Living neural networks are capable of processing information much faster than a modern computer, despite running at significantly lower clock speeds. Therefore, understanding the mechanisms neural networks utilize is an issue of substantial importance. Neuronal interaction dynamics were studied using histiotypic networks growing on microelectrode arrays in vitro. Hierarchical relationships were explored using bursting (when many neurons fire in a short time frame) dynamics, pairwise neuronal activation, and information theoretic measures. Together, these methods reveal that global network activity results from ignition by a small group of burst leader neurons, which form a primary circuit that is responsible for initiating most network-wide burst events. Phase delays between leaders and followers reveal information about the nature of the connection between the two. Physical distance from a burst leader appears to be an important factor in follower response dynamics. Information theory reveals that mutual information between neuronal pairs is also a function of physical distance. Activation relationships in developing networks were studied and plating density was found to play an important role in network connectivity development. These measures provide unique views of network connectivity and hierarchical relationship in vitro which should be included in biologically meaningful models of neural networks.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18075号 / 理博第3953号 / 新制||理||1570(附属図書館) / 30933 / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 中村 卓史, 教授 柴田 大, 教授 畑 浩之 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20172号 / 理博第4257号 / 新制||理||1612(附属図書館) / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 谷森 達, 教授 永江 知文, 教授 鶴 剛 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20909号 / 理博第4361号 / 新制||理||1626(附属図書館) / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 柴田 大, 教授 井岡 邦仁, 教授 川合 光 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21680号 / 医博第4486号 / 新制||医||1036(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 伊佐 正, 教授 村井 俊哉, 教授 松原 和夫 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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Macrophages are a cornerstone in innate immunity, especially important in detecting and killing invading microorganisms. In tumor biology, the macrophages can contribute both to anti-tumor activity and tumor promotion depending on individual tumor microenvironment and therefore have a large impact on both tumor progression and prognosis. Two of the most important functions of macrophages are the ability to phagocytose microorganisms and then kill them through the respiratory burst. Phagocytosis activates the respiratory burst, but the more subtle interactions between these processes are less known. Since phagocytosis and reactive oxygen species production are two attributes that change between the classically and alternatively activated macrophages we decided to compare these two functions in macrophages. Activation of macrophages varies in terms of stimuli and effects. We specifically looked at macrophage activation by tumor cell lines and by chemical stimulation due to caffeine. We hypothesized that the level of oxidation would be directly linked to the level of phagocytosis. We assume that caffeine will increase activity in macrophages and that tumor cell co-incubation will decrease it. We found that there is a high correlation between the level of engulfment and level of respiratory burst. Chemical stimulation with caffeine can lower aggressiveness of macrophages at lower concentration, raise it at higher concentrations and eventually become toxic to the cell. Co-incubation with leukemic cell lines, as well with necrotic cells, affected an increase in aggressiveness.

Wavelength division multiplexed (WDM) optical networks are rapidly becoming the technology of choice in next-generation Internet architectures. This dissertation addresses the important issues of improving four aspects of optical networks, namely, routing efficiency, fairness, differentiated quality of service (QoS) and throughput. A new approach for implementing efficient routing and wavelength assignment in WDM networks is proposed and evaluated. In this approach, the state of a multiple-fiber link is represented by a compact bitmap computed as the logical union of the bitmaps of the free wavelengths in the fibers of this link. A modified Dijkstra's shortest path algorithm and a wavelength assignment algorithm are developed using fast logical operations on the bitmap representation. In optical burst switched (OBS) networks, the burst dropping probability increases as the number of hops in the lightpath of the burst increases. Two schemes are proposed and evaluated to alleviate this unfairness. The two schemes have simple logic, and alleviate the beat-down unfairness problem without negatively impacting the overall throughput of the system. Two similar schemes to provide differentiated services in OBS networks are introduced. A new scheme to improve the fairness of OBS networks based on burst preemption is presented. The scheme uses carefully designed constraints to avoid excessive wasted channel reservations, reduce cascaded useless preemptions, and maintain healthy throughput levels. A new scheme to improve the throughput of OBS networks based on burst preemption is presented. An analytical model is developed to compute the throughput of the network for the special case when the network has a ring topology and the preemption weight is based solely on burst size. The analytical model is quite accurate and gives results close to those obtained by simulation. Finally, a preemption-based scheme for the concurrent improvement of throughput and burst fairness in OBS networks is proposed and evaluated. The scheme uses a preemption weight consisting of two terms: the first term is a function of the size of the burst and the second term is the product of the hop count times the length of the lightpath of the burst.

Optical networking, employing wavelength division multiplexing (WDM), is seen as the technology of the future for the Internet. This dissertation investigates several important problems affecting optical circuit switching (OCS) and optical burst switching (OBS) networks. Novel algorithms and new approaches to improve the performance of these networks through effective routing and channel scheduling are presented. Extensive simulations and analytical modeling have both been used to evaluate the effectiveness of the proposed algorithms in achieving lower blocking probability, better fairness as well as faster switching. The simulation tests were performed over a variety of optical network topologies including the ring and mesh topologies, the U.S. Long-Haul topology, the Abilene high-speed optical network used in Internet 2, the Toronto Metropolitan topology and the European Optical topology. Optical routing protocols previously published in the literature have largely ignored the noise and timing jitter accumulation caused by cascading several wavelength conversions along the lightpath of the data burst. This dissertation has identified and evaluated a new constraint, called the wavelength conversion cascading constraint. According to this constraint, the deployment of wavelength converters in future optical networks will be constrained by a bound on the number of wavelength conversions that a signal can go through when it is switched all-optically from the source to the destination. Extensive simulation results have conclusively demonstrated that the presence of this constraint causes significant performance deterioration in existing routing and wavelength assignment (RWA) algorithms. Higher blocking probability and/or worse fairness have been observed for existing RWA algorithms when the cascading constraint is not ignored. To counteract the negative side effect of the cascading constraint, two constraint-aware routing algorithms are proposed for OCS networks: the desirable greedy algorithm and the weighted adaptive algorithm. The two algorithms perform source routing using link connectivity and the global state information of each wavelength. Extensive comparative simulation results have illustrated that by limiting the negative cascading impact to the minimum extent practicable, the proposed approaches can dramatically decrease the blocking probability for a variety of optical network topologies. The dissertation has developed a suite of three fairness-improving adaptive routing algorithms in OBS networks. The adaptive routing schemes consider the transient link congestion at the moment when bursts arrive and use this information to reduce the overall burst loss probability. The proposed schemes also resolve the intrinsic unfairness defect of existing popular signaling protocols. The extensive simulation results have shown that the proposed schemes generally outperform the popular shortest path routing algorithm and the improvement could be substantial. A two-dimensional Markov chain analytical model has also been developed and used to analyze the burst loss probabilities for symmetrical ring networks. The accuracy of the model has been validated by simulation. Effective proactive routing and preemptive channel scheduling have also been proposed to address the conversion cascading constraint in OBS environments. The proactive routing adapts the fairness-improving adaptive routing mentioned earlier to the environment of cascaded wavelength conversions. On the other hand, the preemptive channel scheduling approach uses a dynamic priority for each burst based on the constraint threshold and the current number of performed wavelength conversions. Empirical results have proved that when the cascading constraint is present, both approaches would not only decrease the burst loss rates greatly, but also improve the transmission fairness among bursts with different hop counts to a large extent.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24409号 / 理博第4908号 / 新制||理||1701(附属図書館) / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 柴田 大, 教授 井岡 邦仁, 教授 橋本 幸士 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM