The main objective of this research is to model and analyse complex electromagnetic problems by means of a new hybridised computational technique combining the frequency domain Method of Moments (MoM), Finite-Difference Time-Domain (FDTD) method and a subgridded Finite-Difference Time-Domain (SGFDTD) method. This facilitates a significant advance in the ability to predict electromagnetic absorption in inhomogeneous, anisotropic and lossy dielectric materials irradiated by geometrically intricate sources. The Method of Moments modelling employed a two-dimensional electric surface patch integral formulation solved by independent linear basis function methods in the circumferential and axial directions of the antenna wires. A similar orthogonal basis function is used on the end surface and appropriate attachments with the wire surface are employed to satisfy the requirements of current continuity. The surface current distributions on structures which may include closely spaced parallel wires, such as dipoles, loops and helical antennas are computed. The results are found to be stable and showed good agreement with less comprehensive earlier work by others. The work also investigated the interaction between overhead high voltage transmission lines and underground utility pipelines using the FDTD technique for the whole structure, combined with a subgridding method at points of interest, particularly the pipeline. The induced fields above the pipeline are investigated and analysed. FDTD is based on the solution of Maxwell's equations in differential form. It is very useful for modelling complex, inhomogeneous structures. Problems arise when open-region geometries are modelled. However, the Perfectly Matched Layer (PML) concept has been employed to circumvent this difficulty. The establishment of edge elements has greatly improved the performance of this method and the computational burden due to huge numbers of time steps, in the order of tens of millions, has been eased to tens of thousands by employing quasi-static methods. This thesis also illustrates the principle of the equivalent surface boundary employed close to the antenna for MoM-FDTD-SGFDTD hybridisation. It depicts the advantage of using hybrid techniques due to their ability to analyse a system of multiple discrete regions by employing the principle of equivalent sources to excite the coupling surfaces. The method has been applied for modelling human body interaction with a short range RFID antenna to investigate and analyse the near field and far field radiation pattern for which the cumulative distribution function of antenna radiation efficiency is presented. The field distributions of the simulated structures show reasonable and stable results at 900 MHz. This method facilitates deeper investigation of the phenomena in the interaction between electromagnetic fields and human tissues.

The tumour microenvironment comprises the non-cancerous cells present in the tumour mass (fibroblasts, endothelial, and immune cells), as well as signalling molecules and extracellular matrix. Tumour growth, invasion, metastasis, and response to therapy are influenced by the tumour microenvironment. Therefore, characterising the cellular and molecular components of the tumour microenvironment, and understanding how they influence tumour progression, represent a crucial aim for the success of cancer therapies. High-grade serous ovarian cancer provides an excellent opportunity to systematically study the tumour microenvironment due to its clinical presentation of advanced disseminated disease and debulking surgery being standard of care. This thesis first presents a case report of a long-term survivor (>10 years) of metastatic high-grade serous ovarian cancer who exhibited concomitant regression/progression of the metastatic lesions (5 samples). We found that progressing metastases were characterized by immune cell exclusion, whereas regressing metastases were infiltrated by CD8+ and CD4+ T cells. Through a T cell - neoepitope challenge assay we demonstrated that pre- dicted neoepitopes were recognised by the CD8+ T cells obtained from blood drawn from the patient, suggesting that regressing tumours were subjected to immune attack. Immune excluded tumours presented a higher expression of immunosuppressive Wnt signalling, while infiltrated tumours showed a higher expression of the T cell chemoattractant CXCL9 and evidence of immunoediting. These findings suggest that multiple distinct tumour immune microenvironments can co-exist within a single individual and may explain in part the hetero- geneous fates of metastatic lesions often observed in the clinic post-therapy. Second, this thesis explores the prevalence of intra-patient tumour microenvironment het- erogeneity in high-grade serous ovarian cancer at diagnosis (38 samples from 8 patients), as well as the effect of chemotherapy on the tumour microenvironment (80 paired samples from 40 patients). Whole transcriptome analysis and image-based quantification of T cells from treatment-naive tumours revealed highly prevalent variability in immune signalling and distinct immune microenvironments co-existing within the same individuals at diagnosis. ConsensusTME, a method that generates consensus immune and stromal cell gene signatures by intersecting state-of-the-art deconvolution methods that predict immune cell populations using bulk RNA data was developed. ConsensusTME improved accuracy and sensitivity of T cell and leukocyte deconvolutions in ovarian cancer samples. As previously observed in the case report, Wnt signalling expression positively correlated with immune cell exclusion. To evaluate the effect of chemotherapy on the tumour microenvironment, we compared site-matched and site-unmatched tumours before and after neoadjuvant chemotherapy. Site- matched samples showed increased cytotoxic immune activation and oligoclonal expansion of T cells after chemotherapy, unlike site-unmatched samples where heterogeneity could not be accounted for. In addition, low levels of immune activation pre-chemotherapy were found to be correlated with immune activation upon chemotherapy treatment. These results cor- roborate that the tumour-immune interface in advanced high-grade serous ovarian cancer is intrinsically heterogeneous, and that chemotherapy induces an immunogenic effect mediated by cytotoxic cells. Finally, the different deconvolution methods were benchmarked along with ConsensusTME in a pan-cancer setting by comparing deconvolution scores to DNA-based purity scores, leukocyte methylation data, and tumour infiltrating lymphocyte counts from image analysis. In so far as it has been benchmarked, unlike the other methods, ConsensusTME performs consistently among the top three methods across cancer-related benchmarks. Additionally, ConsensusTME provides a dynamic and evolvable framework that can integrate newer de- convolution tools and benchmark their performance against itself, thus generating an ever updated version. Overall, this thesis presents a systematic characterisation of the tumour microenvironment of high grade serous ovarian cancer in treatment-naive and chemotherapy treated samples, and puts forward the development of an integrative computational method for the systematic analysis of the tumour microenvironment of different tumour types using bulk RNA data.

Résumé: Cette dissertation s’intéresse aux méthodes numériques dans le domaine de l’acoustique. Les propriétés acoustiques d’un produit sont devenues une part intégrante de la conception. En effet, de nos jours le bruit est perçu comme une nuisance par le consommateur et constitue un critère de vente. Il y a de plus des normes à respecter. Les méthodes numériques permettent de prédire la propagation sonore et constitue dès lors un outil de conception incontournable pour réduire le temps et les coûts de développement d’un produit. Cette dissertation considère la propagation d’ondes acoustiques dans le domaine fréquentiel en tenant compte de la présence d’un écoulement. Nous pouvons citer comme application industrielle, le rayonnement d’une nacelle de réacteur d’avion. Le but de la thèse est de proposer une nouvelle méthode et démontrer ses performances par rapport aux méthodes actuellement utilisées (i.e. la méthode des éléments finis). L’originalité du travail consiste à étendre la méthode de partition de l’unité polynomiale dans le cadre de la propagation acoustique convectée, pour des domaines extérieurs. La simulation acoustique dans des domaines de dimensions infinies est réalisée dans ce travail à l’aide d’un couplage entre éléments finis et éléments infinis. La dissertation présente la formulation de la méthode pour des applications axisymétriques et tridimensionnelles et vérifie la méthode en comparant les résultats numériques obtenus avec des solutions analytiques pour des applications académiques (i.e. propagation dans un conduit, rayonnement d’un multipole, bruit émis par la vibration d’un piston rigide, etc.). Les performances de la méthode sont ensuite analysées. Des courbes de convergences illustrent à une fréquence donnée, la précision de la méthode en fonction du nombre d’inconnues. Tandis que des courbes de performances présentent le temps de calcul nécessaire pour obtenir une solution d’une précision donnée en fonction de la fréquence d’excitation. Ces études de performances montrent l’intérêt de la méthode présentée. Le rayonnement d’un réacteur d’avion a été abordé dans le but de vérifier la méthode sur une application de type industriel. Les résultats illustrent la propagation pour une nacelle axisymétrique en tenant compte de l’écoulement et la présence de matériau absorbant dans la nacelle et compare les résultats obtenus avec la méthode proposée et ceux obtenus avec la méthode des éléments finis. Les performances de la méthode de la partition de l’unité dans le cadre de la propagation convectée en domaines infinis sont présentées pour des applications académiques et de type industriel. Le travail effectué illustre l’intérêt d’utiliser des fonctions polynomiales d’ordre élevé ainsi que les avantages à enrichir l’approximation localement afin d’améliorer la solution sans devoir créer un maillage plus fin. Summary: Environmental considerations are important in the design of many engineering systems and components. In particular, the environmental impact of noise is important over a very broad range of engineering applications and is increasingly perceived and regulated as an issue of occupational safety or health, or more simply as a public nuisance. The acoustic quality is then considered as a criterion in the product design process. Numerical prediction techniques allow to simulate vibro-acoustic responses. The use of such techniques reduces the development time and cost. This dissertation focuses on acoustic convected radiation in outer domains such as it is the case for turbofan radiation. In the current thesis the mapped infinite partition of unity method is implemented within a coupled finite and infinite element model. This method allows to enrich the approximation with polynomial functions. We present axisymmetric and three-dimensional formulations, verify and analyse the performance of the method. The verification compares computed results with the proposed method and analytical solutions for academic applications (i.e. duct propagation, multipole radiation, noise radiated by a vibrating rigid piston, etc.) . Performance analyses are performed with convergence curves plotting, for a given frequency, the accuracy of the computed solution with respect to the number of degrees of freedom or with performance curves, plotting the CPU time required to solve the application within a given accuracy, with respect to the excitation frequency. These performance analyses illustrate the interest of the mapped infinite partition of unity method. We compute the radiation of an axisymmetric turbofan (convected radiation and acoustic treatments). The aim is to verify the method on an industrial application. We illustrate the radiation and compare the mapped infinite partition of unity results with finite element computations. The dissertation presents the mapped partition of unity method as a computationally efficient method and illustrates its performances for academic as well as industrial applications. We suggest to use the method with high order polynomials and take the advantage of the method which allows to locally enrich the approximation. This last point improves the accuracy of the solution and prevent from creating a finer mesh.

The characteristics of fibers suspensions depend on the properties of fibers, the suspending fluid, and fiber-fiber interactions. This thesis demonstrates the development and application of a novel coupled method (lattice Boltzmann and finite element methods) to investigate these relationships. Fibers are modeled as flexible rod particles which are simulated by the finite element method. The fluid flow that causes the fibers to deform is calculated by the lattice Boltzmann method. The method is extended from the two dimensional case to the three dimensional case. Results from simulation show the rigid fiber in simple shear flow produces a good agreement for orientation of a fiber relative to the theoretical study by Jeffery (1922). The flexible fiber exhibits an increase on the rotational period from the rigid fiber due to more deformation shape is revealed during rotation. The simulation technique demonstrates the ability to simulate fiber-fiber interactions to further study of relative viscosity of suspensions in shear flow. Simulation results show that fiber orientation and relative viscosity depend on the fiber characteristics (fiber aspect ratio, fiber flexibility, and volume fraction). The results are verified against known experimental measurements and theoretical results. The broad aim of this research is to better understand the behavior of fibers in fluid flow. It is hoped that future researchers may benefit from the new technique and algorithms developed here.

[pt] A pesquisa tem como objetivo estudar a variação temporal de enquadramentos genéricos e específicos sobre saúde no contexto da pandemia de covid-19 no Brasil. Se trata de um estudo de caso realizado no Twitter sobre o tema da saúde (n = 31.339.922) entre 15 de março e 15 junho de 2020. Como categorias analíticas, se estudaram 3 frames genéricos e 3 específicos sobre saúde em contextos de epidemias. Os frames genéricos foram operacionalizados de forma dedutiva: conflito, atribuição de responsabilidade e moralidade (SEMETKO; VALKENBURG, 2000). Os frames específicos foram operacionalizados com o método indutivo (DE VREESE, 2005): consequências da pandemia, medidas de contenção e métodos de tratamento. Os tweets foram classificados automaticamente mediante um método computacional dictionary based, garantindo a confiabilidade, a validez e a reprodutibilidade (KRIPPENDORFF, 2011; SAMPAIO; LYCARIÃO, 2018). Foi realizada uma série temporal para observar a variação diária da evocação de cada quadro nos 93 dias estudados. Foi construída também uma rede temporal de usuários conectados mediante menções, retweets e respostas, sobre a qual foi calculada a métrica PageRank para medir a sua influência diária sobre a rede. Foram selecionados os dez atores mais proeminentes segundo o seu PageRank na data de maior pico de cada frame da série temporal. Finalmente, foram sistematizadas as informações sobre o contexto de análise e sobre o clima de opinião no Brasil mediante surveys representativos da população brasileira com frequência diária (n = 1.800, ME = mais ou menos 2 por cento, IC = 95 por cento). Os resultados da pesquisa apontam que a ordem de evocação dos frames, do mais ao menos proeminente, foi: conflito, atribuição de responsabilidade, consequências da pandemia, moralidade, medidas de contenção e métodos de tratamento. Em especial, os quadros do conflito, da atribuição de responsabilidade e das consequências da pandemia estiveram fortemente relacionados a um enquadramento negativo, episódico e de interesse humano dos tweets. Por outro lado, os demais frames (moralidade, medidas de contenção e métodos de tratamento) priorizaram enquadramentos temáticos, cujas implicações eram preponderantemente de natureza mais social e menos individual. Se destaca também a significativa presença de perfis anônimos entre os Top10 usuários de cada frame, assim como militantes, especialistas em saúde, influenciadores digitais, jornalistas, órgãos de mídia, políticos e perfis de outra natureza. Por fim, no que se refere ao estudo das condições que estão associadas aos picos mais altos de evocação dos frames genéricos e específicos da série temporal, foi observado um fenômeno que se definiu como sincronização do enquadramento. Se define a sincronização do enquadramento como um fenômeno de ajuste coletivo da frequência ativação em rede de um determinado frame por meio da interação entre os indivíduos e influenciado por quatro fatores: contexto, sucessão de eventos associados, clima de opinião e combinação entre frames e temas. / [en] The research aims to study the temporal variation of generic and specific frames about health in the context of the Covid-19 Pandemic in Brazil. It is a case study conducted on Twitter about health (n = 31,339,922) between March 15 and June 15, 2020. As analytical categories, 3 generic and 3 specific frames about health in epidemic contexts were studied. The generic frames were operationalized deductively: conflict, attribution of responsibility and morality (SEMETKO; VALKENBURG, 2000). The specific frames were operationalized with the inductive method (DE VREESE, 2005): consequences of the pandemic, containment measures, and treatment methods. The tweets were automatically classified using a dictionary-based computational method, ensuring reliability, validity, and reproducibility (KRIPPENDORFF, 2011; SAMPAIO; LYCARIÃO, 2018). A time series was performed to observe the daily variation of the evocation of each frame in the 93 days studied. A temporal network of users connected through mentions, retweets, and replies was also performed, on which the PageRank metric was calculated to measure their daily influence on the network. The ten most prominent actors were selected according to their PageRank on the peak date of each frame of the time series. Finally, information on the context of analysis and on the climate of opinion in Brazil was systematized through representative surveys of the Brazilian population with daily frequency (n = 1,800, ME = plus–minus 2 percent, CI = 95 percent). The results indicate that the order of evocation of the frames, from most to least prominent, was conflict, attribution of responsibility, consequences of the pandemic, morality, containment measures, and treatment methods. In particular, the frames of conflict, attribution of responsibility, and consequences of the pandemic were strongly related to a negative, episodic, and human interest framing of the tweets. On the other hand, the other frames (morality, containment measures and treatment methods), prioritized thematic framings, whose implications were preponderantly of a more social and less individual nature. Also noteworthy is the significant presence of anonymous profiles among the Top10 users of each frame, as well as activists, health experts, digital influencers, journalists, media organizations, politicians, and profiles of another nature, such as fandoms and satirical. Finally, regarding the study of the conditions that explain the highest peaks of evocation of the generic and specific frames in the time series, a phenomenon that was defined in this thesis as framing synchronization was observed. Framing synchronization is defined as the phenomenon of collective adjustment of the frequency of network activation of a given frame through interaction between individuals and influenced by five factors: context, succession of associated events, climate of opinion, and the combination of frames, and issues.

The main objective of this research is to model and analyse complex electromagnetic problems by means of a new hybridised computational technique combining the frequency domain Method of Moments (MoM), Finite-Difference Time-Domain (FDTD) method and a subgridded Finite-Difference Time-Domain (SGFDTD) method. This facilitates a significant advance in the ability to predict electromagnetic absorption in inhomogeneous, anisotropic and lossy dielectric materials irradiated by geometrically intricate sources. The Method of Moments modelling employed a two-dimensional electric surface patch integral formulation solved by independent linear basis function methods in the circumferential and axial directions of the antenna wires. A similar orthogonal basis function is used on the end surface and appropriate attachments with the wire surface are employed to satisfy the requirements of current continuity. The surface current distributions on structures which may include closely spaced parallel wires, such as dipoles, loops and helical antennas are computed. The results are found to be stable and showed good agreement with less comprehensive earlier work by others. The work also investigated the interaction between overhead high voltage transmission lines and underground utility pipelines using the FDTD technique for the whole structure, combined with a subgridding method at points of interest, particularly the pipeline. The induced fields above the pipeline are investigated and analysed. FDTD is based on the solution of Maxwell¿s equations in differential form. It is very useful for modelling complex, inhomogeneous structures. Problems arise when open-region geometries are modelled. However, the Perfectly Matched Layer (PML) concept has been employed to circumvent this difficulty. The establishment of edge elements has greatly improved the performance of this method and the computational burden due to huge numbers of time steps, in the order of tens of millions, has been eased to tens of thousands by employing quasi-static methods. This thesis also illustrates the principle of the equivalent surface boundary employed close to the antenna for MoM-FDTD-SGFDTD hybridisation. It depicts the advantage of using hybrid techniques due to their ability to analyse a system of multiple discrete regions by employing the principle of equivalent sources to excite the coupling surfaces. The method has been applied for modelling human body interaction with a short range RFID antenna to investigate and analyse the near field and far field radiation pattern for which the cumulative distribution function of antenna radiation efficiency is presented. The field distributions of the simulated structures show reasonable and stable results at 900 MHz. This method facilitates deeper investigation of the phenomena in the interaction between electromagnetic fields and human tissues. / Ministry of Higher Education Malaysia and Universiti Tun Hussein Onn Malaysia (UTHM)

Résumé:<p><p>Cette dissertation s’intéresse aux méthodes numériques dans le domaine de l’acoustique. Les propriétés acoustiques d’un produit sont devenues une part intégrante de la conception. En effet, de nos jours le bruit est perçu comme une nuisance par le consommateur et constitue un critère de vente. Il y a de plus des normes à respecter. Les méthodes numériques permettent de prédire la propagation sonore et constitue dès lors un outil de conception incontournable pour réduire le temps et les coûts de développement d’un produit.<p><p>Cette dissertation considère la propagation d’ondes acoustiques dans le domaine fréquentiel en tenant compte de la présence d’un écoulement. Nous pouvons citer comme application industrielle, le rayonnement d’une nacelle de réacteur d’avion. Le but de la thèse est de proposer une nouvelle méthode et démontrer ses performances par rapport aux méthodes actuellement utilisées (i.e. la méthode des éléments finis).<p><p>L’originalité du travail consiste à étendre la méthode de partition de l’unité polynomiale dans le cadre de la propagation acoustique convectée, pour des domaines extérieurs. La simulation acoustique dans des domaines de dimensions infinies est réalisée dans ce travail à l’aide d’un couplage entre éléments finis et éléments infinis.<p><p>La dissertation présente la formulation de la méthode pour des applications axisymétriques et tridimensionnelles et vérifie la méthode en comparant les résultats numériques obtenus avec des solutions analytiques pour des applications académiques (i.e. propagation dans un conduit, rayonnement d’un multipole, bruit émis par la vibration d’un piston rigide, etc.). Les performances de la méthode sont ensuite analysées. Des courbes de convergences illustrent à une fréquence donnée, la précision de la méthode en fonction du nombre d’inconnues. Tandis que des courbes de performances présentent le temps de calcul nécessaire pour obtenir une solution d’une précision donnée en fonction de la fréquence d’excitation. Ces études de performances montrent l’intérêt de la méthode présentée.<p><p>Le rayonnement d’un réacteur d’avion a été abordé dans le but de vérifier la méthode sur une application de type industriel. Les résultats illustrent la propagation pour une nacelle axisymétrique en tenant compte de l’écoulement et la présence de matériau absorbant dans la nacelle et compare les résultats obtenus avec la méthode proposée et ceux obtenus avec la méthode des éléments finis.<p><p>Les performances de la méthode de la partition de l’unité dans le cadre de la propagation convectée en domaines infinis sont présentées pour des applications académiques et de type industriel. Le travail effectué illustre l’intérêt d’utiliser des fonctions polynomiales d’ordre élevé ainsi que les avantages à enrichir l’approximation localement afin d’améliorer la solution sans devoir créer un maillage plus fin.<p><p><p>Summary:<p><p>Environmental considerations are important in the design of many engineering systems and components. In particular, the environmental impact of noise is important over a very broad range of engineering applications and is increasingly perceived and regulated as an issue of occupational safety or health, or more simply as a public nuisance. The acoustic quality is then considered as a criterion in the product design process. Numerical prediction techniques allow to simulate vibro-acoustic responses. The use of such techniques reduces the development time and cost.<p><p>This dissertation focuses on acoustic convected radiation in outer domains such as it is the case for turbofan radiation. In the current thesis the mapped infinite partition of unity method is implemented within a coupled finite and infinite element model. This method allows to enrich the approximation with polynomial functions. <p><p>We present axisymmetric and three-dimensional formulations, verify and analyse the performance of the method. The verification compares computed results with the proposed method and analytical solutions for academic applications (i.e. duct propagation, multipole radiation, noise radiated by a vibrating rigid piston, etc.) .Performance analyses are performed with convergence curves plotting, for a given frequency, the accuracy of the computed solution with respect to the number of degrees of freedom or with performance curves, plotting the CPU time required to solve the application within a given accuracy, with respect to the excitation frequency. These performance analyses illustrate the interest of the mapped infinite partition of unity method.<p><p>We compute the radiation of an axisymmetric turbofan (convected radiation and acoustic treatments). The aim is to verify the method on an industrial application. We illustrate the radiation and compare the mapped infinite partition of unity results with finite element computations.<p><p>The dissertation presents the mapped partition of unity method as a computationally efficient method and illustrates its performances for academic as well as industrial applications. We suggest to use the method with high order polynomials and take the advantage of the method which allows to locally enrich the approximation. This last point improves the accuracy of the solution and prevent from creating a finer mesh.<p> / Doctorat en Sciences de l'ingénieur / info:eu-repo/semantics/nonPublished