br- anion is demonstrated.
Chapter 3 probes the anion recognition characteristics of a series of novel halogen and hydrogen bonding motifs. Evidence for intramolecular hydrogen bond enhanced halogen bonding recognition of halides is presented and the selective recognition of the anion H2PO4- by a [3]rotaxane host is displayed.
Chapter 4 discusses the redox-mediated modulation of the luminescent output of a series of visible and near-infrared emitting lanthanide complexes within cucurbit[8]uril based ternary complexes.
Chapter 5 describes the experimental procedures and characterisation of the compounds presented in Chapters 2-4.
Chapter 6 summarises the conclusions of this thesis.

Keywords: Lanthanide Luminescence
Chemistry
Halogen Bonding
Anion Supramolecular Chemistry
Ternary Complexes
Advisor: Beer, P
Investigating low cost hole transporting materials for perovskite solar cells

Organic-inorganic halide perovskites (CH3NH3PbI3) have attracted strong attention of photovoltaic research community since 2012, benefiting from the low cost of organolmetal halide perovskite precursors and their simple solution processability. However, the chemical instability of this material, especially in high humidity environment, restricts its photovoltaic application in industry. This thesis is focusing on employing novel hole transporting materials (HTMs) for perovskite solar cells (PSCs). Besides their main responsibility acting as a hole selective layer increasing the photovoltaic performance, HTMs can also play an additional role serving as moisture blocking layers, enhancing the stability of PSCs.
Chapter 2 presents the general background knowledge of the physics of solar cells, delving deeper into the working principle of PSCs and related researches about the HTMs and stability of the devices. In chapter 3, the device fabrication techniques and the characterization methods used are presented in details. Commencing from chapter 4, the application of two kinds of HTMs and related studies are discussed. Chapter 4 demonstrates the use of a p-type organic material, PEDOT, on 'regular' structured PSCs, achieving devices with decent power conversion efficiency (PCE) but relatively huge hysteresis and low stabilized power output (SPO). Stability analysis shows this organic material provides a better protection of the perovskite film comparing to that of doped Spiro-OMeTAD, which is the most generally used HTM. Chapter 5 presents a study about CuSCN, an inorganic p-type semiconductor, being applied in PSCs as HTM. The CuSCN based devices show comparable performance to that of Spiro-OMeTAD based devices, but an interfacial degradation mechanism is found to facilitate the perovskite degradation even in inert atmosphere. A facile sealing protocol is established to deal with this problem, leading to super stable photovoltaic devices under thermal stressing. The following chapter 6 demonstrates a CuI doping technique to improve the hole transporting effectiveness of CuSCN layer. This doping technique modifies the morphology of CuSCN film and leads to a substantial improvement in the photovoltaic performance.

Keywords: Photovoltaics
Perovskite
Solar cells
Hole transporting materials
Advisor: Snaith, H
Isotopes in the landscape

This thesis deals with the development of farming landscapes in the Thames Valley from the Neolithic to the Roman period (4000 BCE – 410 CE). The focus is on the major domestic animal species, cattle, sheep and pig, and their roles in the agroecosystem, traced using carbon and nitrogen isotope ratios measured in collagen. The large dataset of faunal isotope values from a limited area, obtained from sites with extensive archaeological and environmental information, allowed a thorough characterisation of variability in isotope values, within and between species, sites, archaeological periods, and landscape regions.
Isotope ratios in a flock of modern sheep showed less variability than archaeological assemblages. Linear mixed models were used to analyse variation in isotope values in 1490 archaeological samples from 23 sites. The pattern of change over time differed for cattle, sheep and pig, reflecting both wide-scale environmental change and changes in animal management. δ13C values of cattle and pigs reflected the loss of primary closed-canopy woodland. Pig management changed from an emphasis on woodland resources to a closer association with settlement and consumption of anthropogenic waste. Herbivore δ15N values probably reflect variations in the intensity of pasture use and association with arable farming. Climatic cooling since the post-glacial thermal maximum cannot explain these varied trajectories of change.
Variation between sites in faunal isotope values was related to landscape regions. Faunal isotope values at individual sites were useful in site interpretation in the context of other evidence. The trend in pig and cattle δ13C values with time was widely found in the UK, as expected if it represents forest clearance. In the Neolithic, cattle management was similar to the UK at central and eastern European Neolithic sites, but pig management was different.
Patterns of faunal isotope values and their changes over time, analysed in the context of archaeological and environmental information, can contribute to the interpretation of sites, and give a unique perspective on changes in farming practice and their effects on the landscape.

Keywords: Environmental archaeology
Romano-British
Domestic animals
Nitrogen--Isotopes
Archaeology
Bronze age
Carbon--Isotopes
Neolithic period
Isoscapes
Iron age
England--Thames Valley
Advisor: Hedges, R
Lee-Thorp, J
Lock, G
French lute-song, 1529-1643

A study of French-texted solo songs and duets with lute or guitar accompaniment notated in tablature, dating from the sixteenth and seventeenth centuries. Connected repertoires include the Parisian chanson, psalm, voix de ville, dialogue, and air de cour. Sources are examined in terms of their background, composers represented in them, relationship to concordant and other musical sources, repertoire, and musical conception. Foreign and manuscript sources are included. Literary references indicating the status of sixteenth-century lute-song, its importance to humanists (including its role in the Académie de Poésie et de Musique), and its position in theatrical works, are considered. Issues of notation, musical and poetic form, prosody, rhythm, ornamentation, lute pitch and tuning, relationship to polyphonic versions, to the ballet de cour, to dance forms, and to solo instrumental styles such as stile brisé are examined. Early references to continuo practice and to the theorbo are noted. Several arguments are developed, including 1. that the sixteenth-century Le Roy publications were conceived primarily as solo lute music, 2. that from the late sixteenth-century onwards lute-songs were initially conceived as melody-bass outlines, and may to an extent be regarded as continuo realisations, and 3. that rhythmic features of the air de cour commonly related to the influence of musique mesurée may also be explained with reference to earlier attempts to adapt the voix de ville to humanist goals, and also to the influence of the Italian villanella. Includes tables and bibliographies. Musical examples, facsimiles, and transcriptions are included in a separate volume.

Keywords: song
lute
French
guitar
music
The piety and charity of London’s female elite, c. 1580-1630

Why was an ideal of elite women's virtue promoted in London c. 1580-1630, and why was it based on their reformed piety and charity? To what extent can elite women’s piety and charity reveal their religious identity, among an elite characterised as 'puritan' by contemporaries and historians? How did women practise piety and charity in a worldly City, and did they share a civic ethos?
This thesis engages with historiographies of urban history, the history of charity and hospitality, and gender history. It concerns over 400 wives and widows of the 331 aldermen elected 1540-1630, and uses 78 widows' wills. Women’s wills are analysed qualitatively save to consider widows' public charitable bequests. From preambles to exceptionally diffuse bequests, wills are an intimate source for studying women’s religious identity through their piety and charity. They reveal women's understanding of their gender in a patriarchal society that fostered an attitude of sorority that is particularly evident in women’s charity and hospitality.
To study the piety and charity of aldermen’s wives extra-testamentary personal evidence complements the wills. Sources written by women themselves include a household book used to reconstruct a woman's charity and hospitality, portraits, devotional works and letters. Sources of praise and abuse authored by men including Stow's Survay, funeral sermons, verse libel and verbal abuse are used to reconstruct ideals and antitypes of elite female virtue and hypocrisy, and are read critically in comparison with other sources to furnish evidence of female piety and social conduct. Chapter II-VII focus on the conforming female elite, comparing contemporary discussion of female piety, charity and religious identity to women's lives and practice in the household and the community, and Chapter VIII considers three Catholic women to ask to what extent the civic ethos shared by reformed City women could accommodate even their recusant kinswomen.

Advisor: Brigden, S
Archer, I