9758
2012
eng
article
1
--
--
--
Augmenting the Connectivity of Planar and Geometric Graphs
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.
Journal of Graph Algorithms and Applications
10.7155/jgaa.00275
urn:nbn:de:bvb:20-opus-97587
In: Journal of Graph Algorithms and Applications (2012) 16: 2, 599-628, DOI: 10.755/jgaa.00275
Deutsches Urheberrecht
Alexander Wolff
Iganz Rutter
Datenverarbeitung; Informatik
open_access
Institut für Informatik
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/9758/Wolff_jgaa-00275.pdf
6429
2012
eng
doctoralthesis
1
2013-02-19
--
2012-10-30
Advances in Distributed Real-Time Sensor/Actuator Systems Operation - Operating Systems, Communication, and Application Design Concepts -
Fortschritte im Betrieb drahtloser Sensor/Aktuator Netzwerke
This work takes a close look at several quite different research areas related to the design of networked embedded sensor/actuator systems. The variety of the topics illustrates the potential complexity of current sensor network applications; especially when enriched with actuators for proactivity and environmental interaction. Besides their conception, development, installation and long-term operation, we'll mainly focus on more "low-level" aspects: Compositional hardware and software design, task cooperation and collaboration, memory management, and real-time operation will be addressed from a local node perspective. In contrast, inter-node synchronization, communication, as well as sensor data acquisition, aggregation, and fusion will be discussed from a rather global network view. The diversity in the concepts was intentionally accepted to finally facilitate the reliable implementation of truly complex systems. In particular, these should go beyond the usual "sense and transmit of sensor data", but show how powerful today's networked sensor/actuator systems can be despite of their low computational performance and constrained hardware: If their resources are only coordinated efficiently!
Diese Arbeit behandelt einige sehr unterschiedliche Forschungsbereiche bezüglich des Designs vernetzter und eingebetteter Sensor/Aktuator-Systeme. Die Vielfalt der Themen zeigt die potenzielle Komplexität aktueller Sensornetzwerk-Anwendungen, insbesondere wenn sie mit Aktuatoren zur Interaktion mit der Umwelt ausgestattet sind. Neben deren Konzeption, Entwicklung, Installation und dem langfristigen Betrieb wird besonders auf diverse "low-level" Aspekte eingegangen: Kompositionelles Hardware- und Software-Design, Task Kooperation und Kollaboration, Speicher-Verwaltung und Echtzeit-Betrieb werden aus lokaler Sicht der Sensorknoten betrachtet. Im Kontrast werden Knoten-Synchronisation, Kommunikation, sowie Sensordatenerfassung, -aggregation und -fusion aus globaler Netzwerk-Sicht diskutiert. Die Vielfalt der behandelten Konzepte wurde bewusst in Kauf genommen, um letztlich die zuverlässige Umsetzung sehr komplexer Systeme zu erleichtern. Insbesondere sollte dies über das übliche "Erfassen und Übertragen von Sensordaten" hinausgehen, und zeigen, wie mächtig heutige vernetzte Sensor/Aktuator-Systeme trotz ihrer geringen Rechenleistung und eingeschränkten Hardware sein können: Wenn ihre Ressourcen effizient koordiniert werden!
urn:nbn:de:bvb:20-opus-76489
7648
X124437
Deutsches Urheberrecht
Marcel Baunach
deu
swd
Eingebettetes System
deu
swd
Drahtloses Sensorsystem
deu
swd
Echtzeitsystem
deu
uncontrolled
Dynamische Speicherverwaltung
deu
uncontrolled
Ressourcenallokation
deu
uncontrolled
Fernwartung
deu
uncontrolled
Betriebssystem
deu
uncontrolled
Verteiltes System
deu
uncontrolled
Lokalisation
eng
uncontrolled
Embedded Systems
eng
uncontrolled
Real-Time Operating Systems
eng
uncontrolled
Localization
eng
uncontrolled
Wireless Sensor/Actuator Systems
eng
uncontrolled
Dynamic Memory Management
Datenverarbeitung; Informatik
open_access
Institut für Informatik
Universität Würzburg
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/6429/dissBaunach.pdf
6699
2012
deu
article
1
2013-07-09
--
--
Cover contact graphs
We study problems that arise in the context of covering certain geometric objects called seeds (e.g., points or disks) by a set of other geometric objects called cover (e.g., a set of disks or homothetic triangles). We insist that the interiors of the seeds and the cover elements are pairwise disjoint, respectively, but they can touch. We call the contact graph of a cover a cover contact graph (CCG). We are interested in three types of tasks, both in the general case and in the special case of seeds on a line: (a) deciding whether a given seed set has a connected CCG, (b) deciding whether a given graph has a realization as a CCG on a given seed set, and (c) bounding the sizes of certain classes of CCG’s. Concerning (a) we give efficient algorithms for the case that seeds are points and show that the problem becomes hard if seeds and covers are disks. Concerning (b) we show that this problem is hard even for point seeds and disk covers (given a fixed correspondence between graph vertices and seeds). Concerning (c) we obtain upper and lower bounds on the number of CCG’s for point seeds.
urn:nbn:de:bvb:20-opus-78845
7884
In: Journal of Computational Geometry (2012) 3(1), 102-131; http://jocg.org/index.php/jocg/article/view/66
Nieves Atienza
Natalia de Castro
Carmen Cortés
M. Ángeles Garrido
Clara I. Grima
Gregorio Hernández
Alberto Márquez
Auxiliadora Moreno-González
Martin Nöllenburg
José Ramón Portillo
Pedro Reyes
Jesús Valenzuela
Maria Trinidad Villar
Alexander Wolff
deu
swd
Informatik
Datenverarbeitung; Informatik
open_access
Institut für Informatik
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/6699/091_jocg_3_1.pdf
12375
2012
eng
287-302
6
article
1
2015-12-22
--
--
Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling
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.
Bioinformatics and Biology Insights
10.4137/BBI.S10193
PMC3516044
urn:nbn:de:bvb:20-opus-123751
This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.
Bioinformatics and Biology Insights 2012:6 287–302. doi: 10.4137/BBI.S10193
J. Zirkel
A. Cecil
F. Schäfer
S. Rahlfs
A. Ouedraogo
K. Xiao
S. Sawadogo
B. Coulibaly
K. Becker
T. Dandekar
eng
uncontrolled
methylene blue
eng
uncontrolled
malaria
eng
uncontrolled
elementary mode analysis
eng
uncontrolled
drug
eng
uncontrolled
resistance
eng
uncontrolled
combination therapy
eng
uncontrolled
pathway
eng
uncontrolled
metabolic flux
Datenverarbeitung; Informatik
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12375/f_3443-BBI-Analyzing-Thiol-Dependent-Redox-Networks-in-the-Presence-of-Methylene-.pdf_4656.pdf
12364
2012
eng
97-128
6
article
1
2015-12-21
--
--
Different evolutionary modifications as a guide to rewire two-component systems
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.
Bioinformatics and Biology Insights
PMC3348925
10.4137/BBI.S9356
urn:nbn:de:bvb:20-opus-123647
This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.
Bioinformatics and Biology Insights 2012:6 97–128. doi: 10.4137/BBI.S9356
Beate Krueger
Torben Friedrich
Frank Förster
Jörg Bernhardt
Roy Gross
Thomas Dandekar
eng
uncontrolled
histidine kinase
eng
uncontrolled
connector
eng
uncontrolled
Mycoplasma
eng
uncontrolled
engineering
eng
uncontrolled
promoter
eng
uncontrolled
sensor
eng
uncontrolled
response regulator
eng
uncontrolled
synthetic biology
eng
uncontrolled
sequence alignment
Datenverarbeitung; Informatik
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12364/f_3168-BBI-Different-Evolutionary-Modifications-as-a-Guide-to-Rewire-Two-Componen.pdf_4288.pdf
12460
2012
eng
e3806
61
article
1
2016-01-19
--
--
The ITS2 Database
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.
Journal of Visual Expression
10.3791/3806
urn:nbn:de:bvb:20-opus-124600
Journal of Visual Expression (61), e3806, doi:10.3791/3806 (2012)
Benjamin Merget
Christian Koetschan
Thomas Hackl
Frank Förster
Thomas Dandekar
Tobias Müller
Jörg Schultz
Matthias Wolf
eng
uncontrolled
homology modeling
eng
uncontrolled
molecular systematics
eng
uncontrolled
internal transcribed spacer 2
eng
uncontrolled
alignment
eng
uncontrolled
genetics
eng
uncontrolled
secondary structure
eng
uncontrolled
ribosomal RNA
eng
uncontrolled
phylogenetic tree
eng
uncontrolled
phylogeny
Datenverarbeitung; Informatik
Chemie und zugeordnete Wissenschaften
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Institut für Pharmazie und Lebensmittelchemie
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12460/jove-61-3806.pdf
12462
2012
eng
309-332
62
article
1
2016-01-19
--
--
Drawing (Complete) Binary Tanglegrams
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.
Algorithmica
10.1007/s00453-010-9456-3
urn:nbn:de:bvb:20-opus-124622
Algorithmica (2012) 62:309–332. doi:10.1007/s00453-010-9456-3
Kevin Buchin
Maike Buchin
Jaroslaw Byrka
Martin Nöllenburg
Yoshio Okamoto
Rodrigo I. Silveira
Alexander Wolff
eng
uncontrolled
NP-hardness
eng
uncontrolled
crossing minimization
eng
uncontrolled
binary tanglegram
eng
uncontrolled
approximation algorithm
eng
uncontrolled
fixed-parameter tractability
Datenverarbeitung; Informatik
open_access
Institut für Informatik
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12462/art_10.1007_s00453-010-9456-3.pdf
13132
2012
eng
e34796
4
7
article
1
2016-04-05
--
--
A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer
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.
PLoS One
10.1371/journal.pone.0034796
urn:nbn:de:bvb:20-opus-131323
PLoS ONE 7(4): e34796. doi:10.1371/journal.pone.0034796
Christine Staiger
Sidney Cadot
Raul Kooter
Marcus Dittrich
Tobias Müller
Gunnar W. Klau
Lodewyk F. A. Wessels
eng
uncontrolled
modules
eng
uncontrolled
protein-interaction networks
eng
uncontrolled
expression signature
eng
uncontrolled
classification
eng
uncontrolled
set
eng
uncontrolled
metastasis
eng
uncontrolled
stability
eng
uncontrolled
survival
eng
uncontrolled
database
eng
uncontrolled
markers
Datenverarbeitung; Informatik
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/13132/Staiger_PlosOne.pdf
13112
2012
eng
1
25
3:27
8
article
1
2016-04-01
--
--
Complexity Classifications for Different Equivalence and Audit Problems for Boolean Circuits
We study Boolean circuits as a representation of Boolean functions and conskier different equivalence, audit, and enumeration problems. For a number of restricted sets of gate types (bases) we obtain efficient algorithms, while for all other gate types we show these problems are at least NP-hard.
Logical Methods in Computer Science
10.2168/LMCS-8(3:27)2012
urn:nbn:de:bvb:20-opus-131121
Logical Methods in Computer Science Vol. 8(3:27)2012, pp. 1–25. DOI:10.2168/LMCS-8(3:27)2012
Elmar Böhler
Nadia Creignou
Matthias Galota
Steffen Reith
Henning Schnoor
Heribert Vollmer
eng
uncontrolled
hierarchy
eng
uncontrolled
satisfiability problems
Datenverarbeitung; Informatik
open_access
Institut für Informatik
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/13112/Boehler_1009_1208.pdf
13444
2012
eng
e45682
9
7
article
1
2016-06-06
--
--
Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state
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.
PLoS One
10.1371/journal.pone.0045682
urn:nbn:de:bvb:20-opus-134447
PLoS ONE 7(9): e45682. doi:10.1371/journal.pone.0045682
Elham Schokraie
Uwe Warnken
Agnes Hotz-Wagenblatt
Markus A. Grohme
Steffen Hengherr
Frank Förster
Ralph O. Schill
Marcus Frohme
Thomas Dandekar
Martina Schnölzer
eng
uncontrolled
life-span regulation
eng
uncontrolled
genes
eng
uncontrolled
Yolk protein
eng
uncontrolled
water stress
eng
uncontrolled
expression
eng
uncontrolled
tolerance
eng
uncontrolled
richtersius coronifer
eng
uncontrolled
superoxide-dismutase
eng
uncontrolled
caenorhabditis elegans
eng
uncontrolled
arabidopsis thaliana
eng
uncontrolled
vitellogenin
Datenverarbeitung; Informatik
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/13444/Schokraie_PLoSOne.pdf