TY - JOUR A1 - Zirkel, J. A1 - Cecil, A. A1 - Schäfer, F. A1 - Rahlfs, S. A1 - Ouedraogo, A. A1 - Xiao, K. A1 - Sawadogo, S. A1 - Coulibaly, B. A1 - Becker, K. A1 - Dandekar, T. T1 - Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling JF - Bioinformatics and Biology Insights N2 - BACKGROUND: In the face of growing resistance in malaria parasites to drugs, pharmacological combination therapies are important. There is accumulating evidence that methylene blue (MB) is an effective drug against malaria. Here we explore the biological effects of both MB alone and in combination therapy using modeling and experimental data. RESULTS: We built a model of the central metabolic pathways in P. falciparum. Metabolic flux modes and their changes under MB were calculated by integrating experimental data (RT-PCR data on mRNAs for redox enzymes) as constraints and results from the YANA software package for metabolic pathway calculations. Several different lines of MB attack on Plasmodium redox defense were identified by analysis of the network effects. Next, chloroquine resistance based on pfmdr/and pfcrt transporters, as well as pyrimethamine/sulfadoxine resistance (by mutations in DHF/DHPS), were modeled in silico. Further modeling shows that MB has a favorable synergism on antimalarial network effects with these commonly used antimalarial drugs. CONCLUSIONS: Theoretical and experimental results support that methylene blue should, because of its resistance-breaking potential, be further tested as a key component in drug combination therapy efforts in holoendemic areas. KW - methylene blue KW - malaria KW - elementary mode analysis KW - drug KW - resistance KW - combination therapy KW - pathway KW - metabolic flux Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-123751 N1 - This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. VL - 6 ER - TY - JOUR A1 - Krueger, Beate A1 - Friedrich, Torben A1 - Förster, Frank A1 - Bernhardt, Jörg A1 - Gross, Roy A1 - Dandekar, Thomas T1 - Different evolutionary modifications as a guide to rewire two-component systems JF - Bioinformatics and Biology Insights N2 - Two-component systems (TCS) are short signalling pathways generally occurring in prokaryotes. They frequently regulate prokaryotic stimulus responses and thus are also of interest for engineering in biotechnology and synthetic biology. The aim of this study is to better understand and describe rewiring of TCS while investigating different evolutionary scenarios. Based on large-scale screens of TCS in different organisms, this study gives detailed data, concrete alignments, and structure analysis on three general modification scenarios, where TCS were rewired for new responses and functions: (i) exchanges in the sequence within single TCS domains, (ii) exchange of whole TCS domains; (iii) addition of new components modulating TCS function. As a result, the replacement of stimulus and promotor cassettes to rewire TCS is well defined exploiting the alignments given here. The diverged TCS examples are non-trivial and the design is challenging. Designed connector proteins may also be useful to modify TCS in selected cases. KW - histidine kinase KW - connector KW - Mycoplasma KW - engineering KW - promoter KW - sensor KW - response regulator KW - synthetic biology KW - sequence alignment Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-123647 N1 - This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. VL - 6 ER - TY - JOUR A1 - Merget, Benjamin A1 - Koetschan, Christian A1 - Hackl, Thomas A1 - Förster, Frank A1 - Dandekar, Thomas A1 - Müller, Tobias A1 - Schultz, Jörg A1 - Wolf, Matthias T1 - The ITS2 Database JF - Journal of Visual Expression N2 - The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution1 and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation. The ITS2 Database presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank accurately reannotated. Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling. In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold. The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE and ProfDistS for multiple sequence-structure alignment calculation and Neighbor Joining tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure. In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses. KW - homology modeling KW - molecular systematics KW - internal transcribed spacer 2 KW - alignment KW - genetics KW - secondary structure KW - ribosomal RNA KW - phylogenetic tree KW - phylogeny Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124600 VL - 61 IS - e3806 ER - TY - JOUR A1 - Buchin, Kevin A1 - Buchin, Maike A1 - Byrka, Jaroslaw A1 - Nöllenburg, Martin A1 - Okamoto, Yoshio A1 - Silveira, Rodrigo I. A1 - Wolff, Alexander T1 - Drawing (Complete) Binary Tanglegrams JF - Algorithmica N2 - A binary tanglegram is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential that both trees are drawn without edge crossings and that the inter-tree edges have as few crossings as possible. It is known that finding a tanglegram with the minimum number of crossings is NP-hard and that the problem is fixed-parameter tractable with respect to that number. We prove that under the Unique Games Conjecture there is no constant-factor approximation for binary trees. We show that the problem is NP-hard even if both trees are complete binary trees. For this case we give an O(n 3)-time 2-approximation and a new, simple fixed-parameter algorithm. We show that the maximization version of the dual problem for binary trees can be reduced to a version of MaxCut for which the algorithm of Goemans and Williamson yields a 0.878-approximation. KW - NP-hardness KW - crossing minimization KW - binary tanglegram KW - approximation algorithm KW - fixed-parameter tractability Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124622 VL - 62 ER - TY - GEN T1 - Jahresbericht 2014 T1 - Annual Report 2014 N2 - Jahresbericht 2014 des Rechenzentrums der Universität Würzburg N2 - Annual Report 2014 of the Computer Center, University of Wuerzburg T3 - Jahresbericht des Rechenzentrums der Universität Würzburg - 2014 KW - Rechenzentrum Universität Würzburg KW - annual report KW - Computer Center University of Wuerzburg KW - Jahresbericht Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124432 UR - https://www.rz.uni-wuerzburg.de/infos/publikationen/ ER - TY - JOUR A1 - Toepfer, Martin A1 - Corovic, Hamo A1 - Fette, Georg A1 - Klügl, Peter A1 - Störk, Stefan A1 - Puppe, Frank T1 - Fine-grained information extraction from German transthoracic echocardiography reports JF - BMC Medical Informatics and Decision Making N2 - 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 Würzburg. 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 Würzburg. Extracted results populate a clinical data warehouse which supports clinical research. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-125509 VL - 15 IS - 91 ER - TY - THES A1 - Hopfner, Marbod T1 - Source Code Analysis, Management, and Visualization for PROLOG T1 - Quelltextanalyse, Verwaltung und Visualisierung für Prolog N2 - This thesis deals with the management and analysis of source code, which is represented in XML. Using the elementary methods of the XML repository, the XML source code representation is accessed, changed, updated, and saved. We reason about the source code, refactor source code and we visualize dependency graphs for call analysis. The visualized dependencies between files, modules, or packages are used to structure the source code in order to get a system, which is easily to comprehend, to modify and to complete. Sophisticated methods have been developed to slice the source code in order to obtain a working package of a large system, containing only a specific functionality. The basic methods, on which the visualizations and analyses are built on can be changed like changing a plug-in. The visualization methods can be reused in order to handle arbitrary source code representations, e.g., JAML, PHPML, PROLOGML. Dependencies of other context can be visualized, too, e.g., ER diagrams, or website references. The tool SCAV supports source code visualization and analyzing methods. N2 - Diese Dissertation beschäftigt sich mit der Verwaltung und Analyse von Quellcode, der in XML repräsentiert ist. Es werden Abhängigkeitsgraphen visualisiert um ein Projekt leichter verstehen zu können. Es kann auch ein Slice einer bestimmten Methode aus dem Projekt erstellt werden. Die Programmierung ist in Modulen gemacht, so dass die Funktionalität leicht erweitert werden kann. KW - Refactoring KW - Software Engineering KW - Refactoring KW - Call Graph KW - Dependency Graph KW - Abhängigskeitsgraph KW - Software Engineering KW - Source Code Visualization KW - Refactoring KW - Call Graph KW - Dependency Graph KW - Abhängigskeitsgraph KW - Software Engineering KW - Source Code Visualization Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-36300 ER - TY - THES A1 - Binder, Andreas T1 - Die stochastische Wissenschaft und zwei Teilsysteme eines Web-basierten Informations- und Anwendungssystems zu ihrer Etablierung T1 - The stochastic science and two subsystems of a web-based information and application system for its establishment N2 - Das stochastische Denken, die Bernoullische Stochastik und dessen informationstechnologische Umsetzung, namens Stochastikon stellen die Grundlage für das Verständnis und die erfolgreiche Nutzung einer stochastischen Wissenschaft dar. Im Rahmen dieser Arbeit erfolgt eine Klärung des Begriffs des stochastischen Denkens, eine anschauliche Darstellung der von Elart von Collani entwickelten Bernoullischen Stochastik und eine Beschreibung von Stochastikon. Dabei werden sowohl das Gesamtkonzept von Stochastikon, sowie die Ziele, Aufgaben und die Realisierung der beiden Teilsysteme namens Mentor und Encyclopedia vorgestellt. Das stochastische Denken erlaubt eine realitätsnahe Sichtweise der Dinge, d.h. eine Sichtweise, die mit den menschlichen Beobachtungen und Erfahrungen im Einklang steht und somit die Unsicherheit über zukünftige Entwicklungen berücksichtigt. Der in diesem Kontext verwendete Begriff der Unsicherheit bezieht sich ausschließlich auf zukünftige Entwicklungen und äußert sich in Variabilität. Quellen der Unsicherheit sind einerseits die menschliche Ignoranz und andererseits der Zufall. Unter Ignoranz wird hierbei die Unwissenheit des Menschen über die unbekannten, aber feststehenden Fakten verstanden, die die Anfangsbedingungen der zukünftigen Entwicklung repräsentieren. Die Bernoullische Stochastik liefert ein Regelwerk und ermöglicht die Entwicklung eines quantitativen Modells zur Beschreibung der Unsicherheit und expliziter Einbeziehung der beiden Quellen Ignoranz und Zufall. Das Modell trägt den Namen Bernoulli-Raum und bildet die Grundlage für die Herleitung quantitativer Verfahren, um zuverlässige und genaue Aussagen sowohl über die nicht-existente zufällige Zukunft (Vorhersageverfahren), als auch über die unbekannte feststehende Vergangenheit (Messverfahren). Das Softwaresystem Stochastikon implementiert die Bernoullische Stochastik in Form einer Reihe autarker, miteinander kommunizierender Teilsysteme. Ziel des Teilsystems Encyclopedia ist die Bereitstellung und Bewertung stochastischen Wissens. Das Teilsystem Mentor dient der Unterstützung des Anwenders bei der Problemlösungsfindung durch Identifikation eines richtigen Modells bzw. eines korrekten Bernoulli-Raums. Der Lösungsfindungsprozess selber enthält keinerlei Unsicherheit. Die ganze Unsicherheit steckt in der Lösung, d.h. im Bernoulli-Raum, der explizit die vorhandene Unwissenheit (Ignoranz) und den vorliegenden Zufall abdeckend enthält. N2 - Stochastic thinking, Bernoulli stochastics and its information technological realization, called Stochastikon, represent the basis for understanding and successfully utilizing stochastic science. This thesis defines the concept of stochastic thinking, introduces Bernoulli stochastics, which has been developed by Elart von Collani, and describes the IT system Stochastikon. The concept and the design of Stochastikon are outlined and the aims, tasks and realizations of the two subsystems Mentor and Encyclopedia are given in detail. Stochastic thinking enables a realistic view of reality. This means a view, which is in agreement with observation and experience and, thus, takes into account uncertainty about future developments. In this context the term of uncertainty is used exclusively with respect to future development and materializes in variability. Sources of uncertainty are on the one hand human ignorance about fixed facts on the one hand and randomness on the other. Bernoulli stochastics makes available a set of rules for developing a quantitative model about uncertainty taking particularly into account the two sources ignorance and randomness. The model is called Bernoulli-Space, which is the basis for reliable and precise quantitative procedures for statements about the random future (prediction procedures) as well as about the unknown fixed past (measurement procedures). The software system, called Stochastikon, implements Bernoulli stochastics based on a set of self-sustained intercommunicating subsystems. The Subsystem Encyclopedia makes stochastical knowledge available, while the Subsystem Mentor supports the user for solving (stochastic) problems by identifying the correct model respectively correct Bernoulli-Space. The problem solving process is free of uncertainty, because all uncertainty is modelled by Bernoulli-space. KW - Stochastik KW - stochastisches Denken KW - Bernoullische Stochastik KW - Bernoulli-Raum KW - Stochastikon KW - stochastic thinking KW - Bernoulli stochastics KW - Bernoullispace KW - Stochastikon Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-26146 ER - TY - THES A1 - Binzenhöfer, Andreas T1 - Performance Analysis of Structured Overlay Networks T1 - Leistungsbewertung Strukturierter Overlay Netze N2 - Overlay networks establish logical connections between users on top of the physical network. While randomly connected overlay networks provide only a best effort service, a new generation of structured overlay systems based on Distributed Hash Tables (DHTs) was proposed by the research community. However, there is still a lack of understanding the performance of such DHTs. Additionally, those architectures are highly distributed and therefore appear as a black box to the operator. Yet an operator does not want to lose control over his system and needs to be able to continuously observe and examine its current state at runtime. This work addresses both problems and shows how the solutions can be combined into a more self-organizing overlay concept. At first, we evaluate the performance of structured overlay networks under different aspects and thereby illuminate in how far such architectures are able to support carrier-grade applications. Secondly, to enable operators to monitor and understand their deployed system in more detail, we introduce both active as well as passive methods to gather information about the current state of the overlay network. N2 - Unter einem Overlay Netz versteht man den Zusammenschluss mehrerer Komponenten zu einer logischen Topologie, die auf einer existierenden physikalischen Infrastruktur aufsetzt. Da zufällige Verbindungen zwischen den einzelnen Teilnehmern aber sehr ineffizient sind, wurden strukturierte Overlay Netze entworfen, bei denen die Beziehungen zwischen den einzelnen Teilnehmern fest vorgeschrieben sind. Solche strukturierten Mechanismen versprechen zwar ein großes Potential, dieses wurde aber noch nicht ausreichend untersucht bzw. wissenschaftlich nachgewiesen. In dieser Arbeit wird mit mathematischen Methoden und ereignisorientierter Simulation die Leistungsfähigkeit von strukturierten Overlay Netzen untersucht. Da diese stark von der aktuellen Situation im Overlay abhängt, entwickeln wir Methoden, mit denen sich sowohl passiv, als auch aktiv, wichtige Systemparameter zur Laufzeit abschätzen bzw. messen lassen. Zusammen führen die vorgeschlagenen Methoden zu selbstorganisierenden Mechanismen, die den aktuellen Zustand des Overlays überwachen, diesen bewerten und sich gegebenenfalls automatisch an die aktuellen Verhältnisse anpassen T3 - Würzburger Beiträge zur Leistungsbewertung Verteilter Systeme - 01/08 KW - Overlay-Netz KW - Leistungsbewertung KW - Peer-to-Peer-Netz KW - Mathematisches Modell KW - Chord KW - Kademlia KW - DHT KW - Overlay KW - Chord KW - Kademlia KW - DHT Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-26291 ER - TY - THES A1 - Pries, Jan Rastin T1 - Performance Optimization of Wireless Infrastructure and Mesh Networks T1 - Leistungsoptimierung von drahtlosen Infrastruktur und Mesh Netzen N2 - Future broadband wireless networks should be able to support not only best effort traffic but also real-time traffic with strict Quality of Service (QoS) constraints. In addition, their available resources are scare and limit the number of users. To facilitate QoS guarantees and increase the maximum number of concurrent users, wireless networks require careful planning and optimization. In this monograph, we studied three aspects of performance optimization in wireless networks: resource optimization in WLAN infrastructure networks, quality of experience control in wireless mesh networks, and planning and optimization of wireless mesh networks. An adaptive resource management system is required to effectively utilize the limited resources on the air interface and to guarantee QoS for real-time applications. Thereby, both WLAN infrastructure and WLAN mesh networks have to be considered. An a-priori setting of the access parameters is not meaningful due to the contention-based medium access and the high dynamics of the system. Thus, a management system is required which dynamically adjusts the channel access parameters based on the network load. While this is sufficient for wireless infrastructure networks, interferences on neighboring paths and self-interferences have to be considered for wireless mesh networks. In addition, a careful channel allocation and route assignment is needed. Due to the large parameter space, standard optimization techniques fail for optimizing large wireless mesh networks. In this monograph, we reveal that biology-inspired optimization techniques, namely genetic algorithms, are well-suitable for the planning and optimization of wireless mesh networks. Although genetic algorithms generally do not always find the optimal solution, we show that with a good parameter set for the genetic algorithm, the overall throughput of the wireless mesh network can be significantly improved while still sharing the resources fairly among the users. N2 - Die Anbindung an das Internet erfolgt zunehmend über drahtlose Netze. Deren Ressourcen sind allerdings limitiert, was die Anzahl der unterstützten Nutzer stark einschränkt. Zudem ist ein Trend dieser Nutzer weg von der Verwendung reiner Datendienste zu Diensten mit Echtzeitanforderungen wie Voice over IP (VoIP) zu erkennen, deren Dienstgüteanforderungen eingehalten werden müssen. Heutige drahtlose Zugangsnetze sind jedoch nur für den herkömmlichen Datenverkehr ausgelegt. Der IEEE 802.11 WLAN Standard unterscheidet zwar zwischen verschiedenen Dienstklassen, gibt aber keine Dienstgütegarantien. Um die Dienstgüte (Quality of Service, QoS), bzw. die vom Nutzer erfahrene Dienstgüte (Quality of Experience, QoE) zu garantieren, müssen die zukünftigen drahtlosen Netze daher sorgfältig geplant und optimiert werden. Um die limitierten Ressourcen auf der Luftschnittstelle effektiv zu nutzen und um Dienstgüteanforderungen für Echtzeitanwendungen einzuhalten, bedarf es eines adaptiven Ressourcenmanagements. Dabei sind sowohl drahtlose Infrastruktur, als auch drahtlose Mesh-Netze zu betrachten. Durch den randomisierten Medienzugriff und die hohe Dynamik im System ist eine a-priori Wahl der Zugangsparameter nicht sinnvoll. Vielmehr wird ein Managementsystem benötigt, das die Zugangsparameter dynamisch in Abhängigkeit der Last in einem Netz wählt. Während dies für drahtlose Infrastrukturnetze ausreicht, müssen in drahtlosen Mesh-Netzen zusätzlich noch Interferenzen von Nachbarpfaden und Eigeninterferenzen berücksichtigt werden. Desweiteren ist eine sorgfältige Planung der Kanalzuweisung und des Routings notwendig, um einerseits den Durchsatz in drahtlosen Mesh-Netzen zu maximieren und andererseits die Ressourcen fair zwischen den Stationen aufzuteilen. Da es dabei eine Vielzahl von Parametern zu berücksichtigen gilt, sind neue Optimierungsmethoden notwendig, die es ermöglichen, auch große Mesh-Netze in annehmbarer Zeit zu planen und zu optimieren. Diese Doktorarbeit arbeitet die folgenden drei Optimierungsmöglichkeiten für drahtlose Zugangsnetze aus: Optimierung der Zugangsparameter in drahtlosen Infrastrukturnetzen, Optimierung von drahtlosen Mesh-Netzen unter Berücksichtigung der QoE und Planung und Optimierung von drahtlosen Mesh-Netzen mit Berücksichtigung einer fairen Ressourcenallokation. Die Ergebnisse und Untersuchungen dieser Arbeit gliedern sich entsprechend dieser Optimierungsmöglichkeiten. T3 - Würzburger Beiträge zur Leistungsbewertung Verteilter Systeme - 01/10 KW - IEEE 802.11 KW - Leistungsbewertung KW - Optimierung KW - Dienstgüte KW - Netzplanung KW - Drahtloses lokales Netz KW - WLAN KW - Mesh Netze KW - Genetische Optimierung KW - WLAN KW - Optimization KW - Mesh Networks KW - Genetic Optimization Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-46097 ER - TY - CHAP A1 - Epplée, Rafael A1 - Langbehn, Eike T1 - Overlapping Architecture: Implementation of Impossible Spaces in Virtual Reality Games N2 - Natural walking in virtual reality games is constrained by the physical boundaries defined by the size of the player’s tracking space. Impossible spaces, a redirected walking technique, enlarge the virtual environment by creating overlapping architecture and letting multiple locations occupy the same physical space. Within certain thresholds, this is subtle to the player. In this paper, we present our approach to implement such impossible spaces and describe how we handled challenges like objects with simulated physics or precomputed global illumination. KW - virtual reality KW - games KW - locomotion Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-246045 ER - TY - THES A1 - Busch, Stephan T1 - Robust, Flexible and Efficient Design for Miniature Satellite Systems T1 - Moderne Kleinstsatelliten - Zwischen Robustheit, Flexibilität und Effizienz N2 - 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. N2 - Miniaturisierte Satellitensysteme übernehmen zunehmend eine entscheidende Rolle in der fortschreitenden Globalisierung und Demokratisierung der Raumfahrt. Großes Innovationspotential und neue Kommerzialisierungschancen verspricht der effektive Einsatz von Kleinstsatelliten in zukünftigen fraktionierten Missionen für Erdbeobachtungs- und Kommunikationsanwendungen. Basierend auf vielen kleinen kooperierenden Systemen können diese Systeme zukünftig große multifunktionale Satelliten ergänzen oder ersetzen. Die Herausforderung bei der Entwicklung miniaturisierter Satellitensysteme ist die Gratwanderung zwischen der im Rahmen der Miniaturisierung notwendigen Effizienz, der für die Erfüllung der Mission geforderten Zuverlässigkeit und der wünschenswerten Wiederverwendbarkeit und Erweiterbarkeit zur Realisierung agiler Kleinstsatellitenserien. Diese Arbeit adressiert verschiedene Aspekte für den optimalen Entwurf robuster, flexibler und effizienter Kleinstsatelliten am Beispiel des UWE Pico-Satelliten Bus der Universität Würzburg. Mit dem Ziel der Entwicklung einer soliden Basisplattform für zukünftige Kleinstsatelliten-Formationen wurden entsprechende Designansätze im Rahmen des UWE-3 Projektes in einem integralen Designansatz konsistent umgesetzt. Neben der Entwicklung von effizienten Redundanzkonzepten mit minimalem Overhead für den optimalen Betrieb auf Ressourcen-limitierten Kleinstsatelliten wurde ein modularer Satellitenbus entworfen, der als eine robuste und erweiterbare Basis für zukünftige Missionen dienen soll. Damit realisiert UWE-3 eine der effizientesten Kleinstsatelliten-Architekturen die in den letzten Jahren in den Orbit gebracht wurde. Dargestellte Missionsergebnisse fassen den erfolgreichen Betrieb des Satelliten seit seinem Launch in Jahr 2013 zusammen. T3 - Forschungsberichte in der Robotik = Research Notes in Robotics - 11 KW - Kleinsatellit KW - Fehlertoleranz KW - Miniaturisierung KW - Modularität KW - Picosatellite KW - Satellit Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-136523 SN - 978-3-945459-10-2 ER - TY - GEN T1 - Jahresbericht 2015 T1 - Annual Report 2015 N2 - Jahresbericht 2015 des Rechenzentrums der Universität Würzburg N2 - Annual Report 2015 of the Computer Center, University of Wuerzburg T3 - Jahresbericht des Rechenzentrums der Universität Würzburg - 2015 KW - Julius-Maximilians-Universität Würzburg. Rechenzentrum KW - annual report KW - Computer Center University of Wuerzburg KW - Jahresbericht KW - RZUW Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-136599 UR - https://www.rz.uni-wuerzburg.de/wir/publikationen/ ER - TY - JOUR A1 - Kuhn, Joachim A1 - Gripp, Tatjana A1 - Flieder, Tobias A1 - Dittrich, Marcus A1 - Hendig, Doris A1 - Busse, Jessica A1 - Knabbe, Cornelius A1 - Birschmann, Ingvild T1 - UPLC-MRM Mass Spectrometry Method for Measurement of the Coagulation Inhibitors Dabigatran and Rivaroxaban in Human Plasma and Its Comparison with Functional Assays JF - PLOS ONE N2 - 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. KW - LC-MS/MS KW - validation KW - serum KW - quantification KW - apixaban KW - diagnostic accuracy KW - performance liquid chromatography KW - factor XA inhibitor KW - direct oral anticoagulants KW - direct thrombin inhibitor Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-136023 VL - 10 IS - 12 ER - TY - JOUR A1 - Singh, Amit K. A1 - Kingston, Joseph J. A1 - Gupta, Shishir K. A1 - Batra, Harsh V. T1 - Recombinant Bivalent Fusion Protein rVE Induces CD4+ and CD8+ T-Cell Mediated Memory Immune Response for Protection Against Yersinia enterocolitica Infection JF - Frontiers in Microbiology N2 - 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. KW - I-tasser KW - Yersinia enterocolitica KW - memory immune responses KW - cytokine profiling KW - CD8+T cells KW - CD4+T cells KW - recombinant protein rVE KW - resistance KW - pneumonic plague KW - pestis infection KW - nonhuman-primates KW - III secretion KW - V-antigen KW - mice KW - vaccine Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-136114 VL - 6 IS - 1407 ER - TY - JOUR A1 - Staiger, Christine A1 - Cadot, Sidney A1 - Kooter, Raul A1 - Dittrich, Marcus A1 - Müller, Tobias A1 - Klau, Gunnar W. A1 - Wessels, Lodewyk F. A. T1 - A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer JF - PLoS One N2 - 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. KW - modules KW - protein-interaction networks KW - expression signature KW - classification KW - set KW - metastasis KW - stability KW - survival KW - database KW - markers Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131323 VL - 7 IS - 4 ER - TY - JOUR A1 - Naseem, Muhammad A1 - Dandekar, Thomas T1 - The Role of Auxin-Cytokinin Antagonism in Plant-Pathogen Interactions JF - PLOS Pathogens N2 - No abstract available. KW - disease KW - pseudomas-syringae KW - arabidpsis thaliana KW - immunity KW - organogenesis KW - transcription KW - resistance KW - crosstalk Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131901 VL - 8 IS - 11 ER - TY - JOUR A1 - Mandel, Alexander A1 - Hörnlein, Alexander A1 - Ifland, Marianus A1 - Lüneburg, Edeltraud A1 - Deckert, Jürgen A1 - Puppe, Frank T1 - Aufwandsanalyse für computerunterstützte Multiple-Choice Papierklausuren T1 - Cost analysis for computer supported multiple-choice paper examinations JF - GMS Journal for Medical Education N2 - 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." N2 - Einleitung: Multiple-Choice-Klausuren spielen immer noch eine herausragende Rolle für fakultätsinterne medizinische Prüfungen. Neben inhaltlichen Arbeiten stellt sich die Frage, wie die technische Abwicklung optimiert werden kann. Für Dozenten in der Medizin gibt es zunehmend drei Optionen zur Durchführung von MC-Klausuren: Papierklausuren mit oder ohne Computerunterstützung oder vollständig elektronische Klausuren. Kritische Faktoren sind der Aufwand für die Formatierung der Klausur, der logistische Aufwand bei der Klausurdurchführung, die Qualität, Schnelligkeit und der Aufwand der Klausurkorrektur, die Bereitstellung der Dokumente für die Einsichtnahme, und die statistische Analyse der Klausurergebnisse. Methoden: An der Universität Würzburg wird seit drei Semestern ein Computerprogramm zur Eingabe und Formatierung der MC-Fragen in medizinischen und anderen Papierklausuren verwendet und optimiert, mit dem im Wintersemester (WS) 2009/2010 elf, im Sommersemester (SS) 2010 zwölf und im WS 2010/11 dreizehn medizinische Klausuren erstellt und anschließend die eingescannten Antwortblätter automatisch ausgewertet wurden. In den letzten beiden Semestern wurden die Aufwände protokolliert. Ergebnisse: Der Aufwand der Formatierung und der Auswertung einschl. nachträglicher Anpassung der Auswertung einer Durchschnittsklausur mit ca. 140 Teilnehmern und ca. 35 Fragen ist von 5-7 Stunden für Klausuren ohne Komplikation im WS 2009/2010 über ca. 2 Stunden im SS 2010 auf ca. 1,5 Stunden im WS 2010/11 gefallen. Einschließlich der Klausuren mit Komplikationen bei der Auswertung betrug die durchschnittliche Zeit im SS 2010 ca. 3 Stunden und im WS 10/11 ca. 2,67 Stunden pro Klausur. Diskussion: Für konventionelle Multiple-Choice-Klausuren bietet die computergestützte Formatierung und Auswertung von Papierklausuren einen beträchtlichen Zeitvorteil für die Dozenten im Vergleich zur manuellen Korrektur von Papierklausuren und benötigt im Vergleich zu rein elektronischen Klausuren eine deutlich einfachere technische Infrastruktur und weniger Personal bei der Klausurdurchführung. KW - Multiple-Choice Prüfungen KW - Automatisierte Prüfungskorrektur KW - Aufwandsanalyse KW - Educational Measurement (I2.399) KW - Self-Evaluation Programs (I2.399.780) KW - Multiple-Choice Examination KW - Cost Analysis Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-134386 VL - 28 IS - 4 ER - TY - JOUR A1 - Schokraie, Elham A1 - Warnken, Uwe A1 - Hotz-Wagenblatt, Agnes A1 - Grohme, Markus A. A1 - Hengherr, Steffen A1 - Förster, Frank A1 - Schill, Ralph O. A1 - Frohme, Marcus A1 - Dandekar, Thomas A1 - Schnölzer, Martina T1 - Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state JF - PLoS One N2 - 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. KW - life-span regulation KW - genes KW - Yolk protein KW - water stress KW - expression KW - tolerance KW - richtersius coronifer KW - superoxide-dismutase KW - caenorhabditis elegans KW - arabidopsis thaliana KW - vitellogenin Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-134447 VL - 7 IS - 9 ER - TY - JOUR A1 - Buga, Ana-Maria A1 - Scholz, Claus Jürgen A1 - Kumar, Senthil A1 - Herndon, James G. A1 - Alexandru, Dragos A1 - Cojocaru, Gabriel Radu A1 - Dandekar, Thomas A1 - Popa-Wagner, Aurel T1 - Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke JF - PLoS One N2 - 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. KW - gamma KW - corticotropin-releasing hormone KW - colony-stimulating factor KW - cerebral ischemia KW - receptor KW - brain KW - protein KW - inhibitor KW - mouse KW - differentiation Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-130657 VL - 7 IS - 12 ER -