VictorJuiz/thesis huggingface dataset:
Exploring new concepts in biomolecular recognition and ligand discovery

Aptamers are short nucleic acids that can bind with high affinity to a variety of biological targets through shape complementary. However, aptamers composed of natural bases are susceptible to nuclease degradation and have a limited range of intermolecular interactions with their targets. Here we introduce novel modifications at one of the four bases in SELEX libraries to enhance the interaction capabilities of the DNA and thereby broaden the target spectrum. Initially, azidoethoxy and propargylamino groups are introduced to C2′ position of thymidine or C5 position of deoxyuridine with benefits of further conjugation to novel functional groups – such as hydrophobic amino acid side chains to supplement protein-like interaction or halogen substituted modifications to add halogen bonding interaction. By providing the additional interactions that are not available in a canonical nucleic acid aptamer, next-generation aptamers with high target binding affinity and kinetic are anticipated. For their uses in SELEX to discover next-generation aptamer, the acceptance of chemically functionalised triphosphates by DNA polymerase is firstly examined. Base-modified nucleotides are better substrates for DNA polymerases than sugar-modified nucleotides due to the steric gate of the enzyme. Especially, 5-propargylamino-iodotriazole-dUTP (5-ITZ-dUTP), a monomer which can potentially allow aptamers to form halogen bonding interaction is used in SELEX. Promisingly, a G-quadruplex streptavidin aptamer containing nine 5-ITZ-dUTPs which has a high affinity to the target is discovered. This aptamer shows 6.5-fold and 9-fold higher binding affinities than the appropriate control sequences which contain non-halogen bearing nucleotides (5-propargylamino-prototriazole-dU or canonical dT). Further studies to demonstrate halogen bonding in aptamer-target interaction are required to confirm this as the first example of halogen bonding in aptamer-protein interactions.

Advisor: Brown, T
The chemistry of ynamides and yndiamides

There have been significant developments in both the synthesis and applications of nitrogen-substituted alkynes since the turn of the millennium, but there is still much that remains unexplored. In continuing these developments, two projects have been completed:
(i) A general copper-catalysed synthesis of ynamides from 1,2-dichloroenamides was achieved with broad substrate scope. This includes the use of acyclic secondary amides, acyclic ureas and sterically hindered enamide partners.
(ii) The first known synthesis of yndiamides was developed, which involves the copper-catalysed coupling of 1,1-dibromoenamides with sulfonamides and phosphoramidates. A preliminary study of yndiamide reactivity in transition metal- and Brønsted acid-catalysed processes was also performed.
Combined with the aid of crystallographic, spectroscopic and computational analyses, more fundamental aspects of these compounds have been uncovered during these studies, including conformational preferences. Questions were also raised as to how these preferences can affect the reactivity and stability of ynamides and yndiamides.

Keywords: Ynamides
Nitrogen
Alkynes
Yndiamides
Copper Catalysis
Heterocycles
Advisor: Anderson, E
Strong edge zero modes in interacting systems

I will discuss how edge spins in certain one-dimensional spin chains retain memory of their initial state for very long times, even with interactions and at infinite temperature. These long coherence times do not require disorder or integrability. I will show how this is a consequence of an "almost" strong edge zero mode that almost commutes with the Hamiltonian, and explain how to compute this operator explicitly with computer-aided algebra. I will examine the effect of this almost strong zero mode on the behaviour of a wide variety of one-dimensional systems analytically, from the ground state to infinite temperature, and from finite size to the thermodynamic limit. I will also examine the effect of the almost strong zero mode on the eigenstate spectrum and the matrix elements of the edge spin, and show that despite the long coherence time of the edge spin, the almost strong zero mode does not induce degeneracies in the entire spectrum, unlike its counterpart exact strong zero mode in non-interacting systems. At special values of the couplings, resonances dramatically limit the coherence time. I will explain how these resonances are related to physical processes which flip the edge spin for no change in the energy of the system, and calculate the coupling strengths for which they appear. I will propose an experimental test of the almost strong zero mode and the long coherence time of the edge spin in a trapped ion chain which is feasible to implement with current technology. Lastly, I will explain how these almost strong edge zero modes in a system with symmetry-protected topological order can be used to form a boundary qubit with both long decoherence and dephasing times.

Advisor: Fendley, P
Elucidating the structures of cationic metal-nitrous oxide complexes using infrared action spectroscopy

Gas-phase metal ion-molecule complexes provide model environments within which to study fundamental molecular interactions involved in ligand activation and metal ion solvation. These complexes also represent entrance-channel species for catalytic reactions. The ligand of interest in this thesis is nitrous oxide, which accounts for 5% of anthropogenic emissions and is a potent greenhouse gas with a warming potential 300 times greater than carbon dioxide. Thus, there is considerable interest in reducing N2O emissions particularly via metal-catalysed N2O reduction. M+/0/-(N2O)n complexes represent entrance-channel species for such reactions and yet, little attention has been given to the structures of M+/0/-(N2O)n complexes. This thesis presents the first experimental investigation on M+$(N2O)n and M+n(N2O) complexes studied via infrared action spectroscopy. The infrared spectra are further interpreted and assigned from simulated spectra based on density functional theory (DFT). A range of M+(N2O)n complexes (M = group 11, group 9, and Li, Al) have been studied in an attempt to draw comparisons between the different M+ electron configurations d10, d8, and closed s-shell, respectively). Spectroscopic signatures for N- and O-bound N2O ligands are observed in all cases however the importance of low-lying electronic states is revealed for the group 9 cations, and insertion complexes inferred for the Li+ ion.
Infrared multi-photon dissociation (IRMPD) studies on M+n(N2O) complexes (M = Au, Co) also present N- and O-bound spectroscopic signatures. However, as the metal cluster size increases, N2O binds preferentially via the terminal N-atom. Larger clusters represent a more effective energy "bath" facilitating annealing to the lowest energy structure.

Keywords: Quantum Chemical Calculations
Photodissociation
Cluster Chemistry
Nitrous Oxide
Physical Chemistry
Infrared Spectroscopy
Metal-Ligand Complex
Advisor: Mackenzie, S
Learning the structure of object categories from incomplete supervision

This thesis aims at learning and predicting the fine-grained structure of visual object categories given input image data. Alleviating the common requirement of collecting an ample amount of manual annotations, we propose several approaches that learn given an incomplete supervisory signal.
Specifically, we begin with an analysis of the amount of supervision needed to learn all visual variations of an object part. Motivated by the gathered observations, a detector of semantic (i.e. nameable) parts supervised with inexpensive web image search data is then proposed. The main challenge of handling a significant amount of annotation noise is addressed with a novel geometry-appearance embedding.
Moving away from semantic part detection, learning generic mid-level elements for understanding the geometry of object categories is brought into focus. A novel architecture that outputs a visual representation suitable for establishing image-to-image semantic correspondences is proposed. The main contribution consists of a new discriminability diversity objective that facilitates learning of sparse image features sensitive to the changes of the geometry of the input.
A similar feature learning machine leveraging the equivariance constraint is later introduced. Differently from existing alternatives, we adapt the method for the noisy settings of the training dataset by means of a novel probabilistic introspection framework. This allows for a selective representation of image pixels that have the potential to result in a correct match.
Inspired by the ability of deep networks to decompose an object into a constellation of pixel-perfect landmarks, an opposite problem of grouping image pixels belonging to an object is addressed. More specifically, we deal with the instance segmentation problem using a deep convolutional architecture that "colors" image pixels with their instance labels. Identifying the convolutional coloring dilemma, a drawback of standard position-agnostic networks that prevents them from solving this task, we propose a correction comprising a novel position-sensitive semi-convolutional operator.
The last tackled task is learning 3D shapes of object categories. Inspired by the human visual system, a deep network that learns by observing an object category in a sequence of videos is described.
Our final contribution is a probabilistic learning scheme that increases robustness of network training and enables test-time confidence predictions. This is achieved by explicitly modeling the distribution of training errors caused by the insufficiencies of the model or by the noise in ground truth annotations.

Keywords: ai
feature learning
machine learning
3d reconstruction
Computer vision
Advisor: Larlus, D
Vedaldi, A
Frequency metrology at the 10^−18 level with an ytterbium ion optical clock

Atomic clocks, the most accurate instruments in existence, are reaching new levels of precision. These devices now find novel uses—from the exploration of relativity [1] to the detection of dark matter [2, 3]—all from same principle: measurement of the frequency of the light that excites a reference atomic transition. The 2S1/2 (F 0) → 2F7/2 (F 3) electric octupole (E3) transition in 171Yb+, with its Δν ≈ 1 nHz [4] linewidth and low sensitivity to external electromagnetic fields, lends itself to this usage [5].
We probe this transition in a single 171Yb+ ion held in a newly-designed endcap RF trap [6]. This design achieves a low temperature rise of 0.14(14)K. Excess micromotion in the trap is automatically compensated, resulting in a fractional frequency uncertainty of the combined RF-Stark and 2nd order Doppler shifts of 3.6 × 10−19. Anomalous phonon heating rates in the radial plane were measured as (−4.9 ± 5.2) s−1 and (−1.3 ± 3.6) s−1 for secular frequencies of 446 kHz and 470 kHz.
The ion’s differential polarisability at λ = 7 μm has been measured, suggesting a reduction in the BBR-related systematic error of the electric quadrupole (E2) transition by a factor of 5 and confirming the results of a previous measurement for the E3, performed using a different method [7]. However, a limitation prevented full confidence in our uncertainty levels.
To pre-stabilize the frequency of our laser a 28 cm long, ultra-stable Fabry-Pérot cavity was constructed and used to drive the E3 atomic resonance with a linewidth of 1.64(2) Hz. Its finesse was measured as 458 000 and, in an atomic lock, a clock stability of 1.9 × 10−15 (τ/1 s)−1/2 was observed. The laser’s frequency was measured and its stability transferred to other wavelengths via a femtosecond optical frequency comb.
An international clock comparison campaign was carried out via satellite-mediated microwave links: the first of its scale, involving 4 National Measurement Institutes (NMIs) and 5 optical atomic clocks. A new technique was developed to analyse the resulting data and to characterize its uncertainty. The lowest fractional uncertainty in the comparison between any pair of clocks was 2.8 × 10−16.
Finally, an absolute measurement of the E3 transition has been carried out through a link to International Atomic Time (TAI), without a local primary standard. The transition frequency was measured to be 642 121 496 772 645.17(22) Hz: the best measurement of this transition to date [8, 9].

Keywords: optical clock
atomic clock
frequency
time
metrology
atomic physics
ytterbium
Advisor: Baird, P
Godun, R
Sterile activation of invariant natural killer T cells by ER-stressed antigen presenting cells

Invariant NKT (iNKT) cells are a subset of innate-like lymphocytes that recognize lipid antigen presented on monomorphic CD1d molecules. These cells have the unique ability to shape immunity during anti-tumour immune responses and other forms of sterile and non-sterile inflammation. Recent studies have highlighted a variety of classes of endogenous and pathogen-derived lipid antigens that can trigger iNKT cell activation under sterile and non-sterile conditions. However, the context and mechanisms that drive the presentation of self-lipid antigens in sterile inflammation remain unclear. Given that ER-stress is prevalent during tumourigenesis coupled with the intersection between the ER-stress pathways and lipid metabolism, we hypothesized that ER-stressed CD1d+ cells might present immunogenic self-lipid(s) on CD1d molecules to activate iNKT cells in sterile conditions. We demonstrate that ER-stressed dendritic cells activated iNKT cells in a CD1d-dependent manner, which in turn promotes dendritic cell maturation. We illustrate that PERK signalling increases CD1d-mediated presentation of immunogenic endogenous lipid species. We demonstrate that the immunogenic self-lipid(s) are likely ceramide-based and loaded onto CD1d in the endosomal/lysosomal compartments. We also investigate the relevance of this mechanism in a human tumour setting by analysing iNKT cell responses to multiple myeloma cell lines and identifying ER-stressed myeloid cells in the tumour microenvironment. In conclusion, this work defines a previously unidentified mechanism that controls iNKT cell activation during sterile inflammation, with a potential role in human health and disease.

Keywords: cancer
ER-stress
iNKT cells
Advisor: Cerundolo, V
Enantioselective desymmetrisation towards the synthesis of daphniphyllum alkaloids

Chapter One introduces the Daphniphyllum alkaloids and the Calyciphylline A- type alkaloid sub-family, including proposed biosyntheses and recently reported total syntheses. The morphan core is introduced, and methods for its synthesis are dis- cussed, with a focus on enantioselective desymmetrising cyclisations.
Chapter Two details the development of a Pd(II)/secondary amine co-catalysed desymmetrising cyclisation for the enantioselective synthesis of the morphan core. The method addresses several limitations of previous methods, and provides access to a broad range of products including trisubstituted alkenes.
Chapter Three details the preparative synthesis of the morphan core via an enantioselective desymmetrisation reaction on up to 20 g scale. Functionalisation of the bicyclic core is discussed, including a diastereoselective hydrogenation to afford the desired stereochemical configuration.
Chapter Four describes the synthesis of the tetracyclic core common to many Daphniphyllum alkaloids. An intramolecular Michael addition reaction is used to form the five-membered lactam, while the seven-membered ring is constructed by ring closing metathesis.
Chapter Five details a range of synthetic strategies investigated in an attempt to construct the pentacyclic core of the Calyciphylline A-type alkaloids in an effort to achieve a total synthesis. Some of the key approaches investigated include an aldol condensation, a 5-endo-dig cyclisation, and a [3+2] cycloaddition.

Keywords: Asymmetric catalysis
Dual catalysis
Organocatalysis
Natural product synthesis
Alkaloids
Enantioselective desymmetrisation
Total synthesis
Advisor: Dixon, DJ
Biodegradable pulsatile release technologies for viral vector based vaccinations

Vaccines are arguably the greatest public health intervention of modern era medicine. Most vaccines, in order to be effective require multiple doses. This is disadvantageous as there is an increasing trend towards non-compliance with subsequent doses. Viral vectored vaccines represent arguably the next generation of vaccines but they too often require a heterologous prime-boost approach such as the use of Adenoviral-MVA vectors. This thesis describes work utilising biodegradable microparticulate and non-microparticulate technologies to attempt to transform vaccination regimes from multiple into one single injection. Both technologies were tested using the heterologous Adenoviral-MVA prime-boost regime. A novel and virus-tailored encapsulation using the solvent triacetin and qPCR-based quantification methodology is proposed for the microencapsulation of MVA virus in biodegradable PLGA or PLA microparticles. Immunogenicity studies comparing routine prime-boost using 2 injections compared to single-dose administration of soluble Adenovirus with encapsulated MVA virus in PLA microparticles, showed comparable immune responses after 8 weeks. However true pulsatile release kinetic based on T-cell and antibody response kinetics was not observed. When experimentally tested with malarial sporozoite challenge the same formulation failed to provide comparable protective immune responses with a single immunisation after 5 weeks. Further work is still required to manufacture more uniform and reproducible formulations. This work is a significant improvement in the field of viral vector encapsulation in solid polymeric matrices, which could benefit not only human vaccination but also veterinary, including fish vaccination, improving quality of life, reducing public health costs and ultimately saving more lives.

Keywords: malaria
viral vectors
microparticles
vaccines
biodegradable
Advisor: Hill, A
Development of feedback algorithms for future linear colliders

The Feedback On Nanosecond Timescales (FONT) intra-train feedback system has been designed to provide beam stabilisation at the interaction point (IP) of a future linear collider, such as the International Linear Collider (ILC). A prototype system based around cavity Beam Position Monitors (BPMs) is installed in the final focus system at the Accelerator Test Facility (ATF2) at KEK, and is designed to demonstrate nanometre-level stabilisation using low-latency beam-based feedback. One focus of this thesis is the development of this prototype system, including the optimisation of the BPM resolution and the improvement of the beam stabilisation performance. The feedback system was tested on trains of two bunches with a separation of 280 ns, for which the position of the first bunch was measured and the subsequent bunch was stabilised. The correction was implemented using a stripline kicker, with a custom power amplifier, and the feedback calculations were performed on a FONT5A digital board built around a Field Programmable Gate Array (FPGA).
Studies of the BPM resolution are presented, highlighting the importance of sample integration of the BPM waveforms in improving the resolution from ˜ 40 nm to ˜ 20 nm. Recent improvements to the FPGA firmware allow for the use of waveform integration during feedback operation. The feedback loop can be configured to include either input from a single BPM to provide local beam stabilisation, or to use signals from two BPMs to stabilise the beam at an intermediate location. Stabilisation to 50 nm and 41 nm have been demonstrated for 1-BPM and 2-BPM feedback respectively.
The ATF2 extraction-line feedback system has demonstrated the latency, resolution and correction range required for an ILC IP feedback system. Simulations were performed to show that a similar feedback system could be used to provide the required level of luminosity recovery and stabilisation for the ILC. The beam transport was modelled using PLACET and the beam-beam interactions were simulated in GUINEA-PIG. A bunch-by-bunch IP feedback system was modelled in Octave, for which various feedback algorithms were investigated. Ground motion, the jitter of the damping-ring extraction kicker and wakefields were modelled and preliminary studies suggested that the proposed feedback system could help achieve ˜ 95% of the design luminosity.

Advisor: Burrows, P
Evaluating the effects of dengue virus and  iminosugar treatment on  cellular unfolded protein response  and redox homeostasis

Dengue virus (DENV) infections cause significant morbidity worldwide. The complex host-viral interactions affecting viral replication and the host immune response result in variable disease severity in affected individuals. This thesis focuses on two such host responses implicated in DENV pathogenesis; unfolded protein response (UPR) and oxidative stress. DENV preferentially activated the proviral and pro-inflammatory IRE1-XBP1 arm of the UPR in monocyte-derived macrophages in vitro. Investigation of redox homeostasis revealed induction of reactive oxygen species and increase in total antioxidant capacity in DENV- infected macrophages. Further evaluation of peripheral blood mononuclear cells during early DENV-infection revealed increased XBP1s and reduced DDIT3 and HSPA5 transcripts in affected individuals who later developed severe dengue disease. Proteomics performed on the cell lysates revealed upregulation of the IRE1-mediated UPR pathway and differential expression of several protein markers in individuals who developed severe disease compared to non-severe disease potentially providing a foundation to develop markers of DENV disease severity.
Iminosugars are broad spectrum antivirals targeting host ER glucosidases causing antiviral effects against DENV. The effects of iminosugars have not previously been studied in DENV-infected dendritic cells. The percentage of infected cells and secretion of DENV were reduced in dendritic cells treated with three DNJ-derived iminosugars in a dose-dependent manner. The specific infectivity was reduced at iminosugar doses exceeding 3.16 M which inhibited -glucosidase I. Furthermore, DENV-induced TNF levels were reduced with iminosugar treatment. Evaluation of the UPR in DENV-infected and 2THO-DNJ treated macrophages revealed a reduction in XBP1s levels compared to untreated cells and an increase in EDEM1 and ERDJ4 transcripts. However, the UPR was not required for the antiviral or anti-inflammatory effects of the iminosugar 2THO-DNJ. ROS levels and antioxidant capacity were also reduced in DENV-infected macrophages following treatment with 2THO-DNJ and MON-DNJ.
Overall, this thesis describes the role of the UPR and oxidative stress in DENV infection and the effect of iminosugars on these host responses.

Keywords: unfolded protein response
iminosugars
dengue virus
Advisor: Zitzmann, N