京都大学 / 新制・課程博士 / 博士(薬学) / 甲第23845号 / 薬博第852号 / 新制||薬||242(附属図書館) / 京都大学大学院薬学研究科薬学専攻 / (主査)教授 髙倉 喜信, 教授 山下 富義, 教授 小野 正博 / 学位規則第4条第1項該当 / Doctor of Pharmaceutical Sciences / Kyoto University / DFAM

Tesis por compendio / [EN] The determination of genetic biomarkers is progressively becoming more extended and popular, being commercialized even in kits for personalized medicine. Establishing specific genotype variations for each patient, such as single nucleotide polymorphisms (SNPs), could be a fundamental tool in the field of diagnosis, prognosis and therapy selection. However, the use of DNA testing is not fully implemented in general healthcare, mainly due to technical and economic barriers associated to the current technologies, which are limited only to specialized centers and large hospitals. In this thesis, the main goal was to overcome these obstacles by developing simpler, faster and more affordable point-of-care (POC) genotyping systems. Allele discrimination was achieved by employing isothermal enzymatic reactions, like recombinase polymerase amplification (RPA), ligation of oligonucleotides and loop-mediated isothermal amplification (LAMP). These processes were integrated to colorimetric indicators and immunoenzymatic assays, in a microarray format. Using compact discs and polycarbonate chips as platforms, the detection was achieved through widespread electronics, like disc-reader, flatbed scanner and smartphone. To demonstrate their capacities, the resulting systems were applied for identifying SNPs in human samples, associated to therapies for tobacco smoking cessation, major depression disorder and blood clotting-related diseases. After selecting the proper conditions, all studied strategies discriminated SNPs in samples containing as low as 100 copies of genomic DNA, with an error rate below 15%. Most importantly, the developed methods have reduced assays times varying between 70 and 140 minutes, at a cost similar to a conventional PCR-based analog, but maintaining or raising amplification efficiency and eliminating the need of specialized temperature cyclers and fluorescence scanners. In conclusion, the biosensors based in isothermal reactions and consumer electronics devices greatly improve the competitivity of POC DNA analysis. It was demonstrated that the technologies developed in this thesis could support genotyping assays in low-resource areas, such as primary healthcare centers and emerging countries. Through this democratization of genetic testing and by performing adequate association studies, molecular diagnostics and personalized medicine practices could have their application extended to the clinical routine. / [ES] La determinación de biomarcadores genéticos es cada vez más extensa y popular, estando incluso comercializándose kits para medicina personalizada. Establecer las variaciones específicas en el genotipo de cada paciente, como los polimorfismos de un solo nucleótido (SNP) podría ser una herramienta fundamental en el campo del diagnóstico, pronóstico y selección de la terapia. Sin embargo, el uso de pruebas de ADN no se encuentra completamente implementado en la atención médica general, principalmente debido a las barreras técnicas y económicas asociadas a las tecnologías actuales, limitadas solamente a centros especializados y grandes hospitales. En esta tesis, el objetivo principal fue superar estos obstáculos mediante el desarrollo de sistemas de genotipado point-of-care (POC), más simples, rápidos y asequibles. La discriminación alélica se logró mediante el uso de reacciones enzimáticas isotermas, como la amplificación de la recombinasa polimerasa (RPA), la ligación de oligonucleótidos y la amplificación isotérmica mediada por bucle (LAMP). Estos procesos se integraron a indicadores colorimétricos y ensayos inmunoenzimáticos en formato de micromatriz. Utilizando discos compactos y chips de policarbonato como plataforma de ensayo, se ha logrado la detección mediante dispositivos electrónicos de consumo, como un lector de discos, escáner documental y teléfono móvil. Para demostrar sus capacidades, los sistemas resultantes se aplicaron a la identificación de SNPs en muestras humanas, asociados a terapias antitabaquismo, para depresión y enfermedades relacionadas con la coagulación de la sangre. Tras seleccionar las condiciones adecuadas, todas las estrategias estudiadas discriminaron SNPs en muestras conteniendo tan solo 100 copias de ADN genómico, con una tasa de error inferior al 15%. Más importante, los métodos desarrollados han reducido los tiempos de ensayo a valores entre 70 y 140 minutos, a un coste similar a un análogo convencional basado en la reacción en cadena de la polimerasa (PCR), pero manteniendo o aumentando la eficiencia de amplificación y eliminando la necesidad de termocicladores y escáneres de fluorescencia. En conclusión, los biosensores basados en reacciones isotérmicas y dispositivos de electrónica de consumo mejoran en gran medida la competitividad del análisis POC de ADN. Se ha demostrado que las tecnologías desarrolladas en esta tesis podrían apoyar los ensayos de genotipado en áreas de recursos escasos, como centros de atención primaria y países emergentes. A través de esta democratización de las pruebas genéticas y realización estudios de asociación adecuados, el diagnóstico molecular y las prácticas en medicina personalizada podrían extender su aplicación a la rutina clínica. / [CA] La determinació de biomarcadors genètics és cada vegada més extensa i popular, estant fins i tot comercialitzant-se kits per a medicina personalitzada. Establir les variacions específiques en el genotip de cada pacient, com els polimorfismes d'un sol nucleòtid (SNP) podria ser una eina fonamental en el camp del diagnòstic, pronòstic i selecció de la teràpia. No obstant això, l'ús de proves d'ADN no es troba completament implementat en l'atenció mèdica general, principalment a causa de les barreres tècniques i econòmiques associades a les tecnologies actuals, limitades solament a centres especialitzats i grans hospitals. En aquesta tesi, l'objectiu principal va ser superar aquests obstacles mitjançant el desenvolupament de sistemes de genotipat point-of-care (POC), més simples, ràpids i assequibles. La discriminació al·lèlica es va aconseguir mitjançant l'ús de reaccions enzimàtiques isotermes, com l'amplificació de la recombinasa polimerasa (RPA), la lligació de oligonucleòtids i l'amplificació isotèrmica mediada per bucle (LAMP). Aquests processos es van integrar a indicadors colorimètrics i assajos inmunoenzimàtics en format de micromatriu. Utilitzant discos compactes i xips de policarbonat com a plataforma d'assaig, s'ha conseguit la detecció mitjançant dispositius electrònics de consum, com un lector de discos, escàner documental i telèfon mòbil. Per a demostrar les seues capacitats, els sistemes resultants es van aplicar a la identificació de polimorfismes en mostres humanes, associats a teràpies antitabaquisme, per a depressió i malalties relacionades amb la coagulació de la sang. Després de seleccionar les condicions adequades, totes les estratègies estudiades van ser capaces de discriminar SNPs en mostres contenint tan sols 100 còpies d'ADN genòmic, amb una taxa d'error inferior al 15%. Més important, els mètodes desenvolupats han reduït els temps d'assaig a valors entre 70 i 140 minuts, a un cost similar a un anàleg convencional basat en la reacció en cadena de la polimerasa (PCR), però mantenint o augmentant l'eficiència d'amplificació i eliminant la necessitat de termocicladors i escàners de fluorescència. En conclusió, els biosensors basats en reaccions isotèrmiques i dispositius d'electrònica de consum milloren en gran manera la competitivitat de l'anàlisi POC del ADN. S'ha demostrat que les tecnologies desenvolupades en aquesta tesi podrien donar suport als assajos de genotipat en àrees de recursos escassos, com a centres d'atenció primària i països emergents. A través d'aquesta democratització de les proves genètiques i realització estudis d'associació adequats, el diagnòstic molecular i les pràctiques en medicina personalitzada podrien estendre la seua aplicació a la rutina clínica. / [PT] A determinação de biomarcadores genéticos está tornando-se cada vez mais extensa e popular, sendo comercializada até em kits para medicina personalizada. O estabelecimento de variações específicas de genotipo para cada paciente, tais como os polimorfismo de nucleotídeo único, pode ser uma ferramenta fundamental no campo do diagnóstico, prognóstico e seleção de terapias. No entanto, o uso de testes de DNA ainda não encontra-se totalmente implementado na área de saúde geral, principalmente devido às barreiras técnicas e econômicas associadas às tecnologias atuais, limitadas apenas a centros especializados e grandes hospitais. Nesta tese, o principal objetivo foi superar esses obstáculos desenvolvendo sistemas de genotipagem point-of-care (POC) de DNA, mais simples, rápidos e acessíveis. A discriminação de alelos foi alcançada empregando reações enzimáticas isotérmicas, como amplificação por recombinase polimerase (RPA), ligação de oligonucleotídeos e amplificação isotérmica mediada por loop (LAMP). Tais processos foram integrados a indicadores colorimétricos e ensaios imunoenzimáticos, em formato micromatriz. Usando discos compactos e chips de policarbonato como plataforma de ensaio, os analitos foram detectados através de dispositivos eletrônicos de consumo, como leitor de disco, scanner de mesa e smartphone. Para demonstrar suas capacidades, os sistemas resultantes foram aplicados para identificação de polimorfismos em amostras de DNA humano, associados a terapias antitabagismo, para depressão e doenças relacionadas à coagulação do sangue. Após a seleção das condições adequadas, todas as estratégias estudadas foram capazes de discriminar SNPs em amostras contendo até 100 cópias de DNA genômico, com uma taxa de erro inferior a 15%. Mais importante, os métodos desenvolvidos reduziram o tempo de ensaio a valores entre 70 e 140 minutos, com um custo similar a um método análogo baseado em reação em cadeia da polimerase (PCR), mas mantendo ou aumentando a eficiência da amplificação e eliminando a necessidade de cicladores de temperatura e scanners de fluorescência especializados. Em conclusão, os biosensores baseados em reações enzimáticas isotérmicas e dispositivos eletrônicos de consumo incrementam grandemente a competitividade da análise POC de DNA. Foi demonstrado que as tecnologias desenvolvidas nesta tese poderiam dar suporte a ensaios de genotipagem em lugares com poucos recursos, como centros de atenção primária e países emergentes. Através desta democratização dos testes genéticos e com a realização de estudos de associação adequados, o diagnóstico molecular e as práticas de medicina personalizada poderiam ter sua aplicação extendida à rotina clínica. / The authors acknowledge the financial support received from the Generalitat Valenciana (GVA-PROMETEOII/2014/040 Project and GRISOLIA/2014/024 PhD grant) and the Spanish Ministry of Economy and Competitiveness (MINECO CTQ2013-45875-R project) / Yamanaka, ES. (2020). Isothermal-based DNA biosensors for application in pharmacogenetics [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/148366 / Compendio

Im Vergleich zum Rest der Erde erfährt die Arktis eine signifikant schnellere Klimaerwärmung, die unter dem Begriff Arktische Verstärkung bekannt ist und mit zahlreichen sich verstärkenden Prozessen und Mechanismen einhergeht. Wolken spielen aufgrund ihrer Mitwirkung in verschiedenen, gegensätzlichen Effekten eine zwiespältige und eine der unsichersten Rollen für die Veränderung des arktischen Klimasystems. Daher ist die Untersuchung arktischer Wolken und ihrer Effekte von essenzieller Bedeutung, um den arktischen Klimawandel besser zu verstehen und in Modellen repräsentieren zu können. Diese Arbeit quantifiziert den bodennahen Strahlungseffekt von Wolken (engl. cloud radiative effect, CRE) aus einer Kombination von flugzeuggetragenen Breitbandstrahlungsmessungen während tiefer Flugabschnitte unter meist bewölkten Bedingungen und Strahlungstransfersimulationen für wolkenlose Bedingungen. Die Flugzeugmessungen wurden über den gegensätzlichen offenen Ozean- und Meereisoberflächen während dreier jahreszeitlich unterschiedlicher Kampagnen in der Umgebung von Spitzbergen aufgenommen. Ziel dieser Arbeit ist die Untersuchung des Einflusses von Oberflächen-, Wolken- und thermodynamischen Eigenschaften sowie Sonnenzenitwinkel (SZW) auf Unterschiede des solaren, thermisch-infraroten (TIR) und gesamten (solar+TIR) CRE, in Bezug auf die verschiedenen Kampagnen und Oberflächentypen. Die Unterschiede des solaren CRE werden überwiegend vom Kontrast der Oberflächenalbedo und vom jahreszeitlich variierenden SZW angetrieben. Der stärkste Abkühlungseffekt wurde im Frühsommer festgestellt und die über offenem Ozean beobachtete Abkühlung war stärker als über Meereis (-259 W m-2 vs. -65 W m-2 im Frühsommer, -108 W m-2 vs. -17 W m-2 im Frühjahr). Außerdem beeinflussen von Wolken ausgelöste Veränderungen der Oberflächenalbedo den solaren CRE je nach SZW und Oberflächentyp. Der TIR CRE zeigte aufgrund der vorherrschenden opaken Wolken und einer Kompensierung von Effekten sich ändernder Temperatur und Feuchte nur schwache Veränderungen zwischen den Kampagnen und Oberflächentypen (etwa 75 W m-2). Daher wird die Variabilität des gesamten CRE von der Schwankung des solaren CRE bestimmt. Über offenem Ozean wurde ein Abkühlungseffekt während aller Kampagnen beobachtet, über Meereis konnte der solare Abkühlungs- den TIR Erwärmungseffekt hingegen nur im Frühsommer ausgleichen. Für die gesamte Region Framstraße resultiert ein mittäglicher erwärmender, neutraler und abkühlender Effekt in Frühjahr, Frühsommer und Spätsommer aus dem Jahresgang der Meereisbedeckung. Zusätzlich zur eher qualitativen Analyse der einzelnen Einflussfaktoren auf die Unterschiede des solaren CRE wird ein Ansatz zur quantitativen Bestimmung dieser Faktoren angeregt. Diese neue Methode basiert auf einer Fallstudie mit sich verändernden Wolken- und Oberflächeneigenschaften senkrecht zur Eiskante während eines Warmlufteinschubs. Trotz signifikant mangelnder Komplexität der dem Fall zugrundeliegenden Parametrisierung werden plausible relative Beiträge von 77 % und 23 % zum Unterschied des solaren CRE zwischen offenem Ozean und Meereis für Oberflächen- respektive Wolkeneigenschaften ermittelt.:Zusammenfassung Abstract 1 General Introduction 1.1 Arctic Amplification – The Accelerated Warming of the Arctic 1.2 Clouds in the Arctic Climate System 2 Definitions and Theory 2.1 Radiative Quantities 2.2 Radiative Energy Budget 2.3 Surface, Cloud, and Atmospheric Properties 3 Motivation and Objectives 3.1 Previous Research on Cloud Radiative Effect 3.2 Aims of the Thesis 4 Observations and Methods 4.1 Aircraft Measurements 4.1.1 Broadband Radiation Measurements 4.1.2 Complementary Observations 4.2 Radiative Transfer Simulations 4.3 Calculation of Cloud Radiative Effect 4.4 Retrieval of Surface Albedo in Cloud-Free Conditions 4.4.1 Sea Ice Albedo and Retrieval of Equivalent Liquid Water Path 4.4.2 Open Ocean Albedo 4.4.3 Albedo of Inhomogeneous Surfaces 4.5 Uncertainty Estimation 4.5.1 Broadband Radiation Measurements 4.5.2 Radiative Transfer Simulations 4.5.3 Cloud Radiative Effect 4.6 Overview of Employed Data sets from all Campaigns 5 Statistical Analysis of Surface Cloud Radiative Effect 5.1 Campaign Characteristics 5.1.1 Sea Ice Distribution and Solar Zenith Angle 5.1.2 Thermodynamic Profiles 5.1.3 Cloud Properties 5.2 Impact of Cloud-Induced Albedo Modification 5.2.1 Impact on Surface Albedo 5.2.2 Impact on Solar Cloud Radiative Effect 5.3 Impact of Flight Altitude 5.4 Observed Cloud Radiative Effect 5.4.1 Solar Cloud Radiative Effect 5.4.2 Thermal-Infrared Cloud Radiative Effect 5.4.3 Total Cloud Radiative Effect 6 Sensitivity of Solar Cloud Radiative Effect to Surface and Cloud Properties 6.1 Introduction of Case 6.1.1 Synoptic Situation 6.1.2 Surface and Cloud Characteristics 6.2 Contributions to Solar Cloud Radiative Effect 6.2.1 Relative Contributions along a Continuous Time Series 6.2.2 Relative Contributions between States 7 Conclusions and Outlook 7.1 Summary and Conclusions 7.2 Outlook A Appendix A.1 Uncertainty Estimation A.1.1 Broadband Radiation Measurements A.1.2 Radiative Transfer Simulations A.1.3 Cloud Radiative Effect List of Figures List of Tables List of Symbols and Acronyms Bibliography Acknowledgements Summary of the Dissertation List of Papers and Author’s Contribution Supervision Statement / Compared to the rest of the globe, the Arctic experiences a significantly more rapid climate warming, which is called Arctic amplification and linked to numerous intensifying processes and mechanisms. Due to their contribution to and modification of various counteracting effects, clouds play one of the most ambiguous and uncertain roles in the change of the Arctic climate system. Thus, the investigation of clouds and their effects in the Arctic is essential to better understand and represent the Arctic climate change. This thesis quantifies the near-surface cloud radiative effect (CRE), which is obtained from a combination of airborne broadband radiation measurements during low-level flight sections under mostly cloudy conditions and radiative transfer simulations for cloud-free conditions. The airborne measurements were acquired over the contrasting open ocean and sea ice surfaces during three seasonally distinct campaigns in the vicinity of Svalbard. The objective of this thesis is to analyze the impact of surface, cloud, and thermodynamic properties as well as solar zenith angle (SZA) on differences of the solar, thermal-infrared (TIR), and total (solar+TIR) CRE with respect to the particular campaigns and surface types. The difference of the solar CRE is found to be predominantly driven by the contrasting surface albedo and the seasonally varying SZA. The strongest solar cooling effect was detected in early summer and the cooling observed over open ocean was stronger compared to sea ice (-259 W m-2 vs. -65 W m-2 in early summer, -108 W m-2 vs. -17 W m-2 in spring). Additionally, modifications of the surface albedo induced by the cloud-related illumination changes affect the solar CRE depending on SZA and surface type. The TIR CRE varied only weakly between campaigns and surface types (around 75 W m-2) due to the predominant opaque clouds and a compensation effect of changing temperature and humidity. Consequently, the variability of the total CRE is driven by the solar CRE variation. While a total cooling effect was present over open ocean during all campaigns, the solar cooling could compensate the TIR warming effect over sea ice only during early summer. For the entire Fram Strait region, the seasonal cycle of the sea ice distribution results in a total warming, neutral, and cooling effect during solar noon in spring, early summer, and late summer. In addition to the rather qualitative analysis of the individual contributors to the CRE differences, an attempt to quantitatively disentangle the contributions is proposed. This new method is based on a case study with varying cloud and surface properties over the sea ice edge during a warm air intrusion. Although the underlying parameterization developed for the case significantly lacks complexity, plausible relative contributions of surface and cloud properties of about 77 % and 23 % to the solar CRE difference between sea ice and open ocean are retrieved.:Zusammenfassung Abstract 1 General Introduction 1.1 Arctic Amplification – The Accelerated Warming of the Arctic 1.2 Clouds in the Arctic Climate System 2 Definitions and Theory 2.1 Radiative Quantities 2.2 Radiative Energy Budget 2.3 Surface, Cloud, and Atmospheric Properties 3 Motivation and Objectives 3.1 Previous Research on Cloud Radiative Effect 3.2 Aims of the Thesis 4 Observations and Methods 4.1 Aircraft Measurements 4.1.1 Broadband Radiation Measurements 4.1.2 Complementary Observations 4.2 Radiative Transfer Simulations 4.3 Calculation of Cloud Radiative Effect 4.4 Retrieval of Surface Albedo in Cloud-Free Conditions 4.4.1 Sea Ice Albedo and Retrieval of Equivalent Liquid Water Path 4.4.2 Open Ocean Albedo 4.4.3 Albedo of Inhomogeneous Surfaces 4.5 Uncertainty Estimation 4.5.1 Broadband Radiation Measurements 4.5.2 Radiative Transfer Simulations 4.5.3 Cloud Radiative Effect 4.6 Overview of Employed Data sets from all Campaigns 5 Statistical Analysis of Surface Cloud Radiative Effect 5.1 Campaign Characteristics 5.1.1 Sea Ice Distribution and Solar Zenith Angle 5.1.2 Thermodynamic Profiles 5.1.3 Cloud Properties 5.2 Impact of Cloud-Induced Albedo Modification 5.2.1 Impact on Surface Albedo 5.2.2 Impact on Solar Cloud Radiative Effect 5.3 Impact of Flight Altitude 5.4 Observed Cloud Radiative Effect 5.4.1 Solar Cloud Radiative Effect 5.4.2 Thermal-Infrared Cloud Radiative Effect 5.4.3 Total Cloud Radiative Effect 6 Sensitivity of Solar Cloud Radiative Effect to Surface and Cloud Properties 6.1 Introduction of Case 6.1.1 Synoptic Situation 6.1.2 Surface and Cloud Characteristics 6.2 Contributions to Solar Cloud Radiative Effect 6.2.1 Relative Contributions along a Continuous Time Series 6.2.2 Relative Contributions between States 7 Conclusions and Outlook 7.1 Summary and Conclusions 7.2 Outlook A Appendix A.1 Uncertainty Estimation A.1.1 Broadband Radiation Measurements A.1.2 Radiative Transfer Simulations A.1.3 Cloud Radiative Effect List of Figures List of Tables List of Symbols and Acronyms Bibliography Acknowledgements Summary of the Dissertation List of Papers and Author’s Contribution Supervision Statement

Paratuberculosis (PTB) has been reported in the Sudan in cattle and goats for more than 50 years but has never been reported in sheep. However, suspicion of the disease in a breeding flock of sheep in Khartoum North locality was made due to a history of unknown cause of loss of weight. Blood and faecal samples were collected from all animals (N = 59): harvested sera were tested for anti-Mycobacterium avium subsp. paratuberculosis (MAP) antibodies by Enzyme Linked Immunosorbent Assay (ELISA); faeces were screened for acid-fast bacilli by Ziehl–Neelsen staining, tested for MAP DNA by recombinase polymerase amplification (RPA) and some faecal samples were cultured for MAP isolation. Typical MAP acid-fast bacilli were seen in 10.2% (6/59) of the faecal smears, 37.5% of the tested faecal samples (12/32) were positive for MAP DNA and only 3 (5.1%) animals were seropositive for MAP. MAP positive cultures were obtained from 2 out the 6 samples showing typical MAP acid-fast bacilli; the isolates were confirmed by real-time PCR and sequencing. As sheep are animals of utmost economic importance as the main export animals for the country, this first report of ovine PTB warrants special considerations and more investigations for planning control programmes of the disease.

Combinatorial approaches in metabolic engineering can make use of randomized mutations and/or overexpression of randomized DNA fragments. When DNA fragments are obtained from a common genome or metagenome and packaged into the same expression vector, this is referred to as a DNA library. Generating quality DNA libraries that incorporate broad genetic diversity is challenging, despite the availability of published protocols. In response, a novel, efficient, and reproducible technique for creating DNA libraries was created in this research based on whole genome amplification using degenerate oligonucleotide primed PCR (DOP-PCR). The approach can produce DNA libraries from nanograms of a template genome or the metagenome of multiple microbial populations. The DOP-PCR primers contain random bases, and thermodynamics of hairpin formation was used to design primers capable of binding randomly to template DNA for amplification with minimal bias. Next-generation high-throughput sequencing was used to determine the design is capable of amplifying up to 98% of template genomic DNA and consistently out-performed other DOP-PCR primers. Application of these new DOP-PCR amplified DNA libraries was demonstrated in multiple strain enrichments to isolate genetic library fragments capable of (i) increasing tolerance of E. coli ER2256 to toxic levels of 1-butanol by doubling the growth rate of the culture, (ii) redirecting metabolism to ethanol and pyruvate production (over 250% increase in yield) in Clostridium cellulolyticum when consuming cellobiose, and (iii) enhancing L-arginine production when used in conjunction with a new synthetic gene circuit. / Ph. D.

The understanding of the impact of site effects on ground motions is crucial for improving the assessment of seismic hazards. Site response analyses (SRA) can numerically accommodate the mechanics behind the wave propagation phenomena near the surface as well as the variability associated with the input motion and soil properties. As a result, SRA constitute a key component of the assessment of site-specific seismic hazards within the probabilistic seismic hazard analysis framework. This work focuses on limitations in SRA, namely, the definition of the elastic half-space (EHS) boundary condition, the selection of input ground motions so that they are compatible with the assumed EHS properties, and the proper consideration of near-surface attenuation effects. Input motions are commonly selected based on similarities between the shear wave velocity (Vs) at the recording station and the materials below the reference depth at the study site (among other aspects such as the intensity of the expected ground motion, distance to rupture, type of source, etc.). This traditional approach disregards the influence of the attenuation in the shallow crust and the degree to which it can alter the estimates of site response. A Vs-κ correction framework for input motions is proposed to render them compatible with the properties of the assumed EHS at the site. An ideal EHS must satisfy the conditions of linearity and homogeneity. It is usually defined at a horizon where no strong impedance contrast will be found below that depth (typically the top of bedrock). However, engineers face challenges when dealing with sites where this strong impedance contrast takes place far beyond the depth of typical Vs measurements. Case studies are presented to illustrate potential issues associated with the selection of the EHS boundary in SRA. Additionally, the relationship between damping values as considered in geotechnical laboratory-based models, and as implied by seismological attenuation parameters measured using ground motions recorded in the field is investigated to propose alternative damping models that can match more closely the attenuation of seismic waves in the field. / Ph. D.

Vibration control is a large branch in control research, because all moving systems may induce desired or undesired vibration. Due to the limitation of passive system's adaptability and changing excitation input, vibration control brings the solution to change system dynamic with desired behavior to fulfill control targets. According to preference, vibration control can be separated into two categories: vibration reduction and vibration amplification. Lots of research papers only examine one aspect in vibration control. The thesis investigates the control development for both control targets with two different control applications: vehicle suspension and ocean wave energy converter. It develops control methods for both systems with simplified modeling setup, then followed by the application of a novel mechanical motion rectifier (MMR) gearbox that uses mechanical one-way clutches in both systems. The flow is from the control for common system to the control design for a specifically designed system. In the thesis, active (model predictive control: MPC), semi-active (Skyhook, skyhook-power driven damper: SH-PDD, hybrid model predictive control: HMPC), and passive control (Latching Control) methods are developed for different applications or control performance comparison on single system. The thesis also studies about new type of system with switching mechanism, in which other papers do not talk too much and possible control research direction to deal with such complicated system in vibration control. The state-space modeling for both systems are provided in the thesis with detailed model of the MMR gearbox. From the simulation, it can be shown that in the vehicle suspension application, the controlled MMR gearbox can be effective in improving vehicle ride comfort by 29.2% compared to that of the traditional hydraulic suspension. In the ocean wave energy converter, the controlled MMR WEC with simple latching control can improve the power generation by 57% compared to the passive MMR WEC. Besides, the passive MMR WEC also shows its advantage on the passive direct drive WEC in power generation improvement. From the control development flow for the MMR system, the limitation of the MMR gearbox is also identified, which introduces the future work in developing active-MMR gearbox by using an electromagnetic clutch. Some possible control development directions on the active-MMR is also mentioned at the end of the thesis to provide reference for future works. / Master of Science / Vibration happens in our daily life in almost all cases. It is a regular or irregular back and forth motion of particles. For example, when we start a vehicle, the engine will do circular motion to drive the wheel, which causes vibration and we feel wave pulses on our body when we sit in the car. However, this kind of vibration is undesirable, since it makes us uncomfortable. The car manufacture designs cushion seats to absorb vibration. This is a way to use hardware to control vibration. However, this is not enough. When vehicle goes through bumps, we do have suspension to absorb vibration transferred from road to our body. The car still experiences a big shock that makes us feel dizzy. On the opposite direction, in some cases when vibration becomes the motion source for energy harvesting, we would like to enhance it. Hardware can be helpful, since by tuning some parameters of an energy harvesting device, it can match with the vibration source to maximize vibration. However, it is still not enough due to low adaptability of a fixed parameter system. To overcome the limitation of hardware, researches begin to think about the way to control vibration, which is the method to change system behavior by using real-time adjustable hardware. By introducing vibration control, the theory behind that started to be investigated. This thesis investigates the vibration control theory application in both cases: vibration reduction and vibration enhancement, which are mentioned above due to opposite application preferences. There are two major applications of vibration control: vehicle suspension control and ocean wave energy converter (WEC) control. The thesis starts from the control development for both fields with general modeling criteria, then followed by control development with specific hardware design-mechanical motion rectifier (MMR) gearbox-applied on both systems. The MMR gearbox is the researcher designed hardware that targets on vibration adjustment with hardware capability, which is similar as the cushion seats mentioned at the beginning of the abstract. However, the MMR cannot have capability to furtherly optimize system vibration, which introduces the necessity of control development based on the existing hardware. In the suspension control application, the control strategy introduced successfully improve the vehicle ride comfort by 29.2%, which means the vehicle body acceleration has been reduced furtherly to let passenger feel less vibration. In the WEC application, the power absorbed from wave has been improved by 57% by applying suitable control strategy. The performance of improvement on vibration control has proved the effect on further vibration optimization beyond hardware limitation.

No description available.

The first experiment was conducted to determine the optimum in vitro culture system for one-cell bovine embryos. Subsequent experiments compared bisection and biopsy for acquisition of cellular material from bovine morulae for DNA amplification by the polymerase chain reaction technique (PCR), and evaluated the use of DNA microinjection, in vitro culture, morula bisection, and PCR for production and selection of transgenic bovine preimplantation embryos. In vivo fertilized one-cell bovine embryos were cultured in TCM-199 (n=46), co-cultured with bovine oviductal epithelial cells (OEC; n=38), or in explanted immature mouse oviducts (n=54). Of the embryos that cleaved once, 52.6, and 30.4 and 0.0% developed to morulae/blastocysts after culture in OEC, TCM-199, and explanted mouse oviducts. Mean cell number for embryos cultured in OEC (24.5) was higher than for embryos cultured in TCM-199 (12.8) or in explanted mouse oviducts (5.9; P<.05). Bovine morulae were subjected to bisection (n=44; 20 to 30 cells) or biopsy (n=50; 8 to 12 cells) to assess embryo development in vitro and compare the efficiency of PCR amplification of an endogenous 18S rRNA. Mean development scores (l1=degenerate, 2=morula, 3=blastocyst) and mean cell number after microsurgery and 48 h of culture did not differ between treatments (P>.05; 2.4 ± .1 and 41.8 ± 2.5 versus 2.3 ± .1 and 48.8 ± 2.9, respectively). Frequency of the 18S rRNA amplifications was similar (P>.05) for demi-morulae (78%; 32/41) and biopsies (81%; 39/48). In the third experiment, in vivo fertilized one- (n=155), two- (n=57) and four-cell (n=62) bovine embryos were collected for pronuclear and nuclear DNA microinjection. Approximately 70% of the embryos were injected with DNA and 30% served as controls. Injection did not affect (P>.05) mean development scores after 144 h of cultured in TCM-199 with OEC. Sixty-five (34%) of the DNA injected embryos developed to morulae and were bisected. Injected DNA was amplified by PCR in 29% (19/65) of the demi-morulae. Frequency of DNA detection was more frequent (P<.01) in morulae injected at the 1-cell stage (50%: 16/32) than at the 2-cell (10%; 1/10) or 4-cell (9%: 2/23) stage. Production and selection of transgenic bovine morulae was most successful when one-cell bovine embryos were microinjected. / Ph. D.

<p>La distribution quantique de clés est une technique cryptographique permettant l'échange de clés secrètes dont la confidentialité est garantie par les lois de la mécanique quantique. Le comportement particulier des particules élémentaires est exploité. En effet, en mécanique quantique, toute mesure sur l'état d'une particule modifie irrémédiablement cet état. En jouant sur cette propriété, deux parties, souvent appelées Alice et Bob, peuvent encoder une clé secrète dans des porteurs quantiques tels que des photons uniques. Toute tentative d'espionnage demande à l'espion, Eve, une mesure de l'état du photon qui transmet un bit de clé et donc se traduit par une perturbation de l'état. Alice et Bob peuvent alors se rendre compte de la présence d'Eve par un nombre inhabituel d'erreurs de transmission.</p> <p>L'information échangée par la distribution quantique n'est pas directement utilisable mais doit être d'abord traitée. Les erreurs de transmissions, qu'elles soient dues à un espion ou simplement à du bruit dans le canal de communication, doivent être corrigées grâce à une technique appelée réconciliation. Ensuite, la connaissance partielle d'un espion qui n'aurait perturbé qu'une partie des porteurs doit être supprimée de la clé finale grâce à une technique dite d'amplification de confidentialité.</p> <p>Cette thèse s'inscrit dans le contexte de la distribution quantique de clé où les porteurs sont des états continus de la lumière. En particulier, une partie importante de ce travail est consacrée au traitement de l'information continue échangée par un protocole particulier de distribution quantique de clés, où les porteurs sont des états cohérents de la lumière. La nature continue de cette information implique des aménagements particuliers des techniques de réconciliation, qui ont surtout été développées pour traiter l'information binaire. Nous proposons une technique dite de réconciliation en tranches qui permet de traiter efficacement l'information continue. L'ensemble des techniques développées a été utilisé en collaboration avec l'Institut d'Optique à Orsay, France, pour produire la première expérience de distribution quantique de clés au moyen d'états cohérents de la lumière modulés continuement.</p> <p>D'autres aspects importants sont également traités dans cette thèse, tels que la mise en perspective de la distribution quantique de clés dans un contexte cryptographique, la spécification d'un protocole complet, la création de nouvelles techniques d'amplification de confidentialité plus rapides à mettre en œuvre ou l'étude théorique et pratique d'algorithmes alternatifs de réconciliation.</p> <p>Enfin, nous étudions la sécurité du protocole à états cohérents en établissant son équivalence à un protocole de purification d'intrication. Sans entrer dans les détails, cette équivalence, formelle, permet de valider la robustesse du protocole contre tout type d'espionnage, même le plus compliqué possible, permis par les lois de la mécanique quantique. En particulier, nous généralisons l'algorithme de réconciliation en tranches pour le transformer en un protocole de purification et nous établissons ainsi un protocole de distribution quantique sûr contre toute stratégie d'espionnage.</p> <p>Quantum key distribution is a cryptographic technique, which allows to exchange secret keys whose confidentiality is guaranteed by the laws of quantum mechanics. The strange behavior of elementary particles is exploited. In quantum mechnics, any measurement of the state of a particle irreversibly modifies this state. By taking advantage of this property, two parties, often called Alice and bob, can encode a secret key into quatum information carriers such as single photons. Any attempt at eavesdropping requires the spy, Eve, to measure the state of the photon and thus to perturb this state. Alice and Bob can then be aware of Eve's presence by a unusually high number of transmission errors.</p> <p>The information exchanged by quantum key distribution is not directly usable but must first be processed. Transmission errors, whether they are caused by an eavesdropper or simply by noise in the transmission channel, must be corrected with a technique called reconciliation. Then, the partial knowledge of an eavesdropper, who would perturb only a fraction of the carriers, must be wiped out from the final key thanks to a technique called privacy amplification.</p> <p>The context of this thesis is the quantum key distribution with continuous states of light as carriers. An important part of this work deals with the processing of continuous information exchanged by a particular protocol, where the carriers are coherent states of light. The continuous nature of information in this case implies peculiar changes to the reconciliation techniques, which have mostly been developed to process binary information. We propose a technique called sliced error correction, which allows to efficiently process continuous information. The set of the developed techniques was used in collaboration with the Institut d'Optique, Orsay, France, to set up the first experiment of quantum key distribution with continuously-modulated coherent states of light.</p> <p>Other important aspects are also treated in this thesis, such as placing quantum key distribution in the context of a cryptosystem, the specification of a complete protocol, the creation of new techniques for faster privacy amplification or the theoretical and practical study of alternate reconciliation algorithms.</p> <p>Finally, we study the security of the coherent state protocol by analyzing its equivalence with an entanglement purification protocol. Without going into the details, this formal equivalence allows to validate the robustness of the protocol against any kind of eavesdropping, even the most intricate one allowed by the laws of quantum mechanics. In particular, we generalize the sliced error correction algorithm so as to transform it into a purification protocol and we thus establish a quantum key distribution protocol secure against any eavesdropping strategy.</p>