Pim (Provirus Integration site for Moloney murine leukemia virus) kinases are a family of three serine/threonine kinases involved in cell cycle, survival and metabolism. These kinases were first identified in malignant cells and are most often associated with their role in cancer. Their role in immunity and lymphocytes is less well known. To date, it has been shown that Pim 1 and/or Pim 2 are important for T lymphocyte survival and activation when the Akt signaling pathway is inhibited by rapamycin. In addition, our laboratory has shown that Pim 2 is critical for BLyS-mediated naive B lymphocyte survival in the presence of rapamycin. This thesis extends the role(s) for Pim 1 and/or 2 to include functions during B cell activation and the generation of immune responses. We found that during in vitro activation of purified resting splenic B cells from wild type mice with a variety of activators that use multiple signaling pathways, including the BCR, TLR and CD40 receptors, both Pim 1 and 2 kinases were induced by 48 hours post-activation, suggesting that they could play a role in B cell activation and differentiation to antibody secreting or memory B cells. Immunization of Pim 1-/-2-/- knockout mice with T cell dependent antigens showed impairment in antibody and antibody secreting cell generation as well as lack of germinal center formation clearly demonstrating an involvement of Pim 1 and/or 2 in the immune response. FACS examination of B cell populations from naive Pim 1-/-2-/- knockout mice revealed normal levels of splenic marginal zone and follicular B cells and T cells, however, decreased numbers of all peritoneal B cell populations and decreased B cells in Peyer's Patches was seen. An examination of serum antibody found in naive Pim 1-/-2-/- knockout mice showed decreased levels of natural antibody, which is likely due to loss of the peritoneal B1 cells but does not explain the significantly decreased TD immune response. To determine whether the defect was B cell intrinsic or a more complex interaction between B and T cells, we determined whether Pim 1-/-2-/- mice would respond to T cell independent, TI-1 and TI-2, antigens. Antibody production and antibody secreting cell formation were also significantly decreased in these mice supporting our notion of a B cell intrinsic defect. To further examine the B cell response problem, we attempted to establish chimeric mice using either bone marrow derived cells or fetal liver cells from WT or Pim 1-/-2-/- donors so that the B cells were derived from Pim 1-/-2-/- mice and the T cells would be WT. Unfortunately, we were not able to consistently engraft and develop mature Pim 1-/-2-/- B cells, which indicate that there is a stem cell defect in these knockout mice that requires further investigation. Because one of the major failures in activated Pim 1-/-2-/- B cells is the generation of antibody secreting cells, an analysis of the expression of transcription factors IRF-4 and BLIMP-1, known to play a role in this process was carried out. Although IRF-4 induction was not affected by the loss of Pim 1 and 2, the number of cells able to increase BLIMP-1 expression was significantly decreased, revealing a partial block in the generation of ASCs. Taken together the data presented in this thesis reveals a new and critical role for Pim 1 and 2 kinases in the humoral immune response.

Depuis la mise en évidence de l’existence des protéines kinases vers la fin des années 1950 cette famille d’enzymes s’est vu attribuer d’importants rôles dans divers mécanismes pathologiques notamment dans des processus de cancérisations. Plus récemment ces enzymes ont été identifiées comme potentiellement impliquées dans d’autres types de maladies telles que les maladies neurodégénératives.Deux projets de recherche seront présentés. Le premier projet expose la conception et la synthèse de nouveaux composés tricycliques de la famille des pyrido[3,4-g]quinazolines. Les propriétés inhibitrices de kinases des premiers dérivés ont été évaluées sur un panel de cinq kinases (CDK5, CK1, GSK3, CLK1 and DYRK1A) connues pour leurs implications dans la maladie d’Alzheimer. L’intérêt de ces nouveaux squelettes tricycliques comme inhibiteurs de kinases a été validé par des activités inhibitrices nanomolaire à l’encontre des kinases DYRK1A et CLK1. D’autre part l’obtention de structures co-crystallographiques d’interaction de deux dérivés avec le site ATP de la kinase CLK1 a permis de rationnaliser la substitution du motif pyrido[3,4-g]quinazoline. Le second projet présente le développement d’un nouveau dérivé de la staurosporine aglycone (K252c) dans lequel la partie lactame a été remplacée par un noyau pyrazole. Une étude préliminaire des propriétés biologiques de l’indolopyrazolocarbazole obtenu met en avant une cytotoxicité, du même ordre de grandeur que K252c, contre les lignées cellulaires K562 (leucémie humaine) et HCT116 (carcinome du colon). En revanche, le composé chef de file s’est révélé être un faible inhibiteur de cibles connues de K252c, les isoformes α and γ de la protéine kinase C et présente un bon potentiel inhibiteur des kinases Pim 1-3. Ce nouveau chemotype pourrait être un inhibiteur de kinases prometteur. / In 1950’s protein kinases were found to play a critical role in cell signaling, rising strong research potential for this enzyme family. Initially investigated for their implications in cancerogenesis they were more recently found to be involved in a wide variety of diseases including neurodegenerative pathologies. Herein will be presented two research projects that offer bright new perspectives for the inhibition of kinases involved whether in neurodegenerative diseases or cancers.First, the design and synthesis of new pyrido[3,4-g]quinazoline derivatives will be described as well as their protein kinase inhibitory potencies toward five CMGC family members (CDK5, CK1, GSK3, CLK1 and DYRK1A) that are known to play a potential role in Alzheimer’s disease. The interest for this original tricyclic heteroaromatic scaffold as modulators of CLK1/ DYRK1A activity was validated by nanomolar potencies. CLK1 co-crystal structures with two inhibitors revealed the binding mode of these compounds within the ATP-binding pocket and led to the synthesis of new diversely substituted pyrido[3,4-g]quinazolines.Then the synthesis of a new derivative of the staurosporine aglycon (K252c), in which the lactam ring was replaced by a pyrazole moiety, will be depicted. The resulting indolopyrazolocarbazole inhibited Pim isoforms 1–3 whereas it did not impair the activity of two known targets of K252c, protein kinase C isoforms α and γ . The lead compound exhibited same cytotoxic activity as K252c toward both human leukemia and colon carcinoma cell lines (K562 and HCT116), strongly suggesting that this new scaffold deserves further investigations for treatment of malignancies associated with kinases activities.

The exceeding supply over demand and very hard competitive conditions are nowadays the main features of the majority of sectors. A successful company is the one that is able to satisfy specific customers' needs, the one that has efficient cooperation with its suppliers throughout the whole supply chain and also the one that is able to speed up the in-house information exchange. Thus the company has to seek constantly new and innovative solutions. This is not possible without standardization and automatization of business processes. This master's thesis is dedicated to one of the possible solutions -- the Product Information Management (PIM). Since it is intended for business managers (without deep IT knowledge), at the beginning it answers the question why it is so important to know master data and to manage it. It specializes in managing product data, brings its comprehensive overview and identifies the advantages and drawbacks of the implementation as well as financial and organizational impacts. The consecutive chapter deals with simplified yet applicable approach to data management analysis (with emphasis on the PIM) and based on research, it mentions main mistakes of the implementation. In addition to the overview of main vendors of the PIM solution, it presents the latest trends in the PIM. Besides internal data synchronization, the thesis analyses several product standards -- the fundamental step towards external data synchronization, the key topic of the practical part. The whole thesis is conceived to provide an organization with a simple yet compact and therefore very effective tool for master product data insight and thus to help it to gain a competitive advantage.

Passive Intermodulation is a type of distortion affecting the sensitive receiving signals in a cellular network, which is a growing problem in the telecommunication field. One way to mitigate this problem is through Passive Intermodulation Cancellation, where the predicted noise in a signal is modeled with polynomials. Recent experiments using neural networks instead of polynomials to model this noise have shown promising results. However, one drawback with neural networks is their lack of explainability. In this work, we identify a suitable method that provides explanations for this use case. We apply this technique to explain the neural networks used for Passive Intermodulation Cancellation and discuss the result with domain expertise. We show that the input space as well as the architecture could be altered, and propose an alternative architecture for the neural network used for Passive Intermodulation Cancellation. This alternative architecture leads to a significant reduction in trainable parameters, a finding which is valuable in a cellular network where resources are heavily constrained. When performing an explainability analysis of the alternative model, the explanations are also more in line with domain expertise. / Passiv Intermodulation är en typ av störning som påverkar de känsliga mottagarsignalerna i ett mobilnät. Detta är ett växande problem inom telekommunikation. Ett tillvägagångssätt för att motverka detta problem är genom passiv intermodulations-annullering, där störningarna modelleras med hjälp av polynomiska funktioner. Nyligen har experiment där neurala nätverk används istället för polynomiska funktioner för att modellera dessa störningar påvisat intressanta resultat. Användandet av neurala nätverk är dock förenat med vissa nackdelar, varav en är svårigheten att tyda och tolka utfall av neurala nätverk. I detta projekt identifieras en passande metod för att erbjuda förklaringar av neurala nätverk tränade för passiv intermodulations-annullering. Vi applicerar denna metod på nämnda neurala nätverk och utvärderar resultatet tillsammans med domänexpertis. Vi visar att formatet på indatan till neurala nätverket kan manipuleras, samt föreslår en alternativ arkitektur för neurala nätverk tränade för passiv intermodulations-annullering. Denna alternativa arkitektur innebär en avsevärd reduktion av antalet träningsbara parametrar, vilket är ett värdefullt resultat i samband med mobilnät där det finns kraftiga begränsningar på hårdvaruresurser. När vi applicerar metoder för att förklara utfall av denna alternativa arkitektur finner vi även att förklaringarna bättre motsvarar förväntningarna från domänexpertis.

La première partie de cette thèse est consacrée au problème de partage de ressources réseaux entre les flux multicast. Tout d'abord, nous proposons MFQ (Multicast Fair Queuing), un mécanisme simple de gestion active de files d'attente qui passe à l'échelle et permettant le partage équitable de la bande passante entre les flux multicast et ceci en utilisant une fonction d'équité configurée à l'avance. Ensuite, nous décrivons SBQ (Service Based Queuing), un ordonnanceur simple utilisant deux files d'attentes afin d'améliorer le partage de ressources entre les flux unicast et multicast. Une nouvelle méthode de re-marquage de paquets multicast dans un réseau DiffServ en se basant sur le nombre de membres est également proposée. Les performances de tous ces mécanismes sont évalués pour plusieurs configurations et trafics réels. Les résultats montrent que MFQ permet d'obtenir le partage de la bande passante entre les flux multicast attendu et que SBQ garantie une allocation équitable de ressources réseaux entre les flux unicast et multicast. Enfin, nous décrivons une extension du service multicast permettant le comptage de nombre de membres dans un groupe multicast aussi bien au niveau de la source multicast qu'au niveau des routeurs intermédiaires. La deuxième partie de cette thèse examine le problème de support de l'IP multicast dans les réseaux intégrant des supports de transmission hétérogènes. Dans une première étape, nous considérons les satellites GEO transparent et nous déterminons les adaptations qui doivent être ajoutées aux différents protocoles de routage multicast. Dans une deuxième étape, nous nous focalisons sur le déploiement de l'IP multicast dans la nouvelle génération de satellites GEO supportant les technologies des multiples sopt-beams et de la commutation à bord. Nous proposons une nouvelle méthode d'encapsulation optimisée pour l'IP multicast et nous développons deux approches permettant la commutation des paquets à bord du satellite: l'approche self-routing et l'approche label switching. Nous présentons le protocole SMRP (Satellite Multicast Routing Protocol) qui traite les messages PIM-SM messages reçus par le entités du système. À la fin de cette thèse, nous présentons et nous montrons les avantages d'un nouveau mécanisme de commutation entre les deux modes du protocole PIM-SM. Ce mécanisme utilise une coordination entre les membres concernés par la commutation. De plus, il prend en compte les contraintes réseaux et les besoins de membres.

There were three main driving forces behind this thesis: global concern over climate change mainly due to uncontrolled carbon dioxide (CO2) emissions, the excitement over the discovery of graphene and its versatile potential, and the potential to design three-dimensional (3D) or two-dimensional (2D) structures, in our case using unique triptycene molecule. We examined two polymeric materials for CO2 adsorption and suggested simple design of disordered carbons suitable for gas adsorption studies. The approach in each task was to examine structural and adsorption properties of materials using detailed atomistic modelling employing Monte Carlo and Molecular Dynamics techniques and where possible provide experimental measurements to validate the simulations. The thesis is presented as a collection of papers and the work can be divided into three independent projects. The aim of the first project is to utilize graphene as an additive in polymer composites in order to increase separation between the polymer chains increasing available surface area. The matrix used is a polymer of intrinsic microporosity (PIM-1), which possess large surface area and narrow nano-sized ( > 2nm) pore distribution attractive for gas separation membrane applications. Adding a filler can reduce aging of the polymer, and enhance permeability across the membrane, often to the expense of loosing selectivity. Therefore, we investigated the packing of PIM-1 chains in presence of discrete 2D graphene platelets and 3D graphene-derived structures and its effect on composite structure and adsorption properties. We found that additives do not alter structural polymer properties at the molecular level preserving the same adsorption capacity and affinity. Potential permeability increase would benefit from the retention of selectivity in the material. Building on design philosophy of materials with intrinsic microporosity we continued further investigation of 3D graphene-derived structures. The idea is that highly concave molecules or polymer chains pack inefficiently creating microporous materials with sufficient surface area for gas adsorption. 3D propeller-like structures were derived from graphene arms connected through the rigid triptycene and other types of cores. The resulting structures created a large amount of micropores and showed similar CO2/CH4 selectivity to activated carbons reported in the literature. It was shown that rigid triptycene core leads to more open structures. The model was also applied to model commercially available activated carbon to predict n- perfluorohexane adsorption. The fitting to experimental structural information proved to be challenging due to trial and error nature of the approach. Nevertheless, the simple packing procedure and diverse structure design have a great potential to serve as a virtual model for porous carbons that possess pore complexity and does not require any previous experimental data to be build on. The last project concerns CO2 adsorption and selectivity over CH4 and N2 in recently reported triptycene-based polymer. The triptycene shape polymer can form a porous 2D network that can be exfoliated into free-standing sheets and potentially used as a membrane. Sheets stack in the bulk material forming anisotropic channel pores. Additionally it contains fluoro- functional groups, which are known to have a high CO2 affinity. We explored pore structure and chemistry of stacked material for gas adsorption and predicted comparable capacity and CO2 selectivity to other microporous covalent materials such as activated carbons and PIMs. The CH4/N2 selectivity was similar to currently most selective material belonging to MOF family. We showed that fluoro-group have a positive effect on CO2 affinity, however predictions are sensitive to the charges of fluorine atoms assigned by different methods.

Cellular response to environmental changes involves a wide repertoire of complex signalling systems often resulting in up and down regulation of various genes. These mechanisms are generally conserved in a variety of organisms. These pathways are also constantly rewired in various organisms, which aid them in maintaining homeostasis and result in species-specific adaptation mechanisms. Protein kinases are central to these mechanisms and orchestrate a multitude of these pathways. This thesis aims to understand the selective forces behind evolution of signalling pathways. More specifically, this thesis focuses on structural and domain architecture differences of protein kinases. Protein kinases are one of the most populated families of proteins in many organisms and it constitutes about 2-3% of proteomes of most of the eukaryotic organisms. These kinases have evolved over ~400 million years and regulate nearly all major signalling pathways. Classification of kinases enables convenient association of kinases to the function and signalling pathway in which they participate. The current scheme of classification is based on the amino acid sequence of the catalytic region, which consists of about 200-300 residues. This scheme proposes division into 7 groups which show gross level similarities in function such as the TK group, which constitutes all tyrosine kinases, or AGC group which constitutes kinases regulated by second messengers. These groups are further divided into ~280 subfamilies providing us insights into function and regulation at a much finer level. This enables ascertaining information about signalling pathways, protein-protein interactions or substrates the kinase phosphorylates. Chapter 1 provides an elaborate introduction to the various types of protein kinases and their roles in signalling processes. This chapter discusses how protein kinases work in a concerted manner with several other players of a signalling pathway to generate a regulated response to external stimuli. Furthermore, it highlights both the evolutionary aspects and dynamical nature of such pathways. The subsequent part of this chapter deals with protein kinases, their evolution, regulation and structural features crucial to catalysis. Protein kinases are regulated in many ways ¬regulation is achieved from within the catalytic domain and also by means of additional domains tethered to the catalytic domain. The regulatory switch is triggered by various cellular and molecular events such as phosphorylation of specific residues, changes in spatial-temporal localization and altered redox states to name a few. The effects of regulatory domains on the overall function have also been discussed. The chapter concludes by highlighting structural analysis carried out to understand the regulatory aspect of kinases and uses this information in rational drug discovery. Chapters 2 and 3 report identification and analysis of a repertoire of protein kinases encoded in the genomes of two of the organisms which are frequently used in comparative genomics. Chapter 2 focuses on the distribution of kinases in Takifugu rubripes, a teleost fish which is a widely used model system for studying human genes. Use of remote homology detection methods identified 519 kinases in fugu. Although the group-wise distribution of kinases shows high similarity to that of human kinases, subfamily distribution shows considerable differences in 22 subfamilies. They are either under or over-represented in fugu. Most noticeable difference is seen for the DYRK subfamily, which is eight times higher in fugu than human. Detailed analysis of the DYRKs revealed interesting insights into and explained partially their high representation in fugu. Only about ten of these kinases classified into these subfamilies showed high sequence similarity and conserved localization signals to the human kinases and kinases commonly found in other eukaryotes such as C.elegans, S.cereviseae and D.melanogaster. Disparity at the level of genome may be attributed to the observation of unique domain architectures characteristic of this genome. A comparison of domain architectures of kinases documented in Pfam with that of the kinases in Takifugu also revealed two kinases with unique domain architectures in fugu; they are associated with Galectin domain and YkyA domains. Despite inconsistencies in the distribution, human and Takifugu kinases subfamilies remarkable similarity is observed in the MAP kinase pathway, which is ubiquitously found across eukaryotic organisms. Nearly 83% of the proteins in this pathway show more than 30% sequence identity between the two organisms thus, validating the use of Takifugu as a model system to study human signalling pathways. While addressing the possibilities of similar expansions of kinases in other teleosts, it was noticed that the Danio rerio genome (zebrafish) had a massively expanded kinome with ~1200 kinases. Chapter 3 explores the possible reasons for the expansion of kinome with kinases specific to Zebrafish. For e.g., the number of kinases from one subfamily (CAMK) is roughly similar to the total number of protein kinases encoded in the human genome. Further, the PIM kinase subfamily is the sole subfamily, which is massively over-represented (~30 times) in this genome. A detailed analysis of PIM kinases of zebrafish revealed that the sequences are divergent from the canonical PIM kinases. Despite this difference, the specific residues, which dictate the functional properties specific to PIM kinases, are highly conserved. These PIM kinases are usually constitutively active, features of which are conserved in PIM kinases of zebrafish as well. Unlike canonical PIM kinases in other eukaryotes, the post-transcriptional regulation of these PIM kinases might be different due to the absence of regulatory regions in the 3'UTR regions of the PIM gene. However, conservation of a S261 phosphorylation site highlights regulation by phosphorylation, which compensates for the constitutively active nature. A massive expansion of the substrate pool of PIM kinases in this genome seems to correlate well with the expansion. Since PIM kinases regulate large number of growth related pathways, we believe that, this might be associated with high regenerative capacity of organs observed in this fish, which makes it an ideal model to study most cancers. While the earlier two chapters primarily focused on the kinase catalytic domain and organism specific changes; the next two chapters address the contribution of domains tethered to the catalytic domain in the overall function of the kinase. Deviations from canonical kinase domain architectures indicate expansion in the functional repertoire of kinases. Chapter 4 is a study on human kinases from the latest revised version of the human genome sequence data. The initial part of the chapter focuses on the differences in the kinase repertoire upon revision of the human genomic data. Seven sequences gleaned from the earlier genomic data are absent and 16 new sequences are added to the kinome dataset according to the latest human genome sequence data. In addition, differences in transcripts for 23 kinases have led to differences in overall length and sub-family classification of these kinases. The identification of the kinome data from this latest version was a mandatory step prior to the study of outlier kinases due to variations in gene transcripts. The domain architectures of the human kinases have been compared with known subfamily-specific domain architectures, in order to identify outliers. Based on the type of domain architecture these outliers have been classified as “rogue” or “hybrid” kinases. Hybrid architecture represent kinases showing high sequence similarity within the kinase domain to a known sub¬family of kinases with the acquisition of non-kinase domains typically found in one of the other subfamilies of kinases. On the other hand rogue architectures belong to kinases with domain architectures not observed in any of the kinase sub-families. A total of 23 outliers have been identified in the human genome-13 hybrids and 10 rogues. The presence of such "hybrid" and "rogue" kinases makes classification of kinases into subfamilies a daunting task and hence necessitates a new method for classification using the full-length sequences. The use of one such alignment-free method, ClaP (Appendix), using full length sequences has been validated for classification of kinases. A similarity metric obtained from full protein sequence comparison further improved the existing methods of classification for 29 kinases, which utilize only the catalytic domain of kinases. Classification based on catalytic domain is incomplete without the knowledge of associated domains, which also have an important role in function. This necessitates a new approach in classification of kinases for function annotation-an integrated one that uses information from the full-length sequence of each kinase. Chapter 5 extends the learning from chapter 4 and aids in identification of 74 "Hybrid" and 18 "Rogue" kinases in other model eukaryotes, Mus musculus, C.elegans, S. Cerevisiae, D. melanogaster and Takifugu rubripes which show significant variations in the overall functions. These sequences due to their hybrid nature might facilitate cross-talk between signalling pathways. Thus annotating the function of each of these 92 outliers has highlighted the use of domain recombination in wiring new pathways and re-wiring existing pathways. Also, these sequences because of their hybrid nature cannot be classified under any of the existing sub-families. Therefore, it has been proposed in this chapter that they be classified as separate sub-family containing sequences with hybrid properties. To validate this, the ClaP method has been extended where the pair-wise distances between two sequences (using full length sequence) has been used to generate phylogenetic trees which have then been subjected to hierarchical clustering to generate sub-family based clusters. Further, a Shannon entropy based score has been used to identify clusters that contain sequences from diverse sub-families grouped together. Upon analysis of these clusters, it was observed that the hybrid and rogue kinases specifically cluster within four clusters with high entropy (constitute large number of sub-families) validating their status as emergent sub-families. In addition, more hybrids and rogues have been identified in these clusters, which have long regions without any domain assignments. Such sequences may contain domain families deviant from those that are currently known and information on their function can be obtained from further genomic studies in future. Lastly, the prevalence of such hybrid and rogue kinases in the genome of a protozoan parasite, P. falciparum has been studied in detail. The role of hybrids and rogues in host-pathogen interaction has been explored. Chapter 6 presents an in-depth analysis of the possible role of charge-neutralization around phosphosites in protein kinases and its substrates. This analysis was a follow up of a study and in collaboration with Dr.Warwicker's group in Manchester, which identified positively charged residues around phosphosites in kinase substrates. The current study not only aims to address the importance of charge neutralization around phosphosites, but also uses this feature for prediction of phosphosites in known structures of kinase substrates. A dataset of phosphosites mapped on a 3-D structure has been used to calculate peak electrostatic potentials around phosphosites based on the solution of a non-linear Poisson-Boltzmann equation. A comparison of peak potentials around phosphosites with that of non-phosphosites reveals a higher positive peak potential at ~10.0 Å radius around the phosphosite. This variation is significantly higher around tyrosine residues in comparison to Ser/Thr residues phosphosites. Further, this distinction in peak potential around the phosphosite is attributed to only certain families like protein kinases and pyruvate kinases. The concept of charge neutralization will therefore show greater success in prediction of phosphosites in such families in comparison to other families with phosphosites. The functional importance of such charge neutralizations has been studied in great detail in the protein kinase domain family due to prior knowledge that certain phosphorylation events contribute to conformational change, which may be correlated to the changes in peak potentials upon phosphorylation. Phosphorylation at certain sites within the kinase catalytic domain often mediates onset of certain signalling events including regulating activity levels of kinases, mediating protein-protein interactions and altering their localization. Therefore, by means of studying conservation patterns of such phosphosites or neutralizing residues, the variations in signalling pathways in homologues with differences in conservation patterns, have been highlighted. Among domain families which do not show clear differences in peak potentials between phosphosites and non-phosphosites, it was noted, in a few cases, that negatively charged ligands bind to the protein in the vicinity of phosphosites, in the un-phosphorylated forms of the protein. Structural studies on a few cases in ligand bound forms indicate a competitive mechanism between phosphorylation and ligand binding which helps in switching between different functional forms. Therefore, the role of phosphorylation as a regulatory mechanism for modulating ligand binding in such domain families has been highlighted. Chapter 7 of the thesis reports a study on disease causing mutations in kinases. So far 180 kinases have been reported to contain disease causing mutations. This chapter particularly focuses on understanding the deleterious effects of non-synonymous missense mutations in kinases. Mutations at certain sites are enriched as seen by the concentration of disease phenotypes upon mutations at these sites in comparison to others. Interactions involving Arginines in sub-domains VIB, VIII, IX and XI are perturbed which affect catalysis. Structural explanation of 10 such mutations, which occur in important sub-domains and not directly implicated in catalysis has been provided. Apart from analyzing the various evolutionary and structural aspects of protein kinases in this thesis an attempt has been made to provide a deeper structural understanding of Msh (MutS Homologues) proteins involved in eukaryotic chromosomal segregation. Chapter 8 deals with Msh4-Msh5 complex, which are eukaryotic homologues of the MutS family of proteins in bacteria. MutS proteins form homodimeric complexes in bacteria that aid in mismatch repair process. There are six MutS homologues in eukaryotes, which form hetero-dimers. Two of the homologues are Msh4 and Msh5, which form hetero-dimeric complexes which is a pre-requisite for its function. They are involved in chromosomal segregation during meiosis-I and aid in resolving Holliday junction DNA. Till date no structure of this complex is available and the exact mode of binding is unclear. In addition, Msh4 and Msh5 display asymmetry in DNA and ATP binding sites. These insights are derived from the severity in phenotypes upon mutation of various residues in these proteins. This work is in collaboration with Dr. Nishant from IISER, Trivandrum. The questions addressed in chapter 8 of the thesis are: What are the structural features that contribute to the asymmetry in function between Msh4 and Msh5 in DNA and ATP binding? Can a structural explanation be provided for each of the 27 mutations causing severe phenotypes (cross-over defects/viability) to predict their role in function of the Msh4-Msh5 complex? Can a prediction be provided for the mode of binding of the Holliday junction DNA? Can residues occurring at interface regions of Msh4 and Msh5 be identified on the basis of the structure which affects the complexation of Msh4 and Msh5? These questions are addressed by homology modelling of the Msh4-Msh5 complex using the Msh2-Msh6 complex as template. Structural explanations have been provided for 23 out of 27 mutations with severe phenotypes. Certain residues in Msh5 are shown to form tighter network of interactions than their counterparts in Msh4 and therefore likely to have a more prominent role in DNA and ATP binding which corroborate with the observed asymmetry in mutant functions. A volume based calculation has been used to suggest a possible mode of binding of the Holliday junction within the cavity of the complex. Finally, the model has been used to predict interface residues that play a crucial role in complexation and function. Experiments are being carried out in Dr. Nishant's laboratory to mutate these residues to validate the model. Chapter 9 summarizes the entire thesis work and also clearly states the chief conclusions from various chapters. Apart from studies embodied in the thesis, the author has been involved in one other study, which is provided as appendix.

[ES] Los satélites de telecomunicación operan en entornos multiportadora, bajo una demanda continua de mayores capacidades de transmisión. Esto ha originado un aumento en los niveles de potencia de RF, frecuencias de trabajo, y número de canales transmitidos, estimulando la aparición de efectos no lineales de alta potencia, como Multipactor, Corona, y la Intermodulación Pasiva (PIM). Entre los efectos anteriores, el PIM es el menos comprendido, debido a su carácter no lineal y su estrecha relación con la fabricación, lo que dificulta el desarrollo de modelos fiables. Los términos de PIM generados en el enlace descendente pueden interferir a la débil señal en el canal de recepción, amenazando la capacidad de recepción del enlace ascendente. Los modelos tradicionales de PIM suelen basarse en una excitación formada por dos portadoras. Aunque se trata de un caso simple y bastante representativo, presenta diferencias importantes con el escenario real multiportadora. El trabajo de este Ph.D. intenta reducir estas diferencias. Para lograrlo, se realizan dos nuevas contribuciones de relevancia para las condiciones reales de operación de los satélites. En concreto, se ha investigado de forma teórica el rol de las fases de las portadoras en el PIM, y se ha propuesto un nuevo modelo que tiene en cuenta el efecto de las portadoras no contribuyentes en un cierto término de PIM, aplicando un nuevo principio de conservación de energía. Los resultados obtenidos con ambos modelos teóricos se ajustan a los datos experimentales. Debido a la compleja naturaleza del PIM, la validación de los componentes de RF de satélites se realiza mediante tests. Por lo tanto, la disponibilidad de bancos de medida de PIM es un tema de interés para la industria espacial. Sin embargo, el diseño de bancos de altas prestaciones es un desafío, ya que su nivel de PIM debe ser inferior al requerido para validar los dispositivos. Para hardware de satélites, la diferencia entre el nivel de las portadoras a transmitir y la señal de RF a detectar es como 185 dBc. En este Ph.D. se proponen unas nuevas arquitecturas integradas de bancos de PIM en guía de ondas, que cubren tanto el PIM conducido como el radiado. Dichas arquitecturas permiten una reducción importante del nivel de PIM residual del sistema de medida, siendo flexibles, capaces de manejar elevados niveles de potencia, y libres de resonancias e interacciones indeseadas. Los elementos claves de estos bancos son unos multiplexores de bajo PIM, que pueden incorporar dos familias de filtros que admiten un elevado número de ceros de transmisión, y por tanto, son capaces de proporcionar un elevado rechazo en la banda de recepción del PIM. Los bancos de medida de PIM conducido por onda reflejada, sin embargo, están expuestos al PIM generado por la carga empleada para absorber las portadoras de alta potencia. Para resolver esta situación, se han propuesto unas nuevas cargas de bajo PIM, que reducen el PIM residual de estos sistemas de medida. Así mismo, se ha elaborado un nuevo tipo de transición para mitigar el PIM respecto a flanges estándar. Para escenarios radiados se ha desarrollado una formulación capaz de relacionar densidades de potencia en el dispositivo bajo test con los niveles detectados en el banco de medida, y que por tanto permiten trasladar especificaciones de PIM del satélite al sistema de medida. Por último, se han mostrado varias campañas de medida de PIM realizadas con bancos implementados acorde a las nuevas arquitecturas propuestas. Las medidas cubren varias bandas de frecuencia y diferentes escenarios (tanto PIM conducido como radiado). Se ha determinado el excepcional nivel de fondo de ruido de PIM logrado en cada banco. Además, se han mostrado resultados obtenidos para medidas de PIM radiado en capas aislantes multicapa y mallas reflectoras, obteniendo interesantes conclusiones en cuanto a geometrías y impacto que tienen en el PIM elementos como los bordes serrados y los remaches. / [CA] Els satèl·lits de telecomunicació operen en entorns multiportadora, sota una demanda contínua de majors capacitats de transmissió. Això ha originat un augment en els nivells de potència de *RF, freqüències de treball, i nombre de canals transmesos, estimulant l'aparició d'efectes no lineals d'alta potència, com *Multipactor, Corona, i la Intermodulació Passiva (*PIM). Entre els efectes anteriors, el *PIM és el menys comprés, a causa del seu caràcter no lineal i la seua estreta relació amb la fabricació, la qual cosa dificulta el desenvolupament de models fiables. Els termes de *PIM generats en l'enllaç descendent poden interferir al feble senyal en el canal de recepció, amenaçant la capacitat de recepció de l'enllaç ascendent. Els models tradicionals de *PIM solen basar-se en una excitació formada per dues portadores. Encara que es tracta d'un cas simple i bastant representatiu, presenta diferències importants amb l'escenari real multiportadora. El treball d'aquest *Ph.D. intenta reduir aquestes diferències. Per a aconseguir-ho, es realitzen dues noves contribucions de rellevància per a les condicions reals d'operació dels satèl·lits . En concret, s'ha investigat de manera teòrica el rol de les fases de les portadores en el *PIM, i s'ha proposat un nou model que té en compte l'efecte de les portadores no contribuents en un cert terme de *PIM, aplicant un nou principi de conservació d'energia. Els resultats obtinguts amb tots dos models teòrics s'ajusten a les dades experimentals. A causa de la complexa naturalesa del *PIM, la validació dels components de *RF de satèl·lits es realitza mitjançant tests. Per tant, la disponibilitat de bancs de mesura de *PIM és un tema d'interés per a la indústria espacial. No obstant això, el disseny de bancs d'altes prestacions és un desafiament, ja que el seu nivell de *PIM ha de ser inferior al requerit per a validar els dispositius. Per a maquinari de satèl·lits , la diferència entre el nivell de les portadores a transmetre i el senyal de *RF a detectar és com 185 *dBc. En aquest *Ph.D. es proposen unes noves arquitectures integrades de bancs de *PIM en guia d'ones, que cobreixen tant el *PIM conduït com el radiat. Aquestes arquitectures permeten una reducció important del nivell de *PIM residual del sistema de mesura, sent flexibles, capaces de manejar elevats nivells de potència, i lliures de ressonàncies i interaccions indesitjades. Els elements claus d'aquests bancs són uns multiplexors de baix *PIM, que poden incorporar dues famílies de filtres que admeten un elevat nombre de zeros de transmissió, i per tant, són capaces de proporcionar un elevat rebuig en la banda de recepció del *PIM. Els bancs de mesura de *PIM conduït per ona reflectida, no obstant això, estan exposats al *PIM generat per la càrrega emprada per a absorbir les portadores d'alta potència. Per a resoldre aquesta situació, s'han proposat unes noves càrregues de baix *PIM, que redueixen el *PIM residual d'aquests sistemes de mesura. Així mateix, s'ha elaborat un nou tipus de transició per a mitigar el *PIM respecte a *flanges estàndard. Per a escenaris radiats s'ha desenvolupat una formulació capaç de relacionar densitats de potència en el dispositiu sota test amb els nivells detectats en el banc de mesura, i que per tant permeten traslladar especificacions de *PIM del satèl·lit al sistema de mesura. Finalment, s'han mostrat diverses campanyes de mesura de *PIM realitzades amb bancs implementats concorde a les noves arquitectures proposades. Les mesures cobreixen diverses bandes de freqüència i diferents escenaris (tant *PIM conduït com radiat). S'ha determinat l'excepcional nivell de fons de soroll de *PIM reeixit en cada banc. A més, s'han mostrat resultats obtinguts per a mesures de *PIM radiat en capes aïllants multicapa i malles reflectores, obtenint interessants conclusions quant a geometries i impacte que tenen en el *PIM elements com les vores serrades i els reblons. / [EN] Modern satellite payloads operate in multicarrier scenarios, under a continuous demand for higher capacity links. This leads to an increase in the RF power levels, frequency of operation, and the number of transmitted channels, thus stimulating non-linear high-power effects, such as Multipactor, Corona, thermal issues and Passive Inter-Modulation (PIM). Among the above-mentioned phenomena, PIM is the less studied, or, at least, understood. This is due to its extreme non-linear nature and its close relation to workmanship, which make very difficult the development of models able to faithfully predict and explain PIM degradation. PIM terms, once ignited in the downlink, may interfere the weak signal to be detected in the uplink channel, thus threatening the payload throughput. Traditional PIM models are based on a two-carriers excitation. This is a simple and quite representative case, but has significant differences with the real multi- carrier scenario. This Ph.D. thesis work tries to diminish this gap by two novel contributions of relevance for real operation conditions. Firstly, the role of the carrier phases (neglected for two-carriers excitation) has been theoretically investigated. Secondly, a new model to account for the effect of non-contributing carriers for a given PIM term has been developed, which is based on a novel energy conservation assumption. The resulting models fit to experimental data. Due to the complexity of PIM modeling, PIM validation of RF components is conducted only by testing. The availability of low PIM test set-ups is therefore of great interest for the space industry. However, the design of low PIM test benches is challenging, as their intrinsic residual PIM has to be below the one requested to validate the test devices. For satellite hardware, the dynamic range between the RF power levels of the transmission carriers and the signal to be detected may be 185 dBc. During this Ph.D. thesis work, novel integrated test bed architectures in waveguide technology, both for conducted and radiated PIM scenarios, have been developed. These architectures consent a mitigation of the residual PIM of the test facility, being at the same time flexible, free from unwanted interactions and spurious resonances, and able to withstand considerable RF power levels for the transmission carriers. The key elements of these set-ups are the low PIM multiplexers, which may integrate two new families of waveguide filters able to provide a high number of transmission zeros, and therefore a high rejection, in the PIM reception channel. The test benches conceived for measuring conducted backward PIM, however, are normally unprotected from the PIM generated by the termination absorbing the high-power transmission carriers. To alleviate this situation, a new type of low PIM terminations in waveguide technology has been proposed and verified with PIM tests, showing a clear benefit in mitigating the residual PIM of the test facilities. Moreover, novel transitions able to improve the PIM performance of standard flanges have also been conceived. Finally, and with regard to radiated scenarios, a novel formulation able to convert payload PIM specifications to a practical PIM test is proposed. This formulation consents to link the power flux densities at the device under test (DUT) with the RF power levels measured by the test bench. Last, a large class of PIM measurements carried out with the novel test bed architectures have been reported. These measurements cover several frequency bands (C-, Ku-, K- and Ka) and different PIM scenarios, both conducted and radiated. The exceptional residual PIM noise floor of each test bed will be pointed out. In addition, PIM tests on an anechoic chamber facility, multi-layer insulation blankets (MLIs) and reflector mesh samples are presented, with interesting considerations about the geometry of the structure and the impact on the PIM performance of typical elements as sawing areas and rivets. / Smacchia, D. (2022). Advanced Techniques for the Characterization and Experimental Validation of Passive Inter-Modulation Effect (PIM) in Space Communications Systems [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/182402 / TESIS

This masters thesis is about mutlicast. There are explained 2nd and 3th layers of the ISO/OSI model multicast addressing. Routers in a network use multicast routing protocols to optimally route multicast packet through the network, this is also in this project. These multicast protocols are DVMRP, protocol PIM in his two modes, PIM Sparse Mode and PIM Dense Mode. Protocol DVMRP uses protocol IGMP, which is described as well. At practical section of this masters thesis is presented connections, by which tests was executed.

Die Forschungsarbeit beabsichtigte den Zusammenhang zwischen Kultur und der wahrgenommenen Bedienbarkeit der PIM Software seitens deutscher und indonesischer Anwender, welcher in zwei Experimenten untersucht wurde, zu erforschen. Die Entwicklung der PIM Technologie in beiden Ländern, sowie deren kultureller Wert, insbesondere Unsicherheitsvermeidung (UA) und Individualismus-Kollektivismus (INCOL), repräsentieren die zentralen Beweggründe der vorliegenden Untersuchung. Der betrachtete kulturelle Hintergrund und die verwendete Methodik stellen die Verbindung zwischen der ersten und zweiten Studie dar. Die Experimente waren in zwei Studien aufgeteilt, da jeder kulturelle Hintergrund ein unterschiedliches Erhebungsdesign benötigt: UA steht in Beziehung mit der ersten vs. der zweiten Aufgabe und INCOL wurde mittels zwei verschiedenen Wegen der Vervollständigung erfasst (Individual- vs. Gruppenaufgabe). Während sich der Fokus der ersten Studie auf den Vergleich zwischen der deutschen und indonesischen Kultur richtet, konzentrierte sich die zweite Studie auf Kulturen zwischen (Deutschland vs. Indonesien) und innerhalb eines Landes (Individualismus vs. Kollektivismus). Die Ergebnisse legen dar, dass deutsche Anwender ein höheres Level an Unsicherheitsvermeidung als indonesische Anwender zeigen. Lediglich hinsichtlich der Zufriedenheit weisen indonesische, verglichen zu deutschen Benutzern, einen höheren Wert auf, wobei der Haupteffekt der Zeit nur bezüglich der Höhe der Effizienz signifikant ist. Es zeigte sich außerdem ein positiver Zusammenhang zwischen UA und der Effizienz beider Aufgaben, sowie eine negative Korrelation zwischen UA und der berichteten Zufriedenheit. Hinsichtlich der Höhe von UA und der Effektivität ließ sich kein negativer Zusammenhang nachweisen. Desweiteren, betreffend INCOL, lässt sich zusammenfassen, dass der Hauptinteraktionseffekt Aufgabe*INCOL statistisch signifikant ist. Bezüglich Effizienz und Zufriedenheit ist entscheidend, dass, je höher die Ausprägung von Individualismus und Kollektivismus auf Seiten der Anwender ist, desto weniger Zeit beanspruchen diese für die Ausführung individueller Aufgaben und desto zufriedener wenden die Benutzer das PIM und GIM Tool an. Mit eingeschlossen ist jedoch, dass sich zwischen Individualismus und Kollektivismus deutscher und indonesischer Bediener kein Zusammenhang mit der Höhe der Effektivität darstellen lasst. Zusammenfassend ist festzuhalten, dass die Entwickler der PIM Software mit einer internationalen Anwendergruppe beachten sollten, dass die Ergebnisse von Usability Messungen seitens Benutzeranfänger in verschiedenen Kulturen unterschiedlich sein können.:1. Abstract 2. Chapter 1: Introduction 3. Chapter 2: Research Paradigm 4. Chapter 3: Uncertainty Avoidance and Usability of Personal Information Management 5. Chapter 4: Do Individualistic and Collective Persons Measure Usability of Personal and Group Information Management differently? A Culturability Study with German and Indonesian Users 6. Chapter 5: Summary and Conclusion 7. References