TY - THES A1 - Sun, Kaipeng T1 - Six Degrees of Freedom Object Pose Estimation with Fusion Data from a Time-of-flight Camera and a Color Camera T1 - 6DOF Posenschätzung durch Datenfusion einer Time-of-Flight-Kamera und einer Farbkamera N2 - 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. N2 - Die 6DOF Posenschätzung von Objekten ist ein fundamentales Problem in vielen praktischen Robotikanwendungen, bei denen sich ein Ziel- oder Hindernisobjekt, einfacher oder komplexer Form, schnell in einer unstrukturierten schwierigen Umgebung bewegt. In dieser Forschungsarbeit wird zur Lösung des Problem ein 6DOF Posenschätzer entwickelt, der auf der Fusion von Daten einer Time-of-Flight-Kamera und einer Farbkamera beruht. Der Algorithmus ist in zwei Phasen unterteilt, ein Annealed Partikel-Filter bestimmt eine grobe Posenschätzung, welche mittels eines Gradientenverfahrens in einer zweiten Phase optimiert wird. In der ersten Phase wird jeder Partikel mittels sparse represenation ausgewertet, auf diese Weise kann eine große Inter-Frame-Bewegung des Zielobjektes gut behandelt werden. In der zweiten Phase wird die genaue Pose des Zielobjektes mittels des konventionellen, auf Entfernungsdaten beruhenden, Iterative Closest Point-Algorithmus aus der groben Schätzung der ersten Stufe berechnet. Der Algorithmus wurde dabei erweitert, so dass auch Informationen über das äußere Erscheinungsbild des Zielobjektes verwendet werden. Zur Kompensation von signifikanten Beleuchtungsschwankungen während des Trackings, wurde eine Modellierung der Ausleuchtung mittels Kugelflächenfunktionen erforscht und in beide Stufen der Posenschätzung integriert. Die Leistungsfähigkeit, Robustheit und Genauigkeit des entwickelten Algorithmus wurde in Experimenten im Innen- und Außenbereich mit verschiedenen Zielobjekten gezeigt. Zudem konnte gezeigt werden, dass die Schätzung mit Hilfe von Grafikprozessoren in Echtzeit möglich ist. T3 - Forschungsberichte in der Robotik = Research Notes in Robotics - 10 KW - Mustererkennung KW - Maschinelles Sehen KW - Sensor KW - 3D Vision KW - 6DOF Pose Estimation KW - Visual Tracking KW - Pattern Recognition KW - Computer Vision KW - 3D Sensor Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-105089 SN - 978-3-923959-97-6 ER - TY - JOUR A1 - Andronic, Joseph A1 - Shirakashi, Ryo A1 - Pickel, Simone U. A1 - Westerling, Katherine M. A1 - Klein, Teresa A1 - Holm, Thorge A1 - Sauer, Markus A1 - Sukhorukov, Vladimir L. T1 - Hypotonic Activation of the Myo-Inositol Transporter SLC5A3 in HEK293 Cells Probed by Cell Volumetry, Confocal and Super-Resolution Microscopy JF - PLoS One N2 - 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. KW - electrolytes KW - isotonic KW - membrane proteins KW - cell membranes KW - hypotonic KW - hypotonic solutions KW - tonicity KW - permeability Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-126408 VL - 10 IS - 3 ER - TY - JOUR A1 - Weiß, Clemens Leonard A1 - Schultz, Jörg T1 - Identification of divergent WH2 motifs by HMM-HMM alignments JF - BMC Research Notes N2 - 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. KW - WH2 domain KW - spire KW - shootin-1 KW - actin nucleation KW - HHblits Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-126413 VL - 8 IS - 18 ER - TY - THES A1 - Kindermann, Philipp T1 - Angular Schematization in Graph Drawing N2 - 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. N2 - Graphen sind häufig verwendete Werkzeuge zur Modellierung von Zusammenhängen zwischen Daten. Ein Graph ist eine binäre Relation zwischen Objekten, das heißt er besteht aus einer Menge von Objekten (Knoten) und einer Menge von Paaren von Objekten (Kanten). Netzwerke sind übliche Beispiele für das Modellieren von Daten als ein Graph. Beispielsweise lassen sich Beziehungen zwischen Personen in einem sozialen Netzwerk oder Netzanbindungen zwischen Computern in einem Telekommunikationsnetz als Graph darstellen. Die modellierten Daten können am anschaulichsten dargestellt werden, indem man die Graphen visualisiert. Der Bereich des Graphenzeichnens behandelt das Problem, Algorithmen zum automatischen Erzeugen von Graphenvisualisierungen zu finden. Das Ziel ist es, eine "gute" Zeichnung zu finden, was durch unterschiedliche Kriterien gemessen werden kann; zum Beispiel durch die Anzahl der Kreuzungen zwischen Kanten oder durch den Platzverbrauch. In dieser Arbeit beschäftigen wir uns mit Winkelschematisierung im Graphenzeichnen. Darunter verstehen wir Zeichnungen, in denen die Winkel (zum Beispiel zwischen Kanten an einem gemeinsamen Knoten oder einem Kreuzungspunkt) möglichst groß gestaltet sind. Die Arbeit besteht aus drei Teilen. Im ersten Teil betrachten wir die Platzierung von Boxen. Boxen sind achsenparallele Rechtecke, die zum Beispiel Text enthalten. Sie können beispielsweise auf einer Karte platziert werden, um wichtige Standorte zu beschriften, oder benutzt werden, um semantische Beziehungen zwischen Wörtern in einem Wortnetzwerk darzustellen. Im zweiten Teil der Arbeit untersuchen wir Graphenzeichnungen, die den Betrachter visuell führen. Im Allgemeinen haben diese Zeichnungen große Winkel zwischen Kanten, die sich in einem Knoten treffen. Außerdem werden die Verbindungen kreuzungsfrei und so gezeichnet, dass es dem menschlichen Auge leicht fällt, ihnen zu folgen. Im dritten und letzten Teil geht es um Kreuzungen mit großen Winkeln. In Zeichnungen mit Kreuzungen ist es wichtig, dass die Winkel zwischen Kanten an Kreuzungspunkten groß sind, vorzugsweise rechtwinklig. KW - graph drawing KW - angular schematization KW - boundary labeling KW - contact representation KW - word clouds KW - monotone drawing KW - smooth orthogonal drawing KW - simultaneous embedding KW - right angle crossing KW - independent crossing KW - Graphenzeichnen KW - Winkel KW - Kreuzung KW - v Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-112549 SN - 978-3-95826-020-7 (print) SN - 978-3-95826-021-4 (online) PB - Würzburg University Press CY - Würzburg ER - TY - RPRT A1 - Kounev, Samuel A1 - Brosig, Fabian A1 - Huber, Nikolaus T1 - The Descartes Modeling Language N2 - 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. KW - Ressourcenmanagement KW - Software Engineering KW - Resource and Performance Management KW - Software Performance Engineering KW - Software Performance Modeling KW - Performance Management KW - Quality-of-Service Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-104887 ER - TY - JOUR A1 - Becker, Martin A1 - Caminiti, Saverio A1 - Fiorella, Donato A1 - Francis, Louise A1 - Gravino, Pietro A1 - Haklay, Mordechai (Muki) A1 - Hotho, Andreas A1 - Loreto, Virrorio A1 - Mueller, Juergen A1 - Ricchiuti, Ferdinando A1 - Servedio, Vito D. P. A1 - Sirbu, Alina A1 - Tria, Franesca T1 - Awareness and Learning in Participatory Noise Sensing JF - PLOS ONE N2 - 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. KW - exposure Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-127675 SN - 1932-6203 VL - 8 IS - 12 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 -