VictorJuiz/thesis huggingface dataset:
Mechanisms of clinical ototoxicity and inner ear protection
Keywords: Cochlea
Utricle
Cisplatin
Ototoxicity
Aminoglycoside
Extracellular vesicle
Deafness

Clinical ototoxicity—permanent hearing loss caused by medications—is estimated to affect millions of patients annually. Two classes of drug are largely to blame: platinum-based chemotherapeutics, primarily cisplatin, and aminoglycoside antibiotics. Development of methods to prevent ototoxicity depends upon an understanding of its mechanisms and may benefit from an understanding of native protective pathways of the inner ear.
As the mechanisms behind cisplatin ototoxicity remain unclear, I first sought, and herein report, a refined mouse model of cisplatin ototoxicity which will allow for further in vivo investigation of cisplatin ototoxicity and potential methods for its prevention. This low-dose, multi-cycle model was found to accurately reproduce cisplatin ototoxicity as it has been described clinically and histopathologically.
I then used this mouse model of cisplatin ototoxicity to investigate cisplatin pharmacokinetics in the cochlea and their role in driving cisplatin ototoxicity. Cisplatin was found to be retained within the cochlea for months following its administration. This initial finding in mice was extended to cochlear tissue samples from deceased human patients. Analysis of intra-cochlear cisplatin distribution in murine and human tissue identified the stria vascularis region of the cochlea as a promising target for intervention.
With the nature of aminoglycoside ototoxicity better understood, I investigated a native inner ear protective pathway which could be leveraged to promote sensory hair cell survival. The improved hair cell survival that has previously been demonstrated as a result of heat stress was found to be mediated by cell-cell communication via extracellular vesicles. Further, hair cell protection against aminoglycosides could be reproduced through the application of exogenous, non-inner ear-derived extracellular vesicles.
In sum, these data provide new insight into mechanisms of ototoxicity and details of cellular pathways which can help protect against it.
Role of posttranslational modifications of histone proteins in epigenetics
Keywords: MS-based interaction proteomics
O-GlcNAcylation
Epigenetics
Protein chemistry

Nature has evolved an additional level of genetic regulation by-passing direct changes in genetic code through the means of posttranslational modifications (PTMs) of nucleobases and histone proteins. Acetylation, methylation, phosphorylation, O-GlcNAcylation, ubiquitination, sumoylation, and ADP ribosylation are few common examples of various histone modifications. Identification of these modifications and subsequent access to homogeneously modified histone proteins are key for understanding the functional consequence of these PTMs. In this doctoral thesis, the role of PTMs of histone proteins in epigenetics was investigated with emphasis on understanding the role of O-GlcNAcylation in particular.
In the second chapter, the functional consequence of O-GlcNAcylation at histone protein, H2B-Ser112 was explored. Homogeneously GlcNAcylated histones and nucleosomes were synthesized using protein chemical reactions. Mass Spectrometry (MS) based quantitative interaction proteomics revealed a direct interaction between GlcNAcylated nucleosomes and the Facilitates Chromatin Transcription (FACT) complex. Preferential binding of FACT to GlcNAcylated nucleosomes provides a molecular mechanism for FACT-driven transcriptional control.
In the third chapter, the physical effect of O-GlcNAcylation on the nucleosome structure is described. Homogeneously GlcNAcylated histone protein, H2A-Thr101 was synthesized. The modified protein was used to reconstitute histone sub-complexes and nucleosomes. Various biophysical studies involving circular dichroism and native mass spectrometry revealed that H2A-T101 GlcNAcylation regulates the stability of the nucleosome structure, suggesting a role in transcriptional activation.
In the fourth chapter, we discuss an interesting scenario where two PTMs – O-GlcNAcylation and phosphorylation – can compete for the same modification site of histone protein, H2B-Ser36. The resulting outcome is possibly a competitive antagonism or cross-talk, which can modulate the overall control of chromatin regulation. Using a "Tag-and-modify" approach, modified histone proteins bearing both modifications was synthesized, and was later used for nucleosome reconstitution. Quantitative interaction proteomics experiments with the modified nucleosome revealed key interacting protein partners for both the modifications.
First-principles Fröhlich electron-phonon coupling and polarons in oxides and polar semiconductors
Keywords: First-principles calculations
polarons
electron-phonon coupling

The Fröhlich coupling describes the interaction between electrons and infrared-active vibrations at long wavelength in polar semiconductors and insulators, and may result in the formation of polaronic quasiparticles. Polarons are electrons dressed by a phonon cloud, which can strongly affect the electronic properties of the crystal. Despite their ubiquitous role in a broad range of technologies, first-principles investigations of the electron-phonon interaction in polar materials are scarce. In this thesis we develop a general formalism for calculating the electron-phonon matrix element in polar semiconductors and insulators from first principles, which represents a generalization of the Fröhlich model and can be used to compute the polar electron-phonon coupling as a straightforward post-processing operation. We apply this procedure to explore an important material for photovoltaics, the hybrid lead halide perovskite CH3NH3PbI3. In this case we show that the temperature dependence of emission line broadening is dominated by Fröhlich coupling. Our method is formulated in conjunction with an ab initio interpolation technique based on maximally localized Wannier functions, which allows to describe all forms of electron-phonon coupling on the same footing. We demonstrate the validity of this approach on the prototypical examples GaN and SrTiO3. Focusing on anatase TiO2, a transition metal oxide of wide technological interest, we establish quantitatively the effect of including the ab initio Fröhlich coupling in the calculation of electron lifetimes. The rest of the thesis is devoted to exploring the quasiparticle properties in doped oxides. In particular, we investigate angle-resolved photoemission spectra from first principles in doped anatase TiO2 by proposing a novel framework that combines our ab initio matrix elements, including the dynamical screening arising from the added carriers, and the cumulant expansion approach. We compare our results with experimental data, and show that the transition from a polaronic to a Fermi liquid regime with increasing doping concentration originates from nonadiabatic polar electron-phonon coupling. We further validate this mechanism by calculating angle-resolved photoemission spectra in the ferromagnetic semiconductor EuO.
An evidence-based approach to the post-marketing withdrawal of medicinal products because of adverse reactions
Keywords: Systematic review
Adverse reaction
Drug withdrawal

Background: The aim of this thesis was to develop an evidence-based approach to the post-marketing withdrawal of medicinal products when harms are attributed to their use.
Methods: Electronic and non-electronic searches were conducted to identify medicinal products withdrawn from the market because of adverse reactions. Data relating to the time periods between launch, first adverse reaction reports and withdrawals, the mechanism through which the adverse reactions occurred, and the countries of withdrawal were extracted. Standard criteria were used to document the levels of evidence used by drug regulators to make the withdrawal decisions; scatter plots and two-by-two tables used to explore the trends over time. A previously published algorithm was used to examine the justification for withdrawals. To examine the benefits and harms of medicinal products before regulatory approval, searches were conducted on drug regulatory websites and scientific databases. The Cochrane criterion was used to examine the risk of bias, Review Manager Software for meta-analysis, and GRADE criterion to rate the quality of evidence.
Results: Improvements in pharmacovigilance over the past six decades have resulted in quicker detection of harms caused by approved medicinal products; however, there have not been corresponding improvements in how quickly harmful products are withdrawn from the market following the reports of harms. Harmful drugs are significantly less likely to be withdrawn in low resource settings. The quality of evidence in drug trials for which regulatory approval decisions are based is on the whole, poor. There is a lack of consistency in the methods used by drug regulators to assess the harms of medicinal products before granting marketing licences.
Conclusions: Universally accepted guidelines for deciding when to withdraw approved medicinal products from the market should be developed. Pharmacovigilance systems in low-resource settings should be strengthened. The methods used to assess harms in clinical trials require improvement.
Neural circuit mechanisms of memory coding in the Drosophila mushroom body
Keywords: mushroom body
sNPF
plasticity
memory
reconsolidation
learning
extinction
acetylcholine
Drosophila

Learning allows animals to adapt their behaviour to changes in the environment. In humans and other mammals, memories are stored in the hippocampus and cerebellum, whereas in insects, they are stored inside the mushroom bodies (MB). Here, MB-intrinsic Kenyon cells (KCs) form plastic synapses to MB output neurons (MBONs) that are modulated by the reinforcing action of dopaminergic neurons (DANs).
Despite decades of research on the MB, the main neurotransmitter underlying the plastic KC → MBON synapse has remained a mystery. Here, I show that this synapse is cholinergic in the fruit fly Drosophila melanogaster. MBONs show fast excitatory responses to direct acetylcholine (ACh) application. KCs synthesise ACh-related proteins ChAT and VAChT. MBONs express and require nicotinic ACh receptors (nAChRs) to become fully activated by odour presentation. Lastly, artificial activation of KCs leads to MBON calcium responses that are blocked by nicotinic antagonists and genetic reduction of VAChT in KCs. Short neuropeptide F (sNPF) may play a role as a modulatory co-transmitter that can either excite or inhibit specific MBONs and DANs.
The retrieval of memories is state-dependent and known to potentially change the original memory. Fruit flies need to be hungry to express appetitive memories. Hunger state depends on insulin signalling that activates the GABAergic MBON MVP2, while appetitive memory retrieval depends on decreased activity in M4/6 MBONs. Here, I show that optogenetic MVP2 activation acutely inhibits M4/6 odour responses, rendering MVP2 an inhibitory MBON interneuron. I also show that other MBONs are functionally connected to DANs, thus linking memory reinforcement and retrieval pathways in a way that enables the updating of the original memory.
These findings show that associative memories in Drosophila are initially formed at cholinergic KC–MBON synapses, and can be retrieved and modified through an intricate KC–MBON–DAN network.
Sri Lanka and the Indian Ocean contacts: internal networks and external connections
Keywords: Kantarodai
Sri Lanka's Maritime trade
Indian Ocean trade
Mantai
Kirinda
Sri Lanka
Sri Lankan archaeology
Sri Lanka's external connections
Jambukolapattana
Mahatittha

This study reconceptualises Sri Lanka’s external trade and interactions from the middle of the first millennium BC to the early second millennium AD. Unlike earlier analyses, mine draws on the excavated material culture from three port-cum-urban centres—Mantai, Kantharodai and Kirinda—which were linked to major urban complexes, interior resource bases and Indian Ocean maritime networks. The scale and intensity of their external trade and connectivity, crafts and industries varied greatly over time and location.
My findings illustrate Sri Lanka's earliest cultural-commercial connections with India from the middle of the first millennium BC. By the beginning of the CE, islanders were trading with the Middle East and the Mediterranean in the west and Southeast Asia and China in the east. The Middle East was a particularly strong connection from about the mid-3rd century. Materials from Southeast Asia and China arrive by the late 7th/8th centuries, with the focus of external trade shifting away from the Middle East to the Far-East around the end of the 10th century, lasting until the 12th/13th centuries and beyond.
My findings demonstrate that internal developments in irrigated agriculture, iron technology, crafts, industries and procurement–distribution networks were crucial for external trade and connectivity. Contrary to the traditional view, I identify local agency as an important driving force behind both internal and external trade in ancient Sri Lanka. The island's external connectivity did not depend on a single factor but was based on specific historical realities which were constantly redefined and reformulated in response to the changing dynamics within and outside Sri Lanka.
The role of LKB1 (STK11) in non-small cell lung cancer
Keywords: Bioactive small molecule screen
Metabolism
3D spheroids
Sub-cutaneous xenografts
RNA Sequencing
Othotopic mouse model

LKB1 is the second most commonly altered tumour suppressor gene in lung adenocarcinoma, the most prevalent form of lung cancer. LKB1 is a "master kinase" that has been shown to phosphorylate up to 13 downstream targets. We hypothesised that LKB1 loss is associated with an increased dependency on alternative, targetable pathways. The overall aims of this project were to better understand the role of LKB1 loss in lung cancer and to identify novel approaches to selectively target LKB1 mutated cells.
We generated isogenic cells with or without LKB1 and used these to study the effect of LKB1 on cell proliferation. Importantly, we used a range of models including 2D culture, 3D spheroids and, sub-cutaneous and orthotopic xenograft models. To understand the role of LKB1 loss in lung cancer, the effect of LKB1 on mRNA expression was analysed using whole genome RNA Sequencing. To identify novel approaches to selectively target LKB1 mutated cells, we used biological screening methods and also investigated the effect of several metabolic inhibitors.
We found that loss of LKB1 expression had no effect on cell proliferation in 2D culture, but was associated with increased growth in 3D spheroids, sub-cutaneous and orthotopic xenografts, as well as greater metastasis in a lung orthotopic model. Gene ontology analysis of the transcriptome identified that genes associated with cAMP signalling and cytoskeletal organisation were differentially expressed between LKB1 deficient and proficient cells. We confirmed that cAMP signalling was increased in LKB1 deficient cells, though there was no difference in sensitivity between LKB1 deficient and proficient cells to cAMP signalling modulators. The bioactive small molecule screen showed that LKB1 deficient cells underwent apoptosis more slowly and therefore, were less sensitive to many compounds, compared with LKB1 proficient cells. Screening in 3D spheroids was a novel approach that we used to identify microtubule inhibitors as potentially selective compounds acting in LKB1 deficient cells. Our RNASeq data suggests that there was a metabolic shift from oxidative phosphorylation to aerobic glycolysis in LKB1 deficient cells, although this did not affect sensitivity to complex I inhibitors. Importantly, LKB1 deficient cells were more sensitive to glucose and glutamine deprivation which suggests that targeting these metabolic pathways may hold the greatest promise to selectively inhibit proliferation in LKB1 mutated cells.
The literary Chinese cosmopolis
Keywords: Silla Korea
Ch'oe Ch'iwon
Inter-Asian studies
Heian Japan
Sugawara no Michizane

The thesis is set against the backdrop of literary Chinese as the cosmopolitan written language across East Asia and examines two contemporary literary Chinese writers in the ninth century: Ch'oe Ch'iwŏn from Silla Korea and Sugawara no Michizane from Heian Japan. Though composition in Chinese characters on the peninsula and the archipelago was ancient, a high-water mark within this community appeared in the ninth century. At that time, literary Chinese was embraced by mainstream literati as the medium for poetry and prose, and competent composition in this international written language came to have political as well as cultural significance. The importance of Ch'oe Ch'iwŏn and Sugawara no Michizane as the great masters of Chinese letters in Korea and Japan derives in part from their talents and in part from the social and political acceptance of Chinese.
This comparative research primarily draws inspiration from Sheldon Pollock's comparison of the Sanskrit cosmopolis and the Latin cosmopolis. Pollock describes the Latin cosmopolis as coercive and the Sanskrit cosmopolis as voluntaristic. I argue that the history of literary Chinese in East Asia provides a third cosmo-political model for the history of interactions among language, literature, and cultural and military power. The literary Chinese cosmopolis can be characterized not as coercive or voluntaristic but as hegemonic. I compare Ch'oe Ch'iwŏn and Sugawara no Michizane for their cosmopolitan identities, transnational experiences, and diglossic worlds. Though there is debate over the appropriateness of the terms "diglossia," "Chinese cosmopolis," and "Sinographic cosmopolis" to describe the world in which Ch'oe and Michizane lived, I argue in favor of "literary Chinese cosmopolis," because I pay attention to the common grammar, syntax, and other linguistic features one must bear in mind when composing in literary Chinese (as opposed to reading). Localism produced vernaculars, but the unity of the community was based on composition in a cosmopolitan language. That cosmopolitan language was literary Chinese, a hyperglossic language, a language that allowed universal communication in East Asia.
Intersecting with various disciplines and bringing several critical fields into conversation, this work contests and refreshes a series of key issues at the heart of discussions on globalization, namely the intrinsic relationship between language and power. How does cultural power emerge from language? How does writing in a "foreign" script articulate ethnic, local identities? As a meditation on language politics, ethics, and the historical situation of an earlier cosmopolitan ecumene (ninth century CE), this work will, I hope, offer insights into the specificities and mechanisms of a past cosmopolitan era in East Asia, even as it establishes a broader historical and ethical context for contemporary debates on globalization.
Opinion formation in dynamic social networks
Keywords: Opinion formation
Social networks

Opinion dynamics in a society of interacting agents may lead to consensus or to the coexistence of different opinions. The interplay between social network change and opinion formation is complex, because the agents, their social interactions and the changing social structure over time, are themselves complex.
DeGroot proposed a prescriptive model for achieving consensus, where agents revise their opinions at each time step by taking a weighted average of the opinions of neighbours. This thesis contains three main contributions. First, we introduce a generalisation of the DeGroot model and examine the long-time behaviour of the model, with and without insistent agents. Second, we consider opinion formation on networks which are themselves dynamic, where the dynamics may be completely random or based on homophily and triadic closure. The weights that agents place on the opinions of neighbours are also dynamic, based on a rule where weights decrease with increased difference in opinions. Third, we examine the effect of a sudden, temporary or permanent shift in the opinions of some agents.
Two dynamics are considered for the network change over time; random switching (RS) network dynamics, and homophily and triadic closure (HT) network dynamics. We prove that the RS network dynamics enhances consensus formation and network connectivity, compared to the HT network dynamics where we show by simulation that different opinions can persist.
We investigate the in uence of the presence of a minority of insistent agents and prove that for a connected static network, insistent agents with the same opinion in uence the final opinions to converge to their own opinion, thus leading to consensus. In contrast, lack of consensus persists when insistent agents have different opinions. This conclusion also holds for the RS network dynamics model. However, for the HT network dynamics model, coexistence of different opinions can persist even when insistent agents have the same opinion. This finding regarding the HT dynamics is of particular interest as it relates to observations in the real-world.
We also investigate the in uence of a sudden shift in the opinions of some agents on the outcome of final opinions. The case of either a temporary shift in opinions or a permanent shift in opinions is examined. Additionally, the in uence of the time of the introduction of a shift, the number and the network positions of initial recipients of the shift in opinions is investigated. The overall effect of an opinion shift is measured by its in uence on the stabilisation time of the final opinions.