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Language Use, Monitoring, and Repair in the Social and Narrative Discourse of Children with and without ADHD
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of Philosoph
Non-Markovian Epidemic Spreading on Complex Networks
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyIn this thesis, we investigate the rate at which an epidemic propagates through a random, complex network. Traditional epidemiology associates a pathogen’s infectiousness and basic reproduction number with the epidemic’s spreading rate but typically assumes homogeneous mixing, thereby neglecting the underlying network structure. Conversely, network theory accounts for structural complexity but often relies on Markovian assumptions with constant spreading rates. In practice, the infectiousness of an individual varies over time, depending on when the infection was contracted. To reconcile these perspectives, we develop a framework that accurately describes the exponential spreading rate of an epidemic in a network under realistic, time-dependent infectiousness. We find an expression for the reproduction number that incorporates key features of a network: degree distribution, assortativity, and clustering. We then connect this network-based reproduction number and the pathogen’s infectiousness profile to the spreading rate of the epidemic. Furthermore, we propose a computationally efficient and exact method to simulate epidemics with arbitrary infectiousness on large networks, surpassing alternative approaches. We extend this method to networks whose structure varies over time and provide a user-friendly software implementation for practical use
An Investigation into Inter-brain Synchrony using Simulation and Experimental Approaches
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyOver the past two decades, advancements in neuroimaging technologies have enabled the simultaneous imaging of two brains with increasing spatial and temporal resolution, revealing that interacting participants can synchronise their brain signals, a phenomenon known as inter-brain synchrony (IBS). This thesis deepens research into how IBS can occur, investigating along several dimensions: the minimal requirements for IBS, the role of the body, and the brain-behaviour relationship. I rely on two research paradigms to carry out this investigation: computer simulations, which examine IBS through an evolutionary framework, and human subject experiments, which include a minimalistic perceptual crossing task in a simple virtual environment and a rhythmic video game experiment. These inquiries lead to several important findings and implications for the study of IBS and social cognition more broadly: 1) the body manifests dynamics at slower behavioural timescales that regulate faster neural signals; 2) the possibility of alpha-band IBS, even in touch-based interactions in minimally shared environments, challenges the notion that IBS is merely an epiphenomenon; 3) the type of interaction (alternating or simultaneous) influences IBS; and 4) greater IBS is not inherently better. Overall, this thesis advances theoretical and empirical understanding of IBS within neuroscience and explore its broader cultural implications
Predicting Future Ant Invasions and Assessing Community Dynamics After Establishment
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyAs humans have spread and increasingly dominated the planet, other species have also been introduced to places beyond their natural dispersal capacity. Some of these species have become costly invasives causing severe damage in human lives and producing negative impacts on the environment and native biodiversity. Invasive ants are among the most damaging invasive species, with hundreds of species known to be spreading around the world. In this dissertation I study pre-establishment risks and post-establishment long term effects from a community perspective using the whole ant family (Hymenoptera: Formicidae). In the first chapter, I include relevant background information to the topic and study systems. In the second chapter, I forecast the risk of establishment for Japan from the global pool of alien ants. I derive potential source hotspots from around the globe using a new workflow built around species distribution modeling. These predictions are intended to help policy-makers implement better preventive programs for cargo coming from different regions of the world. I show that there is a latitudinal effect on the invasion risk and that the remote islands of Japan are at highest risk. The species identified as threats are most numerous in temperate European areas and the subtropical American continent, which could become the main sources of new invasive species to different regions of Japan. In the third chapter, I investigate how seasonality and land cover differences shape the spatial and temporal activity density of ant communities of different historical presence (native vs. alien) to the island of Okinawa in Japan using a hierarchical joint species distribution modeling approach. I demonstrate that, even long after the first introduction, alien ants have a distinct usage of the environment than native ants. Native species' activity is mainly driven by high temperatures with a strong phenological effect which results in high activity during spring and summer. Meanwhile alien species' activity have more types of responses to temperature and humidity, with most of them active at the colder and less humid seasons. Species are also spatially structured by land cover, as expected from invasion ecology, native species are most active in forested areas while alien species dominate urban environments, and both guilds are similarly active in open areas like agricultural land. In the fourth chapter, I include how these studies may be followed, general conclusions and highlight the need for extra preventive measures as the number of potential new invaders is higher than current invaders and past invasions show that alien species are able to exploit niches that native ants cannot, and include potential avenues to continue these research studies
Ion Trapping with a Laser-written 3D Miniaturized Monolithic Linear Paul Trap for Microcavity Integration
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThis thesis investigates the integration of microcavities into linear Paul traps as a critical step toward scalable trapped-ion quantum computing. While trapped ions offer high-fidelity operations and long coherence times, scaling to the large qubit numbers required for fault-tolerant computation presents significant challenges. Efficient photonic interconnects, essential for modular architectures like MUSIQC, can be made possible with an efficient ion-cavity interface. Specifically, a microcavity of length of a few hundred micrometers is desired. To this end, we designed, fabricated, and characterized a miniaturized linear trap compatible with the microcavity integration. We addressed technical barriers such as RF potential distortion from cavity shields, and show that the effect can be suppressed by shield design and enable single-RF driving. In addition, we analyze the impact of dielectric charging on secular frequency shifts and propose a correction method for stray electric fields. This work advances both the theoretical understanding and practical implementation of cavity-integrated ion traps, laying the groundwork for robust, modular trapped-ion quantum processors
Identification of Functional miRNAs Regulating Plasma Membrane Damage-dependent Senescence in Human Fibroblasts
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyDamage to the plasma membrane is common in nature, caused by a variety of triggers ranging from physical damage to cell-autonomous activities. Our previous study has revealed that cellular senescence, a state of irreversible cell cycle arrest that contributes to organismal aging, is one of the cellular outcomes that can be triggered by plasma membrane damage. Upon the induction of plasma membrane damage-dependent senescence (PMD-Sen), human diploid fibroblasts exhibit senescence features, including increased β-galactosidase activity, the manifestation of senescence-associated secretory phenotypes, and the upregulation of senescence marker proteins, including p53, p21, and p16. However, the molecular mechanisms underlying PMD-Sen remain unclear. Given that substantial alterations in gene expression are associated with the onset of senescence, it is essential to investigate the regulatory mechanisms responsible for gene expression changes during cellular senescence. MicroRNAs (miRNAs), a large class of small noncoding RNAs, have been identified as critical regulators of gene expression by targeting messenger RNAs (mRNAs). When miRNAs bind to the 3’ untranslated region (3’UTR) of target mRNAs, they primarily inhibit translation or promote degradation of the target mRNAs. In this study, to identify regulatory miRNA-mRNA pairs in PMD-Sen cells, I performed an integrated analysis of miRNA and mRNA expression profiles in a time-resolved manner. My analysis suggests that a total of 2495 miRNA-mRNA pairs, comprising 65 miRNAs, are involved in the process of PMD-Sen. The results support the hypothesis that miRNAs regulate senescence induction by post-transcriptionally regulating their target mRNAs. Furthermore, an overlap was identified between the set of miRNA-mRNA pairs implicated in PMD-Sen and DNA damage-induced senescence (DDR-Sen), leading to the identification of 41 shared miRNAs in the pairs. This suggests common regulatory miRNA-mRNA pairs across different senescent cell subtypes. Notably, miR-155-5p emerged as the miRNA with the largest number of shared miRNA-mRNA pairs that exhibit a highly negative correlation. These findings imply that miR-155-5p may have a role in PMD-Sen and DDR-Sen
Towards Quantum Networks with Color Centers in Diamond
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyConnecting cryogenic solid-state quantum processors with room-temperature optical links is a key step toward a scalable quantum computer. This thesis presents two technological advancements toward the realization of a spin-ensemble-based quantum transducer using impurity spins in diamond. First, a low-loss dielectric microwave resonator based on rutile (TiO2) was developed, achieving an internal quality factor of Qint ∼ 104 despite incorporating large optical apertures. Second, an optical Fabry–Pérot cavity was stabilized at millikelvin temperatures with sub-0.1 nm root-mean-square cavity length fluctuations, enabling stable cavity locking to the laser in a dilution refrigerator. These components were integrated into a hybrid resonator enabling spatial mode overlap within a diamond sample containing an ensemble of nitrogen-vacancy centers. Measurements at 10 mK revealed spin coherence times of T1 = 1930 s and T2 = 470 µs, and characterized the inhomogeneous broadening of the optical transition. We estimate the current microwave-to-optical conversion efficiency and discuss potential improvements through device and cavity optimization. This work establishes a platform for spin ensemble-based transducers operating at millikelvin temperatures
Dynamic Change of Microglial States Across Onset of Degeneration and Müller Glia- Mediated Regeneration in a Zebrafish Model of Chronic Photoreceptor Degeneration Caused by pde6c Dysfunction
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyMicroglia are immune sentinels of the central nervous system and contribute to the progression of acute retinal degeneration. However, the role of microglia at different stages of chronic degeneration is still unclear. Our lab has previously characterized zebrafish cyclic GMP-dependent phosphodiesterase 6c (pde6c) mutants, in which cones degenerate progressively over the lifespan of the fish. Rods are initially malformed but recover from 4 weeks post fertilization onwards through Müller glia-mediated regeneration. Taking advantage of this unique model, I investigate microglial responses to onset of degeneration and start of regeneration, as well as microglial heterogeneity, in the pde6c mutant retina. At onset of degeneration, microglia play a globally neuroprotective role by phagocytosing dying photoreceptors and upregulating neuroprotectionlinked genes, including p2ry12. I discover three distinct clusters of microglia, which all migrate towards the photoreceptors. Of these, the apoeb-enriched cluster 5d_Mg1 is the most reactive and expresses oxidative phosphorylation genes associated with repair. At start of regeneration, microglia hamper Müller glial proliferation in a time-dependent manner and express proinflammatory cytokine il1b. I discover two homeostasis-associated clusters and two diseaselinked clusters at this stage. One homeostatic cluster patrols the inner retina, while the other is a stem cell niche-associated, apoeb-enriched cluster. The two disease-linked clusters show pro- and anti-inflammatory characteristics respectively, are rare in the sibling, and associate principally with the photoreceptor outer segments in the mutant retina. This work provides the first characterization of microglial states in the homeostatic and chronically degenerating zebrafish retina, identifies candidate microglial states for future investigation, and emphasizes the critical role of timing on the impact of microglia on retinal degeneration
Light Interaction with Cold 87Rb Ground and Rydberg States via an Optical Nanofiber and in an Optical Resonator
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe combination of cold Rydberg atoms and optical nanofibers (ONF) has the potential for creating robust quantum information devices. This thesis presents our work on the interfacing of cold 87Rb Rydberg atoms with an ONF. The first experiment examines creating Rydberg atoms near ONFs, focusing on the highest principal quantum number, n, for observable excitation and studying the behavior of nS1/2, nD3/2 and nD5/2 Rydberg states. We also present a laser locking technique that uses EIT with the Zeeman sublevels of an 87Rb Rydberg level that allows for continuous tuning over 0.6 GHz. In addition, theoretical models of state-insensitive magnetic traps for ground and Rydberg state atoms, based on a combination of ONF light-induced and external magnetic fields, as well as ONF and optical tweezers light-induced magnetic fields are developed. Finally, we present experiments on spin excitations in an ensemble of cold 87Rb atoms coupled to an optical cavity, achieving a spin-wave to single-photon conversion efficiency of χ = 0.75. These investigations strengthen the knowledge for future research on Rydberg atoms, ONFs, and optical resonators for quantum information applications
Information-Theoretical Analysis of Team Dynamics in Football Matches
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThis thesis investigates how coordinated behavior emerges within football teams by applying information-theoretic frameworks to spatiotemporal player tracking data.
The first part of the thesis applies the causal emergence framework to 34 professional football matches, demonstrating that spatially defined macro-level features provide stronger explanatory power than their micro-level origins based on published work. This analysis reveals that emergent coordination is closely linked to match-critical situations including possession rate and shooting.
The second part applies integrated information to the same dataset, revealing higher integration during defensive phases, which is opposite to the causal emergence results. This divergence reflects the frameworks’ differing emphases: integrated information captures internal irreducibility, while causal emergence highlights differentiated roles. Simulation based validation supports this interpretation.
The third part analyzes transfer entropy matrices to uncover latent patterns of players’ interaction. Clustering in TE space reveals consistent separation between static and active phases, while non-negative matrix factorization (NMF) identifies dominant interaction components linked to key match events.
Together, these analyses demonstrate the complementary strengths of causal emergence, integrated information, and transfer entropy in characterizing multiscale patterns of coordination in team sports. The thesis offers practical insights relevant to fields ranging from sports analytics to collective systems