Les microrésonateurs à mode de galerie passifs à base de cristal ou de verre fabriqués par la méthode de fusion possèdent un facteur de qualité limité à quelques 10E8. Ceci est généralement dû à la contamination de la surface du résonateur lors de sa fusion. Dans ces travaux, nous proposons de contourner cette limitation en utilisant des microrésonateurs actifs pour compenser les pertes. Afin de caractériser les microrésonateurs actifs de très haut facteur de qualité ainsi obtenu, nous nous appuyons sur la méthode CRDM (Cavity Ring Down Measurement). Cette méthode interférométrique est d'une part bien adaptée à la caractérisation de résonateurs de très haut facteur de qualité et d'autre part elle permet de remonter de manière univoque aux facteurs de qualité intrinsèque Qo et extrinsèque Qe du résonateur. Dans un régime de compensation de pertes, nous avons pu atteindre tous les régimes de couplage et obtenus des facteurs de qualité intrinsèques excédant les 10E10. En régime d'amplification sélective, nous avons démontré expérimentalement que l'on pouvait obtenir des gains élevés allant jusqu'à 33 dB et des retards de groupe excédant 2,3 µs dans ces microrésonateurs actifs. Ces microrésonateurs de très haut facteur de qualité et de très haute finesse peuvent présenter un couplage modal se manifestant par un doublet de résonances. Une confrontation théorie/expérience avec la méthode CRDM permet de mesurer un écart très faible entre les doublets. Par ailleurs, ces microrésonateurs présentant un fort confinement spatial et une forte surtension, sont propices à l'observation d'effets non-linéaires. Une modélisation intégrant l'effet thermique et l'effet Kerr a été réalisée. Une confrontation théorie/expérience nous a permis d'estimer la puissance réellement injectée dans le mode ainsi qu'à estimer le volume du mode.

The Apollon-10 PW laser chain is a large-scale project aimed at delivering 10 PW pulses to reach intensities of 10^22 W/cm^2. State of the art, high intensity lasers based solely on chirped pulse amplification (CPA) and titanium sapphire (Ti:Sa) crystals are limited to peak powers reaching 1.3 PW with 30-fs pulses as a result of gain narrowing in the amplifiers. To access the multipetawatt regime, gain narrowing can be suppressed with an alternative amplification technique called optical parametric chirped pulse amplification (OPCPA), offering a broader gain bandwidth and pulse durations as short as 10 fs. The Apollon-10 PW laser will exploit a hybrid OPCPA-Ti:Sa-CPA strategy to attain 10-PW pulses with 150 J and 15 fs. It will have two high-gain, low-energy amplification stages (10 fs ,100 mJ range) based on OPCPA in the picosecond and nanosecond timescale and afterwards, and will use Ti:Sa for power amplification to the 100-Joule level.Work in this thesis involves the progression of the development on the Apollon-10 PW front end and is focused on the development of a high contrast, ultrashort seed source supporting 10-fs pulses, stretching these pulses prior to OPCPA and the implementation of the picosecond OPCPA stage with a target of achieving 10-mJ pulses and maintaining its bandwidth. To achieve the final goal of 15-fs, 150-J pulses, the seed source must have a bandwidth supporting 10-fs and a temporal contrast of at least 10^10. Thus from an initial commercial Ti:Sa source delivering 25-fs pulses with a contrast of 10^8, spectral broadening via self-phase modulation and contrast enhancement with cross polarized (XPW) generation was performed. Subsequently, the seed pulses were stretched to a few picoseconds to match the pump for picosecond OPCPA. Strecher designs using an acousto-optic programmable dispersive filter (dazzler) for phase control in this purpose are studied. A compact and straightforward compressor using BK7 glass is used and an associated compressor for pulse monitoring was also studied. Lastly, the picosecond OPCPA stage was implemented in single and dual stage configurations.

Cette thèse, à dominante expérimentale, explore la physique d'une cavité Fabry Pérot dont les miroirs sont des réseaux, en l'occurrence un guide multimode à cristal photonique bidimensionnel, autour de thèmes appliqués, aux télécommunications optiques autour de 1,55µm, et fondamentaux. Les parois d'un tel guide sont constituées d'un réseau périodique de trous d'air gravés au travers d'une hétérostructure semi-conductrice à base d'InP et sont, dans la bande interdite photonique, parfaitement réfléchissantes pour toute onde incidente dans le plan de périodicité. La périodicité le long du guide couple par diffraction de Bragg, des modes guidés de vitesse de groupe "ordinaire" et des modes guidés très lents, analogues à des modes résonnants. L'originalité essentielle de ce couplage est qu'il n'intervient que pour des fenêtres de fréquences et de vecteur d'onde étroites, restant pratiquement silencieux ailleurs. Ce couplage est tout d'abord exploité pour la conception d'un coupleur/découpleur de longueurs d'onde, à extraction latérale et sélective de tout ou partie du signal optique guidé. La suite de la thèse, plus fondamentale, explore les potentialités des régions spectrales autour de ces fenêtres de couplage pour l'émission et le contrôle de photons dans ces structures confinantes et diffractives. Nous présentons un effet expérimental spectaculaire d'exaltation de l'émission spontanée, associé à une augmentation locale de la densité d'états photoniques. Le dernier volet aborde la mesure du spectre ed gain modal: l'effet du ralentissement du mode guidé aux abords de la fenêtre de couplage sur l'amplification ressentie par un signal se propageant sur ce mode y est discutée.

Reverse genetics systems that are based on either viral transcripts or cDNA genome segments cloned in plasmids have recently been reported for some of the dsRNA viruses of the Reoviridae family, namely African horsesickness virus, bluetongue virus and orthoreovirus. For rotaviruses, three reverse genetics systems which only allow the manipulation of a single genome segment have been described. These rotavirus single genome segment reverse genetics systems are not true stand-alone systems because they require a helper virus and a recombinant virus selection step. A true selection-free, plasmid- only or transcript-based reverse genetics system for rotaviruses is lacking. This study sought to identify and characterise the factors that need to be understood and overcome for the development of a rotavirus reverse genetics system using mRNA derived from the in vitro transcription of a consensus nucleotide sequence as well as from double-layered particles. The consensus whole genome sequence of the prototype rotavirus DS-1 and SA11 strains was determined using sequenceindependent whole genome amplification and 454® pyrosequencing. For the rotavirus DS-1 strain, a novel isoleucine in a minor population variant was found at position 397 in a hydrophobic region of VP4. NSP1 contained seven additional amino acids MKSLVEA at the N-terminal end due to an insertion in the consensus nucleotide sequence of genome segment 5. The first 34 nucleotides at the 5'- terminus and last 30 nucleotides at the 3'-terminal end of genome segment 10 (NSP4) of the DS-1 strain were determined in this study. The consensus genome segment 11 (NSP5/6) sequence was 821 bp in length, 148 bp longer than previously reported. The 454® pyrosequence data for a rotavirus SA11 sample with no known passage history revealed a mixed infection with two SA11 strains. One of the strains was a reassortant which contained genome segment 8 (NSP2) from the bovine rotavirus O agent. The other ten consensus genome segments of the two strains could not be differentiated. Novel minor population variants of genome segments 4 (VP4), 9 (VP7) and 10 (NSP4) were identified. Molecular clock phylogenetic analyses of the rotavirus SA11 genomes showed that the two SA11 strains were closely related to the original SA11-H96 strain isolated in 1958. Plasmids containing inserts of the consensus cDNA of the rotavirus DS-1 strain were purchased and used to generate exact capped transcripts by in vitro transcription with a T7 polymerase. Wild-type transcripts of rotavirus SA11 were obtained from in vitro transcription using purified rotavirus SA11 double-layered particles. The purified rotavirus DS-1 and SA11 transcripts were transfected into BSR, COS-7 and MA104 cells. Work on MA104 cells was discontinued due their very low transfection efficacy. In BSR and COS-7 cells, rotavirus DS-1 and SA11 transcripts induced cell death. However, no viable rotavirus was recovered following attempts to infect MA104 cells with the BSR and COS-7 transfected cell lysates. The cell death was determined to be due to apoptotic cell death mechanisms. Immunostaining showed that the DS-1 genome segment 6 (VP6) and SA11 transcripts were translated in transfected BSR and COS-7 cells. Based on visual inspection, the translation seemed to be higher in the retinoic acid-inducible gene-I (RIG-I) deficient BSR cells than in COS-7 cells. This suggested that the transfection of rotavirus transcripts induced an innate immune response which could lead to the development of an antiviral state. Therefore, the innate immune response to rotavirus transcripts was investigated in HEK 293H cells using qRT-PCR and western blot analyses. Results of this investigation showed that RIG-I, but not MDA5 sensed rotavirus transcripts in transfected HEK 293H cells. Furthermore, rotavirus transcripts induced high levels of cellular mRNA encoding the cytokines IFN-1β, IFN-λ1, CXCL10 and TNF-α. Other cytokines namely, IFN-α, IL-10, IL-12 p40 and the kinase RIP1 were not significantly induced. Inhibiting the RNA-dependent protein kinase R (PKR) reduced the induction of cytokines IFN-1β, IFN-λ1, CXCL10 and TNF-α, but the expression levels were not abrogated. The importance of a consensus sequence and the insights gained in the current study regarding the role of the innate immune response after transfection of rotavirus transcripts into cells in culture, should aid the development of a true rotavirus reverse genetics system. / Thesis (PhD (Biochemistry))--North-West University, Potchefstroom Campus, 2013

Reverse genetics systems that are based on either viral transcripts or cDNA genome segments cloned in plasmids have recently been reported for some of the dsRNA viruses of the Reoviridae family, namely African horsesickness virus, bluetongue virus and orthoreovirus. For rotaviruses, three reverse genetics systems which only allow the manipulation of a single genome segment have been described. These rotavirus single genome segment reverse genetics systems are not true stand-alone systems because they require a helper virus and a recombinant virus selection step. A true selection-free, plasmid- only or transcript-based reverse genetics system for rotaviruses is lacking. This study sought to identify and characterise the factors that need to be understood and overcome for the development of a rotavirus reverse genetics system using mRNA derived from the in vitro transcription of a consensus nucleotide sequence as well as from double-layered particles. The consensus whole genome sequence of the prototype rotavirus DS-1 and SA11 strains was determined using sequenceindependent whole genome amplification and 454® pyrosequencing. For the rotavirus DS-1 strain, a novel isoleucine in a minor population variant was found at position 397 in a hydrophobic region of VP4. NSP1 contained seven additional amino acids MKSLVEA at the N-terminal end due to an insertion in the consensus nucleotide sequence of genome segment 5. The first 34 nucleotides at the 5'- terminus and last 30 nucleotides at the 3'-terminal end of genome segment 10 (NSP4) of the DS-1 strain were determined in this study. The consensus genome segment 11 (NSP5/6) sequence was 821 bp in length, 148 bp longer than previously reported. The 454® pyrosequence data for a rotavirus SA11 sample with no known passage history revealed a mixed infection with two SA11 strains. One of the strains was a reassortant which contained genome segment 8 (NSP2) from the bovine rotavirus O agent. The other ten consensus genome segments of the two strains could not be differentiated. Novel minor population variants of genome segments 4 (VP4), 9 (VP7) and 10 (NSP4) were identified. Molecular clock phylogenetic analyses of the rotavirus SA11 genomes showed that the two SA11 strains were closely related to the original SA11-H96 strain isolated in 1958. Plasmids containing inserts of the consensus cDNA of the rotavirus DS-1 strain were purchased and used to generate exact capped transcripts by in vitro transcription with a T7 polymerase. Wild-type transcripts of rotavirus SA11 were obtained from in vitro transcription using purified rotavirus SA11 double-layered particles. The purified rotavirus DS-1 and SA11 transcripts were transfected into BSR, COS-7 and MA104 cells. Work on MA104 cells was discontinued due their very low transfection efficacy. In BSR and COS-7 cells, rotavirus DS-1 and SA11 transcripts induced cell death. However, no viable rotavirus was recovered following attempts to infect MA104 cells with the BSR and COS-7 transfected cell lysates. The cell death was determined to be due to apoptotic cell death mechanisms. Immunostaining showed that the DS-1 genome segment 6 (VP6) and SA11 transcripts were translated in transfected BSR and COS-7 cells. Based on visual inspection, the translation seemed to be higher in the retinoic acid-inducible gene-I (RIG-I) deficient BSR cells than in COS-7 cells. This suggested that the transfection of rotavirus transcripts induced an innate immune response which could lead to the development of an antiviral state. Therefore, the innate immune response to rotavirus transcripts was investigated in HEK 293H cells using qRT-PCR and western blot analyses. Results of this investigation showed that RIG-I, but not MDA5 sensed rotavirus transcripts in transfected HEK 293H cells. Furthermore, rotavirus transcripts induced high levels of cellular mRNA encoding the cytokines IFN-1β, IFN-λ1, CXCL10 and TNF-α. Other cytokines namely, IFN-α, IL-10, IL-12 p40 and the kinase RIP1 were not significantly induced. Inhibiting the RNA-dependent protein kinase R (PKR) reduced the induction of cytokines IFN-1β, IFN-λ1, CXCL10 and TNF-α, but the expression levels were not abrogated. The importance of a consensus sequence and the insights gained in the current study regarding the role of the innate immune response after transfection of rotavirus transcripts into cells in culture, should aid the development of a true rotavirus reverse genetics system. / Thesis (PhD (Biochemistry))--North-West University, Potchefstroom Campus, 2013

This thesis develops and explores two methodologies to assess earthquake ground shaking in southwestern British Columbia based on 1D soil layering and 3D basin structure. To assess site response based on soil layering, microtremor array measurements were conducted at two sites of contrasting geology to estimate Rayleigh-wave dispersion curves. A Bayesian inversion algorithm is developed to invert the dispersion data for the shear-wave velocity (VS) profile together with quantitative uncertainty estimates, accounting rigorously for data error covariance and model parameterization selection. The recovered VS profiles are assessed for reliability by comparison with invasive VS measurements at each site with excellent agreement. Probabilistic site response analysis is conducted based on a sample of VS profiles drawn from the posterior probability density of the microtremor inversion. The quantitative uncertainty analysis shows that the rapid and inexpensive microtremor array method provides sufficient resolution of soil layering for practical characterization of earthquake ground motion. To assess the effects of 3D Georgia basin structure on long-period (> 2 s) ground motion for large scenario earthquakes, numerical 3D finite difference modelling of viscoelastic wave propagation is applied. Both deep (> 40 km) subducting Juan de Fuca plate and crustal (5 km) North America plate earthquakes are simulated in locations congruent with known seismicity. Simulations are calibrated by comparing synthetic waveforms with 36 selected strong- and weak-motion seismograms of the 2001 MW 6.8 Nisqually earthquake. The ratio between predicted peak ground motions in models with and without Georgia basin sediments is applied as a quantitative measure of basin amplification. Steep edges in the upper 1 km of the northwest and southeast extents of the basin are coincident with the appearance of surface waves. Focussing of north-to-northeast propagating surface waves by shallow (< 1 km) basin structure increases ground motion in a localized region of southern Greater Vancouver. This effect occurs for both types of earthquakes located south-southwest of Vancouver at distances greater than ~80 km. The predicted shaking level is increased up to 17 times and the duration of moderate shaking (> 3.4 cm/s) is up to 16 times longer due to the 3D Georgia basin structure. / Graduate

Britų kriminologai Stanley’is Cohenas ir Jockas Youngas sukūrė teorinį modelį, kuris paaiškina, kaip žiniasklaida, manipuliuodama informacija apie narkotinių medžiagų vartojimo keliamą pavojų, sustiprina deviaciją. Magistro darbe, remiantis S. Coheno moralinės panikos ir J. Youngo deviacijos amplifikacijos teorijomis, nagrinėjamas narkotikų baimės poveikis psichiką veikiančių medžiagų kriminalizavimo procesui dabartinėje Lietuvoje. Ginama magistro darbo tezė – narkotikų baimė yra vienas iš psichiką veikiančių medžiagų kriminalizavimo veiksnių dabartinėje Lietuvoje. Atsižvelgiant į problemos specifiką, darbe naudojama metodų trianguliacija – derinami kiekybiniai ir kokybiniai sociologinių tyrimų metodai. VU pirmosios pakopos ir vientisųjų studijų studentų požiūrio anketinė apklausa atskleidė, kaip manipuliavimas informacija viešajame diskurse veikia studentų požiūrį į narkotinių medžiagų vartojimo problemą. Studentų reakcija į narkotinių medžiagų vartojimo problemą – tai pirmasis deviacijos amplifikacijos proceso etapas. Studentai teigia, kad ši problema Lietuvoje yra labai paplitusi ir siūlo ją spręsti represinėmis priemonėmis. Antrasis deviacijos amplifikacijos proceso etapas yra žiniasklaidos reakcija į deviaciją. Atlikus naujienų portalo delfi.lt skaitytojų komentarų kokybinę turinio analizę, nustatyti du moralinės panikos dėl narkotikų požymiai: šių medžiagų vartotojai vaizduojami kaip nevidonai, o narkotinių medžiagų vartojimo problema – kaip nesustabdomai plintanti liga... [toliau žr. visą tekstą] / Sociological and criminological theories illuminated to the role of the mass media in deviance amplification process in the middle of 20th century. British criminologist Stanley Cohen was among the first to draw attention how the mass media is manipulating public fear of illicit drugs users. Another British criminologist Jock Young has developed a theoretical model which theoretically explains the connection between the public reaction to deviance and deviance amplification. He called this explanation the deviance amplification spiral model. J. Young argued that the mass media creates public fear of illicit drugs which exerts pressure upon legislator, police and courts to take action against illicit drugs use. This study is based on S. Cohen's moral panic and J. Young's deviance amplification theories. It is grounded in the analysis of data collected in four sociological investigations: (1) Vilnius University students attitudes survey; (2) qualitative content analysis of the readers' comments in the news portal delfi.lt; (3) qualitative and quantitative content analysis of the Lithuanian Parliament's plenary meeting stenographs and (4) expert interviews. The main thesis: the drugs fear is one of the factors of psychoactive substances criminalization in present-day Lithuania. Vilnius University students attitudes survey results show that the most of the respondents are convinced that illicit drugs problem is very widespread in present-day Lithuania, and the most effective way... [to full text]

This research focuses on the development of polymer microfabrication technologies for the realization of two major components of a pneumatic tactile display: a microactuator array and a complementary microvalve (control) array. The concept, fabrication, and characterization of a kinematically-stabilized polymeric microbubble actuator (¡°endoskeletal microbubble actuator¡±) were presented. A systematic design and modeling procedure was carried out to generate an optimized geometry of the corrugated diaphragm to satisfy membrane deflection, force, and stability requirements set forth by the tactile display goals. A refreshable Braille cell as a tactile display prototype has been developed based on a 2x3 endoskeletal microbubble array and an array of commercial valves. The prototype can provide both a static display (which meets the displacement and force requirement of a Braille display) and vibratory tactile sensations. Along with the above capabilities, the device was designed to meet the criteria of lightness and compactness to permit portable operation. The design is scalable with respect to the number of tactile actuators while still being simple to fabricate. In order to further reduce the size and cost of the tactile display, a microvalve array can be integrated into the tactile display system to control the pneumatic fluid that actuates the microbubble actuator. A piezoelectrically-driven and hydraulically-amplified polymer microvalve has been designed, fabricated, and tested. An incompressible elastomer was used as a solid hydraulic medium to convert the small axial displacement of a piezoelectric actuator into a large valve head stroke while maintaining a large blocking force. The function of the microvalve as an on-off switch for a pneumatic microbubble tactile actuator was demonstrated. To further reduce the cost of the microvalve, a laterally-stacked multilayer PZT actuator has been fabricated using diced PZT multilayer, high aspect ratio SU-8 photolithography, and molding of electrically conductive polymer composite electrodes.

The human body is composed of trillions of cells closely working together to maintain a functional organism. Every cell is unique in molecular composition and can acquire genetic variations that might cause it to turn pathological. It is essential to develop improved tools to better understand the development of normal and disease tissue, ideally enabling single-cell expression studies in preserved context of complex tissue with single-nucleotide resolution. This thesis presents the development and application of a new in situ method for localized detection and genotyping of individual transcripts directly in cells and tissues. The described technique utilizes padlock probes and target-primed rolling circle amplification and is highly suitable for sensitive in situ analysis. First, a new strategy for directed cleavage of single stranded DNA was investigated, e.g. nucleic acid targets with extended 3´ ends, for successful initiation of rolling circle amplification. The presented cleavage strategy is simple and applicable for subsequent enzymatic reactions, e.g. ligation and polymerization. Specific cleavage of long target overhangs was demonstrated in synthetic oligonucleotides and in genomic DNA and the detection efficiency was substantially increased. For multiplex detection and genotyping of individual transcripts in single cells, a new in situ method was developed. The technique showed a satisfactorily detection efficiency and was later applied as a general mutation analysis tool for detection of KRAS point mutations in complex tumor tissue sections, e.g. formalin-fixed, paraffin-embedded tumor tissues and cytologic tumor imprints. Mutation status was assessed in patient samples by in situ padlock probe detection and results were confirmed by DNA-sequencing.  Finally, the method was adapted for simultaneous detection of individual mRNA molecules and endogenous protein modifications in single cells using padlock probes and in situ PLA. This assay will be useful for gene expression analysis and exploration of new drugs with vague effector sites. To our knowledge, no other technique exists today that offers in situ transcript detection with single-nucleotide resolution in heterogeneous tissues. The method will especially be suitable for discrimination of highly similar transcripts, e.g. splice variants, SNPs and point mutations, within gene expression studies and for cancer diagnostics.

Intra- and intercellular information is communicated by posttranslational modifications (PTMs) and protein-protein interactions, transducing information over cell membranes and to the nucleus. A cells capability to respond to stimuli by several highly complex and dynamic signaling networks provides the basis for rapid responses and is fundamental for the cellular collaborations required in a multicellular organism. Having received diverse stimuli, being positioned at various stages of the cell cycle or, for the case of cancer, containing altered genetic background, each cell in a population is slightly different from its neighbor. However, bulk analyses of interactions will only reveal an average, but not the true variation within a population. Thus studies of interacting endogenous biomolecules in situ are essential to acquire a comprehensive view of cellular functions and communication. In situ proximity ligation assay (in situ PLA) was developed to investigate individual endogenous protein-protein interactions in fixed cells and tissues and was later applied for detection for PTMs. Progression of signals in a pathway can branch out in different directions and induce expression of different target genes. Hence simultaneous measurement of protein activity and gene expression provides a tool to determine the balance and progression of these signaling events. To obtain this in situ PLA was combined with padlock probes, providing an assay that can interrogate both PTMs and mRNA expression at a single cell level. Thereby different nodes of the signaling pathway as well as drug effects on different types of molecules could be investigated simultaneously. In addition to regulation of gene expression, protein-DNA interactions present a mechanism to manage accessibility of the genomic DNA in an inheritable manner, providing the basis for lineage commitment, via e.g. histone PTMs. To enable analyses of protein-DNA interactions in situ we developed a method that utilizes the proximity dependence of PLA and the sequence selectivity of padlock probes. This thesis presents new methods providing researchers with a set of tools to address cellular functions and communication in complex microenvironments, to improve disease diagnostics and to contribute to hopefully finding cures.