TY - JOUR A1 - Becker, Martin A1 - Caminiti, Saverio A1 - Fiorella, Donato A1 - Francis, Louise A1 - Gravino, Pietro A1 - Haklay, Mordechai (Muki) A1 - Hotho, Andreas A1 - Loreto, Virrorio A1 - Mueller, Juergen A1 - Ricchiuti, Ferdinando A1 - Servedio, Vito D. P. A1 - Sirbu, Alina A1 - Tria, Franesca T1 - Awareness and Learning in Participatory Noise Sensing JF - PLOS ONE N2 - The development of ICT infrastructures has facilitated the emergence of new paradigms for looking at society and the environment over the last few years. Participatory environmental sensing, i.e. directly involving citizens in environmental monitoring, is one example, which is hoped to encourage learning and enhance awareness of environmental issues. In this paper, an analysis of the behaviour of individuals involved in noise sensing is presented. Citizens have been involved in noise measuring activities through the WideNoise smartphone application. This application has been designed to record both objective (noise samples) and subjective (opinions, feelings) data. The application has been open to be used freely by anyone and has been widely employed worldwide. In addition, several test cases have been organised in European countries. Based on the information submitted by users, an analysis of emerging awareness and learning is performed. The data show that changes in the way the environment is perceived after repeated usage of the application do appear. Specifically, users learn how to recognise different noise levels they are exposed to. Additionally, the subjective data collected indicate an increased user involvement in time and a categorisation effect between pleasant and less pleasant environments. KW - exposure Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-127675 SN - 1932-6203 VL - 8 IS - 12 ER - TY - JOUR A1 - Zirkel, J. A1 - Cecil, A. A1 - Schäfer, F. A1 - Rahlfs, S. A1 - Ouedraogo, A. A1 - Xiao, K. A1 - Sawadogo, S. A1 - Coulibaly, B. A1 - Becker, K. A1 - Dandekar, T. T1 - Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling JF - Bioinformatics and Biology Insights N2 - BACKGROUND: In the face of growing resistance in malaria parasites to drugs, pharmacological combination therapies are important. There is accumulating evidence that methylene blue (MB) is an effective drug against malaria. Here we explore the biological effects of both MB alone and in combination therapy using modeling and experimental data. RESULTS: We built a model of the central metabolic pathways in P. falciparum. Metabolic flux modes and their changes under MB were calculated by integrating experimental data (RT-PCR data on mRNAs for redox enzymes) as constraints and results from the YANA software package for metabolic pathway calculations. Several different lines of MB attack on Plasmodium redox defense were identified by analysis of the network effects. Next, chloroquine resistance based on pfmdr/and pfcrt transporters, as well as pyrimethamine/sulfadoxine resistance (by mutations in DHF/DHPS), were modeled in silico. Further modeling shows that MB has a favorable synergism on antimalarial network effects with these commonly used antimalarial drugs. CONCLUSIONS: Theoretical and experimental results support that methylene blue should, because of its resistance-breaking potential, be further tested as a key component in drug combination therapy efforts in holoendemic areas. KW - methylene blue KW - malaria KW - elementary mode analysis KW - drug KW - resistance KW - combination therapy KW - pathway KW - metabolic flux Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-123751 N1 - This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. VL - 6 ER - TY - JOUR A1 - Krueger, Beate A1 - Friedrich, Torben A1 - Förster, Frank A1 - Bernhardt, Jörg A1 - Gross, Roy A1 - Dandekar, Thomas T1 - Different evolutionary modifications as a guide to rewire two-component systems JF - Bioinformatics and Biology Insights N2 - Two-component systems (TCS) are short signalling pathways generally occurring in prokaryotes. They frequently regulate prokaryotic stimulus responses and thus are also of interest for engineering in biotechnology and synthetic biology. The aim of this study is to better understand and describe rewiring of TCS while investigating different evolutionary scenarios. Based on large-scale screens of TCS in different organisms, this study gives detailed data, concrete alignments, and structure analysis on three general modification scenarios, where TCS were rewired for new responses and functions: (i) exchanges in the sequence within single TCS domains, (ii) exchange of whole TCS domains; (iii) addition of new components modulating TCS function. As a result, the replacement of stimulus and promotor cassettes to rewire TCS is well defined exploiting the alignments given here. The diverged TCS examples are non-trivial and the design is challenging. Designed connector proteins may also be useful to modify TCS in selected cases. KW - histidine kinase KW - connector KW - Mycoplasma KW - engineering KW - promoter KW - sensor KW - response regulator KW - synthetic biology KW - sequence alignment Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-123647 N1 - This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. VL - 6 ER - TY - JOUR A1 - Merget, Benjamin A1 - Koetschan, Christian A1 - Hackl, Thomas A1 - Förster, Frank A1 - Dandekar, Thomas A1 - Müller, Tobias A1 - Schultz, Jörg A1 - Wolf, Matthias T1 - The ITS2 Database JF - Journal of Visual Expression N2 - The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution1 and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation. The ITS2 Database presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank accurately reannotated. Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling. In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold. The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE and ProfDistS for multiple sequence-structure alignment calculation and Neighbor Joining tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure. In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses. KW - homology modeling KW - molecular systematics KW - internal transcribed spacer 2 KW - alignment KW - genetics KW - secondary structure KW - ribosomal RNA KW - phylogenetic tree KW - phylogeny Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124600 VL - 61 IS - e3806 ER - TY - JOUR A1 - Buchin, Kevin A1 - Buchin, Maike A1 - Byrka, Jaroslaw A1 - Nöllenburg, Martin A1 - Okamoto, Yoshio A1 - Silveira, Rodrigo I. A1 - Wolff, Alexander T1 - Drawing (Complete) Binary Tanglegrams JF - Algorithmica N2 - A binary tanglegram is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential that both trees are drawn without edge crossings and that the inter-tree edges have as few crossings as possible. It is known that finding a tanglegram with the minimum number of crossings is NP-hard and that the problem is fixed-parameter tractable with respect to that number. We prove that under the Unique Games Conjecture there is no constant-factor approximation for binary trees. We show that the problem is NP-hard even if both trees are complete binary trees. For this case we give an O(n 3)-time 2-approximation and a new, simple fixed-parameter algorithm. We show that the maximization version of the dual problem for binary trees can be reduced to a version of MaxCut for which the algorithm of Goemans and Williamson yields a 0.878-approximation. KW - NP-hardness KW - crossing minimization KW - binary tanglegram KW - approximation algorithm KW - fixed-parameter tractability Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124622 VL - 62 ER - 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 -