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 - THES A1 - Kindermann, Philipp T1 - Angular Schematization in Graph Drawing N2 - Graphs are a frequently used tool to model relationships among entities. A graph is a binary relation between objects, that is, it consists of a set of objects (vertices) and a set of pairs of objects (edges). Networks are common examples of modeling data as a graph. For example, relationships between persons in a social network, or network links between computers in a telecommunication network can be represented by a graph. The clearest way to illustrate the modeled data is to visualize the graphs. The field of Graph Drawing deals with the problem of finding algorithms to automatically generate graph visualizations. The task is to find a "good" drawing, which can be measured by different criteria such as number of crossings between edges or the used area. In this thesis, we study Angular Schematization in Graph Drawing. By this, we mean drawings with large angles (for example, between the edges at common vertices or at crossing points). The thesis consists of three parts. First, we deal with the placement of boxes. Boxes are axis-parallel rectangles that can, for example, contain text. They can be placed on a map to label important sites, or can be used to describe semantic relationships between words in a word network. In the second part of the thesis, we consider graph drawings visually guide the viewer. These drawings generally induce large angles between edges that meet at a vertex. Furthermore, the edges are drawn crossing-free and in a way that makes them easy to follow for the human eye. The third and final part is devoted to crossings with large angles. In drawings with crossings, it is important to have large angles between edges at their crossing point, preferably right angles. N2 - Graphen sind häufig verwendete Werkzeuge zur Modellierung von Zusammenhängen zwischen Daten. Ein Graph ist eine binäre Relation zwischen Objekten, das heißt er besteht aus einer Menge von Objekten (Knoten) und einer Menge von Paaren von Objekten (Kanten). Netzwerke sind übliche Beispiele für das Modellieren von Daten als ein Graph. Beispielsweise lassen sich Beziehungen zwischen Personen in einem sozialen Netzwerk oder Netzanbindungen zwischen Computern in einem Telekommunikationsnetz als Graph darstellen. Die modellierten Daten können am anschaulichsten dargestellt werden, indem man die Graphen visualisiert. Der Bereich des Graphenzeichnens behandelt das Problem, Algorithmen zum automatischen Erzeugen von Graphenvisualisierungen zu finden. Das Ziel ist es, eine "gute" Zeichnung zu finden, was durch unterschiedliche Kriterien gemessen werden kann; zum Beispiel durch die Anzahl der Kreuzungen zwischen Kanten oder durch den Platzverbrauch. In dieser Arbeit beschäftigen wir uns mit Winkelschematisierung im Graphenzeichnen. Darunter verstehen wir Zeichnungen, in denen die Winkel (zum Beispiel zwischen Kanten an einem gemeinsamen Knoten oder einem Kreuzungspunkt) möglichst groß gestaltet sind. Die Arbeit besteht aus drei Teilen. Im ersten Teil betrachten wir die Platzierung von Boxen. Boxen sind achsenparallele Rechtecke, die zum Beispiel Text enthalten. Sie können beispielsweise auf einer Karte platziert werden, um wichtige Standorte zu beschriften, oder benutzt werden, um semantische Beziehungen zwischen Wörtern in einem Wortnetzwerk darzustellen. Im zweiten Teil der Arbeit untersuchen wir Graphenzeichnungen, die den Betrachter visuell führen. Im Allgemeinen haben diese Zeichnungen große Winkel zwischen Kanten, die sich in einem Knoten treffen. Außerdem werden die Verbindungen kreuzungsfrei und so gezeichnet, dass es dem menschlichen Auge leicht fällt, ihnen zu folgen. Im dritten und letzten Teil geht es um Kreuzungen mit großen Winkeln. In Zeichnungen mit Kreuzungen ist es wichtig, dass die Winkel zwischen Kanten an Kreuzungspunkten groß sind, vorzugsweise rechtwinklig. KW - graph drawing KW - angular schematization KW - boundary labeling KW - contact representation KW - word clouds KW - monotone drawing KW - smooth orthogonal drawing KW - simultaneous embedding KW - right angle crossing KW - independent crossing KW - Graphenzeichnen KW - Winkel KW - Kreuzung KW - v Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-112549 SN - 978-3-95826-020-7 (print) SN - 978-3-95826-021-4 (online) PB - Würzburg University Press CY - Würzburg ER - TY - INPR A1 - Nassourou, Mohamadou T1 - Assisting Analysis and Understanding of Quran Search Results with Interactive Scatter Plots and Tables N2 - The Quran is the holy book of Islam consisting of 6236 verses divided into 114 chapters called suras. Many verses are similar and even identical. Searching for similar texts (e.g verses) could return thousands of verses, that when displayed completely or partly as textual list would make analysis and understanding difficult and confusing. Moreover it would be visually impossible to instantly figure out the overall distribution of the retrieved verses in the Quran. As consequence reading and analyzing the verses would be tedious and unintuitive. In this study a combination of interactive scatter plots and tables has been developed to assist analysis and understanding of the search result. Retrieved verses are clustered by chapters, and a weight is assigned to each cluster according to number of verses it contains, so that users could visually identify most relevant areas, and figure out the places of revelation of the verses. Users visualize the complete result and can select a region of the plot to zoom in, click on a marker to display a table containing verses with English translation side by side. KW - Text Mining KW - Visualisierung KW - Koran KW - Information Visualization KW - Visual Text Mining KW - Scatter Plot KW - Quran Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-55840 ER - TY - INPR A1 - Nassourou, Mohamadou T1 - Assisting Understanding, Retention, and Dissemination of Religious Texts Knowledge with Modeling, and Visualization Techniques: The Case of The Quran N2 - Learning a book in general involves reading it, underlining important words, adding comments, summarizing some passages, and marking up some text or concepts. Once deeper understanding is achieved, one would like to organize and manage her/his knowledge in such a way that, it could be easily remembered and efficiently transmitted to others. In this paper, books organized in terms of chapters consisting of verses, are considered as the source of knowledge to be modeled. The knowledge model consists of verses with their metadata and semantic annotations. The metadata represent the multiple perspectives of knowledge modeling. Verses with their metadata and annotations form a meta-model, which will be published on a web Mashup. The meta-model with linking between its elements constitute a knowledge base. An XML-based annotation system breaking down the learning process into specific tasks, helps constructing the desired meta-model. The system is made up of user interfaces for creating metadata, annotating chapters’ contents according to user selected semantics, and templates for publishing the generated knowledge on the Internet. The proposed software system improves comprehension and retention of knowledge contained in religious texts through modeling and visualization. The system has been applied to the Quran, and the result obtained shows that multiple perspectives of information modeling can be successfully applied to religious texts. It is expected that this short ongoing study would motivate others to engage in devising and offering software systems for cross-religions learning. KW - Wissensmanagement KW - Koran KW - Knowledge Modeling KW - Meta-model KW - Knowledge Management KW - Content Management KW - Quran Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-55927 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 - Wolff, Alexander A1 - Rutter, Iganz T1 - Augmenting the Connectivity of Planar and Geometric Graphs JF - Journal of Graph Algorithms and Applications N2 - In this paper we study connectivity augmentation problems. Given a connected graph G with some desirable property, we want to make G 2-vertex connected (or 2-edge connected) by adding edges such that the resulting graph keeps the property. The aim is to add as few edges as possible. The property that we consider is planarity, both in an abstract graph-theoretic and in a geometric setting, where vertices correspond to points in the plane and edges to straight-line segments. We show that it is NP-hard to � nd a minimum-cardinality augmentation that makes a planar graph 2-edge connected. For making a planar graph 2-vertex connected this was known. We further show that both problems are hard in the geometric setting, even when restricted to trees. The problems remain hard for higher degrees of connectivity. On the other hand we give polynomial-time algorithms for the special case of convex geometric graphs. We also study the following related problem. Given a planar (plane geometric) graph G, two vertices s and t of G, and an integer c, how many edges have to be added to G such that G is still planar (plane geometric) and contains c edge- (or vertex-) disjoint s{t paths? For the planar case we give a linear-time algorithm for c = 2. For the plane geometric case we give optimal worst-case bounds for c = 2; for c = 3 we characterize the cases that have a solution. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-97587 ER - TY - JOUR A1 - Krenzer, Adrian A1 - Heil, Stefan A1 - Fitting, Daniel A1 - Matti, Safa A1 - Zoller, Wolfram G. A1 - Hann, Alexander A1 - Puppe, Frank T1 - Automated classification of polyps using deep learning architectures and few-shot learning JF - BMC Medical Imaging N2 - Background Colorectal cancer is a leading cause of cancer-related deaths worldwide. The best method to prevent CRC is a colonoscopy. However, not all colon polyps have the risk of becoming cancerous. Therefore, polyps are classified using different classification systems. After the classification, further treatment and procedures are based on the classification of the polyp. Nevertheless, classification is not easy. Therefore, we suggest two novel automated classifications system assisting gastroenterologists in classifying polyps based on the NICE and Paris classification. Methods We build two classification systems. One is classifying polyps based on their shape (Paris). The other classifies polyps based on their texture and surface patterns (NICE). A two-step process for the Paris classification is introduced: First, detecting and cropping the polyp on the image, and secondly, classifying the polyp based on the cropped area with a transformer network. For the NICE classification, we design a few-shot learning algorithm based on the Deep Metric Learning approach. The algorithm creates an embedding space for polyps, which allows classification from a few examples to account for the data scarcity of NICE annotated images in our database. Results For the Paris classification, we achieve an accuracy of 89.35 %, surpassing all papers in the literature and establishing a new state-of-the-art and baseline accuracy for other publications on a public data set. For the NICE classification, we achieve a competitive accuracy of 81.13 % and demonstrate thereby the viability of the few-shot learning paradigm in polyp classification in data-scarce environments. Additionally, we show different ablations of the algorithms. Finally, we further elaborate on the explainability of the system by showing heat maps of the neural network explaining neural activations. Conclusion Overall we introduce two polyp classification systems to assist gastroenterologists. We achieve state-of-the-art performance in the Paris classification and demonstrate the viability of the few-shot learning paradigm in the NICE classification, addressing the prevalent data scarcity issues faced in medical machine learning. KW - machine learning KW - deep learning KW - endoscopy KW - gastroenterology KW - automation KW - image classification KW - transformer KW - deep metric learning KW - few-shot learning Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-357465 VL - 23 ER - TY - JOUR A1 - Becker, Martin A1 - Caminiti, Saverio A1 - Fiorella, Donato A1 - Francis, Louise A1 - Gravino, Pietro A1 - Haklay, Mordechai (Muki) A1 - Hotho, Andreas A1 - Loreto, Virrorio A1 - Mueller, Juergen A1 - Ricchiuti, Ferdinando A1 - Servedio, Vito D. P. A1 - Sirbu, Alina A1 - Tria, Franesca T1 - Awareness and Learning in Participatory Noise Sensing JF - PLOS ONE N2 - The development of ICT infrastructures has facilitated the emergence of new paradigms for looking at society and the environment over the last few years. Participatory environmental sensing, i.e. directly involving citizens in environmental monitoring, is one example, which is hoped to encourage learning and enhance awareness of environmental issues. In this paper, an analysis of the behaviour of individuals involved in noise sensing is presented. Citizens have been involved in noise measuring activities through the WideNoise smartphone application. This application has been designed to record both objective (noise samples) and subjective (opinions, feelings) data. The application has been open to be used freely by anyone and has been widely employed worldwide. In addition, several test cases have been organised in European countries. Based on the information submitted by users, an analysis of emerging awareness and learning is performed. The data show that changes in the way the environment is perceived after repeated usage of the application do appear. Specifically, users learn how to recognise different noise levels they are exposed to. Additionally, the subjective data collected indicate an increased user involvement in time and a categorisation effect between pleasant and less pleasant environments. KW - exposure Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-127675 SN - 1932-6203 VL - 8 IS - 12 ER - TY - JOUR A1 - Wienrich, Carolin A1 - Döllinger, Nina A1 - Hein, Rebecca T1 - Behavioral Framework of Immersive Technologies (BehaveFIT): How and why virtual reality can support behavioral change processes JF - Frontiers in Virtual Reality N2 - The design and evaluation of assisting technologies to support behavior change processes have become an essential topic within the field of human-computer interaction research in general and the field of immersive intervention technologies in particular. The mechanisms and success of behavior change techniques and interventions are broadly investigated in the field of psychology. However, it is not always easy to adapt these psychological findings to the context of immersive technologies. The lack of theoretical foundation also leads to a lack of explanation as to why and how immersive interventions support behavior change processes. The Behavioral Framework for immersive Technologies (BehaveFIT) addresses this lack by 1) presenting an intelligible categorization and condensation of psychological barriers and immersive features, by 2) suggesting a mapping that shows why and how immersive technologies can help to overcome barriers and finally by 3) proposing a generic prediction path that enables a structured, theory-based approach to the development and evaluation of immersive interventions. These three steps explain how BehaveFIT can be used, and include guiding questions for each step. Further, two use cases illustrate the usage of BehaveFIT. Thus, the present paper contributes to guidance for immersive intervention design and evaluation, showing that immersive interventions support behavior change processes and explain and predict 'why' and 'how' immersive interventions can bridge the intention-behavior-gap. KW - immersive technologies KW - behavior change KW - intervention design KW - intervention evaluation KW - framework KW - virtual reality KW - intention-behavior-gap KW - human-computer interaction Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-258796 VL - 2 ER - TY - INPR A1 - Dandekar, Thomas T1 - Biological heuristics applied to cosmology suggests a condensation nucleus as start of our universe and inflation cosmology replaced by a period of rapid Weiss domain-like crystal growth N2 - Cosmology often uses intricate formulas and mathematics to derive new theories and concepts. We do something different in this paper: We look at biological processes and derive from these heuristics so that the revised cosmology agrees with astronomical observations but does also agree with standard biological observations. We show that we then have to replace any type of singularity at the start of the universe by a condensation nucleus and that the very early period of the universe usually assumed to be inflation has to be replaced by a period of rapid crystal growth as in Weiss magnetization domains. Impressively, these minor modifications agree well with astronomical observations including removing the strong inflation perturbations which were never observed in the recent BICEP2 experiments. Furthermore, looking at biological principles suggests that such a new theory with a condensation nucleus at start and a first rapid phase of magnetization-like growth of the ordered, physical laws obeying lattice we live in is in fact the only convincing theory of the early phases of our universe that also is compatible with current observations. We show in detail in the following that such a process of crystal creation, breaking of new crystal seeds and ultimate evaporation of the present crystal readily leads over several generations to an evolution and selection of better, more stable and more self-organizing crystals. Moreover, this explains the “fine-tuning” question why our universe is fine-tuned to favor life: Our Universe is so self-organizing to have enough offspring and the detailed physics involved is at the same time highly favorable for all self-organizing processes including life. This biological theory contrasts with current standard inflation cosmologies. The latter do not perform well in explaining any phenomena of sophisticated structure creation or self-organization. As proteins can only thermodynamically fold by increasing the entropy in the solution around them we suggest for cosmology a condensation nucleus for a universe can form only in a “chaotic ocean” of string-soup or quantum foam if the entropy outside of the nucleus rapidly increases. We derive an interaction potential for 1 to n-dimensional strings or quantum-foams and show that they allow only 1D, 2D, 4D or octonion interactions. The latter is the richest structure and agrees to the E8 symmetry fundamental to particle physics and also compatible with the ten dimensional string theory E8 which is part of the M-theory. Interestingly, any other interactions of other dimensionality can be ruled out using Hurwitz compositional theorem. Crystallization explains also extremely well why we have only one macroscopic reality and where the worldlines of alternative trajectories exist: They are in other planes of the crystal and for energy reasons they crystallize mostly at the same time, yielding a beautiful and stable crystal. This explains decoherence and allows to determine the size of Planck´s quantum h (very small as separation of crystal layers by energy is extremely strong). Ultimate dissolution of real crystals suggests an explanation for dark energy agreeing with estimates for the “big rip”. The halo distribution of dark matter favoring galaxy formation is readily explained by a crystal seed starting with unit cells made of normal and dark matter. That we have only matter and not antimatter can be explained as there may be right handed mattercrystals and left-handed antimatter crystals. Similarly, real crystals are never perfect and we argue that exactly such irregularities allow formation of galaxies, clusters and superclusters. Finally, heuristics from genetics suggest to look for a systems perspective to derive correct vacuum and Higgs Boson energies. KW - heuristics KW - inflation KW - cosmology KW - crystallization KW - crystal growth KW - E8 symmetry KW - Hurwitz theorem KW - evolution KW - Lee Smolin Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-183945 ER -