Drosophila melanogaster has been integral to unravelling the mechanisms of animalian immunity. Diverse species of Drosophila with sequenced genomes have been used to characterize how immune systems respond to natural selection. However, Drosophila is an incredibly speciose lineage, especially so in the subgenus Drosophila. Of the 12 genomes sequenced in 2007, ushering in the era of Drosophila comparative genomics, only three were subgenus Drosophila flies, and none were from the lesser- characterized Immigrans-Tripunctata clade. Recently, multiple Immigrans-Tripunctata clade Drosophila have been sequenced, including the transcriptome of Drosophila neotestacea. I investigated the realized immune responses of D. neotestacea to characterize the immune repertoire of this divergent lineage. The signalling pathways of D. neotestacea were largely conserved, though there were interesting patterns of evolution in antimicrobial peptide genes (AMPs). One of these AMPs, a diptericin, was highly dissimilar to diptericins in D. melanogaster, and conserved in other subgenus Drosophila flies. This prompted me to characterize the evolution of the diptericin gene family in Drosophila. I found that Drosophila diptericins have evolved under positive selection, and display intriguing differences in net charge to well-conserved diptericin domains. I assessed the expression profile of this divergent D. neotestacea diptericin, and found that it did not respond to Serratia bacterial challenge, unlike diptericin in D. melanogaster. I also highlight a potential novel drosocin-like AMP conserved throughout the subgenus Drosophila. These results agree that signalling pathways are highly conserved in diverse insects, including Drosophila. However seemingly-conserved effectors of the Drosophila immune response (such as AMPs) may have previously unappreciated variation in expression and function. / Graduate / 0718 / 0353 / 0369 / markhans@uvic.ca

<p>This thesis report is focused on the growth of Pt/Mg multilayers and the studies of the sputter yield amplification effect in these. The main application is to use the multilayers as X-ray mirrors reflecting an X-ray wavelength of 17 Å. This wavelength is important for astronomical applications in general, and solar imaging applications in particular.</p><p>For periodic X-ray multilayer mirrors only a certain specific wavelength of X-rays can be reflected. What wavelength that is reflected depends on the individual layer thicknesses of the materials that are constituting the multilayer. These thicknesses can be determined using modified Bragg’s law and are approximately a quarter of the wavelength.</p><p>In order to obtain the exact desired layer thickness of each individual layer it is necessary to understand the growth processes and the effects that are going on during deposition of such multilayer mirrors. It has been shown that when depositing multilayers consisting of one very light and one very heavy material, like e.g. Pt and Mg, the deposition rate of the light element is non-linear with deposition time for thin layers. This is because of backscattered energetic neutrals from the heavy target material, which affects the growing film. Furthermore, a sputter yield amplification is present for thin layers when a light element is grown on top of a heavy element, i.e. for Mg on top of Pt.</p><p>Dual DC magnetron sputtering has been used to grow the Pt/Mg multilayers, and the influence of the backscattered energetic neutrals and the sputter yield amplification effect has been studied for Ar and Kr sputtering gases at pressures ranging from 3 up to 9 mTorr. The individual layer thicknesses have been obtained from simulations of hard X-ray reflectivity measurements using the IMD program. The number of backscattered energetic neutrals and their energies at the target have been calculated using the TRIM code.</p><p>Using the results obtained it is now possible to predict and compensate for the non-linear deposition rate of Mg.</p>

This thesis report is focused on the growth of Pt/Mg multilayers and the studies of the sputter yield amplification effect in these. The main application is to use the multilayers as X-ray mirrors reflecting an X-ray wavelength of 17 Å. This wavelength is important for astronomical applications in general, and solar imaging applications in particular. For periodic X-ray multilayer mirrors only a certain specific wavelength of X-rays can be reflected. What wavelength that is reflected depends on the individual layer thicknesses of the materials that are constituting the multilayer. These thicknesses can be determined using modified Bragg’s law and are approximately a quarter of the wavelength. In order to obtain the exact desired layer thickness of each individual layer it is necessary to understand the growth processes and the effects that are going on during deposition of such multilayer mirrors. It has been shown that when depositing multilayers consisting of one very light and one very heavy material, like e.g. Pt and Mg, the deposition rate of the light element is non-linear with deposition time for thin layers. This is because of backscattered energetic neutrals from the heavy target material, which affects the growing film. Furthermore, a sputter yield amplification is present for thin layers when a light element is grown on top of a heavy element, i.e. for Mg on top of Pt. Dual DC magnetron sputtering has been used to grow the Pt/Mg multilayers, and the influence of the backscattered energetic neutrals and the sputter yield amplification effect has been studied for Ar and Kr sputtering gases at pressures ranging from 3 up to 9 mTorr. The individual layer thicknesses have been obtained from simulations of hard X-ray reflectivity measurements using the IMD program. The number of backscattered energetic neutrals and their energies at the target have been calculated using the TRIM code. Using the results obtained it is now possible to predict and compensate for the non-linear deposition rate of Mg.

Several fabrication techniques for surface micromachined 3-D structures have been developed for RF components. The fabrication techniques all have in common the use of epoxy patterning and subsequent metallization. Techniques and structures such as embedded conductors, epoxy-core conductors, a reverse-side exposure technique, a multi-exposure scheme, and inclined patterning are presented. The epoxy-core conductor technique makes it easy to fabricate high-aspect-ratio (10-20:1), tall (~1mm) RF subelements as well as potentially very complex structures by taking advantage of advanced epoxy processes. To demonstrate feasibility and usefulness of the developed fabrication techniques for RF applications, two test vehicles are employed. One is a solenoid type RF inductor, and the other is a millimeter wave radiating structure such as a W-band quarter-wavelength monopole antenna. The embedded inductor approach provides mechanical robustness and package compatibility as well as good electrical performance. An inductor with a peak Q-factor of 21 and an inductance of 2.6nH at 4.5GHz has been fabricated on a silicon substrate. In addition, successful integration with a CMOS power amplifier has been demonstrated. A high-aspect-ratio inductor fabricated using epoxy core conductors shows a maximum Q-factor of 84 and an inductance of 1.17nH at 2.6GHz on a glass substrate with a height of 900um and a single turn. Successful W-band monopole antenna fabrication is demonstrated. A monopole with a height of 800um shows its radiating resonance at 85GHz with a return loss of 16dB. In addition to the epoxy-based devices, an advanced tunable ferroelectric device architecture is introduced. This architecture enables a low-loss conductor device; a reduced intermodulation distortion (IMD) device; and a compact tunable LC module. A single-finger capacitor having a low-loss conductor with an electrode gap of 1.2um and an electrode thickness of 2.2um has been fabricated using a reverse-side exposure technique, showing a tunability of 33% at 10V. It shows an improved Q-factor of 21.5. Reduced IMD capacitors consist of wide RF gaps and narrowly spaced high resistivity electrodes with a gap of 2um and a width of 2um within the wide gap. A 14um gap and a 20um gap capacitor show improved IMD performance compared to a 4um gap capacitor by 6dB and 15dB, respectively, while the tunability is approximately 21% at 30V for all three devices due to the narrowly spaced multi-pair high resistivity DC electrodes within the gap. Finally, a compact tunable LC module is implemented by forming the narrow gap capacitor in an inductor shape. The resonance frequency of this device is variable as a function of DC bias and a frequency tunability of 1.1%/V is achieved. The RF components developed in this thesis illustrate the usefulness of the application of micromachining technology to this application area, especially as frequencies of operation of RF systems continue to increase (and therefore wavelengths continue to shrink).

La maladie d'Alzheimer (MA) se caractérise par l'accumulation de l'amyloïde β (Aβ) dans le cerveau. Des indications suggèrent un lien étroit entre la MA et la neuroinflammation. Cependant, l'aspect moléculaire des réactions immunitaires innées contre l'Aβ n'a pas été élucidé. Nous avons utilisé la drosophile pour étudier l'impact des réactions immunitaires innées sur la MA. Au cours de ma thèse, j'ai: (1) mis en place un modèle drosophile de la MA pour l'étude du rôle des réactions inflammatoires, (2) montré que la voie inflammatoire IMD exerce un rôle neuroprotecteur empêchant le développement de phénotypes associés à la MA (3) généré l'interactome de la voie IMD utile lors de l'étude des mécanismes liant la MA à la neuroinflammation, et (4) introduit un crible génétique visant à identifier des gènes modificateurs de la MA. Nous estimons que nos résultats pourraient servir de base à de nouvelles interventions thérapeutiques contre la MA.

L’avènement de l’IDM (Ingénierie Dirigée par les Modèles) a suscité beaucoup d’intérêt de la part des organisations qui de fait commencent à transformer leur processus de développement traditionnel en un processus de développement dirigé par les modèles, appelé aussi processus IDM.Au moment où ces processus commencent à émerger, nous notons l’absence d’un langage dédié pour les modéliser et les mettre en œuvre. Le standard SPEM 2.0 propose des concepts génériques qui sont supposés être capables de décrire tout type de processus logiciel. Cependant, les concepts de SPEM ne capturent pas la nature exacte des processus IDM. D’autre part, une autre insuffisance majeure de SPEM réside dans le fait qu’il n’intègre pas les concepts relatifs à la mise en œuvre des processus.L’objectif de cette thèse est triple : (1) proposer une extension de SPEM dans laquelle les concepts centraux des processus IDM sont réifiés ; (2) proposer un langage dédié à la modélisation comportementale des processus IDM ; (3) proposer une architecture conceptuelle d’un environnement logiciel d’aide à la modélisation et à la mise en œuvre des processus IDM.Pour valider notre approche, un prototype a été développé sous l’environnement TOPCASED. Ce prototype fournit d’une part un éditeur graphique pour la modélisation structurelle et comportementale des processus IDM et d’autre part un environnement de mise en œuvre s’appuyant sur les modèles comportementaux des processus. Nous avons également appliqué notre approche à une étude de cas significatif: le processus UWE (UML-based Web Engineering), qui est un processus IDM dédié au développement d’applications web. / With the emergence of MDE, many organizations have been starting to transform their traditional software development processes into model-driven processes. Kleppe and al. define a model-driven software development as “a process of developing software using different models on different levels of abstraction with (automated) transformations between these models”.While model-driven development processes – called MDE processes – have started to appear, a tool-supported Process Modeling Language (PML) for describing and enacting such processes is still lacking. The concepts of SPEM 2.0 are quite generic since they are supposed to allow describing any kind of software. However, SPEM 2.0 concepts do not succeed in capturing the exact nature of most activities and artifacts of model-driven development. In addition, another major weakness of SPEM 2.0 is the lack of concepts for process enactment.The objective of this thesis is threefold: (1) provide an extension of SPEM that reifies the MDE concepts; (2) provide a language dedicated to behavioral modeling of MDE processes; (3) provide a conceptual architecture of a PSEE (Process-centered Software Engineering Environment) that guides process designer at modeling phase and developers at enactment time.To validate our approach, a prototype of this PSEE is developed under the TOPCASED environment. This prototype provides a graphical editor for structural and behavioral modeling of MDE processes, and a process enactment engine based on process behavior models. We have also applied our approach to a significant case study: the UWE (UML-based Web Engineering) process, which is a MDE process dedicated to web applications development.

La presente investigación lleva como título “Propuesta de Gestión para mantener la Rugosidad dentro de los Niveles de Servicio del contrato de concesión”. La investigación se enfoca en dar una alternativa de gestión que asegure mantener los niveles de servicio en lo referente a la calidad del pavimento cuando la carretera se encuentra en estado de conservación reduciendo el costo que se va a invertir en años futuros teniendo como base datos obtenidos desde el año 2010 al 2015. El deterioro prematuro del pavimento se ve afectado cuando no se tiene un plan de conservación adecuado que conlleve a programar y ejecutar actividades de mantenimiento rutinario y periódico con la finalidad de mantener los niveles de servicio en carreteras concesionadas. Esto conlleva que la condiciones de las redes viales se encuentren por debajo de lo que resulta deseable y conveniente, presentando un ciclo vicioso de la vía (Construcción – Abandono – Destrucción – Reconstrucción). La investigación es de tipo cuantitativo no experimental, descriptivo, correlacional y explicativo. Su diseño es longitudinal ya que tiene como referencia datos obtenidos desde el año 2010 al 2015. Se analizaron dos propuestas de gestión de conservación vial teniendo como base los datos procesados de los años 2010 al 2015 para obtener una alternativa que logre cumplir con el objetivo principal de ésta investigación. Finalmente se concluye que es posible formular una propuesta de gestión vial que permita optimizar el presupuesto de mantenimiento en los años proyectados conservando la calidad del pavimento. Analizando la posibilidad y conveniencia de postergar el mantenimiento periódico considerando que los valores de rugosidad, estén dentro de los niveles admisibles reemplazándolo por intervenciones de menor costo. This research is entitled "Management Proposal to maintain the roughness within Service Level concession contract." The research focuses on providing an alternative management to ensure maintain service levels in terms of the quality of the pavement when the road condition in reducing the cost to be reversed in future years on the basis of data from 2010 to 2015. Premature pavement deterioration is affected when there is no proper conservation plan that may lead to program and implement activities of routine and periodic maintenance in order to maintain service levels in toll roads. This means that the conditions of the road networks are below what is desirable and convenient, featuring a vicious cycle route (Construction - Abandonment - Destruction - Reconstruction). The research is not experimental, descriptive, correlational and quantitative explanatory. Its design is longitudinal and whose reference data from 2010 to 2015. Two proposals for road maintenance management on the basis of processed data for the years 2010 to 2015 for an alternative that would meet the main objective of this research is analyzed. Finally we conclude that it is possible to formulate a proposal for road management for optimizing the maintenance budget in projected years preserving the quality of the pavement. Analyzing the possibility and desirability of postponing regular maintenance considering that the roughness values, are within acceptable levels by replacing lower-cost interventions.

Residential energy visualization has increased in popularity during the past years, due to both legislation and an increased focus on the environmental impact of buildings. Meanwhile, the European energy efficiency directive has raised a debate on legislation on individual metering and charging (IMC), in which many negative voices among property owners and developers are being raised. The controversies bring interesting aspects to the analysis of energy visualization and its prerequisite IMC. This thesis will analyze the possibilities and barriers to implement residential energy visualization in new buildings in Stockholm, and the focus will be on local developers' perspective. The purpose of the thesis is to establish Stockholm developers' willingness to pay (WTP) for an IMC and energy visualization solution. The thesis defines perceived utility as the driving force for WTP, and accordingly the developer WTP is analyzed by evaluation of the developers' perceived utility of different technical aspects of an energy visualization solution. The solution has been modularized into three modules; IMC of hot water, IMC of heating and residential visualization. The hypothesis is that utility of the solution modules is perceived differently depending on developer ownership and developer business model; if the developer builds for property management or to sell. The empirical data has been collected through twelve in-depth interviews with developers in Stockholm. The developers were of different size, ownership and with different business models. When looking at the developers from an overall perspective, the analysis shows that there is some willingness to pay for IMC of hot water but none for IMC of heating. It can also be seen that residential visualization is something that the developers have some interest in although the overall WTP is considered low. Although environmental and fairness aspects are often mentioned by the developers in the context of IMC and energy visualization, operational and financial utility seem to be more influential in driving willingness to pay and as these utilities are not perceived, the overall WTP is low or non-existent for IMC and energy visualization. The hypothesis that developers would perceive utility differently depending on ownership or business model, if they build for property management of for sales, could not be proven. There are possibly tendencies for such differences but in this study such patterns were not clear enough to state the hypothesis as true. Additional to the WTP and developer groups, insights and takeaways are presented. The insights and takeaways are based on opportunities and risks that developers perceive with IMC and visualization, as well as requirements they have on the systems.

The innate immune system is a critical first line of defense against invading pathogens. Innate immunity directly detects pathogens, sets up an appropriate adaptive response, and can directly kill pathogens. Drosophila may lack an adaptive immune response, but have a robust innate immune system with a variety of defense effector mechanisms. While the responses to bacteria, fungi, and RNA viruses have been well characterized, not much is known about the response to DNA viruses. My studies have set out to characterize the Drosophila immune response to a DNA virus, utilizing the large dsDNA virus, Invertebrate Iridescent Virus 6 (IIV-6). IIV-6 infection causes shortened lifespan, and in later stages of infection, flies present with abdominal swelling and iridescent blue color. Our objectives were to identify pathways flies use to protect themselves from IIV-6 infection, determine how this protection is mediated, and to identify any immune inhibitors that IIV-6 uses to suppress innate immune signaling. I have found that IIV-6 strongly up-regulates a class of stress proteins with unknown function, termed Turandots, after infection in vivo or in vitro. This induction is dependent upon viral replication, requires JAK-STAT activation, and activation of p38b MAPK. In addition, the unpaireds, which function as JAK-STAT ligands, are upregulated after IIV-6 infection in a p38b-dependent manner. Together, this data suggests that p38b activation leads to production of unpaired cytokines and activation of JAK-STAT signaling to induce Turandots. I have also found that IIV-6 infected cells secrete protective factors. This response is induced within 12 hours of IIV-6 infection, exosome-mediated, and provides robust protection to naive cells challenged with an mCherry-expressing strain of IIV-6. Additionally, IIV-6 inhibits two major immune responses in Drosophila, the IMD and Toll pathways. Stimulation of IIV-6 infected Drosophila S2* cells with either IMD or Toll stimulators results in very poor antimicrobial peptide responses. Yet, IMD and Relish are still cleaved upon stimulation in IIV-6 infected cells, indicating that the block is downstream. In support of this finding, IIV-6 infected flies respond very poorly to infection with the enterobacteria Erwinia carotovora carotovora compared to mock-injected flies.

Le convertisseur analogique-numérique (ADC), fait fonction d’interface entre les domaines de représentation analogique et numérique des systèmes mixtes de traitement du signal.Il est un élément central en cela que ses performances circonscrivent celles des traitements numériques qui lui succèdent et a fortiori celles de son dispositif hôte. C’est notamment le casdes récepteurs radioélectriques numériques à large bande instantanée. De fait, ces systèmes voient leurs performances de dynamiques instantanées monotonale (DTDR) et bitonale (STDR)– i.e. leur capacité à traiter simultanément des composantes de faible puissance en présence d’une ou plusieurs autres composantes de plus forte puissance – limitées par la linéarité de leur ADC.Ce dernier caractère est quantifié par les performances de dynamique sans raies parasites (SFDR)et distorsion d’intermodulation (IMD) d’un ADC.Les critères de DTDR et de STDR sont essentiels pour les récepteurs radios numériques de guerre électronique conçus pour le traitement des signaux de radiocommunications. En effet, ces dispositifs sont employés à l’établissement de la situation tactique de l’environnement électromagnétique à des fins de support de manoeuvres militaires. La fidélité de la représentation numérique du signal analogique reçu est donc critique. Ainsi, cette thèse vise à étudier la linéarisation des ADC, i.e. l’augmentation des SFDR et IMD, en vue de l’amélioration des dynamiques instantanées de ces récepteurs.Dans ce manuscrit, nous traitons cette problématique selon deux axes différents. Le premier consiste à corriger les distorsions introduites par un ADC au moyen de tables de correspondances(LUT) pré-remplies. À cette fin, nous proposons un algorithme de remplissage de LUT procédant d’une méthode de la littérature par la réduction de moitié du nombre de coefficients à déterminer pour estimer la non-linéarité intégrale (INL) d’un ADC. Sur la base de cette nouvelle méthode,nous développons une approche de correction des non-linéarités dynamiques introduites par un ADC reposant sur une paire de LUT statiques et présentons un exemple d’algorithme permettant de l’opérer. Le second axe du manuscrit repose sur la modélisation comportementale de l’ADC par les séries de Volterra à temps discrets et leurs dérivés. En premier lieu, nous considérons les trois problématiques fondamentales de cette approche de linéarisation : la modélisation ;l’identification de modèle ; et l’inversion de modèle. Puis, nous définissons trois solutions de linéarisation d’ADC aveugles. Enfin, nous analysons l’implémentation sur circuits à réseaux logiques programmables (FPGA) de l’un de ces algorithmes afin d’évaluer la pertinence d’uneopération en temps-réel des échantillons de sortie d’un ADC échantillonnant à une fréquence d’environ 400 MHz. / The analog-to-digital converter (ADC) is a central component of mixed signal systems as the interface between the analog and digital representation spaces. Its performance bounds that of the device it is integrated in. Indeed, ADC linearity is essential for maintaining in the digital space the reliability of its input signal and then that of the information it carries.Wideband digital radio receivers are particularly sensitive to ADC non-linearities. Single-tone and dual-tone dynamic range (respectively STDR and DTDR) of such systems – i.e. the abilityto process simultaneously signal components with high power ratio – are limited by the spurious free dynamic range (SFDR) and intermodulation distortion (IMD) of their internal ADC.DTDR et de STDR are key metrics for electronic warfare wideband digital radio receivers developed for radiocommunication signal processing. As a matter of fact, these equipments are employed for analyzing the tactical situation of the radiofrequency spectrum in order to support military maneuvers. Hence, signal integrity is critical. This thesis deals with the ADC linearization issue in this context. Thus, it aims to study techniques for increasing ADC SFDRand IMD for the purpose of improving dynamic ranges of electronic warfare wideband digitalr eceivers.In this dissertation, the problematic of ADC linearization is approached in two different ways.On the one hand, we consider distortion compensation using pre-filled look-up tables (LUT). Wepropose an algorithm for filling LUTs that stems from an existing method by halving the numberof coefficients required for the integral non-linearity (INL) estimation. Then, based on this new method, we develop an approach for correcting ADC dynamic non-linearities using a couple ofstatic LUTs and we present an example of algorithm for operating this method. On the other hand,we study linearization solutions that rely on behavioural modelling of ADCs using discrete-time Volterra series and its derivatives. First, we address the three fundamental issues of this approach:modelling ; model identification ; and model inversion. Then, we propose three blind linearization algorithms. Finally, we consider the implementation on field programmable gate array (FPGA) of one of them for the purpose of evaluating the relevance of real-time linearization of an ADC sampling at about 400 MHz.