VictorJuiz/thesis huggingface dataset:
Molecular pathways leading to sleep and wakefulness in Drosophila
Keywords: sleep
dFB neurons
Drosophila

Sleep is a universal and highly conserved phenomenon across species; yet its operational mechanisms remain one of the greatest biological mysteries. In Drosophila, sleep homeostasis is largely mediated by the activity of neurons projecting to the dorsal fan-shaped body (dFB). Dopamine promotes wakefulness by inhibiting the activity of dFB neurons, switching them to a silent state. This wake-promoting effect is hypothesised to require the exocytosis of the potassium “leak” channel, Sandman, to the plasma membrane, where it exerts its effects by blunting the firing of the neurons. In the chronically sleep-deprived flies bearing a mutation for the crossveinless-c (cv-c) gene, the dFB neurons were previously found in electrical quiescence as well. It is therefore possible that in these mutants, Sandman resides at the plasma membrane of the neurons, reducing their excitability and causing insomnia in the flies. However, the signals responsible for Sandman’s recycling to and from the plasma membrane remain elusive.
To visualise the exo-endocytic pathway of Sandman, I attempted to localise the channel with different fluorescent probes and identify proteins acting in the same pathway using genetic interaction experiments. Depletion of Sandman from the dFB neurons rescues the sleep loss of cv-c mutants, supporting the notion that insomnia in these flies results from the channel’s presence at the plasma membrane. As cv-c encodes for a Rho GTPase-activating protein (Rho-GAP) and small GTPases are often regulated by neurotrophin-related pathways, sleep induction involving the Cv-c-Sandman pathway may further couple to the upstream action of neurotrophic molecules.
dFB-restricted interference with Toll-6, a receptor with neurotrophic function, reduces sleep. Toll-6/cv-c mutants mirror the sleepless phenotype of cv-c mutants, suggesting that Toll-6 may signal through Cv-c, conveying sleep pressure to the neurons. A mutation for Drosophila neurotrophin 1 (DNT1), a ligand of Toll-6, also diminishes sleep. RNAi-mediated knockdown of DNT1 in the R5 neurons, a defined input to the dFB, decreases sleep and abolishes sleep drive encoded by the circuit.
It is proposed here that activity-dependent release of DNT1 from the R5 neurons signals sleep pressure that is transduced by the Toll-6 receptor in the dFB neurons. Activation of the receptor likely feeds into a small GTPase cascade that involves Cv-c and Sandman.
Bifunctional iminophosphorane superbase catalysed enantioselective intramolecular michael reactions
Keywords: organocatalysis
heteroatom Michael reaction
superbase BIMP
enantioselective

Chapter 1 introduces the strategies to prepare enantioenriched compounds, specifically focusing on tertiary amine-based and superbasic bifunctional organocatalysis. Bifunctional iminophosphorane (BIMP) catalysis will then be detailed in its discovery and applications.
Chapter 2 outlines the development of a squaramide BIMP-catalysed enantioselective intramolecular aza-Michael reaction (IAMR) of both aromatic and aliphatic ureas to tethered α,β-unsaturated esters, furnishing decorated enantioenriched hydroquinazolines.
Chapter 3 demonstrates the enantioselective preparation of structurally diverse enantioenriched cyclic ethers via a BIMP-catalysed intramolecular oxy-Michael reaction (IOMR) of alcohols to tethered α,β-unsaturated esters and amides. The improved efficiency (1 day vs 7 days) and a far broader scope than the previous syntheses will be described. Subsequently, the pronucleophile scope of the IOMR will be extended to phenols and benzylic alcohols, thereby delivering enantioenriched dihydro-(iso)-benzofurans and iso chromans.
Phylogenomics and biogeography of the calamoid palms
Keywords: rattan
arecaceae
phylogenomics
Asia-Pacific
calamoideae
fossil calibration
biogeography
divergence time estimation
molecular dating
systematics

Tropical rainforests are the most diverse terrestrial biome, but their origins remain incompletely understood. Detailed analyses of the temporal and spatial context of the evolution of old and species-rich tropical rainforest lineages have potential to yield novel insights. However, only few such analyses are currently available.
The palm subfamily Calamoideae is proposed here as an appropriate study system to address this knowledge gap. It has a rich fossil record, comprises 555 species, and has a pantropical distribution with the centre of diversity in the Asia-Pacific region. There is a general understanding of its taxonomy, phylogeny, and distribution, but species-level relationships, divergence times, and biogeographic history of the subfamily are known only in vague outlines.
Here, three steps were undertaken to realise the full potential of the Calamoideae for providing new insights into the origins of tropical rainforests. First, targeted sequencing of 971 genes of 75 species was conducted, resulting in a robust phylogenomic framework of the Calamoideae. Second, sequencing was expanded to 653 calamoid specimens representing 502 species (90%) of the Calamoideae, resulting in 381 species (68%) in the final species-level phylogeny after data filtering. Divergence times were estimated based on four dating strategies, indicating an Early Cretaceous age of crown Calamoideae but an Oligocene and Miocene origin of most extant species. Finally, ancestral ranges and dispersal patterns were inferred for the Calamoideae in the Asia-Pacific region following the testing of 198 biogeographic models, showing that the subfamily reached its broad distribution during the Oligocene and Miocene convergence of Australia and Asia, and that migration pathways closely followed a stepping-stone model with dispersals out of the centre and into the periphery of the Asia-Pacific region.
This work represents the largest densely sampled and dated molecular phylogeny of any major pantropical rainforest lineage to date and elucidates the biogeographic history of a characteristic component of the tropical rainforests in the Asia-Pacific region in unprecedented detail. It is hoped that it will serve as a detailed framework for future comparative analyses.
Some contributions to stochastic differential equations
Keywords: aronson estimates
vorticity equation
forward-backward SDEs
Cameron-Martin formula
McKean-Vlasov SDEs
quadratic BSDEs
diffusion processes
strong solution

This thesis elaborates topics on a type of McKean–Vlasov stochastic differential equations and forward–backward stochastic differential equations arising from physics models.
Mainly, this thesis is divided into three parts. Chapter 2 consists of preliminary definitions and results from the theory of parabolic equations, stochastic differential equations and backward stochastic differential equations. Some key results are summarised for subsequent developments.
Motivated by the random vortex method for the Navier–Stokes equation, Chapter 3 studies a special type of McKean–Vlasov stochastic differential equation (MVSDE), whose kernel function is assumed to be continuous except at few singularities in Rd. With some technical estimates, we establish the existence and uniqueness of both the weak and the strong solutions to the MVSDE theoretically. The numerical simulations are also conducted to approximate the MVSDE and the corresponding velocity field in the three dimensional space.
Chapter 4 is devoted to studying a system of forward-backward stochastic differential equations (FBSDEs) arising from the porous medium equation. The gererating function of the backward equation for this class of FBSDEs has quadratic growth in the variable Z. We construct the unique solution on a small time interval by using a fixed point argument, and further extend the study to a class of quadratic FBSDEs with more general growth conditions.
Macroecological consequences of biotic and abiotic factors in marine ecosystems through time
Keywords: species distributions
fossil record
planktonic foraminifera
spatial sampling standardization
ecological release
Antell GT
Gawain Antell

This dissertation statistically investigated putative biotic and abiotic drivers of ecological characteristics over the spatial scale of ocean basins and temporal scale of millennia to millions of years. For three fundamental hypotheses in evolutionary ecology, I compared patterns of natural experiments from the fossil record against expectations from theory. The first empirical study appraised the hypothesis that competition restricts geographic distributions at the species level, and thus taxa are more widespread when in the presence of fewer competitors, such as after mass extinction events. Contrary to the prediction of competitive exclusion, brachiopod and bivalve distributions were invariant to inferred biotic pressure, while habitat type and lineage age had detectable effects on range expansion or contraction on the scale of geologic stages across the Phanerozoic. The second study estimated the degree to which plankton modulate thermal preferences vs. migrate in response to glacial–interglacial climate fluctuations. Species conserved abiotic niches over the Middle–Late Pleistocene study interval, suggesting marine species will track preferred environments rather than adapt to Anthropogenic climate warming. The final study explored relative niche change within lineages vs. across an evolutionary tree of macroperforate planktonic foraminifera. The stark stasis observed within lineages could suggest niches evolve primarily during speciation, but any signal of such punctuated equilibrium was undetectable statistically with the small phylogenetic tree and large variance within and between species. Together, these results add perspective to longstanding debates about the scaling of population- to species-level ecology and micro- to macro-evolution.
Layered double hydroxide based materials for carbon dioxide capture
Keywords: core-shell
layered double oxide
Layered double hydroxide
carbon dioxide

This thesis discusses the development of layered double hydroxides (LDHs), layered double oxides (LDOs) and their composites for use in CO2 capture.
Chapter One introduces LDHs, providing a background into their flexible composition and versatile application. A brief description of core@shell materials is also provided. Materials used in CO2 capture in research and industry are discussed and compared. A background to the polyurethane (PU) curing process is also introduced.
Chapter Two investigates the acidity and basicity of solvent treated LDHs and LDOs (aqueous miscible organic (AMO) and aqueous immiscible organic (AIM) solvents). Their Brønsted and Lewis acidities and basicities are probed using titration, in situ fourier transformed infrared spectroscopy and temperature programmed desorption (TPD) respectively. Solid state NMR (ssNMR) is used to probe both the composition and surface sites, and a novel hypothesis regarding solvent interactions upon calcination is proposed. The CO22 adsorption of solvent treated LDOs are tested to determine the optimal solvent for the process.
Chapter Three focuses on determining both the chemical and process parameters that affect the CO2 capture performance of MgxAl LDH/LDOs in CO2 capture. Process parameters, such as calcination temperature, calcination time and heating ramp rate, are investigated. Spectroscopic techniques, including ssNMR, TPD and surface hydroxyl titration, are used to observe the differences in the materials in order to determine the physicochemical factors that control CO2 capture performance. By combining the result from Chapters Two and Three, an MgxAl LDH optimised for CO2 capture is synthesised.
Chapter Four describes the synthesis of carbon@Mg2Al LDH core@shell materials. The effects of varying LDH composition upon the morphology and growth of the core@shells are investigated. The series of materials is explored for synergy with regards to CO2 capture with minimal pre-treatment. Calcination parameters for carbon@Mg2Al LDH are varied and optimised for the CO2 capture. Different carbon-based core materials are investigated in order to improve the overall CO2 capacities of the core@shell composites. Post-synthesis modifications, such as solvent and ammonia treatment, are also investigated for potential improvement on CO2 capture.
Chapter Five is a preliminary study of use of LDH-based materials during the curing of polyurethanes (PUs), with the ultimate goal of reducing curing time and eliminating CO2 production during the curing.
Chapter Six includes the experimental details of the work described in this thesis. Lastly, the findings of the work of this thesis is summarised in Chapter Seven. Any supplementary information and other data referred to in the main text are found in the Appendices.
The heirs of Theodore: Aḥob of Qatar and the development of the East Syriac exegetical tradition
Keywords: the Physiologus
scholia
Basil of Caesarea,
church architecture
Aḥob of Qatar
The Commentary on Genesis-Exodus 9:32
East Syriac exegesis
cosmology
Theodore of Mopsuestia
East Syriac liturgy
the Denḥa-Grigor Commentary
Isaac Shbadnaya
the School of Seleucia
Jewish exegesis
Nathniel of Shirzor
the language of Qatar
Bar Bahlul’s Lexicon
East Syriac Christology
Theodore bar Koni
the Anonymous Commentary
Isho‘dad of Merv

This thesis is a study of Aḥob of Qatar, an important but under-researched late 6th-century East Syriac biblical commentator, and his surviving Old Testament exegetical works (mostly in the form of scholia). It further examines what can be deduced of Aḥob’s influence on the later East Syriac exegetical tradition, and it details the originality of his exegesis, especially in comparison with earlier and/or contemporary Greek and Syriac sources. My argument will be twofold: 1) Aḥob’s exegetical and theological impact on the East Syriac exegetical tradition was more extensive than previously considered, and 2) Aḥob represents a distinct voice within the East Syriac exegetical tradition and so should not be equated with a presumed harmonized monologue in East Syriac biblical exegesis which repeats Theodore of Mopsuestia’s (350-428) exegesis and theology line-by-line.
In Chapter 1, I examine the surviving biographical data relating to Aḥob’s life and works. In Chapter 2, I present an annotated edition and English translation of Aḥob’s Cause of the Psalms and surviving attributed Old Testament scholia, as well as a discussion of disputed scholia and spurious scholia connected to Aḥob. In Chapters 3 and 4, I analyze Aḥob’s Old Testament exegetical works as they were used and developed by later East Syriac writers and manuscript traditions, including Nathniel of Shirzor’s (ca. 600) Cause of the Psalms, The Commentary on Genesis-Exodus 9:32 (first half of the 8th century), Theodore bar Koni’s Scholion (792/793), the Denḥa-Grigor Commentary (first half of the 9th century?), Isho‘dad of Merv’s (fl. ca. 850) Commentary on Genesis, 1 Samuel, and Psalms, the Anonymous Commentary (10th century), Bar Bahlul’s Lexicon (mid-10th century-early 20th century), and Isaac Shbadnaya’s (fl. 1439/1440) prose commentary on his Poem on God’s Governance from ‘In the Beginning’ until Eternity. In Chapter 5, I investigate four aspects of Aḥob’s Old Testament exegetical works: 1) their original form, 2) their original purpose, 3) their multiple sources, and 4) their overall distinctiveness within the East Syriac exegetical tradition. I conclude this thesis with an Appendix, which presents an edition of the Introduction and select parts of thirteen psalms from the Denḥa-Grigor Commentary, to which Aḥob’s Psalm scholia are connected.
Nature-watching and affective encounters with more-than-human beings in post-reform Beijing
Keywords: Affect
Urban nature
Cross-species relateness
More-than-human ethnography

Cities as purely social spaces have long held sway over dominant understandings of cities. This thesis sets out to make visible the many ways that more-than-human beings permeate urban life to unsettle the deeply ingrained assumption of “anti-nature” cities. To do so, It scrutinises a variety of visual practices to engage with an array of living beings in Beijing that I refer to as “nature-watching” (ziran guancha 自然观察). I argue that nature-watching practices create a condition of affective and intense encounters with more-than-beings, and foster the flourishing of cross-species relatedness in the city. By drawing on a mixture of ethnographic methods including participant observation, visual methods and crucially my participant learning experience, it seeks to unveil how Beijing nature-watchers are enabled to learn to sense, know, open up to, care for and build civic solidarity with more-than-human beings in new ways. This thesis suggests a research agenda to conceive cities anew as more-than-human spaces, and to call for attention to the caring and relational potentials of visual practices.
Carbon dioxide utilisation in block polymers: catalysis and functional materials
Keywords: Polymer materials
Block polymers
Carbon dioxide utilization
Polymers
Catalysis

The following thesis describes the synthesis of block polymers comprising polycarbonates (derived from carbon dioxide) and polyesters, and their evaluation as functional materials and possible renewable alternatives to current petrochemical-based plastics. The preparation of the polymers utilises efficient and sequence-controlled polymerisation catalysis, combining lactone ring-opening polymerisation (ROP) and epoxide/CO2 ring-opening copolymerisation (ROCOP) cycles through a single catalyst.
Chapter 2 evaluates heterodinuclear zinc(II)/magnesium(II) catalysts for the switchable polymerisation catalysis of lactone and epoxide/CO2. The heterodinuclear catalyst, [LZnMg(OBzNMe2)2] where L = macrocyclic ancillary ligand, OBzNMe2 = parasubstituted benzoate, is initially assessed for the preparation of ABA-type triblock polymers, but because of poor end-group fidelity the development of a new organometallic catalyst, [LZnMg(C6F5)2] is undertaken. The organometallic catalyst shows strong performance with equivalent high activity for epoxide/CO2 ROCOP and enhanced activity for lactone ROP compared with the benzoate variant. Importantly, it delivers higher molar mass ABA triblock polymers (Mn > 20 kg mol-1 ) with block sequence-selectivity and with excellent end-group fidelity.
Chapter 3 further explores the application of the organometallic Zn(II)/Mg(II) catalyst in switchable polymerisation catalysis. High molar mass ABA triblock polymers (38 < Mn < 71 kg mol-1) with varying degrees of CO2 utilisation (6 – 23 wt %) are prepared by controlling the starting monomer stoichiometry, with the final materials comprising hard polycarbonate “A” blocks and a soft polyester “B” block. The effects of varying the relative block ratio on the thermal and mechanical characteristics of the polymers are analysed, and their performance as toughened plastics, elastomers, and pressure-sensitive adhesives is evaluated.
Chapter 4 investigates the synthesis and thermal/mechanical effects of changing the polymer architecture by varying the initiating alcohol groups, from linear to stars. A range of tri-, tetra-, and hexafunctional star block polymers are synthesised from vinyl-cyclohexene oxide (vCHO), CO2, and ε-decalactone (ε-DL). It also investigates the selective postpolymerisation modification of the polycarbonate block at fixed relative block composition. Multi-arm star-like polymers are fashioned using a “core-first” approach by employing chaintransfer agents with varying numbers of hydroxyl groups. Trends in thermomechanical and morphological characteristics for both the non-modified and modified polymers are analysed in relation to molar mass (overall and individual arm) and number of star ‘arms’, and a preliminary assessment of particular advantages/disadvantages for star vs. linear architectures in these polymers is presented.
Automated and verified deep learning
Keywords: Neural network verificaiton
Meta learning
Optimization
Neural networks

In the last decade, deep learning has enabled remarkable progress in various fields such as image recognition, machine translation, and speech recognition. We are also witnessing an explosion in the range of applications. However, there are many challenges that stand in the way of the widespread deployment of deep learning. In this thesis, we focus on two of the key challenges, namely, neural network verification and automated machine learning.
Firstly, deep neural networks are infamous for being `black boxes' and making unexpected mistakes. For reliable AI, we want systems that are consistent with specifications like fairness, unbiasedness and robustness. We focus on verifying the adversarial robustness of neural networks, which aims at proving the existence or non-existence of an adversarial example. This non-convex problem is commonly approximated with a convex relaxation. We make two important contributions in this direction. First, we propose a specialised dual solver for a new convex relaxation. This was essential because although the relaxation is tighter than previous relaxations, it has an exponential number of constraints that make the existing dual solvers inapplicable. Second, we design a tighter relaxation for the problem of verifying robustness to input perturbations within the probability simplex. The size of our relaxation is linear in the number of neurons, which enables us to design simpler and efficient algorithms. Empirically, we demonstrate the performance by verifying the respective specifications on common verification benchmarks.
Secondly, deep neural networks require extensive human effort and expertise. We consider automated machine learning or meta learning which aims at automating the process of applying machine learning. We make three contributions in this context. First, we propose efficient approximations for the bi-level formulation of meta learning. We show its efficiency in the context of learning to generate synthetic data for training neural networks by optimizing state-of-the-art photorealistic renderers. Second, we propose a technique to automatically optimize the learning rate of gradient-based meta learning algorithms. We demonstrate a substantial reduction in the need to tune training hyperparameters. Third, we show an application by tackling video segmentation as a meta learning problem and demonstrating state-of-the-art results on common benchmarks.
Halogen bonding and chalcogen bonding host systems for charged guest recognition
Keywords: ion-pair recognition
rotaxanes
anion recognition
catenanes

This thesis describes the preparation of halogen bonding and chalcogen bonding macrocyclic and mechanically interlocked systems for the recognition of anions and ion-pairs.
Chapter 1 introduces the field of supramolecular host-guest chemistry, with particular focus on the recognition of anions and ion-pair species. The synthesis and applications of mechanically interlocked molecules are also reviewed.
Chapter 2 details the fundamental charged guest recognition properties of a novel family of σ-hole [2]rotaxanes incorporated with multiple halogen bonding and chalcogen bonding triazole-based donor motifs.
Chapter 3 investigates the anion sensing capability of halogen bonding receptors functionalised with photo- and redox-active reporter groups. This entails the construction of zinc(II) metalloporphyrin-BODIPY [2]rotaxanes for the dual optical- and electrochemical sensing of anions.
Chapter 4 describes the exploitation of halogen bonding and chalcogen bonding interactions to mediate ion-pair recognition in heteroditopic/multitopic macrocyclic and catenane host systems.
Chapter 5 summarises the conclusion of this thesis.
Chapter 6 provides the experimental procedures employed in this work, including synthetic protocols and characterisation of novel compounds.