VictorJuiz/thesis huggingface dataset:
Electrochemical analysis of natural aqueous media
Keywords: Electrochemical analysis
Electrochemistry
sensors

This thesis focuses on investigations of electroanalytical methods to study natural aqueous media particularly considering analyte quantification with high chloride levels (seawater) or low electrolyte concentrations (drinking water). The two extremes correspond to different voltammetric regimes where high ionic strength suppresses transport via ionic migration and the voltammetry is said to be ‘fully supported’ and mass transport is dominated by diffusion, whilst in the near absence of electrolyte diffusion is strongly coupled with migration.
The fundamentals of electrochemistry and the principles of electrochemical methods used in this thesis are introduced in Chapter 1. The chemistry of natural water is discussed in Chapter 2. Experimental methods and non-electrochemical based techniques including simulation software are described in Chapter 3.
The investigations of seawater and drinking water each consist of two chapters. In the study of seawater, Chapter 4 suggests the possible toxicity of silver nanoparticles in seawater is assessed in the light of studies of the oxygen reduction reaction on a silver electrode where the toxic superoxide was found to be produced as a reaction intermediate with a lifetime on the voltammetric timescale in seawater media. Chapter 5 builds on the work in Chapter 4 to realise a bespoke chemical sensor for chloride in seawater based on anodic stripping voltammetry of silver chloride in the very high ionic strength seawater medium.
On the other hand, the research in drinking water aims to sketch a methodology of chloride quantification to overcome current challenges in performing electrochemical experiments under low ionic strength conditions without the addition of extra electrolytes. Prior to sensor development, some fundamental studies were undertaken to characterise stripping voltammetry under low ionic strength conditions. First, the simulation and experimental investigation of the deposition and stripping voltammetry from ideal fully supported conditions (with a ratio of electrolyte concentration to analyte concentration ~100) to weakly support (electrolyte concentration: analyte concentration <100) and even self-support conditions (in absence of any supporting electrolyte) is discussed in Chapter 6. Then, deposition and stripping voltammetry is used in chloride analysis in self-support mineral water solution without added reagents (Chapter 7)
The effects of energetic substrate manipulation on myocardial metabolism and cardiac function
Keywords: heart failure
cardiology
metabolism
MRS
MRI

The healthy human heart uses fat and glucose as its predominant metabolic substrates, approximately in a ratio of 70% to 30%. In heart failure, substrate oxidation is decreased as is ATP production. Free fatty acid uptake and oxidation is reduced, while glucose uptake and glycolysis are increased, although pyruvate oxidation falls. This thesis set out to establish the links between myocardial substrate metabolism and function in the healthy and the failing human heart, at rest and at stress.
In chapter 3, an inhibitor of lipolysis, nicotinic acid, is compared to a lipid infusion in normal human subjects and in rats. While the lipid infusion increases cardiac contractility, a decline in both contractility and PCr/ATP ratio is shown with the nicotinic acid. This is revealed to result from inhibition in lipolysis combined with reduction in glucose stimulated insulin secretion, hence the heart is starved of energetic substrate, revealing metabolism’s importance and close link to contractile function.
In chapters 4 and 5, lipid infusion is further shown in the failing human heart to increase contractility and PCr/ATP ratio at rest as well as increasing maximum available cardiac work. It is demonstrated that the failing heart displays substrate flexibility with an ability to take up higher amounts of free fatty acids when their availability is increased and increase their uptake during rapid pacing stress. In addition, the failing heart is not shown to be oxygen starved and oxygen consumption increases during the lipid infusion without deleterious consequence.
In chapter 6, in normal human subjects, vasodilator stress with glyceryl trinitrate is shown to greatly increase myocardial ATP demand while inhibiting mitochondrial ATP production, creating a mismatch between supply and demand and resulting in a fall in PCr/ATP ratio. A higher baseline PCr/ATP is shown to be protective against stress induced changes, confirming the importance of PCr/ATP as a target for interventions.
Together, these data show myocardial metabolism is an important target for heart failure therapeutics and that it may be manipulated via increasing availability of free fatty acids.
Formal verification meets stochastic analysis
Keywords: recombination problem
stochastic analysis
formal verification

The thesis goal is to explore the relations between Formal Verification techniques in Computer Science and Stochastic Analysis in Mathematics. They both deal with probabilistic dynamical systems, implying that the number of connections is significant. The Formal Verification studies dynamical systems' properties, which are specified in terms of logic statements. This discipline has been successfully applied to multiple industry problems, such as
verification of'' Software, Microprocessors or Neural Networks. The models studied have a countable states space and this can be considered the main obstacle to extend Formal Verification techniques for the computation of likelihoods in the case of Stochastic Differential Equations. However, the most studied properties in Formal Verification have a clear characterization in Mathematics. In this thesis, we focus on the safety property
always'', which can be characterized as an exit time in the theory of Stochastic Analysis.
The main difficulties are twofold. Firstly, if we are particularly interested in discretizing the states space - going from a continuous, uncountable space to a finite countable one - it is very likely to have an explosion of the cardinality of the states space. This leads to problems both in time and memory complexity. We find a new characterization of the barycenter of a discrete probability measure, which allows us to introduce a new algorithm for the recombination problem. Then, we use the algorithm to build recombining trees in order to approximate weakly stochastic processes, solving the exponential explosion of the cardinality of the states space. Secondly, one has to consider the approximation error: if the probability to exit from a safety region has not an analytical closed-form, a numerical scheme must be considered and therefore it is important to analyse the error. We introduce a grid-free approach for the computation of Probabilistic Safety Regions using Malliavin Calculus.
Brain mechanisms underlying fatigue and its impact on the motivation to exert effort
Keywords: frontal lobe
fatigue
reward
magnetic resonance imaging
decision-making
choice behaviour
exertion
dopamine
ventral striatum
psychopharmacology
computational modelling
Parkinson's disease
effort
motivation

Fatigue, a feeling of tiredness or exhaustion, increases with effortful exertion and impacts motivation and performance. While healthy people typically recover during periods of rest, persistent forms of fatigue are a debilitating symptom in many medical conditions and in particular in Parkinson’s disease (PD). To date, the neural and computational mechanisms in the brain that underlie fatigue and its impact on the willingness to exert effort are still poorly understood. Using physical effort-based decision-making paradigms and trial-by-trial self-report ratings in combination with a novel computational model, functional Magnetic Resonance Imaging and pharmacological manipulation, this thesis addresses the following outstanding research questions: How are brain systems implicated in effort-based decision-making impacted by momentary levels of fatigue in healthy individuals (Chapter 2)? Do people prioritise effort or reward information before option selection and are these preferences associated with fatigue and motivation to exert effort (Chapter 3)? How does fatigue develop as a function of effort, rest and rewards (Chapter 4), and what are the specific effects of dopaminergic medication in PD patients (Chapter 5)? Finally, how closely linked are dynamic changes in fatigue ratings and in the motivation to exert effort (Chapter 6)?
Together, the findings suggest that levels of fatigue fluctuate on a moment-to-moment basis as a function of the recent history of effortful exertion and rest, with underlying recoverable and unrecoverable components, impacting people’s sensitivity to efforts and the subjective value of exerting effort to obtain rewards. Separate frontal sub-regions signalled recoverable and unrecoverable fatigue states, while current fatigue levels were integrated with value in the ventral striatum and the frontal pole. Dopaminergic medication affected self-reported fatigue, playing a differential role in recovery. In addition to these insights, the studies demonstrate that the paradigms and the computational model developed here may provide new approaches for the assessment and quantification of pathological forms of fatigue and associated deficits in motivation and might thereby help identify potential avenues for prevention and treatment.
Molecular diagnosis of infectious disease and cancer via synthetic biological methods
Keywords: biosensor
synthetic biology
RT-LAMP
cancer
microbiology
diagnostic
therapeutic

Synthetic biology is an emerging field that unveils a new dimension to biology, where the disciplines of engineering and biological sciences are brought together to program novel biological entities or re-wire existing ones. The ultimate goal is to achieve de novo engineering of biological systems to address the most pressing societal issues ranging from environmental and industrial to healthcare while accelerating the progress of fundamental biological research to answer important questions about life. However, the complications, instability and insecurity of a genetic network have hindered the translation of synthetic biological technologies into real-world applications. This thesis aims to contribute partly to these challenges and seeks to address two of the most urgent global health threats at the moment, the COVID-19 pandemic and cancer.
To support the testing strategy for COVID-19, I begin by re-purposing a traditional cell-free enzymatic reaction, RT-LAMP to detect multiple targets on the SARS-CoV-2 RNA genome. Reported here are proof-of-concept experiments to demonstrate the diagnostic sensitivity and specificity of this method and highlight the practicality of using RT-LAMP as a rapid diagnostic test for COVID-19. To refine the testing method, I introduce a molecular switch that reduces the false positive likelihood by preventing self- and off-target amplification. In particular, the adoption of molecular switch has seen a drop of the false positive rate from 60 % to 0 % in a RT-LAMP experiment with 20 replicates. Through a large-scale clinical validation, this optimised RT-LAMP is shown to provide COVID-19 diagnosis within a short turn-around time at point-of-care setting.
To design a diagnostic for colorectal cancer, I first develop a bacterial whole-cell biosensor by expressing a specific single-domain antibody on the outer membrane of Escherichia coli BL21 to confer binding specificity to a cancer biomarker, carcinoembryonic antigen. I then demonstrate the diagnostic sensitivity of the whole-cell biosensor in a biological agglutination assay format. To transform the whole-cell biosensor into a potential in vivo diagnostic and therapeutic agent, I adopt two different top-down approaches to generate synthetic biological chasses, SimCell and minicell, which are non-replicable, non-growing and metabolically active. These chasses allow the housing and actuation of synthetic circuits without any interference from the host genome, which can thus be exploited for a wide range of healthcare-related applications.
Overall, the research on the cell-free system and genome-less chassis described herein provides a genetically stable and secure system to help synthetic biology reach its translational potential.
Lung measurement and quantification of lung heterogeneity using the inspired sinewave test
Keywords: Lung diseases
Inspired Sinewave Test
Lung heterogeneity

The lung is a complex organ. The most familiar and significant lung disease, chronic obstructive pulmonary disease (COPD), can be severely debilitating. Additionally, acute lung injury in the critically ill can be life-threatening. Lung diseases are known to be correlated with the heterogeneity of the lung (ventilation mismatch and perfusion mismatch). Currently, there is no “standard” method for assessing lung heterogeneity. Many lung function tests and computational methods have been proposed to diagnose and monitor lung heterogeneity. The Inspired Sinewave Test (IST) is a non-invasive and practical test to investigate lung pathophysiology.
To investigate the usability of the IST, we compare the IST results to similar lung function tests (current “standard” tests). A mathematical lung simulation is developed to enable the IST to quantify lung heterogeneity. This simulation is proved to work with the IST by testing with simulated data and sensitivity analysis. The resulting validated process is implemented in thirteen pigs (pre-injury and post-injury) and 104 human volunteers (healthy and COPD patients, including different phenotypes). The IST lung heterogeneity measurement is compared to CT scan results.
The IST results show that it is potentially a suitable device for bedside monitoring in mechanically ventilated patients. Additionally, by using the lung simulation, lung heterogeneity can be quantified by the IST using 60 s and 180 s period tracer gas. The ventilation and perfusion heterogeneity in injured animals are found to be higher than in non-injured animals. There is no clear distinction between healthy subjects and patients with COPD in the COPD human data set. The multiple alveolar compartments lung simulation is proposed to boost the COPD prediction accuracy using only IST data.
The results in this thesis suggest the translation of the IST into human medicine as a tool for detection and prevention of lung injury. Future investigations are proposed, which could potentially improve the works in this thesis.
Co-evolution of bats and viruses and how it has shaped host biology
Keywords: ERV
endogenous viruses
immunology
bats
syncytin
evolution
EVE

Although the general link between bats and viral diseases is clear, tracing outbreaks to their bat origins can be difficult. It is believed that the lack of symptoms in bats may be caused by their long co-evolution with viruses, their immunological traits, or evolutionary adjustments arising from endogenized viral genes.
Our work confirmed that, despite a small genome size, bats have a comparable diversity of endogenous retroviruses (ERVs) to other mammals. Some of these ERVs are suffi- ciently preserved to be expressed, with potential effects for host biology. We detected an unusual diversity of complex retroviruses, which are generally rare in endogenous form, and a novel class of recombinant retrovirus with an alpharetrovirus-like envelope which has not previously been seen in mammalian genomes.
In parallel we studied Toll-like receptors (TLRs) in bats, a class of innate immunity recep- tors. Although highly conserved in vertebrates, the viral and bacterial ligand recognition properties of TLRs can have subtle variations between species, which may have driven the evolutionary pathways of interactions with infectious diseases. We found that bat species differ between each other with respect to the array of TLR genes and discuss these in the context of a broader mammalian profile.
In addition, we studied the mammalian ACE2 receptor, which is an entry receptor for SARS viruses. With coronaviruses which can change tropism quickly, the host range can at least partially be predicted with knowledge of the receptor specificity. We analysed the ACE2 SARS binding region of several vertebrates and discovered that it can vary even between related species e.g. bats.
Collectively these results strengthen the unique position the Chiroptera order has in regards to its relationship with viruses, both exogenous and endogenous and confirm the special role of bats among other mammals as virus reservoirs.
How to design, optimise and implement a fibre-tip Fabry-Pérot cavity for quantum networks of atoms and photons
Keywords: atomic physics
fibre Fabry-Pérot cavities
cavity quantum electrodynamics
quantum optics
quantum networks

One of the most exciting prospects of quantum physics today is to simulate large quantum systems, intractable by classical computation, by connecting many smaller systems together. A cavity-based quantum network of atoms and photons constitutes one such approach, where each cavity interfaces between stationary atomic qubits in a node and photonic qubits travelling along optical fibre channels. For this scheme to work well, the cavity-based interface must be faithful and well-controlled.
In this thesis, we construct a fibre-tip Fabry-Pérot cavity by aligning two optical fibre-tips against each other, where each has a concave, mirror-coated surface. Three properties make it highly suitable for interfacing: a small mode volume for strong atom-photon coupling, directly fibre-coupled cavity light, and optical access for trapped atoms. For the latter, we design a scheme that allows for a 2D reconfigurable array of atoms, held in the cavity mode by holographically-generated optical tweezers. Our particular design will allow us to move atoms independently of one another.
We find the atom-cavity system parameters for optimal single photon generation, absorption and remote state transfer using V-STIRAP (vacuum-stimulated emission by Raman adiabatic passage). Using master equations and the Nelder-Mead algorithm, we optimise both the parameters and V-STIRAP pulse shapes to do this.
We assemble the first fibre cavity formed of two single-mode fibres in ultra-high vacuum. Aligning two single-mode fibres is particularly demanding; we overcome this with an assembly method that gives permanent sub-micron alignment precision, unlike other similar cavities that need realigning using a translation stage. We fully characterise the cavity's parameters, then test it by probabilistically loading atoms from a magneto-optical trap, measuring the Purcell-enhanced fluorescence from the cavity.
Altogether, our advances facilitate deterministically controlled, strongly-coupled and networked quantum systems.
The use of iPSC-derived neurons to investigate the role of clusterin trafficking in Alzheimer’s disease
Keywords: CRISPR/Cas9
neurons
APOJ
Clusterin (CLU)
iPSC
Alzheimer's disease (AD)

Clusterin’s role in neurodegeneration and Alzheimer’s disease (AD) remains unclear. Clusterin (CLU) protein expression and trafficking are altered in response to stress; the treatment of rodent neurons with beta-amyloid (Aβ) increases intracellular retention and reduces secretion of clusterin proteins. CLU knockdown in rodent neurons provides protection against Aβ-induced toxicity including cell death indicating clusterin may mediate Aβ toxicity.
Although traditionally referred to as a highly glycosylated and secreted protein, clusterin can also be found intracellularly. However, the biogenesis, structure, and functional importance of these intracellular proteins remains debated.
In this thesis, CRISPR/Cas9 genome engineering was used to remove exon 2 from CLU, since this exon contains the endoplasmic reticulum (ER) signal peptide required for the generation of glycosylated, secreted clusterin proteins. This generated heterozygous and homozygous exon 2 knockout (KO) iPSC lines. These were then differentiated into neurons and treated with Aβ to compare cellular and genetic responses of KO and control cells.
The data demonstrated that heterozygous KO neurons responded similarly to control neurons when treated with Aβ, displaying both cell death and neurite retraction indicating no altered sensitivity. Furthermore, Aβ treatment, and not neuronal genotype, was identified as the largest contributor to gene expression changes measured by RNA-Seq. In contrast, homozygous exon 2 KO was sufficient to generate intracellular, non-glycosylated clusterin proteins, and prevent secretion. This manifested as reduced sensitivity to Aβ: neurons displayed cell death but no evidence of neurite damage indicating exon 2 KO provides partial protection to iPSC-neurons.
Metabolic flux analysis in Euglena gracilis
Keywords: flux balance analysis
metabolic flux analysis
Euglena gracilis
carbon metabolism

In this study, 13C metabolic flux analysis and flux balance analysis are used to investigate the metabolic phenotypes of Euglena gracilis grown on glucose, acetate, ethanol and pyruvate. A set of metabolic flux maps of E. gracilis are presented. These flux maps emphasise the limited contribution of plastidic metabolic processes and the oxidative pentose phosphate pathway in heterotrophic metabolism of E. gracilis. Comparison of the flux maps of wild-type and aplastidic E. gracilis on glucose reveals that disruption of chloroplast increases demand for the cofactors required for cell maintenance, resulting in higher fluxes through the central pathways of carbohydrate oxidation and a decrease in carbon conversion efficiency in aplastidic cells. Moreover, flux maps of E. gracilis on different respiratory substrates emphasise the importance of the glyoxylate shunt and malate dehydrogenase in supporting anaplerosis when grown on acetate and ethanol, but not on pyruvate in which the precursor for gluconeogenesis is mainly provided by pyruvate carboxylase. The flux maps reported in this study reveal the impact of chloroplast disruption on the metabolic phenotype of Euglena and provide new insights into the metabolism of substrates differing in carbon composition and chemical redox potential.
Enter Xiuhquilitl: indigo in the Spanish Empire, c.1550-1700
Keywords: Atlantic trade
Indigo
colonial Latin America
natural dyes
merchant networks -Iberian Atlantic
early modern Spain
Yucatan
Guatemala

Over the course of the sixteenth century, the burgeoning globalising forces of exploration and discovery transformed the indigo trade in Asia and the Americas, the histories of blue, and woad producing regions in Europe. Around 1560, the Spanish Crown found indigo-producing plants grew wild in parts of New Spain, and across the Captaincy General of Guatemala; settlers turned with enthusiasm to the new industry, and by 1600 indigo ranked third on the list of exports from the Spanish colonies – after bullion, and cochineal, contending for its place with cattle hides. Previous studies of colonial Mesoamerican indigo have concentrated on eighteenth century production methods and the problematic of indigenous labour, rarely following the blue dye past the port of Seville, to the dyer’s vat or the artist’s studio. Processes of reception, accommodation (sometimes rejection), and commodification, the initial development of manufacturing techniques and the diffusion of these new practices, have been left unexamined. This thesis seeks to address some of these, neglected chapters in the history of indigo, constructing a narrative that integrates the experiences of producers and consumers, considering the materiality of indigo (in its raw, and multiple finished forms). Drawing on selected case studies from across the Empire, I examine the production, trade, and consumption of New World indigo over the course of two centuries – between 1550 and 1750 – focusing on the individuals and groups, connections and interactions that determined its path from an unfamiliar, exotic dye, to a commodity circulated globally.