@unpublished{Nassourou2011, author = {Nassourou, Mohamadou}, title = {Using Machine Learning Algorithms for Categorizing Quranic Chaptersby Major Phases of Prophet Mohammad's Messengership}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-66862}, year = {2011}, abstract = {This paper discusses the categorization of Quranic chapters by major phases of Prophet Mohammad's messengership using machine learning algorithms. First, the chapters were categorized by places of revelation using Support Vector Machine and na{\"i}ve Bayesian classifiers separately, and their results were compared to each other, as well as to the existing traditional Islamic and western orientalists classifications. The chapters were categorized into Meccan (revealed in Mecca) and Medinan (revealed in Medina). After that, chapters of each category were clustered using a kind of fuzzy-single linkage clustering approach, in order to correspond to the major phases of Prophet Mohammad's life. The major phases of the Prophet's life were manually derived from the Quranic text, as well as from the secondary Islamic literature e.g hadiths, exegesis. Previous studies on computing the places of revelation of Quranic chapters relied heavily on features extracted from existing background knowledge of the chapters. For instance, it is known that Meccan chapters contain mostly verses about faith and related problems, while Medinan ones encompass verses dealing with social issues, battles…etc. These features are by themselves insufficient as a basis for assigning the chapters to their respective places of revelation. In fact, there are exceptions, since some chapters do contain both Meccan and Medinan features. In this study, features of each category were automatically created from very few chapters, whose places of revelation have been determined through identification of historical facts and events such as battles, migration to Medina…etc. Chapters having unanimously agreed places of revelation were used as the initial training set, while the remaining chapters formed the testing set. The classification process was made recursive by regularly augmenting the training set with correctly classified chapters, in order to classify the whole testing set. Each chapter was preprocessed by removing unimportant words, stemming, and representation with vector space model. The result of this study shows that, the two classifiers have produced useable results, with an outperformance of the support vector machine classifier. This study indicates that, the proposed methodology yields encouraging results for arranging Quranic chapters by phases of Prophet Mohammad's messengership.}, subject = {Koran}, language = {en} } @article{VainshteinSanchezBrazmaetal.2010, author = {Vainshtein, Yevhen and Sanchez, Mayka and Brazma, Alvis and Hentze, Matthias W. and Dandekar, Thomas and Muckenthaler, Martina U.}, title = {The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67869}, year = {2010}, abstract = {Background: Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results: The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions: ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see "Additional Files" section) and at: http://www.alice-dsl.net/evgeniy. vainshtein/ICEP/}, subject = {Microarray}, language = {en} } @phdthesis{Schlosser2011, author = {Schlosser, Daniel}, title = {Quality of Experience Management in Virtual Future Networks}, doi = {10.25972/OPUS-5719}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-69986}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {Aktuell beobachten wir eine drastische Vervielf{\"a}ltigung der Dienste und Anwendungen, die das Internet f{\"u}r den Datentransport nutzen. Dabei unterscheiden sich die Anforderungen dieser Dienste an das Netzwerk deutlich. Das Netzwerkmanagement wird durch diese Diversit{\"a}t der nutzenden Dienste aber deutlich erschwert, da es einem Datentransportdienstleister kaum m{\"o}glich ist, die unterschiedlichen Verbindungen zu unterscheiden, ohne den Inhalt der transportierten Daten zu analysieren. Netzwerkvirtualisierung ist eine vielversprechende L{\"o}sung f{\"u}r dieses Problem, da sie es erm{\"o}glicht f{\"u}r verschiedene Dienste unterschiedliche virtuelle Netze auf dem gleichen physikalischen Substrat zu betreiben. Diese Diensttrennung erm{\"o}glicht es, jedes einzelne Netz anwendungsspezifisch zu steuern. Ziel einer solchen Netzsteuerung ist es, sowohl die vom Nutzer erfahrene Dienstg{\"u}te als auch die Kosteneffizienz des Datentransports zu optimieren. Dar{\"u}ber hinaus wird es mit Netzwerkvirtualisierung m{\"o}glich das physikalische Netz so weit zu abstrahieren, dass die aktuell fest verzahnten Rollen von Netzwerkbesitzer und Netzwerkbetreiber entkoppelt werden k{\"o}nnen. Dar{\"u}ber hinaus stellt Netzwerkvirtualisierung sicher, dass unterschiedliche Datennetze, die gleichzeitig auf dem gleichen physikalischen Netz betrieben werden, sich gegenseitig weder beeinflussen noch st{\"o}ren k{\"o}nnen. Diese Arbeit  besch{\"a}ftigt sich mit ausgew{\"a}hlten Aspekten dieses Themenkomplexes und fokussiert sich darauf, ein virtuelles Netzwerk mit bestm{\"o}glicher Dienstqualit{\"a}t f{\"u}r den Nutzer zu betreiben und zu steuern. Daf{\"u}r wird ein Top-down-Ansatz gew{\"a}hlt, der von den Anwendungsf{\"a}llen, einer m{\"o}glichen Netzwerkvirtualisierungs-Architektur und aktuellen M{\"o}glichkeiten der Hardwarevirtualisierung ausgeht. Im Weiteren fokussiert sich die Arbeit dann in Richtung Bestimmung und Optimierung der vom Nutzer erfahrenen Dienstqualit{\"a}t (QoE) auf Applikationsschicht und diskutiert M{\"o}glichkeiten zur Messung und {\"U}berwachung von wesentlichen Netzparametern in virtualisierten Netzen.}, subject = {Netzwerkmanagement}, language = {en} } @unpublished{Nassourou2012, author = {Nassourou, Mohamadou}, title = {Towards a Knowledge-Based Learning System for The Quranic Text}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-70003}, year = {2012}, abstract = {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.}, subject = {Wissensbanksystem}, language = {en} } @unpublished{Nassourou2011, author = {Nassourou, Mohamadou}, title = {Computing Generic Causes of Revelation of the Quranic Verses Using Machine Learning Techniques}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-66083}, year = {2011}, abstract = {Because many verses of the holy Quran are similar, there is high probability that, similar verses addressing same issues share same generic causes of revelation. In this study, machine learning techniques have been employed in order to automatically derive causes of revelation of Quranic verses. The derivation of the causes of revelation is viewed as a classification problem. Initially the categories are based on the verses with known causes of revelation, and the testing set consists of the remaining verses. Based on a computed threshold value, a na{\"i}ve Bayesian classifier is used to categorize some verses. After that, using a decision tree classifier the remaining uncategorized verses are separated into verses that contain indicators (resultative connectors, causative expressions…), and those that do not. As for those verses having indicators, each one is segmented into its constituent clauses by identification of the linking indicators. Then a dominant clause is extracted and considered either as the cause of revelation, or post-processed by adding or subtracting some terms to form a causal clause that constitutes the cause of revelation. Concerning remaining unclassified verses without indicators, a naive Bayesian classifier is again used to assign each one of them to one of the existing classes based on features and topics similarity. As for verses that could not be classified so far, manual classification was made by considering each verse as a category on its own. The result obtained in this study is encouraging, and shows that automatic derivation of Quranic verses' generic causes of revelation is achievable, and reasonably reliable for understanding and implementing the teachings of the Quran.}, subject = {Text Mining}, language = {en} } @unpublished{Nassourou2011, author = {Nassourou, Mohamadou}, title = {Design and Implementation of a Model-driven XML-based Integrated System Architecture for Assisting Analysis, Understanding, and Retention of Religious Texts:The Case of The Quran}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-65737}, year = {2011}, abstract = {Learning a book in general involves reading it, underlining important words, adding comments, summarizing some passages, and marking up some text or concepts. Once deeper understanding is achieved, one would like to organize and manage her/his knowledge in such a way that, it could be easily remembered and efficiently transmitted to others. This paper discusses about modeling religious texts using semantic XML markup based on frame-based knowledge representation, with the purpose of assisting understanding, retention, and sharing of knowledge they contain. In this study, books organized in terms of chapters made up of verses are considered as the source of knowledge to model. Some metadata representing the multiple perspectives of knowledge modeling are assigned to each chapter and verse. Chapters and verses with their metadata form a meta-model, which is represented using frames, and published on a web mashup. An XML-based annotation and visualization system equipped with user interfaces for creating static and dynamic metadata, annotating chapters' contents according to user selected semantics, and templates for publishing generated knowledge on the Internet, has been developed. The system has been applied to the Quran, and the result obtained shows that multiple perspectives of information modeling can be successfully applied to religious texts, in order to support analysis, understanding, and retention of the texts.}, subject = {Wissensrepr{\"a}sentation}, language = {en} } @unpublished{Nassourou2011, author = {Nassourou, Mohamadou}, title = {Computer-based Textual Documents Collation System for Reconstructing the Original Text from Automatically Identified Base Text and Ranked Witnesses}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-65749}, year = {2011}, abstract = {Given a collection of diverging documents about some lost original text, any person interested in the text would try reconstructing it from the diverging documents. Whether it is eclecticism, stemmatics, or copy-text, one is expected to explicitly or indirectly select one of the documents as a starting point or as a base text, which could be emended through comparison with remaining documents, so that a text that could be designated as the original document is generated. Unfortunately the process of giving priority to one of the documents also known as witnesses is a subjective approach. In fact even Cladistics, which could be considered as a computer-based approach of implementing stemmatics, does not present or recommend users to select a certain witness as a starting point for the process of reconstructing the original document. In this study, a computational method using a rule-based Bayesian classifier is used, to assist text scholars in their attempts of reconstructing a non-existing document from some available witnesses. The method developed in this study consists of selecting a base text successively and collating it with remaining documents. Each completed collation cycle stores the selected base text and its closest witness, along with a weighted score of their similarities and differences. At the end of the collation process, a witness selected more often by majority of base texts is considered as the probable base text of the collection. Witnesses' scores are weighted using a weighting system, based on effects of types of textual modifications on the process of reconstructing original documents. Users have the possibility to select between baseless and base text collation. If a base text is selected, the task is reduced to ranking the witnesses with respect to the base text, otherwise a base text as well as ranking of the witnesses with respect to the base text are computed and displayed on a bar diagram. Additionally this study includes a recursive algorithm for automatically reconstructing the original text from the identified base text and ranked witnesses.}, subject = {Textvergleich}, language = {en} } @unpublished{Nassourou2011, author = {Nassourou, Mohamadou}, title = {Philosophical and Computational Approaches for Estimating and Visualizing Months of Revelations of Quranic Chapters}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-65784}, year = {2011}, abstract = {The question of why the Quran structure does not follow its chronology of revelation is a recurring one. Some Islamic scholars such as [1] have answered the question using hadiths, as well as other philosophical reasons based on internal evidences of the Quran itself. Unfortunately till today many are still wondering about this issue. Muslims believe that the Quran is a summary and a copy of the content of a preserved tablet called Lawhul-Mahfuz located in the heaven. Logically speaking, this suggests that the arrangement of the verses and chapters is expected to be similar to that of the Lawhul-Mahfuz. As for the arrangement of the verses in each chapter, there is unanimity that it was carried out by the Prophet himself under the guidance of Angel Gabriel with the recommendation of God. But concerning the ordering of the chapters, there are reports about some divergences [3] among the Prophet's companions as to which chapter should precede which one. This paper argues that Quranic chapters might have been arranged according to months and seasons of revelation. In fact, based on some verses of the Quran, it is defendable that the Lawhul-Mahfuz itself is understood to have been structured in terms of the months of the year. In this study, philosophical and mathematical arguments for computing chapters' months of revelation are discussed, and the result is displayed on an interactive scatter plot.}, subject = {Text Mining}, language = {en} } @phdthesis{Selbach2011, author = {Selbach, Stefan}, title = {Hybride bitparallele Volltextsuche}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-66476}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {Der große Vorteil eines q-Gramm Indexes liegt darin, dass es m{\"o}glich ist beliebige Zeichenketten in einer Dokumentensammlung zu suchen. Ein Nachteil jedoch liegt darin, dass bei gr{\"o}ßer werdenden Datenmengen dieser Index dazu neigt, sehr groß zu werden, was mit einem deutlichem Leistungsabfall verbunden ist. In dieser Arbeit wird eine neuartige Technik vorgestellt, die die Leistung eines q-Gramm Indexes mithilfe zus{\"a}tzlicher M-Matrizen f{\"u}r jedes q-Gramm und durch die Kombination mit einem invertierten Index erh{\"o}ht. Eine M-Matrix ist eine Bit-Matrix, die Informationen {\"u}ber die Positionen eines q-Gramms enth{\"a}lt. Auch bei der Kombination von zwei oder mehreren Q-Grammen bieten diese M-Matrizen Informationen {\"u}ber die Positionen der Kombination. Dies kann verwendet werden, um die Komplexit{\"a}t der Zusammenf{\"u}hrung der q-Gramm Trefferlisten f{\"u}r eine gegebene Suchanfrage zu reduzieren und verbessert die Leistung des n-Gramm-invertierten Index. Die Kombination mit einem termbasierten invertierten Index beschleunigt die durchschnittliche Suchzeit zus{\"a}tzlich und vereint die Vorteile beider Index-Formate. Redundante Informationen werden in dem q-Gramm Index reduziert und weitere Funktionalit{\"a}t hinzugef{\"u}gt, wie z.B. die Bewertung von Treffern nach Relevanz, die M{\"o}glichkeit, nach Konzepten zu suchen oder Indexpartitionierungen nach Wichtigkeit der enthaltenen Terme zu erstellen.}, subject = {Information Retrieval}, language = {de} } @article{SchmidSchindelinCardonaetal.2010, author = {Schmid, Benjamin and Schindelin, Johannes and Cardona, Albert and Longair, Martin and Heisenberg, Martin}, title = {A high-level 3D visualization API for Java and ImageJ}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67851}, year = {2010}, abstract = {Background: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Results: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Conclusions: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.}, subject = {Visualisierung}, language = {en} } @phdthesis{Duelli2012, author = {Duelli, Michael}, title = {Heuristic Design and Provisioning of Resilient Multi-Layer Networks}, doi = {10.25972/OPUS-5600}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-69433}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {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.}, subject = {Mehrschichtsystem}, language = {en} } @phdthesis{Saska2009, author = {Saska, Martin}, title = {Trajectory planning and optimal control for formations of autonomous robots}, isbn = {978-3-923959-56-3}, doi = {10.25972/OPUS-4622}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-53175}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2009}, abstract = {In this thesis, we present novel approaches for formation driving of nonholonomic robots and optimal trajectory planning to reach a target region. The methods consider a static known map of the environment as well as unknown and dynamic obstacles detected by sensors of the formation. The algorithms are based on leader following techniques, where the formation of car-like robots is maintained in a shape determined by curvilinear coordinates. Beyond this, the general methods of formation driving are specialized and extended for an application of airport snow shoveling. Detailed descriptions of the algorithms complemented by relevant stability and convergence studies will be provided in the following chapters. Furthermore, discussions of the applicability will be verified by various simulations in existing robotic environments and also by a hardware experiment.}, subject = {Autonomer Roboter}, language = {en} } @phdthesis{Fehler2010, author = {Fehler, Manuel}, title = {Kalibrierung Agenten-basierter Simulationen}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-64762}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {In der vorliegenden Arbeit wird das Problem der Kalibrierung Agenten-basierter Simulationen (ABS) behandelt, also das Problem, die Parameterwerte eines Agenten-basierten Simulationsmodells so einzustellen, dass valides Simulationsverhalten erreicht wird. Das Kalibrierungsproblem f{\"u}r Simulationen an sich ist nicht neu und ist im Rahmen klassischer Simulationsparadigmen, wie z.B. der Makro-Simulation, fester Bestandteil der Forschung. Im Vergleich zu den dort betrachteten Kalibrierungsproblemen zeichnet sich das Kalibrierungsproblem f{\"u}r ABS jedoch durch eine Reihe zus{\"a}tzlicher Herausforderungen aus, welche die direkte Anwendung existierender Kalibrierungsverfahren in begrenzter Zeit erschweren, bzw. nicht mehr sinnvoll zulassen. Die L{\"o}sung dieser Probleme steht im Zentrum dieser Dissertation: Das Ziel besteht darin, den Nutzer bei der Kalibrierung von ABS auf der Basis von unzureichenden, potentiell fehlerhaften Daten und Wissen zu unterst{\"u}tzen. Dabei sollen drei Hauptprobleme gel{\"o}st werden: 1)Vereinfachung der Kalibrierung großer Agenten-Parametermengen auf der Mikro- Ebene in Agenten-basierten Simulationen durch Ausnutzung der spezifischen Struktur von ABS (n{\"a}mlich dem Aufbau aus einer Menge von Agentenmodellen). 2)Kalibrierung Agenten-basierter Simulationen, so dass auf allen relevanten Beobachtungsebenen valides Simulationsverhalten erzeugt wird (mindestens Mikro und Makro-Ebene). Als erschwerende Randbedingung muss die Kalibrierung unter der Voraussetzung einer Makro-Mikro-Wissensl{\"u}cke durchgef{\"u}hrt werden. 3)Kalibrierung Agenten-basierter Simulationen auf der Mikro-Ebene unter der Voraussetzung, dass zur Kalibrierung einzelner Agentenmodelle nicht ausreichend und potentiell verf{\"a}lschte Daten zur Verhaltensvalidierung zur Verf{\"u}gung stehen. Hierzu wird in dieser Arbeit das sogenannte Makro-Mikro-Verfahren zur Kalibrierung von Agenten-basierten Simulationen entwickelt. Das Verfahren besteht aus einem Basisverfahren, das im Verlauf der Arbeit um verschiedene Zusatzverfahren erweitert wird. Das Makro-Mikro-Verfahren und seine Erweiterungen sollen dazu dienen, die Modellkalibrierung trotz stark verrauschter Daten und eingeschr{\"a}nktem Wissen {\"u}ber die Wirkungszusammenh{\"a}nge im Originalsystem geeignet zu erm{\"o}glichen und dabei den Kalibrierungsprozess zu beschleunigen: 1) Makro-Mikro-Kalibrierungsverfahren: Das in dieser Arbeit entwickelte Makro- Mikro-Verfahren unterst{\"u}tzt den Nutzer durch eine kombinierte Kalibrierung auf der Mikro- und der Makro-Beobachtungsebene, die gegebenenfalls durch Zwischenebenen erweitert werden kann. Der Grundgedanke des Verfahrens besteht darin, das Kalibrierungsproblem in eines auf aggregierter Verhaltensebene und eines auf der Ebene des Mikro-Agentenverhaltens aufzuteilen. Auf der Makro-Ebene wird nach validen idealen aggregierten Verhaltensmodellen (IVM) der Agenten gesucht. Auf der Mikro-Ebene wird versucht die individuellen Modelle der Agenten auf Basis des erw{\"u}nschten Gesamtverhaltens und der ermittelten IVM so zu kalibrieren, das insgesamt Simulationsverhalten entsteht, das sowohl auf Mikro- als auch auf Makro-Ebene valide ist. 2) Erweiterung 1: Robuste Kalibrierung: Um den Umgang mit potentiell verrauschten Validierungskriterien (d.h. mit verrauschten Daten {\"u}ber ein Originalsystem, auf denen die Validierungskriterien der Simulation beruhen) und Modellteilen w{\"a}hrend der Kalibrierung von ABS zu erm{\"o}glichen, wird eine robuste Kalibrierungstechnik zur Anwendung im Makro-Mikro-Verfahren entwickelt. 3) Erweiterung 2: Kalibrierung mit Heterogenit{\"a}tssuche: Als zweite Erweiterung des Makro-Mikro-Verfahrens wird ein Verfahren entwickelt, das das Problem des unklaren Detaillierungsgrades von ABS auf der Ebene der Parameterwerte adressiert. Prinzipiell kann zwar jeder Agent unterschiedliche Parameterwerte verwenden, obwohl eine geringere Heterogenit{\"a}t zur Erzeugung validen Verhaltens ausreichend w{\"a}re. Die entwickelte Erweiterung versucht, w{\"a}hrend der Kalibrierung, eine geeignete Heterogenit{\"a}tsauspr{\"a}gung f{\"u}r die Parameterwerte der Agenten zu ermitteln. Unter einer Heterogenit{\"a}tsauspr{\"a}gung wird dabei eine Einteilung der simulierten Agenten in Gruppen mit jeweils gleichen Parameterwerten verstanden. Die Heterogenit{\"a}tssuche dient dazu, einen Kompromiss zu finden zwischen der Notwendigkeit, sehr große Parametersuchr{\"a}ume durchsuchen zu m{\"u}ssen und gleichzeitig den Suchraum so klein wie m{\"o}glich halten zu wollen.}, subject = {Computersimulation}, language = {de} } @phdthesis{Sun2014, author = {Sun, Kaipeng}, title = {Six Degrees of Freedom Object Pose Estimation with Fusion Data from a Time-of-flight Camera and a Color Camera}, isbn = {978-3-923959-97-6}, doi = {10.25972/OPUS-10508}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-105089}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {Object six Degrees of Freedom (6DOF) pose estimation is a fundamental problem in many practical robotic applications, where the target or an obstacle with a simple or complex shape can move fast in cluttered environments. In this thesis, a 6DOF pose estimation algorithm is developed based on the fused data from a time-of-flight camera and a color camera. The algorithm is divided into two stages, an annealed particle filter based coarse pose estimation stage and a gradient decent based accurate pose optimization stage. In the first stage, each particle is evaluated with sparse representation. In this stage, the large inter-frame motion of the target can be well handled. In the second stage, the range data based conventional Iterative Closest Point is extended by incorporating the target appearance information and used for calculating the accurate pose by refining the coarse estimate from the first stage. For dealing with significant illumination variations during the tracking, spherical harmonic illumination modeling is investigated and integrated into both stages. The robustness and accuracy of the proposed algorithm are demonstrated through experiments on various objects in both indoor and outdoor environments. Moreover, real-time performance can be achieved with graphics processing unit acceleration.}, subject = {Mustererkennung}, language = {en} } @article{AndronicShirakashiPickeletal.2015, author = {Andronic, Joseph and Shirakashi, Ryo and Pickel, Simone U. and Westerling, Katherine M. and Klein, Teresa and Holm, Thorge and Sauer, Markus and Sukhorukov, Vladimir L.}, title = {Hypotonic Activation of the Myo-Inositol Transporter SLC5A3 in HEK293 Cells Probed by Cell Volumetry, Confocal and Super-Resolution Microscopy}, series = {PLoS One}, volume = {10}, journal = {PLoS One}, number = {3}, doi = {10.1371/journal.pone.0119990}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-126408}, year = {2015}, abstract = {Swelling-activated pathways for myo-inositol, one of the most abundant organic osmolytes in mammalian cells, have not yet been identified. The present study explores the SLC5A3 protein as a possible transporter of myo-inositol in hyponically swollen HEK293 cells. To address this issue, we examined the relationship between the hypotonicity-induced changes in plasma membrane permeability to myo-inositol Pino [m/s] and expression/localization of SLC5A3. Pino values were determined by cell volumetry over a wide tonicity range (100-275 mOsm) in myo-inositol-substituted solutions. While being negligible under mild hypotonicity (200-275 mOsm), Pino grew rapidly at osmolalities below 200 mOsm to reach a maximum of ∼3 nm/s at 100-125 mOsm, as indicated by fast cell swelling due to myo-inositol influx. The increase in Pino resulted most likely from the hypotonicity-mediated incorporation of cytosolic SLC5A3 into the plasma membrane, as revealed by confocal fluorescence microscopy of cells expressing EGFP-tagged SLC5A3 and super-resolution imaging of immunostained SLC5A3 by direct stochastic optical reconstruction microscopy (dSTORM). dSTORM in hypotonic cells revealed a surface density of membrane-associated SLC5A3 proteins of 200-2000 localizations/μm2. Assuming SLC5A3 to be the major path for myo-inositol, a turnover rate of 80-800 myo-inositol molecules per second for a single transporter protein was estimated from combined volumetric and dSTORM data. Hypotonic stress also caused a significant upregulation of SLC5A3 gene expression as detected by semiquantitative RT-PCR and Western blot analysis. In summary, our data provide first evidence for swelling-mediated activation of SLC5A3 thus suggesting a functional role of this transporter in hypotonic volume regulation of mammalian cells.}, language = {en} } @article{WeissSchultz2015, author = {Weiß, Clemens Leonard and Schultz, J{\"o}rg}, title = {Identification of divergent WH2 motifs by HMM-HMM alignments}, series = {BMC Research Notes}, volume = {8}, journal = {BMC Research Notes}, number = {18}, doi = {10.1186/s13104-015-0981-7}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-126413}, year = {2015}, abstract = {Background The actin cytoskeleton is a hallmark of eukaryotic cells. Its regulation as well as its interaction with other proteins is carefully orchestrated by actin interaction domains. One of the key players is the WH2 motif, which enables binding to actin monomers and filaments and is involved in the regulation of actin nucleation. Contrasting conserved domains, the identification of this motif in protein sequences is challenging, as it is short and poorly conserved. Findings To identify divergent members, we combined Hidden-Markov-Model (HMM) to HMM alignments with orthology predictions. Thereby, we identified nearly 500 proteins containing so far not annotated WH2 motifs. This included shootin-1, an actin binding protein involved in neuron polarization. Among others, WH2 motifs of 'proximal to raf' (ptr)-orthologs, which are described in the literature, but not annotated in genome databases, were identified. Conclusion In summary, we increased the number of WH2 motif containing proteins substantially. This identification of candidate regions for actin interaction could steer their experimental characterization. Furthermore, the approach outlined here can easily be adapted to the identification of divergent members of further domain families.}, language = {en} } @phdthesis{Kindermann2016, author = {Kindermann, Philipp}, title = {Angular Schematization in Graph Drawing}, publisher = {W{\"u}rzburg University Press}, address = {W{\"u}rzburg}, isbn = {978-3-95826-020-7 (print)}, doi = {10.25972/WUP-978-3-95826-021-4}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-112549}, school = {W{\"u}rzburg University Press}, pages = {184}, year = {2016}, abstract = {Graphs are a frequently used tool to model relationships among entities. A graph is a binary relation between objects, that is, it consists of a set of objects (vertices) and a set of pairs of objects (edges). Networks are common examples of modeling data as a graph. For example, relationships between persons in a social network, or network links between computers in a telecommunication network can be represented by a graph. The clearest way to illustrate the modeled data is to visualize the graphs. The field of Graph Drawing deals with the problem of finding algorithms to automatically generate graph visualizations. The task is to find a "good" drawing, which can be measured by different criteria such as number of crossings between edges or the used area. In this thesis, we study Angular Schematization in Graph Drawing. By this, we mean drawings with large angles (for example, between the edges at common vertices or at crossing points). The thesis consists of three parts. First, we deal with the placement of boxes. Boxes are axis-parallel rectangles that can, for example, contain text. They can be placed on a map to label important sites, or can be used to describe semantic relationships between words in a word network. In the second part of the thesis, we consider graph drawings visually guide the viewer. These drawings generally induce large angles between edges that meet at a vertex. Furthermore, the edges are drawn crossing-free and in a way that makes them easy to follow for the human eye. The third and final part is devoted to crossings with large angles. In drawings with crossings, it is important to have large angles between edges at their crossing point, preferably right angles.}, language = {en} } @techreport{KounevBrosigHuber2014, author = {Kounev, Samuel and Brosig, Fabian and Huber, Nikolaus}, title = {The Descartes Modeling Language}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-104887}, pages = {91}, year = {2014}, abstract = {This technical report introduces the Descartes Modeling Language (DML), a new architecture-level modeling language for modeling Quality-of-Service (QoS) and resource management related aspects of modern dynamic IT systems, infrastructures and services. DML is designed to serve as a basis for self-aware resource management during operation ensuring that system QoS requirements are continuously satisfied while infrastructure resources are utilized as efficiently as possible.}, subject = {Ressourcenmanagement}, language = {en} } @article{BeckerCaminitiFiorellaetal.2013, author = {Becker, Martin and Caminiti, Saverio and Fiorella, Donato and Francis, Louise and Gravino, Pietro and Haklay, Mordechai (Muki) and Hotho, Andreas and Loreto, Virrorio and Mueller, Juergen and Ricchiuti, Ferdinando and Servedio, Vito D. P. and Sirbu, Alina and Tria, Franesca}, title = {Awareness and Learning in Participatory Noise Sensing}, series = {PLOS ONE}, volume = {8}, journal = {PLOS ONE}, number = {12}, issn = {1932-6203}, doi = {10.1371/journal.pone.0081638}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-127675}, pages = {e81638}, year = {2013}, abstract = {The development of ICT infrastructures has facilitated the emergence of new paradigms for looking at society and the environment over the last few years. Participatory environmental sensing, i.e. directly involving citizens in environmental monitoring, is one example, which is hoped to encourage learning and enhance awareness of environmental issues. In this paper, an analysis of the behaviour of individuals involved in noise sensing is presented. Citizens have been involved in noise measuring activities through the WideNoise smartphone application. This application has been designed to record both objective (noise samples) and subjective (opinions, feelings) data. The application has been open to be used freely by anyone and has been widely employed worldwide. In addition, several test cases have been organised in European countries. Based on the information submitted by users, an analysis of emerging awareness and learning is performed. The data show that changes in the way the environment is perceived after repeated usage of the application do appear. Specifically, users learn how to recognise different noise levels they are exposed to. Additionally, the subjective data collected indicate an increased user involvement in time and a categorisation effect between pleasant and less pleasant environments.}, language = {en} } @article{ZirkelCecilSchaeferetal.2012, author = {Zirkel, J. and Cecil, A. and Sch{\"a}fer, F. and Rahlfs, S. and Ouedraogo, A. and Xiao, K. and Sawadogo, S. and Coulibaly, B. and Becker, K. and Dandekar, T.}, title = {Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling}, series = {Bioinformatics and Biology Insights}, volume = {6}, journal = {Bioinformatics and Biology Insights}, doi = {10.4137/BBI.S10193}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-123751}, pages = {287-302}, year = {2012}, abstract = {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.}, language = {en} }