This thesis deals with the issue of wireless sensor networks and communication protocols. Is explained of what the network is composed, what standards are used and in what sectors are most often used. The main scope of work is to introduce with the localization algorithms using in WSN. Algorithms are clearly divided into groups according to the methods used. In work is describes the structure used simulation tools J-Sim, for creating a wireless sensor network. To create network will be then applied different localization algorithms, which must first be implemented in a simulator using Java code. All generated classes and the algorithms are detailed described in the work. Results from simulations are detailed and graphically displays for individual localization algorithms.

La modification post-traductionnelle par les « Small Ubiquitin-Like MOdifyers (SUMOs) » est un processus majeur de régulation qui influence plus d’une centaine de protéines. Cette modification (SUMOylation) touche plusieurs fonctions nucléaires telles que la réparation de l’ADN, la réplication et la transcription. La SUMOylation affecte une protéine le plus souvent en permettant la formation de nouvelles interactions protéine-protéines avec des facteurs de régulations qui possèdent un court segment hydrophobe dans leur séquence connu sous le nom de « SUMO interacting motif (SIM) ». Bien que les interactions SUMO-SIMs soient bien documentées, la description de leur régulation n’est pas complète. Cette thèse décrit des études fonctionnelles et structurales sur différents mécanismes de régulation des interactions SUMO-SIMs. Plus précisément, elle décrit les effets de l’acétylation et de la queue N-terminale des protéines SUMOs sur leur capacité à réguler les interactions entre SUMOs et les SIMs de trois protéines : le suppresseur de tumeur « promyelocytic leukemia (PML) », le corépresseur de transcription « Death Domain Associated Protein 6 (Daxx) » et « Protein Inhibitor of Activated STAT (PIAS) », une ligase E3 pour SUMO. La première étude décrit l’effet de l’acétylation de SUMO1 sur sa capacité à interagir avec les SIMs de PML et de Daxx. À partir d’expériences de titrage calorimétrique et d’études cristallographiques, nous avons démontré que l’acétylation précise de certains résidus conservés chez SUMO1 (K39 et K46) réduit fortement l’affinité avec les deux SIMs testés. En contraste, nous démontrons que l’acétylation du résidu K37 sur SUMO1 à un effet inhibiteur spécifique pour le SIM de Daxx. Les structures cristallographiques des complexes formés entre les variants acétylés de SUMO1 avec les SIMs concordent avec les données des titrages et suggère une plasticité dans la formation des liens sur la surface d’interaction. Partant de ce constat, nous postulons que la plasticité observée dans la structure des complexes acétylés démontre un mécanisme de régulation des interactions SUMO-SIMs par l’acétylation de résidus conservés chez SUMO1. Dans la deuxième étude, nous avons identifié un deuxième SIM à l’extrémité C-terminale de protéines de la famille (PIAS1-2-3). Nous démontrons que ce SIM est capable de lier SUMO1 et que structurellement la phosphorylation de résidus clés dans ce domaine ainsi que l’acétylation de SUMO1 peut contrôler cette interaction. Une comparaison avec le premier SIM des variants PIAS démontre que les deux SIMs sont affectés différemment par la phosphorylation et l’acétylation. En outre, nous avons déterminé que le nouveau SIM identifié joue un rôle important dans la formation d’un complexe ternaire répresseur de la transcription, formé des protéines PIAS, SUMO1 et de l’enzyme de conjugaison « UBiquitin Conjugating enzyme E2I (UBC9) ». Pris ensemble, ces résultats donnent une description atomique de l’interaction d’un nouveau SIM chez PIAS avec SUMO1 et décris comment la phosphorylation et l’acétylation peuvent sélectivement réguler la spécificité des SIM trouvés chez les variants PIAS. Finalement, dans la dernière étude, nous avons exploré le rôle de la queue N-terminale des paralogues SUMO1 et 2 sur sa capacité à moduler les interactions SUMO-SIMs. Nous avons démontré que la queue N-terminale de SUMO1, mais pas SUMO2, avait un effet auto-inhibiteur sur les interactions SUMO-SIMs et que cet effet dépendait de la présence de résidus chargés négativement présent dans le SIM. Aussi, nous avons démontré que l’effet auto-inhibiteur était spécifique à la surface d’interaction des SIMs sur SUMO1. De plus à partir d’études cristallographiques et de calorimétrie, nous avons démontré que l’effet auto-inhibiteur de la queue N-terminale de SUMO1 peut être neutralisé par la présence de zinc. La structure cristallographique du complexe entre SUMO1 et le SIM de PML démontre que le zinc stabilise la formation de liens entre des résidus chargés négativement du SIM et de la queue N-terminale de SUMO1. De plus, le zinc induit la formation d’une hélice α dans la queue N-terminale de SUMO1 qui est normalement intrinsèquement désordonnée. En résumé, cette étude donne une description atomique de l’effet de l’acétylation sur les interactions SUMO-SIMs, décris un nouveau SIM dans la famille de protéines PIAS et identifie un nouveau rôle de la queue N-terminale de SUMO1 ainsi que comment cette région peut définir la sélectivité des paralogues SUMOs. / Post-translational modification with the « Small Ubiquitin-Like MOdifyer (SUMO) » is a major regulatory process (commonly referred to as SUMOylation) that regulates hundreds of proteins associated with a diverse array of biological activities including several nuclear functions such as DNA repair, replication and transcription. SUMOylation of a protein can impact its function in many ways most often by providing an additional binding surface for forming protein-protein interactions with regulatory factors through short hydrophobic regions on their binding partners known as « SUMO interacting motif (SIM) ». Although SUMO-SIM interactions are well documented, there are nevertheless outstanding questions that still need to be addressed regarding their controlling mechanisms. This thesis reports functional and structural studies on the regulatory mechanisms that govern SUMO-SIM interactions. More precisely, we studied how acetylation and the amino-terminal tail of SUMO proteins affects the interaction of SUMO with model SIMs from three proteins: the « promyelocytic leukemia (PML) » tumor suppressor, the transcriptional corepressor « Death Domain Associated Protein 6 (Daxx) » and the SUMO E3 ligase « Protein Inhibitor of Activated STAT (PIAS) ». The first study reports the role that acetylation of SUMO1 plays on its binding to the SIMs of PML and Daxx. Isothermal Titration Calorimetry (ITC) experiments demonstrated that acetylation of SUMO1 at conserved residues (K39 and K46) dramatically reduces the binding to the SIMs of PML and Daxx. In contrast, SUMO1 acetylation at K37 dramatically reduced binding to the SIM of Daxx but only had minimal impact on binding to the SIM of PML. Crystal structures of the SUMO1 acetylated variants bound to the two SIMs support the ITC titrations and suggest that there is plasticity in SUMO-SIM interactions. The plasticity observed in the structures of these complexes would provide a robust mechanism for regulating SUMO-SIM interactions using a combination of signalling mechanisms that control post-translational modifications. In the second study, we identified and characterized a novel SIM at the C-terminal extremity of three of the four known variants of the PIAS-family proteins (PIAS1-2-3). We demonstrated that this SIM binds to SUMO1 and structurally show that phosphorylation of the SIM or acetylation at select lysine residues of SUMO1 alters this interaction. In addition, we determined that it plays an important role in the formation of ternary complex made of SUMO1, PIAS1 and the « UBiquitin Conjugating enzyme E2I (UBC9) » in human cells. Together, these results provide an atomic description of the interaction between the C-terminal SIM of PIAS proteins and SUMO1 as well as important insight into how posttranslational modifications selectively regulate the specificity of the SIMs found in PIAS1-2-3. Finally, our third study explores the intrinsically disordered N-terminal tail of SUMO paralogs and their ability to regulate SUMO-SIM interactions. We demonstrate that the N-terminal region of SUMO1, but not SUMO2, has an auto-inhibitory effect on the binding to SIMs and that this effect is dependent on the presence of acidic or phosphorylated residues that within the SIM. In addition, we also determined that this inhibition does not affect the interaction of SUMO1 with its E2 conjugating enzyme UBC9. Using titration calorimetry and crystallographic screening, we identified zinc as a negative regulator of this auto-inhibitory effect. The crystallographic structure of the complex between SUMO1 and the SIM of PML shows that zinc stabilises the formation of interactions with the negatively charged residues within the SIM and the N-terminal tail of SUMO1. Interestingly, zinc also appears to stabilize the formation of an α-helix within the N-terminal tail of SUMO1 which is normally intrinsically disordered. In summary, this thesis describes the underlying atomic regulatory mechanisms of SUMO-SIM interactions by acetylation, reveals a novel SIM within the PIAS SUMO E3 ligase family and describes an unprecedented role of the N-terminal region of SUMO1 and provides important insight on how this region can define SUMO paralog specificity.

Network intrusion detection systems (NIDSs) are a major component in cybersecurity and can be implemented with open-source software. Active communities and researchers continue to improve projects and rulesets used for detecting threats to keep up with the rapid development of the internet. With the combination of security information management, automated threat detection updates and widely used software, the NIDS security can be maximized. However, it is not clear how different combinations of software and basic settings affect network performance. The main purpose in this thesis was to find out how multithreading, standard ruleset configurations and near real-time data shipping affect Snort IDS’ online and offline performance. Investigations and results were designed to guide researchers or companies to enable maximum security with minimum impact on connectivity. Software used in performance testing was limited to Snort 2.9.17.1-WIN64 (IDS), Snort 3.1.0.0 (IDS), PulledPork (rule management) and Open Distro for Elasticsearch (information management). To increase the replicability of this study, the experimentation method was used, and network traffic generation was limited to 1.0 Gbit/s hardware. Offline performance was tested with traffic recorded from a webserver during February 2021 to increase the validity of test results, but detection of attacks was not the focus. Through experimentation it was found that multithreading enabled 68-74% less runtime for offline analysis on an octa-thread system. On the same system, Snort’s drop rate was reduced from 9.0% to 1.1% by configuring multiple packet threads for 1.0 Gbit/s traffic. Secondly, Snort Community and Proofpoint ET Open rulesets showed approximately 1% and 31% dropped packets, respectively. Finally, enabling data shipping services to integrate Snort with Open Distro for Elasticsearch (ODFE) did not have any negative impact on throughput, network delay or Snort’s drop rate. However, the usability of ODFE needs further investigation. In conclusion, Snort 3 multithreading enabled major performance benefits but not all open-source rules were available. In future work, the shared security information management solution could be expanded to include multiple Snort sensors, triggers, alerting (email) and suggested actions for detected threats.

<p>Simultaneous dual-isotope SPECT imaging has a number of applications, for exam- ple, cardiac, brain and cancer imaging. The major concern in simultaneous dual- isotope SPECT is the significant crosstalk contamination between the different isotopes used. The current study focuses on a method of crosstalk compensation between two isotopes in simultaneous dual isotope SPECT acquisition applied to cancer imaging using ^99mTc/¹¹¹In and breast SPECT using ^99mTc/¹²³I. Monte Carlo (MC), which is thought to offer the most realistic crosstalk and scatter compensation modelling, in typical implementations, has inherent long calculation times (often several hours or days) associated with it. This makes MC unsuitable for clinical applications. We have previously incorporated convolution based forced detection into SIMIND Monte Carlo (MC) program which have made MC feasible to use in clinical time frames. In order to evaluate the accuracy of our accelerated MC program a number of point source simulation results were compared to experimentally acquired data in terms of spatial resolution and detector sensitivity. We have developed an iterative MC based image reconstruction technique that simulates the photon down-scatter from one isotope into the acquisition window of a second isotope. The MC based estimation of scatter contamination contained in projection views is then used to compensate for the photon contamination during iterative reconstruction. We use a modified ordered subset expectation maximization (OSEM) alogrithm, named as simultaneous ordered subset-expectation maximization (Sim-OSEM), to perform this step. We have undertaken a number of simulation tests and phantom studies to verify this approach in case of both of the dual-isotope combinations (i.e. ^99mTc/¹¹¹In and ^99mTc/¹²³I). In breast SPECT studies three different breast sizes were simulated. For each of the breast sizes ten combinations of lesions with 3 lesions per combination, were selected randomly for acquisition and reconstruction of simulation data. The images reconstructed using Sim-OSEM showed crosstalk compensation when compared with images reconstructed using simultaneously (with crosstalk) acquired projection data using analytical attenuation based reconstruction. In case of Sim-OSEM the lesion to background ratios were much closer to actual values compared to images reconstructed for both separately (without crosstalk) and simultaneously (with crosstalk) acquired projection data using analytical attenuation based reconstruction. Activity estimation is also possible with Sim-OSEM and yielded accurate estimates of lesion activities with relatively small error compared to deposited activities. The proposed reconstruction technique also evaluated by reconstruction of experimentally acquired projection phantom data in case of ^99mTc/¹¹¹In. Reconstruction using Sim-OSEM showed very promising results in terms of crosstalk and small angle scatter compensation and uniformity of background compared to analytical attenuation based reconstruction after triple energy window (TEW) based scatter correction of projection data. In our case images obtained using Sim-OSEM showed more uniform background even when compared to the images reconstructed for separately acquired projection data using analytical attenuation based reconstruction may be due to better correction of photons scattered at small angle and got detected under photopeak.</p> / Master of Science (MSc)

Immersive simulations beskrivs ofta som spel som betonar spelarens immersion genom att uppmuntra problemlösning inom mekaniskt konsekventa spelvärldar. Studien syftar på att kartlägga gemensamma drag hos immersive simulations genom spelmekanisk analys med målet att minska allmän oklarhet kring termens innebörd. En enkät publiceras online som efterfrågar de speltitlar som bäst representerar immersive sims inom sex olika kategorier. De populäraste titlarna per kategori analyseras med mål att besvara en uppsättning frågor som formuleras genom granskning av litteratur. Listan av frågor utökas under analysens gång för att fånga upp så många mekaniska egenskaper som möjligt. Likheter och skillnader mellan spelen presenteras och diskuteras med syfte att etablera egenskaper som verkar mer eller mindre viktiga för genren. Studiens resultat pekar på många gemensamma aspekter inom navigering, strid och till viss del smygning hos samtliga verk. Skillnader syns i spelvärldens uppbyggnad och mängden interaktiva system. En framtida studie skulle kunna utföra en liknande analys på ytterligare verk för att få en mer enhetlig bild av genrens mekaniska egenskaper.

Dans ce mémoire, je présenterai les outils que nous avons développés dans le cadre de ma maîtrise. Tout d'abord, je présenterai un outil d'analyse de données génomiques nommé Versatile Aggregrate Profiler (VAP). Ensuite, je présenterai un outil d'identification de profils agrégés similaires nommé vap_sim ainsi que la méthodologie utilisée afin d'obtenir un paramétrage adéquat de l'outil pouvant s'adapter assez facilement aux différents profils agrégés. Au troisième chapitre, je présenterai un outil de validation de formats génomiques nommé Genomic Format Validator (GFV) permettant d'identifier simplement et rapidement les erreurs de structure et de logique dans un fichier de données génomiques. Finalement, au dernier chapitre, je présenterai trois outils complémentaires à VAP.

Made available in DSpace on 2015-04-14T13:48:21Z (GMT). No. of bitstreams: 1 467137.pdf: 936811 bytes, checksum: 4e9e634ce4210eb116c751213b5e98b2 (MD5) Previous issue date: 2015-01-20 / This dissertation will analyze the Confer?ncias C?vicas (1904-1906) and the spelling book Terra Ga?cha (2013), both by Jo?o Sim?es Lopes Neto. On this basis, we intend to comprehend how the author has organized and expressed his ideas concerning the Brazilian nation, what were his inspirations and the lines of thought that most influenced him. With this in mind, this research aims to increase the understanding about Lopes Neto and his work. In other words, the objective is to understand him not only as a regionalist writer but as an intellectual who, from your region, thought about the Brazilian nation. This expansion of perspective about Lopes Neto contributes to a better understanding of the author and his work. When thinking about the Brazilian nation, Lopes Neto realized the lack of a civic education able to awaken in people "the spirit of the nation". Trying to solve this problem the author created a complex narrative in order to pay attention to the virtues and vices of the Brazilian nation, its different regions and cultures. For example, the spelling book would be a tool for teaching in Rio Grande do Sul. So it has special focus on the gaucho culture and tries to demonstrate that the various regions form the nation. / A presente disserta??o tem como objetivo analisar as Confer?ncias C?vicas (1904-1906) e o livro de leitura Terra Ga?cha (2013), ambos de Jo?o Sim?es Lopes Neto. Com base nessa an?lise visamos compreender como o autor organizou e exprimiu suas ideias acerca da tem?tica da na??o brasileira, quais foram as suas inspira??es e as correntes de pensamento que mais o influenciaram. Isto posto, esta pesquisa visa alargar o campo de compreens?o no que se refere ? Jo?o Sim?es Lopes Neto e sua obra, pois o objetivo ? compreend?-lo como um intelectual que a partir de sua regi?o refletiu sobre a na??o brasileira, e n?o apenas como um escritor regionalista, plano ao qual ficou relegado. Esse alargamento da perspectiva acerca do autor colabora para uma melhor compreens?o do mesmo e de sua obra, pois Jo?o Sim?es Lopes Neto ao refletir sobre a na??o brasileira percebeu a falta de uma educa??o c?vica capaz de despertar nas pessoas o esp?rito da na??o. Para tentar resolver esse problema o autor criou uma narrativa complexa de identifica??o, visando atentar para as virtudes e v?cios da na??o brasileira, as suas diversas regi?es e culturas. O livro de leitura, por exemplo, tendo em vista que seria um instrumento para o ensino no Rio Grande do Sul, conta com um enfoque especial na cultura ga?cha, buscando demonstrar que as diversas regi?es s?o formadoras da na??o.

Learning the knowledge and procedures of the Assessment of Basic Learning Abilities (ABLA) is a major practical priority for direct-care service providers who work with individuals with intellectual disabilities (IDs) and autism spectrum disorders (ASDs). The present study compared the effects of two training conditions involving a self-instructional manual (SIM) alone and its combination with a Web-based computer-aided personalized system of instruction (WebCAPSI) program (SIM plus WebCAPSI) on teaching knowledge and implementation of the ABLA to university students. A multiple-baseline design across training conditions was used. The results indicate that the SIM combined with passing unit tests delivered via WebCAPSI was beneficial for knowledge acquisition while viewing demonstration videos was beneficial for conducting the ABLA. The findings suggest that a combination of a SIM combined with unit tests delivered via WebCAPSI and videos provides an effective approach to teach both knowledge and application of behavioural procedures to potential knowledge users.

Learning the knowledge and procedures of the Assessment of Basic Learning Abilities (ABLA) is a major practical priority for direct-care service providers who work with individuals with intellectual disabilities (IDs) and autism spectrum disorders (ASDs). The present study compared the effects of two training conditions involving a self-instructional manual (SIM) alone and its combination with a Web-based computer-aided personalized system of instruction (WebCAPSI) program (SIM plus WebCAPSI) on teaching knowledge and implementation of the ABLA to university students. A multiple-baseline design across training conditions was used. The results indicate that the SIM combined with passing unit tests delivered via WebCAPSI was beneficial for knowledge acquisition while viewing demonstration videos was beneficial for conducting the ABLA. The findings suggest that a combination of a SIM combined with unit tests delivered via WebCAPSI and videos provides an effective approach to teach both knowledge and application of behavioural procedures to potential knowledge users.

Optical microscopy is a cornerstone of biomedical research. Advances in optical techniques enable specific, high resolution, sterile, and biologically compatible imaging. In particular, beam shaping has been used to tailor microscopy techniques to enhance microscope performance. The aim of this Thesis is to investigate the use of novel beam shaping techniques in emerging optical microscopy methods, and to apply these methods in biomedicine. To overcome the challenges associated with high resolution imaging of large specimens, the use of Airy beams and related techniques are applied to light-sheet microscopy. This approach increases the field-of-view that can be imaged at high resolution by over an order of magnitude compared to standard Gaussian beam based light-sheet microscopy, has reduced phototoxicity, and can be implemented with a low-cost optical system. Advanced implementations show promise for imaging at depth within turbid tissue, in particular for neuroscience. Super-resolution microscopy techniques enhance the spatial resolution of optical methods. Structured illumination microscopy is investigated as an alternative for electron microscopy in disease diagnosis, capable of visualising pathologically relevant features of kidney disease. Separately, compact optical manipulation methods are developed with the aim of adding functionality to super-resolution techniques.