@article{DuLauterbachLietal.2020, author = {Du, Shitong and Lauterbach, Helge A. and Li, Xuyou and Demisse, Girum G. and Borrmann, Dorit and N{\"u}chter, Andreas}, title = {Curvefusion — A Method for Combining Estimated Trajectories with Applications to SLAM and Time-Calibration}, series = {Sensors}, volume = {20}, journal = {Sensors}, number = {23}, issn = {1424-8220}, doi = {10.3390/s20236918}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-219988}, year = {2020}, abstract = {Mapping and localization of mobile robots in an unknown environment are essential for most high-level operations like autonomous navigation or exploration. This paper presents a novel approach for combining estimated trajectories, namely curvefusion. The robot used in the experiments is equipped with a horizontally mounted 2D profiler, a constantly spinning 3D laser scanner and a GPS module. The proposed algorithm first combines trajectories from different sensors to optimize poses of the planar three degrees of freedom (DoF) trajectory, which is then fed into continuous-time simultaneous localization and mapping (SLAM) to further improve the trajectory. While state-of-the-art multi-sensor fusion methods mainly focus on probabilistic methods, our approach instead adopts a deformation-based method to optimize poses. To this end, a similarity metric for curved shapes is introduced into the robotics community to fuse the estimated trajectories. Additionally, a shape-based point correspondence estimation method is applied to the multi-sensor time calibration. Experiments show that the proposed fusion method can achieve relatively better accuracy, even if the error of the trajectory before fusion is large, which demonstrates that our method can still maintain a certain degree of accuracy in an environment where typical pose estimation methods have poor performance. In addition, the proposed time-calibration method also achieves high accuracy in estimating point correspondences.}, language = {en} } @unpublished{Dandekar2019, author = {Dandekar, Thomas}, title = {Biological heuristics applied to cosmology suggests a condensation nucleus as start of our universe and inflation cosmology replaced by a period of rapid Weiss domain-like crystal growth}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-183945}, pages = {24}, year = {2019}, abstract = {Cosmology often uses intricate formulas and mathematics to derive new theories and concepts. We do something different in this paper: We look at biological processes and derive from these heuristics so that the revised cosmology agrees with astronomical observations but does also agree with standard biological observations. We show that we then have to replace any type of singularity at the start of the universe by a condensation nucleus and that the very early period of the universe usually assumed to be inflation has to be replaced by a period of rapid crystal growth as in Weiss magnetization domains. Impressively, these minor modifications agree well with astronomical observations including removing the strong inflation perturbations which were never observed in the recent BICEP2 experiments. Furthermore, looking at biological principles suggests that such a new theory with a condensation nucleus at start and a first rapid phase of magnetization-like growth of the ordered, physical laws obeying lattice we live in is in fact the only convincing theory of the early phases of our universe that also is compatible with current observations. We show in detail in the following that such a process of crystal creation, breaking of new crystal seeds and ultimate evaporation of the present crystal readily leads over several generations to an evolution and selection of better, more stable and more self-organizing crystals. Moreover, this explains the "fine-tuning" question why our universe is fine-tuned to favor life: Our Universe is so self-organizing to have enough offspring and the detailed physics involved is at the same time highly favorable for all self-organizing processes including life. This biological theory contrasts with current standard inflation cosmologies. The latter do not perform well in explaining any phenomena of sophisticated structure creation or self-organization. As proteins can only thermodynamically fold by increasing the entropy in the solution around them we suggest for cosmology a condensation nucleus for a universe can form only in a "chaotic ocean" of string-soup or quantum foam if the entropy outside of the nucleus rapidly increases. We derive an interaction potential for 1 to n-dimensional strings or quantum-foams and show that they allow only 1D, 2D, 4D or octonion interactions. The latter is the richest structure and agrees to the E8 symmetry fundamental to particle physics and also compatible with the ten dimensional string theory E8 which is part of the M-theory. Interestingly, any other interactions of other dimensionality can be ruled out using Hurwitz compositional theorem. Crystallization explains also extremely well why we have only one macroscopic reality and where the worldlines of alternative trajectories exist: They are in other planes of the crystal and for energy reasons they crystallize mostly at the same time, yielding a beautiful and stable crystal. This explains decoherence and allows to determine the size of Planck´s quantum h (very small as separation of crystal layers by energy is extremely strong). Ultimate dissolution of real crystals suggests an explanation for dark energy agreeing with estimates for the "big rip". The halo distribution of dark matter favoring galaxy formation is readily explained by a crystal seed starting with unit cells made of normal and dark matter. That we have only matter and not antimatter can be explained as there may be right handed mattercrystals and left-handed antimatter crystals. Similarly, real crystals are never perfect and we argue that exactly such irregularities allow formation of galaxies, clusters and superclusters. Finally, heuristics from genetics suggest to look for a systems perspective to derive correct vacuum and Higgs Boson energies.}, language = {en} } @article{GehrkeBalbachRauchetal.2019, author = {Gehrke, Alexander and Balbach, Nico and Rauch, Yong-Mi and Degkwitz, Andreas and Puppe, Frank}, title = {Erkennung von handschriftlichen Unterstreichungen in Alten Drucken}, series = {Bibliothek Forschung und Praxis}, volume = {43}, journal = {Bibliothek Forschung und Praxis}, number = {3}, issn = {1865-7648}, doi = {10.1515/bfp-2019-2083}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-193377}, pages = {447 -- 452}, year = {2019}, abstract = {Die Erkennung handschriftlicher Artefakte wie Unterstreichungen in Buchdrucken erm{\"o}glicht R{\"u}ckschl{\"u}sse auf das Rezeptionsverhalten und die Provenienzgeschichte und wird auch f{\"u}r eine OCR ben{\"o}tigt. Dabei soll zwischen handschriftlichen Unterstreichungen und waagerechten Linien im Druck (z. B. Trennlinien usw.) unterschieden werden, da letztere nicht ausgezeichnet werden sollen. Im Beitrag wird ein Ansatz basierend auf einem auf Unterstreichungen trainierten Neuronalen Netz gem{\"a}ß der U-Net Architektur vorgestellt, dessen Ergebnisse in einem zweiten Schritt mit heuristischen Regeln nachbearbeitet werden. Die Evaluationen zeigen, dass Unterstreichungen sehr gut erkannt werden, wenn bei der Binarisierung der Scans nicht zu viele Pixel der Unterstreichung wegen geringem Kontrast verloren gehen. Zuk{\"u}nftig sollen die Worte oberhalb der Unterstreichung mit OCR transkribiert werden und auch andere Artefakte wie handschriftliche Notizen in alten Drucken erkannt werden.}, language = {de} } @article{WickHarteltPuppe2019, author = {Wick, Christoph and Hartelt, Alexander and Puppe, Frank}, title = {Staff, symbol and melody detection of Medieval manuscripts written in square notation using deep Fully Convolutional Networks}, series = {Applied Sciences}, volume = {9}, journal = {Applied Sciences}, number = {13}, issn = {2076-3417}, doi = {10.3390/app9132646}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-197248}, year = {2019}, abstract = {Even today, the automatic digitisation of scanned documents in general, but especially the automatic optical music recognition (OMR) of historical manuscripts, still remains an enormous challenge, since both handwritten musical symbols and text have to be identified. This paper focuses on the Medieval so-called square notation developed in the 11th-12th century, which is already composed of staff lines, staves, clefs, accidentals, and neumes that are roughly spoken connected single notes. The aim is to develop an algorithm that captures both the neumes, and in particular its melody, which can be used to reconstruct the original writing. Our pipeline is similar to the standard OMR approach and comprises a novel staff line and symbol detection algorithm based on deep Fully Convolutional Networks (FCN), which perform pixel-based predictions for either staff lines or symbols and their respective types. Then, the staff line detection combines the extracted lines to staves and yields an F\(_1\) -score of over 99\% for both detecting lines and complete staves. For the music symbol detection, we choose a novel approach that skips the step to identify neumes and instead directly predicts note components (NCs) and their respective affiliation to a neume. Furthermore, the algorithm detects clefs and accidentals. Our algorithm predicts the symbol sequence of a staff with a diplomatic symbol accuracy rate (dSAR) of about 87\%, which includes symbol type and location. If only the NCs without their respective connection to a neume, all clefs and accidentals are of interest, the algorithm reaches an harmonic symbol accuracy rate (hSAR) of approximately 90\%. In general, the algorithm recognises a symbol in the manuscript with an F\(_1\) -score of over 96\%.}, language = {en} } @phdthesis{Peng2019, author = {Peng, Dongliang}, title = {An Optimization-Based Approach for Continuous Map Generalization}, edition = {1. Auflage}, publisher = {W{\"u}rzburg University Press}, address = {W{\"u}rzburg}, isbn = {978-3-95826-104-4}, doi = {10.25972/WUP-978-3-95826-105-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-174427}, school = {W{\"u}rzburg University Press}, pages = {xv, 132}, year = {2019}, abstract = {Maps are the main tool to represent geographical information. Geographical information is usually scale-dependent, so users need to have access to maps at different scales. In our digital age, the access is realized by zooming. As discrete changes during the zooming tend to distract users, smooth changes are preferred. This is why some digital maps are trying to make the zooming as continuous as they can. The process of producing maps at different scales with smooth changes is called continuous map generalization. In order to produce maps of high quality, cartographers often take into account additional requirements. These requirements are transferred to models in map generalization. Optimization for map generalization is important not only because it finds optimal solutions in the sense of the models, but also because it helps us to evaluate the quality of the models. Optimization, however, becomes more delicate when we deal with continuous map generalization. In this area, there are requirements not only for a specific map but also for relations between maps at difference scales. This thesis is about continuous map generalization based on optimization. First, we show the background of our research topics. Second, we find optimal sequences for aggregating land-cover areas. We compare the A\$^{\!\star}\$\xspace algorithm and integer linear programming in completing this task. Third, we continuously generalize county boundaries to provincial boundaries based on compatible triangulations. We morph between the two sets of boundaries, using dynamic programming to compute the correspondence. Fourth, we continuously generalize buildings to built-up areas by aggregating and growing. In this work, we group buildings with the help of a minimum spanning tree. Fifth, we define vertex trajectories that allow us to morph between polylines. We require that both the angles and the edge lengths change linearly over time. As it is impossible to fulfill all of these requirements simultaneously, we mediate between them using least-squares adjustment. Sixth, we discuss the performance of some commonly used data structures for a specific spatial problem. Seventh, we conclude this thesis and present open problems.}, subject = {Generalisierung }, language = {en} } @article{OberdoerferLatoschik2019, author = {Oberd{\"o}rfer, Sebastian and Latoschik, Marc Erich}, title = {Knowledge encoding in game mechanics: transfer-oriented knowledge learning in desktop-3D and VR}, series = {International Journal of Computer Games Technology}, volume = {2019}, journal = {International Journal of Computer Games Technology}, doi = {10.1155/2019/7626349}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-201159}, pages = {7626349}, year = {2019}, abstract = {Affine Transformations (ATs) are a complex and abstract learning content. Encoding the AT knowledge in Game Mechanics (GMs) achieves a repetitive knowledge application and audiovisual demonstration. Playing a serious game providing these GMs leads to motivating and effective knowledge learning. Using immersive Virtual Reality (VR) has the potential to even further increase the serious game's learning outcome and learning quality. This paper compares the effectiveness and efficiency of desktop-3D and VR in respect to the achieved learning outcome. Also, the present study analyzes the effectiveness of an enhanced audiovisual knowledge encoding and the provision of a debriefing system. The results validate the effectiveness of the knowledge encoding in GMs to achieve knowledge learning. The study also indicates that VR is beneficial for the overall learning quality and that an enhanced audiovisual encoding has only a limited effect on the learning outcome.}, language = {en} } @phdthesis{Niebler2019, author = {Niebler, Thomas}, title = {Extracting and Learning Semantics from Social Web Data}, doi = {10.25972/OPUS-17866}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178666}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2019}, abstract = {Making machines understand natural language is a dream of mankind that existed since a very long time. Early attempts at programming machines to converse with humans in a supposedly intelligent way with humans relied on phrase lists and simple keyword matching. However, such approaches cannot provide semantically adequate answers, as they do not consider the specific meaning of the conversation. Thus, if we want to enable machines to actually understand language, we need to be able to access semantically relevant background knowledge. For this, it is possible to query so-called ontologies, which are large networks containing knowledge about real-world entities and their semantic relations. However, creating such ontologies is a tedious task, as often extensive expert knowledge is required. Thus, we need to find ways to automatically construct and update ontologies that fit human intuition of semantics and semantic relations. More specifically, we need to determine semantic entities and find relations between them. While this is usually done on large corpora of unstructured text, previous work has shown that we can at least facilitate the first issue of extracting entities by considering special data such as tagging data or human navigational paths. Here, we do not need to detect the actual semantic entities, as they are already provided because of the way those data are collected. Thus we can mainly focus on the problem of assessing the degree of semantic relatedness between tags or web pages. However, there exist several issues which need to be overcome, if we want to approximate human intuition of semantic relatedness. For this, it is necessary to represent words and concepts in a way that allows easy and highly precise semantic characterization. This also largely depends on the quality of data from which these representations are constructed. In this thesis, we extract semantic information from both tagging data created by users of social tagging systems and human navigation data in different semantic-driven social web systems. Our main goal is to construct high quality and robust vector representations of words which can the be used to measure the relatedness of semantic concepts. First, we show that navigation in the social media systems Wikipedia and BibSonomy is driven by a semantic component. After this, we discuss and extend methods to model the semantic information in tagging data as low-dimensional vectors. Furthermore, we show that tagging pragmatics influences different facets of tagging semantics. We then investigate the usefulness of human navigational paths in several different settings on Wikipedia and BibSonomy for measuring semantic relatedness. Finally, we propose a metric-learning based algorithm in adapt pre-trained word embeddings to datasets containing human judgment of semantic relatedness. This work contributes to the field of studying semantic relatedness between words by proposing methods to extract semantic relatedness from web navigation, learn highquality and low-dimensional word representations from tagging data, and to learn semantic relatedness from any kind of vector representation by exploiting human feedback. Applications first and foremest lie in ontology learning for the Semantic Web, but also semantic search or query expansion.}, subject = {Semantik}, language = {en} } @article{DjebkoPuppeKayal2019, author = {Djebko, Kirill and Puppe, Frank and Kayal, Hakan}, title = {Model-based fault detection and diagnosis for spacecraft with an application for the SONATE triple cube nano-satellite}, series = {Aerospace}, volume = {6}, journal = {Aerospace}, number = {10}, issn = {2226-4310}, doi = {10.3390/aerospace6100105}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-198836}, pages = {105}, year = {2019}, abstract = {The correct behavior of spacecraft components is the foundation of unhindered mission operation. However, no technical system is free of wear and degradation. A malfunction of one single component might significantly alter the behavior of the whole spacecraft and may even lead to a complete mission failure. Therefore, abnormal component behavior must be detected early in order to be able to perform counter measures. A dedicated fault detection system can be employed, as opposed to classical health monitoring, performed by human operators, to decrease the response time to a malfunction. In this paper, we present a generic model-based diagnosis system, which detects faults by analyzing the spacecraft's housekeeping data. The observed behavior of the spacecraft components, given by the housekeeping data is compared to their expected behavior, obtained through simulation. Each discrepancy between the observed and the expected behavior of a component generates a so-called symptom. Given the symptoms, the diagnoses are derived by computing sets of components whose malfunction might cause the observed discrepancies. We demonstrate the applicability of the diagnosis system by using modified housekeeping data of the qualification model of an actual spacecraft and outline the advantages and drawbacks of our approach.}, language = {en} } @article{LodaKrebsDanhofetal.2019, author = {Loda, Sophia and Krebs, Jonathan and Danhof, Sophia and Schreder, Martin and Solimando, Antonio G. and Strifler, Susanne and Rasche, Leo and Kort{\"u}m, Martin and Kerscher, Alexander and Knop, Stefan and Puppe, Frank and Einsele, Hermann and Bittrich, Max}, title = {Exploration of artificial intelligence use with ARIES in multiple myeloma research}, series = {Journal of Clinical Medicine}, volume = {8}, journal = {Journal of Clinical Medicine}, number = {7}, issn = {2077-0383}, doi = {10.3390/jcm8070999}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-197231}, pages = {999}, year = {2019}, abstract = {Background: Natural language processing (NLP) is a powerful tool supporting the generation of Real-World Evidence (RWE). There is no NLP system that enables the extensive querying of parameters specific to multiple myeloma (MM) out of unstructured medical reports. We therefore created a MM-specific ontology to accelerate the information extraction (IE) out of unstructured text. Methods: Our MM ontology consists of extensive MM-specific and hierarchically structured attributes and values. We implemented "A Rule-based Information Extraction System" (ARIES) that uses this ontology. We evaluated ARIES on 200 randomly selected medical reports of patients diagnosed with MM. Results: Our system achieved a high F1-Score of 0.92 on the evaluation dataset with a precision of 0.87 and recall of 0.98. Conclusions: Our rule-based IE system enables the comprehensive querying of medical reports. The IE accelerates the extraction of data and enables clinicians to faster generate RWE on hematological issues. RWE helps clinicians to make decisions in an evidence-based manner. Our tool easily accelerates the integration of research evidence into everyday clinical practice.}, language = {en} } @article{LopezArreguinMontenegro2019, author = {Lopez-Arreguin, A. J. R. and Montenegro, S.}, title = {Improving engineering models of terramechanics for planetary exploration}, series = {Results in Engineering}, volume = {3}, journal = {Results in Engineering}, doi = {10.1016/j.rineng.2019.100027}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-202490}, pages = {100027}, year = {2019}, abstract = {This short letter proposes more consolidated explicit solutions for the forces and torques acting on typical rover wheels, that can be used as a method to determine their average mobility characteristics in planetary soils. The closed loop solutions stand in one of the verified methods, but at difference of the previous, observables are decoupled requiring a less amount of physical parameters to measure. As a result, we show that with knowledge of terrain properties, wheel driving performance rely in a single observable only. Because of their generality, the formulated equations established here can have further implications in autonomy and control of rovers or planetary soil characterization.}, language = {en} } @misc{FunkenTscherner2019, author = {Funken, Matthias and Tscherner, Michael}, title = {Jahresbericht 2018 des Rechenzentrums der Universit{\"a}t W{\"u}rzburg}, edition = {1. Auflage}, organization = {Rechenzentrum (Universit{\"a}t W{\"u}rzburg)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-188265}, pages = {76}, year = {2019}, abstract = {Eine {\"U}bersicht {\"u}ber die Aktivit{\"a}ten des Rechenzentrums im Jahr 2018.}, subject = {Julius-Maximilians-Universit{\"a}t W{\"u}rzburg}, language = {de} } @article{PetschkeStaab2019, author = {Petschke, Danny and Staab, Torsten E.M.}, title = {DDRS4PALS: a software for the acquisition and simulation of lifetime spectra using the DRS4 evaluation board}, series = {SoftwareX}, volume = {10}, journal = {SoftwareX}, doi = {10.1016/j.softx.2019.100261}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-202276}, pages = {100261}, year = {2019}, abstract = {Lifetime techniques are applied to diverse fields of study including materials sciences, semiconductor physics, biology, molecular biophysics and photochemistry. Here we present DDRS4PALS, a software for the acquisition and simulation of lifetime spectra using the DRS4 evaluation board (Paul Scherrer Institute, Switzerland) for time resolved measurements and digitization of detector output pulses. Artifact afflicted pulses can be corrected or rejected prior to the lifetime calculation to provide the generation of high-quality lifetime spectra, which are crucial for a profound analysis, i.e. the decomposition of the true information. Moreover, the pulses can be streamed on an (external) hard drive during the measurement and subsequently downloaded in the offline mode without being connected to the hardware. This allows the generation of various lifetime spectra at different configurations from one single measurement and, hence, a meaningful comparison in terms of analyzability and quality. Parallel processing and an integrated JavaScript based language provide convenient options to accelerate and automate time consuming processes such as lifetime spectra simulations.}, language = {en} } @phdthesis{Borrmann2018, author = {Borrmann, Dorit}, title = {Multi-modal 3D mapping - Combining 3D point clouds with thermal and color information}, isbn = {978-3-945459-20-1}, issn = {1868-7474}, doi = {10.25972/OPUS-15708}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157085}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2018}, abstract = {Imagine a technology that automatically creates a full 3D thermal model of an environment and detects temperature peaks in it. For better orientation in the model it is enhanced with color information. The current state of the art for analyzing temperature related issues is thermal imaging. It is relevant for energy efficiency but also for securing important infrastructure such as power supplies and temperature regulation systems. Monitoring and analysis of the data for a large building is tedious as stable conditions need to be guaranteed for several hours and detailed notes about the pose and the environment conditions for each image must be taken. For some applications repeated measurements are necessary to monitor changes over time. The analysis of the scene is only possible through expertise and experience. This thesis proposes a robotic system that creates a full 3D model of the environment with color and thermal information by combining thermal imaging with the technology of terrestrial laser scanning. The addition of a color camera facilitates the interpretation of the data and allows for other application areas. The data from all sensors collected at different positions is joined in one common reference frame using calibration and scan matching. The first part of the thesis deals with 3D point cloud processing with the emphasis on accessing point cloud data efficiently, detecting planar structures in the data and registering multiple point clouds into one common coordinate system. The second part covers the autonomous exploration and data acquisition with a mobile robot with the objective to minimize the unseen area in 3D space. Furthermore, the combination of different modalities, color images, thermal images and point cloud data through calibration is elaborated. The last part presents applications for the the collected data. Among these are methods to detect the structure of building interiors for reconstruction purposes and subsequent detection and classification of windows. A system to project the gathered thermal information back into the scene is presented as well as methods to improve the color information and to join separately acquired point clouds and photo series. A full multi-modal 3D model contains all the relevant geometric information about the recorded scene and enables an expert to fully analyze it off-site. The technology clears the path for automatically detecting points of interest thereby helping the expert to analyze the heat flow as well as localize and identify heat leaks. The concept is modular and neither limited to achieving energy efficiency nor restricted to the use in combination with a mobile platform. It also finds its application in fields such as archaeology and geology and can be extended by further sensors.}, subject = {Punktwolke}, language = {en} } @article{PfitznerMayNuechter2018, author = {Pfitzner, Christian and May, Stefan and N{\"u}chter, Andreas}, title = {Body weight estimation for dose-finding and health monitoring of lying, standing and walking patients based on RGB-D data}, series = {Sensors}, volume = {18}, journal = {Sensors}, number = {5}, doi = {10.3390/s18051311}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-176642}, pages = {1311}, year = {2018}, abstract = {This paper describes the estimation of the body weight of a person in front of an RGB-D camera. A survey of different methods for body weight estimation based on depth sensors is given. First, an estimation of people standing in front of a camera is presented. Second, an approach based on a stream of depth images is used to obtain the body weight of a person walking towards a sensor. The algorithm first extracts features from a point cloud and forwards them to an artificial neural network (ANN) to obtain an estimation of body weight. Besides the algorithm for the estimation, this paper further presents an open-access dataset based on measurements from a trauma room in a hospital as well as data from visitors of a public event. In total, the dataset contains 439 measurements. The article illustrates the efficiency of the approach with experiments with persons lying down in a hospital, standing persons, and walking persons. Applicable scenarios for the presented algorithm are body weight-related dosing of emergency patients.}, language = {en} } @phdthesis{Fleszar2018, author = {Fleszar, Krzysztof}, title = {Network-Design Problems in Graphs and on the Plane}, edition = {1. Auflage}, publisher = {W{\"u}rzburg University Press}, address = {W{\"u}rzburg}, isbn = {978-3-95826-076-4 (Print)}, doi = {10.25972/WUP-978-3-95826-077-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-154904}, school = {W{\"u}rzburg University Press}, pages = {xi, 204}, year = {2018}, abstract = {A network design problem defines an infinite set whose elements, called instances, describe relationships and network constraints. It asks for an algorithm that, given an instance of this set, designs a network that respects the given constraints and at the same time optimizes some given criterion. In my thesis, I develop algorithms whose solutions are optimum or close to an optimum value within some guaranteed bound. I also examine the computational complexity of these problems. Problems from two vast areas are considered: graphs and the Euclidean plane. In the Maximum Edge Disjoint Paths problem, we are given a graph and a subset of vertex pairs that are called terminal pairs. We are asked for a set of paths where the endpoints of each path form a terminal pair. The constraint is that any two paths share at most one inner vertex. The optimization criterion is to maximize the cardinality of the set. In the hard-capacitated k-Facility Location problem, we are given an integer k and a complete graph where the distances obey a given metric and where each node has two numerical values: a capacity and an opening cost. We are asked for a subset of k nodes, called facilities, and an assignment of all the nodes, called clients, to the facilities. The constraint is that the number of clients assigned to a facility cannot exceed the facility's capacity value. The optimization criterion is to minimize the total cost which consists of the total opening cost of the facilities and the total distance between the clients and the facilities they are assigned to. In the Stabbing problem, we are given a set of axis-aligned rectangles in the plane. We are asked for a set of horizontal line segments such that, for every rectangle, there is a line segment crossing its left and right edge. The optimization criterion is to minimize the total length of the line segments. In the k-Colored Non-Crossing Euclidean Steiner Forest problem, we are given an integer k and a finite set of points in the plane where each point has one of k colors. For every color, we are asked for a drawing that connects all the points of the same color. The constraint is that drawings of different colors are not allowed to cross each other. The optimization criterion is to minimize the total length of the drawings. In the Minimum Rectilinear Polygon for Given Angle Sequence problem, we are given an angle sequence of left (+90°) turns and right (-90°) turns. We are asked for an axis-parallel simple polygon where the angles of the vertices yield the given sequence when walking around the polygon in counter-clockwise manner. The optimization criteria considered are to minimize the perimeter, the area, and the size of the axis-parallel bounding box of the polygon.}, subject = {Euklidische Ebene}, language = {en} } @phdthesis{Wojtkowiak2018, author = {Wojtkowiak, Harald}, title = {Planungssystem zur Steigerung der Autonomie von Kleinstsatelliten}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-163569}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2018}, abstract = {Der Betrieb von Satelliten wird sich in Zukunft gravierend {\"a}ndern. Die bisher ausge{\"u}bte konventionelle Vorgehensweise, bei der die Planung der vom Satelliten auszuf{\"u}hrenden Aktivit{\"a}ten sowie die Kontrolle hier{\"u}ber ausschließlich vom Boden aus erfolgen, st{\"o}ßt bei heutigen Anwendungen an ihre Grenzen. Im schlimmsten Fall verhindert dieser Umstand sogar die Erschließung bisher ungenutzter M{\"o}glichkeiten. Der Gewinn eines Satelliten, sei es in Form wissenschaftlicher Daten oder der Vermarktung satellitengest{\"u}tzter Dienste, wird daher nicht optimal ausgesch{\"o}pft. Die Ursache f{\"u}r dieses Problem l{\"a}sst sich im Grunde auf eine ausschlaggebende Tatsache zur{\"u}ckf{\"u}hren: Konventionelle Satelliten k{\"o}nnen ihr Verhalten, d.h. die Folge ihrer T{\"a}tigkeiten, nicht eigenst{\"a}ndig anpassen. Stattdessen erstellt das Bedienpersonal am Boden - vor allem die Operatoren - mit Hilfe von Planungssoftware feste Ablaufpl{\"a}ne, die dann in Form von Kommandosequenzen von den Bodenstationen aus an die jeweiligen Satelliten hochgeladen werden. Dort werden die Befehle lediglich {\"u}berpr{\"u}ft, interpretiert und strikt ausgef{\"u}hrt. Die Abarbeitung erfolgt linear. Situationsbedingte {\"A}nderungen, wie sie vergleichsweise bei der Codeausf{\"u}hrung von Softwareprogrammen durch Kontrollkonstrukte, zum Beispiel Schleifen und Verzweigungen, {\"u}blich sind, sind typischerweise nicht vorgesehen. Der Operator ist daher die einzige Instanz, die das Verhalten des Satelliten mittels Kommandierung, per Upload, beeinflussen kann, und auch nur dann, wenn ein direkter Funkkontakt zwischen Satellit und Bodenstation besteht. Die dadurch m{\"o}glichen Reaktionszeiten des Satelliten liegen bestenfalls bei einigen Sekunden, falls er sich im Wirkungsbereich der Bodenstation befindet. Außerhalb des Kontaktfensters kann sich die Zeitschranke, gegeben durch den Orbit und die aktuelle Position des Satelliten, von einigen Minuten bis hin zu einigen Stunden erstrecken. Die Signallaufzeiten der Funk{\"u}bertragung verl{\"a}ngern die Reaktionszeiten um weitere Sekunden im erdnahen Bereich. Im interplanetaren Raum erstrecken sich die Zeitspannen aufgrund der immensen Entfernungen sogar auf mehrere Minuten. Dadurch bedingt liegt die derzeit technologisch m{\"o}gliche, bodengest{\"u}tzte, Reaktionszeit von Satelliten bestenfalls im Bereich von einigen Sekunden. Diese Einschr{\"a}nkung stellt ein schweres Hindernis f{\"u}r neuartige Satellitenmissionen, bei denen insbesondere nichtdeterministische und kurzzeitige Ph{\"a}nomene (z.B. Blitze und Meteoreintritte in die Erdatmosph{\"a}re) Gegenstand der Beobachtungen sind, dar. Die langen Reaktionszeiten des konventionellen Satellitenbetriebs verhindern die Realisierung solcher Missionen, da die verz{\"o}gerte Reaktion erst erfolgt, nachdem das zu beobachtende Ereignis bereits abgeschlossen ist. Die vorliegende Dissertation zeigt eine M{\"o}glichkeit, das durch die langen Reaktionszeiten entstandene Problem zu l{\"o}sen, auf. Im Zentrum des L{\"o}sungsansatzes steht dabei die Autonomie. Im Wesentlichen geht es dabei darum, den Satelliten mit der F{\"a}higkeit auszustatten, sein Verhalten, d.h. die Folge seiner T{\"a}tigkeiten, eigenst{\"a}ndig zu bestimmen bzw. zu {\"a}ndern. Dadurch wird die direkte Abh{\"a}ngigkeit des Satelliten vom Operator bei Reaktionen aufgehoben. Im Grunde wird der Satellit in die Lage versetzt, sich selbst zu kommandieren. Die Idee der Autonomie wurde im Rahmen der zugrunde liegenden Forschungsarbeiten umgesetzt. Das Ergebnis ist ein autonomes Planungssystem. Dabei handelt es sich um ein Softwaresystem, mit dem sich autonomes Verhalten im Satelliten realisieren l{\"a}sst. Es kann an unterschiedliche Satellitenmissionen angepasst werden. Ferner deckt es verschiedene Aspekte des autonomen Satellitenbetriebs, angefangen bei der generellen Entscheidungsfindung der T{\"a}tigkeiten, {\"u}ber die zeitliche Ablaufplanung unter Einbeziehung von Randbedingungen (z.B. Ressourcen) bis hin zur eigentlichen Ausf{\"u}hrung, d.h. Kommandierung, ab. Das Planungssystem kommt als Anwendung in ASAP, einer autonomen Sensorplattform, zum Einsatz. Es ist ein optisches System und dient der Detektion von kurzzeitigen Ph{\"a}nomenen und Ereignissen in der Erdatmosph{\"a}re. Die Forschungsarbeiten an dem autonomen Planungssystem, an ASAP sowie an anderen zu diesen in Bezug stehenden Systemen wurden an der Professur f{\"u}r Raumfahrttechnik des Lehrstuhls Informatik VIII der Julius-Maximilians-Universit{\"a}t W{\"u}rzburg durchgef{\"u}hrt.}, subject = {Planungssystem}, language = {de} } @phdthesis{Baier2018, author = {Baier, Pablo A.}, title = {Simulator for Minimally Invasive Vascular Interventions: Hardware and Software}, isbn = {978-3-945459-22-5}, doi = {10.25972/OPUS-16119}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-161190}, school = {Universit{\"a}t W{\"u}rzburg}, pages = {118}, year = {2018}, abstract = {A complete simulation system is proposed that can be used as an educational tool by physicians in training basic skills of Minimally Invasive Vascular Interventions. In the first part, a surface model is developed to assemble arteries having a planar segmentation. It is based on Sweep Surfaces and can be extended to T- and Y-like bifurcations. A continuous force vector field is described, representing the interaction between the catheter and the surface. The computation time of the force field is almost unaffected when the resolution of the artery is increased. The mechanical properties of arteries play an essential role in the study of the circulatory system dynamics, which has been becoming increasingly important in the treatment of cardiovascular diseases. In Virtual Reality Simulators, it is crucial to have a tissue model that responds in real time. In this work, the arteries are discretized by a two dimensional mesh and the nodes are connected by three kinds of linear springs. Three tissue layers (Intima, Media, Adventitia) are considered and, starting from the stretch-energy density, some of the elasticity tensor components are calculated. The physical model linearizes and homogenizes the material response, but it still contemplates the geometric nonlinearity. In general, if the arterial stretch varies by 1\% or less, then the agreement between the linear and nonlinear models is trustworthy. In the last part, the physical model of the wire proposed by Konings is improved. As a result, a simpler and more stable method is obtained to calculate the equilibrium configuration of the wire. In addition, a geometrical method is developed to perform relaxations. It is particularly useful when the wire is hindered in the physical method because of the boundary conditions. The physical and the geometrical methods are merged, resulting in efficient relaxations. Tests show that the shape of the virtual wire agrees with the experiment. The proposed algorithm allows real-time executions and the hardware to assemble the simulator has a low cost.}, subject = {Computersimulation}, language = {en} } @article{ZimmererFischbachLatoschik2018, author = {Zimmerer, Chris and Fischbach, Martin and Latoschik, Marc Erich}, title = {Semantic Fusion for Natural Multimodal Interfaces using Concurrent Augmented Transition Networks}, series = {Multimodal Technologies and Interaction}, volume = {2}, journal = {Multimodal Technologies and Interaction}, number = {4}, issn = {2414-4088}, doi = {10.3390/mti2040081}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-197573}, year = {2018}, abstract = {Semantic fusion is a central requirement of many multimodal interfaces. Procedural methods like finite-state transducers and augmented transition networks have proven to be beneficial to implement semantic fusion. They are compliant with rapid development cycles that are common for the development of user interfaces, in contrast to machine-learning approaches that require time-costly training and optimization. We identify seven fundamental requirements for the implementation of semantic fusion: Action derivation, continuous feedback, context-sensitivity, temporal relation support, access to the interaction context, as well as the support of chronologically unsorted and probabilistic input. A subsequent analysis reveals, however, that there is currently no solution for fulfilling the latter two requirements. As the main contribution of this article, we thus present the Concurrent Cursor concept to compensate these shortcomings. In addition, we showcase a reference implementation, the Concurrent Augmented Transition Network (cATN), that validates the concept's feasibility in a series of proof of concept demonstrations as well as through a comparative benchmark. The cATN fulfills all identified requirements and fills the lack amongst previous solutions. It supports the rapid prototyping of multimodal interfaces by means of five concrete traits: Its declarative nature, the recursiveness of the underlying transition network, the network abstraction constructs of its description language, the utilized semantic queries, and an abstraction layer for lexical information. Our reference implementation was and is used in various student projects, theses, as well as master-level courses. It is openly available and showcases that non-experts can effectively implement multimodal interfaces, even for non-trivial applications in mixed and virtual reality.}, language = {en} } @phdthesis{Budig2018, author = {Budig, Benedikt}, title = {Extracting Spatial Information from Historical Maps: Algorithms and Interaction}, edition = {1. Auflage}, publisher = {W{\"u}rzburg University Press}, address = {W{\"u}rzburg}, isbn = {978-3-95826-092-4}, doi = {10.25972/WUP-978-3-95826-093-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-160955}, school = {W{\"u}rzburg University Press}, pages = {viii, 160}, year = {2018}, abstract = {Historical maps are fascinating documents and a valuable source of information for scientists of various disciplines. Many of these maps are available as scanned bitmap images, but in order to make them searchable in useful ways, a structured representation of the contained information is desirable. This book deals with the extraction of spatial information from historical maps. This cannot be expected to be solved fully automatically (since it involves difficult semantics), but is also too tedious to be done manually at scale. The methodology used in this book combines the strengths of both computers and humans: it describes efficient algorithms to largely automate information extraction tasks and pairs these algorithms with smart user interactions to handle what is not understood by the algorithm. The effectiveness of this approach is shown for various kinds of spatial documents from the 16th to the early 20th century.}, subject = {Karte}, language = {en} } @misc{FunkenTscherner2018, author = {Funken, Matthias and Tscherner, Michael}, title = {Jahresbericht 2017 des Rechenzentrums der Universit{\"a}t W{\"u}rzburg}, edition = {1. Auflage}, organization = {Rechenzentrum (Universit{\"a}t W{\"u}rzburg)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168537}, pages = {68}, year = {2018}, abstract = {Eine {\"U}bersicht {\"u}ber die Aktivit{\"a}ten des Rechenzentrums im Jahr 2017.}, subject = {Julius-Maximilians-Universit{\"a}t W{\"u}rzburg}, language = {de} } @article{NaglerNaegeleGillietal.2018, author = {Nagler, Matthias and N{\"a}gele, Thomas and Gilli, Christian and Fragner, Lena and Korte, Arthur and Platzer, Alexander and Farlow, Ashley and Nordborg, Magnus and Weckwerth, Wolfram}, title = {Eco-Metabolomics and Metabolic Modeling: Making the Leap From Model Systems in the Lab to Native Populations in the Field}, series = {Frontiers in Plant Science}, volume = {9}, journal = {Frontiers in Plant Science}, number = {1556}, issn = {1664-462X}, doi = {10.3389/fpls.2018.01556}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189560}, year = {2018}, abstract = {Experimental high-throughput analysis of molecular networks is a central approach to characterize the adaptation of plant metabolism to the environment. However, recent studies have demonstrated that it is hardly possible to predict in situ metabolic phenotypes from experiments under controlled conditions, such as growth chambers or greenhouses. This is particularly due to the high molecular variance of in situ samples induced by environmental fluctuations. An approach of functional metabolome interpretation of field samples would be desirable in order to be able to identify and trace back the impact of environmental changes on plant metabolism. To test the applicability of metabolomics studies for a characterization of plant populations in the field, we have identified and analyzed in situ samples of nearby grown natural populations of Arabidopsis thaliana in Austria. A. thaliana is the primary molecular biological model system in plant biology with one of the best functionally annotated genomes representing a reference system for all other plant genome projects. The genomes of these novel natural populations were sequenced and phylogenetically compared to a comprehensive genome database of A. thaliana ecotypes. Experimental results on primary and secondary metabolite profiling and genotypic variation were functionally integrated by a data mining strategy, which combines statistical output of metabolomics data with genome-derived biochemical pathway reconstruction and metabolic modeling. Correlations of biochemical model predictions and population-specific genetic variation indicated varying strategies of metabolic regulation on a population level which enabled the direct comparison, differentiation, and prediction of metabolic adaptation of the same species to different habitats. These differences were most pronounced at organic and amino acid metabolism as well as at the interface of primary and secondary metabolism and allowed for the direct classification of population-specific metabolic phenotypes within geographically contiguous sampling sites.}, language = {en} } @article{PetschkeStaab2018, author = {Petschke, Danny and Staab, Torsten E.M.}, title = {DLTPulseGenerator: a library for the simulation of lifetime spectra based on detector-output pulses}, series = {SoftwareX}, volume = {7}, journal = {SoftwareX}, doi = {10.1016/j.softx.2018.04.002}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-176883}, pages = {122-128}, year = {2018}, abstract = {The quantitative analysis of lifetime spectra relevant in both life and materials sciences presents one of the ill-posed inverse problems and, hence, leads to most stringent requirements on the hardware specifications and the analysis algorithms. Here we present DLTPulseGenerator, a library written in native C++ 11, which provides a simulation of lifetime spectra according to the measurement setup. The simulation is based on pairs of non-TTL detector output-pulses. Those pulses require the Constant Fraction Principle (CFD) for the determination of the exact timing signal and, thus, the calculation of the time difference i.e. the lifetime. To verify the functionality, simulation results were compared to experimentally obtained data using Positron Annihilation Lifetime Spectroscopy (PALS) on pure tin.}, language = {en} } @phdthesis{Ostermayer2017, author = {Ostermayer, Ludwig}, title = {Integration of Prolog and Java with the Connector Architecture CAPJa}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-150713}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Modern software is often realized as a modular combination of subsystems for, e. g., knowledge management, visualization, verification, or the interaction with users. As a result, software libraries from possibly different programming languages have to work together. Even more complex the case is if different programming paradigms have to be combined. This type of diversification of programming languages and paradigms in just one software application can only be mastered by mechanisms for a seamless integration of the involved programming languages. However, the integration of the common logic programming language Prolog and the popular object-oriented programming language Java is complicated by various interoperability problems which stem on the one hand from the paradigmatic gap between the programming languages, and on the other hand, from the diversity of the available Prolog systems. The subject of the thesis is the investigation of novel mechanisms for the integration of logic programming in Prolog and object-oriented programming in Java. We are particularly interested in an object-oriented, uniform approach which is not specific to just one Prolog system. Therefore, we have first identified several important criteria for the seamless integration of Prolog and Java from the object-oriented perspective. The main contribution of the thesis is a novel integration framework called the Connector Architecture for Prolog and Java (CAPJa). The framework is completely implemented in Java and imposes no modifications to the Java Virtual Machine or Prolog. CAPJa provides a semi-automated mechanism for the integration of Prolog predicates into Java. For compact, readable, and object-oriented queries to Prolog, CAPJa exploits lambda expressions with conditional and relational operators in Java. The communication between Java and Prolog is based on a fully automated mapping of Java objects to Prolog terms, and vice versa. In Java, an extensible system of gateways provides connectivity with various Prolog system and, moreover, makes any connected Prolog system easily interchangeable, without major adaption in Java.}, subject = {Logische Programmierung}, language = {en} } @phdthesis{Aschenbrenner2017, author = {Aschenbrenner, Doris}, title = {Human Robot Interaction Concepts for Human Supervisory Control and Telemaintenance Applications in an Industry 4.0 Environment}, isbn = {978-3-945459-18-8}, doi = {10.25972/OPUS-15052}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-150520}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {While teleoperation of technical highly sophisticated systems has already been a wide field of research, especially for space and robotics applications, the automation industry has not yet benefited from its results. Besides the established fields of application, also production lines with industrial robots and the surrounding plant components are in need of being remotely accessible. This is especially critical for maintenance or if an unexpected problem cannot be solved by the local specialists. Special machine manufacturers, especially robotics companies, sell their technology worldwide. Some factories, for example in emerging economies, lack qualified personnel for repair and maintenance tasks. When a severe failure occurs, an expert of the manufacturer needs to fly there, which leads to long down times of the machine or even the whole production line. With the development of data networks, a huge part of those travels can be omitted, if appropriate teleoperation equipment is provided. This thesis describes the development of a telemaintenance system, which was established in an active production line for research purposes. The customer production site of Braun in Marktheidenfeld, a factory which belongs to Procter \& Gamble, consists of a six-axis cartesian industrial robot by KUKA Industries, a two-component injection molding system and an assembly unit. The plant produces plastic parts for electric toothbrushes. In the research projects "MainTelRob" and "Bayern.digital", during which this plant was utilised, the Zentrum f{\"u}r Telematik e.V. (ZfT) and its project partners develop novel technical approaches and procedures for modern telemaintenance. The term "telemaintenance" hereby refers to the integration of computer science and communication technologies into the maintenance strategy. It is particularly interesting for high-grade capital-intensive goods like industrial robots. Typical telemaintenance tasks are for example the analysis of a robot failure or difficult repair operations. The service department of KUKA Industries is responsible for the worldwide distributed customers who own more than one robot. Currently such tasks are offered via phone support and service staff which travels abroad. They want to expand their service activities on telemaintenance and struggle with the high demands of teleoperation especially regarding security infrastructure. In addition, the facility in Marktheidenfeld has to keep up with the high international standards of Procter \& Gamble and wants to minimize machine downtimes. Like 71.6 \% of all German companies, P\&G sees a huge potential for early information on their production system, but complains about the insufficient quality and the lack of currentness of data. The main research focus of this work lies on the human machine interface for all human tasks in a telemaintenance setup. This thesis provides own work in the use of a mobile device in context of maintenance, describes new tools on asynchronous remote analysis and puts all parts together in an integrated telemaintenance infrastructure. With the help of Augmented Reality, the user performance and satisfaction could be raised. A special regard is put upon the situation awareness of the remote expert realized by different camera viewpoints. In detail the work consists of: - Support of maintenance tasks with a mobile device - Development and evaluation of a context-aware inspection tool - Comparison of a new touch-based mobile robot programming device to the former teach pendant - Study on Augmented Reality support for repair tasks with a mobile device - Condition monitoring for a specific plant with industrial robot - Human computer interaction for remote analysis of a single plant cycle - A big data analysis tool for a multitude of cycles and similar plants - 3D process visualization for a specific plant cycle with additional virtual information - Network architecture in hardware, software and network infrastructure - Mobile device computer supported collaborative work for telemaintenance - Motor exchange telemaintenance example in running production environment - Augmented reality supported remote plant visualization for better situation awareness}, subject = {Fernwartung}, language = {en} } @phdthesis{Houshiar2017, author = {Houshiar, Hamidreza}, title = {Documentation and mapping with 3D point cloud processing}, isbn = {978-3-945459-14-0}, doi = {10.25972/OPUS-14449}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144493}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {3D point clouds are a de facto standard for 3D documentation and modelling. The advances in laser scanning technology broadens the usability and access to 3D measurement systems. 3D point clouds are used in many disciplines such as robotics, 3D modelling, archeology and surveying. Scanners are able to acquire up to a million of points per second to represent the environment with a dense point cloud. This represents the captured environment with a very high degree of detail. The combination of laser scanning technology with photography adds color information to the point clouds. Thus the environment is represented more realistically. Full 3D models of environments, without any occlusion, require multiple scans. Merging point clouds is a challenging process. This thesis presents methods for point cloud registration based on the panorama images generated from the scans. Image representation of point clouds introduces 2D image processing methods to 3D point clouds. Several projection methods for the generation of panorama maps of point clouds are presented in this thesis. Additionally, methods for point cloud reduction and compression based on the panorama maps are proposed. Due to the large amounts of data generated from the 3D measurement systems these methods are necessary to improve the point cloud processing, transmission and archiving. This thesis introduces point cloud processing methods as a novel framework for the digitisation of archeological excavations. The framework replaces the conventional documentation methods for excavation sites. It employs point clouds for the generation of the digital documentation of an excavation with the help of an archeologist on-site. The 3D point cloud is used not only for data representation but also for analysis and knowledge generation. Finally, this thesis presents an autonomous indoor mobile mapping system. The mapping system focuses on the sensor placement planning method. Capturing a complete environment requires several scans. The sensor placement planning method solves for the minimum required scans to digitise large environments. Combining this method with a navigation system on a mobile robot platform enables it to acquire data fully autonomously. This thesis introduces a novel hole detection method for point clouds to detect obscured parts of a captured environment. The sensor placement planning method selects the next scan position with the most coverage of the obscured environment. This reduces the required number of scans. The navigation system on the robot platform consist of path planning, path following and obstacle avoidance. This guarantees the safe navigation of the mobile robot platform between the scan positions. The sensor placement planning method is designed as a stand alone process that could be used with a mobile robot platform for autonomous mapping of an environment or as an assistant tool for the surveyor on scanning projects.}, subject = {3D Punktwolke}, language = {en} } @article{KaltdorfSchulzeHelmprobstetal.2017, author = {Kaltdorf, Kristin Verena and Schulze, Katja and Helmprobst, Frederik and Kollmannsberger, Philip and Dandekar, Thomas and Stigloher, Christian}, title = {Fiji macro 3D ART VeSElecT: 3D automated reconstruction tool for vesicle structures of electron tomograms}, series = {PLoS Computational Biology}, volume = {13}, journal = {PLoS Computational Biology}, number = {1}, doi = {10.1371/journal.pcbi.1005317}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-172112}, year = {2017}, abstract = {Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial.}, language = {en} } @misc{OPUS4-15355, title = {Jahresbericht 2016 des Rechenzentrums der Universit{\"a}t W{\"u}rzburg}, edition = {1. Auflage}, organization = {Rechenzentrum (Universit{\"a}t W{\"u}rzburg)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-153558}, pages = {72}, year = {2017}, abstract = {Das Dokument umfasst eine j{\"a}hrliche Zusammenfassung der Aktivit{\"a}ten des Rechenzentrums als zentraler IT-Dienstleister der Universit{\"a}t W{\"u}rzburg}, subject = {Jahresbericht}, language = {de} } @article{vonMammenWagnerKnoteetal.2017, author = {von Mammen, Sebastian Albrecht and Wagner, Daniel and Knote, Andreas and Taskin, Umut}, title = {Interactive simulations of biohybrid systems}, series = {Frontiers in Robotics and AI}, volume = {4}, journal = {Frontiers in Robotics and AI}, issn = {2296-9144}, doi = {10.3389/frobt.2017.00050}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-195755}, year = {2017}, abstract = {In this article, we present approaches to interactive simulations of biohybrid systems. These simulations are comprised of two major computational components: (1) agent-based developmental models that retrace organismal growth and unfolding of technical scaffoldings and (2) interfaces to explore these models interactively. Simulations of biohybrid systems allow us to fast forward and experience their evolution over time based on our design decisions involving the choice, configuration and initial states of the deployed biological and robotic actors as well as their interplay with the environment. We briefly introduce the concept of swarm grammars, an agent-based extension of L-systems for retracing growth processes and structural artifacts. Next, we review an early augmented reality prototype for designing and projecting biohybrid system simulations into real space. In addition to models that retrace plant behaviors, we specify swarm grammar agents to braid structures in a self-organizing manner. Based on this model, both robotic and plant-driven braiding processes can be experienced and explored in virtual worlds. We present an according user interface for use in virtual reality. As we present interactive models concerning rather diverse description levels, we only ensured their principal capacity for interaction but did not consider efficiency analyzes beyond prototypic operation. We conclude this article with an outlook on future works on melding reality and virtuality to drive the design and deployment of biohybrid systems.}, language = {en} } @article{FisselerMuellerWeichert2017, author = {Fisseler, Denis and M{\"u}ller, Gerfrid G. W. and Weichert, Frank}, title = {Web-Based scientific exploration and analysis of 3D scanned cuneiform datasets for collaborative research}, series = {Informatics}, volume = {4}, journal = {Informatics}, number = {4}, issn = {2227-9709}, doi = {10.3390/informatics4040044}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-197958}, pages = {44}, year = {2017}, abstract = {The three-dimensional cuneiform script is one of the oldest known writing systems and a central object of research in Ancient Near Eastern Studies and Hittitology. An important step towards the understanding of the cuneiform script is the provision of opportunities and tools for joint analysis. This paper presents an approach that contributes to this challenge: a collaborative compatible web-based scientific exploration and analysis of 3D scanned cuneiform fragments. The WebGL -based concept incorporates methods for compressed web-based content delivery of large 3D datasets and high quality visualization. To maximize accessibility and to promote acceptance of 3D techniques in the field of Hittitology, the introduced concept is integrated into the Hethitologie-Portal Mainz, an established leading online research resource in the field of Hittitology, which until now exclusively included 2D content. The paper shows that increasing the availability of 3D scanned archaeological data through a web-based interface can provide significant scientific value while at the same time finding a trade-off between copyright induced restrictions and scientific usability.}, language = {en} } @article{KunzLiangNillaetal.2016, author = {Kunz, Meik and Liang, Chunguang and Nilla, Santosh and Cecil, Alexander and Dandekar, Thomas}, title = {The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development}, series = {Database}, volume = {2016}, journal = {Database}, doi = {10.1093/database/baw041}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147369}, pages = {baw041}, year = {2016}, abstract = {The drug-minded protein interaction database (DrumPID) has been designed to provide fast, tailored information on drugs and their protein networks including indications, protein targets and side-targets. Starting queries include compound, target and protein interactions and organism-specific protein families. Furthermore, drug name, chemical structures and their SMILES notation, affected proteins (potential drug targets), organisms as well as diseases can be queried including various combinations and refinement of searches. Drugs and protein interactions are analyzed in detail with reference to protein structures and catalytic domains, related compound structures as well as potential targets in other organisms. DrumPID considers drug functionality, compound similarity, target structure, interactome analysis and organismic range for a compound, useful for drug development, predicting drug side-effects and structure-activity relationships.}, language = {en} } @article{AliMontenegro2016, author = {Ali, Qasim and Montenegro, Sergio}, title = {Decentralized control for scalable quadcopter formations}, series = {International Journal of Aerospace Engineering}, volume = {2016}, journal = {International Journal of Aerospace Engineering}, doi = {10.1155/2016/9108983}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146704}, pages = {9108983}, year = {2016}, abstract = {An innovative framework has been developed for teamwork of two quadcopter formations, each having its specified formation geometry, assigned task, and matching control scheme. Position control for quadcopters in one of the formations has been implemented through a Linear Quadratic Regulator Proportional Integral (LQR PI) control scheme based on explicit model following scheme. Quadcopters in the other formation are controlled through LQR PI servomechanism control scheme. These two control schemes are compared in terms of their performance and control effort. Both formations are commanded by respective ground stations through virtual leaders. Quadcopters in formations are able to track desired trajectories as well as hovering at desired points for selected time duration. In case of communication loss between ground station and any of the quadcopters, the neighboring quadcopter provides the command data, received from the ground station, to the affected unit. Proposed control schemes have been validated through extensive simulations using MATLAB®/Simulink® that provided favorable results.}, language = {en} } @article{AliMontenegro2016, author = {Ali, Qasim and Montenegro, Sergio}, title = {Explicit Model Following Distributed Control Scheme for Formation Flying of Mini UAVs}, series = {IEEE Access}, volume = {4}, journal = {IEEE Access}, number = {397-406}, doi = {10.1109/ACCESS.2016.2517203}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146061}, year = {2016}, abstract = {A centralized heterogeneous formation flight position control scheme has been formulated using an explicit model following design, based on a Linear Quadratic Regulator Proportional Integral (LQR PI) controller. The leader quadcopter is a stable reference model with desired dynamics whose output is perfectly tracked by the two wingmen quadcopters. The leader itself is controlled through the pole placement control method with desired stability characteristics, while the two followers are controlled through a robust and adaptive LQR PI control method. Selected 3-D formation geometry and static stability are maintained under a number of possible perturbations. With this control scheme, formation geometry may also be switched to any arbitrary shape during flight, provided a suitable collision avoidance mechanism is incorporated. In case of communication loss between the leader and any of the followers, the other follower provides the data, received from the leader, to the affected follower. The stability of the closed-loop system has been analyzed using singular values. The proposed approach for the tightly coupled formation flight of mini unmanned aerial vehicles has been validated with the help of extensive simulations using MATLAB/Simulink, which provided promising results.}, language = {en} } @article{LugrinLatoschikHabeletal.2016, author = {Lugrin, Jean-Luc and Latoschik, Marc Erich and Habel, Michael and Roth, Daniel and Seufert, Christian and Grafe, Silke}, title = {Breaking Bad Behaviors: A New Tool for Learning Classroom Management Using Virtual Reality}, series = {Frontiers in ICT}, volume = {3}, journal = {Frontiers in ICT}, number = {26}, doi = {10.3389/fict.2016.00026}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147945}, year = {2016}, abstract = {This article presents an immersive virtual reality (VR) system for training classroom management skills, with a specific focus on learning to manage disruptive student behavior in face-to-face, one-to-many teaching scenarios. The core of the system is a real-time 3D virtual simulation of a classroom populated by twenty-four semi-autonomous virtual students. The system has been designed as a companion tool for classroom management seminars in a syllabus for primary and secondary school teachers. This will allow lecturers to link theory with practice using the medium of VR. The system is therefore designed for two users: a trainee teacher and an instructor supervising the training session. The teacher is immersed in a real-time 3D simulation of a classroom by means of a head-mounted display and headphone. The instructor operates a graphical desktop console, which renders a view of the class and the teacher whose avatar movements are captured by a marker less tracking system. This console includes a 2D graphics menu with convenient behavior and feedback control mechanisms to provide human-guided training sessions. The system is built using low-cost consumer hardware and software. Its architecture and technical design are described in detail. A first evaluation confirms its conformance to critical usability requirements (i.e., safety and comfort, believability, simplicity, acceptability, extensibility, affordability, and mobility). Our initial results are promising and constitute the necessary first step toward a possible investigation of the efficiency and effectiveness of such a system in terms of learning outcomes and experience.}, language = {en} } @article{AnkenbrandWeberBeckeretal.2016, author = {Ankenbrand, Markus J. and Weber, Lorenz and Becker, Dirk and F{\"o}rster, Frank and Bemm, Felix}, title = {TBro: visualization and management of de novo transcriptomes}, series = {Database}, volume = {2016}, journal = {Database}, doi = {10.1093/database/baw146}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147954}, pages = {baw146}, year = {2016}, abstract = {RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro's modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers.}, language = {en} } @article{BaierBaierSaipSchillingetal.2016, author = {Baier, Pablo A. and Baier-Saip, J{\"u}rgen A. and Schilling, Klaus and Oliveira, Jauvane C.}, title = {Simulator for Minimally Invasive Vascular Interventions: Hardware and Software}, series = {Presence}, volume = {25}, journal = {Presence}, number = {2}, issn = {1531-3263}, doi = {10.1162/PRES_a_00250}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-140580}, pages = {108-128}, year = {2016}, abstract = {In the present work, a simulation system is proposed that can be used as an educational tool by physicians in training basic skills of minimally invasive vascular interventions. In order to accomplish this objective, initially the physical model of the wire proposed by Konings has been improved. As a result, a simpler and more stable method was obtained to calculate the equilibrium configuration of the wire. In addition, a geometrical method is developed to perform relaxations. It is particularly useful when the wire is hindered in the physical method because of the boundary conditions. Then a recipe is given to merge the physical and the geometrical methods, resulting in efficient relaxations. Moreover, tests have shown that the shape of the virtual wire agrees with the experiment. The proposed algorithm allows real-time executions, and furthermore, the hardware to assemble the simulator has a low cost.}, 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} } @misc{OPUS4-12443, title = {Jahresbericht 2014}, organization = {Rechenzentrum (Universit{\"a}t W{\"u}rzburg)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124432}, pages = {90}, year = {2016}, abstract = {Jahresbericht 2014 des Rechenzentrums der Universit{\"a}t W{\"u}rzburg}, subject = {Rechenzentrum Universit{\"a}t W{\"u}rzburg}, language = {de} } @phdthesis{Busch2016, author = {Busch, Stephan}, title = {Robust, Flexible and Efficient Design for Miniature Satellite Systems}, isbn = {978-3-945459-10-2}, doi = {10.25972/OPUS-13652}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-136523}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Small satellites contribute significantly in the rapidly evolving innovation in space engineering, in particular in distributed space systems for global Earth observation and communication services. Significant mass reduction by miniaturization, increased utilization of commercial high-tech components, and in particular standardization are the key drivers for modern miniature space technology. This thesis addresses key fields in research and development on miniature satellite technology regarding efficiency, flexibility, and robustness. Here, these challenges are addressed by the University of Wuerzburg's advanced pico-satellite bus, realizing a generic modular satellite architecture and standardized interfaces for all subsystems. The modular platform ensures reusability, scalability, and increased testability due to its flexible subsystem interface which allows efficient and compact integration of the entire satellite in a plug-and-play manner. Beside systematic design for testability, a high degree of operational robustness is achieved by the consequent implementation of redundancy of crucial subsystems. This is combined with efficient fault detection, isolation and recovery mechanisms. Thus, the UWE-3 platform, and in particular the on-board data handling system and the electrical power system, offers one of the most efficient pico-satellite architectures launched in recent years and provides a solid basis for future extensions. The in-orbit performance results of the pico-satellite UWE-3 are presented and summarize successful operations since its launch in 2013. Several software extensions and adaptations have been uploaded to UWE-3 increasing its capabilities. Thus, a very flexible platform for in-orbit software experiments and for evaluations of innovative concepts was provided and tested.}, subject = {Kleinsatellit}, language = {en} } @misc{OPUS4-13659, title = {Jahresbericht 2015}, organization = {Rechenzentrum (Universit{\"a}t W{\"u}rzburg)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-136599}, pages = {88}, year = {2016}, abstract = {Jahresbericht 2015 des Rechenzentrums der Universit{\"a}t W{\"u}rzburg}, subject = {Julius-Maximilians-Universit{\"a}t W{\"u}rzburg. Rechenzentrum}, language = {de} } @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} } @article{ToepferCorovicFetteetal.2015, author = {Toepfer, Martin and Corovic, Hamo and Fette, Georg and Kl{\"u}gl, Peter and St{\"o}rk, Stefan and Puppe, Frank}, title = {Fine-grained information extraction from German transthoracic echocardiography reports}, series = {BMC Medical Informatics and Decision Making}, volume = {15}, journal = {BMC Medical Informatics and Decision Making}, number = {91}, doi = {doi:10.1186/s12911-015-0215-x}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-125509}, year = {2015}, abstract = {Background Information extraction techniques that get structured representations out of unstructured data make a large amount of clinically relevant information about patients accessible for semantic applications. These methods typically rely on standardized terminologies that guide this process. Many languages and clinical domains, however, lack appropriate resources and tools, as well as evaluations of their applications, especially if detailed conceptualizations of the domain are required. For instance, German transthoracic echocardiography reports have not been targeted sufficiently before, despite of their importance for clinical trials. This work therefore aimed at development and evaluation of an information extraction component with a fine-grained terminology that enables to recognize almost all relevant information stated in German transthoracic echocardiography reports at the University Hospital of W{\"u}rzburg. Methods A domain expert validated and iteratively refined an automatically inferred base terminology. The terminology was used by an ontology-driven information extraction system that outputs attribute value pairs. The final component has been mapped to the central elements of a standardized terminology, and it has been evaluated according to documents with different layouts. Results The final system achieved state-of-the-art precision (micro average.996) and recall (micro average.961) on 100 test documents that represent more than 90 \% of all reports. In particular, principal aspects as defined in a standardized external terminology were recognized with f 1=.989 (micro average) and f 1=.963 (macro average). As a result of keyword matching and restraint concept extraction, the system obtained high precision also on unstructured or exceptionally short documents, and documents with uncommon layout. Conclusions The developed terminology and the proposed information extraction system allow to extract fine-grained information from German semi-structured transthoracic echocardiography reports with very high precision and high recall on the majority of documents at the University Hospital of W{\"u}rzburg. Extracted results populate a clinical data warehouse which supports clinical research.}, language = {en} } @article{KuhnGrippFliederetal.2015, author = {Kuhn, Joachim and Gripp, Tatjana and Flieder, Tobias and Dittrich, Marcus and Hendig, Doris and Busse, Jessica and Knabbe, Cornelius and Birschmann, Ingvild}, title = {UPLC-MRM Mass Spectrometry Method for Measurement of the Coagulation Inhibitors Dabigatran and Rivaroxaban in Human Plasma and Its Comparison with Functional Assays}, series = {PLOS ONE}, volume = {10}, journal = {PLOS ONE}, number = {12}, doi = {10.1371/journal.pone.0145478}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-136023}, pages = {e0145478}, year = {2015}, abstract = {Introduction The fast, precise, and accurate measurement of the new generation of oral anticoagulants such as dabigatran and rivaroxaban in patients' plasma my provide important information in different clinical circumstances such as in the case of suspicion of overdose, when patients switch from existing oral anticoagulant, in patients with hepatic or renal impairment, by concomitant use of interaction drugs, or to assess anticoagulant concentration in patients' blood before major surgery. Methods Here, we describe a quick and precise method to measure the coagulation inhibitors dabigatran and rivaroxaban using ultra-performance liquid chromatography electrospray ionization-tandem mass spectrometry in multiple reactions monitoring (MRM) mode (UPLC-MRM MS). Internal standards (ISs) were added to the sample and after protein precipitation; the sample was separated on a reverse phase column. After ionization of the analytes the ions were detected using electrospray ionization-tandem mass spectrometry. Run time was 2.5 minutes per injection. Ion suppression was characterized by means of post-column infusion. Results The calibration curves of dabigatran and rivaroxaban were linear over the working range between 0.8 and 800 mu g/L (r > 0.99). Limits of detection (LOD) in the plasma matrix were 0.21 mu g/L for dabigatran and 0.34 mu g/L for rivaroxaban, and lower limits of quantification (LLOQ) in the plasma matrix were 0.46 mu g/L for dabigatran and 0.54 mu g/L for rivaroxaban. The intraassay coefficients of variation (CVs) for dabigatran and rivaroxaban were < 4\% and 6\%; respectively, the interassay CVs were < 6\% for dabigatran and < 9\% for rivaroxaban. Inaccuracy was < 5\% for both substances. The mean recovery was 104.5\% (range 83.8-113.0\%) for dabigatran and 87.0\%(range 73.6-105.4\%) for rivaroxaban. No significant ion suppressions were detected at the elution times of dabigatran or rivaroxaban. Both coagulation inhibitors were stable in citrate plasma at -20 degrees C, 4 degrees C and even at RT for at least one week. A method comparison between our UPLC-MRM MS method, the commercially available automated Direct Thrombin Inhibitor assay (DTI assay) for dabigatran measurement from CoaChrom Diagnostica, as well as the automated anti-Xa assay for rivaroxaban measurement from Chromogenix both performed by ACL-TOP showed a high degree of correlation. However, UPLC-MRM MS measurement of dabigatran and rivaroxaban has a much better selectivity than classical functional assays measuring activities of various coagulation factors which are susceptible to interference by other coagulant drugs. Conclusions Overall, we developed and validated a sensitive and specific UPLC-MRM MS assay for the quick and specific measurement of dabigatran and rivaroxaban in human plasma.}, language = {en} } @article{SinghKingstonGuptaetal.2015, author = {Singh, Amit K. and Kingston, Joseph J. and Gupta, Shishir K. and Batra, Harsh V.}, title = {Recombinant Bivalent Fusion Protein rVE Induces CD4+ and CD8+ T-Cell Mediated Memory Immune Response for Protection Against Yersinia enterocolitica Infection}, series = {Frontiers in Microbiology}, volume = {6}, journal = {Frontiers in Microbiology}, number = {1407}, doi = {10.3389/fmicb.2015.01407}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-136114}, year = {2015}, abstract = {Studies investigating the correlates of immune protection against Yersinia infection have established that both humoral and cell mediated immune responses are required for the comprehensive protection. In our previous study, we established that the bivalent fusion protein (rVE) comprising immunologically active regions of Y pestis LcrV (100-270 aa) and YopE (50-213 aa) proteins conferred complete passive and active protection against lethal Y enterocolitica 8081 challenge. In the present study, cohort of BALB/c mice immunized with rVE or its component proteins rV, rE were assessed for cell mediated immune responses and memory immune protection against Y enterocolitica 8081 rVE immunization resulted in extensive proliferation of both CD4 and CD8 T cell subsets; significantly high antibody titer with balanced IgG1: IgG2a/IgG2b isotypes (1:1 ratio) and up regulation of both Th1 (INF-\(\alpha\), IFN-\(\gamma\), IL 2, and IL 12) and Th2 (IL 4) cytokines. On the other hand, rV immunization resulted in Th2 biased IgG response (11:1 ratio) and proliferation of CD4+ T-cell; rE group of mice exhibited considerably lower serum antibody titer with predominant Th1 response (1:3 ratio) and CD8+ T-cell proliferation. Comprehensive protection with superior survival (100\%) was observed among rVE immunized mice when compared to the significantly lower survival rates among rE (37.5\%) and rV (25\%) groups when IP challenged with Y enterocolitica 8081 after 120 days of immunization. Findings in this and our earlier studies define the bivalent fusion protein rVE as a potent candidate vaccine molecule with the capability to concurrently stimulate humoral and cell mediated immune responses and a proof of concept for developing efficient subunit vaccines against Gram negative facultative intracellular bacterial pathogens.}, language = {en} } @phdthesis{Ullmann2015, author = {Ullmann, Tobias}, title = {Characterization of Arctic Environment by Means of Polarimetric Synthetic Aperture Radar (PolSAR) Data and Digital Elevation Models (DEM)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-115719}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {The ecosystem of the high northern latitudes is affected by the recently changing environmental conditions. The Arctic has undergone a significant climatic change over the last decades. The land coverage is changing and a phenological response to the warming is apparent. Remotely sensed data can assist the monitoring and quantification of these changes. The remote sensing of the Arctic was predominantly carried out by the usage of optical sensors but these encounter problems in the Arctic environment, e.g. the frequent cloud cover or the solar geometry. In contrast, the imaging of Synthetic Aperture Radar is not affected by the cloud cover and the acquisition of radar imagery is independent of the solar illumination. The objective of this work was to explore how polarimetric Synthetic Aperture Radar (PolSAR) data of TerraSAR-X, TanDEM-X, Radarsat-2 and ALOS PALSAR and interferometric-derived digital elevation model data of the TanDEM-X Mission can contribute to collect meaningful information on the actual state of the Arctic Environment. The study was conducted for Canadian sites of the Mackenzie Delta Region and Banks Island and in situ reference data were available for the assessment. The up-to-date analysis of the PolSAR data made the application of the Non-Local Means filtering and of the decomposition of co-polarized data necessary. The Non-Local Means filter showed a high capability to preserve the image values, to keep the edges and to reduce the speckle. This supported not only the suitability for the interpretation but also for the classification. The classification accuracies of Non-Local Means filtered data were in average +10\% higher compared to unfiltered images. The correlation of the co- and quad-polarized decomposition features was high for classes with distinct surface or double bounce scattering and a usage of the co-polarized data is beneficial for regions of natural land coverage and for low vegetation formations with little volume scattering. The evaluation further revealed that the X- and C-Band were most sensitive to the generalized land cover classes. It was found that the X-Band data were sensitive to low vegetation formations with low shrub density, the C-Band data were sensitive to the shrub density and the shrub dominated tundra. In contrast, the L-Band data were less sensitive to the land cover. Among the different dual-polarized data the HH/VV-polarized data were identified to be most meaningful for the characterization and classification, followed by the HH/HV-polarized and the VV/VH-polarized data. The quad-polarized data showed highest sensitivity to the land cover but differences to the co-polarized data were small. The accuracy assessment showed that spectral information was required for accurate land cover classification. The best results were obtained when spectral and radar information was combined. The benefit of including radar data in the classification was up to +15\% accuracy and most significant for the classes wetland and sparse vegetated tundra. The best classifications were realized with quad-polarized C-Band and multispectral data and with co-polarized X-Band and multispectral data. The overall accuracy was up to 80\% for unsupervised and up to 90\% for supervised classifications. The results indicated that the shortwave co-polarized data show promise for the classification of tundra land cover since the polarimetric information is sensitive to low vegetation and the wetlands. Furthermore, co-polarized data provide a higher spatial resolution than the quad-polarized data. The analysis of the intermediate digital elevation model data of the TanDEM-X showed a high potential for the characterization of the surface morphology. The basic and relative topographic features were shown to be of high relevance for the quantification of the surface morphology and an area-wide application is feasible. In addition, these data were of value for the classification and delineation of landforms. Such classifications will assist the delineation of geomorphological units and have potential to identify locations of actual and future morphologic activity.}, subject = {Mackenzie-River-Delta}, language = {en} } @phdthesis{Winkler2015, author = {Winkler, Marco}, title = {On the Role of Triadic Substructures in Complex Networks}, publisher = {epubli GmbH}, address = {Berlin}, isbn = {978-3-7375-5654-5}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-116022}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {In the course of the growth of the Internet and due to increasing availability of data, over the last two decades, the field of network science has established itself as an own area of research. With quantitative scientists from computer science, mathematics, and physics working on datasets from biology, economics, sociology, political sciences, and many others, network science serves as a paradigm for interdisciplinary research. One of the major goals in network science is to unravel the relationship between topological graph structure and a network's function. As evidence suggests, systems from the same fields, i.e. with similar function, tend to exhibit similar structure. However, it is still vague whether a similar graph structure automatically implies likewise function. This dissertation aims at helping to bridge this gap, while particularly focusing on the role of triadic structures. After a general introduction to the main concepts of network science, existing work devoted to the relevance of triadic substructures is reviewed. A major challenge in modeling triadic structure is the fact that not all three-node subgraphs can be specified independently of each other, as pairs of nodes may participate in multiple of those triadic subgraphs. In order to overcome this obstacle, we suggest a novel class of generative network models based on so called Steiner triple systems. The latter are partitions of a graph's vertices into pair-disjoint triples (Steiner triples). Thus, the configurations on Steiner triples can be specified independently of each other without overdetermining the network's link structure. Subsequently, we investigate the most basic realization of this new class of models. We call it the triadic random graph model (TRGM). The TRGM is parametrized by a probability distribution over all possible triadic subgraph patterns. In order to generate a network instantiation of the model, for all Steiner triples in the system, a pattern is drawn from the distribution and adjusted randomly on the Steiner triple. We calculate the degree distribution of the TRGM analytically and find it to be similar to a Poissonian distribution. Furthermore, it is shown that TRGMs possess non-trivial triadic structure. We discover inevitable correlations in the abundance of certain triadic subgraph patterns which should be taken into account when attributing functional relevance to particular motifs - patterns which occur significantly more frequently than expected at random. Beyond, the strong impact of the probability distributions on the Steiner triples on the occurrence of triadic subgraphs over the whole network is demonstrated. This interdependence allows us to design ensembles of networks with predefined triadic substructure. Hence, TRGMs help to overcome the lack of generative models needed for assessing the relevance of triadic structure. We further investigate whether motifs occur homogeneously or heterogeneously distributed over a graph. Therefore, we study triadic subgraph structures in each node's neighborhood individually. In order to quantitatively measure structure from an individual node's perspective, we introduce an algorithm for node-specific pattern mining for both directed unsigned, and undirected signed networks. Analyzing real-world datasets, we find that there are networks in which motifs are distributed highly heterogeneously, bound to the proximity of only very few nodes. Moreover, we observe indication for the potential sensitivity of biological systems to a targeted removal of these critical vertices. In addition, we study whole graphs with respect to the homogeneity and homophily of their node-specific triadic structure. The former describes the similarity of subgraph distributions in the neighborhoods of individual vertices. The latter quantifies whether connected vertices are structurally more similar than non-connected ones. We discover these features to be characteristic for the networks' origins. Moreover, clustering the vertices of graphs regarding their triadic structure, we investigate structural groups in the neural network of C. elegans, the international airport-connection network, and the global network of diplomatic sentiments between countries. For the latter we find evidence for the instability of triangles considered socially unbalanced according to sociological theories. Finally, we utilize our TRGM to explore ensembles of networks with similar triadic substructure in terms of the evolution of dynamical processes acting on their nodes. Focusing on oscillators, coupled along the graphs' edges, we observe that certain triad motifs impose a clear signature on the systems' dynamics, even when embedded in a larger network structure.}, subject = {Netzwerk}, language = {en} } @inproceedings{AliMontenegro2015, author = {Ali, Qasim and Montenegro, Sergio}, title = {A Simple Approach to Quadrocopter Formation Flying Test Setup for Education and Development}, series = {INTED2015 Proceedings}, booktitle = {INTED2015 Proceedings}, publisher = {International Academy of Technology, Education and Development (IATED)}, isbn = {978-84-606-5763-7}, issn = {2340-1079}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-114495}, pages = {2776 -- 2784}, year = {2015}, abstract = {A simple test setup has been developed at Institute of Aerospace Information Technology, University of W{\"u}rzburg, Germany to realize basic functionalities for formation flight of quadrocopters. The test environment is planned to be utilized for developing and validating the algorithms for formation flying capability in real environment as well as for education purpose. An already existing test bed for single quadrocopter was extended with necessary inter-communication and distributed control mechanism to test the algorithms for formation flights in 2 degrees of freedom (roll / pitch). This study encompasses the domain of communication, control engineering and embedded systems programming. Bluetooth protocol has been used for inter-communication between two quadrocopters. A simple approach of PID control in combination with Kalman filter has been exploited. MATLAB Instrument Control Toolbox has been used for data display, plotting and analysis. Plots can be drawn in real-time and received information can also be stored in the form of files for later use and analysis. The test setup has been developed indigenously and at considerably low cost. Emphasis has been placed on simplicity to facilitate students learning process. Several lessons have been learnt during the course of development of this setup. Proposed setup is quite flexible that can be modified as per changing requirements.}, subject = {Flugk{\"o}rper}, language = {en} } @phdthesis{Hartmann2015, author = {Hartmann, Matthias}, title = {Optimization and Design of Network Architectures for Future Internet Routing}, issn = {1432-8801}, doi = {10.25972/OPUS-11416}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-114165}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {At the center of the Internet's protocol stack stands the Internet Protocol (IP) as a common denominator that enables all communication. To make routing efficient, resilient, and scalable, several aspects must be considered. Care must be taken that traffic is well balanced to make efficient use of the existing network resources, both in failure free operation and in failure scenarios. Finding the optimal routing in a network is an NP-complete problem. Therefore, routing optimization is usually performed using heuristics. This dissertation shows that a routing optimized with one objective function is often not good when looking at other objective functions. It can even be worse than unoptimized routing with respect to that objective function. After looking at failure-free routing and traffic distribution in different failure scenarios, the analysis is extended to include the loop-free alternate (LFA) IP fast reroute mechanism. Different application scenarios of LFAs are examined and a special focus is set on the fact that LFAs usually cannot protect all traffic in a network even against single link failures. Thus, the routing optimization for LFAs is targeted on both link utilization and failure coverage. Finally, the pre-congestion notification mechanism PCN for network admission control and overload protection is analyzed and optimized. Different design options for implementing the protocol are compared, before algorithms are developed for the calculation and optimization of protocol parameters and PCN-based routing. The second part of the thesis tackles a routing problem that can only be resolved on a global scale. The scalability of the Internet is at risk since a major and intensifying growth of the interdomain routing tables has been observed. Several protocols and architectures are analyzed that can be used to make interdomain routing more scalable. The most promising approach is the locator/identifier (Loc/ID) split architecture which separates routing from host identification. This way, changes in connectivity, mobility of end hosts, or traffic-engineering activities are hidden from the routing in the core of the Internet and the routing tables can be kept much smaller. All of the currently proposed Loc/ID split approaches have their downsides. In particular, the fact that most architectures use the ID for routing outside the Internet's core is a poor design, which inhibits many of the possible features of a new routing architecture. To better understand the problems and to provide a solution for a scalable routing design that implements a true Loc/ID split, the new GLI-Split protocol is developed in this thesis, which provides separation of global and local routing and uses an ID that is independent from any routing decisions. Besides GLI-Split, several other new routing architectures implementing Loc/ID split have been proposed for the Internet. Most of them assume that a mapping system is queried for EID-to-RLOC mappings by an intermediate node at the border of an edge network. When the mapping system is queried by an intermediate node, packets are already on their way towards their destination, and therefore, the mapping system must be fast, scalable, secure, resilient, and should be able to relay packets without locators to nodes that can forward them to the correct destination. The dissertation develops a classification for all proposed mapping system architectures and shows their similarities and differences. Finally, the fast two-level mapping system FIRMS is developed. It includes security and resilience features as well as a relay service for initial packets of a flow when intermediate nodes encounter a cache miss for the EID-to-RLOC mapping.}, subject = {Netzwerk}, language = {en} } @phdthesis{Freiberg2015, author = {Freiberg, Martina}, title = {UI-, User-, \& Usability-Oriented Engineering of Participative Knowledge-Based Systems}, publisher = {W{\"u}rzburg University Press}, isbn = {978-3-95826-012-2 (print)}, doi = {10.25972/WUP-978-3-95826-013-9}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-106072}, school = {W{\"u}rzburg University Press}, pages = {232}, year = {2015}, abstract = {Knowledge-based systems (KBS) face an ever-increasing interest in various disciplines and contexts. Yet, the former aim to construct the 'perfect intelligent software' continuously shifts to user-centered, participative solutions. Such systems enable users to contribute their personal knowledge to the problem solving process for increased efficiency and an ameliorated user experience. More precisely, we define non-functional key requirements of participative KBS as: Transparency (encompassing KBS status mediation), configurability (user adaptability, degree of user control/exploration), quality of the KB and UI, and evolvability (enabling the KBS to grow mature with their users). Many of those requirements depend on the respective target users, thus calling for a more user-centered development. Often, also highly expertise domains are targeted — inducing highly complex KBs — which requires a more careful and considerate UI/interaction design. Still, current KBS engineering (KBSE) approaches mostly focus on knowledge acquisition (KA) This often leads to non-optimal, little reusable, and non/little evaluated KBS front-end solutions. In this thesis we propose a more encompassing KBSE approach. Due to the strong mutual influences between KB and UI, we suggest a novel form of intertwined UI and KB development. We base the approach on three core components for encompassing KBSE: (1) Extensible prototyping, a tailored form of evolutionary prototyping; this builds on mature UI prototypes and offers two extension steps for the anytime creation of core KBS prototypes (KB + core UI) and fully productive KBS (core KBS prototype + common framing functionality). (2) KBS UI patterns, that define reusable solutions for the core KBS UI/interaction; we provide a basic collection of such patterns in this work. (3) Suitable usability instruments for the assessment of the KBS artifacts. Therewith, we do not strive for 'yet another' self-contained KBS engineering methodology. Rather, we motivate to extend existing approaches by the proposed key components. We demonstrate this based on an agile KBSE model. For practical support, we introduce the tailored KBSE tool ProKEt. ProKEt offers a basic selection of KBS core UI patterns and corresponding configuration options out of the box; their further adaption/extension is possible on various levels of expertise. For practical usability support, ProKEt offers facilities for quantitative and qualitative data collection. ProKEt explicitly fosters the suggested, intertwined development of UI and KB. For seamlessly integrating KA activities, it provides extension points for two selected external KA tools: For KnowOF, a standard office based KA environment. And for KnowWE, a semantic wiki for collaborative KA. Therewith, ProKEt offers powerful support for encompassing, user-centered KBSE. Finally, based on the approach and the tool, we also developed a novel KBS type: Clarification KBS as a mashup of consultation and justification KBS modules. Those denote a specifically suitable realization for participative KBS in highly expertise contexts and consequently require a specific design. In this thesis, apart from more common UI solutions, we particularly also introduce KBS UI patterns especially tailored towards Clarification KBS.}, subject = {Wissensbasiertes System}, language = {en} } @article{SirbuBeckerCaminitietal.2015, author = {S{\^i}rbu, Alina and Becker, Martin and Caminiti, Saverio and De Baets, Bernard and Elen, Bart and Francis, Louise and Gravino, Pietro and Hotho, Andreas and Ingarra, Stefano and Loreto, Vittorio and Molino, Andrea and Mueller, Juergen and Peters, Jan and Ricchiuti, Ferdinando and Saracino, Fabio and Servedio, Vito D.P. and Stumme, Gerd and Theunis, Jan and Tria, Francesca and Van den Bossche, Joris}, title = {Participatory Patterns in an International Air Quality Monitoring Initiative}, series = {PLoS ONE}, volume = {10}, journal = {PLoS ONE}, number = {8}, doi = {10.1371/journal. pone.0136763}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151379}, pages = {e0136763}, year = {2015}, abstract = {The issue of sustainability is at the top of the political and societal agenda, being considered of extreme importance and urgency. Human individual action impacts the environment both locally (e.g., local air/water quality, noise disturbance) and globally (e.g., climate change, resource use). Urban environments represent a crucial example, with an increasing realization that the most effective way of producing a change is involving the citizens themselves in monitoring campaigns (a citizen science bottom-up approach). This is possible by developing novel technologies and IT infrastructures enabling large citizen participation. Here, in the wider framework of one of the first such projects, we show results from an international competition where citizens were involved in mobile air pollution monitoring using low cost sensing devices, combined with a web-based game to monitor perceived levels of pollution. Measures of shift in perceptions over the course of the campaign are provided, together with insights into participatory patterns emerging from this study. Interesting effects related to inertia and to direct involvement in measurement activities rather than indirect information exposure are also highlighted, indicating that direct involvement can enhance learning and environmental awareness. In the future, this could result in better adoption of policies towards decreasing pollution.}, language = {en} } @article{AppelScholzMuelleretal.2015, author = {Appel, Mirjam and Scholz, Claus-J{\"u}rgen and M{\"u}ller, Tobias and Dittrich, Marcus and K{\"o}nig, Christian and Bockstaller, Marie and Oguz, Tuba and Khalili, Afshin and Antwi-Adjei, Emmanuel and Schauer, Tamas and Margulies, Carla and Tanimoto, Hiromu and Yarali, Ayse}, title = {Genome-Wide Association Analyses Point to Candidate Genes for Electric Shock Avoidance in Drosophila melanogaster}, series = {PLoS ONE}, volume = {10}, journal = {PLoS ONE}, number = {5}, doi = {10.1371/journal.pone.0126986}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-152006}, pages = {e0126986}, year = {2015}, abstract = {Electric shock is a common stimulus for nociception-research and the most widely used reinforcement in aversive associative learning experiments. Yet, nothing is known about the mechanisms it recruits at the periphery. To help fill this gap, we undertook a genome-wide association analysis using 38 inbred Drosophila melanogaster strains, which avoided shock to varying extents. We identified 514 genes whose expression levels and/or sequences covaried with shock avoidance scores. We independently scrutinized 14 of these genes using mutants, validating the effect of 7 of them on shock avoidance. This emphasizes the value of our candidate gene list as a guide for follow-up research. In addition, by integrating our association results with external protein-protein interaction data we obtained a shock avoidance- associated network of 38 genes. Both this network and the original candidate list contained a substantial number of genes that affect mechanosensory bristles, which are hairlike organs distributed across the fly's body. These results may point to a potential role for mechanosensory bristles in shock sensation. Thus, we not only provide a first list of candidate genes for shock avoidance, but also point to an interesting new hypothesis on nociceptive mechanisms.}, language = {en} } @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} } @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} } @phdthesis{Klein2014, author = {Klein, Dominik Werner}, title = {Design and Evaluation of Components for Future Internet Architectures}, issn = {1432-8801}, doi = {10.25972/OPUS-9313}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-93134}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {Die derzeitige Internetarchitektur wurde nicht in einem geplanten Prozess konzipiert und entwickelt, sondern hat vielmehr eine evolutionsartige Entwicklung hinter sich. Ausl{\"o}ser f{\"u}r die jeweiligen Evolutionsschritte waren dabei meist aufstrebende Anwendungen, welche neue Anforderungen an die zugrundeliegende Netzarchitektur gestellt haben. Um diese Anforderungen zu erf{\"u}llen, wurden h{\"a}ufig neuartige Dienste oder Protokolle spezifiziert und in die bestehende Architektur integriert. Dieser Prozess ist jedoch meist mit hohem Aufwand verbunden und daher sehr tr{\"a}ge, was die Entwicklung und Verbreitung innovativer Dienste beeintr{\"a}chtigt. Derzeitig diskutierte Konzepte wie Software-Defined Networking (SDN) oder Netzvirtualisierung (NV) werden als eine M{\"o}glichkeit angesehen, die Altlasten der bestehenden Internetarchitektur zu l{\"o}sen. Beiden Konzepten gemein ist die Idee, logische Netze {\"u}ber dem physikalischen Substrat zu betreiben. Diese logischen Netze sind hochdynamisch und k{\"o}nnen so flexibel an die Anforderungen der jeweiligen Anwendungen angepasst werden. Insbesondere erlaubt das Konzept der Virtualisierung intelligentere Netzknoten, was innovative neue Anwendungsf{\"a}lle erm{\"o}glicht. Ein h{\"a}ufig in diesem Zusammenhang diskutierter Anwendungsfall ist die Mobilit{\"a}t sowohl von Endger{\"a}ten als auch von Diensten an sich. Die Mobilit{\"a}t der Dienste wird hierbei ausgenutzt, um die Zugriffsverz{\"o}gerung oder die belegten Ressourcen im Netz zu reduzieren, indem die Dienste zum Beispiel in f{\"u}r den Nutzer geographisch nahe Datenzentren migriert werden. Neben den reinen Mechanismen bez{\"u}glich Dienst- und Endger{\"a}temobilit{\"a}t sind in diesem Zusammenhang auch geeignete {\"U}berwachungsl{\"o}sungen relevant, welche die vom Nutzer wahrgenommene Dienstg{\"u}te bewerten k{\"o}nnen. Diese L{\"o}sungen liefern wichtige Entscheidungshilfen f{\"u}r die Migration oder {\"u}berwachen m{\"o}gliche Effekte der Migration auf die erfahrene Dienstg{\"u}te beim Nutzer. Im Falle von Video Streaming erm{\"o}glicht ein solcher Anwendungsfall die flexible Anpassung der Streaming Topologie f{\"u}r mobile Nutzer, um so die Videoqualit{\"a}t unabh{\"a}ngig vom Zugangsnetz aufrechterhalten zu k{\"o}nnen. Im Rahmen dieser Doktorarbeit wird der beschriebene Anwendungsfall am Beispiel einer Video Streaming Anwendung n{\"a}her analysiert und auftretende Herausforderungen werden diskutiert. Des Weiteren werden L{\"o}sungsans{\"a}tze vorgestellt und bez{\"u}glich ihrer Effizienz ausgewertet. Im Detail besch{\"a}ftigt sich die Arbeit mit der Leistungsanalyse von Mechanismen f{\"u}r die Dienstmobilit{\"a}t und entwickelt eine Architektur zur Optimierung der Dienstmobilit{\"a}t. Im Bereich Endger{\"a}temobilit{\"a}t werden Verbesserungen entwickelt, welche die Latenz zwischen Endger{\"a}t und Dienst reduzieren oder die Konnektivit{\"a}t unabh{\"a}ngig vom Zugangsnetz gew{\"a}hrleisten. Im letzten Teilbereich wird eine L{\"o}sung zur {\"U}berwachung der Videoqualit{\"a}t im Netz entwickelt und bez{\"u}glich ihrer Genauigkeit analysiert.}, subject = {Leistungsbewertung}, language = {en} } @phdthesis{Fink2014, author = {Fink, Martin}, title = {Crossings, Curves, and Constraints in Graph Drawing}, publisher = {W{\"u}rzburg University Press}, isbn = {978-3-95826-002-3 (print)}, doi = {10.25972/WUP-978-3-95826-003-0}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-98235}, school = {W{\"u}rzburg University Press}, pages = {222}, year = {2014}, abstract = {In many cases, problems, data, or information can be modeled as graphs. Graphs can be used as a tool for modeling in any case where connections between distinguishable objects occur. Any graph consists of a set of objects, called vertices, and a set of connections, called edges, such that any edge connects a pair of vertices. For example, a social network can be modeled by a graph by transforming the users of the network into vertices and friendship relations between users into edges. Also physical networks like computer networks or transportation networks, for example, the metro network of a city, can be seen as graphs. For making graphs and, thereby, the data that is modeled, well-understandable for users, we need a visualization. Graph drawing deals with algorithms for visualizing graphs. In this thesis, especially the use of crossings and curves is investigated for graph drawing problems under additional constraints. The constraints that occur in the problems investigated in this thesis especially restrict the positions of (a part of) the vertices; this is done either as a hard constraint or as an optimization criterion.}, subject = {Graphenzeichnen}, language = {en} } @phdthesis{Jarschel2014, author = {Jarschel, Michael}, title = {An Assessment of Applications and Performance Analysis of Software Defined Networking}, issn = {1432-8801}, doi = {10.25972/OPUS-10079}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-100795}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {With the introduction of OpenFlow by the Stanford University in 2008, a process began in the area of network research, which questions the predominant approach of fully distributed network control. OpenFlow is a communication protocol that allows the externalization of the network control plane from the network devices, such as a router, and to realize it as a logically-centralized entity in software. For this concept, the term "Software Defined Networking" (SDN) was coined during scientific discourse. For the network operators, this concept has several advantages. The two most important can be summarized under the points cost savings and flexibility. Firstly, it is possible through the uniform interface for network hardware ("Southbound API"), as implemented by OpenFlow, to combine devices and software from different manufacturers, which increases the innovation and price pressure on them. Secondly, the realization of the network control plane as a freely programmable software with open interfaces ("Northbound API") provides the opportunity to adapt it to the individual circumstances of the operator's network and to exchange information with the applications it serves. This allows the network to be more flexible and to react more quickly to changing circumstances as well as transport the traffic more effectively and tailored to the user's "Quality of Experience" (QoE). The approach of a separate network control layer for packet-based networks is not new and has already been proposed several times in the past. Therefore, the SDN approach has raised many questions about its feasibility in terms of efficiency and applicability. These questions are caused to some extent by the fact that there is no generally accepted definition of the SDN concept to date. It is therefore a part of this thesis to derive such a definition. In addition, several of the open issues are investigated. This Investigations follow the three aspects: Performance Evaluation of Software Defined Networking, applications on the SDN control layer, and the usability of SDN Northbound-API for creation application-awareness in network operation. Performance Evaluation of Software Defined Networking: The question of the efficiency of an SDN-based system was from the beginning one of the most important. In this thesis, experimental measurements of the performance of OpenFlow-enabled switch hardware and control software were conducted for the purpose of answering this question. The results of these measurements were used as input parameters for establishing an analytical model of the reactive SDN approach. Through the model it could be determined that the performance of the software control layer, often called "Controller", is crucial for the overall performance of the system, but that the approach is generally viable. Based on this finding a software for analyzing the performance of SDN controllers was developed. This software allows the emulation of the forwarding layer of an SDN network towards the control software and can thus determine its performance in different situations and configurations. The measurements with this software showed that there are quite significant differences in the behavior of different control software implementations. Among other things it has been shown that some show different characteristics for various switches, in particular in terms of message processing speed. Under certain circumstances this can lead to network failures. Applications on the SDN control layer: The core piece of software defined networking are the intelligent network applications that operate on the control layer. However, their development is still in its infancy and little is known about the technical possibilities and their limitations. Therefore, the relationship between an SDN-based and classical implementation of a network function is investigated in this thesis. This function is the monitoring of network links and the traffic they carry. A typical approach for this task has been built based on Wiretapping and specialized measurement hardware and compared with an implementation based on OpenFlow switches and a special SDN control application. The results of the comparison show that the SDN version can compete in terms of measurement accuracy for bandwidth and delay estimation with the traditional measurement set-up. However, a compromise has to be found for measurements below the millisecond range. Another question regarding the SDN control applications is whether and how well they can solve existing problems in networks. Two programs have been developed based on SDN in this thesis to solve two typical network issues. Firstly, the tool "IPOM", which enables considerably more flexibility in the study of effects of network structures for a researcher, who is confined to a fixed physical test network topology. The second software provides an interface between the Cloud Orchestration Software "OpenNebula" and an OpenFlow controller. The purpose of this software was to investigate experimentally whether a pre-notification of the network of an impending relocation of a virtual service in a data center is sufficient to ensure the continuous operation of that service. This was demonstrated on the example of a video service. Usability of the SDN Northbound API for creating application-awareness in network operation: Currently, the fact that the network and the applications that run on it are developed and operated separately leads to problems in network operation. SDN offers with the Northbound-API an open interface that enables the exchange between information of both worlds during operation. One aim of this thesis was to investigate whether this interface can be exploited so that the QoE experienced by the user can be maintained on high level. For this purpose, the QoE influence factors were determined on a challenging application by means of a subjective survey study. The application is cloud gaming, in which the calculation of video game environments takes place in the cloud and is transported via video over the network to the user. It was shown that apart from the most important factor influencing QoS, i.e., packet loss on the downlink, also the type of game type and its speed play a role. This demonstrates that in addition to QoS the application state is important and should be communicated to the network. Since an implementation of such a state conscious SDN for the example of Cloud Gaming was not possible due to its proprietary implementation, in this thesis the application "YouTube video streaming" was chosen as an alternative. For this application, status information is retrievable via the "Yomo" tool and can be used for network control. It was shown that an SDN-based implementation of an application-aware network has distinct advantages over traditional network management methods and the user quality can be obtained in spite of disturbances.}, subject = {Leistungsbewertung}, language = {en} } @phdthesis{Hock2014, author = {Hock, David Rog{\´e}r}, title = {Analysis and Optimization of Resilient Routing in Core Communication Networks}, issn = {1432-8801}, doi = {10.25972/OPUS-10168}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-101681}, school = {Universit{\"a}t W{\"u}rzburg}, pages = {175}, year = {2014}, abstract = {Routing is one of the most important issues in any communication network. It defines on which path packets are transmitted from the source of a connection to the destination. It allows to control the distribution of flows between different locations in the network and thereby is a means to influence the load distribution or to reach certain constraints imposed by particular applications. As failures in communication networks appear regularly and cannot be completely avoided, routing is required to be resilient against such outages, i.e., routing still has to be able to forward packets on backup paths even if primary paths are not working any more. Throughout the years, various routing technologies have been introduced that are very different in their control structure, in their way of working, and in their ability to handle certain failure cases. Each of the different routing approaches opens up their own specific questions regarding configuration, optimization, and inclusion of resilience issues. This monograph investigates, with the example of three particular routing technologies, some concrete issues regarding the analysis and optimization of resilience. It thereby contributes to a better general, technology-independent understanding of these approaches and of their diverse potential for the use in future network architectures. The first considered routing type, is decentralized intra-domain routing based on administrative IP link costs and the shortest path principle. Typical examples are common today's intra-domain routing protocols OSPF and IS-IS. This type of routing includes automatic restoration abilities in case of failures what makes it in general very robust even in the case of severe network outages including several failed components. Furthermore, special IP-Fast Reroute mechanisms allow for a faster reaction on outages. For routing based on link costs, traffic engineering, e.g. the optimization of the maximum relative link load in the network, can be done indirectly by changing the administrative link costs to adequate values. The second considered routing type, MPLS-based routing, is based on the a priori configuration of primary and backup paths, so-called Label Switched Paths. The routing layout of MPLS paths offers more freedom compared to IP-based routing as it is not restricted by any shortest path constraints but any paths can be setup. However, this in general involves a higher configuration effort. Finally, in the third considered routing type, typically centralized routing using a Software Defined Networking (SDN) architecture, simple switches only forward packets according to routing decisions made by centralized controller units. SDN-based routing layouts offer the same freedom as for explicit paths configured using MPLS. In case of a failure, new rules can be setup by the controllers to continue the routing in the reduced topology. However, new resilience issues arise caused by the centralized architecture. If controllers are not reachable anymore, the forwarding rules in the single nodes cannot be adapted anymore. This might render a rerouting in case of connection problems in severe failure scenarios infeasible.}, subject = {Leistungsbewertung}, language = {en} } @article{Hurtienne2013, author = {Hurtienne, J{\"o}rn}, title = {Inter-coder reliability of categorising force-dynamic events in human-technology interaction}, volume = {1}, number = {1}, issn = {2197-2796}, doi = {10.1515/gcla-2013-0005}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-194127}, pages = {59-78}, year = {2013}, abstract = {Two studies are reported that investigate how readily accessible and applicable ten force-dynamic categories are to novices in describing short episodes of human-technology interaction (Study 1) and that establish a measure of inter-coder reliability when re-classifying these episodes into force-dynamic categories (Study 2). The results of the first study show that people can easily and confidently relate their experiences with technology to the definitions of force-dynamic events (e.g. "The driver released the handbrake" as an example of restraint removal). The results of the second study show moderate agreement between four expert coders across all ten force-dynamic categories (Cohen's kappa = .59) when re-classifying these episodes. Agreement values for single force-dynamic categories ranged between 'fair' and 'almost perfect', i.e. between kappa = .30 and .95. Agreement with the originally intended classifications of study 1 was higher than the pure inter-coder reliabilities. Single coders achieved an average kappa of .71, indicating substantial agreement. Using more than one coder increased kappas to almost perfect: up to .87 for four coders. A qualitative analysis of the predicted versus the observed number of category confusions revealed that about half of the category disagreement could be predicted from strong overlaps in the definitions of force-dynamic categories. From the quantitative and qualitative results, guidelines are derived to aid the better training of coders in order to increase inter-coder reliability.}, language = {en} } @phdthesis{Lehrieder2013, author = {Lehrieder, Frank}, title = {Performance Evaluation and Optimization of Content Distribution using Overlay Networks}, doi = {10.25972/OPUS-6420}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-76018}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2013}, abstract = {The work presents a performance evaluation and optimization of so-called overlay networks for content distribution in the Internet. Chapter 1 describes the importance which have such networks in today's Internet, for example, for the transmission of video content. The focus of this work is on overlay networks based on the peer-to-peer principle. These are characterized by the fact that users who download content, also contribute to the distribution process by sharing parts of the data to other users. This enables efficient content distribution because each user not only consumes resources in the system, but also provides its own resources. Chapter 2 of the monograph contains a detailed description of the functionality of today's most popular overlay network BitTorrent. It explains the various components and their interaction. This is followed by an illustration of why such overlay networks for Internet service providers (ISPs) are problematic. The reason lies in the large amount of inter-ISP traffic that is produced by these overlay networks. Since this inter-ISP traffic leads to high costs for ISPs, they try to reduce it by improved mechanisms for overlay networks. One optimization approach is the use of topology awareness within the overlay networks. It provides users of the overlay networks with information about the underlying physical network topology. This allows them to avoid inter-ISP traffic by exchanging data preferrentially with other users that are connected to the same ISP. Another approach to save inter-ISP traffic is caching. In this case the ISP provides additional computers in its network, called caches, which store copies of popular content. The users of this ISP can then obtain such content from the cache. This prevents that the content must be retrieved from locations outside of the ISP's network, and saves costly inter-ISP traffic in this way. In the third chapter of the thesis, the results of a comprehensive measurement study of overlay networks, which can be found in today's Internet, are presented. After a short description of the measurement methodology, the results of the measurements are described. These results contain data on a variety of characteristics of current P2P overlay networks in the Internet. These include the popularity of content, i.e., how many users are interested in specific content, the evolution of the popularity and the size of the files. The distribution of users within the Internet is investigated in detail. Special attention is given to the number of users that exchange a particular file within the same ISP. On the basis of these measurement results, an estimation of the traffic savings that can achieved by topology awareness is derived. This new estimation is of scientific and practical importance, since it is not limited to individual ISPs and files, but considers the whole Internet and the total amount of data exchanged in overlay networks. Finally, the characteristics of regional content are considered, in which the popularity is limited to certain parts of the Internet. This is for example the case of videos in German, Italian or French language. Chapter 4 of the thesis is devoted to the optimization of overlay networks for content distribution through caching. It presents a deterministic flow model that describes the influence of caches. On the basis of this model, it derives an estimate of the inter-ISP traffic that is generated by an overlay network, and which part can be saved by caches. The results show that the influence of the cache depends on the structure of the overlay networks, and that caches can also lead to an increase in inter-ISP traffic under certain circumstances. The described model is thus an important tool for ISPs to decide for which overlay networks caches are useful and to dimension them. Chapter 5 summarizes the content of the work and emphasizes the importance of the findings. In addition, it explains how the findings can be applied to the optimization of future overlay networks. Special attention is given to the growing importance of video-on-demand and real-time video transmissions.}, subject = {Leistungsbewertung}, 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{KarlDandekar2013, author = {Karl, Stefan and Dandekar, Thomas}, title = {Jimena: Efficient computing and system state identification for genetic regulatory networks}, series = {BMC Bioinformatics}, volume = {14}, journal = {BMC Bioinformatics}, doi = {10.1186/1471-2105-14-306}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-128671}, year = {2013}, abstract = {Background: Boolean networks capture switching behavior of many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states is necessary. The high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such as apoptosis or proliferation allows for the modeling of a wider range of node interactions than continuous activator-inhibitor models, but suffers from scaling problems for networks which contain nodes with more than ~10 inputs. Many GRNs from literature or new gene expression experiments exceed those limitations and a new approach was developed. Results: (i) As a part of our new GRN simulation framework Jimena we introduce and setup Boolean-tree-based data structures; (ii) corresponding algorithms greatly expedite the calculation of the polynomial interpolation in almost all cases, thereby expanding the range of networks which can be simulated by this model in reasonable time. (iii) Stable states for discrete models are efficiently counted and identified using binary decision diagrams. As application example, we show how system states can now be sampled efficiently in small up to large scale hormone disease networks (Arabidopsis thaliana development and immunity, pathogen Pseudomonas syringae and modulation by cytokinins and plant hormones). Conclusions: Jimena simulates currently available GRNs about 10-100 times faster than the previous implementation of the polynomial interpolation model and even greater gains are achieved for large scale-free networks. This speed-up also facilitates a much more thorough sampling of continuous state spaces which may lead to the identification of new stable states. Mutants of large networks can be constructed and analyzed very quickly enabling new insights into network robustness and behavior.}, language = {en} } @article{GageikStrohmeierMontenegro2013, author = {Gageik, Nils and Strohmeier, Michael and Montenegro, Sergio}, title = {Waypoint flight parameter comparison of an autonomous UAV}, series = {International Journal of Artificial Intelligence \& Applications (IJAIA)}, journal = {International Journal of Artificial Intelligence \& Applications (IJAIA)}, doi = {10.5121/ijaia.2013.4304}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-96833}, year = {2013}, abstract = {The present paper compares the effect of different waypoint parameters on the flight performance of a special autonomous indoor UAV (unmanned aerial vehicle) fusing ultrasonic, inertial, pressure and optical sensors for 3D positioning and controlling. The investigated parameters are the acceptance threshold for reaching a waypoint as well as the maximal waypoint step size or block size. The effect of these parameters on the flight time and accuracy of the flight path is investigated. Therefore the paper addresses how the acceptance threshold and step size influence the speed and accuracy of the autonomous flight and thus influence the performance of the presented autonomous quadrocopter under real indoor navigation circumstances. Furthermore the paper demonstrates a drawback of the standard potential field method for navigation of such autonomous quadrocopters and points to an improvement.}, language = {en} } @article{GageikStrohmeierMontenegro2013, author = {Gageik, Nils and Strohmeier, Michael and Montenegro, Sergio}, title = {An Autonomous UAV with an Optical Flow Sensor for Positioning and Navigation}, series = {International Journal of Advanced Robotic Systems}, journal = {International Journal of Advanced Robotic Systems}, doi = {10.5772/56813}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-96368}, year = {2013}, abstract = {A procedure to control all six DOF (degrees of freedom) of a UAV (unmanned aerial vehicle) without an external reference system and to enable fully autonomous flight is presented here. For 2D positioning the principle of optical flow is used. Together with the output of height estimation, fusing ultrasonic, infrared and inertial and pressure sensor data, the 3D position of the UAV can be computed, controlled and steered. All data processing is done on the UAV. An external computer with a pathway planning interface is for commanding purposes only. The presented system is part of the AQopterI8 project, which aims to develop an autonomous flying quadrocopter for indoor application. The focus of this paper is 2D positioning using an optical flow sensor. As a result of the performed evaluation, it can be concluded that for position hold, the standard deviation of the position error is 10cm and after landing the position error is about 30cm.}, language = {en} } @phdthesis{Herrmann2013, author = {Herrmann, Christian}, title = {Robotic Motion Compensation for Applications in Radiation Oncology}, isbn = {978-3-923959-88-4}, doi = {10.25972/OPUS-6727}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-79045}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2013}, abstract = {Aufgrund vieler Verbesserungen der Behandlungsmethoden im Laufe der letzten 60 Jahre, erlaubt die Strahlentherapie heutzutage pr{\"a}zise Behandlungen von statischen Tumoren. Jedoch birgt die Bestrahlung von sich bewegenden Tumoren noch große Herausforderungen in sich, da bewegliche Tumore oft den Behandlungsstrahl verlassen. Dabei reduziert sich die Strahlendosis im Tumor w{\"a}hrend sich diese im umliegenden gesunden Gewebe erh{\"o}ht. Diese Forschungsarbeit zielt darauf ab, die Grenzen der Strahlentherapie zu erweitern, um pr{\"a}zise Behandlungen von beweglichen Tumoren zu erm{\"o}glichen. Der Fokus der Arbeit liegt auf der Erstellung eines Echtzeitsystems zur aktiven Kompensation von Tumorbewegungen durch robotergest{\"u}tzte Methoden. W{\"a}hrend Behandlungen befinden sich Patienten auf einer Patientenliege, mit der statische Lagerungsfehler vor Beginn einer Behandlung korrigiert werden. Die in dieser Arbeit verwendete Patientenliege "HexaPOD" ist ein paralleler Manipulator mit sechs Freiheitsgraden, der große Lasten innerhalb eines eingeschr{\"a}nkten Arbeitsbereichs pr{\"a}zise positionieren kann. Obwohl der HexaPOD urspr{\"u}nglich nicht f{\"u}r dynamische Anwendungen konzipiert wurde, wird dieser f{\"u}r eine dauerhafte Bewegungskompensation eingesetzt, in dem Patienten so bewegt werden, dass Tumore pr{\"a}zise im Zentralstrahl w{\"a}hrend der Dauer einer gesamten Behandlung verbleiben. Um ein echtzeitf{\"a}higes Kompensationssystem auf Basis des HexaPODs zu realisieren, muss eine Reihe an Herausforderungen bew{\"a}ltigt werden. Echtzeitaspekte werden einerseits durch die Verwendung eines harten Echtzeitbetriebssystems abgedeckt, andererseits durch die Messung und Sch{\"a}tzung von Latenzzeiten aller physikalischen Gr{\"o}ßen im System, z.B. Messungen der Tumor- und Atemposition. Neben der konsistenten und durchg{\"a}ngigen Ber{\"u}cksichtigung von akkuraten Zeitinformation, werden alle software-induzierten Latenzen adaptiv ausgeglichen. Dies erfordert Vorhersagen der Tumorposition in die nahe Zukunft. Zahlreiche Pr{\"a}diktoren zur Atem- und Tumorpositionsvorhersage werden vorgeschlagen und anhand verschiedenster Metriken evaluiert. Erweiterungen der Pr{\"a}diktionsalgorithmen werden eingef{\"u}hrt, die sowohl Atem- als auch Tumorpositionsinformationen fusionieren, um Vorhersagen ohne explizites Korrelationsmodell zu erm{\"o}glichen. Die Vorhersagen bestimmen den zuk{\"u}nftigen Bewegungspfad des HexaPODs, um Tumorbewegungen zu kompensieren. Dazu werden verschiedene Regler entwickelt, die eine Trajektorienverfolgung mit dem HexaPOD erm{\"o}glichen. Auf der Basis von linearer und nicht-linearer dynamischer Modellierung des HexaPODs mit Methoden der Systemidentifikation, wird zun{\"a}chst ein modellpr{\"a}diktiver Regler entwickelt. Ein zweiter Regler wird auf Basis einer Annahme {\"u}ber das Arbeitsprinzip des internen Reglers im HexaPOD entworfen. Schließlich wird ein dritter Regler vorgeschlagen, der beide vorhergehenden Regler miteinander kombiniert. F{\"u}r jeden dieser Regler werden vergleichende Ergebnisse aus Experimenten mit realer Hardware und menschlichen Versuchspersonen pr{\"a}sentiert und diskutiert. Dar{\"u}ber hinaus wird die geeignete Wahl von freien Parametern in den Reglern vorgestellt. Neben einer pr{\"a}zisen Verfolgung der Referenztrajektorie spielt der Patientenkomfort eine entscheidende Rolle f{\"u}r die Akzeptanz des Systems. Es wird gezeigt, dass die Regler glatte Trajektorien realisieren k{\"o}nnen, um zu garantieren, dass sich Patienten wohl f{\"u}hlen w{\"a}hrend ihre Tumorbewegung mit Genauigkeiten im Submillimeterbereich ausgeglichen wird. Gesamtfehler werden im Kompensationssystem analysiert, in dem diese zu Trajektorienverfolgungsfehlern und Pr{\"a}diktionsfehlern in Beziehung gesetzt werden. Durch Ausnutzung von Eigenschaften verschiedener Pr{\"a}diktoren wird gezeigt, dass die Startzeit des Systems bis die Verfolgung der Referenztrajektorie erreicht ist, wenige Sekunden betr{\"a}gt. Dies gilt insbesondere f{\"u}r den Fall eines initial ruhenden HexaPODs und ohne Vorwissen {\"u}ber Tumorbewegungen. Dies zeigt die Eignung des Systems f{\"u}r die sehr kurz fraktionierten Behandlungen von Lungentumoren. Das Tumorkompensationssystem wurde ausschließlich auf Basis von klinischer Standard-Hardware entwickelt, die in vielen Behandlungsr{\"a}umen zu finden ist. Durch ein einfaches und flexibles Design k{\"o}nnen Behandlungsr{\"a}ume in kosteneffizienter Weise um M{\"o}glichkeiten der Bewegungskompensation erg{\"a}nzt werden. Dar{\"u}ber hinaus werden aktuelle Behandlungsmethoden wie intensit{\"a}tsmodulierte Strahlentherapie oder Volumetric Modulated Arc Therapy in keiner Weise eingeschr{\"a}nkt. Aufgrund der Unterst{\"u}tzung verschiedener Kompensationsmodi kann das System auf alle beweglichen Tumore angewendet werden, unabh{\"a}ngig davon ob die Bewegungen vorhersagbar (Lungentumore) oder nicht vorhersagbar (Prostatatumore) sind. Durch Integration von geeigneten Methoden zur Tumorpositionsbestimmung kann das System auf einfache Weise zur Kompensation von anderen Tumoren erweitert werden.}, subject = {Robotik}, language = {en} } @phdthesis{Baunach2012, author = {Baunach, Marcel}, title = {Advances in Distributed Real-Time Sensor/Actuator Systems Operation - Operating Systems, Communication, and Application Design Concepts -}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-76489}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {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!}, subject = {Eingebettetes System}, language = {en} } @phdthesis{Dang2012, author = {Dang, Nghia Duc}, title = {Konzeption und Evaluation eines hybriden, skalierbaren Werkzeugs zur mechatronischen Systemdiagnose am Beispiel eines Diagnosesystems f{\"u}r freie Kfz-Werkst{\"a}tten}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-70774}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {Die Entwicklung eines wissensbasierten Systems, speziell eines Diagnosesystems, ist eine Teildisziplin der k{\"u}nstlichen Intelligenz und angewandten Informatik. Im Laufe der Forschung auf diesem Gebiet wurden verschiedene L{\"o}sungsans{\"a}tze mit unterschiedlichem Erfolg bei der Anwendung in der Kraftfahrzeugdiagnose entwickelt. Diagnosesysteme in Vertragswerkst{\"a}tten, das heißt in Fahrzeughersteller gebundenen Werkst{\"a}tten, wenden haupts{\"a}chlich die fallbasierte Diagnostik an. Zum einen h{\"a}lt sich hier die Fahrzeugvielfalt in Grenzen und zum anderen besteht eine Meldepflicht bei neuen, nicht im System vorhandenen F{\"a}llen. Die freien Werkst{\"a}tten verf{\"u}gen nicht {\"u}ber eine solche Datenbank. Somit ist der fallbasierte Ansatz schwer umsetzbar. In freien Werkst{\"a}tten - Fahrzeughersteller unabh{\"a}ngigen Werkst{\"a}tten - basiert die Fehlersuche haupts{\"a}chlich auf Fehlerb{\"a}umen. Wegen der wachsenden Fahrzeugkomplexit{\"a}t, welche wesentlich durch die stark zunehmende Anzahl der durch mechatronische Systeme realisierten Funktionen bedingt ist, und der steigenden Typenvielfalt ist die gef{\"u}hrte Fehlersuche in freien Werkst{\"a}tten nicht immer zielf{\"u}hrend. Um die Unterst{\"u}tzung des Personals von freien Werkst{\"a}tten bei der zuk{\"u}nftigen Fehlersuche zu gew{\"a}hrleisten, werden neue Generationen von herstellerunabh{\"a}ngigen Diagnosetools ben{\"o}tigt, die die Probleme der Variantenvielfalt und Komplexit{\"a}t l{\"o}sen. In der vorliegenden Arbeit wird ein L{\"o}sungsansatz 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 f{\"u}r die erstellten Diagnosemodelle behandelt. Die Diagnose ist symptombasiert und die Inferenzmechanismen zur Verarbeitung des Diagnosewissens sind eine Kombination aus Propagierung der abweichenden physikalischen Gr{\"o}ßen 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 Werkst{\"a}tten. Die Evaluierung der entwickelten L{\"o}sung bei der Wissenserhebung in Form von Modellerstellungen und Modellierungsworkshops sowie Feldtests dient nicht nur zur Best{\"a}tigung des entwickelten Ansatzes, sondern auch zur Ideenfindung f{\"u}r die Integration der entwickelten Tools in die existierende IT-Infrastruktur.}, subject = {Diagnosesystem}, language = {de} } @phdthesis{Zinner2012, author = {Zinner, Thomas}, title = {Performance Modeling of QoE-Aware Multipath Video Transmission in the Future Internet}, doi = {10.25972/OPUS-6106}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-72324}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {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.}, subject = {Video{\"u}bertragung}, language = {en} } @phdthesis{Schroeter2012, author = {Schr{\"o}ter, Martin}, title = {Newton Methods for Image Registration}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-71490}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {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.}, subject = {Newton-Verfahren}, 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} } @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} } @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} } @article{KruegerFriedrichFoersteretal.2012, author = {Krueger, Beate and Friedrich, Torben and F{\"o}rster, Frank and Bernhardt, J{\"o}rg and Gross, Roy and Dandekar, Thomas}, title = {Different evolutionary modifications as a guide to rewire two-component systems}, series = {Bioinformatics and Biology Insights}, volume = {6}, journal = {Bioinformatics and Biology Insights}, doi = {10.4137/BBI.S9356}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-123647}, pages = {97-128}, year = {2012}, abstract = {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.}, language = {en} } @article{MergetKoetschanHackletal.2012, author = {Merget, Benjamin and Koetschan, Christian and Hackl, Thomas and F{\"o}rster, Frank and Dandekar, Thomas and M{\"u}ller, Tobias and Schultz, J{\"o}rg and Wolf, Matthias}, title = {The ITS2 Database}, series = {Journal of Visual Expression}, volume = {61}, journal = {Journal of Visual Expression}, number = {e3806}, doi = {10.3791/3806}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124600}, year = {2012}, abstract = {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.}, language = {en} } @article{BuchinBuchinByrkaetal.2012, author = {Buchin, Kevin and Buchin, Maike and Byrka, Jaroslaw and N{\"o}llenburg, Martin and Okamoto, Yoshio and Silveira, Rodrigo I. and Wolff, Alexander}, title = {Drawing (Complete) Binary Tanglegrams}, series = {Algorithmica}, volume = {62}, journal = {Algorithmica}, doi = {10.1007/s00453-010-9456-3}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124622}, pages = {309-332}, year = {2012}, abstract = {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.}, language = {en} } @article{StaigerCadotKooteretal.2012, author = {Staiger, Christine and Cadot, Sidney and Kooter, Raul and Dittrich, Marcus and M{\"u}ller, Tobias and Klau, Gunnar W. and Wessels, Lodewyk F. A.}, title = {A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer}, series = {PLoS One}, volume = {7}, journal = {PLoS One}, number = {4}, doi = {10.1371/journal.pone.0034796}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-131323}, pages = {e34796}, year = {2012}, abstract = {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.}, language = {en} } @article{NaseemDandekar2012, author = {Naseem, Muhammad and Dandekar, Thomas}, title = {The Role of Auxin-Cytokinin Antagonism in Plant-Pathogen Interactions}, series = {PLOS Pathogens}, volume = {8}, journal = {PLOS Pathogens}, number = {11}, doi = {10.1371/journal.ppat.1003026}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-131901}, pages = {e1003026}, year = {2012}, abstract = {No abstract available.}, language = {en} } @article{SchokraieWarnkenHotzWagenblattetal.2012, author = {Schokraie, Elham and Warnken, Uwe and Hotz-Wagenblatt, Agnes and Grohme, Markus A. and Hengherr, Steffen and F{\"o}rster, Frank and Schill, Ralph O. and Frohme, Marcus and Dandekar, Thomas and Schn{\"o}lzer, Martina}, title = {Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state}, series = {PLoS One}, volume = {7}, journal = {PLoS One}, number = {9}, doi = {10.1371/journal.pone.0045682}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134447}, pages = {e45682}, year = {2012}, abstract = {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.}, language = {en} } @article{BugaScholzKumaretal.2012, author = {Buga, Ana-Maria and Scholz, Claus J{\"u}rgen and Kumar, Senthil and Herndon, James G. and Alexandru, Dragos and Cojocaru, Gabriel Radu and Dandekar, Thomas and Popa-Wagner, Aurel}, title = {Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke}, series = {PLoS One}, volume = {7}, journal = {PLoS One}, number = {12}, doi = {10.1371/journal.pone.0050985}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-130657}, pages = {e50985}, year = {2012}, abstract = {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.}, language = {en} } @article{BoehlerCreignouGalotaetal.2012, author = {B{\"o}hler, Elmar and Creignou, Nadia and Galota, Matthias and Reith, Steffen and Schnoor, Henning and Vollmer, Heribert}, title = {Complexity Classifications for Different Equivalence and Audit Problems for Boolean Circuits}, series = {Logical Methods in Computer Science}, volume = {8}, journal = {Logical Methods in Computer Science}, number = {3:27}, doi = {10.2168/LMCS-8(3:27)2012}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-131121}, pages = {1 -- 25}, year = {2012}, abstract = {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.}, language = {en} } @article{AtienzadeCastroCortesetal.2012, author = {Atienza, Nieves and de Castro, Natalia and Cort{\´e}s, Carmen and Garrido, M. {\´A}ngeles and Grima, Clara I. and Hern{\´a}ndez, Gregorio and M{\´a}rquez, Alberto and Moreno-Gonz{\´a}lez, Auxiliadora and N{\"o}llenburg, Martin and Portillo, Jos{\´e} Ram{\´o}n and Reyes, Pedro and Valenzuela, Jes{\´u}s and Trinidad Villar, Maria and Wolff, Alexander}, title = {Cover contact graphs}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-78845}, year = {2012}, abstract = {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.}, subject = {Informatik}, language = {de} } @article{WolffRutter2012, author = {Wolff, Alexander and Rutter, Iganz}, title = {Augmenting the Connectivity of Planar and Geometric Graphs}, series = {Journal of Graph Algorithms and Applications}, journal = {Journal of Graph Algorithms and Applications}, doi = {10.7155/jgaa.00275}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-97587}, year = {2012}, abstract = {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.}, language = {en} } @article{BuchheimKellerKoetschanetal.2011, author = {Buchheim, Mark A. and Keller, Alexander and Koetschan, Christian and F{\"o}rster, Frank and Merget, Benjamin and Wolf, Matthias}, title = {Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life}, series = {PLoS ONE}, volume = {6}, journal = {PLoS ONE}, number = {2}, doi = {10.1371/journal.pone.0016931}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-140866}, pages = {e16931}, year = {2011}, abstract = {Background: Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta. Methodology/Principal Findings: Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses. Conclusions/Significance: Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.}, language = {en} } @phdthesis{Reitwiessner2011, author = {Reitwießner, Christian}, title = {Multiobjective Optimization and Language Equations}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-70146}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {Praktische Optimierungsprobleme beinhalten oft mehrere gleichberechtigte, sich jedoch widersprechende Kriterien. Beispielsweise will man bei einer Reise zugleich m{\"o}glichst schnell ankommen, sie soll aber auch nicht zu teuer sein. Im ersten Teil dieser Arbeit wird die algorithmische Beherrschbarkeit solcher mehrkriterieller Optimierungsprobleme behandelt. Es werden zun{\"a}chst verschiedene L{\"o}sungsbegriffe diskutiert und auf ihre Schwierigkeit hin verglichen. Interessanterweise stellt sich heraus, dass diese Begriffe f{\"u}r ein einkriterielles Problem stets gleich schwer sind, sie sich ab zwei Kriterien allerdings stark unterscheiden k{\"o}nen (außer es gilt P = NP). In diesem Zusammenhang wird auch die Beziehung zwischen Such- und Entscheidungsproblemen im Allgemeinen untersucht. Schließlich werden neue und verbesserte Approximationsalgorithmen f{\"u}r verschieden Varianten des Problems des Handlungsreisenden gefunden. Dabei wird mit Mitteln der Diskrepanztheorie eine Technik entwickelt, die ein grundlegendes Hindernis der Mehrkriteriellen Optimierung aus dem Weg schafft: Gegebene L{\"o}sungen so zu kombinieren, dass die neue L{\"o}sung in allen Kriterien m{\"o}glichst ausgewogen ist und gleichzeitig die Struktur der L{\"o}sungen nicht zu stark zerst{\"o}rt wird. Der zweite Teil der Arbeit widmet sich verschiedenen Aspekten von Gleichungssystemen f{\"u}r (formale) Sprachen. Einerseits werden konjunktive und Boolesche Grammatiken untersucht. Diese sind Erweiterungen der kontextfreien Grammatiken um explizite Durchschnitts- und Komplementoperationen. Es wird unter anderem gezeigt, dass man bei konjunktiven Grammatiken die Vereinigungsoperation stark einschr{\"a}nken kann, ohne dabei die erzeugte Sprache zu {\"a}ndern. Außerdem werden bestimmte Schaltkreise untersucht, deren Gatter keine Wahrheitswerte sondern Mengen von Zahlen berechnen. F{\"u}r diese Schaltkreise wird das {\"A}quivalenzproblem betrachtet, also die Frage ob zwei gegebene Schaltkreise die gleiche Menge berechnen oder nicht. Es stellt sich heraus, dass, abh{\"a}ngig von den erlaubten Gattertypen, die Komplexit{\"a}t des {\"A}quivalenzproblems stark variiert und f{\"u}r verschiedene Komplexit{\"a}tsklassen vollst{\"a}ndig ist, also als (parametrisierter) Vertreter f{\"u}r diese Klassen stehen kann.}, subject = {Mehrkriterielle Optimierung}, language = {en} } @phdthesis{Staehle2011, author = {Staehle, Barbara}, title = {Modeling and Optimization Methods for Wireless Sensor and Mesh Networks}, doi = {10.25972/OPUS-4967}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-64884}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {Im Internet der Zukunft werden Menschen nicht nur mit Menschen, sondern auch mit „Dingen", und sogar „Dinge" mit „Dingen" kommunizieren. Zus{\"a}tzlich wird das Bed{\"u}rfnis steigen, immer und {\"u}berall Zugang zum Internet zu haben. Folglich gewinnen drahtlose Sensornetze (WSNs) und drahtlose Mesh-Netze (WMNs) an Bedeutung, da sie Daten {\"u}ber die Umwelt ins Internet liefern, beziehungsweise einfache Internet-Zugangsm{\"o}glichkeiten schaffen. In den vier Teilen dieser Arbeit werden unterschiedliche Modellierungs- und Optimierungsmethoden f{\"u}r WSNs und WMNs vorgestellt. Der Energieverbrauch ist die wichtigste Metrik, wenn es darum geht die Kommunikation in einem WSN zu optimieren. Da sich in der Literatur sehr viele unterschiedliche Energiemodelle finden, untersucht der erste Teil der Arbeit welchen Einfluss unterschiedliche Energiemodelle auf die Optimierung von WSNs haben. Aufbauend auf diesen {\"U}berlegungen besch{\"a}ftigt sich der zweite Teil der Arbeit mit drei Problemen, die {\"u}berwunden werden m{\"u}ssen um eine standardisierte energieeffiziente Kommunikations-L{\"o}sung f{\"u}r WSNs basierend auf IEEE 802.15.4 und ZigBee zu realisieren. F{\"u}r WMNs sind beide Probleme von geringem Interesse, die Leistung des Netzes jedoch umso mehr. Der dritte Teil der Arbeit f{\"u}hrt daher Algorithmen f{\"u}r die Berechnung des Max-Min fairen (MMF) Netzwerk-Durchsatzes in WMNs mit mehreren Linkraten und Internet-Gateways ein. Der letzte Teil der Arbeit untersucht die Auswirkungen des LRA-Konzeptes. Dessen grundlegende Idee ist die folgende. Falls f{\"u}r einen Link eine niedrigere Datenrate als theoretisch m{\"o}glich verwendet wird, sinkt zwar der Link-Durchsatz, jedoch ist unter Umst{\"a}nden eine gr{\"o}ßere Anzahl von gleichzeitigen {\"U}bertragungen m{\"o}glich und der Gesamt-Durchsatz des Netzes kann sich erh{\"o}hen. Mithilfe einer analytischen LRA Formulierung und einer systematischen Studie kann gezeigt werden, dass eine netzwerkweite Zuordnung robusterer Datenraten als n{\"o}tig zu einer Erh{\"o}hung des MMF Netzwerk-Durchsatzes f{\"u}hrt. Desweitern kann gezeigt werden, dass sich LRA positiv auf die Leistungsf{\"a}higkeit eines IEEE 802.11 WMNs auswirkt und f{\"u}r die Optimierung des Netzes genutzt werden kann.}, subject = {Drahtloses Sensorsystem}, language = {en} } @phdthesis{Schmidt2011, author = {Schmidt, Marco}, title = {Ground Station Networks for Efficient Operation of Distributed Small Satellite Systems}, isbn = {978-3-923959-77-8}, doi = {10.25972/OPUS-4984}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-64999}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {The field of small satellite formations and constellations attracted growing attention, based on recent advances in small satellite engineering. The utilization of distributed space systems allows the realization of innovative applications and will enable improved temporal and spatial resolution in observation scenarios. On the other side, this new paradigm imposes a variety of research challenges. In this monograph new networking concepts for space missions are presented, using networks of ground stations. The developed approaches combine ground station resources in a coordinated way to achieve more robust and efficient communication links. Within this thesis, the following topics were elaborated to improve the performance in distributed space missions: Appropriate scheduling of contact windows in a distributed ground system is a necessary process to avoid low utilization of ground stations. The theoretical basis for the novel concept of redundant scheduling was elaborated in detail. Additionally to the presented algorithm was a scheduling system implemented, its performance was tested extensively with real world scheduling problems. In the scope of data management, a system was developed which autonomously synchronizes data frames in ground station networks and uses this information to detect and correct transmission errors. The system was validated with hardware in the loop experiments, demonstrating the benefits of the developed approach.}, subject = {Kleinsatellit}, language = {en} } @unpublished{Nassourou2011, author = {Nassourou, Mohamadou}, title = {A Rule-based Statistical Classifier for Determining a Base Text and Ranking Witnesses In Textual Documents Collation Process}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-57465}, 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 histogram.}, subject = {Textvergleich}, language = {en} } @unpublished{Nassourou2011, author = {Nassourou, Mohamadou}, title = {Assisting Understanding, Retention, and Dissemination of Religious Texts Knowledge with Modeling, and Visualization Techniques: The Case of The Quran}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-55927}, 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. In this paper, books organized in terms of chapters consisting of verses, are considered as the source of knowledge to be modeled. The knowledge model consists of verses with their metadata and semantic annotations. The metadata represent the multiple perspectives of knowledge modeling. Verses with their metadata and annotations form a meta-model, which will be published on a web Mashup. The meta-model with linking between its elements constitute a knowledge base. An XML-based annotation system breaking down the learning process into specific tasks, helps constructing the desired meta-model. The system is made up of user interfaces for creating metadata, annotating chapters' contents according to user selected semantics, and templates for publishing the generated knowledge on the Internet. The proposed software system improves comprehension and retention of knowledge contained in religious texts through modeling and visualization. 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. It is expected that this short ongoing study would motivate others to engage in devising and offering software systems for cross-religions learning.}, subject = {Wissensmanagement}, language = {en} } @unpublished{Nassourou2011, author = {Nassourou, Mohamadou}, title = {Design and Implementation of Architectures for Interactive Textual Documents Collation Systems}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-56601}, year = {2011}, abstract = {One of the main purposes of textual documents collation is to identify a base text or closest witness to the base text, by analyzing and interpreting differences also known as types of changes that might exist between those documents. Based on this fact, it is reasonable to argue that, explicit identification of types of changes such as deletions, additions, transpositions, and mutations should be part of the collation process. The identification could be carried out by an interpretation module after alignment has taken place. Unfortunately existing collation software such as CollateX1 and Juxta2's collation engine do not have interpretation modules. In fact they implement the Gothenburg model [1] for collation process which does not include an interpretation unit. Currently both CollateX and Juxta's collation engine do not distinguish in their critical apparatus between the types of changes, and do not offer statistics about those changes. This paper presents a model for both integrated and distributed collation processes that improves the Gothenburg model. The model introduces an interpretation component for computing and distinguishing between the types of changes that documents could have undergone. Moreover two architectures implementing the model in order to solve the problem of interactive collation are discussed as well. Each architecture uses CollateX library, and provides on the one hand preprocessing functions for transforming input documents into CollateX input format, and on the other hand a post-processing module for enabling interactive collation. Finally simple algorithms for distinguishing between types of changes, and linking collated source documents with the collation results are also introduced.}, subject = {Softwarearchitektur}, language = {en} } @unpublished{Nassourou2011, author = {Nassourou, Mohamadou}, title = {Assisting Analysis and Understanding of Quran Search Results with Interactive Scatter Plots and Tables}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-55840}, year = {2011}, abstract = {The Quran is the holy book of Islam consisting of 6236 verses divided into 114 chapters called suras. Many verses are similar and even identical. Searching for similar texts (e.g verses) could return thousands of verses, that when displayed completely or partly as textual list would make analysis and understanding difficult and confusing. Moreover it would be visually impossible to instantly figure out the overall distribution of the retrieved verses in the Quran. As consequence reading and analyzing the verses would be tedious and unintuitive. In this study a combination of interactive scatter plots and tables has been developed to assist analysis and understanding of the search result. Retrieved verses are clustered by chapters, and a weight is assigned to each cluster according to number of verses it contains, so that users could visually identify most relevant areas, and figure out the places of revelation of the verses. Users visualize the complete result and can select a region of the plot to zoom in, click on a marker to display a table containing verses with English translation side by side.}, subject = {Text Mining}, language = {en} } @unpublished{Nassourou2011, author = {Nassourou, Mohamadou}, title = {A Knowledge-based Hybrid Statistical Classifier for Reconstructing the Chronology of the Quran}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-54712}, year = {2011}, abstract = {Computationally categorizing Quran's chapters has been mainly confined to the determination of chapters' revelation places. However this broad classification is not sufficient to effectively and thoroughly understand and interpret the Quran. The chronology of revelation would not only improve comprehending the philosophy of Islam, but also the easiness of implementing and memorizing its laws and recommendations. This paper attempts estimating possible chapters' dates of revelation through their lexical frequency profiles. A hybrid statistical classifier consisting of stemming and clustering algorithms for comparing lexical frequency profiles of chapters, and deriving dates of revelation has been developed. The classifier is trained using some chapters with known dates of revelation. Then it classifies chapters with uncertain dates of revelation by computing their proximity to the training ones. The results reported here indicate that the proposed methodology yields usable results in estimating dates of revelation of the Quran's chapters based on their lexical contents.}, subject = {Text Mining}, language = {en} } @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} } @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{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{MandelHoernleinIflandetal.2011, author = {Mandel, Alexander and H{\"o}rnlein, Alexander and Ifland, Marianus and L{\"u}neburg, Edeltraud and Deckert, J{\"u}rgen and Puppe, Frank}, title = {Aufwandsanalyse f{\"u}r computerunterst{\"u}tzte Multiple-Choice Papierklausuren}, series = {GMS Journal for Medical Education}, volume = {28}, journal = {GMS Journal for Medical Education}, number = {4}, doi = {10.3205/zma000767}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134386}, pages = {1-15, Doc55}, year = {2011}, abstract = {Introduction: Multiple-choice-examinations are still fundamental for assessment in medical degree programs. In addition to content related research, the optimization of the technical procedure is an important question. Medical examiners face three options: paper-based examinations with or without computer support or completely electronic examinations. Critical aspects are the effort for formatting, the logistic effort during the actual examination, quality, promptness and effort of the correction, the time for making the documents available for inspection by the students, and the statistical analysis of the examination results. Methods: Since three semesters a computer program for input and formatting of MC-questions in medical and other paper-based examinations is used and continuously improved at Wuerzburg University. In the winter semester (WS) 2009/10 eleven, in the summer semester (SS) 2010 twelve and in WS 2010/11 thirteen medical examinations were accomplished with the program and automatically evaluated. For the last two semesters the remaining manual workload was recorded. Results: The cost of the formatting and the subsequent analysis including adjustments of the analysis of an average examination with about 140 participants and about 35 questions was 5-7 hours for exams without complications in the winter semester 2009/2010, about 2 hours in SS 2010 and about 1.5 hours in the winter semester 2010/11. Including exams with complications, the average time was about 3 hours per exam in SS 2010 and 2.67 hours for the WS 10/11. Discussion: For conventional multiple-choice exams the computer-based formatting and evaluation of paper-based exams offers a significant time reduction for lecturers in comparison with the manual correction of paper-based exams and compared to purely electronically conducted exams it needs a much simpler technological infrastructure and fewer staff during the exam."}, language = {de} } @article{Zeeshan2010, author = {Zeeshan, Ahmed}, title = {Towards Performance Measurement and Metrics Based Analysis of PLA Applications}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-68188}, year = {2010}, abstract = {This article is about a measurement analysis based approach to help software practitioners in managing the additional level complexities and variabilities in software product line applications. The architecture of the proposed approach i.e. ZAC is designed and implemented to perform preprocessesed source code analysis, calculate traditional and product line metrics and visualize results in two and three dimensional diagrams. Experiments using real time data sets are performed which concluded with the results that the ZAC can be very helpful for the software practitioners in understanding the overall structure and complexity of product line applications. Moreover the obtained results prove strong positive correlation between calculated traditional and product line measures.}, subject = {Programmierbare logische Anordnung}, language = {en} } @phdthesis{Oechsner2010, author = {Oechsner, Simon}, title = {Performance Challenges and Optimization Potential of Peer-to-Peer Overlay Technologies}, doi = {10.25972/OPUS-4159}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-50015}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {In today's Internet, building overlay structures to provide a service is becoming more and more common. This approach allows for the utilization of client resources, thus being more scalable than a client-server model in this respect. However, in these architectures the quality of the provided service depends on the clients and is therefore more complex to manage. Resource utilization, both at the clients themselves and in the underlying network, determine the efficiency of the overlay application. Here, a trade-off exists between the resource providers and the end users that can be tuned via overlay mechanisms. Thus, resource management and traffic management is always quality-of-service management as well. In this monograph, the three currently significant and most widely used overlay types in the Internet are considered. These overlays are implemented in popular applications which only recently have gained importance. Thus, these overlay networks still face real-world technical challenges which are of high practical relevance. We identify the specific issues for each of the considered overlays, and show how their optimization affects the trade-offs between resource efficiency and service quality. Thus, we supply new insights and system knowledge that is not provided by previous work.}, subject = {Overlay-Netz}, language = {en} }