Mammalian genomes are characterised by unique regions of non-methylated DNA known as CpG islands (CGIs). These genomic elements are characterised by a high density of CpGs and an elevated GC content compared to the surrounding, bulk of the genome. CGIs are prevalently associated with the 5’ end of genes and represent key nucleation sites where specific transcription factors and chromatin modifiers are recruited to impact on gene function. This thesis is focused at understanding the biochemical properties of the recently discovered H3K36-specific histone demethylase, KDM2A. This enzyme is specifically recruited to CGIs but how it interfaces with local chromatin in vivo remains unknown. Using defined chromatin templates in vitro, this study demonstrates that KDM2A binding to DNA relies on a zinc finger CXXC domain that preferentially recognizes non-methylated CpGs. In particular, nucleosomes represent a major barrier to KDM2A binding and chromatin substrates are interpreted by the CXXC domain through specific interaction with CpGs within linker DNAs. Moreover, the adjacent PHD domain does not contribute to KDM2A binding to chromatin. Together these observations suggest that sequence, methylation status and accessibility of DNA define how CGI chromatin is interpreted by CXXC domain proteins. In particular, the precise targeting of KDM2A to CGIs contributes to the creation of a unique chromatin architecture that highlights gene regulatory regions within large and complex mammalian genomes.

The power usage of the communication technology industry and the consistent energy-related pollution are becoming major societal and economic concerns. These concern stimulated academia and industry to an intense activity in the new research area of green cellular networks. Bandwidth Efficiency (BE) is one of the most important metrics to select candidate technologies for next-generation wireless communications systems. Nevertheless, the important goal is to design new innovative network architecture and technologies needed to encounter the explosive development in cellular data demand without increasing the power consumption. As a result, Energy Efficiently (EE) has become another significant metric for evaluating the performance of wireless communications systems. MIMO technology has drawn lots of attention in wireless communication, as it gives substantial increases in link range and throughput without an additional increase in bandwidth or transmits power. Multi-user MIMO (MU-MIMO) regarded when evolved Base Station equipped with multiple antennas communicates with several User Terminal (UEs) at the same time. MU-MIMO is capable of improving either the reliability or the BE by improving either the multiplexing gains or diversity gains. A proposed new idea in MU-MIMO refers to the system that uses hundreds of antennas to serve dozens of UEs simultaneously. This so-called, Large Scale-MIMO (LS MIMO) regarded as a candidate technique for future wireless communication systems. An analysis is conducted to investigate the performance of the proposed uplink and downlink of LS MIMO systems with different linear processing techniques at the base station. The most common precoding and receive combining are considered: minimum mean squared error (MMSE), maximum ratio transmission/combining (MRT/MRC), and zero-forcing (ZF)processing. The fundamental problems answered on how to select the number of (BS) antennas M, number of active (UEs) K, and the transmit power to cover a given area with maximal EE. The EE is defined as the number of bits transferred per Joule of energy. A new power consumption model is proposed to emphasise that the real power scales faster with M and K than scaling linearly. The new power consumption model is utilised for deriving closed-form EE maximising values of the number of BS antennas, number of active UEs and transmit power under the assumption that ZF processing is deployed in the uplink and downlink transmissions for analytic convenience. This analysis is then extended to the imperfect CSI case and to symmetric multi-cell scenarios. These expressions provide valuable design understandings on the interaction between systems parameters, propagation environment, and different components of the power consumption model. Analytical results are assumed only for ZF with perfect channel state information (CSI) to compute closed-form expression for the optimal number of UEs, number of BS antennas, and transmit power. Numerical results are provided (a) for all the investigated schemes with perfect CSI and in a single-cell scenario; (b) for ZF with imperfect CSI, and in a multi-cell scenario. The simulation results show that (a) an LS MIMO with 100 - 200 BS antennas are the correct number of antennas for energy efficiency maximisation; (b) these number of BS antennas should serve number of active UEs of the same size; (c) since the circuit power increases the transmit power should increase with number of BS antennas; (d) the radiated power antenna is in the range of 10-100 mW and decreases with number of BS antennas; (e) ZF processing provides the highest EE in all the scenarios due to active interference-suppression at affordable complexity. Therefore, these are highly relevant results that prove LS MIMO is the technique to achieve high EE in future cellular networks.

Recently, interference alignment (IA) has emerged as a promising technique to effectively mitigate interference in wireless communication systems. It has also evolved as a powerful technique to achieve the optimal degrees of freedom of interference channel. IA can be constructed in many domains such as space, time, frequency and codes. Currently, most researches on developing IA assume that channel state information (CSI) is well-known at the transceiver. However, in practice, perfect CSI at the transceiver can¡¦t be obtained due to many factors such as channel estimation error, quantization error, and feedback error. Under our investigation, the performance of IA is very sensitive to imperfect CSI. Therefore, this thesis proposes a spatial domain IA scheme for the three-user multiple-input multiple-output (MIMO) downlink interference channels, and analyzes the effect of channel estimation errors by modeling the estimation error as independent complex Gaussian random variables. The approximated bit error rate (BER) for the system with MIMO Zero-Forcing equalizer using IA is derived.

Rapid development processes and higher customer requirements lead to increasing integration of software solutions in the automotive industry’s products. Today, several electronic control units communicate by bus systems like CAN and provide computation of complex algorithms. This increasingly requires a controlled timing behavior. The following diploma thesis investigates how the timing analysis tool SymTA/S can be used in the software development process of the ZF Friedrichshafen AG.Within the scope of several scenarios, the benefits of using it, the difficulties in using it and the questions that can not be answered by the timing analysis tool are examined. (new: additional files)

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / Em se tratando de comunicaÃÃes mÃveis, a troca de informaÃÃes sobre os estados do canal entre as antenas receptoras e transmissoras à uma importante ferramenta para a melhoria do desempenho do sistema. Assim, nesse trabalho foram analisados sistemas MIMO multiplexados espacialmente, Spatially Multiplexed MIMO (SM-MIMO), com informaÃÃes do estado do canal no transmissor, Channel State Information (CSI), limitadas e duas tÃcnicas de detecÃÃo linear do sinal e prÃ-equalizaÃÃo do sinal Zero Forcing (ZF) e Minimum Mean Square Error (MMSE). Para essa limitaÃÃo dois esquemas foram considerados: Quantization Codebook (QC) e Compressive Sensing (CS). Compressive Sensing à usado para gerar um CSI comprimido a ser enviado pelas antenas receptoras por um canal de feedback a fim de reduzir a quantidade de informaÃÃo enviada pelas mesmas. Portanto, nesse trabalho, o desempenho das duas tÃcnicas foram comparadas por simulaÃÃes computacionais das curvas da taxa de erro de bit, Bit Error Rate (BER), de acordo com a variaÃÃo da relaÃÃo sinal ruÃdo, Signal to Noise Ratio (SNR), considerando as duas abordagens QC e CS. AlÃm disso, a presenÃa do erro de quantizaÃÃo e do ruÃdo, no canal de feedback, tambÃm foi avaliada para o esquema de CS. / Concerning to mobile communications, the information exchange over the channel states between receiving antennas and transmiting antennas is an important tool to enhance the system performance. Thus, in this work, spatially multiplexed MIMO (SM-MIMO) systems with limited Channel State Information (CSI) were analyzed considering two techniques of linear signal detection and pre-equalization Zero Forcing (ZF) and Minimum Mean Square Error (MMSE). Due to this limitation two schemes were considered: Quantization Codebook (QC) e Compressive Sensing (CS). Compressive Sensing is used to generate a reduced CSI feedback to the transmitter in order to reduce feedback load into the system. Therefore, in this work, the performance of the techniques were compared by computational simulations of Bit Error Rate (BER) curves according to the variation of the Signal to Noise Ratio (SNR) for the two considered approaches QC and CS. Furthermore, the presence of quantization error and noise, in the feedback link, were also evaluated for the CS scheme.

Rapid development processes and higher customer requirements lead to increasing integration of software solutions in the automotive industry’s products. Today, several electronic control units communicate by bus systems like CAN and provide computation of complex algorithms. This increasingly requires a controlled timing behavior. The following diploma thesis investigates how the timing analysis tool SymTA/S can be used in the software development process of the ZF Friedrichshafen AG.Within the scope of several scenarios, the benefits of using it, the difficulties in using it and the questions that can not be answered by the timing analysis tool are examined

We introduce the Partition Principle PP, an axiom introduced by Russell in the context of its similarities and differences with the Axiom of Choice AC. We start by proving some properties of PP, and AC, and show that AC, entails PP. To address the problem of whether the converse holds, we develop the Zermelo-Fraenkel ZF set theory and examine its consistency and build a model in which AC, fails. We follow this with a discussion of forcing, a technique introduced by Paul Cohen to build new models of set theory from existing ones, which have differing properties from the starting model. We conclude by examining candidate models called permutation models where AC, fails, which may be useful as candidate models for forcing a model in which PP, holds but AC, does not. We conjecture that such a model exists, and that PP, does not entail AC. / Thesis / Master of Science (MSc)

<p>Early Xenopus laevis development involves highly complex morphogenic movements. Two key movements are gastrulation, which establishes germ layer spatial arrangement, and neurulation, which results in the folding and closure of the neural tube. Multiple signaling pathways are involved in regulating cell adhesion, migration, shape and polarity during these processes to ensure normal development. Two of the most characterized pathways are the canonical and non-canonical Wnt pathways. However, the roles of all the individual molecules involved are not fully understood. In this thesis I provide initial characterization of the POZ-ZF transcription factor xZnf131. Znf131 is a transcriptional activator and its binding partner Kaiso negatively regulates this function. Since Znf131 and Kaiso display antagonistic roles and Kaiso mediates Wnt signaling and morphogenesis during Xenopus gastrulation and neurulation I hypothesize that xZnf131 is also required to regulate morphogenesis during these key developmental events.</p> <p>Like other POZ-ZF proteins, xZnf131 contains an amino-terminal POZ domain and a carboxy-terminal ZF domain comprised of five zinc fingers. xZnf131 is continuously expressed through early Xenopus development but was spatially localized to the dorsal and anterior structures of the embryo, notably the neural plate. Morpholino oligonucleotide (MO) knockdown of xZnf131 resulted in severe defects in notochord and neural plate formation, with abnormal cell morphology, typical of non-canonical Wnt misregulation. Interestingly, xZnf131 overexpression produced phenotypes very similar to xZnf131 knockdown suggesting that xZnf131 protein levels need to be tightly maintained to regulate the correct/normal morphogenic movements during Xenopus gastrulation and neurulation.</p> <p>Our findings indicate that xZnf131 plays a role in the morphogenic movements during Xenopus gastrulation and neurulation. Our data provides a useful foundation for future experiments to elucidate the biological mechanism of xZnf131 action during these key developmental processes.</p> / Master of Science (MSc)

Devido à sua importância em turbulência causada por ondas de deriva e à aplicação com propósitos em diagnósticos de plasma, a investigação de fluxos zonais (ZF) e modos acústicos geodésicos (GAM) tem atraído bastante atenção na literatura em física de plasmas. Nesta tese, primeiramente consideramos efeitos de equilíbrio com rotação poloidal e toroidal nestes modos, posteriormente investigamos efeitos diamagnéticos em GAM a partir de um modelo de dois fluido, no qual incluímos viscosidade paralela de íons e, na parte final, consideramos amortecimento de Landau e efeitos diamagnéticos simultaneamente no estudo de GAM, porém, a partir do modelo girocinético. Efeitos diamagnéticos são causados por termos que envolvem gradientes de densidade e de temperatura provenientes da função Maxwelliana de equilíbrio. O acoplamento entre os harmônicos poloidais, $m = \\pm1$, e as derivadas radiais de quantidades macroscópicas do plasma é responsável pelo aumento no valor da frequência no GAM de alta frequência e pela instabilidade no GAM de baixa frequência. Este tipo de instabilidade, que é proporcional à frequência diamagnética de elétrons e à razão entre os gradientes de temperatura e de densidade, é mais propenso a ocorrer em posições radiais em que o fator segurança é alto. Modos geodésicos são fracamente amortecidos devido a um mecânismo não colisional conhecido por amortecimento de Landau, o qual é causado pela interação entre a onda eletrostática e partículas carregadas, íons no caso, e a taxa de amortecimento é maior próximo ao centro da coluna de plasma, onde o fator de segurança assume valores mais baixos. O equilíbrio MHD com rotação foi investigado em três regimes com relação às superfícies magnéticas: isotérmico, adiabático e isométrico. Foi observado que o gradiente de temperatura possui sentido oposto em relação à velocidade de rotação poloidal apenas no regime isométrico. Ao considerar equilíbrio com rotação e superfícies magnéticas isotérmicas e incluir fluxo de calor na equação da energia, observamos que ZF apresentam frequência não-nula, a qual é proporcional à velocidade de rotação poloidal e inversamente proporcional ao fator de segurança. Como direções futuras ressaltamos que é importante considerar efeitos eletromagnéticos, estudar automodos geodésicos e incluir o efeito de partículas aprisionadas para o desenvolvimento da física de ZF e GAM. Tal desenvolvimento beneficiará tanto a área de transporte em tokamaks como a área de diagnósticos, na qual a obtenção do perfil radial da temperatura de íons e do fator de segurança é um dos objetivos. Nesta área, um novo tipo de diagnóstico conhecido como espectroscopia em modos acústicos geodésicos está sendo desenvolvido baseado no estudo de automodos. / Due to the important role in drift wave turbulence and applications for plasma diagnostic purposes, the investigation of zonal flows (ZF) and associated geodesic acoustic modes (GAM) has arisen much attention in the plasma physics literature. In this thesis, first we consider equilibrium poloidal and toroidal rotation effects on these modes using the ideal MHD model, then we investigate diamagnetic effects on GAM using a two fluid model that includes parallel ion viscosity, and, in the final step, we include both Landau damping and diamagnetic effects on the study of GAM within the framework of the gyrokinetic model. By diamagnetic effects we mean the density and temperature radial gradients terms coming from the equilibrium Maxwellian distribution function. The effects caused by the coupling between the $m = \\pm1$ poloidal harmonics and the radial derivatives of equilibrium macroscopic quantities are responsible for an increase in the frequency value of the high frequency GAM and for an instability in the low frequency GAM. This instability, which is proportional to the electron drift frequency and the ratio between ion temperature and density gradients, are more likely to occur in radial positions where the safety factor is high. We observe that geodesic modes are slowly damped by a collisionlees mechanism known as Landau damping which is caused by the wave particle interaction between the eletrostatic potential and the íons. This damping is enhanced near the center of the plasma column, where the safety factor has lower values. Equilibrium MHD with plasma rotation were investigated in three regimes regarding the magnetic surfaces: isotherm, adiabatic and isometric. It is found that the temperature gradient has opposite directions compared to the poloidal rotation only for the isometric regime. By considering equilibrium rotation with isotherm magnetic surfaces and including heat flux we observed that ZF has a non-zero frequency which is proportional to the poloidal velocity and the inverse of the safety factor. For future directions we point out that electromagnetic effects, geodesic eigenmodes and trapped particles physics should be important for the development of the ZF and GAM physics, either in the area of anomalous transport caused by drift wave turbulence or for diagnostic purposes for obtaining the radial profile of the ion temperature and the safety factor. In this area, a new kind of diagnostic known as geodesic acoustic mode spectroscopy is being developing based on the study of eigenmodes.

Cette thèse a permis de travailler sur l'efficacité d'un canal des systèmes massifs MIMO pour lesquels il faille déterminer le débit à l'Uplink des terminaux présents dans leurs cellules respectives. Comme hypothèse, la bande de fréquence en mode TDD est réutilisée dans chaque cellule. Tous les symboles sont propagés de manière asynchrone par les terminaux présents dans les cellules, n'empêchant pas de fait des interactions intra et inter symboles au niveau des stations de base. Ces signaux rencontrent beaucoup d'obstacles sur leur trajet qui entraînent des retards, des pertes de signaux (destructifs), des régénérations de signaux (constructifs) avec divers types de modulation (amplitude, fréquentielle, phase), etc. L’affaiblissement du trajet dans le canal est mis en exergue avec les différentes valeurs prises par le coefficient d'atténuation choisi lors des simulations. Face à cette situation, il a fallu rechercher le meilleur et robuste estimateur de canal à un temps de cohérence donné. La méthode MMSE (Minimum Mean Square Error) est retenue, comparée à d'autres. Pour la performance des systèmes massifs MIMO, nous nous sommes appesantis sur les méthodes de diversité des antennes (diversité d'ordre N), les méthodes de coding, les méthodes d'accès OFDMA et les méthodes d'égalisation pour montrer qu'effectivement le fait d'utiliser de nombreuses antennes au niveau des stations de base améliore et contribue aux gains recherchés en débits. Avec les systèmes massifs MIMO, nous avons montré que l'apport antennaire est bien reconnu dans la gestion des interférences. Un algorithme de calcul de débit à l'Uplink a été réalisé avec trois récepteurs conventionnels que sont le MRC (Maximum Ratio Combiner), le ZF (Zero-Forcing) et le MMSE (Minimum Mean Square Error). Les simulations ont permis de comparer les différentes approches. En faisant varier la puissance de contamination des symboles pilotes, nous observons la convergence des courbes ZF et MMSE. Si le nombre des cellules L augmentent, nous constatons que plus la puissance de contamination des symboles pilotes (pp) est élevée, plus la capacité diminue dans le canal. Après plusieurs itérations, notre algorithme converge vers une asymptote (régime stationnaire et linéaire) où les échantillons à la sortie des détecteurs s’approchent de la séquence de données émises. Le SINR obtenu avec les détecteurs conventionnels permet le calcul des débits respectifs dans le canal avec le théorème de SHANNON. / This thesis made it possible to work on the efficiency of a channel of massive MIMO systems for which it is necessary to determine the throughput at the Uplink of the terminals present in their respective cells. As an assumption, the frequency band in TDD mode is reused in each cell. All symbols are propagated asynchronously by the terminals present in the cells, not effectively preventing intra- and inter-symbol interactions at the base stations. These signals encounter many obstacles on their path that lead to delays, signal losses (destructive), signal regenerations (constructive) with various types of modulation (amplitude, frequency, phase), etc. The path loss in the channel is highlighted with the different values taken by the attenuation coefficient chosen during the simulations. Faced with this situation, it was necessary to look for the best and most robust channel estimator at a given consistency time. The MMSE (Minimum Mean Square Error) method is used, compared to others. For the performance of massive MIMO systems, we have focused on antenna diversity methods (N-order diversity), coding methods, OFDMA access methods and equalization methods to show that effectively using multiple antennas at base stations improves and contributes to the desired rate gains. With massive MIMO systems, we have shown that antennar contribution is well recognized in interference management. An algorithm for calculating the flow rate at the Uplink was developed using three conventional receivers: the MRC (Maximum Ratio Combiner), the ZF (Zero-Forcing) and the MMSE (Minimum Mean Square Error). The simulations made it possible to compare the different approaches. By varying the contamination power of the pilot symbols, we observe the convergence of the ZF and MMSE curves. If the number of L cells increases, we find that the higher the contamination power of the pilot symbols (pp), the lower the capacity in the channel. After several iterations, our algorithm converges to an asymptote (stationary and linear regime) where the samples at the detector output approach the transmitted data sequence. The SINR obtained with conventional detectors allows the calculation of the respective flows in the channel with the SHANNON theorem.