VictorJuiz/thesis huggingface dataset:
Natural product inspired synthesis of cysteine-derived tetramates for antibacterial activity
Keywords: Natural product
Tetramic acid derivatives synthesis
Antibacterial activity

This thesis describes the synthesis and evaluation of cysteine-derived tetramate (pyrrolidine-2,4-dione) derivatives for the development of novel antibacterial drugs.
Chapter 1 gives a brief overview of the history of antibiotics and clinically available antibacterial drugs. It addresses the need for novel antibacterial drugs due to the emergence of bacterial resistance. While exploring different chemical approaches to tackle the problem of drug resistance, it highlights the re-emergence of natural products as a crucial source for drug development. In particular, it focuses on tetramic acid containing natural products and discusses their value in antibacterial drug discovery, their properties and synthesis. In the end, it exposes the need for optimisation of cysteine-derived tetramates due to their apparent reduction of antibacterial activity when tested in vitro in the presence of blood, hence establishing the hypotheses and aims of this project.
Chapter 2 describes the synthesis, structural and brief antibacterial evaluation of a library of cysteine-derived tetramates with increased hydrophilicity by incorporation of pendant heterocyclic rings. An effective synthetic protocol for accessing polar tetramate derivates is established and a computational study has developed detailed understanding of the controlling factors of the key Dieckmann cyclisation step. Direct evidence of strong metal chelation in these tetramate systems is also demonstrated.
Chapter 3 and 4 discuss chemical modifications on cysteine-derived tetramates to modulate their metal chelation property. Structural dependency of the metal binding ability is established, with a library of cysteine-derived tetramates exhibiting evidence for reduced metal chelation. The antibacterial activity of these tetramates is evaluated in relation with their metal binding ability.
Chapter 5 provides a detailed biological evaluation of the synthesised cysteine-derived tetramates with regard to their antibacterial potency, physiochemical properties and metal chelation ability. The potential for multi-targeting mechanisms coupled with a low cytotoxicity is also briefly addressed. It demonstrates the types of structural modifications possible to assess hydrophilic cysteine-derived tetramates with reduced metal chelation, while preserving their selective Gram-positive activity with MIC against MRSA < 8 μg/ml.
English literature and the invention of atheism, 1564–1611
Keywords: fictive writing
Atheism
Douay–Rheims Bible
Reformation
Cicero
Henry Smith
Christopher Marlowe
prose fiction
George Gifford
Machiavellianism
Philippe Du-Plessis-Mornay
William Bullein
Secularisation
construction of interiority
William Rainolds
William Whitaker
ethos
influence of Marlowe
rhetorical invention
religious polemic
John Lyly
Philip Sidney
invention of atheism
Gregory Martin
prosopopoeia
Scepticism
separatism
disputations
puritanism
translation
Epicureanism
inward/outward atheism
Calvinism
morality drama
classical rhetoric
Catholicism
fictional dialogues
Unbelief
classical reception
Cyril Tourneur
Renaissance

By the 1580s, Western European writers were discussing atheism with increasing urgency. The Greek term ἄθεος and its Latin equivalent atheos had largely fallen out of use since the decline of the Roman Empire. When these terms were readopted in the early sixteenth century, first by writers in France and soon after in Germany, Italy, and the British Isles, they immediately gained currency, becoming central to political, religious, and literary discourses. This thesis examines writing about atheists and atheism in sixteenth-century England from the 1560s to the early seventeenth century. Rather than seeking historical evidence for rising levels of ‘real’ atheism during this period, this thesis explores the role of literature in ‘inventing’ atheism as a cultural category. I use ‘unbelief’ to refer to lack of belief in the existence of God or gods and argue that ‘atheism’ is a conceptualisation of unbelief explicitly developed to attack and discredit unbelievers. Following an initial survey of the histories of atheism and unbelief, I examine the objectives and rhetorical strategies of three forms of writing in which the development of early modern conceptions of atheism is most visible. Firstly, dialogues with fictive atheists written by John Lyly, George Gifford, and Philip Sidney; secondly, the religious polemics of William Whitaker, William Rainolds, and Henry Smith; and finally, dramatic representations of atheism by Christopher Marlowe. These chapters demonstrate that atheism is a hostile designation of unbelief which emerged in response to post-Reformation anxieties about religious division and the recovery of ancient philosophies of unbelief, such as Epicurean annihilationism and Stoic pantheism. Ultimately, this thesis shows how literary techniques that allow motives and inner convictions to be inferred as ‘character’ and ‘voice’ contributed to the emergence of the atheist as a powerfully imagined cultural presence in dialogues, plays, and polemics.
Childhood divided: child soliders and gang members in the Western imagination
Keywords: socio-legal
childhood
child soldiers
gangs

In many parts of the world, child soldiers are widely understood as innocent victims in need of international protection, while young gang members are viewed as deviant agents in need of state control and punishment. Yet many young people join these groups for very similar reasons. This thesis asks how these opposing images emerged in the United States and United Kingdom and what might explain their divergence. It first considers what is known about the realities of children who join groups that engage in violence. In doing so, it undermines common assumptions about forced recruitment vs. volunteerism and illustrates how many child soldiers and young gang members are motivated by parallel societal, community, interpersonal, and individual factors. It then traces the ways in which child soldiers and young gang members have been portrayed from the 16th to early 21st centuries, showing how the perception and treatment of these figures has changed drastically over time, shaped and reshaped amidst debates about human nature, changing political and economic realities, and shifting group and state interests. Finally, it explores how laws, government rhetoric, and academic work portray child soldiers and young gang members today (2018- 2020), examining dominant narratives and identifying potential cracks in those frameworks. The analysis ultimately reveals how one society can construct two opposed images of childhood based primarily on adult interests, ideas, and insecurities, as well as how those simplistic constructions can impact the worlds of young people themselves. Overlooking the parallels between child soldiers and young gang members risks not only perpetuating those inaccuracies, but also overlooking broader social, racial, and economic inequalities that at once shape and transcend both figures.
Temporal expectations in the context of spatial expectations and stimulus competition
Keywords: neuroscience
cognition
attention

With this thesis, I investigated the effects of combined temporal and spatial expectations. In addition, I examined temporal expectations in the context of spatially and temporally competing distractors. In a parallel line of research, I studied the effects of aging on these functions. In Chapter 1, I introduce the subject of temporal expectations, review how they interact with other top-down biases, and argue why they should be investigated in the context of distraction. I also review theories of cognitive aging and motivate the investigation of age-related changes in the context of the main subjects of this thesis. In Chapter 2, I show that both behavioural performance and neural markers of pre-target processing can be modulated flexibly and beneficially by combined temporal and spatial expectations. I also show that neural markers of expectation seem to have behavioural relevance, and that temporal and spatial expectations can interact both neurally and behaviourally, when lateralised effects are investigated. I further demonstrate that aging compromises lateralised effects of spatio-temporal expectations. In Chapter 3, I show that perceptual effects of temporal expectations on stimulus competition depend on the stimulus context. Temporal expectations act independently of competition when stimuli are presented in different hemifields but can impair performance with intrahemifield competition. I further show that aging can spare the ability to suppress irrelevant information, and that older adults benefit from temporal expectations. In Chapter 4, I explore the effects of temporal expectations for a target stimulus when stimuli compete over time. I show that target-related behavioural performance can be increased, and pre-target distractor representations relatively decreased. In Chapter 5, I draw commonalities and differences across experimental Chapters 2-4, discussing temporal expectations in the context of isolated and competing stimuli, the relevance of lateralised effects of temporal expectations, age-related findings, and future questions and directions for research.
Small molecule reactivity of zirconocene hydrazides, imides and silylamides
Keywords: hydrazide
boranes
zirconocene
small molecule reactivity
silylamide
alkynes
imide
silanes

This thesis reports the reactivity of zirconocene hydrazides, imides and silylamides, as well as the reactivity of titanium permethylpentalene complexes. Particular focus is paid to the reactions of hydrazides and imides with boranes and silanes, and reactions of silylamides with terminal alkynes, boranes and silanes.
Luís Fróis’s História de Japam: aims and methods
Keywords: Jesuit's letters
Japanese mission
Luís Fróis
Society of Jesus
História de Japam
Japan

The focus of the thesis is the work of the Portuguese Jesuit missionary Luís Fróis (1532-97). It refutes the view of the historiography that has considered his magnum opus the História de Japam, produced between 1584-93, as bona fide and as one of the most reliable sources on the basis that he was often either a protagonist or an eyewitness of the events that he relates. As it will be shown in this work, Fróis is selective in the manner in which he deletes, adds or avoids facts, or simply creates narratives purposefully composing an edifying account. Fróis takes the opportunity to put forward his view of the mission by fusing history and sacred rhetoric, such as the use of rhetorical devices, to elevate the volume of the message that had previously been recorded in the Jesuits’ correspondence, or sometimes silencing it completely. For this reason, I argue that Fróis should be considered not only the first historian of the mission, but also the first editor of the history of the Japanese mission by writers who took part in the evangelisation of this country. Through the reading of Fróis’s História there is an underlying theme of the ‘opposite cultures’ between Japan and Europe. This is not so much born out of a fascination with a very different culture, as some historians have alluded, but my readings are rather that it serves in justifying the Jesuit’s controversial method of accommodation implemented at the time in the archipelago. It also signals to a belief of the incommensurability between these cultures, reflecting on a decrease in the dialogue and the beginning of an increase in the distancing between these societies.
In the História anything that is controversial or could depict the missionaries in a bad light is avoided or minimised; the Jesuits’ errors are usually blamed on their enemies. The theme of diabolism is closely analysed, and it is concluded that it serves rhetorically to exonerate the missionaries’ failings and as a reflection of a true conviction in the sixteenth century of the Devil’s presence among pagans.
Viscoelasticity of upper mantle utilizing high-resolution techniques
Keywords: viscoelasticity
transient creep
amplitude-dependent attenuation
low-temperature plasticity
apparatus compliance
dislocation damping
single-crystal olivine

In this study, we developed a high-temperature, uniaxial creep apparatus to investigate the nonlinear viscoelasticity of geological materials at a wide range of temperatures (room temperature to 1330°C), frequencies (0.01 Hz to 100 Hz), and bias stresses (maximum load of 5 kN). This apparatus allows us to conduct creep tests (i.e., constant bias stress) and forced oscillation tests simultaneously, and these capabilities allow us to investigate viscoelastic phenomena relevant to postseismic relaxation, glacial isostatic adjustment, and tidal dissipation in exoplanets.

We characterize the complex spring compliance of the apparatus by conducting several calibration experiments using single-crystal sapphire. Based on experiments conducted on sapphire samples with different lengths, we demonstrate that the apparatus compliance is dependent on frequency and sample length, but not on the oscillation amplitude or bias stress. We validate this calibration by measuring the viscoelastic properties of aluminum and stainless steel and comparing our results to previously published results at similar conditions. Based on this calibration, we constrain the parameter space within which reliable measurements of attenuation and Young’s modulus can be made with this apparatus.

We use this newly calibrated apparatus to conduct a series of experiments to examine viscoelasticity in single-crystal San Carlos olivine. Our results reveal that an increase in the bias stress causes an increase in attenuation, demonstrating that attenuation increases with increasing dislocation density. The magnitude of attenuation ranges from 0.1 to 100, and the Young’s modulus ranges from 40 GPa to the unrelaxed modulus. These experiments demonstrate that the critical stress amplitude demarcating the transition from linear to nonlinear viscoelasticity is approximately at ~1 MPa. Furthermore, these experiments exhibit a peak in attenuation as a function of stress amplitude at approximately 1.2 MPa stress amplitude, although the position of the peak depends on the bias stress and temperature.

The shape of hysteresis loops is inconsistent with models for attenuation based on dislocation breakaway from point defects. Instead, we suggest our data are consistent with nonlocalized friction models in which the restoring force is controlled by the backstress associated with the long-range stress fields of dislocations and the onset of nonlinear dissipation is controlled by the plastic yield strength of olivine.
Learning visual concepts with fewer human annotations
Keywords: Object Recognition
Machine Learning
Weakly-supervised Learning
Unsupervised Learning
Computer Vision
Artificial Intelligence
Neural Physics

This thesis explores the use of modern deep neural networks to learn visual concepts with fewer human annotations on data. While data is abundant and increasingly easier to collect, most deep learning methods need extensive human labelling to be trained, which is often costly and may require expert-level knowledge. In this thesis we explore alternatives to human labelling by considering synthetic data, as well as partially and completely unlabelled data. We will study these alternatives within two visual concepts related to human-level intelligence: intuitive physics and object recognition. For the former, we will focus on synthetic and unlabelled real sequences while for the latter we will focus on collections of images of natural categories that are scarcely annotated.
The first part of this thesis explores the ability of recent convolutional neural networks to learn physics through long term prediction. We first show that from limited visual data it is possible to make accurate future predictions of systems obeying the Newton’s laws of physics. We propose to work on more complex synthetic and real data than standard benchmarks. For real data, we also develop an automatic self-supervised labelling method. Second, we propose a meta-learning pipeline that is able to infer environment properties from past experiences without any need for annotations. In particular, this understands causal concepts such as solidity. To conclude our work on physics we explore physical plausibility. Inspired from recent research on neural physics, we propose a generative architecture with a structured latent space that works on unlabelled data. Our model is not only quantitatively superior to prior art but has also a deeper understanding of the relations between objects in a scene.
The second part of this thesis is dedicated to object recognition. We consider the realistic scenario where data annotation is incomplete i.e lots of images are unlabelled. We make contributions in three different scenarios with decreasing levels of annotations. For each of them, we strongly advocate a systematic use of self-supervision as a pre-training step as well as self-training in the last step of training. We first introduce a novel semi-supervised learning method which performs optimisation alternatively on labelled and unlabelled data. Albeit simple, our method can work with as few as ten labelled instances per class. Next, we develop a clustering method that is initialised from supervision on other datasets. Clustering is then performed thanks to a new way of extracting pairwise similarity between two images: by comparing the rank of the most activated neurons of their network embedding. Finally, we extend the use of pairwise similarity to the nearest neighbours in the network embedding space and propose a clustering method that works without any supervised signal on different types of data.
Cavity optomechanics with nm-thick membranes
Keywords: Thermodynamics
NEMS and MEMS
Quantum Foundations
Cavity Optomechanics

This thesis focuses on fast and sensitive readout of mechanical motion to answer questions in the foundations of physics. By coupling a silicon nitride membrane to different readout cavities I have explored the thermodynamic costs of time keeping and carried out a bench-top experiment to put bounds on the theory of classical channel gravity. In order to reach these aims, I have developed real time displacement measurements of the motion of a nm-thick silicon nitride membrane. For this, a lumped element LC circuit is capacitively coupled to the metallized silicon nitride membrane. This approach allows for the estimation of key parameters without the need for frequency matching or cryogenic cooling. I demonstrate electromechanical characterization of several mechanical modes of the silicon nitride membrane. In addition, I show optomechanically induced transparency on chip in this high loss cavity.
The real time displacement measurements of the membrane’s motion allow the device to be operated as a thermomechanical clock and to be used to investigate a thermodynamic trade-off in a nanoscale clock. The system follows a trade-off derived for the idealised quantum setting, indicating a fundamental universality of a relation previously predicted to hold in the quantum regime.
This system is compatible with cryogenic temperatures, allowing me to actuate and detect the resonance frequency of a membrane at low temperatures. At these temperatures, one can perform tests of the theory of classical channel gravity which models the gravitational interaction as a classical measurement channel. The theory predicts a density dependent heating effect due to the gravitational interactions within the membrane itself. Bounds could be put on this theory using a membrane capacitively coupled to a 3D superconducting microwave cavity which has a much higher Q factor than the LC circuit. With this cavity, I achieved 10 mHz resolution of the mechanical signal, which is required for an accurate estimation of the mode temperature and thus to put bounds on the theory.
Efficient methods for simulating stochastic reaction-diffusion models on evolving domains
Keywords: reaction-diffusion master equation
mathematical biology
stochastic modelling

Mathematical modelling of complex biological phenomena allows us to under- stand the contributions of different processes to observed behaviours. Many of these phenomena involve the reaction and diffusion of biomolecules and so we use so-called reaction-diffusion models to describe them mathematically. By discretising space into compartments and letting system dynamics be governed by the reaction-diffusion master equation, it is possible to derive and simulate a stochastic model of reaction and diffusion on an arbitrary domain. However, there are many implementation choices involved in this process, such as the choice of discretisation and method of derivation of the diffusive jump rates, and it is not clear a priori how these affect model predictions.
To shed light on how model implementation choices affect simulation results, in this thesis we explore how a variety of discretisations and methods for deriva- tion of the diffusive jump rates affect the outputs of stochastic simulations of reaction-diffusion models, in particular using Turing’s model of pattern forma- tion as a key example. While only minor differences are observed for simple reaction-diffusion systems, there can be vast differences in model predictions for systems that include complicated reaction kinetics, such as Turing’s model of pattern formation.
To date, very few works have considered domain growth for stochastic models. Hence, we consider both static and uniformly growing domains and demon- strate that domain growth can impact how the different diffusive jump rates affect simulation results. Furthermore, we consider discretisations of the do- main using complex meshes. Using complex meshes allows models to cap- ture geometric characteristics of a system. We investigate the effects of using complex meshes and the corresponding choices of diffusive jump rates on sim- ulation results. This thesis highlights that care must be taken in using the reaction-diffusion master equation to make predictions as to the dynamics of stochastic reaction-diffusion systems.