VictorJuiz/thesis huggingface dataset:
Forward looking logics and automata
Keywords: minimization
logics
automata
logical characterization

This thesis is concerned with extending properties of regular word languages to richer structures. We consider intricate properties like the relationship between one-way and two-way temporal logics, minimization of automata, and the ability to effectively characterize logics. We investigate whether these properties can be extended to tree languages or word languages over an infinite alphabet.
It is known that linear temporal logic (LTL) is as expressive as first-order logic over finite words [Kam68, GPSS80]. LTL is a unidirectional logic, that can only navigate forwards in a word, hence it is quite surprising that it can capture all of first-order logic. In fact, one of the main ideas of the proof of [GPSS80] is to show that the expressiveness of LTL is not increased if modalities for navigating backwards are added. It is also known that an extension of bidirectional LTL to ordered trees, called Conditional XPath, is first-order complete [Mar04]. We investigate whether the unidirectional fragment of Conditional XPath is also first-order complete. We show that this is not the case. In fact we show that there is a strict hierarchy of expressiveness consisting of languages that are all weaker than first-order logic. Unidirectional Conditional XPath is contained in the lowest level of this hierarchy.
In the second part of the thesis we consider data word languages. That is, word languages over an infinite alphabet. We extend the theorem of Myhill and Nerode to a class of automata for data word languages, called deterministic finite memory automata (DMA). We give a characterization of the languages that are accepted by DMA, and also provide an algorithm for minimizing DMA.
Finally we extend theorems of Büchi, Schützenberger, McNaughton, and Papert to data word languages. A theorem of Büchi states that a language is regular iff it can be defined in monadic second-order logic. Schützenberger, McNaughton, and Papert have provided an effective characterization of first-order logic, that is, an algorithm for deciding whether a regular language can be defined in first-order logic. We provide a counterpart of Büchi's theorem for data languages. More precisely we define a new logic and we show that it has the same expressiveness as non-deterministic finite memory automata. We then turn to a smaller class of data languages, those that are recognized by algebraic objects called orbit finite data monoids. We define a second new logic and show that it can define precisely the languages accepted by orbit finite data monoids. We provide an effective characterization of a first-order variant of this second logic, as well as of restrictions of first-order logic, such as its two variable fragment and local variants.
Quasi-static impact of foldcore sandwich panels
Keywords: origami
folded shell structures
curved-crease
quasi-static impact
single-curved sandwich shell
foldcore

This thesis considered the design of new and improved foldcore sandwich panels suitable for high-performance energy absorption applications. This was achieved by utilising origami geometry design techniques to alter foldcore structures such that they possessed different mechanical behaviours and failure modes. The major findings of this thesis were in three areas as follows.
First, a modified planar foldcore geometry was developed by introducing sub-folds into a standard foldcore pattern. The new geometry, deemed the indented foldcore, successfully triggered a high-order failure mode known as a travelling hinge line failure mode. This was found to have a much higher energy absorption than the plate buckling failure mode seen in an unmodified foldcore structure. A comprehensive numerical, theoretical, and experimental analysis was conducted on the indented core, which included the development of a new foldcore prototyping method that utilised 3D printed moulds. It was shown that compared to available commercial honeycomb cores, the indented foldcore had an improved uniformity of energy absorption, but weaker overall peak and crushing stresses.
Second, rigid origami design principles were used to develop extended foldcore geometries. New parametrisations were presented for three patterns, to complete a set of Miura-derivative geometries termed first-level derivatives. The first-level derivative parametrisations were then combined to create complex, piecewise geometries, with compatible faceted sandwich face geometry also developed. Finally, a method to generate rigid-foldable, curved-crease geometry from Miura-derivative straight-crease geometry was presented. All geometry was validated with physical prototypes and was compiled into a MATLAB Toolbox.
Third, the performance of these extended foldcore geometries under impact loadings was investigated. An investigation of curved-crease foldcores showed that they were stronger than straight-crease foldcores, and at certain configurations can potentially match the strength, energy-absorption under quasi-static impact loads, and out-of-plane stiffness of a honeycomb core. A brief investigation of foldcores under low-velocity impact loadings showed that curved-crease foldcores, unlike straight-crease foldcores, strengthened under dynamic loadings, however not to the same extent as honeycomb. Finally, an investigation of single-curved foldcore sandwich shells was conducted. It was seen that foldcore shells could not match the energy-absorption capability of an over-expanded honeycomb shell, but certain core types did exhibit other attributes that might be exploitable with future research, including superior initial strength and superior uniformity of response.
Origin and evolution of the Santiaguito lava dome complex, Guatemala
Keywords: lava domes
volcanology
Santiaguito

Subduction zone volcanoes are a major natural hazard, frequently endangering lives and livelihoods. The eruptive history of many subduction zone volcanoes includes the extrusion of blocky, silicic lava that forms domes or flows, but we do not yet understand what determines the duration of dome-forming behaviour, what path magma may take to the surface, or how these systems may change over time.
This thesis presents an investigation of the Santiaguito complex of lava domes and flows in Guatemala, which has been erupting continuously since its inception in 1922. The Santiaguito lavas are predominantly dacitic to andesitic, with a gradual reduction in SiO2 content from ~66 wt% in the 1920s, to ~62 wt% in 2002. This is consistent with a ~15% decrease in the extent of fractional crystallization over that time. The compositions of plagioclase phenocryst cores indicate a diminished role for magma mixing after the 1940s.
I model the Santiaguito system as progressively extracting magma from an extensive, chemically-stratified storage zone. Petrological data are consistent with a storage zone extending from ~25 to ~12 km depth, and magma storage temperatures of ~940 to ~980°C. Phenocryst-hosted apatites suggest melt in this storage zone contained 401 to 1199 ppm S, 600 to 1300 ppm F, and 4100 to 6200 ppm Cl. Ascending magma may pass slowly through a conduit bottleneck, or plug, at shallow depths; groundmass texture suggests that melt rigidifies at or near the base this plug. Pre-eruptive melt volatile concentrations suggest time-averaged fluxes of 40 to 263 Mg d-1 SO2, 32 to 145 Mg d-1 HF, and 247 to 708 Mg d-1 HCl, giving ratios of 0.6 to 0.8 HF/SO2, and 2.7 to 6.2 HCl/SO2. These results are consistent with the few direct measurements of SO2 at Santiaguito, and with measured halogen emissions from other silicic dome-forming systems.
Uncovering latent features in massive open online courses
Keywords: Machine learning
network analysis
online learning
education

Massive Open Online Courses (MOOCs) bring together a global crowd of thousands of learners for several weeks or months. We use social network analysis and community detection to uncover the latent features of online discussions in MOOCs. We begin by using data from two successive instances of a popular business strategy MOOC to filter observed communication patterns and arrive at the "significant" interaction networks between learners. We then use complex network analysis to explore the vulnerability and information diffusion potential of the discussion forums. While network analysis offers a vibrant post-hoc analytical framework, it fails to answer a fundamental question: can we devise a model to represent the generation of the dataset at hand?
Moving from the structural properties of global-scale discussion to the discussion content itself, we employ existing educational theories to qualitatively content-analyse over 6,500 forum posts from a particular MOOC. We then use a generative model - Bayesian Non-negative Matrix Factorization (BNMF) - to extract communities of learners based on the nature of their online forum posts. We observe that the inferred communities are differentiated by the nature and topic of dialogue, as well as their composite students' demographic and course performance indicators. While qualitative analysis confirms these detected communities, additional quantitative sensitivity analysis shows that they are not crisply defined, illuminating key challenges of applying Machine Learning techniques to model noisy and incomplete learner data.
We conclude by discussing the key insights of this work for online education, namely, that different discussion topics and pedagogical practices promote varying levels of peer-to-peer engagement. Additional qualitative investigations reveal that many learners feel a sense of "content-overload" when deciding to participate in online discussions, often leading to their disengagement. These insights call for an interdisciplinary effort to help create relevant and personalized learning experiences in massive scale online settings.
Single molecule fluorescence studies of viral transcription
Keywords: single-molecule fluorescence
viral transcription
Reoviridae

Rotaviruses are the single most common cause of fatal and severe childhood diarrhoeal illness worldwide (>125 million cases annually). Rotavirus shares structural and functional features with many viruses, such as the presence of segmented double-stranded RNA genomes selectively and tightly packed with a conserved number of transcription complexes in icosahedral capsids. Nascent transcripts exit the capsid through 12 channels, but it is unknown whether these channels specialise in specific transcripts or simply act as general exit conduits; a detailed description of this process is needed for understanding viral replication and genomic organisation. To test these opposing models, a novel single-molecule assay was developed for the capture and identification (CID) of newly synthesised specific RNA transcripts. CID combines the hybridisation of transcripts with biotinylated and FRET compatible labelled ssDNAs with the implementation of recent developments in single molecule fluorescence such as alternating laser excitation (ALEX) and total internal reflection fluorescence (TIRF) microscopy. CID identifies and quantifies specific transcripts of rotavirus based on a FRET/Stoichiometry (E*/S) value of the hybridised labelled probes. I used CID to pull down the capsid on the surface slide and identify partially extruded transcripts of three different segments 2, 6 and 11. The findings presented in this thesis support a model in which each channel specialises in extruding transcripts of a specific segment, that in turn is linked to a single transcription complex. The method can be extended to study other transcription systems including E.coli, and can be further developed as a potential diagnostic tool.
On the endurance of indigenous religious culture in Ptolemaic and Roman Egypt: evidence of material culture
Keywords: Egyptian religious culture
Egyptian priests
Alexandrian tombs
Graeco-Roman Egypt
hard-stone statuary
Egyptian numismatics
Egyptian temples

The aim of this thesis is to examine changes in the status of traditional Egyptian religious culture during the Ptolemaic and Roman periods, from 331 BCE to 313 CE. Four distinct categories of material culture are examined: monumental construction of temples and civic buildings, traditional hard-stone sculpture, Alexandrian tombs, and Roman coins. These bodies of evidence were chosen because each offers a unique perspective, reflecting respectively the personal inclinations and official attitudes of both the culturally Hellenic and indigenous elites, which have not previously been studied in this context. Examined together for the first time, these categories reveal commonalities that show clearly the progression of the status of indigenous religious culture. From this, it is argued that, despite being economically disadvantaged by the Roman administration, the high status of this culture persisted in Egyptian society under both the Ptolemies and the Romans.
Patterns of Egyptian temple and classical civic building show that Egypt's indigenous elite controlled the resources allocated for temple construction under the Ptolemies, but that the Romans gradually transferred this land into the management of the culturally Hellenic elite. This resulted in a decrease in Egyptian temple building after the first century CE and a corresponding increase in classical construction from then on. The production of hard-stone statues is shown for the first time to reveal that the indigenous elite had the resources and cultural confidence to continue and develop their traditions under the Ptolemies, while the sharp decrease at the start of the Roman period reflects their diminution in autonomy and prosperity under Roman rule.
New analysis of traditional elements and motifs in the tombs of Alexandrian elites shows that this group respected and adopted indigenous religious customs and beliefs, with a higher incidence of indigenous imagery in the Roman period compared with the Ptolemaic period. In a similar way, well-informed Egyptian religious iconography rendered in a classical style on Alexandrian coins demonstrates the respect of the Roman authorities for Egyptian religious cults and institutions at an official level.
In sum, it is argued that indigenous religious culture largely maintained its privileged economic and social status throughout the Ptolemaic period, despite political upheavals. Under Roman rule, the individuals and institutions representing Egyptian religious culture were disadvantaged economically; however, its social importance and standing were preserved and it continued to enjoy respect.
Lim-only domain proteins in developmental haematopoiesis
Keywords: Zebrafish
Haematopoietic Stem Cell
Lmo proteins

The production of adult blood initiates from the haematopoietic stem cell (HSC). This clinically important cell has the capacity to maintain all blood lineages throughout the lifetime of an organism. HSCs emerge de novo from the haemogenic endothelium in the ventral wall of the embryonic dorsal aorta, from where they go on to seed adult sites of haematopoiesis. We have shown that Lmo4a is required for the emergence of HSCs in the zebrafish, and go on to demonstrate that Lmo4a regulates expression of the critical transcription factor, gata2a. Strikingly, both over- and under-expression of gata2a in the dorsal aorta severely diminishes HSC production. The LIM-only domain protein Lmo4 has previously been shown to interact with the known haematopoietic regulator, Ldb1. Together with our collaborators, we have identified novel binding partners of Lmo4 in mouse erythroleukaemic cells. Our functional analysis shows that many of these partners are also necessary for HSC emergence, thus revealing several new potential regulators of HSC formation. Given that these proteins were identified in an in vitro model of definitive erythropoiesis, it is remarkable that they also appear to act together in vivo at the level of HSC formation, and our data suggests that a transcriptional complex containing Lmo4 and these partners may directly repress gata2a. The related protein Lmo2 is also known to bind Ldb1. Together with Scl, Lmo2 is a master regulator of the haemangioblast programme. We have been utilising this activity, together with recent structural studies, to identify functionally important residues in the Lmo2 molecule. As a cell’s transcriptional programme drives both normal and pathological development, and misexpression of both Lmo2 and Lmo4 is involved in a variety of oncogenic states, the work presented in this thesis is likely to inform efforts to develop therapeutically relevant reagents.
Applications of optical-cavity-based spectroscopic techniques in the condensed phase
Keywords: molecular orientation
evanescent wave CRDS
magnetic field effects
cavity ring-down spectroscopy
cryptochrome
broadband CEAS
laser spectroscopy
cavity enhanced absorption spectroscopy
radical pair
photobleaching
optical cavity
fluorescence

Cavity ring-down spectroscopy (CRDS) and cavity enhanced absorption spectroscopy (CEAS) are two well-established absorption spectroscopic techniques originally developed for gas-phase samples. Condensed-phase applications of these techniques still remain rare, complicated as they are by additional background losses induced by condensed-phase samples as well as the intracavity components in which the sample is constrained. This thesis is concerned with the development and application of optical-cavity-based techniques in the condensed phase.
Polarization-dependent evanescent wave CRDS (EW-CRDS) has been used to study the molecular orientation at the solid/air and solid/liquid interfaces. An increase in average orientation angle with respect to the surface normal has been observed for both methylene blue and coumarin molecules as a function of coverage at the fused silica/air interface. An orientation-angle-dependent photobleaching of pyridin molecules at the fused silica/methanol interface have also been observed. EW-CRDS has also been used to monitor slow in situ photobleaching of thin dye films deposited on the prism surface. The photobleaching dynamics is interpreted as a combination of first- and second-order processes.
A significant fraction of this thesis has been devoted to studying magnetic field effects (MFEs) on the kinetics of the radical pair (RP) reactions in solution, in an effort to understand the ability of animals to sense the geomagnetic field. Two novel optical-cavity-based techniques – broadband CEAS (BBCEAS) and CRDS have been developed for this purpose. BBCEAS uses a supercontinuum (SC) source as the cavity light source and a CCD camera as photodetector, enabling simultaneous acquisition of absorption spectrum across the whole visible region (400 – 800 nm). In CRDS, a tunable optical parametric oscillator has been used as the cavity light source. Combined with the switching of external magnetic field (SEMF) method, this technique allows the decay kinetics of the geminate RPs to be monitored, with nanosecond resolution. Both BBCEAS and CRDS provide sensitivity superior to single-pass transient absorption (TA), a technique traditionally used in the MFE studies. A series of photochemical systems have been studied by BBCEAS and CRDS, respectively, among which, the MFEs of drosophila melanogaster cryptochrome has been observed. Importantly, this is the first time an MFE has been observed in an animal cryptochrome, and provides key supporting evidence for the cryptochrome hypothesis of magnetoreception in animals. Besides the optical-cavity-based techniques, a novel fluorescence detection method of MFEs has also been demonstrated. This technique proved ultrahigh sensitivity when applicable.
Cationic titanium amidinate and guanidinate complexes
Keywords: catalysis
Titanium
Inorganic chemistry

This Thesis describes the synthesis and characterisation of half-sandwich complexes supported by κ1-amidinate and κ1-guanidinate ligands as well as the cationic species produced on activation. The chemistry of the cationic species is detailed and DFT studies which have also been carried out to elucidate the bonding in relevant complexes are also presented.
Decisions under uncertainty: common processes in birds, fish and humans
Keywords: Decision Making
Sturnus vulgaris
Animal Behaviour
Starlings
Decision Making in Animals
Comparative Cognition

Decision making is a framework we impose on a vast universe of possible behaviors to better understand the advantages and disadvantages of acting in different ways. Decisions under uncertainty are of particular interest because stochasticity is a feature of environments both today and throughout evolutionary history. As a result, we might expect decision makers (DMs) to have evolved mechanisms to handle variability. In this dissertation, I examine common decision processes in several model species: European starlings (Sturnus vulgaris), Banded tetras (Astyanax fasciatus) and humans (Homo sapiens). The broad range of approaches discussed include currencies DMs are expected to maximize (Risk Sensitivity Theory, Expected Utility), the currencies DMs do maximize (e.g. long versus short term rate maximizing models), the representation of outcomes in memory (Scalar Expectancy Theory) as well as explicit choice mechanisms (Sequential Choice Model). The first section of this thesis discusses responses to risk, offering humans and starlings choices between options which deliver certain or variable outcomes. Starlings demonstrate sensitivity to changes in the probability of variable outcomes and strong support for local rate maximization. Humans appear similarly sensitive to their own accuracy when task difficulty is varied. When the DM’s affective state was manipulated, neither humans nor starlings exhibit changes in risk preferences, but the effectiveness of these manipulations used could not be confirmed. Another topic of inquiry is the effect of the DM’s state at the time of valuation learning. State dependent valuation learning is demonstrated for the first time in a fish species, but Within Trial Contrast is not observed in starlings. Lastly, two experiments find strong support for the Sequential Choice Model, a promising new model of the mechanism of choice. Taken together, these experiments offer a glimpse into shared decision processes, but leave open questions about the mechanisms through which value is acquired.