VictorJuiz/thesis huggingface dataset:
Assessing sensorimotor plasticity with multimodal magnetic resonance imaging
Keywords: Somatosensory cortex
Motor Cortex
Plasticity

The sensorimotor network receives a rich variety of somesthetic afferents and outputs considerable motor efferents, both of which drive experience-dependent plasticity in the system. It remains unclear to what extent subtle changes in somaesthesis and motor function extrinsic to the brain drive plasticity in the functional organisation and anatomy of the sensorimotor network. This thesis contains a series of multimodal MRI experiments to investigate how altered-use and disuse can induce plastic changes in the sensorimotor network of the human brain.
In Chapter 3, a method of mapping digit somatotopy in primary somatosensory cortex at the single-subject level using 7.0 tesla fMRI was developed and applied for a study of healthy participants. Using a phase-encoding paradigm, digit representations were accurately mapped in under 10 minutes. These maps were reproducible over time and comparable to a standard block design.
In Chapter 4, a further fMRI study assessed the potential for short-term reorganisation of digit representations in primary somatosensory cortex following a manipulation whereby the right index and right middle fingers were glued together for 24 hours. There was a marked shift in the cortical overlap of adjacent digits after the glued manipulation, not seen across an equivalent control period, providing strong evidence for short-term remapping of primary somatosensory cortex.
In Chapter 5, a patient study investigated plasticity associated with chronic unilateral disuse of the upper limb. A cross-sectional comparison with control participants showed reduced grey matter density in the posterior right temporoparietal junction, and increased radial diffusivity in the white matter of the right superior longitudinal fasciculus, consistent with change in the right ventral attention network. A complementary longitudinal study in Chapter 6 investigated structural plasticity associated with rehabilitation of the disused limb. There were localised increases in grey matter density, notably in the right temporoparietal junction, further implicating a potential role for regions responsible for egocentric attention in regaining upper limb use.
In Chapter 7, a further patient study investigated candidate predictive biomarkers at the sub-acute stage of stroke recovery, identifying CST-lesion cross-section and sensorimotor network strength as correlates of motor function, which warrant further study.
The results of the studies presented in this thesis provide a novel insight into the nature and time frame of functional and structural plasticity associated with altered use and disuse. Further study of how subtle changes in our sensory and motor use shape the sensorimotor network is warranted, particularly in the context of disuse in non-neurological clinical populations.
The detection, structure and uses of extended haplotype identity in population genetic data
Keywords: ancestry
haplotype estimation
identity by descent
extended haplotype sharing

In large-scale population genomic data sets, individual chromosomes are likely to share extended regions of haplotype identity with others in the sample. Patterns of local haplotype sharing can be highly informative about many processes including historical demography, selection and recombination. However, in outbred diploid populations, the identification of extended shared haplotypes is not straightforward, particularly in the presence of low levels of genotyping error. Here, we introduce a model-based method for accurately detecting extended haplotype sharing between sets of individuals from unphased data. We describe two implementations of the algorithm that can be applied to data sets consisting of thousands of samples. The method leads naturally to an approach for statistical haplotype estimation, which is shown to be comparable in accuracy to current methods. By applying the method to genome-wide SNP data from over 5,000 samples from the UK we show that the N50 maximal haplotype sharing between unrelated samples is typically 2cM, consistent with a population history of rapid exponential growth that started approx. 125 generations ago. In contrast, within two Greek population isolates of approx. 700 individuals the N50 for maximal haplotype sharing is 12.5cM, while for an unrelated Greek sample of the same size the N50 is 1.3cM. By assessing the size and geographical distribution of maximal haplotype sharing within and between all Greek cohorts, we make inference on the extent of isolatedness of each cohort and on recent migration. We additionally date recent coancestry to about 10 generations for the isolates and 90 generations for the unrelated sample, and finnally attempt to date the time of divergence between them.
Gravity anomalies, flexure, and the long-term rigidity of the continental lithosphere
Keywords: gravity model
India
Te
inversion

The cause and distribution of spatial variations in the mechanical properties of the continental lithosphere are fundamental questions for modern geology. In this study variations in long-term lithospheric rigidity have been investigated. These investigations used profile- and grid-based flexural models of the lithosphere’s response to geologically imposed topographic, or buried, loads. These models were constrained by topographic and gravity data allowing recovery of best fitting rigidity values.
In Oman a Cretaceous ophiolite acts as a significant load on the continental crust. Flexural models along profiles orthogonal to the ophiolite strike show that the observed gravity data can be best modelled by an elastic beam with standard thickness (Te) of 30 km. Along strike there is shown to be significant variation in the foreland shape and the observed gravity signal. This, it is proposed, relates to the complex tectonic processes which occurred as the ophiolite was obducted.
The Himalayan foreland has been the focus of controversy over the recovered long-term rigidity of the continents, with recovered Te values ranging from 40 to over 90 km. Both profile- and grid-based techniques show that Te is high (>70 km) in the foreland region. Across the India-Eurasia collisional system as a whole Te values are variable. Beneath the Tibetan plateau recovered values are generally low (<10 km), while the plateau margins are marked by regions of higher rigidity.
Recovered Te values across the Arabia-Eurasia collisional system range from over 60 km in the foreland region to close to zero beneath the high Zagros mountains. In the eastern part of the foreland, flexural models match the gravity data; however, they disagree with sediment thickness data for the material infilling the foreland. This discrepancy is interpreted in terms of de-coupling of the flexural lithosphere from the shallower crustal levels, caused by the presence of significant salt deposits in this region.
Application of grid-based techniques to South America, North America and Europe recover a broad range of Te values from ∼0 to over 90 km. The low Te values are explained in active orogenic belts in terms of current processes acting to weaken the lithosphere, and in the continental interiors as the relics of past orogenic events. High Te values in the continental interiors correlate with ancient cratonic cores which have undergone little deformation since their formation in the Archean.
This study shows that Te variations have a critical influence on the development of large compressional orogenic belts. In the Himalayan and Andean orogens there is a correlation between the over-thrusting of the orogenic belt and high Te foreland regions. Where lower Te regions are seen, less over thrusting is apparent, and in the case of the India-Eurasia collisional system out-flow of lower crustal material may be occurring.
"'As I said to you before': Paul's witness to formative early Christian instruction
Keywords: early Christianity
catechesis
kerygma
formative instruction
St Paul

This study addresses the question of formative early Christian preaching and teaching. Unlike previous approaches, I eschew synthesis across a broad range and focus instead on the earliest extant Christian source: the letters of Paul.
My method draws on ancient communication practices, primarily represented in ancient rhetoric, wherein communicators rely on knowledge they presume their interlocutors to possess. Passages are analyzed according to the type of appeal to Paul's initial teaching: (1) explicit reminders of previous teaching, (2) direct appeals to knowledge not explicitly linked to previous teaching, and (3) indirect appeals to knowledge about practices, beliefs, conventions, etc.
The reconstruction focuses on 1 Thessalonians, 1 Corinthians and Romans. 1 Thessalonians and 1 Corinthians represent neophyte and well-established Pauline communities, respectively, while Romans is of interest because it represents non-Pauline believers.
I proceed with a comparative analysis of 1 Thessalonians and 1 Corinthians. Chapter 4 lays out the rhetorical situation for these letters while chapters 5-7 investigate the three types of appeal respectively, each closing with a comparison of similar material in each letter. Chapter 8 summarizes and concludes this discussion, providing the basis for my subsequent analysis of Romans.
Finally, I compare the picture from the Thessalonian and Corinthian communities with Paul's letter to the Romans (chapter 9). Topics he expects his Roman audience to know indicate points of expected congruence between Paul's own teaching and that of others. By contrast, topics that receive significant expansion in Romans suggest perceived potential for conflict.
In this dissertation I identify consistent elements of early Christian instruction, ranging from Christology to apocalyptic cosmology, while also noting possible conflict. My approach places the reconstruction of early Christian teaching on firmer methodological footing than previous attempts have done and offers a rhetorically sensitive account of the teaching and how it was used.
Reconstructing North-West African palaeoclimate from speleothem geochemistry: past climate variability and implications for human history
Keywords: palaeoclimate
proxy development
climate change
stalagmite
Morocco
speleothem
cadmium
Sahara
North Africa

Climate north of the Atlas Mountain belt in NW Africa is dominated by extratropical disturbances. However, climatic controls to the south, where climate transitions from extratropical to tropical regimes, are poorly understood due to a paucity of both instrumental and palaeoclimate data. In this thesis past climate change between the High Atlas Mountains and Sahara Desert is reconstructed using the stable isotopic composition and radiometric dating of speleothems. A high-resolution record from the mid-Holocene and a discontinuous record covering the past 400,000 years are developed. Supplemented by U-Th dating of a further four samples, these records indicate increased humidity in this area concomitant with the wider African Humid Period, and indicate a link between the West African Monsoon and humidity north of 30°N. Reconstructed glacial-interglacial scale increases in humidity overlap with "green Sahara" conditions and evidence a recurrent humid corridor connecting NW Africa and the central Sahara that is highly relevant to discussions of prehistoric human migrations. Evidence for a strong influence of high-latitude and solar forcing on decadal to millennial time- scales in this area is also presented. Further to this work, the potential of cadmium-to-calcite ratios as a novel proxy for palaeo-hydrology is confirmed using an annually-resolved trace element, stable isotope and calcite fabric dataset from a North Moroccan stalagmite. The first measurements of cadmium-to-calcite ratios in natural speleothem are here presented, and the palaeoclimatic significance and potential of this proxy for aiding the quantitative reconstruction of changes in calcite precipitation behaviour are demonstrated.
Charge transfer of Rydberg hydrogen molecules and atoms at doped silicon surfaces
Keywords: Jellium
image-charge
Rydberg

The work of this thesis focuses on the interaction of high Rydberg states of hydrogen molecules and atoms with various doped Si semiconductor surfaces with the results compared with those obtained with an atomically flat gold surface. The major part of the thesis was carried out using para-H₂ molecular Rydberg states with principal quantum number n = 17 - 21 and core rotational quantum number N⁺ = 2. Subsequently, this study was continued using H atomic Rydberg states with principal quantum number n = 29 - 34. The high Rydberg states have been produced using two-step laser excitation. For close Rydberg surface separation (< 6 n² a.u.), the Rydberg states may be ionized due to an attractive surface potential experienced by the Rydberg electron, and the remaining ion core may be detected by applying an external electric field.
An efficient ion detectability method is introduced to compare the many surface ionization profiles quantitatively. The p-type doped Si surfaces enhance the detected ion-signal more than the n-type doped Si surfaces due to the presence of widely distributed positive dopant charge fields in the p-type doped Si surfaces. As the dopant density increases, the area sampled by the resultant ions becomes effectively more neutral, and the decay rate of the potential from the surface dopant charge with distance from the surface becomes more rapid. Therefore, the minimum ionization distance is also reduced with increasing dopant density. It is found that the detected ion-signal decreases with increasing dopant density of both p- and n- type doped Si surfaces. The higher-n Rydberg states have shown higher ion detectability than that of lower-n Rydberg states and this variation also becomes smaller when increasing the dopant density.
Experiments involving H2 Rydberg molecules incident on various doped Si surfaces in the presence of a Stark field at the point of excitation are also presented here. The surface ionization profiles produced via both electron and ion detection schemes are measured by changing the Stark polarization. Positive surface dopant charges oppose production of backscattered electrons and negative surface dopant charges enhance the electron-signal. For the electron detection scheme, lightly doped n-type Si surfaces show higher detectability but in the case of p-type Si surfaces the more heavily doped Si surfaces give a higher detected signal. This different behaviour of the detected ion or electron signal implies a different production mechanism.
Theoretical trajectory simulations were also carried out based on a new 2D surface potential model. The results qualitatively agree with the experimental results and explain the changes of the surface ionization profiles between the various dopant types and dopant densities of the Si surfaces.
Single molecule studies of F1-ATPase and the application of external torque
Keywords: molecule
interferometry
trap
tweezer
molecular
back
rotation
biophysics
single
assay
motor
optical
study
F1
laser
focal
plane
ATP synthase
rotary

F1-ATPase, the sector of ATP synthase where the synthesis of cellular ATP occurs, is a rotary molecular motor in its own right. Driven by ATP hydrolysis, direct observation of the rotation of the central axis within single molecules of F1 is possible. Operating at close to 100% efficiency, F1 from thermophilic Bacillus has been shown to produce ~40pN&dot;nm of torque during rotation.
This thesis details the groundwork required for the direct measurement of the torque produced by F1 using a rotary angle clamp, an optical trapping system specifically designed for application to rotary molecular motors. Proof-of-concept experiments will be presented thereby demonstrating the ability to directly manipulate single F1 molecules from Escherichia coli and yeast mitochondria (Saccharomyces cerevisiae), along with activation of F1 out of its inhibited state by the application of external torque.
Despite in-depth knowledge of the rotary mechanism of F1 from thermophilic Bacillus, the rotation of F1 from Escherichia coli is relatively poorly understood. A detailed mechanical characterization of E.coli F1 will be presented here, with particular attention to the ground states within the catalytic cycle, notably the ATP-binding state, the catalytic state and the inhibited state. The fundamental mechanism of E.coli F1 appears to depart little from that of F1 from thermophilic Bacillus, although, at room temperature, chemical processes occur faster within the E.coli enzyme, in line with considerations regarding the physiological conditions of the different species. Also presented here is the verification of the rotary nature of yeast mitochondrial F1. The torque produced by F1 from thermophilic Bacillus, E.coli and yeast mitochondria is the same, within experimental error, despite their diverse evolutionary and environmental origins.
Applications of calcium isotopes in marine carbonates in the Recent and Phanerozoic
Keywords: Cretaceous
Oceanic Anoxic Events
biomineralization
calcium isotopes
carbonate

The applications of calcium-isotope measurements in marine carbonates are explored in several different contexts within this thesis. As a record of global ion fluxes, seawater calcium-isotope ratios can be used as tracers for large weathering imbalances, which develop as a feedback system in response to intervals of climate change. This approach provides valuable constraints on the complex climatic and oceanographic phenomena known as the Oceanic Anoxic Events. Over much longer timescales, the calcium-isotope ratio of seawater is influenced by steady-state processes that reflect the evolution of seawater chemistry. To understand these influences, the modern calcium-isotope budget is assessed quantitatively using a compilation of marine carbonate samples, revealing several distinctive components of the carbonate burial sink that can affect the steady-state balance of the calcium cycle. Changes in the major ion composition of seawater and in the organisms that contribute to sedimentary carbonate burial are shown to contribute significantly to the geological record of seawater calcium-isotope ratios. The importance of skeletal carbonate in the calcium cycle leads to another application of calcium isotopes towards understanding biomineralization. This large and complex topic is approached with calcium-isotope data from two unique growth experiments that constrain some of the mechanisms by which biogenic aragonite acquires its geochemical signatures. This range of topics presents a diverse, but by no means exclusive, sample of the topics that are accessible for investigation through calcium-isotope analysis. The potential of this isotopic tool is demonstrated by the breadth of environments and timescales represented in this work.
Essays in economic and financial history
Keywords: demographic transition
LTCM
great crash
Leverage
industrial revolution
Malthus
financial crisis

Division One: “Malthus Gets Fat” (Two Chapters)
Chapter One develops a simple dynamic model to examine the takeoff from a Malthusian economy to a modern growth regime. It finds that several factors, most notably the rate of technological progress and the economic structure, determine the fastest rate at which the population can grow without declining living standards; this is termed maximum sustainable population growth. It is only when this maximum sustainable rate exceeds the peak rate at which a society expands that takeoff can occur. I also investigate the effects of trade and international income transfers on the ability to sustain takeoff. It is also shown that present income growth is not necessarily indicative of the ability to sustain takeoff and that factors which increase current income growth may actually inhibit takeoff, and vice versa.
Chapter Two applies the sustainable population growth framework to Britain during the Industrial Revolution. The model shows a dramatic increase in sustainable population growth at the time of the Industrial Revolution, well before the beginning of modern levels of income growth. The main contributions to the British breakout were technological improvements and structural change away from agricultural production. At least until the middle of the 19th Century, coal, capital and trade played a minor role.
Division Two: “Leverage and Financial Market Instability” (Four Chapters)
Chapter One develops a model of how leverage induces explosive behavior in financial markets. I show that when levered investors become too large relative to the market as a whole, the demand curve for securities can suddenly become upward-sloping as levered investors are exposed to forced liquidations. The size and leverage of all levered investors defines the minimum elasticity-adjusted market size for stability or MinEAMASS, which is the smallest elasticity-adjusted market size that can support the group of levered investors analyzed. This gives rise to a measure of instability that can predict when markets become vulnerable to a leverage-driven market liquidity crisis.
Chapter Two iterates the model of Chapter One forward in time to generate an inflating bubble that suddenly bursts, reproducing many of Kindleberger's (1996) stylized facts about the dynamics of bubbles in a simple framework.
Chapter Three applies my measure of instability in a historical investigation of the 1998 demise of hedge fund Long-Term Capital Management (LTCM). I find that a forced liquidation of LTCM threatened to destabilize some financial markets, particularly for bank funding and equity volatility.
Chapter Four discusses how the model applied to the stock market crash of 1929. There the evidence suggests that a tightening of margin requirements in the first nine months of 1929 combined with price declines in September and early October caused enough investors to become constrained that the market was tipped into instability, triggering the sudden crash of October and November.