D. Tech. (Department of Process Control and Computer Systems, Faculty of Engineering and Technology), Vaal University of Technology. / In this research study, a scheme to minimise interference in converged mobile cellular networks (MCNs) and wireless sensor networks (WSNs) was designed and implemented. The focus was the mitigation of interference that arises when proximity service (ProSe)-enabled sensors engage in a device-to device (D2D) communication to alert smartphone users upon the detection of explosives at highly crowded areas like shopping malls. D2D is a technology that academia and industry experts believe will play a prominent role in the implementation of the next generation of mobile networks, specifically, the fifth generation (5G). However, the full roll out of D2D is being impeded by the interference that the technology introduces to the cellular network. D2D devices cause a significant amount of interference to the primary cellular network especially when radio resources are shared. In the downlink phase, primary user equipment is likely to suffer from interference emanating from a D2D transmitter. On the other hand, the immobile base station is affected by interference caused by the D2D transmitter in the uplink phase. This type of interference can be avoided or reduced if radio resources are allocated intelligently under strict coordination of the base station. An NP-hard optimisation problem was formulated and finding a solution to this problem in 1 ms is not possible. 5G has a frame structure duration of 10 ms with 10 subframes of 1 ms each. Heuristic algorithms were then developed to mitigate the interference affecting the primary network that could carry out resource allocation within the fast-scheduling period of 1 ms. Smartphones have progressed into devices capable of generating massive volumes of data. The challenge is that battery technology is not keeping up with the pace of smartphone technology, so any additional feature that designers want to add, is met with a lot of contempt from customers who are concerned about their smartphone batteries depleting rapidly. In this context, the strategy must be energy-efficient for smartphone users to embrace it. A system level simulator was developed using MATLAB to evaluate the efficacy of the proposed design. Extensive simulation results showed that ProSe-enabled sensors can safely be integrated into cellular networks participating in D2D communication with smart phones, without introducing significant harm to the primary cellular network. The results showed that after implementing the proposed strategy, overall user throughput decreased by 3.63 %. In cellular networks, this is a modest figure since a reduction of up to 5% is acceptable to both users and network providers. The figure generally capped in service level agreements signed between network providers and users is 5%. The proposed technique also resulted in a 0 % reduction in SINR of CUEs in a cellular network, according to the findings. In terms of D2D link throughput for different D2D transmit levels, the method proposed in this research work surpassed a similar scheme proposed in literature by an average of 18.3%.

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The ever increasing demands of Internet users caused by the introduction of new high bandwidth applications and online services as well as the growing number of users and devices connected to the Internet, bring many challenges for the operators, especially in the last mile section of the network. Next generation access architectures are expected to offer high sustainable bandwidth per user. They also need to support a much larger service areas to decrease number of current central offices and hence potentially save the network expenditures in the future. Obviously, it requires high capacity and low loss transmission and optical fiber technology is the only future proof candidates for broadband access. Although this technology has already been widely deployed in the core networks, it is hard to use the same expensive devices made for core segment to solve the last mile bottlenecks, due to the low number of users sharing the network resources (and deployment cost). Therefore, the next generation optical access (NGOA) networks need to be designed with consideration of cost efficiency in the first place.   Network reliability is also turning to be an important aspect for the NGOA networks as a consequence of long reach, high client count and new services requiring uninterrupted access. Consequently, new architectures not only need to be cost efficient but also they should fulfill the increasing reliability requirements.   Although several NGOA alternatives have been proposed in the literatures, there is not yet an agreement on a single architecture. As described earlier, network expenditure and reliability performance are the two main factors to be considered. Therefore, this thesis concentrates on finding a suitable alternative for future broadband access by evaluating the reliability performance and total cost of ownership for several NGOA candidates. In particular, in this thesis we analyze the tradeoff between the cost needed to deploy backup resources and the reliability performance improvement obtained by the provided survivability mechanism.   First, we identified the suitable NGOA candidates by comparing two main groups of optical access networks, namely passive optical networks (PONs) and active optical networks (AONs), in terms of cost, reliability performance and power consumption. The initial results have shown that wavelength division multiplexing PON (WDM PON) is the most promising alternative for the NGOA networks because of its high potential capacity, low cost and power consumption. So we continued our studies by investigating two WDM-based PON architectures regarding their cost and reliability performance. The study has also included a proposed fiber layout compatible with these two candidates aiming to minimize the required investment needed to offer protection. Our primary results confirmed that hybrid PON (HPON) is the best alternative for the NGOA networks. Therefore we further analyzed this candidate considering several variants of HPON. The most important components and sections of the HPON, which need to be protected to decrease the impact of each failure in the network have been identified. Based on these outcomes, two resilience architectures protecting the shared part of the HPON were proposed and their reliability performance parameters as well as cost of protection were evaluated. According to the results, using our proposed protection schemes a considerable improvement in reliability performance of the HPON variants can be provided at minor extra investment. We also introduced a cost efficient HPON architecture with different levels of protection for users with various reliability requirements, i.e. the protection of shared parts of the access network for all the connected users and end-to-end resilience scheme for some selected ones (e.g., business users). To gain an overall view on the cost efficiency of the proposed architecture, we evaluated the investment required for deploying these schemes considering several network upgrading paths towards a protected network. Moreover, a sensitivity analysis investigating the influence of network deployments time and the density of the users with higher availability requirements was presented.   In summary, we have shown that HPON is able to fulfill the main NGOA requirements such as high bandwidth per-user, large coverage and client count. The work carried out in the thesis has proved that HPON can also offer high reliability performance while keeping the network expenditures at an acceptable level. Moreover, low power consumption and high flexibility in resource allocation of this architecture, makes it a winning candidate for the NGOA networks. Therefore, HPON is a promising architecture to be deployed as NGOA network in the near future considering the fact that components are soon to be available in the market. / <p>QC 20130530</p> / FP7 EU project, Optical Access Seamless Evolution(OASE)

The next generation wireless system (NGWS) has been conceived as a ubiquitous wireless environment. It integrates existing heterogeneous access networks, as well as future networks, and will offer high speed data, real-time applications (e.g. Voice over IP, videoconference ) and real-time multimedia (e.g. real-time audio and video) support with a certain Quality of Service (QoS) level to mobile users. It is required that the mobile nodes have the capability of selecting services that are offered by each provider and determining the best path through the various networks. Efficient radio resource management (RRM) is one of the key issues required to support global roaming of the mobile users among different network architectures of the NGWS and a precise call admission control (CAC) scheme satisfies the requirements of high network utilization, cost reduction, minimum handover latency and high-level QoS of all the connections. This thesis is going to describe an adaptive class-based CAC algorithm, which is expected to prioritize the arriving channel resource requests, based on user¿s classification and channel allocation policy. The proposed CAC algorithm couples with Fuzzy Logic (FL) and Pre-emptive Resume (PR) theories to manage and improve the performance of the integrated wireless network system. The novel algorithm is assessed using a mathematical analytic method to measure the performance by evaluating the handover dropping probability and the system utilization.

In this thesis, an inverse source (IS) approach is considered for the constrained design of static-passive electromagnetic skins (SP-EMSs). By leveraging the ill-posedness/non-uniqueness of the IS problem at hand, a generalized solution framework is devised for the synthesis of SP-EMSs that simultaneously comply with (i) complex wireless coverage requirements and (ii) manufacturing and installation constraints. These two design goals can be decoupled and tackled separately through the employment of non-radiating (NR) currents. The flexibility of the IS-based formulation is demonstrated in practice with the implementation of two synthesis strategies dealing with different classes of design constraints. Representative results from a wide set of numerical experiments are reported to prove the effectiveness and the computational efficiency of the proposed method as a suitable tool for a real and effective realization of the so-called smart electromagnetic environment (SEME).

Microfluidics is a versatile tool with many applications in biology. Its ability to manipulate small volumes of liquid precisely has led to the development of many microfluidic assay platforms. They could handle small amounts of samples and carry out analysis with high sensitivity and throughput. Microfluidic assays have provided new insights into scarce biological samples at higher resolution. In this thesis, we developed microfluidic tools to conduct low input ChIP-seq and ChIRP-seq. We applied them to a variety of samples profiling different targets. The native MOWChIP-seq platform was developed to map RNA polymerase II, transcription factors and histone deacetylase binding in 1,000-50,000 cells. We examined mouse prefrontal cortex and cerebellum using this technology. We found extensive differences that correlated with distinct neurological functions of the brain regions. The same platform and workflow were used to profile five key histone modifications in human lung tumor and normal tissue samples. Integrative analysis with gene expression data revealed extensive chromatin remodeling in lung tumor. Spatial histone modification mapping was conducted in mouse neocortex in a similar fashion. We generated an epigenomic tomography that demonstrated the molecular state of the brain in 3D. Lastly, we developed a microfluidic version of the ChIRP-seq process which successfully conducted the assay using only 500K cells. This improvement makes ChIRP-seq in tissue samples feasible. / Doctor of Philosophy / Microfluidics is a type of technology that can control small volumes of liquid in a miniature system. It can carry out reactions on very small scales with higher precision and sensitivity than conventional methods. Microfluidics has found many uses in the field of biology, especially dealing with samples available in limited quantities. These low input microfluidic platforms have helped researchers gain new knowledge on many complex questions. In this thesis, we developed microfluidic tools to carry out low input ChIP-seq and ChIRP-seq. These are two established techniques used to map where certain targets are located on the genome of an organism. These targets include specific chemical modifications to the wrapper protein of DNA (histone modification), proteins that take part in transcription and expression of genes (RNA polymerase II, transcription factors) and other molecules. Our nMOWChIP-seq system removed the need for fixation by chemicals. It was able to examine RNA polymerase II, transcription factors and other enzymes using 1,000-50,000 cells. Traditional ChIP-seq requires more than 10 million cells and time-consuming chemical treatment steps. Our technology greatly improved sensitivity and ease of use. We also used this platform to test five important histone modifications in human lung tumors and healthy tissues. We constructed a spatial map of histone modification in mouse brain by analyzing slices of the cortex. Finally, we developed a microfluidic version of ChIRP-seq process to map locations of long non-coding RNAs in cultured human cells. The cells needed for a successful test were reduced to 500K from 20 million of the original workflow.

Der Ribonukleinsäure (RNS) Stoffwechsel umfasst verschiedene Schritte, beginnend mit der Transkription der RNS über die Translation bis zum RNA Abbau. Poly(A) Schwänze befinden sich am Ende der meisten der Boten-RNS, schützen die RNA vor Abbau und stimulieren Translation. Die Deadenylierung von Poly(A) Schwänzen limitiert den Abbau von RNS. Bisher wurde RNS Abbau meist im Kontext von cytoplasmatischen Prozessen untersucht, ob und wie RNS Deadenylierung und Abbau in Nukleus erfolgen ist bisher unklar. Es wurde daher eine neue Methode zur genomweiten Bestimmung von Poly(A) Schwanzlänge entwickelt, welche FLAM-Seq genannt wurde. FLAM-Seq wurde verwendet um Zelllinien, Organoide und C. elegans RNS zu analysieren und es wurde eine signifikante Korrelation zwischen 3’-UTR und Poly(A) Länge gefunden, sowie für viele Gene ein Zusammenhang von alternativen 3‘-UTR Isoformen und Poly(A) Länge. Die Untersuchung von Poly(A) Schwänzen von nicht-gespleißten RNS Molekülen zeige, dass deren Poly(A) Schwänze eine Länge von mehr als 200 nt hatten. Die Analyse wurde durch eine Inhibition des Spleiß-Prozesses validiert. Die Verwendung von Methoden zur Markierung von RNS, welche die zeitliche Auflösung der RNS Prozessierung ermöglicht, deutete auf eine Deadenylierung der Poly(A) Schwänze schon wenige Minuten nach deren Synthesis hin. Die Analyse von subzellulären Fraktionen zeigte, dass diese initiale Deadenylierung ein Prozess im Nukleus ist. Dieser Prozess ist gen-spezifisch und Poly(A) Schwänze von bestimmten Typen von Transkripten, wie nuklearen langen nicht-kodierende RNS Molekülen waren nicht deadenyliert. Um Enzyme zu identifizieren, welche die Deadenylierung im Zellkern katalysieren, wurden verschiedene Methoden wie RNS-abbauende Cas Systeme, siRNAs oder shRNA Zelllinien verwendet. Trotz einer effizienten Reduktion der RNS Expression entsprechender Enzymkomplexe konnten keine molekularen Phänotypen identifiziert werden welche die Poly(A) Länge im Zellkern beeinflussen. / The RNA metabolism involves different steps from transcription to translation and decay of messenger RNAs (mRNAs). Most mRNAs have a poly(A) tail attached to their 3’-end, which protects them from degradation and stimulates translation. Removal of the poly(A) tail is the rate-limiting step in RNA decay controlling stability and translation. It is yet unclear if and to what extent RNA deadenylation occurs in the mammalian nucleus. A novel method for genome-wide determination of poly(A) tail length, termed FLAM-Seq, was developed to overcome current challenges in sequencing mRNAs, enabling genome-wide analysis of complete RNAs, including their poly(A) tail sequence. FLAM-Seq analysis of different model systems uncovered a strong correlation between poly(A) tail and 3’-UTR length or alternative polyadenylation. Cytosine nucleotides were further significantly enriched in poly(A) tails. Analyzing poly(A) tails of unspliced RNAs from FLAM-Seq data revealed the genome-wide synthesis of poly(A) tails with a length of more than 200 nt. This could be validated by splicing inhibition experiments which uncovered potential links between the completion of splicing and poly(A) tail shortening. Measuring RNA deadenylation kinetics using metabolic labeling experiments hinted at a rapid shortening of tails within minutes. The analysis of subcellular fractions obtained from HeLa cells and a mouse brain showed that initial deadenylation is a nuclear process. Nuclear deadenylation is gene specific and poly(A) tails of lncRNAs retained in the nucleus were not shortened. To identify enzymes responsible for nuclear deadenylation, RNA targeting Cas-systems, siRNAs and shRNA cell lines were used to different deadenylase complexes. Despite efficient mRNA knockdown, subcellular analysis of poly(A) tail length by did not yield molecular phenotypes of changing nuclear poly(A) tail length.

Streptococcus suis (S. suis) is an important opportunistic pathogen, which can cause septicemia and meningitis in pigs and humans. Previous in vivo observations in S. suisinfected pigs revealed lesions at the choroid plexus (CP). In vitro experiments with primary porcine CP epithelial cells (PCPEC) and human CP epithelial papilloma (HIBCPP) cells demonstrated that S. suis can invade and traverse the CP epithelium, and that the CP contributes to the inflammatory response via cytokine expression. Here, next generation sequencing (RNA-seq) was used to compare global transcriptome profiles of PCPEC and HIBCPP cells challenged with S. suis serotype (ST) 2 infected in vitro, and of pigs infected in vivo. Identified differentially expressed genes (DEGs) were, amongst others, involved in inflammatory responses and hypoxia. The RNA-seq data were validated via quantitative PCR of selected DEGs. Employing Gene Set Enrichment Analysis (GSEA), 18, 28, and 21 enriched hallmark gene sets (GSs) were identified for infected HIBCPP cells, PCPEC, and in the CP of pigs suffering from S. suis ST2 meningitis, respectively, of which eight GSs overlapped between the three different sample sets. The majority of these GSs are involved in cellular signaling and pathways, immune response, and development, including inflammatory response and hypoxia. In contrast, suppressed GSs observed during in vitro and in vivo S. suis ST2 infections included those, which were involved in cellular proliferation and metabolic processes. This study suggests that similar cellular processes occur in infected human and porcine CP epithelial cells, especially in terms of inflammatory response.

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