TY - THES A1 - Baunach, Marcel T1 - Advances in Distributed Real-Time Sensor/Actuator Systems Operation - Operating Systems, Communication, and Application Design Concepts - T1 - Fortschritte im Betrieb drahtloser Sensor/Aktuator Netzwerke N2 - This work takes a close look at several quite different research areas related to the design of networked embedded sensor/actuator systems. The variety of the topics illustrates the potential complexity of current sensor network applications; especially when enriched with actuators for proactivity and environmental interaction. Besides their conception, development, installation and long-term operation, we'll mainly focus on more "low-level" aspects: Compositional hardware and software design, task cooperation and collaboration, memory management, and real-time operation will be addressed from a local node perspective. In contrast, inter-node synchronization, communication, as well as sensor data acquisition, aggregation, and fusion will be discussed from a rather global network view. The diversity in the concepts was intentionally accepted to finally facilitate the reliable implementation of truly complex systems. In particular, these should go beyond the usual "sense and transmit of sensor data", but show how powerful today's networked sensor/actuator systems can be despite of their low computational performance and constrained hardware: If their resources are only coordinated efficiently! N2 - Diese Arbeit behandelt einige sehr unterschiedliche Forschungsbereiche bezüglich des Designs vernetzter und eingebetteter Sensor/Aktuator-Systeme. Die Vielfalt der Themen zeigt die potenzielle Komplexität aktueller Sensornetzwerk-Anwendungen, insbesondere wenn sie mit Aktuatoren zur Interaktion mit der Umwelt ausgestattet sind. Neben deren Konzeption, Entwicklung, Installation und dem langfristigen Betrieb wird besonders auf diverse "low-level" Aspekte eingegangen: Kompositionelles Hardware- und Software-Design, Task Kooperation und Kollaboration, Speicher-Verwaltung und Echtzeit-Betrieb werden aus lokaler Sicht der Sensorknoten betrachtet. Im Kontrast werden Knoten-Synchronisation, Kommunikation, sowie Sensordatenerfassung, -aggregation und -fusion aus globaler Netzwerk-Sicht diskutiert. Die Vielfalt der behandelten Konzepte wurde bewusst in Kauf genommen, um letztlich die zuverlässige Umsetzung sehr komplexer Systeme zu erleichtern. Insbesondere sollte dies über das übliche "Erfassen und Übertragen von Sensordaten" hinausgehen, und zeigen, wie mächtig heutige vernetzte Sensor/Aktuator-Systeme trotz ihrer geringen Rechenleistung und eingeschränkten Hardware sein können: Wenn ihre Ressourcen effizient koordiniert werden! KW - Eingebettetes System KW - Drahtloses Sensorsystem KW - Echtzeitsystem KW - Dynamische Speicherverwaltung KW - Ressourcenallokation KW - Fernwartung KW - Betriebssystem KW - Verteiltes System KW - Lokalisation KW - Embedded Systems KW - Real-Time Operating Systems KW - Localization KW - Wireless Sensor/Actuator Systems KW - Dynamic Memory Management Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-76489 ER - TY - THES A1 - Dang, Nghia Duc T1 - Konzeption und Evaluation eines hybriden, skalierbaren Werkzeugs zur mechatronischen Systemdiagnose am Beispiel eines Diagnosesystems für freie Kfz-Werkstätten T1 - Conception and evaluation of a hybrid, scalable tool for mechatronical system diagnosis on the example of a diagnostic system for independent car repair shops N2 - Die Entwicklung eines wissensbasierten Systems, speziell eines Diagnosesystems, ist eine Teildisziplin der künstlichen Intelligenz und angewandten Informatik. Im Laufe der Forschung auf diesem Gebiet wurden verschiedene Lösungsansätze mit unterschiedlichem Erfolg bei der Anwendung in der Kraftfahrzeugdiagnose entwickelt. Diagnosesysteme in Vertragswerkstätten, das heißt in Fahrzeughersteller gebundenen Werkstätten, wenden hauptsächlich die fallbasierte Diagnostik an. Zum einen hält sich hier die Fahrzeugvielfalt in Grenzen und zum anderen besteht eine Meldepflicht bei neuen, nicht im System vorhandenen Fällen. Die freien Werkstätten verfügen nicht über eine solche Datenbank. Somit ist der fallbasierte Ansatz schwer umsetzbar. In freien Werkstätten - Fahrzeughersteller unabhängigen Werkstätten - basiert die Fehlersuche hauptsächlich auf Fehlerbäumen. Wegen der wachsenden Fahrzeugkomplexität, welche wesentlich durch die stark zunehmende Anzahl der durch mechatronische Systeme realisierten Funktionen bedingt ist, und der steigenden Typenvielfalt ist die geführte Fehlersuche in freien Werkstätten nicht immer zielführend. Um die Unterstützung des Personals von freien Werkstätten bei der zukünftigen Fehlersuche zu gewährleisten, werden neue Generationen von herstellerunabhängigen Diagnosetools benötigt, die die Probleme der Variantenvielfalt und Komplexität lösen. In der vorliegenden Arbeit wird ein Lösungsansatz vorgestellt, der einen qualitativen, modellbasierten Diagnoseansatz mit einem auf heuristischem Diagnosewissen basierenden Ansatz vereint. Neben der Grundlage zur Wissenserhebung werden in dieser Arbeit die theoretische Grundlage zur Beherrschung der Variantenvielfalt sowie die Tests für die erstellten Diagnosemodelle behandelt. Die Diagnose ist symptombasiert und die Inferenzmechanismen zur Verarbeitung des Diagnosewissens sind eine Kombination aus Propagierung der abweichenden physikalischen Größen im Modell und der Auswertung des heuristischen Wissens. Des Weiteren werden in dieser Arbeit verschiedene Aspekte der Realisierung der entwickelten theoretischen Grundlagen dargestellt, zum Beispiel: Systemarchitektur, Wissenserhebungsprozess, Ablauf des Diagnosevorgangs in den Werkstätten. Die Evaluierung der entwickelten Lösung bei der Wissenserhebung in Form von Modellerstellungen und Modellierungsworkshops sowie Feldtests dient nicht nur zur Bestätigung des entwickelten Ansatzes, sondern auch zur Ideenfindung für die Integration der entwickelten Tools in die existierende IT-Infrastruktur. N2 - The development of a knowledge-based system - in particular a diagnostic system - is a branch of artificial intelligence and applied computer science. Throughout the research in this field, various approaches have been developed with varying degrees of success in the application in automotive diagnostics. Diagnostic systems in authorized garages i.e. in garages bound to vehicle manufacturers mainly apply case-based diagnosis. In those cases first the variance of vehicles is limited and second there is a reporting obligation of new, yet not existing cases within the system. The independent repair shops do not have such a database. Thus, the case-based approach is difficult to implement. In independent garages - car manufacturer independent garages - the troubleshooting is mainly based on fault trees. Because of the growing complexity of vehicles, which is mainly due to the rapidly increasing number of functions realized by mechatronic systems and the increasing variety of vehicle types, guided troubleshooting for independent garages is not always productive. To ensure the support of the staff of independent garages in the future troubleshooting, new generations of multivendor diagnostic tools are needed to solve the problems of the variety and complexity. In the present paper an approach is presented which combines a qualitative, model-based diagnostic approach to a heuristic diagnostic knowledge-based approach. In addition to the basis for knowledge collection in this study the theoretical basis for the control of the variety and the tests for the generated diagnosis models are discussed. The diagnosis is symptom-based and the inference mechanisms for processing of diagnostic knowledge are a combination of propagation of the different physical parameters in the model and the evaluation of heuristic knowledge. Furthermore, various aspects of the implementation of the developed theoretical basis are presented in this thesis, for example: system architecture, knowledge collection process, the course of action of the diagnostic process in the workshops. The evaluation of the developed solution for the collection of knowledge in the form of preparation of models and modeling workshops, as well as field tests not only serves to validate the developed approach, but also to find ideas for the integration of the developed tools into the existing IT infrastructure. KW - Diagnosesystem KW - Künstliche Intelligenz KW - Modellbasierte Diagnose KW - Werkstattdiagnose KW - hybride Diagnose KW - skalierbare Diagnose KW - Inferenz KW - Angewandte Informatik KW - aftermarket diagnostic KW - model-base diagnosis KW - hybrid Diagnostic Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-70774 ER - TY - THES A1 - Zinner, Thomas T1 - Performance Modeling of QoE-Aware Multipath Video Transmission in the Future Internet T1 - Leistungsmodellierung einer Mehrpfad Video Übertragung im zukünftigen Internet unter Berücksichtigung der QoE N2 - Internet applications are becoming more and more flexible to support diverge user demands and network conditions. This is reflected by technical concepts, which provide new adaptation mechanisms to allow fine grained adjustment of the application quality and the corresponding bandwidth requirements. For the case of video streaming, the scalable video codec H.264/SVC allows the flexible adaptation of frame rate, video resolution and image quality with respect to the available network resources. In order to guarantee a good user-perceived quality (Quality of Experience, QoE) it is necessary to adjust and optimize the video quality accurately. But not only have the applications of the current Internet changed. Within network and transport, new technologies evolved during the last years providing a more flexible and efficient usage of data transport and network resources. One of the most promising technologies is Network Virtualization (NV) which is seen as an enabler to overcome the ossification of the Internet stack. It provides means to simultaneously operate multiple logical networks which allow for example application-specific addressing, naming and routing, or their individual resource management. New transport mechanisms like multipath transmission on the network and transport layer aim at an efficient usage of available transport resources. However, the simultaneous transmission of data via heterogeneous transport paths and communication technologies inevitably introduces packet reordering. Additional mechanisms and buffers are required to restore the correct packet order and thus to prevent a disturbance of the data transport. A proper buffer dimensioning as well as the classification of the impact of varying path characteristics like bandwidth and delay require appropriate evaluation methods. Additionally, for a path selection mechanism real time evaluation mechanisms are needed. A better application-network interaction and the corresponding exchange of information enable an efficient adaptation of the application to the network conditions and vice versa. This PhD thesis analyzes a video streaming architecture utilizing multipath transmission and scalable video coding and develops the following optimization possibilities and results: Analysis and dimensioning methods for multipath transmission, quantification of the adaptation possibilities to the current network conditions with respect to the QoE for H.264/SVC, and evaluation and optimization of a future video streaming architecture, which allows a better interaction of application and network. N2 - Die Applikationen im Internet passen sich immer besser an unterschiedliche Anforderungen der Nutzer und variierende Netzwerkbedingungen an. Neue Mechanismen ermöglichen die zielgerichtete Anpassung der Anwendungsqualität und damit der benötigten Bandbreite. Im Falle von Videostreaming ermöglicht der skalierbare Videocodec H.264/SVC, die flexible Veränderung der Bildwiederholungsrate, der Auflösung des Videos und der Bildqualität an die vorhandenen Ressourcen im Netzwerk. Um eine gute vom Nutzer erfahrene Dienstgüte (Quality of Experience, QoE) zu garantieren, muss die Videoqualität richtig angepasst und optimiert werden. Aber nicht nur die Anwendungen des heutigen Internets haben sich verändert. Gerade in den letzten Jahren entstanden neue Netzwerk- und Transporttechnologien, welche eine flexiblere und effizientere Nutzung der Kommunikationsnetze erlauben. Eine dieser Techniken ist die Virtualisierung von Netzwerken. Sie erlaubt es auf einem gemeinsamen physikalischen Netz verschiedene logische Netze zu betreiben, die zum Beispiel Anwendungs-abhängige Adressierung unterstützen, eigene Namensgebung erlauben oder ein individuelles Ressourcen Management ermöglichen. Neuartige Transportmechanismen wie Mehrpfadübertragung auf Netzwerk- und Transportebene des ISO/OSI Stacks streben eine effiziente Ausnutzung der zur Verfügung stehenden Übertragungsmöglichkeiten an. Doch die simultane Übertragung von Daten über heterogene Kommunikationspfade und –technologien führt unausweichlich zu einer Veränderung der Reihenfolge, in der die Pakete ankommen. Es werden zusätzliche Mechanismen und Puffer benötigt, um die ursprüngliche Paketreihenfolge wieder herzustellen und so einen störenden Einfluss auf den Datentransport zu verhindern. Die richtige Dimensionierung dieser Puffer sowie die Klassifizierung des Einflusses von variierenden Pfadparametern wie Bandbreite und Verzögerungen setzen passende Evaluierungsmethoden voraus. Darüber hinaus werden für die Auswahl von geeigneten Pfaden aus einer Menge vorhandener Pfade echtzeitfähige Bewertungsmechanismen benötigt. Eine bessere Interaktion zwischen Applikationen und Netzwerk und der damit verbundene Informationsaustausch ermöglicht die effiziente Anpassung der Applikationsqualität an das Netzwerk und umgekehrt. Diese Doktorarbeit analysiert eine auf Mehrpfadübertragung und skalierbarer Videokodierung basierende Videostreaming Architektur und erarbeitet die folgenden Optimierungsmöglichkeiten und Auswertungen: Analyse- und Dimensionierungsmethoden für Mehrpfadübertragung, Quantifizierung der Anpassungsmöglichkeiten von SVC an das Netzwerk unter Berücksichtigung der QoE und Evaluierung und Optimierung einer zukünftigen Videostreaming Architektur, welche eine stärkere Interaktion zwischen Applikation und Netzwerk ermöglicht. T3 - Würzburger Beiträge zur Leistungsbewertung Verteilter Systeme - 03/12 KW - Videoübertragung KW - H.264 SVC KW - Modellierung KW - Quality-of-Experience KW - Mehrpfadübertragung KW - Multipath Transmission KW - Video Streaming KW - H.264/SVC KW - QoE KW - Performance Modeling Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-72324 ER - TY - THES A1 - Schröter, Martin T1 - Newton Methods for Image Registration T1 - Newton-Methoden zur Bildregistrierung N2 - Consider the situation where two or more images are taken from the same object. After taking the first image, the object is moved or rotated so that the second recording depicts it in a different manner. Additionally, take heed of the possibility that the imaging techniques may have also been changed. One of the main problems in image processing is to determine the spatial relation between such images. The corresponding process of finding the spatial alignment is called “registration”. In this work, we study the optimization problem which corresponds to the registration task. Especially, we exploit the Lie group structure of the set of transformations to construct efficient, intrinsic algorithms. We also apply the algorithms to medical registration tasks. However, the methods developed are not restricted to the field of medical image processing. We also have a closer look at more general forms of optimization problems and show connections to related tasks. N2 - Wir betrachten Problemstellungen, in denen zwei Bilder von ein und demselben Objekt aufgenommen wurden. Nach der ersten Aufnahme hat sich allerdings das Objekt bewegt oder deformiert, so dass es sich in den nächsten Bildern auf eine andere Weise darstellt. Zudem kann sich die Aufnahmetechnik geändert haben. Eine der Hauptprobleme in der Bildverarbeitung ist es, die räumliche Korrespondenz zwischen solchen Bildern zu bestimmen. Die zugehörige Aufgabe, eine solche räumliche Übereinstimmung zu finden, nennt man "Registrierung". In dieser Arbeit untersuchen wir das mit der Registrierung verbundene Optimierungsproblem. Insbesondere nutzen wir die Lie-Gruppen-Struktur der Menge der zulässigen Transformationen aus, um effiziente, intrinsische Argorithmen zu entwickeln. Wir wenden diese dann auf Probleme der medizinischen Bildregistrierung an, jedoch sind unsere Methoden nicht auf dieses Feld beschränkt. Wir werfen auch einen genaueren Blick auf eine allgemeinere Form von Optimierungsproblemen und zeigen Verknüpfungen zu verwandten Fragestellungen auf. KW - Newton-Verfahren KW - Registrierung KW - Stochastische Optimierung KW - Newton Methods KW - Image Registration KW - Stochastic Algorithms KW - Optimization on Lie Groups Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-71490 ER - TY - INPR A1 - Nassourou, Mohamadou T1 - Towards a Knowledge-Based Learning System for The Quranic Text N2 - In this research, an attempt to create a knowledge-based learning system for the Quranic text has been performed. The knowledge base is made up of the Quranic text along with detailed information about each chapter and verse, and some rules. The system offers the possibility to study the Quran through web-based interfaces, implementing novel visualization techniques for browsing, querying, consulting, and testing the acquired knowledge. Additionally the system possesses knowledge acquisition facilities for maintaining the knowledge base. KW - Wissensbanksystem KW - Wissensmanagement KW - Text Mining KW - Visualisierung KW - Koran KW - Knowledge-based System KW - Knowledge Management System KW - Text Mining KW - Visualization KW - Quran Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-70003 ER - TY - THES A1 - Duelli, Michael T1 - Heuristic Design and Provisioning of Resilient Multi-Layer Networks T1 - Heuristische Planung und Betrieb von ausfallsicheren Mehrschichtnetzen N2 - To jointly provide different services/technologies, like IP and Ethernet or IP and SDH/SONET, in a single network, equipment of multiple technologies needs to be deployed to the sites/Points of Presence (PoP) and interconnected with each other. Therein, a technology may provide transport functionality to other technologies and increase the number of available resources by using multiplexing techniques. By providing its own switching functionality, each technology creates connections in a logical layer which leads to the notion of multi-layer networks. The design of such networks comprises the deployment and interconnection of components to suit to given traffic demands. To prevent traffic loss due to failures of networking equipment, protection mechanisms need to be established. In multi-layer networks, protection usually can be applied in any of the considered layers. In turn, the hierarchical structure of multi-layer networks also bears shared risk groups (SRG). To achieve a cost-optimal resilient network, an appropriate combination of multiplexing techniques, technologies, and their interconnections needs to be found. Thus, network design is a combinatorial problem with a large parameter and solution space. After the design stage, the resources of a multi-layer network can be provided to traffic demands. Especially, dynamic capacity provisioning requires interaction of sites and layers, as well as accurate retrieval of constraint information. In recent years, generalized multiprotocol label switching (GMPLS) and path computation elements (PCE) have emerged as possible approaches for these challenges. Like the design, the provisioning of multi-layer networks comprises a variety of optimization parameters, like blocking probability, resilience, and energy efficiency. In this work, we introduce several efficient heuristics to approach the considered optimization problems. We perform capital expenditure (CAPEX)-aware design of multi-layer networks from scratch, based on IST NOBEL phase 2 project's cost and equipment data. We comprise traffic and resilience requirements in different and multiple layers as well as different network architectures. On top of the designed networks, we consider the dynamic provisioning of multi-layer traffic based on the GMPLS and PCE architecture. We evaluate different PCE deployments, information retrieval strategies, and re-optimization. Finally, we show how information about provisioning utilization can be used to provide a feedback for network design. N2 - Um in einem Netz verschiedene Dienste/Schichten, z.B. IP und Ethernet oder IP und SDH/SONET, parallel anbieten zu können, müssen Komponenten mehrerer Technologien an den Standorten verbaut und miteinander verbunden werden. Hierbei kann eine Technologie eine Transportschicht für andere Technologien fungieren und die Zahl der verfügbaren Ressourcen durch Multiplex Techniken erhöhen. Durch die Bereitstellung eigener Switching Funktionalität erzeugt jede Technologie Verbindungen in einer logischen Schicht. Dies führt zu der Bezeichnung Mehrschichtnetz (engl. multi-layer network). Die Planung solcher Netze hat das Verbauen und Verbinden von Komponenten zum Ziel, so dass gegebene Verkehrsströme realisiert werden können. Um Unterbrechungen der Verkehrsströme aufgrund von Fehlern in den Netzkomponenten zu verhinden, müssen Schutzmechanismen eingebaut werden. In Mehrschichtnetzen können solche Schutzmechanismen in jeder beliebigen Schicht betrachtet werden. Allerdings birgt die hierarchische Struktur von Mehrschichtnetzen das Risiko von shared risk groups (SRG). Um ein Kosten-optimales ausfallsicheres Netz zu erhalten, muss eine passende Kombination aus Multiplex Techniken, Technologien und deren Verbindungen gefunden werden. Die Netzplanung ist daher ein kombinatorisches Problem mit einem großen Parameter- und Lösungsraum. Nach der Planungsphase können die Ressourcen eines Mehrschichtnetzes für Verkehrsströme vorgehalten werden. Die Betrachtung von dynamischer Kapazitätsanforderungen erfordert die Interaktion von Knoten und Schichten sowie akkurate Gewinnung von Informationen zur Auslastung. In jüngster Zeit sind das Generalized Multiprotocol Label Switching (GMPLS) und das Path Computation Element (PCE) als mögliche Lösungsansätze für diese Herausforderungen entstanden. Wie in der Planung beinhaltet auch der Betrieb von Mehrschichtnetzen eine Vielzahl von Optimierungsparametern, wie die Blockierungswahrscheinlichkeit, Ausfallsicherheit und Energie-Effizienz. In dieser Arbeit, führen wir verschiedene effiziente Heuristiken ein, um die betrachteten Optimierungsprobleme anzugehen. Wir planen Mehrschichtnetze von Grund auf und minimieren hinsichtlich der Anschaffungskosten basierend auf den Kosten- und Komponenten-Daten des IST NOBEL Phase 2 Projekts. Wir berücksichtigen Anforderungen der Verkehrsströme und Ausfallsicherheit in verschiedenen Schichten und in mehreren Schichten gleichzeitig sowie verschiedene Netzarchitekturen. Aufsetzend auf dem geplanten Netz betrachten wir den Betrieb von Mehrschichtnetzen mit dynamischen Verkehr basiert auf der GMPLS und PCE Architektur. Wir bewerten verschiedene PCE Installationen, Strategien zur Informationsgewinnung und Re-Optimierung. Abschließend, zeigen wir wie Information über die Auslastung im Betrieb genutzt werden kann um Rückmeldung an die Netzplanung zu geben. T3 - Würzburger Beiträge zur Leistungsbewertung Verteilter Systeme - 02/12 KW - Mehrschichtsystem KW - Planung KW - Ressourcenmanagement KW - Ausfallsicheres System KW - Mehrschichtnetze KW - Pfadberechnungselement KW - Ausfallsicherheit KW - Multi-Layer KW - Design KW - Resilience KW - Resource Management KW - Path Computation Element Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-69433 ER - TY - JOUR A1 - Zirkel, J. A1 - Cecil, A. A1 - Schäfer, F. A1 - Rahlfs, S. A1 - Ouedraogo, A. A1 - Xiao, K. A1 - Sawadogo, S. A1 - Coulibaly, B. A1 - Becker, K. A1 - Dandekar, T. T1 - Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling JF - Bioinformatics and Biology Insights N2 - BACKGROUND: In the face of growing resistance in malaria parasites to drugs, pharmacological combination therapies are important. There is accumulating evidence that methylene blue (MB) is an effective drug against malaria. Here we explore the biological effects of both MB alone and in combination therapy using modeling and experimental data. RESULTS: We built a model of the central metabolic pathways in P. falciparum. Metabolic flux modes and their changes under MB were calculated by integrating experimental data (RT-PCR data on mRNAs for redox enzymes) as constraints and results from the YANA software package for metabolic pathway calculations. Several different lines of MB attack on Plasmodium redox defense were identified by analysis of the network effects. Next, chloroquine resistance based on pfmdr/and pfcrt transporters, as well as pyrimethamine/sulfadoxine resistance (by mutations in DHF/DHPS), were modeled in silico. Further modeling shows that MB has a favorable synergism on antimalarial network effects with these commonly used antimalarial drugs. CONCLUSIONS: Theoretical and experimental results support that methylene blue should, because of its resistance-breaking potential, be further tested as a key component in drug combination therapy efforts in holoendemic areas. KW - methylene blue KW - malaria KW - elementary mode analysis KW - drug KW - resistance KW - combination therapy KW - pathway KW - metabolic flux Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-123751 N1 - This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. VL - 6 ER - TY - JOUR A1 - Krueger, Beate A1 - Friedrich, Torben A1 - Förster, Frank A1 - Bernhardt, Jörg A1 - Gross, Roy A1 - Dandekar, Thomas T1 - Different evolutionary modifications as a guide to rewire two-component systems JF - Bioinformatics and Biology Insights N2 - Two-component systems (TCS) are short signalling pathways generally occurring in prokaryotes. They frequently regulate prokaryotic stimulus responses and thus are also of interest for engineering in biotechnology and synthetic biology. The aim of this study is to better understand and describe rewiring of TCS while investigating different evolutionary scenarios. Based on large-scale screens of TCS in different organisms, this study gives detailed data, concrete alignments, and structure analysis on three general modification scenarios, where TCS were rewired for new responses and functions: (i) exchanges in the sequence within single TCS domains, (ii) exchange of whole TCS domains; (iii) addition of new components modulating TCS function. As a result, the replacement of stimulus and promotor cassettes to rewire TCS is well defined exploiting the alignments given here. The diverged TCS examples are non-trivial and the design is challenging. Designed connector proteins may also be useful to modify TCS in selected cases. KW - histidine kinase KW - connector KW - Mycoplasma KW - engineering KW - promoter KW - sensor KW - response regulator KW - synthetic biology KW - sequence alignment Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-123647 N1 - This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. VL - 6 ER - TY - JOUR A1 - Merget, Benjamin A1 - Koetschan, Christian A1 - Hackl, Thomas A1 - Förster, Frank A1 - Dandekar, Thomas A1 - Müller, Tobias A1 - Schultz, Jörg A1 - Wolf, Matthias T1 - The ITS2 Database JF - Journal of Visual Expression N2 - The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution1 and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation. The ITS2 Database presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank accurately reannotated. Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling. In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold. The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE and ProfDistS for multiple sequence-structure alignment calculation and Neighbor Joining tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure. In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses. KW - homology modeling KW - molecular systematics KW - internal transcribed spacer 2 KW - alignment KW - genetics KW - secondary structure KW - ribosomal RNA KW - phylogenetic tree KW - phylogeny Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124600 VL - 61 IS - e3806 ER - TY - JOUR A1 - Buchin, Kevin A1 - Buchin, Maike A1 - Byrka, Jaroslaw A1 - Nöllenburg, Martin A1 - Okamoto, Yoshio A1 - Silveira, Rodrigo I. A1 - Wolff, Alexander T1 - Drawing (Complete) Binary Tanglegrams JF - Algorithmica N2 - A binary tanglegram is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential that both trees are drawn without edge crossings and that the inter-tree edges have as few crossings as possible. It is known that finding a tanglegram with the minimum number of crossings is NP-hard and that the problem is fixed-parameter tractable with respect to that number. We prove that under the Unique Games Conjecture there is no constant-factor approximation for binary trees. We show that the problem is NP-hard even if both trees are complete binary trees. For this case we give an O(n 3)-time 2-approximation and a new, simple fixed-parameter algorithm. We show that the maximization version of the dual problem for binary trees can be reduced to a version of MaxCut for which the algorithm of Goemans and Williamson yields a 0.878-approximation. KW - NP-hardness KW - crossing minimization KW - binary tanglegram KW - approximation algorithm KW - fixed-parameter tractability Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124622 VL - 62 ER - TY - JOUR A1 - Staiger, Christine A1 - Cadot, Sidney A1 - Kooter, Raul A1 - Dittrich, Marcus A1 - Müller, Tobias A1 - Klau, Gunnar W. A1 - Wessels, Lodewyk F. A. T1 - A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer JF - PLoS One N2 - Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single genes classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single genes classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single genes classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single genes sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single genes classifiers for predicting outcome in breast cancer. KW - modules KW - protein-interaction networks KW - expression signature KW - classification KW - set KW - metastasis KW - stability KW - survival KW - database KW - markers Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131323 VL - 7 IS - 4 ER - TY - JOUR A1 - Naseem, Muhammad A1 - Dandekar, Thomas T1 - The Role of Auxin-Cytokinin Antagonism in Plant-Pathogen Interactions JF - PLOS Pathogens N2 - No abstract available. KW - disease KW - pseudomas-syringae KW - arabidpsis thaliana KW - immunity KW - organogenesis KW - transcription KW - resistance KW - crosstalk Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131901 VL - 8 IS - 11 ER - TY - JOUR A1 - Schokraie, Elham A1 - Warnken, Uwe A1 - Hotz-Wagenblatt, Agnes A1 - Grohme, Markus A. A1 - Hengherr, Steffen A1 - Förster, Frank A1 - Schill, Ralph O. A1 - Frohme, Marcus A1 - Dandekar, Thomas A1 - Schnölzer, Martina T1 - Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state JF - PLoS One N2 - Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state. KW - life-span regulation KW - genes KW - Yolk protein KW - water stress KW - expression KW - tolerance KW - richtersius coronifer KW - superoxide-dismutase KW - caenorhabditis elegans KW - arabidopsis thaliana KW - vitellogenin Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-134447 VL - 7 IS - 9 ER - TY - JOUR A1 - Buga, Ana-Maria A1 - Scholz, Claus Jürgen A1 - Kumar, Senthil A1 - Herndon, James G. A1 - Alexandru, Dragos A1 - Cojocaru, Gabriel Radu A1 - Dandekar, Thomas A1 - Popa-Wagner, Aurel T1 - Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke JF - PLoS One N2 - Background: Because most human stroke victims are elderly, studies of experimental stroke in the aged rather than the young rat model may be optimal for identifying clinically relevant cellular responses, as well for pinpointing beneficial interventions. Methodology/Principal Findings: We employed the Affymetrix platform to analyze the whole-gene transcriptome following temporary ligation of the middle cerebral artery in aged and young rats. The correspondence, heat map, and dendrogram analyses independently suggest a differential, age-group-specific behaviour of major gene clusters after stroke. Overall, the pattern of gene expression strongly suggests that the response of the aged rat brain is qualitatively rather than quantitatively different from the young, i.e. the total number of regulated genes is comparable in the two age groups, but the aged rats had great difficulty in mounting a timely response to stroke. Our study indicates that four genes related to neuropathic syndrome, stress, anxiety disorders and depression (Acvr1c, Cort, Htr2b and Pnoc) may have impaired response to stroke in aged rats. New therapeutic options in aged rats may also include Calcrl, Cyp11b1, Prcp, Cebpa, Cfd, Gpnmb, Fcgr2b, Fcgr3a, Tnfrsf26, Adam 17 and Mmp14. An unexpected target is the enzyme 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 in aged rats, a key enzyme in the cholesterol synthesis pathway. Post-stroke axonal growth was compromised in both age groups. Conclusion/Significance: We suggest that a multi-stage, multimodal treatment in aged animals may be more likely to produce positive results. Such a therapeutic approach should be focused on tissue restoration but should also address other aspects of patient post-stroke therapy such as neuropathic syndrome, stress, anxiety disorders, depression, neurotransmission and blood pressure. KW - gamma KW - corticotropin-releasing hormone KW - colony-stimulating factor KW - cerebral ischemia KW - receptor KW - brain KW - protein KW - inhibitor KW - mouse KW - differentiation Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-130657 VL - 7 IS - 12 ER - TY - JOUR A1 - Böhler, Elmar A1 - Creignou, Nadia A1 - Galota, Matthias A1 - Reith, Steffen A1 - Schnoor, Henning A1 - Vollmer, Heribert T1 - Complexity Classifications for Different Equivalence and Audit Problems for Boolean Circuits JF - Logical Methods in Computer Science N2 - We study Boolean circuits as a representation of Boolean functions and conskier different equivalence, audit, and enumeration problems. For a number of restricted sets of gate types (bases) we obtain efficient algorithms, while for all other gate types we show these problems are at least NP-hard. KW - hierarchy KW - satisfiability problems Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131121 VL - 8 IS - 3:27 SP - 1 EP - 25 ER - TY - JOUR A1 - Atienza, Nieves A1 - de Castro, Natalia A1 - Cortés, Carmen A1 - Garrido, M. Ángeles A1 - Grima, Clara I. A1 - Hernández, Gregorio A1 - Márquez, Alberto A1 - Moreno-González, Auxiliadora A1 - Nöllenburg, Martin A1 - Portillo, José Ramón A1 - Reyes, Pedro A1 - Valenzuela, Jesús A1 - Trinidad Villar, Maria A1 - Wolff, Alexander T1 - Cover contact graphs N2 - We study problems that arise in the context of covering certain geometric objects called seeds (e.g., points or disks) by a set of other geometric objects called cover (e.g., a set of disks or homothetic triangles). We insist that the interiors of the seeds and the cover elements are pairwise disjoint, respectively, but they can touch. We call the contact graph of a cover a cover contact graph (CCG). We are interested in three types of tasks, both in the general case and in the special case of seeds on a line: (a) deciding whether a given seed set has a connected CCG, (b) deciding whether a given graph has a realization as a CCG on a given seed set, and (c) bounding the sizes of certain classes of CCG’s. Concerning (a) we give efficient algorithms for the case that seeds are points and show that the problem becomes hard if seeds and covers are disks. Concerning (b) we show that this problem is hard even for point seeds and disk covers (given a fixed correspondence between graph vertices and seeds). Concerning (c) we obtain upper and lower bounds on the number of CCG’s for point seeds. KW - Informatik Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-78845 ER - TY - JOUR A1 - Wolff, Alexander A1 - Rutter, Iganz T1 - Augmenting the Connectivity of Planar and Geometric Graphs JF - Journal of Graph Algorithms and Applications N2 - In this paper we study connectivity augmentation problems. Given a connected graph G with some desirable property, we want to make G 2-vertex connected (or 2-edge connected) by adding edges such that the resulting graph keeps the property. The aim is to add as few edges as possible. The property that we consider is planarity, both in an abstract graph-theoretic and in a geometric setting, where vertices correspond to points in the plane and edges to straight-line segments. We show that it is NP-hard to � nd a minimum-cardinality augmentation that makes a planar graph 2-edge connected. For making a planar graph 2-vertex connected this was known. We further show that both problems are hard in the geometric setting, even when restricted to trees. The problems remain hard for higher degrees of connectivity. On the other hand we give polynomial-time algorithms for the special case of convex geometric graphs. We also study the following related problem. Given a planar (plane geometric) graph G, two vertices s and t of G, and an integer c, how many edges have to be added to G such that G is still planar (plane geometric) and contains c edge- (or vertex-) disjoint s{t paths? For the planar case we give a linear-time algorithm for c = 2. For the plane geometric case we give optimal worst-case bounds for c = 2; for c = 3 we characterize the cases that have a solution. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-97587 ER -