Dokument-ID Dokumenttyp Verfasser/Autoren Herausgeber Haupttitel Abstract Auflage Verlagsort Verlag Erscheinungsjahr Seitenzahl Schriftenreihe Titel Schriftenreihe Bandzahl ISBN Quelle der Hochschulschrift Konferenzname Quelle:Titel Quelle:Jahrgang Quelle:Heftnummer Quelle:Erste Seite Quelle:Letzte Seite URN DOI Abteilungen OPUS4-6429 Dissertation Baunach, Marcel Advances in Distributed Real-Time Sensor/Actuator Systems Operation - Operating Systems, Communication, and Application Design Concepts - 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! 2012 urn:nbn:de:bvb:20-opus-76489 Institut für Informatik OPUS4-6106 Dissertation Zinner, Thomas Performance Modeling of QoE-Aware Multipath Video Transmission in the Future Internet 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. 2012 urn:nbn:de:bvb:20-opus-72324 10.25972/OPUS-6106 Institut für Informatik OPUS4-5947 Dissertation Schröter, Martin Newton Methods for Image Registration 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. 2012 urn:nbn:de:bvb:20-opus-71490 Institut für Mathematik OPUS4-5739 unpublished Nassourou, Mohamadou Towards a Knowledge-Based Learning System for The Quranic Text 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. 2012 urn:nbn:de:bvb:20-opus-70003 Institut für deutsche Philologie OPUS4-5600 Dissertation Duelli, Michael Heuristic Design and Provisioning of Resilient Multi-Layer Networks 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. 2012 urn:nbn:de:bvb:20-opus-69433 10.25972/OPUS-5600 Institut für Informatik OPUS4-12375 Wissenschaftlicher Artikel Zirkel, J.; Cecil, A.; Schäfer, F.; Rahlfs, S.; Ouedraogo, A.; Xiao, K.; Sawadogo, S.; Coulibaly, B.; Becker, K.; Dandekar, T. Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling 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. 2012 287-302 Bioinformatics and Biology Insights 6 urn:nbn:de:bvb:20-opus-123751 10.4137/BBI.S10193 Theodor-Boveri-Institut für Biowissenschaften OPUS4-12364 Wissenschaftlicher Artikel Krueger, Beate; Friedrich, Torben; Förster, Frank; Bernhardt, Jörg; Gross, Roy; Dandekar, Thomas Different evolutionary modifications as a guide to rewire two-component systems 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. 2012 97-128 Bioinformatics and Biology Insights 6 urn:nbn:de:bvb:20-opus-123647 10.4137/BBI.S9356 Theodor-Boveri-Institut für Biowissenschaften OPUS4-12460 Wissenschaftlicher Artikel Merget, Benjamin; Koetschan, Christian; Hackl, Thomas; Förster, Frank; Dandekar, Thomas; Müller, Tobias; Schultz, Jörg; Wolf, Matthias The ITS2 Database 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. 2012 Journal of Visual Expression 61 e3806 urn:nbn:de:bvb:20-opus-124600 10.3791/3806 Theodor-Boveri-Institut für Biowissenschaften OPUS4-12462 Wissenschaftlicher Artikel Buchin, Kevin; Buchin, Maike; Byrka, Jaroslaw; Nöllenburg, Martin; Okamoto, Yoshio; Silveira, Rodrigo I.; Wolff, Alexander Drawing (Complete) Binary Tanglegrams 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. 2012 309-332 Algorithmica 62 urn:nbn:de:bvb:20-opus-124622 10.1007/s00453-010-9456-3 Institut für Informatik OPUS4-13132 Wissenschaftlicher Artikel Staiger, Christine; Cadot, Sidney; Kooter, Raul; Dittrich, Marcus; Müller, Tobias; Klau, Gunnar W.; Wessels, Lodewyk F. A. A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer 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. 2012 e34796 PLoS One 7 4 urn:nbn:de:bvb:20-opus-131323 10.1371/journal.pone.0034796 Theodor-Boveri-Institut für Biowissenschaften OPUS4-13190 Wissenschaftlicher Artikel Naseem, Muhammad; Dandekar, Thomas The Role of Auxin-Cytokinin Antagonism in Plant-Pathogen Interactions No abstract available. 2012 e1003026 PLOS Pathogens 8 11 urn:nbn:de:bvb:20-opus-131901 10.1371/journal.ppat.1003026 Theodor-Boveri-Institut für Biowissenschaften OPUS4-13444 Wissenschaftlicher Artikel Schokraie, Elham; Warnken, Uwe; Hotz-Wagenblatt, Agnes; Grohme, Markus A.; Hengherr, Steffen; Förster, Frank; Schill, Ralph O.; Frohme, Marcus; Dandekar, Thomas; Schnölzer, Martina Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state 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. 2012 e45682 PLoS One 7 9 urn:nbn:de:bvb:20-opus-134447 10.1371/journal.pone.0045682 Theodor-Boveri-Institut für Biowissenschaften OPUS4-13065 Wissenschaftlicher Artikel Buga, Ana-Maria; Scholz, Claus Jürgen; Kumar, Senthil; Herndon, James G.; Alexandru, Dragos; Cojocaru, Gabriel Radu; Dandekar, Thomas; Popa-Wagner, Aurel Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke 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. 2012 e50985 PLoS One 7 12 urn:nbn:de:bvb:20-opus-130657 10.1371/journal.pone.0050985 Theodor-Boveri-Institut für Biowissenschaften OPUS4-13112 Wissenschaftlicher Artikel Böhler, Elmar; Creignou, Nadia; Galota, Matthias; Reith, Steffen; Schnoor, Henning; Vollmer, Heribert Complexity Classifications for Different Equivalence and Audit Problems for Boolean Circuits 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. 2012 24 Logical Methods in Computer Science 8 3:27 1 25 urn:nbn:de:bvb:20-opus-131121 10.2168/LMCS-8(3:27)2012 Institut für Informatik OPUS4-9758 Wissenschaftlicher Artikel Wolff, Alexander; Rutter, Iganz Augmenting the Connectivity of Planar and Geometric Graphs 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. 2012 Journal of Graph Algorithms and Applications urn:nbn:de:bvb:20-opus-97587 10.7155/jgaa.00275 Institut für Informatik