In heterogeneous dense networks where spectrum is shared, users privacy remains one of the major challenges. When the receivers are not only interested in their own signals but also in eavesdropping other users' signals, the cross talk becomes information leakage.We propose a novel and efficient secrecy rate enhancing relay strategy EFFIN for information leakage neutralization. The relay matrix is chosen such that the effective leakage channel (spectral and spatial) is zero. Thus, it ensures secrecy regardless of receive processing employed at eavesdroppers and does not rely on wiretaps codes to ensure secrecy, unlike other physical layer security techniques such as artificial noise. EFFIN achieves a higher sum secrecy rate over several state-of-the-art baseline methods.

In heterogeneous dense networks where spectrum is shared, users' privacy remains one of the major challenges. On a multi-antenna relay-assisted multi-carrier interference channel, each user shares the spectral and spatial resources with all other users. When the receivers are not only interested in their own signals but also in eavesdropping other users' signals, the cross talk on the spectral and spatial channels becomes information leakage. In this paper, we propose a novel secrecy rate enhancing relay strategy that utilizes both spectral and spatial resources, termed as information leakage neutralization. To this end, the relay matrix is chosen such that the effective channel from the transmitter to the colluding eavesdropper is equal to the negative of the effective channel over the relay to the colluding eavesdropper and thus the information leakage to zero. Interestingly, the optimal relay matrix in general is not block-diagonal which encourages users' encoding over the frequency channels. We proposed two information leakage neutralization strategies, namely efficient information leakage neutralization (EFFIN) and local-optimized information leakage neutralization (LOPTIN). EFFIN provides a simple and efficient design of relay processing matrix and precoding matrices at the transmitters in the scenario of limited power and computational resources. LOPTIN, despite its higher complexity, provides a better sum secrecy rate performance by optimizing the relay processing matrix and the precoding matrices jointly. The proposed methods are shown to improve the sum secrecy rates over several state-of-the-art baseline methods.

Motivation: Although various high-throughput technologies provide a lot of valuable information, each of them is giving an insight into different aspects of cellular activity and each has its own limitations. Thus, a complete and systematic understanding of the cellular machinery can be achieved only by a combined analysis of results coming from different approaches. However, methods and tools for integration and analysis of heterogenous biological data still have to be developed. Results: This work presents systemic analysis of basic cellular processes, i.e. cell viability and cell cycle, as well as embryonic stem cell pluripotency and differentiation. These phenomena were studied using several high-throughput technologies, whose combined results were analysed with existing and novel clustering and hit selection algorithms. This thesis also introduces two novel data management and data analysis tools. The first, called DSViewer, is a database application designed for integrating and querying results coming from various genome-wide experiments. The second, named PhenoFam, is an application performing gene set enrichment analysis by employing structural and functional information on families of protein domains as annotation terms. Both programs are accessible through a web interface. Conclusions: Eventually, investigations presented in this work provide the research community with novel and markedly improved repertoire of computational tools and methods that facilitate the systematic analysis of accumulated information obtained from high-throughput studies into novel biological insights.

In heterogeneous dense networks where spectrum is shared, users privacy remains one of the major challenges. When the receivers are not only interested in their own signals but also in eavesdropping other users' signals, the cross talk becomes information leakage.We propose a novel and efficient secrecy rate enhancing relay strategy EFFIN for information leakage neutralization. The relay matrix is chosen such that the effective leakage channel (spectral and spatial) is zero. Thus, it ensures secrecy regardless of receive processing employed at eavesdroppers and does not rely on wiretaps codes to ensure secrecy, unlike other physical layer security techniques such as artificial noise. EFFIN achieves a higher sum secrecy rate over several state-of-the-art baseline methods.

In heterogeneous dense networks where spectrum is shared, users' privacy remains one of the major challenges. On a multi-antenna relay-assisted multi-carrier interference channel, each user shares the spectral and spatial resources with all other users. When the receivers are not only interested in their own signals but also in eavesdropping other users' signals, the cross talk on the spectral and spatial channels becomes information leakage. In this paper, we propose a novel secrecy rate enhancing relay strategy that utilizes both spectral and spatial resources, termed as information leakage neutralization. To this end, the relay matrix is chosen such that the effective channel from the transmitter to the colluding eavesdropper is equal to the negative of the effective channel over the relay to the colluding eavesdropper and thus the information leakage to zero. Interestingly, the optimal relay matrix in general is not block-diagonal which encourages users' encoding over the frequency channels. We proposed two information leakage neutralization strategies, namely efficient information leakage neutralization (EFFIN) and local-optimized information leakage neutralization (LOPTIN). EFFIN provides a simple and efficient design of relay processing matrix and precoding matrices at the transmitters in the scenario of limited power and computational resources. LOPTIN, despite its higher complexity, provides a better sum secrecy rate performance by optimizing the relay processing matrix and the precoding matrices jointly. The proposed methods are shown to improve the sum secrecy rates over several state-of-the-art baseline methods.

Background Systematic, large-scale RNA interference (RNAi) approaches are very valuable to systematically investigate biological processes in cell culture or in tissues of organisms such as Drosophila. A notorious pitfall of all RNAi technologies are potential false positives caused by unspecific knock-down of genes other than the intended target gene. The ultimate proof for RNAi specificity is a rescue by a construct immune to RNAi, typically originating from a related species. Methodology/Principal Findings We show that primary sequence divergence in areas targeted by Drosophila melanogaster RNAi hairpins in five non-melanogaster species is sufficient to identify orthologs for 81% of the genes that are predicted to be RNAi refractory. We use clones from a genomic fosmid library of Drosophila pseudoobscura to demonstrate the rescue of RNAi phenotypes in Drosophila melanogaster muscles. Four out of five fosmid clones we tested harbour cross-species functionality for the gene assayed, and three out of the four rescue a RNAi phenotype in Drosophila melanogaster. Conclusions/Significance The Drosophila pseudoobscura fosmid library is designed for seamless cross-species transgenesis and can be readily used to demonstrate specificity of RNAi phenotypes in a systematic manner.

Die Auswahl eines passenden Wortes aus semantisch verbundenen Wettbewerbern ist eine wesentliche Funktion der Sprachproduktion. Neuere strittige Befunde scheinen traditionellen lexikalischen Selektionsmodellen zu widersprechen. Der swinging lexical network (SLN) Ansatz offeriert eine kompetitiven Bezugsrahmen, der spezifische Voraussetzungen formuliert, unter denen semantische Erleichterungs- als auch Interferenzeffekte in Bildbenennungsparadigmen beobachtet werden können. Diese spezifischen Voraussetzungen betreffen a) die Manipulation eines Trade-offs zwischen konzeptueller Erleichterung und lexikalischer Interferenz, b) das Ausmaß an lexikalischer Kohortenaktivierung und c) die flexible Anpassungsfähigkeit des Sprachproduktionssystems. Die Trade-off-Annahme wurde durch Einflüsse von Assoziationen auf die Benennungslatenz untersucht (Studie 1), wenn Stimuli im kontinuierlichen Benennungsparadigma in einer scheinbar zufälligen Reihenfolge benannt werden. Information über den Einfluss lexikalischer Kohortenaktivierung auf die Wortproduktion wurde durch Manipulation semantischer Distanz und durch Kombination des kontinuierlichen Benennungsparadigmas mit ereignis-korrelierten Potentialen (EKPs) gewonnen (Studie 2). Zur Überprüfung der Flexibilitätsannahme werden Benennungslatenzen von Homophonen mittels Bild-Wort-Interferenzparadigma untersucht, nachdem Versuchspersonen wiederholt linguistische Mehrdeutigkeit verarbeiten haben (Studie 3). Die Ergebnisse zeigen semantische Interferenzeffekte für assoziativ und für eng kategorial verbundene Stimuli im kontinuierlichen Benennungsparadigma (Studie 1 & 2) und Erleichterungseffekte für Homophone im PWI, nachdem das kognitive System sich auf Mehrdeutigkeit adaptiert hatte (Studie 3). Eng kategorial verbundene Stimuli modulierten EKP-Komponenten in der P1, zwischen 250 und 400 ms und im N400-Zeitfenster, welche mit Wortproduktions-prozessen in Verbindung gebracht werden. / The selection of an appropriate word from other meaning-related competitors is a main function of language production. Recent inconclusive findings have casted doubt about traditional lexical selection accounts. The swinging lexical network (SLN) account presents a competitive framework that formulates specific conditions under which semantic facilitation or interference effects can be observed in picture naming paradigms. These specific conditions concern a) the manipulation of the trade-off between conceptual facilitation and lexical interference, b) the extent of lexical cohort activation and c) the flexible nature of the language production system. The trade-off assumption was assessed by investigating the impact of associations on naming latencies in the continuous naming paradigm in which semantically related items are named within a seemingly random sequence (Study 1). Information for the understanding of lexical cohort activation on word production was obtained by manipulating semantic distance in the continuous naming paradigm combined with event-related potentials (ERP; Study 2). Aiming at testing the flexibility assumption, effects of unrelated meaning alternatives of homophones in a picture-word interference (PWI) paradigm were investigated, after participants repeatedly processed linguistic ambiguities (Study 3). Results show semantic interference for associates and for closely related category co-ordinates in the continuous naming paradigm (Study 1 & 2), and facilitation effects for homophone names in the PWI after the cognitive system adapted to the processing of linguistic ambiguities (Study 3). Closely related stimuli modulated ERPs in the P1, between 250 and 400 ms, and in the N400 time window, which are known to be associated with single word naming processes. These results support the SLN model and enhance the understanding of semantic and cognitive factors that shape the microstructure of language production.

Tumormodelle, in denen die maligne Transformation durch definierte Onkogene experimentell ausgelöst und unterhalten wird, bieten vielfältige Möglichkeiten, die komplexen Mechanismen der Tumorentstehung und Therapieresistenz zu untersuchen und neue Ansätze für Diagnostik und Therapie auszuarbeiten. KRAS-Onkogen-„getriebene“ Transformationsmodelle spiegeln neben anderen tumorspezifischen Veränderungen insbesondere die charakteristischen Änderungen des Transkriptoms wider. In der vorliegenden Arbeit wird ein Modell für Ovarialtumore auf Grundlage von Rose Zellen („Rat ovarian surface epithelium“) verwendet, um die Rolle von Transkriptionsfaktoren, welche durch die KRAS-vermittelte Signaltransduktion hoch reguliert werden, zu untersuchen. Die KRAS-transfomierten Derivate der normalen Rose Zellen zeigen die typischen Merkmale von ankerunabhängigen und invasiven Tumorzellen. Aufgrund der hohen Komplexität sind die Interaktionen zwischen der zytoplasmatischen Signaltransduktion und dem durch sie regulierten Transkriptionsfaktornetzwerk noch weitgehend unverstanden. Die Transkriptionsfaktoren Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1 und RelA wurden systematisch mittels RNA-Interferenz in KRAS-transformierten Rose Zellen transient ausgeschaltet. Danach wurden Proliferation, Morphologie (epithelial-mesenchymale Transition, EMT) und Ankerunabhängigkeit der Zellen bestimmt. Alle untersuchten Transkriptionsfaktoren beeinflussten die KRAS-induzierten morphologischen Veränderungen teilweise, belegt durch die Abnahme der EMT-Merkmale nach siRNA-vermittelter Ausschaltung. Der Knock-down der Transkriptionsfaktoren Otx1, Gfi1 und RelA hemmte die Proliferation, während Fosl1, Hmga2, Klf6 und JunB die generelle Proliferationsfähigkeit nicht beeinflussten, jedoch spezifisch die ankerunabhängige Proliferation blockierten. Diesen Faktoren kommt daher eine spezifische Funktion in der neoplastischen Transformation zu, da die Ankerunabhängigkeit sehr gut mit der Tumorigenität korreliert ist. Um die Beteiligung der Transkriptionsfaktoren an der Deregulation von Zielgenen zu erfassen, wurden Genexpressionsmuster aller Zellen, in denen jeweils ein Faktor durch siRNA ausgeschaltet war, mittels Microarray-Analyse identifiziert. Auf dieser Grundlage wurde ein Netzwerk-Modell der regulatorischen Interaktionen zwischen den Transkriptionsfaktoren berechnet. Die Existenz der beiden funktionellen Gruppen wurde im Modell bestätigt. Darüber hinaus zeigte sich eine gegenseitige Abhängigkeit des transkriptionellen Netzwerks und der zytoplasmatischen Signaltransduktion, gemessen mittels Proteinanalyse der mitogenabhängigen Signalkinasen (MAPK). Diese wird als kompensatorische Regulation interpretiert, welche trotz Pertubation, experimentell durch siRNA, das effiziente Überleben der transformierten Zellen sicherstellt. Die vorliegende Studie schafft somit die Voraussetzung und Motivation, das reduzierte Netzwerk aus sieben Komponenten auf alle differentiell exprimierten Transkriptionsfaktoren zu erweitern. Möglicherweise behindern solche Regulationskreise in der klinischen Situation die effektive Wirkung zielgerichteter Therapien. / Tumor models, in which malignant transformation was experimentally triggered and maintained through defined oncogenes, offer manifold opportunities to determine the complex mechanisms of tumor progression and resistance to therapies, and to develop new strategies for diagnosis and therapy. Particularly, KRAS oncogene driven models of transformation reflect the characteristic alterations of the transcriptome, among other tumor specific changes. In the present work a model for ovarian cancer based on Rose („Rat ovarian surface epithelium“) cells has been used to evaluate the role of transcription factors, which are up-regulated through KRAS dependent signaling. The KRAS transformed derivates of normal ROSE cells exhibit typical characteristics of anchorage-independent and invasive tumor cells. Due to the high complexity of cellular networks, the interactions between cytoplasmic signalling and their regulated transcription factors are not well understood. The transcription factors Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1 and RelA were systematically eliminated by transient RNA interference in KRAS transformed ROSE cells. The proliferation, morphology (epithelial-mesenchymal transition, EMT) and anchorage-independence of the cells were determined. All of the selected transcription factors had partial effect on the KRAS induced morphologic changes, documented by reduction of EMT-properties after siRNA treatment. The knock-down of the transcription factors Otx1, Gfi1 and RelA blocked proliferation in general, whereas Fosl1, Hmga2, Klf6 and JunB had no influence on proliferation but specifically blocked the anchorage-independence. Thus, these factors exhibited essential functions in the process of neoplastic transformation, because the anchorage-independence correlates very well with tumorigenicity. In order to elucidate the involvement of the transcription factors in the genetic deregulation of their target genes, microarray based gene expression profiles were determined from all cells in which one factor was eliminated by siRNA. Based on these data, a network model of regulatory interactions among these transcription factors was calculated. The existence of both functional groups was confirmed by the model. Furthermore, an interdependence of the transcriptional networks and cytoplasmatic signaling was observed by protein analysis of the mitogen dependent signal kinases (MAPK). This was interpreted as compensatory regulation, which in spite of experimental perturbation by siRNA, permitted efficient survival of the transformed cells. Thus, the present work provides the basis and motivation to extend the reduced network composed of seven components to all regulated transcription factors. Potentially, such regulatory networks diminish the efficacy of targeted therapies in clinical situations.

In vielen humanen Neoplasien findet sich eine erhöhte Aktivität des Raf-Mek-Erk-Signaltransduktionsweges. Zunächst wurde davon ausgegangen, dass diese erhöhte Aktivität hauptsächlich durch die Ras-Onkogene hervorgerufen wird. Doch mittlerweile konnten auch Mutationen der Raf Gene in humanen Neoplasien nachgewiesen werden. Gegen Raf und Mek konnten eine Anzahl von Enzyminhibitoren entwickelt werden. Der Nachteil vieler dieser Inhibitoren ist, dass sie nicht zwischen den einzelnen Kinaseisoformen unterscheiden können. In dieser Arbeit ist es nun das erste Mal gelungen, jede Komponente des Raf-Mek-Erk-Signaltransduktionsweges einzeln mittels RNA Interferenz effizient zu inhibieren. Dabei konnte die Rolle der verschiedenen Isoformen in der Proliferation, Morphologie und Genex-pression von transformierten Zellen definiert werden. In den NIH3T3-pEJ Zellen konnte A-Raf erstmals eine antiapoptotische Rolle zugewiesen werden. Diese Hemmung der Apoptose läuft möglicherweise über einen Mek2-abhängigen Weg und ist an die Mitochondrien gekoppelt. Für die beiden Mek Kinasen konnten unter-schiedliche Funktionen in der Signalweiterleitung gezeigt werden. Mek2 spielt die Hauptrolle in der Aktivierung der beiden Substratkinasen Erk1 und Erk2. Der Verlust der Mek1 Isoform wird dagegen möglicherweise durch eine erhöhte Expression von Mek2 kompensiert und wirkt sich nicht so stark auf die Phosphorylierung von Erk1/2 aus. Durch die Verwendung von Erk1 und Erk2 spezifischen siRNAs konnte eine Trennung zwischen der Proliferationsre-gulation und der Kontrolle der morphologischen Transformation herausgearbeitet werden. Durch die Verwendung von Mikroarrays ist es gelungen, beiden Phänotypen ein Genexpres-sionsprofil zuzuordnen. Neben Unterschieden zwischen den verschiedenen Kinaseisoformen konnten neue, potentielle Feedbacks beschrieben werden. / In many human neoplasia an increased activity of the RAF/MEK/ERK- signaling pathway is found. First it was assumed that this raised activity is caused primarily by the RAS onco-genes. However, meanwhile mutations in the RAF genes could be also proved in human neo-plasia. A number of enzyme inhibitors have been developed against the RAF and MEK pro-teins. The disadvantage of many of these inhibitors is that they cannot distinguish between the different kinase isoforms. In this work it has succeeded the first time to inhibit every compo-nent of the RAF/MEK/ERK- signaling pathway individually by means of interference RNA. Beside this, the role of the different isoforms in the proliferation, morphology and genetic profile of transformed cells could be defined. For the first time A-Raf could be assigned an anti-apoptotic role in NIH3T3-pEJ cells. This inhibition of the apoptosis possibly runs through a Mek2-dependent way and is coupled to the mitochondria. For both Mek kinases different functions could be shown in the downstream signaling. Mek2 plays the leading role in the activation of both downstream kinases Erk1 and Erk2. The loss of the Mek1 isoform expression is possibly compensated through an increased expression of Mek2 and does not affect the phosphorylation of Erk1 / 2 so strongly. A discri-mination between the regulation of proliferation and the control of the morphological trans-formation could be worked out by the use of Erk1 and Erk2 specific siRNAs. By the use of micorarray an expression profile of both phenotypes has assigned. Beside differences between the different kinases new, potential feedback pathways could be described.

P-Glykoprotein als Produkt des MDR1-Gens stellt einen gut untersuchten Mediator der Multidrugresistenz (MDR) in humanen Malignomen dar. Die Überexpression dieses ABC-Transporters steht in Korrelation zu einer erniedrigten Tumorremission und einer kürzeren Überlebensrate der Patienten. Bisherige Versuche, das Protein über niedermolekulare Substanzen (MDR-Modulatoren) zu inhibieren, vermochten in allen bisherigen klinischen Studien nicht zu überzeugen, so daß diese bis heute keinen Eingang in Standardtherapieschemata gefunden haben. Ziel dieser Arbeit war es, mittels RNA-Interferenz Strategien die Expression von MDR1 zu hemmen und eine Reversion der zellulären Chemoresistenz sowohl im Zellkultur- als auch im Tiermodell zu erreichen. Für die in vitro Untersuchungen an drei humanen multidrug-resistenten Karzinomzellinien wurden verschiedene siRNA (short interfering) Duplexe und shRNA (short hairpin)-exprimierende Vektoren gegen die MDR1 mRNA entwickelt. Die Behandlung der Zellen mit siRNAs führte zu einer bis zu 91 %igen Inhibition der MDR1 mRNA-Expression und zu einer Sensitivierung der Zellen gegenüber dem Anthrazyklin um 89 %. Diese Effekte konnte über einen Zeitraum von drei bis fünf Tagen aufrechterhalten werden. Die stabile Expression von anti-MDR1 shRNAs führte in zwei der untersuchten Zellmodelle zu einer dauerhaften und kompletten Überwindung des MDR1-abhängigen Resistenzphänotyps. Im Mausmodell konnte durch intratumorale Applikation des anti-MDR1 shRNA-kodierenden Vektors mittels low-volume Jet-Injektion eine komplette Reversion der MDR1-Überexpression sowie eine Wiederherstellung der Chemosensitivität gegenüber Doxorubicin in dem resistenten Tumormodell erreicht werden. Die Effizienz der kombinierten Gen- und Chemotherapie wird durch die Verminderung des in vivo Tumorwachstums auf das Volumen des von der sensiblen Zellinien-abgeleiteten Tumors reflektiert. / Multidrug resistance (MDR) is the major cause of failure of effective chemotherapeutic treatment of disseminated neoplasms. The "classical" MDR phenotype of human malignancies is mediated by drug extrusion by the adenosine triphosphate binding cassette (ABC)-transporter P-glycoprotein (MDR1/P-gp). For stable reversal of "classical" MDR in three human cancer cell lines by RNA interference (RNAi) technology, two small interfering RNA (siRNA) constructs and four H1-RNA gene promoter-driven expression vectors encoding anti-MDR1/P-gp short hairpin RNA (shRNA) molecules were constructed. In all cellular systems, siRNAs could specifically inhibit MDR1 expression up to 91% at the mRNA and protein levels. Resistance against daunorubicin was decreased to a maximum of 89%. The introduction of anti-MDR1/P-gp shRNA expression vectors leads in two of the three human cancer cell lines to a complete reversion of the MDR phenotype. The reversal of MDR was accompanied by a complete suppression of MDR1/P-gp expression on mRNA and protein level, and by a considerable increased intracellular anthracyline accumulation in the anti-MDR1/P-gp shRNA-treated cells. In a mouse xenograft model a complete in vivo restoration of MDR1 overexpression and chemosensitivity to doxorubicin could be obtained by intratumorally jet-injected anti-MDR1 shRNA in a multidrug resistant human cancer tumor model.