@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{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}
}
@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{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{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{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{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}
}
@phdthesis{Herrler2007,
  author    = {Herrler, Rainer},
  title     = {Agentenbasierte Simulation zur Ablaufoptimierung in Krankenh{\"a}usern und anderen verteilten, dynamischen Umgebungen},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-24483},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2007},
  abstract  = {Verteilte dynamische Systeme unter lokalen und globalen Gesichtspunkten zu optimieren ist eine schwierige Aufgabe. Zwar sind grunds{\"a}tzliche Auswirkungen einzelner Maßnahmen h{\"a}ufig bekannt, durch widerstrebende Ziele, Wechselwirkungen zwischen Prozessen und Nebenwirkungen von Maßnahmen ist ein analytisches Vorgehen bei der Optimierung nicht m{\"o}glich. Besonders schwierig wird es, wenn lokale Einheiten einerseits ihre Ziele und Autonomie behalten sollen, aber durch zentrale Vorgaben bzw. Anreize so gesteuert werden sollen, dass ein {\"u}bergeordnetes Ziel erreicht wird. Ein praktisches Beispiel dieses allgemeinen Optimierungsproblems findet sich im Gesundheitswesen. Das Management von modernen Kliniken ist stets mit dem Problem konfrontiert, die Qualit{\"a}t der Pflege zu gew{\"a}hrleisten und gleichzeitig kosteneffizient zu arbeiten. Hier gilt es unter gegeben Rahmenbedingungen und bei Respektierung der Autonomie der Funktionseinheiten, Optimierungsmaßnahmen zu finden und durchzuf{\"u}hren. Vorhandene Werkzeuge zur Simulation und Modellierung bieten f{\"u}r diese Aufgabe keine ausreichend guten Vorgehensmodelle und Modellierungsmechanismen. Die agentenbasierte Simulation erm{\"o}glicht die Abbildung solcher Systeme und die Durchf{\"u}hrung von Simulationsexperimenten zur Bewertung einzelner Maßnahmen. Es werden L{\"o}sungswege und Werkzeuge vorgestellt und evaluiert, die den Benutzer bei der Formalisierung des Wissens und der Modellierung solch komplexer Szenarien unterst{\"u}tzen und ein systematisches Vorgehen zur Optimierung erm{\"o}glichen.},
  subject      = {Simulation},
  language  = {de}
}
@misc{Hoehn2006,
  type      = {Master Thesis},
  author    = {H{\"o}hn, Winfried},
  title     = {Mustererkennung in Fr{\"u}hdrucken},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-30429},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2006},
  abstract  = {No abstract available},
  subject      = {Mustererkennung},
  language  = {de}
}
@phdthesis{Hossfeld2009,
  author    = {Hoßfeld, Tobias},
  title     = {Performance Evaluation of Future Internet Applications and Emerging User Behavior},
  doi       = {10.25972/OPUS-3067},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-37570},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {In future telecommunication systems, we observe an increasing diversity of access networks. The separation of transport services and applications or services leads to multi-network services, i.e., a future service has to work transparently to the underlying network infrastructure. Multi-network services with edge-based intelligence, like P2P file sharing or the Skype VoIP service, impose new traffic control paradigms on the future Internet. Such services adapt the amount of consumed bandwidth to reach different goals. A selfish behavior tries to keep the QoE of a single user above a certain level. Skype, for instance, repeats voice samples depending on the perceived end-to-end loss. From the viewpoint of a single user, the replication of voice data overcomes the degradation caused by packet loss and enables to maintain a certain QoE. The cost for this achievement is a higher amount of consumed bandwidth. However, if the packet loss is caused by congestion in the network, this additionally required bandwidth even worsens the network situation. Altruistic behavior, on the other side, would reduce the bandwidth consumption in such a way that the pressure on the network is released and thus the overall network performance is improved. In this monograph, we analyzed the impact of the overlay, P2P, and QoE paradigms in future Internet applications and the interactions from the observing user behavior. The shift of intelligence toward the edge is accompanied by a change in the emerging user behavior and traffic profile, as well as a change from multi-service networks to multi-networks services. In addition, edge-based intelligence may lead to a higher dynamics in the network topology, since the applications are often controlled by an overlay network, which can rapidly change in size and structure as new nodes can leave or join the overlay network in an entirely distributed manner. As a result, we found that the performance evaluation of such services provides new challenges, since novel key performance factors have to be first identified, like pollution of P2P systems, and appropriate models of the emerging user behavior are required, e.g. taking into account user impatience. As common denominator of the presented studies in this work, we focus on a user-centric view when evaluating the performance of future Internet applications. For a subscriber of a certain application or service, the perceived quality expressed as QoE will be the major criterion of the user's satisfaction with the network and service providers. We selected three different case studies and characterized the application's performance from the end user's point of view. Those are (1) cooperation in mobile P2P file sharing networks, (2) modeling of online TV recording services, and (3) QoE of edge-based VoIP applications. The user-centric approach facilitates the development of new mechanisms to overcome problems arising from the changing user behavior. An example is the proposed CycPriM cooperation strategy, which copes with selfish user behavior in mobile P2P file sharing system. An adequate mechanism has also been shown to be efficient in a heterogeneous B3G network with mobile users conducting vertical handovers between different wireless access technologies. The consideration of the user behavior and the user perceived quality guides to an appropriate modeling of future Internet applications. In the case of the online TV recording service, this enables the comparison between different technical realizations of the system, e.g. using server clusters or P2P technology, to properly dimension the installed network elements and to assess the costs for service providers. Technologies like P2P help to overcome phenomena like flash crowds and improve scalability compared to server clusters, which may get overloaded in such situations. Nevertheless, P2P technology invokes additional challenges and different user behavior to that seen in traditional client/server systems. Beside the willingness to share files and the churn of users, peers may be malicious and offer fake contents to disturb the data dissemination. Finally, the understanding and the quantification of QoE with respect to QoS degradations permits designing sophisticated edge-based applications. To this end, we identified and formulated the IQX hypothesis as an exponential interdependency between QoE and QoS parameters, which we validated for different examples. The appropriate modeling of the emerging user behavior taking into account the user's perceived quality and its interactions with the overlay and P2P paradigm will finally help to design future Internet applications.},
  subject      = {Leistungsbewertung},
  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}
}
@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}
}