2024-03-29T11:30:50Z
http://sdvcmr-prod-oai01:8080/oai/
oai:qucosa:de:qucosa:10837
2021-03-29T08:12:48Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
status-type:publishedVersion
openaire
Zu Berechenbarkeitsfragen der Idealtheorie.
urn:nbn:de:bsz:15-qucosa-36195
ger
Informatik, Datenverarbeitung
info:eu-repo/classification/ddc/000
ddc:000
Apel, Joachim
Universität Leipzig
1998-09-04
info:eu-repo/semantics/publishedVersion
2004-11-28
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A10837
https://ul.qucosa.de/api/qucosa%3A10837/attachment/ATT-0/
oai:qucosa:de:qucosa:10854
2021-03-29T08:13:01Z
qucosa:ubl
doc-type:report
doc-type:Text
open_access
ddc:000
ddc:500
openaire
Übersicht über die Habilitationen an der Fakultät für Mathematik und Informatik der Universität Leipzig von 1993 bis 1997
urn:nbn:de:bsz:15-qucosa-36360
ger
info:eu-repo/classification/ddc/500
ddc:500
info:eu-repo/classification/ddc/000
ddc:000
Mathematik
Informatik, Datenverarbeitung
Universität Leipzig
2004-11-28
1999-03-12
info:eu-repo/semantics/openAccess
doc-type:report
info:eu-repo/semantics/report
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A10854
https://ul.qucosa.de/api/qucosa%3A10854/attachment/ATT-0/
oai:qucosa:de:qucosa:10855
2021-11-16T08:58:33Z
qucosa:ubl
doc-type:report
doc-type:Text
open_access
ddc:000
ddc:500
openaire
Übersicht über die Promotionen an der Fakultät für Mathematik und Informatik der Universität Leipzig von 1993 bis 1997
urn:nbn:de:bsz:15-qucosa-36376
ger
Mathematik
Informatik, Datenverarbeitung
info:eu-repo/classification/ddc/500
ddc:500
info:eu-repo/classification/ddc/000
ddc:000
Universität Leipzig
2004-11-28
info:eu-repo/semantics/openAccess
doc-type:report
info:eu-repo/semantics/report
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A10855
https://ul.qucosa.de/api/qucosa%3A10855/attachment/ATT-0/
oai:qucosa:de:qucosa:10867
2021-03-29T08:13:11Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
ddc:500
status-type:publishedVersion
openaire
Investigations in Belnap's Logic of Inconsistent and Unknown Information
urn:nbn:de:bsz:15-qucosa-36489
eng
Nuel Belnap schlug 1977 eine vierwertige Logik vor, die -- im Gegensatz zur klassischen Logik -- die Faehigkeit haben sollte, sowohl mit widerspruechlicher als auch mit fehlender Information umzugehen. Diese Logik hat jedoch den Nachteil, dass sie Saetze der Form 'wenn ..., dann ...' nicht ausdruecken kann. Ausgehend von dieser Beobachtung analysieren wir die beiden nichtklassischen Aspekte, Widerspruechlichkeit und fehlende Information, indem wir eine dreiwertige Logik entwickeln, die mit widerspruechlicher Information umgehen kann und eine Modallogik, die mit fehlender Information umgehen kann. Beide Logiken sind nicht monoton. Wir untersuchen Eigenschaften, wie z.B. Kompaktheit, Entscheidbarkeit, Deduktionstheoreme und Berechnungkomplexitaet dieser Logiken. Es stellt sich heraus, dass die dreiwertige Logik, nicht kompakt und ihre Folgerungsmenge im Allgemeinen nicht rekursiv aufzaehlbar ist. Beschraenkt man sich hingegen auf endliche Formelmengen, so ist die Folgerungsmenge rekursiv entscheidbar, liegt in der Klasse $\Sigma_2^P$ der polynomiellen Zeithierarchie und ist DIFFP-schwer. Wir geben ein auf semantischen Tableaux basierendes, korrektes und vollstaendiges Berechnungsverfahren fuer endliche Praemissenmengen an. Darueberhinaus untersuchen wir Abschwaechungen der Kompaktheitseigenschaft. Die nichtmonotone auf S5-Modellen basierende Modallogik stellt sich als nicht minder komplex heraus. Auch hier untersuchen wir eine sinnvolle Abschwaechung der Kompaktheitseigenschaft. Desweiteren studieren wir den Zusammenhang zu anderen nichtmonotonen Modallogiken wie Moores autoepistemischer Logik (AEL) und McDermotts NML-2. Wir zeigen, dass unsere Logik zwischen AEL und NML-2 liegt. Schliesslich koppeln wir die entworfene Modallogik mit der dreiwertigen Logik. Die dabei enstehende Logik MKT ist eine Erweiterung des nichtmonotonen Fragments von Belnaps Logik. Wir schliessen unsere Betrachtungen mit einem Vergleich von MKT und verschiedenen informationstheoretischen Logiken, wie z.B. Nelsons N und Heytings intuitionistischer Logik ab.
Mathematik
Informatik, Datenverarbeitung
Multi-valued Logic, Nonmonotonic Logic, Paraconsistency
info:eu-repo/classification/ddc/500
ddc:500
info:eu-repo/classification/ddc/000
ddc:000
Weber, Stefan
Universität Leipzig
1998-01-01
1998-12-03
info:eu-repo/semantics/publishedVersion
2004-11-28
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A10867
https://ul.qucosa.de/api/qucosa%3A10867/attachment/ATT-0/
oai:qucosa:de:qucosa:10871
2021-03-29T08:13:13Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
status-type:publishedVersion
openaire
Ein mechanisches Finite-Elemente-Modell des menschlichen Kopfes
urn:nbn:de:bsz:15-qucosa-36521
ger
In dieser Arbeit wird ein dreidimensionales Modell des menschlichen Kopfes beschrieben, das es erlaubt, mit der Methode der Finiten Elemente mechanische Einfluesse auf den Kopf zu modellieren. Eine exakte Geometriebeschreibung eines individuellen Modells wird aus einem Kernspintomogramm des Kopfes gewonnen. Ausgehend von diesen medizinischen Bilddaten wird die diskrete Darstellung des Kopfes als Verbund finiter Elemente mit einem Gittergenerator gewonnen. Dieser schnelle und stabile Algorithmus ermoeglicht die Erstellung von raeumlich hochaufgeloesten Finite-Elemente-Repraesentationen des Schaedels und interner neuroanatomischer Strukturen. Es besteht die Auswahl zwischen anisotropen und isotropen Wuerfel- und Tetraedernetzen. Auf deren Basis werden die dem physikalischen Geschehen zugrundeliegenden Differentialgleichungen mittels der Finite-Elemente-Methode numerisch geloest. Die FE-Analysen umfassen statische, dynamische und modale Simulationsrechnungen. Die zur Durchfuehrung der Simulationen noetigen numerischen Verfahren wurden optimiert und auf einer parallelen Rechnerarchitektur implementiert. Jeder der oben genannten Analysearten ist eine klinisch-relevante Anwendung zugeordnet. Mit der nichtlinearen statischen Analyse werden die mechanischen Konsequenzen von Tumorwachstum untersucht, die dynamische Analyse dient dem Studium der Auswirkungen von fokalen Gewalteinwirkungen auf den Kopf und die modale Analyse gibt Aufschluss ueber das Schwingungsverhalten des Kopfes. Die Validierung des Modells wird durch den Vergleich von Simulationsergebnissen mit experimentell ermittelten Daten erzielt.
A new FEM-based approach to model the mechanical response of the head is presented.To overcome restrictions of previous approaches our head model is based on individual datasets of the head obtained from magnetic resonance imaging (MRI). The use of parallel computers allows to carry out biomechanical simulations based on FE meshes with a spatial resolution about five times higher than that of previous models. A totally automatic procedure to generate FE meshes of the head starting from MR datasets is used. Models for individual clinical cases can be set up within minutes and clinically relevant simulations (impact studies, tumor growth consequences) are carried out and discussed by comparing simulation results with experimentally obtained data.
Informatik, Datenverarbeitung
Finite-Elemente-Methode, Biomechanik, Netzgenerierung, Kopf, Gehirn, Simulation,
info:eu-repo/classification/ddc/000
ddc:000
Hartmann, Ulrich
Universität Leipzig
1999-01-01
1999-10-06
info:eu-repo/semantics/publishedVersion
2004-11-28
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A10871
https://ul.qucosa.de/api/qucosa%3A10871/attachment/ATT-0/
oai:qucosa:de:qucosa:10890
2021-03-29T08:13:28Z
qucosa:ubl
doc-type:report
doc-type:Text
open_access
ddc:000
ddc:500
openaire
Übersicht über die Habilitationen an der Fakultät für Mathematik und Informatik der Universität Leipzig von 1998 bis 2000
urn:nbn:de:bsz:15-qucosa-36702
ger
info:eu-repo/classification/ddc/500
ddc:500
info:eu-repo/classification/ddc/000
ddc:000
Mathematik
Informatik, Datenverarbeitung
Universität Leipzig
2004-11-28
2001-08-06
info:eu-repo/semantics/openAccess
doc-type:report
info:eu-repo/semantics/report
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A10890
https://ul.qucosa.de/api/qucosa%3A10890/attachment/ATT-0/
oai:qucosa:de:qucosa:10906
2021-11-16T09:00:40Z
qucosa:ubl
doc-type:report
doc-type:Text
open_access
ddc:000
ddc:500
openaire
Übersicht über die Promotionen an der Fakultät für Mathematik und Informatik der Universität Leipzig von 1998 bis 2000
urn:nbn:de:bsz:15-qucosa-36857
ger
Mathematik
Informatik, Datenverarbeitung
info:eu-repo/classification/ddc/500
ddc:500
info:eu-repo/classification/ddc/000
ddc:000
Universität Leipzig
2004-11-28
info:eu-repo/semantics/openAccess
doc-type:report
info:eu-repo/semantics/report
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A10906
https://ul.qucosa.de/api/qucosa%3A10906/attachment/ATT-0/
oai:qucosa:de:qucosa:10960
2021-03-29T08:14:20Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
status-type:publishedVersion
openaire
Event-Oriented Dynamic Adaptation of Workflows: Model, Architecture and Implementation
urn:nbn:de:bsz:15-qucosa-37372
eng
Workflow management is widely accepted as a core technology to support long-term business processes in heterogeneous and distributed environments. However, conventional workflow management systems do not provide sufficient flexibility support to cope with the broad range of failure situations that may occur during workflow execution. In particular, most systems do not allow to dynamically adapt a workflow due to a failure situation, e.g., to dynamically drop or insert execution steps. As a contribution to overcome these limitations, this dissertation introduces the agent-based workflow management system AgentWork. AgentWork supports the definition, the execution and, as its main contribution, the event-oriented and semi-automated dynamic adaptation of workflows. Two strategies for automatic workflow adaptation are provided. Predictive adaptation adapts workflow parts affected by a failure in advance (predictively), typically as soon as the failure is detected. This is advantageous in many situations and gives enough time to meet organizational constraints for adapted workflow parts. Reactive adaptation is typically performed when predictive adaptation is not possible. In this case, adaptation is performed when the affected workflow part is to be executed, e.g., before an activity is executed it is checked whether it is subject to a workflow adaptation such as dropping, postponement or replacement. In particular, the following contributions are provided by AgentWork: A Formal Model for Workflow Definition, Execution, and Estimation: In this context, AgentWork first provides an object-oriented workflow definition language. This language allows for the definition of a workflows control and data flow. Furthermore, a workflows cooperation with other workflows or workflow systems can be specified. Second, AgentWork provides a precise workflow execution model. This is necessary, as a running workflow usually is a complex collection of concurrent activities and data flow processes, and as failure situations and dynamic adaptations affect running workflows. Furthermore, mechanisms for the estimation of a workflows future execution behavior are provided. These mechanisms are of particular importance for predictive adaptation. Mechanisms for Determining and Processing Failure Events and Failure Actions: AgentWork provides mechanisms to decide whether an event constitutes a failure situation and what has to be done to cope with this failure. This is formally achieved by evaluating event-condition-action rules where the event-condition part describes under which condition an event has to be viewed as a failure event. The action part represents the necessary actions needed to cope with the failure. To support the temporal dimension of events and actions, this dissertation provides a novel event-condition-action model based on a temporal object-oriented logic. Mechanisms for the Adaptation of Affected Workflows: In case of failure situations it has to be decided how an affected workflow has to be dynamically adapted on the node and edge level. AgentWork provides a novel approach that combines the two principal strategies reactive adaptation and predictive adaptation. Depending on the context of the failure, the appropriate strategy is selected. Furthermore, control flow adaptation operators are provided which translate failure actions into structural control flow adaptations. Data flow operators adapt the data flow after a control flow adaptation, if necessary. Mechanisms for the Handling of Inter-Workflow Implications of Failure Situations: AgentWork provides novel mechanisms to decide whether a failure situation occurring to a workflow affects other workflows that communicate and cooperate with this workflow. In particular, AgentWork derives the temporal implications of a dynamic adaptation by estimating the duration that will be needed to process the changed workflow definition (in comparison with the original definition). Furthermore, qualitative implications of the dynamic change are determined. For this purpose, so-called quality measuring objects are introduced. All mechanisms provided by AgentWork include that users may interact during the failure handling process. In particular, the user has the possibility to reject or modify suggested workflow adaptations. A Prototypical Implementation: Finally, a prototypical Corba-based implementation of AgentWork is described. This implementation supports the integration of AgentWork into the distributed and heterogeneous environments of real-world organizations such as hospitals or insurance business enterprises.
Informatik, Datenverarbeitung
Databases, Workflow Management, Adaptive Systems, Computer-Supported Therapy
info:eu-repo/classification/ddc/000
ddc:000
Müller, Robert
Universität Leipzig
2003-01-01
2003-01-14
info:eu-repo/semantics/publishedVersion
2004-11-28
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A10960
https://ul.qucosa.de/api/qucosa%3A10960/attachment/ATT-0/
oai:qucosa:de:qucosa:11024
2021-03-29T08:15:07Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Interfaces for Modular Surgical Planning and Assistance Systems
urn:nbn:de:bsz:15-qucosa-38601
eng
Modern surgery of the 21st century relies in many aspects on computers or, in a wider sense, digital data processing. Department administration, OR scheduling, billing, and - with increasing pervasion - patient data management are performed with the aid of so called Surgical Information Systems (SIS) or, more general, Hospital Information Systems (HIS).
Computer Assisted Surgery (CAS) summarizes techniques which assist a surgeon in the preparation and conduction of surgical interventions. Today still predominantly based on radiology images, these techniques include the preoperative determination of an optimal surgical strategy and intraoperative systems which aim at increasing the accuracy of surgical manipulations.
CAS is a relatively young field of computer science. One of the unsolved "teething troubles" of CAS is the absence of technical standards for the interconnectivity of CAS system. Current CAS systems are usually "islands of information" with no connection to other devices within the operating room or hospital-wide information systems. Several workshop reports and individual publications point out that this situation leads to ergonomic, logistic, and economic limitations in hospital work. Perioperative processes are prolonged by the manual installation and configuration of an increasing amount of technical devices. Intraoperatively, a large amount of the surgeons'' attention is absorbed by the requirement to monitor and operate systems. The need for open infrastructures which enable the integration of CAS devices from different vendors in order to exchange information as well as commands among these devices through a network has been identified by numerous experts with backgrounds in medicine as well as engineering.
This thesis contains two approaches to the integration of CAS systems:
- For perioperative data exchange, the specification of new data structures as an amendment to the existing DICOM standard for radiology image management is presented. The extension of DICOM towards surgical application allows for the seamless integration of surgical planning and reporting systems into DICOM-based Picture Archiving and Communication Systems (PACS) as they are installed in most hospitals for the exchange and long-term archival of patient images and image-related patient data.
- For the integration of intraoperatively used CAS devices, such as, e.g., navigation systems, video image sources, or biosensors, the concept of a surgical middleware is presented. A c++ class library, the TiCoLi, is presented which facilitates the configuration of ad-hoc networks among the modules of a distributed CAS system as well as the exchange of data streams, singular data objects, and commands between these modules. The TiCoLi is the first software library for a surgical field of application to implement all of these services.
To demonstrate the suitability of the presented specifications and their implementation, two modular CAS applications are presented which utilize the proposed DICOM extensions for perioperative exchange of surgical planning data as well as the TiCoLi for establishing an intraoperative network of autonomous, yet not independent, CAS modules.
Die moderne Hochleistungschirurgie des 21. Jahrhunderts ist auf vielerlei Weise abhängig von Computern oder, im weiteren Sinne, der digitalen Datenverarbeitung. Administrative Abläufe, wie die Erstellung von Nutzungsplänen für die verfügbaren technischen, räumlichen und personellen Ressourcen, die Rechnungsstellung und - in zunehmendem Maße - die Verwaltung und Archivierung von Patientendaten werden mit Hilfe von digitalen Informationssystemen rationell und effizient durchgeführt. Innerhalb der Krankenhausinformationssysteme (KIS, oder englisch HIS) stehen für die speziellen Bedürfnisse der einzelnen Fachabteilungen oft spezifische Informationssysteme zur Verfügung. Chirurgieinformationssysteme (CIS, oder englisch SIS) decken hierbei vor allen Dingen die Bereiche Operationsplanung sowie Materialwirtschaft für spezifisch chirurgische Verbrauchsmaterialien ab.
Während die genannten HIS und SIS vornehmlich der Optimierung administrativer Aufgaben dienen, stehen die Systeme der Computerassistierten Chirugie (CAS) wesentlich direkter im Dienste der eigentlichen chirugischen Behandlungsplanung und Therapie. Die CAS verwendet Methoden der Robotik, digitalen Bild- und Signalverarbeitung, künstlichen Intelligenz, numerischen Simulation, um nur einige zu nennen, zur patientenspezifischen Behandlungsplanung und zur intraoperativen Unterstützung des OP-Teams, allen voran des Chirurgen. Vor allen Dingen Fortschritte in der räumlichen Verfolgung von Werkzeugen und Patienten ("Tracking"), die Verfügbarkeit dreidimensionaler radiologischer Aufnahmen (CT, MRT, ...) und der Einsatz verschiedener Robotersysteme haben in den vergangenen Jahrzehnten den Einzug des Computers in den Operationssaal - medienwirksam - ermöglicht. Weniger prominent, jedoch keinesfalls von untergeordnetem praktischen Nutzen, sind Beispiele zur automatisierten Überwachung klinischer Messwerte, wie etwa Blutdruck oder Sauerstoffsättigung.
Im Gegensatz zu den meist hochgradig verteilten und gut miteinander verwobenen Informationssystemen für die Krankenhausadministration und Patientendatenverwaltung, sind die Systeme der CAS heutzutage meist wenig oder überhaupt nicht miteinander und mit Hintergrundsdatenspeichern vernetzt. Eine Reihe wissenschaftlicher Publikationen und interdisziplinärer Workshops hat sich in den vergangen ein bis zwei Jahrzehnten mit den Problemen des Alltagseinsatzes von CAS Systemen befasst. Mit steigender Intensität wurde hierbei auf den Mangel an infrastrukturiellen Grundlagen für die Vernetzung intraoperativ eingesetzter CAS Systeme miteinander und mit den perioperativ eingesetzten Planungs-, Dokumentations- und Archivierungssystemen hingewiesen. Die sich daraus ergebenden negativen Einflüsse auf die Effizienz perioperativer Abläufe - jedes Gerät muss manuell in Betrieb genommen und mit den spezifischen Daten des nächsten Patienten gefüttert werden - sowie die zunehmende Aufmerksamkeit, welche der Operateur und sein Team auf die Überwachung und dem Betrieb der einzelnen Geräte verwenden muss, werden als eine der "Kinderkrankheiten" dieser relativ jungen Technologie betrachtet und stehen einer Verbreitung über die Grenzen einer engagierten technophilen Nutzergruppe hinaus im Wege.
Die vorliegende Arbeit zeigt zwei parallel von einander (jedoch, im Sinne der Schnittstellenkompatibilität, nicht gänzlich unabhängig voneinander) zu betreibende Ansätze zur Integration von CAS Systemen.
- Für den perioperativen Datenaustausch wird die Spezifikation zusätzlicher Datenstrukturen zum Transfer chirurgischer Planungsdaten im Rahmen des in radiologischen Bildverarbeitungssystemen weit verbreiteten DICOM Standards vorgeschlagen und an zwei Beispielen vorgeführt. Die Erweiterung des DICOM Standards für den perioperativen Einsatz ermöglicht hierbei die nahtlose Integration chirurgischer Planungssysteme in existierende "Picture Archiving and Communication Systems" (PACS), welche in den meisten Fällen auf dem DICOM Standard basieren oder zumindest damit kompatibel sind. Dadurch ist einerseits der Tatsache Rechnung getragen, dass die patientenspezifische OP-Planung in hohem Masse auf radiologischen Bildern basiert und andererseits sicher gestellt, dass die Planungsergebnisse entsprechend der geltenden Bestimmungen langfristig archiviert und gegen unbefugten Zugriff geschützt sind - PACS Server liefern hier bereits wohlerprobte Lösungen.
- Für die integration intraoperativer CAS Systeme, wie etwa Navigationssysteme, Videobildquellen oder Sensoren zur Überwachung der Vitalparameter, wird das Konzept einer "chirurgischen Middleware" vorgestellt. Unter dem Namen TiCoLi wurde eine c++ Klassenbibliothek entwickelt, auf deren Grundlage die Konfiguration von ad-hoc Netzwerken während der OP-Vorbereitung mittels plug-and-play Mechanismen erleichtert wird. Nach erfolgter Konfiguration ermöglicht die TiCoLi den Austausch kontinuierlicher Datenströme sowie einzelner Datenpakete und Kommandos zwischen den Modulen einer verteilten CAS Anwendung durch ein Ethernet-basiertes Netzwerk. Die TiCoLi ist die erste frei verfügbare Klassenbibliothek welche diese Funktionalitäten dediziert für einen Einsatz im chirurgischen Umfeld vereinigt.
Zum Nachweis der Tauglichkeit der gezeigten Spezifikationen und deren Implementierungen, werden zwei modulare CAS Anwendungen präsentiert, welche die vorgeschlagenen DICOM Erweiterungen zum perioperativen Austausch von Planungsergebnissen sowie die TiCoLi zum intraoperativen Datenaustausch von Messdaten unter echzeitnahen Anforderungen verwenden.
info:eu-repo/classification/ddc/000
ddc:000
Computerassistierte Chirurgie, Systemintegration, TIMMS, PACS, DICOM, HIS, CIS
Computer assisted surgery, system integration, TIMMS, PACS, DICOM, HIS, CIS
Gessat, Michael
Lemke, Heinz U.
Burgert, Oliver
Scheuermann, Gerik
Wörn, Heinz
Universität Leipzig
2010-07-14
2010-02-17
2010-06-22
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11024
https://ul.qucosa.de/api/qucosa%3A11024/attachment/ATT-0/
oai:qucosa:de:qucosa:11020
2021-03-29T08:15:04Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Learning OWL Class Expressions
urn:nbn:de:bsz:15-qucosa-38351
eng
With the advent of the Semantic Web and Semantic Technologies, ontologies have become one of the most prominent paradigms for knowledge representation and reasoning. The popular ontology language OWL, based on description logics, became a W3C recommendation in 2004 and a standard for modelling ontologies on the Web. In the meantime, many studies and applications using OWL have been reported in research and industrial environments, many of which go beyond Internet usage and employ the power of ontological modelling in other fields such as biology, medicine, software engineering, knowledge management, and cognitive systems.
However, recent progress in the field faces a lack of well-structured ontologies with large amounts of instance data due to the fact that engineering such ontologies requires a considerable investment of resources. Nowadays, knowledge bases often provide large volumes of data without sophisticated schemata. Hence, methods for automated schema acquisition and maintenance are sought. Schema acquisition is closely related to solving typical classification problems in machine learning, e.g. the detection of chemical compounds causing cancer. In this work, we investigate both, the underlying machine learning techniques and their application to knowledge acquisition in the Semantic Web.
In order to leverage machine-learning approaches for solving these tasks, it is required to develop methods and tools for learning concepts in description logics or, equivalently, class expressions in OWL. In this thesis, it is shown that methods from Inductive Logic Programming (ILP) are applicable to learning in description logic knowledge bases. The results provide foundations for the semi-automatic creation and maintenance of OWL ontologies, in particular in cases when extensional information (i.e. facts, instance data) is abundantly available, while corresponding intensional information (schema) is missing or not expressive enough to allow powerful reasoning over the ontology in a useful way. Such situations often occur when extracting knowledge from different sources, e.g. databases, or in collaborative knowledge engineering scenarios, e.g. using semantic wikis. It can be argued that being able to learn OWL class expressions is a step towards enriching OWL knowledge bases in order to enable powerful reasoning, consistency checking, and improved querying possibilities. In particular, plugins for OWL ontology editors based on learning methods are developed and evaluated in this work.
The developed algorithms are not restricted to ontology engineering and can handle other learning problems. Indeed, they lend themselves to generic use in machine learning in the same way as ILP systems do. The main difference, however, is the employed knowledge representation paradigm: ILP traditionally uses logic programs for knowledge representation, whereas this work rests on description logics and OWL. This difference is crucial when considering Semantic Web applications as target use cases, as such applications hinge centrally on the chosen knowledge representation format for knowledge interchange and integration. The work in this thesis can be understood as a broadening of the scope of research and applications of ILP methods. This goal is particularly important since the number of OWL-based systems is already increasing rapidly and can be expected to grow further in the future.
The thesis starts by establishing the necessary theoretical basis and continues with the specification of algorithms. It also contains their evaluation and, finally, presents a number of application scenarios. The research contributions of this work are threefold:
The first contribution is a complete analysis of desirable properties of refinement operators in description logics. Refinement operators are used to traverse the target search space and are, therefore, a crucial element in many learning algorithms. Their properties (completeness, weak completeness, properness, redundancy, infinity, minimality) indicate whether a refinement operator is suitable for being employed in a learning algorithm. The key research question is which of those properties can be combined. It is shown that there is no ideal, i.e. complete, proper, and finite, refinement operator for expressive description logics, which indicates that learning in description logics is a challenging machine learning task. A number of other new results for different property combinations are also proven. The need for these investigations has already been expressed in several articles prior to this PhD work. The theoretical limitations, which were shown as a result of these investigations, provide clear criteria for the design of refinement operators. In the analysis, as few assumptions as possible were made regarding the used description language.
The second contribution is the development of two refinement operators. The first operator supports a wide range of concept constructors and it is shown that it is complete and can be extended to a proper operator. It is the most expressive operator designed for a description language so far. The second operator uses the light-weight language EL and is weakly complete, proper, and finite. It is straightforward to extend it to an ideal operator, if required. It is the first published ideal refinement operator in description logics. While the two operators differ a lot in their technical details, they both use background knowledge efficiently.
The third contribution is the actual learning algorithms using the introduced operators. New redundancy elimination and infinity-handling techniques are introduced in these algorithms. According to the evaluation, the algorithms produce very readable solutions, while their accuracy is competitive with the state-of-the-art in machine learning. Several optimisations for achieving scalability of the introduced algorithms are described, including a knowledge base fragment selection approach, a dedicated reasoning procedure, and a stochastic coverage computation approach.
The research contributions are evaluated on benchmark problems and in use cases. Standard statistical measurements such as cross validation and significance tests show that the approaches are very competitive. Furthermore, the ontology engineering case study provides evidence that the described algorithms can solve the target problems in practice. A major outcome of the doctoral work is the DL-Learner framework. It provides the source code for all algorithms and examples as open-source and has been incorporated in other projects.
info:eu-repo/classification/ddc/000
ddc:000
Machine Learning, OWL, Description Logics, Inductive Logic Programming, Supervised Learning, Semantic Web, RDF, SPARQL, symbolic learning, refinement operators
Maschinelles Lernen, OWL, Beschreibungslogiken, überwachtes Lernen, Semantisches Web, RDF, SPARQL, symbolisches Lernen, Refinementoperatoren
Lehmann, Jens
Fähnrich, Klaus-Peter
Fanizzi, Nicola
Universität Leipzig
2010-06-24
2010-01-05
2010-06-09
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11020
https://ul.qucosa.de/api/qucosa%3A11020/attachment/ATT-0/
oai:qucosa:de:qucosa:11028
2021-03-29T08:15:10Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Genealogy Reconstruction: Methods and applications in cancer and wild populations
urn:nbn:de:bsz:15-qucosa-38656
eng
Genealogy reconstruction is widely used in biology when relationships among entities are studied. Phylogenies, or evolutionary trees, show the differences between species. They are of profound importance because they help to obtain better understandings of evolutionary processes. Pedigrees, or family trees, on the other hand visualize the relatedness between individuals in a population. The reconstruction of pedigrees and the inference of parentage in general is now a cornerstone in molecular ecology. Applications include the direct infer- ence of gene flow, estimation of the effective population size and parameters describing the population’s mating behaviour such as rates of inbreeding.
In the first part of this thesis, we construct genealogies of various types of cancer. Histopatho- logical classification of human tumors relies in part on the degree of differentiation of the tumor sample. To date, there is no objective systematic method to categorize tumor subtypes by maturation. We introduce a novel algorithm to rank tumor subtypes according to the dis- similarity of their gene expression from that of stem cells and fully differentiated tissue, and thereby construct a phylogenetic tree of cancer. We validate our methodology with expression data of leukemia and liposarcoma subtypes and then apply it to a broader group of sarcomas and of breast cancer subtypes. This ranking of tumor subtypes resulting from the application of our methodology allows the identification of genes correlated with differentiation and may help to identify novel therapeutic targets. Our algorithm represents the first phylogeny-based tool to analyze the differentiation status of human tumors.
In contrast to asexually reproducing cancer cell populations, pedigrees of sexually reproduc- ing populations cannot be represented by phylogenetic trees. Pedigrees are directed acyclic graphs (DAGs) and therefore resemble more phylogenetic networks where reticulate events are indicated by vertices with two incoming arcs. We present a software package for pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatel- lites and single nucleotide polymorphism (SNPs) in the second part of the thesis. If available, the algorithm makes use of prior information such as known relationships (sub-pedigrees) or the age and sex of individuals. Statistical confidence is estimated by Markov chain Monte Carlo (MCMC) sampling. The accuracy of the algorithm is demonstrated for simulated data as well as an empirical data set with known pedigree. The parentage inference is robust even in the presence of genotyping errors. We further demonstrate the accuracy of the algorithm on simulated clonal populations. We show that the joint estimation of parameters of inter- est such as the rate of self-fertilization or clonality is possible with high accuracy even with marker panels of moderate power. Classical methods can only assign a very limited number of statistically significant parentages in this case and would therefore fail. The method is implemented in a fast and easy to use open source software that scales to large datasets with many thousand individuals.:Abstract v
Acknowledgments vii
1 Introduction 1
2 Cancer Phylogenies 7
2.1 Introduction..................................... 7
2.2 Background..................................... 9
2.2.1 PhylogeneticTrees............................. 9
2.2.2 Microarrays................................. 10
2.3 Methods....................................... 11
2.3.1 Datasetcompilation ............................ 11
2.3.2 Statistical Methods and Analysis..................... 13
2.3.3 Comparison of our methodology to other methods . . . . . . . . . . . 15
2.4 Results........................................ 16
2.4.1 Phylogenetic tree reconstruction method. . . . . . . . . . . . . . . . . 16
2.4.2 Comparison of tree reconstruction methods to other algorithms . . . . 28
2.4.3 Systematic analysis of methods and parameters . . . . . . . . . . . . . 30
2.5 Discussion...................................... 32
3 Wild Pedigrees 35
3.1 Introduction..................................... 35
3.2 The molecular ecologist’s tools of the trade ................... 36
3.2.1 3.2.2 3.2.3
3.2.1 Sibship inference and parental reconstruction . . . . . . . . . . . . . . 37
3.2.2 Parentage and paternity inference .................... 39
3.2.3 Multigenerational pedigree reconstruction . . . . . . . . . . . . . . . . 40
3.3 Background..................................... 40
3.3.1 Pedigrees .................................. 40
3.3.2 Genotypes.................................. 41
3.3.3 Mendelian segregation probability .................... 41
3.3.4 LOD Scores................................. 43
3.3.5 Genotyping Errors ............................. 43
3.3.6 IBD coefficients............................... 45
3.3.7 Bayesian MCMC.............................. 46
3.4 Methods....................................... 47
3.4.1 Likelihood Model.............................. 47
3.4.2 Efficient Likelihood Calculation...................... 49
3.4.3 Maximum Likelihood Pedigree ...................... 51
3.4.4 Full siblings................................. 52
3.4.5 Algorithm.................................. 53
3.4.6 Missing Values ............................... 56
3.4.7 Allelefrequencies.............................. 58
3.4.8 Rates of Self-fertilization.......................... 60
3.4.9 Rates of Clonality ............................. 60
3.5 Results........................................ 61
3.5.1 Real Microsatellite Data.......................... 61
3.5.2 Simulated Human Population....................... 62
3.5.3 SimulatedClonalPlantPopulation.................... 64
3.6 Discussion...................................... 71
4 Conclusions 77
A FRANz 79
A.1 Availability ..................................... 79
A.2 Input files...................................... 79
A.2.1 Maininputfile ............................... 79
A.2.2 Knownrelationships ............................ 80
A.2.3 Allele frequencies.............................. 81
A.2.4 Sampling locations............................. 82
A.3 Output files..................................... 83
A.4 Web 2.0 Interface.................................. 86
List of Figures 87
List of Tables 88
List Abbreviations 90
Bibliography 92
Curriculum Vitae I
info:eu-repo/classification/ddc/000
ddc:000
pedigree, microsatellite, phylogeny, MCMC, liposarcoma, self-fertilization, clonal, phylogenetic networks
Stammbaum, Microsatellites, Phylogenie, MCMC, Liposarcoma, Phylogenetische Netzwerke, Selbstbefruchtung
Riester, Markus
Stadler, Peter F.
Bryant, David
Universität Leipzig
2010-07-02
2010-04-07
2010-06-23
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11028
https://ul.qucosa.de/api/qucosa%3A11028/attachment/ATT-0/
oai:qucosa:de:qucosa:11029
2021-03-29T08:15:11Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Gene order rearrangement methods for the reconstruction of phylogeny
urn:nbn:de:bsz:15-qucosa-38666
ger
The study of phylogeny, i.e. the evolutionary history of species, is a central problem in biology and a key for understanding characteristics of contemporary species. Many problems in this area can be formulated as combinatorial optimisation problems which makes it particularly
interesting for computer scientists. The reconstruction of the phylogeny of species can be based on various kinds of data, e.g. morphological properties or characteristics of the genetic information of the species. Maximum parsimony is a popular and widely used method for phylogenetic reconstruction aiming for an explanation of the observed data requiring the least evolutionary changes.
A certain property of the genetic information gained much interest for the reconstruction of phylogeny in recent time: the organisation of the genomes of species, i.e. the arrangement of the genes on the chromosomes. But the idea to reconstruct phylogenetic information
from gene arrangements has a long history. In Dobzhansky and Sturtevant (1938) it was already pointed out that “a comparison of the different gene arrangements in the same chromosome may, in certain cases, throw light on the historical relationships of these structures, and consequently on the history of the species as a whole”. This kind of data
is promising for the study of deep evolutionary relationships because gene arrangements are believed to evolve slowly (Rokas and Holland, 2000). This seems to be the case especially for mitochondrial genomes which are available for a wide range of species (Boore, 1999).
The development of methods for the reconstruction of phylogeny from gene arrangement data has made considerable progress during the last years. Prominent examples are the computation of parsimonious evolutionary scenarios, i.e. a shortest sequence of rearrangements
transforming one arrangement of genes into another or the length of such a minimal scenario (Hannenhalli and Pevzner, 1995b; Sankoff, 1992; Watterson et al., 1982); the reconstruction of parsimonious phylogenetic trees from gene arrangement data (Bader et al.,
2008; Bernt et al., 2007b; Bourque and Pevzner, 2002; Moret et al., 2002a); or the computation of the similarities of gene arrangements (Bergeron et al., 2008a; Heber et al., 2009).
1
1 Introduction
The central theme of this work is to provide efficient algorithms for modified versions of fundamental genome rearrangement problems using more plausible rearrangement models.
Two types of modified rearrangement models are explored.
The first type is to restrict the set of allowed rearrangements as follows. It can be observed that certain groups of genes are preserved during evolution. This may be caused by functional constraints which prevented the destruction (Lathe et al., 2000; Sémon and Duret, 2006; Xie et al., 2003), certain properties of the rearrangements which shaped the gene
orders (Eisen et al., 2000; Sankoff, 2002; Tillier and Collins, 2000), or just because no destructive rearrangement happened since the speciation of the gene orders. It can be assumed that gene groups, found in all studied gene orders, are not acquired independently.
Accordingly, these gene groups should be preserved in plausible reconstructions of the course of evolution, in particular the gene groups should be present in the reconstructed putative ancestral gene orders. This can be achieved by restricting the set of rearrangements, which
are allowed for the reconstruction, to those which preserve the gene groups of the given gene orders. Since it is difficult to determine functionally what a gene group is, it has been proposed to consider common combinatorial structures of the gene orders as gene groups
(Marcotte et al., 1999; Overbeek et al., 1999).
The second considered modification of the rearrangement model is extending the set of allowed rearrangement types. Different types of rearrangement operations have shuffled the gene orders during evolution. It should be attempted to use the same set of rearrangement
operations for the reconstruction otherwise distorted or even wrong phylogenetic conclusions may be obtained in the worst case.
Both possibilities have been considered for certain rearrangement problems before. Restricted sets of allowed rearrangements have been used successfully for the computation of parsimonious rearrangement scenarios consisting of inversions only where the gene groups
are identified as common intervals (Bérard et al., 2007; Figeac and Varré, 2004). Extending the set of allowed rearrangement operations is a delicate task. On the one hand it is unknown which rearrangements have to be regarded because this is part of the phylogeny to
be discovered. On the other hand, efficient exact rearrangement methods including several operations are still rare, in particular when transpositions should be included. For example, the problem to compute shortest rearrangement scenarios including transpositions is still of
unknown computational complexity. Currently, only efficient approximation algorithms are known (e.g. Bader and Ohlebusch, 2007; Elias and Hartman, 2006).
Two problems have been studied with respect to one or even both of these possibilities in the scope of this work.
The first one is the inversion median problem. Given the gene orders of some taxa, this problem asks for potential ancestral gene orders such that the corresponding inversion scenario is parsimonious, i.e. has a minimum length. Solving this problem is an essential component 2 of algorithms for computing phylogenetic trees from gene arrangements (Bourque and Pevzner, 2002; Moret et al., 2002a, 2001). The unconstrained inversion median problem is NP-hard (Caprara, 2003). In Chapter 3 the inversion median problem is studied under the additional constraint to preserve gene groups of the input gene orders. Common intervals, i.e. sets of genes that appear consecutively in the gene orders, are used for modelling gene groups. The problem of finding such ancestral gene orders is called the preserving inversion median problem. Already the problem of finding a shortest inversion scenario for two gene orders is NP-hard (Figeac and Varré, 2004).
Mitochondrial gene orders are a rich source for phylogenetic investigations because they are known for more than 1 000 species. Four rearrangement operations are reported at least in the literature to be relevant for the study of mitochondrial gene order evolution (Boore, 1999): That is inversions, transpositions, inverse transpositions, and tandem duplication random loss (TDRL). Efficient methods for a plausible reconstruction of genome rearrangements for mitochondrial gene orders using all four operations are presented in Chapter 4.
An important rearrangement operation, in particular for the study of mitochondrial gene orders, is the tandem duplication random loss operation (e.g. Boore, 2000; Mauro et al., 2006). This rearrangement duplicates a part of a gene order followed by the random loss of one of the redundant copies of each gene. The gene order is rearranged depending on which copy is lost. This rearrangement should be regarded for reconstructing phylogeny from gene order data. But the properties of this rearrangement operation have rarely been studied
(Bouvel and Rossin, 2009; Chaudhuri et al., 2006). The combinatorial properties of the TDRL operation are studied in Chapter 5. The enumeration and counting of sorting TDRLs, that is TDRL operations reducing the distance, is studied in particular. Closed formulas for computing the number of sorting TDRLs and methods for the enumeration are presented. Furthermore, TDRLs are one of the operations considered in Chapter 4. An interesting property of this rearrangement, distinguishing it from other rearrangements, is its
asymmetry. That is the effects of a single TDRL can (in the most cases) not be reversed with a single TDRL. The use of this property for phylogeny reconstruction is studied in Section 4.3.
This thesis is structured as follows. The existing approaches obeying similar types of modified rearrangement models as well as important concepts and computational methods to related problems are reviewed in Chapter 2. The combinatorial structures of gene orders that
have been proposed for identifying gene groups, in particular common intervals, as well as the computational approaches for their computation are reviewed in Section 2.2. Approaches for computing parsimonious pairwise rearrangement scenarios are outlined in Section 2.3.
Methods for the computation genome rearrangement scenarios obeying biologically motivated constraints, as introduced above, are detailed in Section 2.4. The approaches for the inversion median problem are covered in Section 2.5. Methods for the reconstruction of phylogenetic
trees from gene arrangement data are briefly outlined in Section 2.6.3
1 Introduction
Chapter 3 introduces the new algorithms CIP, ECIP, and TCIP for solving the preserving inversion median problem. The efficiency of the algorithm is empirically studied for simulated as well as mitochondrial data. The description of algorithms CIP and ECIP is based on Bernt et al. (2006b). TCIP has been described in Bernt et al. (2007a, 2008b). But the
theoretical foundation of TCIP is extended significantly within this work in order to allow for more than three input permutations.
Gene order rearrangement methods that have been developed for the reconstruction of the phylogeny of mitochondrial gene orders are presented in the fourth chapter. The presented algorithm CREx computes rearrangement scenarios for pairs of gene orders. CREx regards the four types of rearrangement operations which are important for mitochondrial gene orders.
Based on CREx the algorithm TreeREx for assigning rearrangement events to a given tree is developed. The quality of the CREx reconstructions is analysed in a large empirical study for simulated gene orders. The results of TreeREx are analysed for several mitochondrial data sets. Algorithms CREx and TreeREx have been published in Bernt et al. (2008a, 2007c).
The analysis of the mitochondrial gene orders of Echinodermata was included in Perseke et al. (2008). Additionally, a new and simple method is presented to explore the potential of the CREx method. The new method is applied to the complete mitochondrial data set.
The problem of enumerating and counting sorting TDRLs is studied in Chapter 5. The theoretical results are covered to a large extent by Bernt et al. (2009b). The missing combinatorial explanation for some of the presented formulas is given here for the first time.
Therefor, a new method for the enumeration and counting of sorting TDRLs has been developed (Bernt et al., 2009a).
info:eu-repo/classification/ddc/000
ddc:000
Phylogenie
Phylogeny
Bernt, Matthias
Middendorf, Martin
Sagot, Marie-France
Universität Leipzig
2010-06-28
2009-12-09
2010-01-29
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11029
https://ul.qucosa.de/api/qucosa%3A11029/attachment/ATT-0/
oai:qucosa:de:qucosa:11034
2021-03-29T08:15:14Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Kleene-Schützenberger and Büchi Theorems for Weighted Timed Automata
urn:nbn:de:bsz:15-qucosa-38791
978-3-8325-2500-2
eng
In 1994, Alur and Dill introduced timed automata as a simple mathematical model for modelling the behaviour of real-time systems.
In this thesis, we extend timed automata with weights. More detailed, we equip both the states and transitions of a timed automaton with weights taken from an appropriate mathematical structure. The weight of a transition determines the weight for taking this transition, and the weight of a state determines the weight for letting time elapse in this state. Since the weight for staying in a state depends on time, this model, called weighted timed automata, has many interesting applications, for instance, in operations research and scheduling. We give characterizations for the behaviours of weighted timed automata in terms of rational expressions and logical formulas. These formalisms are useful for the specification of real-time systems with continuous resource consumption. We further investigate the relation between the behaviours of weighted timed automata and timed automata. Finally, we present important decidability results for weighted timed automata.
info:eu-repo/classification/ddc/000
ddc:000
Weighted Timed Automata, Real-Time Systems, Weighted Logic
Gewichtete Zeitautomaten, Echtzeitsysteme, gewichtete Logik
Quaas, Karin
Droste, Manfred
Bouyer, Patricia
Universität Leipzig
2010-07-08
2009-11-24
2010
2010-03-24
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11034
https://ul.qucosa.de/api/qucosa%3A11034/attachment/ATT-0/
oai:qucosa:de:qucosa:11041
2021-03-29T08:15:19Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Force Distribution in Macromolecules
urn:nbn:de:bsz:15-qucosa-39367
eng
All living organisms utilize thousands of molecular building blocks to perform mechanical tasks. These building blocks are mostly proteins, and their mechanical properties define the way they can be utilized by the cell. The spectrum ranges from rope like structures that give hold and stability to our bodies to microscopic engines helping us to perform or sense mechanical work.
An increasing number of biological processes are revealed to be driven by force and well-directed distribution of strain is the very base of many of these mechanisms. We need to be able to observe the distribution of strain within bio-molecules if we want to gain detailed insight into the function of these highly complex nano-machines. Only by theoretical understanding and prediction of mechanical processes on the molecular level will we be able to rationally tailor proteins to mimic specific biological functions.
This thesis aims at understanding the molecular mechanics of a wide range of biological molecules, such as the muscle protein titin or silk fibers.
We introduce Force Distribution Analysis (FDA), a new approach to directly study the forces driving molecular processes, instead of indirectly observing them by means of coordinate changes.
info:eu-repo/classification/ddc/000
ddc:000
Force distribution, molecular dynamics, mechanical resistance, protein
Kraftverteilung, mechanische widerstandsfähigkeit, protein
Stacklies, Wolfram
Gräter, Frauke
Stadler, Peter F.
Helms, Volkhard
Universität Leipzig
CAS-MPG Partner Institute for Computational Biology (PICB)
2010-08-05
2010-02-23
2010-07-02
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11041
https://ul.qucosa.de/api/qucosa%3A11041/attachment/ATT-0/
oai:qucosa:de:qucosa:11047
2021-03-29T08:15:23Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Self-Organized Specialization and Controlled Emergence in Organic Computing Systems
urn:nbn:de:bsz:15-qucosa-39591
eng
In this chapter we studied a first approach to generate suitable rule sets for solving classification problems on systems of autonomous, memory constrained components. It was shown that a multi agent system that uses interacting Pittsburgh-style classifier systems
can evolve appropiate rule sets. The system evolves specialists for parts of the classification problem and cooperation between them. In this way the components overcome their restricted memory size and are able to solve the entire problem. It was shown that the communication topology between the components strongly influences the average number of components that a request has to pass until it is classified. It was also shown that the introduction of communication costs into the fitness function leads to a more even distribution of knowledge between the components and reduces the communication overhead without influencing the classification performance very much.
If the system is used to generate rule sets to solve classification tasks on real hardware systems, communication cost in the training phase can thus lead to a better knowledge distribution and small communication cost. That is, in this way the system will be more robust against the loss of single components and longer reliable in case of limited energy
resources.
info:eu-repo/classification/ddc/000
ddc:000
Organic, computing, system
kontrollierte Hilfe
Scheidler, Alexander
Middendorf, Martin
Schmeck, Hartmut
Universität Leipzig
2011-06-29
2009-12-11
2010-02-11
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11047
https://ul.qucosa.de/api/qucosa%3A11047/attachment/ATT-0/
oai:qucosa:de:qucosa:11055
2021-03-29T08:15:29Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
tRNomics: Genomic Organization and Processing Patterns of tRNAs
urn:nbn:de:bsz:15-qucosa-61063
eng
Surprisingly little is known about the organization and distribution of
tRNAs and tRNA-related sequences on a genome-wide scale. While tRNA
complements are usually reported in passing as part of genome annotation
efforts, and peculiar features such as the tandem arrangements of tRNAs
in Entamoeba histolytica have been described in some detail,
comparative studies are rare. We therefore set out to systematically
survey the genomic arrangement of tRNAs in a wide range of eukaryotes
to identify common patterns and taxon-specific peculiarities. We found that tRNA
complements evolve rapidly and that tRNA locations are subject to rapid
turnover. At the phylum level, distributions of tRNA numbers are very broad,
with standard deviations on the order of the mean. Even within fairly closely related species, we observe dramatic changes in local organization. Consistent with this variability, syntenic conservation of tRNAs is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. We conclude that the genomic organization of tRNAs shows complex, lineage-specific patterns characterized by extensive variability, and that this variability is in striking contrast to the extreme levels of sequence-conservation of the tRNA genes themselves. Our comprehensive analysis of eukaroyotic tRNA distributions provides a basis for further studies into the interplay between tRNA gene arrangements and genome organization in general.
Secondly, we focused on the investigation of small non-coding RNAs (ncRNAs) from whole transcriptome data. Since ncRNAs constitute a significant part of the transcriptome, we explore this data to detect and classify patterns derived from transcriptome-associated loci. We selected three distinct ncRNA classes: microRNAs, snoRNAs and tRNAs, all of which undergo maturation processes that lead to the production of shorter RNAs. After mapping the sequences to the reference genome, specific patterns of short reads were observed. These read patterns appeared to reflect RNA processing and, if so, should specify the RNA transcripts from which they are derived. In order to investigate whether the short read patterns carry information on the particular ncRNA class from which they orginate, we performed a random forest classification on the three
distinct ncRNA classes listed above. Then, after exploring the potential
classification of general groups of ncRNAs, we focused on the identification of small RNA fragments derived from tRNAs. After mapping transcriptome sequence data to reference genomes, we searched for specific short read patterns reflecting tRNA processing. In this context, we devised a common tRNA coordinate system based on conservation and secondary structure information that allows vector representation of processing products and thus comparison of different tRNAs by anticodon and
amino acid.
We report patterns of tRNA processing that seem to be conserved across species.
Though the mechanisms and functional implications underlying these patterns remain to be clarified, our analysis suggests that each type of tRNA exhibits a specific pattern and thus appears to undergo a characteristic maturation process.
info:eu-repo/classification/ddc/000
ddc:000
tRNAs, genomic organizations, clusters, transcriptome, HTS, small RNA, block expression
tRNA, Genomische Organisation, Prozessierungsmuster von tRNAs
Bermudez Santana, Clara Isabel
Stadler, Peter F.
Westhof, Eric
Universität Leipzig
2010-09-15
2010-05-05
2010-09-13
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11055
https://ul.qucosa.de/api/qucosa%3A11055/attachment/ATT-0/
https://ul.qucosa.de/api/qucosa%3A11055/attachment/ATT-1/
oai:qucosa:de:qucosa:11065
2021-03-29T08:15:37Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
A Neural Network Model of Invariant Object Identification
urn:nbn:de:bsz:15-qucosa-62050
eng
Invariant object recognition is maybe the most basic and fundamental property of our visual system. It is the basis of many other cognitive tasks, like motor actions and social interactions. Hence, the theoretical understanding and modeling of invariant object recognition is one of the central problems in computational neuroscience.
Indeed, object recognition consists of two different tasks: classification and identification.
The focus of this thesis is on object identification under the basic geometrical
transformations shift, scaling, and rotation. The visual system can
perform shift, size, and rotation invariant object identification.
This thesis consists of two parts. In the first part, we present and investigate the VisNet model proposed by Rolls. The generalization problems of VisNet triggered our development of a new neural network model for invariant object identification. Starting point for an improved generalization behavior is the search for an operation that extracts images features that are invariant under shifts, rotations, and scalings. Extracting invariant features guarantees that an object seen once in a specific pose can be identified in any pose.
We present and investigate our model in the second part of this thesis.
info:eu-repo/classification/ddc/000
ddc:000
invariante Objekterkennung, Neuronales Netz, Fourier Transformation
invariant object identification, neural network, Fourier transform
Wilhelm, Hedwig
Jost, Juergen
Wiskott, Laurenz
Universität Leipzig
2010-11-03
2010-07-05
2010-10-28
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11065
https://ul.qucosa.de/api/qucosa%3A11065/attachment/ATT-0/
oai:qucosa:de:qucosa:11071
2021-03-29T08:15:41Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
The long and the short of computational ncRNA prediction
urn:nbn:de:bsz:15-qucosa-62158
eng
Non-coding RNAs (ncRNAs) are transcripts that function directly as RNA molecule without ever being translated to protein.
The transcriptional output of eukaryotic cells is diverse, pervasive, and multi-layered. It consists of spliced as well as unspliced transcripts of both protein-coding messenger RNAs and functional ncRNAs. However, it also contains degradable non-functional by-products and artefacts - certainly a reason why ncRNAs have long been wrongly disposed as transcriptional noise.
Today, RNA-controlled regulatory processes are broadly recognized for a variety of ncRNA classes. The thermoresponsive ROSE ncRNA (repression of heat shock gene expression) is only one example of a regulatory ncRNA acting at the post-transcriptional level via conformational changes of its secondary structure.
Bioinformatics helps to identify novel ncRNAs in the bulk of genomic and transcriptomic sequence data which are produced at ever increasing rates. However, ncRNA annotation is unfortunately not part of generic genome annotation pipelines. Dedicated computational searches for particular ncRNAs are veritable research projects in their own right. Despite best efforts, ncRNAs across the animal phylogeny remain to a large extent uncharted territory.
This thesis describes a comprehensive collection of exploratory bioinformatic field studies designed to de novo predict ncRNA genes in a series of computational screens and in a multitude of newly sequenced genomes. Non-coding RNAs can be divided into subclasses (families) according to peculiar functional, structural, or compositional similarities. A simple but eligible and frequently applied criterion to classify RNA species is length. In line, the thesis is structured into two parts: We present a series of pilot-studies investigating (1) the short and (2) the long ncRNA repertoire of several model species by means of state-of-the-art bioinformatic techniques.
In the first part of the thesis, we focus on the detection of short ncRNAs exhibiting thermodynamically stable and evolutionary conserved secondary structures. We provide evidence for the presence of short structured ncRNAs in a variety of different species, ranging from bacteria to insects and higher eukaryotes. In particular, we highlight drawbacks and opportunities of RNAz-based ncRNA prediction at several hitherto scarcely investigated scenarios, as for example ncRNA prediction in the light of whole genome duplications. A recent microarray study provides experimental evidence for our approach. Differential expression of at least one-sixth of our drosophilid RNAz predictions has been reported. Beyond the means of RNAz, we moreover manually compile sophisticated annotation of short ncRNAs in schistosomes. Obviously, accumulating knowledge about the genetic material of malaria causing parasites which infect millions of humans world-wide is of utmost scientific interest.
Since the performance of any comparative genomics approach is limited by the quality of its input alignments, we introduce a novel light-weight and performant genome-wide alignment approach: NcDNAlign. Although the tool is optimized for speed rather than sensitivity and requires only a minor fraction of CPU time compared to existing programs, we demonstrate that it is basically as sensitive and specific as competing approaches when applied to genome-wide ncRNA gene finding and analysis of ultra-conserved regions.
By design, however, prediction approaches that search for regions with an excess of mutations that maintain secondary structure motifs will miss ncRNAs that are unstructured or whose structure is not well conserved in evolution.
In the second part of the thesis, we therefore overcome secondary structure prediction and, based on splice site detection, develop novel strategies specifically designed to identify long ncRNAs in genomic sequences - probably the open problem in current RNA research. We perform splice site anchored gene-finding in drosophilids, nematodes, and vertebrate genomes and, at least for a subset of obtained candidate genes, provide experimental evidence for expression and the existence of novel spliced transcripts undoubtedly confirming our approach.
In summary, we found evidence for a large number of previously undescribed RNAs which consolidates the idea of non-coding RNAs as an abundant class of regulatory active transcripts. Certainly, ncRNA prediction is a complex task. This thesis, however, rationally advises how to unveil the RNA complement of newly sequenced genomes. Since our results have already established both subsequent computational as well as experimental studies, we believe to have enduringly stimulated the field of RNA research and to have contributed to an enriched view on the subject.
info:eu-repo/classification/ddc/000
ddc:000
ncRNA Vorhersage, komparative Genomik, Vorhersage von Spleiss-Stellen
ncRNA prediction, comparative genomics, splice site prediction
Rose, Dominic
Stadler, Peter F.
Morgenstern, Burkhard
Universität Leipzig
2010-11-12
2010-01-06
2010-03-11
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11071
https://ul.qucosa.de/api/qucosa%3A11071/attachment/ATT-0/
oai:qucosa:de:qucosa:11107
2021-03-29T08:16:06Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Model Driven Development and Maintenance of Business Logic for Information Systems
urn:nbn:de:bsz:15-qucosa-64148
eng
Since information systems become more and more important in today\''s society, business firms, organizations, and individuals rely on these systems to manage their daily business and social activities. The dependency of possibly critical business processes on complex IT systems requires a strategy that supports IT departments in reducing the time needed to implement changed or new domain requirements of functional departments. In this context, software models help to manage system\''s complexity and provide a tool for communication and documentation purposes. Moreover, software engineers tend to use automated software model processing such as code generation to improve development and maintenance processes. Particularly in the context of web-based information systems, a number of model driven approaches were developed. However, we believe that compared to the user interface layer and the persistency layer, there could be a better support of consistent approaches providing a suitable architecture for the consistent model driven development of business logic.
To ameliorate this situation, we developed an architectural blueprint consisting of meta models, tools, and a method support for model driven development and maintenance of business logic from analysis until system maintenance. This blueprint, which we call Amabulo infrastructure, consists of five layers and provides concepts and tools to set up and apply concrete infrastructures for model driven development projects. Modeling languages can be applied as needed. In this thesis we focus on business logic layers of J2EE applications. However, concrete code generation rules can be adapted easily for different target platforms.
After providing a high-level overview of our Amabulo infrastructure, we describe its layers in detail: The Visual Model Layer is responsible for all visual modeling tasks. For this purpose, we discuss requirements for visual software models for business logic, analyze several visual modeling languages concerning their usefulness, and provide an UML profile for business logic models.
The Abstract Model Layer provides an abstract view on the business logic model in the form of a domain specific model, which we call Amabulo model. An Amabulo model is reduced to pure logical information concerning business logic aspects. It focuses on information that is relevant for the code generation. For this purpose, an Amabulo model integrates model elements for process modeling, state modeling, and structural modeling. It is used as a common interface between visual modeling languages and code generators. Visual models of the Visual Model Layer are automatically transformed into an Amabulo model.
The Abstract System Layer provides a formal view onto the system in the form of a Coloured Petri Net (CPN). A Coloured Petri Net representation of the modeled business logic is a formal structure and independent of the actual business logic implementation. After an Amabulo model is automatically transformed into a CPN, it can be analyzed and simulated before any line of code is generated.
The Code Generation Layer is responsible for code generation. To support the design and implementation of project-specific code generators, we discuss several aspects of code integration issues and provide object-oriented design approaches to tackle the issues. Then, we provide a conceptual mapping of Amabulo model elements into architectural elements of a J2EE infrastructure. This mapping explicitly considers robustness features, which support a later manual integration of generated critical code artifacts and external systems. The Application Layer is the target layer of an Amabulo infrastructure and comprises generated code artifacts. These artifacts are instances of a specific target platform specification, and they can be modified for integration purposes with development tools.
Through the contributions in this thesis, we aim to provide an integrated set of solutions to support an efficient model driven development and maintenance process for the business logic of information systems. Therefore, we provide a consistent infrastructure blueprint that considers modeling tasks, model analysis tasks, and code generation tasks. As a result, we see potential for reducing the development and maintenance efforts for changed domain requirements and simultaneously guaranteeing robustness and maintainability even after several changes.
info:eu-repo/classification/ddc/000
ddc:000
Informatik, Softwaretechnik, Modelbasierte Softwareentwicklung
Computer Science, Software Engineering, Model Driven Development
Brückmann, Tobias
Gruhn, Volker
Hasselbring, Wilhelm
Universität Leipzig
2011-01-20
2010-06-28
2010-12-17
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11107
https://ul.qucosa.de/api/qucosa%3A11107/attachment/ATT-0/
oai:qucosa:de:qucosa:11113
2021-03-29T08:16:10Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
ddc:004
ddc:020
openaire
Digital Intelligence – Möglichkeiten und Umsetzung einer informatikgestützten Frühaufklärung: Digital Intelligence – opportunities and implementation of a data-driven foresight
urn:nbn:de:bsz:15-qucosa-64230
ger
Das Ziel der Digital Intelligence bzw. datengetriebenen Strategischen Frühaufklärung ist, die Zukunftsgestaltung auf Basis valider und fundierter digitaler Information mit vergleichsweise geringem Aufwand und enormer Zeit- und Kostenersparnis zu unterstützen. Hilfe bieten innovative Technologien der (halb)automatischen Sprach- und Datenverarbeitung wie z. B. das Information Retrieval, das (Temporal) Data, Text und Web Mining, die Informationsvisualisierung, konzeptuelle Strukturen sowie die Informetrie. Sie ermöglichen, Schlüsselthemen und latente Zusammenhänge aus einer nicht überschaubaren, verteilten und inhomogenen Datenmenge wie z. B. Patenten, wissenschaftlichen Publikationen, Pressedokumenten oder Webinhalten rechzeitig zu erkennen und schnell und zielgerichtet bereitzustellen. Die Digital Intelligence macht somit intuitiv erahnte Muster und Entwicklungen explizit und messbar.
Die vorliegende Forschungsarbeit soll zum einen die Möglichkeiten der Informatik zur datengetriebenen Frühaufklärung aufzeigen und zum zweiten diese im pragmatischen Kontext umsetzen.
Ihren Ausgangspunkt findet sie in der Einführung in die Disziplin der Strategischen Frühaufklärung und ihren datengetriebenen Zweig – die Digital Intelligence.
Diskutiert und klassifiziert werden die theoretischen und insbesondere informatikbezogenen Grundlagen der Frühaufklärung – vor allem die Möglichkeiten der zeitorientierten Datenexploration.
Konzipiert und entwickelt werden verschiedene Methoden und Software-Werkzeuge, die die zeitorientierte Exploration insbesondere unstrukturierter Textdaten (Temporal Text Mining) unterstützen. Dabei werden nur Verfahren in Betracht gezogen, die sich im Kontext einer großen Institution und den spezifischen Anforderungen der Strategischen Frühaufklärung pragmatisch nutzen lassen. Hervorzuheben sind eine Plattform zur kollektiven Suche sowie ein innovatives Verfahren zur Identifikation schwacher Signale.
Vorgestellt und diskutiert wird eine Dienstleistung der Digital Intelligence, die auf dieser Basis in einem globalen technologieorientierten Konzern erfolgreich umgesetzt wurde und eine systematische Wettbewerbs-, Markt- und Technologie-Analyse auf Basis digitaler Spuren des Menschen ermöglicht.:Kurzzusammenfassung 2
Danksagung 3
Inhaltsverzeichnis 5
Tabellenverzeichnis 9
Abbildungsverzeichnis 10
A – EINLEITUNG 13
1 Hintergrund und Motivation 13
2 Beitrag und Aufbau der Arbeit 16
B – THEORIE 20
B0 – Digital Intelligence 20
3 Herleitung und Definition der Digital Intelligence 21
4 Abgrenzung zur Business Intelligence 23
5 Übersicht über unterschiedliche Textsorten 24
6 Informetrie: Bibliometrie, Szientometrie, Webometrie 29
7 Informationssysteme im Kontext der Digital Intelligence 31
B1 – Betriebswirtschaftliche Grundlagen der Digital Intelligence 36
8 Strategische Frühaufklärung 37
8.1 Facetten und historische Entwicklung 37
8.2 Methoden 41
8.3 Prozess 42
8.4 Bestimmung wiederkehrender Termini 44
8.5 Grundlagen der Innovations- und Diffusionsforschung 49
B2 – Informatik-Grundlagen der Digital Intelligence 57
9 Von Zeit, Daten, Text, Metadaten zu multidimensionalen zeitorientierten (Text)Daten 59
9.1 Zeit – eine Begriffsbestimmung 59
9.1.1 Zeitliche Grundelemente und Operatoren 59
9.1.2 Lineare, zyklische und verzweigte Entwicklungen 62
9.1.3 Zeitliche (Un)Bestimmtheit 62
9.1.4 Zeitliche Granularität 63
9.2 Text 63
9.2.1 Der Text und seine sprachlich-textuellen Ebenen 63
9.2.2 Von Signalen und Daten zu Information und Wissen 65
9.3 Daten 65
9.3.1 Herkunft 65
9.3.2 Datengröße 66
9.3.3 Datentyp und Wertebereich 66
9.3.4 Datenstruktur 67
9.3.5 Dimensionalität 68
9.4 Metadaten 69
9.5 Zusammenfassung und multidimensionale zeitorientierte Daten 70
10 Zeitorientierte Datenexplorationsmethoden 73
10.1 Zeitorientierte Datenbankabfragen und OLAP 76
10.2 Zeitorientiertes Information Retrieval 78
10.3 Data Mining und Temporal Data Mining 79
10.3.1 Repräsentationen zeitorientierter Daten 81
10.3.2 Aufgaben des Temporal Data Mining 86
10.4 Text Mining und Temporal Text Mining 91
10.4.1 Grundlagen des Text Mining 98
10.4.2 Entwickelte, genutzte und lizensierte Anwendungen des Text Mining 107
10.4.3 Formen des Temporal Text Mining 110
10.4.3.1 Entdeckung kausaler und zeitorientierter Regeln 110
10.4.3.2 Identifikation von Abweichungen und Volatilität 111
10.4.3.3 Identifikation und zeitorientierte Organisation von Themen 112
10.4.3.4 Zeitorientierte Analyse auf Basis konzeptueller Strukturen 116
10.4.3.5 Zeitorientierte Analyse von Frequenz, Vernetzung und Hierarchien 117
10.4.3.6 Halbautomatische Identifikation von Trends 121
10.4.3.7 Umgang mit dynamisch aktualisierten Daten 123
10.5 Web Mining und Temporal Web Mining 124
10.5.1 Web Content Mining 125
10.5.2 Web Structure Mining 126
10.5.3 Web Usage Mining 127
10.5.4 Temporal Web Mining 127
10.6 Informationsvisualisierung 128
10.6.1 Visualisierungstechniken 130
10.6.1.1 Visualisierungstechniken nach Datentypen 130
10.6.1.2 Visualisierungstechniken nach Darstellungsart 132
10.6.1.3 Visualisierungstechniken nach Art der Interaktion 137
10.6.1.4 Visualisierungstechniken nach Art der visuellen Aufgabe 139
10.6.1.5 Visualisierungstechniken nach Visualisierungsprozess 139
10.6.2 Zeitorientierte Visualisierungstechniken 140
10.6.2.1 Statische Repräsentationen 141
10.6.2.2 Dynamische Repräsentationen 145
10.6.2.3 Ereignisbasierte Repräsentationen 147
10.7 Zusammenfassung 152
11 Konzeptuelle Strukturen 154
12 Synopsis für die zeitorientierte Datenexploration 163
C – UMSETZUNG EINES DIGITAL-INTELLIGENCESYSTEMS 166
13 Bestimmung textbasierter Indikatoren 167
14 Anforderungen an ein Digital-Intelligence-System 171
15 Beschreibung der Umsetzung eines Digital-Intelligence-Systems 174
15.1 Konzept einer Dienstleistung der Digital Intelligence 175
15.1.1 Portalnutzung 177
15.1.2 Steckbriefe 178
15.1.3 Tiefenanalysen 180
15.1.4 Technologiescanning 185
15.2 Relevante Daten für die Digital Intelligence (Beispiel) 187
15.3 Frühaufklärungs-Plattform 188
15.4 WCTAnalyze und automatische Extraktion themenspezifischer Ereignisse 197
15.5 SemanticTalk 200
15.6 Halbautomatische Identifikation von Trends 204
15.6.1 Zeitreihenkorrelation 205
15.6.2 HD-SOM-Scanning 207
D – ZUSAMMENFASSUNG 217
Anhang A: Prozessbilder entwickelter Anwendungen des (Temporal) Text Mining 223
Anhang B: Synopsis der zeitorientierten Datenexploration 230
Literaturverzeichnis 231
Selbstständigkeitserklärung 285
Wissenschaftlicher Werdegang des Autors 286
Veröffentlichungen 287
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/003
ddc:003
info:eu-repo/classification/ddc/004
ddc:004
info:eu-repo/classification/ddc/006
ddc:006
info:eu-repo/classification/ddc/020
ddc:020
info:eu-repo/classification/ddc/025
ddc:025
info:eu-repo/classification/ddc/028
ddc:028
Information Retrieval; Text Mining; Data Mining
Digital Intelligence; datengetriebene Strategische Frühaufklärung; (halb)automatische Sprach- und Datenverarbeitung; Information Retrieval; (Temporal) Data, Text und Web Mining; Informationsvisualisierung; konzeptuelle Strukturen; Informetrie; Informationslogistik
digital intelligence; data driven foresight; information retrieval; (temporal) data, text and web mining; information visualisation; informetrics
Walde, Peter
Heyer, Gerhard
Gurevych, Iryna
Universität Leipzig
2011-01-18
2010-01-31
2010-12-15
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11113
https://ul.qucosa.de/api/qucosa%3A11113/attachment/ATT-0/
oai:qucosa:de:qucosa:11159
2021-03-29T08:16:45Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Expanding the repertoire of bacterial (non-)coding RNAs
urn:nbn:de:bsz:15-qucosa-67816
eng
The detection of non-protein-coding RNA (ncRNA) genes in bacteria and their diverse regulatory mode of action moved the experimental and bio-computational analysis of ncRNAs into the focus of attention. Regulatory ncRNA transcripts are not translated to proteins but function directly on the RNA level. These typically small RNAs have been found to be involved in diverse processes such as (post-)transcriptional regulation and modification, translation, protein translocation, protein degradation and sequestration.
Bacterial ncRNAs either arise from independent primary transcripts or their mature sequence is generated via processing from a precursor. Besides these autonomous transcripts, RNA regulators (e.g. riboswitches and RNA thermometers) also form chimera with protein-coding sequences. These structured regulatory elements are encoded within the messenger RNA and directly regulate the expression of their “host” gene.
The quality and completeness of genome annotation is essential for all subsequent analyses. In contrast to protein-coding genes ncRNAs lack clear statistical signals on the sequence level. Thus, sophisticated tools have been developed to automatically identify ncRNA genes. Unfortunately, these tools are not part of generic genome annotation pipelines and therefore computational searches for known ncRNA genes are the starting point of each study. Moreover, prokaryotic genome annotation lacks essential features of protein-coding genes. Many known ncRNAs regulate translation via base-pairing to the 5’ UTR (untranslated region) of mRNA transcripts. Eukaryotic 5’ UTRs have been routinely annotated by sequencing of ESTs (expressed sequence tags) for more than a decade. Only recently, experimental setups have been developed to systematically identify these elements on a genome-wide scale in prokaryotes.
The first part of this thesis, describes three experimental surveys of exploratory field studies to analyze transcript organization in pathogenic bacteria. To identify ncRNAs in Pseudomonas aeruginosa we used a combination of an experimental RNomics approach and ncRNA prediction. Besides already known ncRNAs we identified and validated the expression of six novel RNA genes.
Global detection of transcripts by next generation RNA sequencing techniques unraveled an unexpectedly complex transcript organization in many bacteria. These ultra high-throughput methods give us the appealing opportunity to analyze the complete RNA output of any species at once. The development of the differential RNA sequencing (dRNA-seq) approach enabled us to analyze the primary transcriptome of Helicobacter pylori and Xanthomonas campestris. For the first time we generated a comprehensive and precise transcription start site (TSS) map for both species and provide a general framework for the analysis of dRNA-seq data. Focusing on computer-aided analysis we developed new tools to annotate TSS, detect small protein-coding genes and to infer homology of newly detected transcripts. We discovered hundreds of TSS in intergenic regions, upstream of protein-coding genes, within operons and antisense to annotated genes. Analysis of 5’ UTRs (spanning from the TSS to the start codon of the adjacent protein-coding gene) revealed an unexpected size diversity ranging from zero to several hundred nucleotides. We identified and validated the expression of about 60 and about 20 ncRNA candidates in Helicobacter and Xanthomonas, respectively. Among these ncRNA candidates we found several small protein-coding genes that have previously evaded annotation in both species. We showed that the combination of dRNA-seq and computational analysis is a powerful method to examine prokaryotic transcriptomes.
Experimental setups are time consuming and often combined with huge costs. Another limitation of experimental approaches is that genes which are expressed in specific developmental stages or stress conditions are likely to be missed. Bioinformatic tools build an alternative to overcome such restraints. General approaches usually depend on comparative genomic data and evolutionary signatures are used to analyze the (non-)coding potential of multiple sequence alignments. In the second part of my thesis we present our major update of the widely used ncRNA gene finder RNAz and introduce RNAcode, an efficient tool to asses local protein-coding potential of genomic regions.
RNAz has been successfully used to identify structured RNA elements in all domains of life. However, our own experience and the user feedback not only demonstrated the applicability of the RNAz approach, but also helped us to identify limitations of the current implementation. Using a much larger training set and a new classification model we significantly improved the prediction accuracy of RNAz.
During transcriptome analysis we repeatedly identified small protein-coding genes that have not been annotated so far. Only a few of those genes are known to date and standard proteincoding gene finding tools suffer from the lack of training data. To avoid an excess of false positive predictions, gene finding software is usually run with an arbitrary cutoff of 40-50 amino acids and therefore misses the small sized protein-coding genes. We have implemented RNAcode which is optimized for emerging applications not covered by standard protein-coding gene annotation software. In addition to complementing classical protein gene annotation, a major field of application of RNAcode is the functional classification of transcribed regions. RNA sequencing analyses are likely to falsely report transcript fragments (e.g. mRNA degradation products) as non-coding. Hence, an evaluation of the protein-coding potential of these fragments is an essential task. RNAcode reports local regions of high coding potential instead of complete protein-coding genes. A training on known protein-coding sequences is not necessary and RNAcode can therefore be applied to any species. We showed this with our analysis of the Escherichia coli genome where the current annotation could be accurately reproduced. We furthermore identified novel small protein-coding genes with RNAcode in this extensively studied genome. Using transcriptome and proteome data we found compelling evidence that several of the identified candidates are bona fide proteins.
In summary, this thesis clearly demonstrates that bioinformatic methods are mandatory to analyze the huge amount of transcriptome data and to identify novel (non-)coding RNA genes. With the major update of RNAz and the implementation of RNAcode we contributed to complete the repertoire of gene finding software which will help to unearth hidden treasures of the RNA World.
info:eu-repo/classification/ddc/000
ddc:000
Transkriptom, kleine RNAs, Transkriptanalyse, vergleichende Genomik
transcriptome, small RNAs, transcript analysis, comparative genomics
Findeiß, Sven
Stadler, Peter F.
Hess, Wolfgang R.
Universität Leipzig
2011-05-02
2011-07-02
2011-07-03
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11159
https://ul.qucosa.de/api/qucosa%3A11159/attachment/ATT-0/
oai:qucosa:de:qucosa:11168
2021-03-29T08:16:51Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Evolution von Ontologien in den Lebenswissenschaften
urn:nbn:de:bsz:15-qucosa-68078
ger
In den Lebenswissenschaften haben sich Ontologien in den letzten Jahren auf breiter Front durchgesetzt und sind in vielen Anwendungs- und Analyseszenarien kaum mehr wegzudenken. So etablierten sich nach und nach immer mehr domänenspezifische Ontologien, z.B. Anatomie-Ontologien oder Ontologien zur Beschreibung der Funktionen von Genen oder Proteinen. Da das Wissen in den Lebenswissenschaften sich rapide ändert und weiterentwickelt, müssen die entsprechenden Ontologien ständig angepasst und verändert werden, um einen möglichst aktuellen Wissensstand zu repräsentieren. Nutzer von Ontologien müssen mit dieser Evolution umgehen können, d.h. um \\\\\\\"Up-to-Date\\\\\\\" zu sein, sollten die aktuellsten Versionen einer Ontologie verwendet werden. Dies ist häufig nur schwer umsetzbar, da die Evolution weitreichende Einflüsse auf existierende Datenbestände, Analyseergebnisse oder Anwendungen haben kann. Innerhalb dieser Dissertation stehen Werkzeuge und Algorithmen zum Umgang mit sich ständig ändernden Ontologien im Bereich der Lebenswissenschaften im Mittelpunkt.
Zunächst wird ein generelles Framework für quantitative Evolutionsanalysen eingeführt. Das Framework wird für eine umfassende Analyse der Evolution zahlreicher Ontologien der Lebenswissenschaften verwendet. Die Analysen zeigen, dass alle untersuchten Ontologien stetig verändert (angepasst) werden und ein signifikantes Wachstum aufweisen. Auch für auf Ontologien basierte Mappings, d.h. Verknüpfungen zwischen Datenquellen und Ontologien (Annotation-Mapping) sowie zwischen Ontologien selbst (Ontologie-Mapping), liegen starke und häufige Veränderungen vor. Es besteht somit ein Bedarf, die Evolution von Ontologien in den Lebenswissenschaften und deren Konsequenzen zu unterstützen, d.h. Nutzern von sich ständig ändernden Ontologien angemessene Algorithmen/Werkzeuge bereitzustellen. Die Erkenntnisse aus den durchgeführten Analysen bilden die Basis für die nachfolgenden Arbeiten.
Eine immer wiederkehrende Aufgabe im Rahmen der Ontologieevolution besteht in der Bestimmung von Änderungen zwischen zwei Versionen einer Ontologie, d.h. worin besteht der Unterschied und wie hat sich die neuere Version aus der alten Version heraus entwickelt. Das Ergebnis, d.h. der Diff (die Differenz) zwischen den beiden Ontologieversionen, bildet die Basis für weitere Aufgaben wie beispielsweise die Anpassung abhängiger Daten. Innerhalb der Arbeit wird ein neuartiger auf Regeln basierter Algorithmus vorgestellt, welcher den Diff zwischen zwei Ontologieversionen bestimmt. Es werden sowohl einfache wie auch komplexe Änderungen erkannt, was eine kompakte, intuitive und verständliche Diff-Repräsentation garantiert. Es wird theoretisch wie praktisch gezeigt, dass ein vollständiger Diff bestimmt wird, was eine korrekte Migration von Ontologieversionen ermöglicht.
Ein weiterer Schwerpunkt der Arbeit liegt in der Bestimmung änderungsintensiver bzw. stabiler Regionen in einer Ontologie. Dazu wird die Notation von Ontologieregionen und zugehörige Metrikern zur Beurteilung ihrer Änderungsintensität (Stabilität) eingeführt. Ein neuartiger automatisierter Algorithmus erlaubt die Bestimmung (in)stabiler Ontologieregionen auf Basis veröffentlichter Ontologieversionen in einem vorgegebenen Zeitraum. Durch erkannte Änderungen zwischen Ontologieversionen und mit Hilfe der Ontologiestruktur werden änderungsintensive bzw. stabile Ontologieregionen erkannt. Die Evaluierung anhand großer Ontologien der Lebenswissenschaften zeigt, dass der Algorithmus in der Lage ist (in)stabile Ontologieregionen automatisiert zu bestimmen.
Abschließend wird das webbasierte System OnEX und dessen Versionierungsansatz präsentiert. OnEX ermöglicht einen benutzerfreundlichen und interaktiven Zugang zu Informationen über die Evolution und Änderungen in Ontologien der Lebenswissenschaften. Nutzer können Ontologien aus ihrem Interessengebiet bzgl. Evolution untersuchen, indem sie beispielsweise Änderungen an einer Ontologieversion einsehen, welche in einer Analyse oder Anwendung genutzt werden soll. Der OnEX zugrunde liegende Versionierungsansatz ermöglicht eine skalierbare und speichereffiziente Versionierung großer Ontologien durch die Nutzung von Zeitstempeln. Mit Hilfe des Ansatzes konnten 16 Ontologien mit ca. 700 Versionen seit 2002 versioniert und Nutzern über OnEX für Evolutionsanalysen zugänglich gemacht werden.
info:eu-repo/classification/ddc/000
ddc:000
Ontologie, Evolution, Lebenswissenschaften
ontology, evolution, life sciences
Hartung, Michael
Rahm, Erhard
Sure, York
Universität Leipzig
2011-05-10
2011-11-01
2011-04-20
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11168
https://ul.qucosa.de/api/qucosa%3A11168/attachment/ATT-0/
oai:qucosa:de:qucosa:11202
2021-03-29T08:17:14Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Evolutionäre Sprachtransformation: Ereignismodell und Rekonstruktionsverfahren für Sprachwandel
urn:nbn:de:bsz:15-qucosa-69531
ger
Verwandte Sprachen besitzen Wörter gleichen Ursprungs. Im Laufe der Geschichte ändern diese Wörter ihre Gestalt und lassen sich heute in ähnlicher Form in verschiedenen Sprachen als Kognate wiederfinden. In dieser Arbeit wird ein formales Modell zur Beschreibung dieser Änderungen mit Hilfe von kodierten, lexikalischen Wortlisten entwickelt. Das Modell ist geeignet, automatisch und objektiv die Evolution idealisierter Sprachen mit Hilfe eines Sprach-Phylogeniebaumes abzubilden. Dabei werden die einzelnen Buchstabenveränderungen verwandter Wörter und die rekonstruierten Protoformen untersucht. Insbesondere interessieren solche Buchstabenveränderungen, die für mehrere Wörter einer Sprache synchron stattgefunden haben. Ein weiterer Bestandteil des evolutionären Modells ist die Identifikation von Kognaten, um die möglichen Buchstabenersetzungen zwischen den verwandten Wörtern untersuchen zu können.
Für die Rekonstruktion linguistisch plausibler Buchstabenveränderungen und Kognatzuweisungen entlang einer Sprachphylogenie wird ein parsimonisches Kostenmodell verwendet, welches die verschiedenen Sprach- und Transformationsverläufe bewertet. Die Suche nach der plausibelsten Lösung ist NP-vollständig, so dass für den enorm großen Suchraum ein Annäherungsverfahren vorgeschlagen wird. Ausgehend von einer geeigneten Rekonstruktion wird durch sukzessives und minimales Verändern einzelner Transformationen oder Kognatzuweisungen mit Hilfe eines speziell entwickelten Approximationsverfahrens nicht nur eine lokal maximale Lösung, sondern eine global beste Lösung angenähert.
Mit dem gewählten umfassenden Ansatz des untersuchten Rekonstruktionsmodells ist eine Sprachentwicklung für kleine Wortlisten in angemessener Zeit berechenbar. Als großer Vorteil ist die Nachvollziehbarkeit aller Einzeltransformationen für den linguistischen Diskurs anzusehen. Insbesonders die Identifikation regulärer Buchstabenersetzungen mit möglicher Interpretation als Lautwandel früherer Sprachen ist hierbei von Bedeutung.
Related languages contain words of the same origin. Through time these words
change. Remaining similarities between these words can be detected in different
languages. In this work, transformations across lexical wordlist are used to
model these changes. To reconstruct the possible pathways of language change
an algorithm is choosen that calculates the phylogeny, the appropriate protolanguage
and the cognate sets. An evaluation function detects plausible evolutions.
Because of the enormous amount of possible solutions an approximative
method is proposed that continuously modifies and improves possible solutions.
info:eu-repo/classification/ddc/000
ddc:000
Linguistik, Sprachphylogenie, Kognate, Transformationen, Evolution, Lautwandel, Protoform, Rekonstruktion, Automatisch, Verfahren, Modell, Wortlisten, Parsimonie
Evolution, Wordlist, Transformation, Method, Computational, Protoword, Linguistik, Language, Kognate, Parsimony
Jung, Hagen
Cysouw, Michael
Dress, Andreas
Middendorf, Martin
Max-Planck-Institut für evolutionäre Anthropologie
2011-06-10
2010-10-29
2011-06-06
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11202
https://ul.qucosa.de/api/qucosa%3A11202/attachment/ATT-0/
oai:qucosa:de:qucosa:11230
2021-03-29T08:17:36Z
qucosa:ubl
doc-type:Other
doc-type:Text
open_access
ddc:000
openaire
Ansatz zur Interaktion mit dreidimensional visualisierten Softwaremodellen
urn:nbn:de:bsz:15-qucosa-71070
ger
Softwaresysteme sind komplexe immaterielle Systeme mit einer Vielzahl von Bestandteilen und Beziehungen. Um den Aufbau, die Funktionsweise und die Entwicklung von Softwaresystemen besser zu verstehen, eignen sich Softwarevisualisierungen, welche die abstrakte Datengrundlage in eine visuelle Repräsentation übertragen. Auf Grund der Masse und der Komplexität der in der Visualisierung enthaltenen Informationen, kommt es schnell zur Unübersichtlichkeit, was sich negativ auf den Prozess des Verstehens auswirkt. Zur Beherrschung der Komplexität muss der Betrachter daher die Gesamtheit zuerst in mehrere Perspektiven unterteilen, um diese anschließend gezielt nach verschiedenen Aspekten untersuchen zu können.
Die dafür benötigten Interaktionsmöglichkeiten sind Gegenstand der Untersuchungen in dieser Arbeit, wobei im Wesentlichen Visualisierungen der Struktur von Software als Ausgangspunkt genutzt werden. Insbesondere wird der Frage nachgegangen, wie die Interaktion gestaltet werden kann, damit der Benutzer ein möglichst umfassendes Verständnis der Struktur erlangt.
Zur Umsetzung der theoretischen Erkenntnisse wird ein Prototyp vorgestellt, der automatisiert aus den Strukturinformationen eines Ecore-Modells eine interaktive dreidimensionale Softwarevisualisierung der Struktur im freien standardisierten Format Extensible 3D generiert. Der Prozess der Visualisierung wird dabei durch Werkzeuge des openArchitectureWare-Frameworks realisiert. Zur Integration in den Entwicklungsprozess ist der Prototyp in ein Plugin für Eclipse eingebettet.:1 Einleitung
1.1 Motivation
1.2 Ziele
1.3 Aufbau
2 Softwarevisualisierung
2.1 Visualisierung
2.1.1 Grundlagen
2.1.2 Aufgaben und Ziele
2.1.3 Teilgebiete
2.2 Definition
2.3 Ziele und Aufgaben
2.4 Visualisierungspipeline
2.5 Visualisierungstechniken
2.5.1 Graphen
2.5.2 Visuelle Metaphern
2.6 Taxonomie für Softwarevisualisierungen
3 Interaktion mit einer Softwarevisualisierung
3.1 Einordnung
3.2 Definition
3.3 Ziele
3.4 Benutzungsschnittstelle
3.5 Aufbau der Benutzungsschnittstelle
3.5.1 Anwendungsschnittstelle
3.5.2 Dialogschnittstelle
3.5.3 Ein-/Ausgabenschnittstelle
3.6 Interaktionstechnik
3.7 Taxonomie der Interaktionstechniken
3.8 Konzept zur Interaktion mit einer Softwarevisualisierung
4 Technische Grundlagen des Prototyps
4.1 Eclipse
4.2 Das openArchitectureWare-Framework
4.2.1 Modellgetriebene Softwareentwicklung
4.2.2 Aufbau des Frameworks
4.2.3 oAW-Workflow
4.2.4 Ecore
4.2.5 Xtend Modell-zu-Modell-Transformationen
4.3 Extensible 3D
4.3.1 Grundlagen
4.3.2 Szenegraph
4.3.3 Ereignismodell
4.3.4 X3D-Prototypen
5 Basisprototyp
5.1 Funktionsweise
5.2 Einordnung
5.3 Visualisierungsprozess des Generators
5.3.1 Modelltransformation von Ecore zu Graph
5.3.2 Modellmodifikation des Graphen
5.3.3 Modelltransformation von Graph zu X3D
5.4 Ansatzpunkte der Erweiterung
6 Erweiterung des Prototyps für die Interaktion
6.1 Benutzungsschnittstelle
6.1.1 Direkte Manipulation
6.1.2 Manipulation nach Elementtyp
6.1.3 Navigation durch Pakethierarchie und Klassengraph
6.1.4 Identifikation nach Bezeichner und Tooltip
6.2 Architektur des interaktiven X3D-Modells
6.3 Erweiterung des Generators
6.3.1 Anpassung der Transformationen des Basisprototyps
6.3.2 Modelltransformation in ein interaktives X3D-Modell
6.4 Integration in das Eclipse-Plugin
7 Fazit und Ausblick
info:eu-repo/classification/ddc/000
ddc:000
Softwarevisualisierung, 3D, Interaktion, Extensible 3D, openArchitectureWare, Eclipse
Softwarevisualisation, interaction, x3d
Kovacs, Pascal
Eisenecker, Ulrich
Universität Leipzig
2011-08-15
2010-04-22
2010-04-22
info:eu-repo/semantics/openAccess
doc-type:Other
info:eu-repo/semantics/other
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11230
https://ul.qucosa.de/api/qucosa%3A11230/attachment/ATT-0/
oai:qucosa:de:qucosa:11229
2021-03-29T08:17:35Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Molecular Morphology: Phylogenetically Informative Characters Derived from Sequence Data
urn:nbn:de:bsz:15-qucosa-71028
eng
A fundamental problem in biology is the reconstruction of the relatedness of all (extant) species.
Traditionally, systematists employ visually recognizable characters of organisms for classification and evolutionary analysis. Recent developments in molecular and computational biology, however, lead to a whole different perspective on how to address the problem of inferring relatedness. The discovery of molecules, carrying genetic information, and the comparison of their primary structure has, in a rather short period of time, revolutionized our understanding of the phylogenetic relationship of many organisms.
These novel approaches, however, turned out to bear similar problems as previous techniques. Moreover, they created new ones. Hence, taxonomists came to realize that even with this new type of data not all problematic relationships could be unambiguously resolved. The search for complementary approaches has led to the utilization of rare genomic changes and other characters which are largely independent from the primary structure of the underlying sequence(s). These “higher order” characters are thought to be evolutionary conserved in certain lineages and largely unaffected by primary sequence data-based problems, allowing for a better resolution of the Tree of Life.
The central aim of this thesis is the utilization of molecular characters of higher order in connection with their consistent and comparable extraction from a given data set. Two novel methods are presented that allow such an inference. This is complemented with the search for and analysis of known and novel molecular characteristics to study the relationships among Metazoa, both intra- as well as interspecific.
The first method tackles a common problem in phylogenetic analyses: the inference of reliable data set. As part of this thesis a pipeline was created for the automated annotation of metazoan mitochondrial genomes. Data thus obtained constitutes a reliable and standardized starting point for all downstream analyses, e.g. genome rearrangement studies.
The second method utilizes a subclass of gaps, namely those which define an approximate split of a given data set. The definition and inference of such split-inducing indels (splids) is based on two basic principles. First, indels at the same position, i.e. sharing the same end points in two sequences, are likely homologous. Second, independent single-residue insertions and deletions tend to occur more frequently than multi-residue indels. It is shown that trees based on splids recover most of the undisputed monophyletic groups while influence of the underlying alignment algorithm is relatively small.
Mitochondrial markers are a valuable tool for the understanding of small and large scale population structure. The non-coding control region of mitochondrial DNA (mtDNA) often contains a higher amount of variability compared to genes encoding proteins and non-coding RNAs. A case study on a small scale population structure investigates the control region of the European Fire-bellied Toad in order to find highly variable parts which are of potential importance to develop informative genetic markers. A particular focus is placed on the investigation of the evolutionary dynamics of the repetitive region at an inter- and intraspecific level. This includes understanding mechanisms underlying its evolution, i.e. by exploring the impact of secondary structure on slipped strand mispairing during mtDNA replication.
The 7SK RNA is a key player in the regulation of polymerase II (Pol-II) transcription, interacting with at least three known proteins: It mediates the inhibition of the Positive Transcription Elongation Factor b (P-TEFb) by the HEXIM1/2 proteins, thereby repressing transcript elongation by Pol-II. A highly specific interaction with LARP7 (La-Related Protein 7), on the other hand, regulates its stability. 7SK RNA is capped at its 5’ end by a highly specific methyltransferase MePCE (Methylphosphate Capping Enzyme). Employing sequence and structure similarity it is shown that the 7SK RNA as well as its protein binding partners have a much earlier evolutionary origin than previously expected. Furthermore, this study presents a good illustration of the pitfalls of using markers of higher order for phylogenetic inference.
info:eu-repo/classification/ddc/000
ddc:000
molekulare Morphologie, Insertionen/Deletionen, Annotation mitochondrialer DNS
molecular morphology, indels, mitochondrial genome annotation
Donath, Alexander
Stadler, Peter F.
Mosig, Axel
Universität Leipzig
2011-07-22
2011-09-05
2011-07-07
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11229
https://ul.qucosa.de/api/qucosa%3A11229/attachment/ATT-0/
oai:qucosa:de:qucosa:11231
2021-03-29T08:17:37Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Understanding and improving high-throughput sequencing data production and analysis
urn:nbn:de:bsz:15-qucosa-71102
eng
Advances in DNA sequencing revolutionized the field of genomics over the last 5 years. New sequencing instruments make it possible to rapidly generate large amounts of sequence data at substantially lower cost. These high-throughput sequencing technologies (e.g. Roche 454 FLX, Life Technology SOLiD, Dover Polonator, Helicos HeliScope and Illumina Genome Analyzer) make whole genome sequencing and resequencing, transcript sequencing as well as quantification of gene expression, DNA-protein interactions and DNA methylation feasible at an unanticipated scale.
In the field of evolutionary genomics, high-throughput sequencing permitted studies of whole genomes from ancient specimens of different hominin groups. Further, it allowed large-scale population genetics studies of present-day humans as well as different types of sequence-based comparative genomics studies in primates. Such comparisons of humans with closely related apes and hominins are important not only to better understand human origins and the biological background of what sets humans apart from other organisms, but also for understanding the molecular basis for diseases and disorders, particularly those that affect uniquely human traits, such as speech disorders, autism or schizophrenia. However, while the cost and time required to create comparative data sets have been greatly reduced, the error profiles and limitations of the new platforms differ significantly from those of previous approaches. This requires a specific experimental design in order to circumvent these issues, or to handle them during data analysis.
During the course of my PhD, I analyzed and improved current protocols and algorithms for next generation sequencing data, taking into account the specific characteristics of these new sequencing technologies. The presented approaches and algorithms were applied in different projects and are widely used within the department of Evolutionary Genetics at the Max Planck Institute of Evolutionary Anthropology. In this thesis, I will present selected analyses from the whole genome shotgun sequencing of two ancient hominins and the quantification of gene expression from short-sequence tags in five tissues from three primates.
info:eu-repo/classification/ddc/000
ddc:000
Hochdurchsatzsequenzierung,Machinenlernen,Genexpression,Neandertal
Next Generation Sequencing,High-throughput sequencing,Machine Learning,Gene expression,Neanderthal
Kircher, Martin
Kelso, Janet
Nekrutenko, Anton
Stadler, Peter F.
Universität Leipzig
2011-07-27
2011-02-22
2011-11-07
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11231
https://ul.qucosa.de/api/qucosa%3A11231/attachment/ATT-0/
https://ul.qucosa.de/api/qucosa%3A11231/attachment/ATT-1/
oai:qucosa:de:qucosa:11305
2021-03-29T08:18:29Z
qucosa:ubl
doc-type:book
doc-type:Text
open_access
ddc:000
status-type:publishedVersion
openaire
Systemintegration: eine qualitative Erhebung aus der Sicht von Integrationsdienstleistern
urn:nbn:de:bsz:15-qucosa-78607
978-3-941608-15-3
ger
urn:nbn:de:bsz:15-qucosa-155763
qucosa:13006
Systemintegration hat auf Grund des Einsatzes heterogener Systeme eine fortlaufende Bedeutung für viele Unternehmen und vor allem für Integrationsdienstleister. Die Praxis der Integration stimmt nicht immer mit den aktuellen Forschungsthemen überein. Diese qualitative Erhebung liefert einen Zustandsbericht über Herausforderungen und Probleme denen Integrationsdienstleister täglich begegnen und dient der Identifikation von praxisrelevanten Forschungsfragen.
Systemintegration, Integration Engineering, qualitative Erhebung, Integrationsdienstleistung
Systemsintegration, Integration Engineering, qualitative Study, Integration Services
info:eu-repo/classification/ddc/000
ddc:000
Gebauer, Martin
Stefan, Fred
Leipziger Informatik-Verbund (LIV)
Universität Leipzig
Institut für Angewandte Informatik (InfAI) e.V. an der Universität Leipzig
2011
info:eu-repo/semantics/publishedVersion
2011-11-28
Leipziger Beiträge zur Informatik
Leipziger Beiträge zur Informatik
info:eu-repo/semantics/openAccess
doc-type:book
info:eu-repo/semantics/book
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11305
https://ul.qucosa.de/api/qucosa%3A11305/attachment/ATT-0/
oai:qucosa:de:qucosa:11314
2021-03-29T08:18:35Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Towards a complete sequence homology concept: Limitations and applications
urn:nbn:de:bsz:15-qucosa-79199
eng
Historically, the paradigm of similarity of protein sequences implying common structure, function and ancestry was generalized based on studies of globular domains. The implications of sequence similarity among non-globular protein segments have not been studied to the same extent; nevertheless, homology considerations are silently extended for them. This appears especially detrimental in the case of transmembrane helices (TMs) and signal peptides (SPs) where sequence similarity is necessarily a consequence of physical requirements rather than common ancestry. Since the matching of SPs/TMs creates the illusion of matching hydrophobic cores, the inclusion of SPs/TMs into domain models can give rise to wrong annotations. More than 1001 domains among the 10,340 models of Pfam release 23 and 18 domains of SMART version 6 (out of 809) contain SP/TM regions. As expected, fragment mode HMM searches generate promiscuous hits limited to solely the SP/TM part among clearly unrelated proteins. More worryingly, this work shows explicit examples that the scores of clearly false-positive hits, even in globalmode searches, can be elevated into the significance range just by matching the hydrophobic runs. In the PIR iProClass database v3.74 using conservative criteria, this study finds that at least between 2.1% and 13.6% of its annotated Pfam hits appear unjustified for a set of validated domain models. Thus, false positive domain hits enforced by SP/TM regions can lead to dramatic annotation errors where the hit has nothing in common with the problematic domain model except the SP/TM region itself. A workflow of flagging problematic hits arising from SP/TM-containing models for critical reconsideration by annotation users is provided.
While E-value guided extrapolation of protein domain annotation from libraries such as Pfam with the HMMER suite is indispensable for hypothesizing about the function of experimentally uncharacterized protein sequences, it can also complicate the annotation problem. In HMMER2, the E-value is computed from the score via a logistic function or via a domain model-specific extreme value distribution (EVD); the lower of the two is returned as E-value for the domain hit in the query sequence. We demonstrated that, for thousands of domain models, this treatment results in switching from the EVD to the statistical model with the logistic function when scores grow (for Pfam release 23, 99% in the global mode and 75% in the fragment mode). If the score corresponding to the breakpoint results in an E-value above a user-defined threshold (e.g., 0.1), a critical score region with conflicting E-values from the logistic function (below the threshold) and from EVD (above the threshold) does exist. Thus, this switch will affect E-value guided annotation decisions in an automated mode. To emphasize, switching in the fragment mode is of no practical relevance since it occurs only at E-values far below 0.1. Unfortunately, a critical score region does exist for 185 domain models in the hmmpfam and 1748 domain models in the hmmsearch global-search mode. For 145 out the respective 185 models, the critical score region is indeed populated by actual sequences. In total, 24.4% of their hits have a logistic function-derived E-value<0.1 when the EVD provides an E-value>0.1. Examples of false annotations are provided and the appropriateness of a logistic function as alternative to the EVD is critically discussed. This work shows that misguided E-value computation coupled with non-globular regions embedded in domain model library not only causes annotation errors in public databases but also limits the extrapolation power of protein function prediction tasks.
So far, the preceding work has demonstrated that sequence homology
considerations widely used to transfer functional annotation to uncharacterized protein sequences require special precautions in the case of non-globular sequence segments including membrane-spanning stretches from non-polar residues. We found that there are two types of transmembrane helices (TMs) in membrane-associated proteins. On the one hand, there are so-called simple TMs with elevated hydrophobicity, low sequence complexity and extraordinary enrichment in long aliphatic residues. They merely serve as membrane-anchoring device. In contrast, so-called complex TMs have lower hydrophobicity, higher sequence complexity and some functional residues. These TMs have additional roles besides membrane anchoring such as intramembrane complex formation, ligand binding or a catalytic role. Simple and complex TMs can occur both in single- and multi-membrane-spanning proteins essentially in any type of topology. Whereas simple TMs have the potential to confuse searches for sequence homologues and to generate unrelated hits with seemingly convincing statistical significance, complex TMs contain essential evolutionary information. For extending the homologyconcept onto membrane proteins, we provide a necessary quantitative criterion to distinguish simple TMs in query sequences prior to their usage in homology searches based on assessment of hydrophobicity and sequence complexity of the TM sequence segments.
Theoretical insights from this work were applied to problems of function
prediction for specific uncharacterized gene/protein sequences (for example, APMAP and ARXES) and for the functional classification of TM-containing proteins.
info:eu-repo/classification/ddc/000
ddc:000
Proteinsequenz; Homologie; Transmembranhelix; Sequenzkomplexität
Protein sequence; Homology; Transmembrane helix; Sequence complexity
Wong, Wing-Cheong
Eisenhaber, Frank
Dandekar, Thomas
Stadler, Peter
Universität Leipzig
2011-12-14
2011-08-11
2011-08-11
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11314
https://ul.qucosa.de/api/qucosa%3A11314/attachment/ATT-0/
oai:qucosa:de:qucosa:11311
2021-03-29T08:18:33Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Transcriptional Regulatory Elements: Detection and Evolutionary Analysis
urn:nbn:de:bsz:15-qucosa-78960
eng
A major challenge in life sciences is the understanding of mechanisms that regulate the expression of genes. An important step towards this goal is the ability to identify transcriptional regulatory elements like binding sites for transcription factors. In computational biology, a popular approach for this task is comparative sequence analysis using both distantly as well as closely related species. Although this method has successfully identified conserved regulatory regions, the majority of binding sites can change rapidly even between closely related species. This makes it difficult to detect them using DNA sequences alone. In this thesis, we introduce two new approaches for the detection and evolutionary analysis of transcriptional elements that consider the challenges of binding site turnover.
In the first part, we develop a method for detecting homologous motifs in a given set of sequences in order to obtain evidence for evolutionary events and turnover. Based on a detailed theoretical scaffold, we develop a simple, but effective and efficient heuristic for assembling local pairwise sequence alignments into a local multiple sequence alignment. This kind of multiple alignment only contains conserved motifs represented in columns which satisfy the order implied by the underlying sequences. By favoring motifs that are contained in a great range of sequences, our method is additionally able to detect even small conserved motifs. Furthermore, the calculation of the initial local pairwise alignments is generic. This allows the use of fast heuristic methods in case of large data sets while exact alignment programs can be used for small data sets where detailed information is needed. Application to artificial as well as biological data sets demonstrate the capabilities of our algorithm.
In the second part, we propose a conceptually simple, but mathematically non-trivial, phenomenological model for the binding site turnover at a genomic locus. The model is based on the assumption that binding sites have a constant rate of origination and a constant decay rate per binding site. The elementary derivation of the transient probability distribution is affirmed by simulations of sequence evolution as well as biological data. Based on the derived distribution, we develop a phenomenological model of binding site number dynamics in order to detect changes in selective constraints acting on transcription factor binding sites. Using a maximum likelihood implementation as well as exploratory data analysis, we show the functionality of the model by identifying functionally important changes in the evolutionary turnover rates on biological data.
Each part of this thesis leads to the development of a new program. While Tracker allows the computation of conserved homologous motifs and their representation in a local multiple alignment, Creto determines the evolutionary turnover rates for arbitrary clades of a phylogenetic tree with given binding site numbers at the final taxa. Both software tools are freely available to the scientific community for further research in this important and exciting field.
info:eu-repo/classification/ddc/000
ddc:000
Transkription, Genregulation, Bioinformatik, Evolution
regulatory elements, transcription factor, regulation, bioinformatics, evolution
Otto, Wolfgang
Stadler, Peter. F.
Morgenstern, Burkhard
Universität Leipzig
2011-12-06
2011-12-07
2011-11-29
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11311
https://ul.qucosa.de/api/qucosa%3A11311/attachment/ATT-0/
oai:qucosa:de:qucosa:11325
2021-03-29T08:18:43Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Language Engineering for Information Extraction
urn:nbn:de:bsz:15-qucosa-81757
eng
Accompanied by the cultural development to an information society and knowledge economy and driven by the rapid growth of the World Wide Web and decreasing prices for technology and disk space, the world\''s knowledge is evolving fast, and humans are challenged with keeping up.
Despite all efforts on data structuring, a large part of this human knowledge is still hidden behind the ambiguities and fuzziness of natural language. Especially domain language poses new challenges by having specific syntax, terminology and morphology. Companies willing to exploit the information contained in such corpora are often required to build specialized systems instead of being able to rely on off the shelf software libraries and data resources. The engineering of language processing systems is however cumbersome, and the creation of language resources, annotation of training data and composition of modules is often enough rather an art than a science. The scientific field of Language Engineering aims at providing reliable information, approaches and guidelines of how to design, implement, test and evaluate language processing systems.
Language engineering architectures have been a subject of scientific work for the last two decades and aim at building universal systems of easily reusable components. Although current systems offer comprehensive features and rely on an architectural sound basis, there is still little documentation about how to actually build an information extraction application. Selection of modules, methods and resources for a distinct usecase requires a detailed understanding of state of the art technology, application demands and characteristics of the input text. The main assumption underlying this work is the thesis that a new application can only occasionally be created by reusing standard components from different repositories. This work recapitulates existing literature about language resources, processing resources and language engineering architectures to derive a theory about how to engineer a new system for information extraction from a (domain) corpus.
This thesis was initiated by the Daimler AG to prepare and analyze unstructured information as a basis for corporate quality analysis. It is therefore concerned with language engineering in the area of Information Extraction, which targets the detection and extraction of specific facts from textual data. While other work in the field of information extraction is mainly concerned with the extraction of location or person names, this work deals with automotive components, failure symptoms, corrective measures and their relations in arbitrary arity.
The ideas presented in this work will be applied, evaluated and demonstrated on a real world application dealing with quality analysis on automotive domain language. To achieve this goal, the underlying corpus is examined and scientifically characterized, algorithms are picked with respect to the derived requirements and evaluated where necessary. The system comprises language identification, tokenization, spelling correction, part of speech tagging, syntax parsing and a final relation extraction step. The extracted information is used as an input to data mining methods such as an early warning system and a graph based visualization for interactive root cause analysis. It is finally investigated how the unstructured data facilitates those quality analysis methods in comparison to structured data. The acceptance of these text based methods in the company\''s processes further proofs the usefulness of the created information extraction system.
info:eu-repo/classification/ddc/000
ddc:000
Textanalyse, Qualitätsanalyse, Informationsextraktion
Text Mining, Information Extraction, Quality Analysis, Language Engineering
Schierle, Martin
Heyer, Gerhard
Wrobel, Stefan
Martin Schierle
2012-01-10
2011-12-07
2011-07-12
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11325
https://ul.qucosa.de/api/qucosa%3A11325/attachment/ATT-0/
oai:qucosa:de:qucosa:11334
2021-03-29T08:18:50Z
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doc-type:doctoralThesis
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Towards a Brain-inspired Information
Processing System: Modelling and Analysis of
Synaptic Dynamics: Towards a Brain-inspired InformationProcessing System: Modelling and Analysis ofSynaptic Dynamics
urn:nbn:de:bsz:15-qucosa-82128
eng
Biological neural systems (BNS) in general and the central nervous system (CNS) specifically
exhibit a strikingly efficient computational power along with an extreme flexible and adaptive basis
for acquiring and integrating new knowledge. Acquiring more insights into the actual mechanisms
of information processing within the BNS and their computational capabilities is a core objective
of modern computer science, computational sciences and neuroscience. Among the main reasons
of this tendency to understand the brain is to help in improving the quality of life of people suffer
from loss (either partial or complete) of brain or spinal cord functions. Brain-computer-interfaces
(BCI), neural prostheses and other similar approaches are potential solutions either to help these
patients through therapy or to push the progress in rehabilitation. There is however a significant
lack of knowledge regarding the basic information processing within the CNS. Without a better
understanding of the fundamental operations or sequences leading to cognitive abilities, applications
like BCI or neural prostheses will keep struggling to find a proper and systematic way to
help patients in this regard. In order to have more insights into these basic information processing
methods, this thesis presents an approach that makes a formal distinction between the essence
of being intelligent (as for the brain) and the classical class of artificial intelligence, e.g. with
expert systems. This approach investigates the underlying mechanisms allowing the CNS to be
capable of performing a massive amount of computational tasks with a sustainable efficiency and
flexibility. This is the essence of being intelligent, i.e. being able to learn, adapt and to invent.
The approach used in the thesis at hands is based on the hypothesis that the brain or specifically a
biological neural circuitry in the CNS is a dynamic system (network) that features emergent capabilities.
These capabilities can be imported into spiking neural networks (SNN) by emulating the
dynamic neural system. Emulating the dynamic system requires simulating both the inner workings
of the system and the framework of performing the information processing tasks. Thus, this
work comprises two main parts. The first part is concerned with introducing a proper and a novel
dynamic synaptic model as a vital constitute of the inner workings of the dynamic neural system.
This model represents a balanced integration between the needed biophysical details and being
computationally inexpensive. Being a biophysical model is important to allow for the abilities of
the target dynamic system to be inherited, and being simple is needed to allow for further implementation
in large scale simulations and for hardware implementation in the future. Besides, the
energy related aspects of synaptic dynamics are studied and linked to the behaviour of the networks
seeking for stable states of activities. The second part of the thesis is consequently concerned with
importing the processing framework of the dynamic system into the environment of SNN. This
part of the study investigates the well established concept of binding by synchrony to solve the information binding problem and to proposes the concept of synchrony states within SNN. The
concepts of computing with states are extended to investigate a computational model that is based
on the finite-state machines and reservoir computing. Biological plausible validations of the introduced
model and frameworks are performed. Results and discussions of these validations indicate
that this study presents a significant advance on the way of empowering the knowledge about the
mechanisms underpinning the computational power of CNS. Furthermore it shows a roadmap on
how to adopt the biological computational capabilities in computation science in general and in
biologically-inspired spiking neural networks in specific. Large scale simulations and the development
of neuromorphic hardware are work-in-progress and future work. Among the applications
of the introduced work are neural prostheses and bionic automation systems.
info:eu-repo/classification/ddc/000
ddc:000
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spiking neural networks, synaptic dynamics, synchrony, synaptic energy, finite state machine
El-Laithy, Karim
Bogdan, Martin
Georgiou, Julius
Universität Leipzig
2012-01-12
2011-09-16
2011-12-19
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11334
https://ul.qucosa.de/api/qucosa%3A11334/attachment/ATT-0/
oai:qucosa:de:qucosa:11349
2021-03-29T08:19:02Z
qucosa:ubl
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Entwicklungspfad Service Engineering 2.0: Neue Perspektiven für die Dienstleistungsentwicklung
urn:nbn:de:bsz:15-qucosa-83437
978-3-941608-16-0
ger
urn:nbn:de:bsz:15-qucosa-155763
qucosa:13006
Das Service Engineering hat sich innerhalb der letzten Jahre zunehmend als eine wissenschaftliche Fachdisziplin etabliert. Das vorliegende Heft bietet in kompakter Form einen kurzen Abriss über die Entwicklung dieses Bereiches der Wissenschaft und kondensiert die Grundideen und bisher in der Forschung betrachteten Aspekte. Darüber hinaus erfolgt eine Auseinandersetzung mit neuen Anforderungen seitens der veränderten Dienstleistungswirtschaft. Aus diesen ergibt sich, dass bisherige Ansätze des Service Engineerings grundlegend weiterentwickelt und neue Ansätze bereitgestellt werden müssen. Diese bilden die Entwicklungspfade für ein Service Engineering 2.0.
Service Engineering, Dienstleistungsentwicklung
Service Engienering, Service Science, New Service Development
info:eu-repo/classification/ddc/000
ddc:000
Dienstleistung
Meyer, Kyrill
Böttcher, Martin
Leipziger Informatik Verbund
Institut für Angewandte Informatik (InfAI) e.V. an der Universität Leipzig
Universität Leipzig
2012
info:eu-repo/semantics/publishedVersion
2012-02-16
Leipziger Beiträge zur Informatik
Leipziger Beiträge zur Informatik
info:eu-repo/semantics/openAccess
doc-type:book
info:eu-repo/semantics/book
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11349
https://ul.qucosa.de/api/qucosa%3A11349/attachment/ATT-0/
oai:qucosa:de:qucosa:11348
2021-03-29T08:19:01Z
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Development of a Surgical Assistance System for Guiding Transcatheter Aortic Valve Implantation
urn:nbn:de:bsz:15-qucosa-83426
eng
Development of image-guided interventional systems is growing up rapidly in the recent years. These new systems become an essential part of the modern minimally invasive surgical procedures, especially for the cardiac surgery. Transcatheter aortic valve implantation (TAVI) is a recently developed surgical technique to treat severe aortic valve stenosis in elderly and high-risk patients. The placement of stented aortic valve prosthesis is crucial and typically performed under live 2D fluoroscopy guidance. To assist the placement of the prosthesis during the surgical procedure, a new fluoroscopy-based TAVI assistance system has been developed.
The developed assistance system integrates a 3D geometrical aortic mesh model and anatomical valve landmarks with live 2D fluoroscopic images. The 3D aortic mesh model and landmarks are reconstructed from interventional angiographic and fluoroscopic C-arm CT system, and a target area of valve implantation is automatically estimated using these aortic mesh models. Based on template-based tracking approach, the overlay of visualized 3D aortic mesh model, landmarks and target area of implantation onto fluoroscopic images is updated by approximating the aortic root motion from a pigtail catheter motion without contrast agent. A rigid intensity-based registration method is also used to track continuously the aortic root motion in the presence of contrast agent. Moreover, the aortic valve prosthesis is tracked in fluoroscopic images to guide the surgeon to perform the appropriate placement of prosthesis into the estimated target area of implantation. An interactive graphical user interface for the surgeon is developed to initialize the system algorithms, control the visualization view of the guidance results, and correct manually overlay errors if needed.
Retrospective experiments were carried out on several patient datasets from the clinical routine of the TAVI in a hybrid operating room. The maximum displacement errors were small for both the dynamic overlay of aortic mesh models and tracking the prosthesis, and within the clinically accepted ranges. High success rates of the developed assistance system were obtained for all tested patient datasets.
The results show that the developed surgical assistance system provides a helpful tool for the surgeon by automatically defining the desired placement position of the prosthesis during the surgical procedure of the TAVI.
Die Entwicklung bildgeführter interventioneller Systeme wächst rasant in den letzten Jahren. Diese neuen Systeme werden zunehmend ein wesentlicher Bestandteil der technischen Ausstattung bei modernen minimal-invasiven chirurgischen Eingriffen. Diese Entwicklung gilt besonders für die Herzchirurgie. Transkatheter Aortenklappen-Implantation (TAKI) ist eine neue entwickelte Operationstechnik zur Behandlung der schweren Aortenklappen-Stenose bei alten und Hochrisiko-Patienten. Die Platzierung der Aortenklappenprothese ist entscheidend und wird in der Regel unter live-2D-fluoroskopischen Bildgebung durchgeführt. Zur Unterstützung der Platzierung der Prothese während des chirurgischen Eingriffs wurde in dieser Arbeit ein neues Fluoroskopie-basiertes TAKI Assistenzsystem entwickelt.
Das entwickelte Assistenzsystem überlagert eine 3D-Geometrie des Aorten-Netzmodells und anatomischen Landmarken auf live-2D-fluoroskopische Bilder. Das 3D-Aorten-Netzmodell und die Landmarken werden auf Basis der interventionellen Angiographie und Fluoroskopie mittels eines C-Arm-CT-Systems rekonstruiert. Unter Verwendung dieser Aorten-Netzmodelle wird das Zielgebiet der Klappen-Implantation automatisch geschätzt. Mit Hilfe eines auf Template Matching basierenden Tracking-Ansatzes wird die Überlagerung des visualisierten 3D-Aorten-Netzmodells, der berechneten Landmarken und der Zielbereich der Implantation auf fluoroskopischen Bildern korrekt überlagert. Eine kompensation der Aortenwurzelbewegung erfolgt durch Bewegungsverfolgung eines Pigtail-Katheters in Bildsequenzen ohne Kontrastmittel. Eine starrere Intensitätsbasierte Registrierungsmethode wurde verwendet, um kontinuierlich die Aortenwurzelbewegung in Bildsequenzen mit Kontrastmittelgabe zu detektieren. Die Aortenklappenprothese wird in die fluoroskopischen Bilder eingeblendet und dient dem Chirurg als Leitfaden für die richtige Platzierung der realen Prothese. Eine interaktive Benutzerschnittstelle für den Chirurg wurde zur Initialisierung der Systemsalgorithmen, zur Steuerung der Visualisierung und für manuelle Korrektur eventueller Überlagerungsfehler entwickelt.
Retrospektive Experimente wurden an mehreren Patienten-Datensätze aus der klinischen Routine der TAKI in einem Hybrid-OP durchgeführt. Hohe Erfolgsraten des entwickelten Assistenzsystems wurden für alle getesteten Patienten-Datensätze erzielt.
Die Ergebnisse zeigen, dass das entwickelte chirurgische Assistenzsystem ein hilfreiches Werkzeug für den Chirurg bei der Platzierung Position der Prothese während des chirurgischen Eingriffs der TAKI bietet.
info:eu-repo/classification/ddc/000
ddc:000
Computer assistierte Chirurgie, Medizinische Bildverarbeitung, Transkatheter Aortenklappenimplantation
Computer Assisted Surgery, Medical image processing, Transcatheter Aortic Valve Implantation
KARAR, Mohamed Esmail Abdel Razek Hassan
Burgert, Oliver
Deserno, Thomas
Scheuermann, Gerik
Universität Leipzig
2012-02-03
2011-10-06
2012-01-26
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11348
https://ul.qucosa.de/api/qucosa%3A11348/attachment/ATT-0/
oai:qucosa:de:qucosa:11359
2021-03-29T08:19:09Z
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Computational Studies on the Evolution of Metabolism
urn:nbn:de:bsz:15-qucosa-84188
eng
Living organisms throughout evolution have developed desired properties, such as the ability
of maintaining functionality despite changes in the environment or their inner structure, the
formation of functional modules, from metabolic pathways to organs, and most essentially
the capacity to adapt and evolve in a process called natural selection. It can be observed in
the metabolic networks of modern organisms that many key pathways such as the citric acid
cycle, glycolysis, or the biosynthesis of most amino acids are common to all of them.
Understanding the evolutionary mechanisms behind this development of complex biological
systems is an intriguing and important task of current research in biology as well as artificial
life. Several competing hypotheses for the formation of metabolic pathways and the mecha-
nisms that shape metabolic networks have been discussed in the literature, each of which finds
support from comparative analysis of extant genomes. However, while being powerful tools
for the investigation of metabolic evolution, these traditional methods do not allow to look
back in evolution far enough to the time when metabolism had to emerge and evolve to the
form we can observe today. To this end, simulation studies have been introduced to discover
the principles of metabolic evolution and the sources for the emergence of metabolism prop-
erties. These approaches differ considerably in the realism and explicitness of the underlying
models. A difficult trade-off between realism and computational feasibility has to be made
and further modeling decisions on many scales have to be taken into account, requiring the
combination of knowledge from different fields such as chemistry, physics, biology and last
but not least also computer science.
In this thesis, a novel computational model for the in silico evolution of early metabolism
is introduced. It comprises all the components on different scales to resemble a situation of
evolving metabolic protocells in an RNA-world. Therefore, the model contains a minimal
RNA-based genetics and an evolving metabolism of catalytic ribozymes that manipulate a
rich underlying chemistry. To allow the metabolic organization to escape from the confines
of the chemical space set by the initial conditions of the simulation and in general an open-
ended evolution, an evolvable sequence-to-function map is used. At the heart of the metabolic
subsystem is a graph-based artificial chemistry equipped with a built-in thermodynamics. The
generation of the metabolic reaction network is realized as a rule-based stochastic simulation.
The necessary reaction rates are calculated from the chemical graphs of the reactants on
the fly. The selection procedure among the population of protocells is based on the optimal metabolic yield of the protocells, which is computed using flux balance analysis.
The introduced computational model allows for profound investigations of the evolution of
early metabolism and the underlying evolutionary mechanisms. One application in this thesis
is the study of the formation of metabolic pathways. Therefore, four established hypothe-
ses, namely the backwards evolution, forward evolution, patchwork evolution and the shell
hypothesis, are discussed within the realms of this in silico evolution study. The metabolic
pathways of the networks, evolved in various simulation runs, are determined and analyzed
in terms of their evolutionary direction. The simulation results suggest that the seemingly
mutually exclusive hypotheses may well be compatible when considering that different pro-
cesses dominate different phases in the evolution of a metabolic system. Further, it is found
that forward evolution shapes the metabolic network in the very early steps of evolution. In
later and more complex stages, enzyme recruitment supersedes forward evolution, keeping a
core set of pathways from the early phase. Backward evolution can only be observed under
conditions of steady environmental change. Additionally, evolutionary history of enzymes
and metabolites were studied on the network level as well as for single instances, showing a
great variety of evolutionary mechanisms at work.
The second major focus of the in silico evolutionary study is the emergence of complex system
properties, such as robustness and modularity. To this end several techniques to analyze the
metabolic systems were used. The measures for complex properties stem from the fields of
graph theory, steady state analysis and neutral network theory. Some are used in general
network analysis and others were developed specifically for the purpose introduced in this
work. To discover potential sources for the emergence of system properties, three different
evolutionary scenarios were tested and compared. The first two scenarios are the same as
for the first part of the investigation, one scenario of evolution under static conditions and
one incorporating a steady change in the set of ”food” molecules. A third scenario was
added that also simulates a static evolution but with an increased mutation rate and regular
events of horizontal gene transfer between protocells of the population. The comparison of all
three scenarios with real world metabolic networks shows a significant similarity in structure
and properties. Among the three scenarios, the two static evolutions yield the most robust
metabolic networks, however, the networks evolved under environmental change exhibit their
own strategy to a robustness more suited to their conditions. As expected from theory,
horizontal gene transfer and changes in the environment seem to produce higher degrees
of modularity in metabolism. Both scenarios develop rather different kinds of modularity,
while horizontal gene transfer provides for more isolated modules, the modules of the second
scenario are far more interconnected.
info:eu-repo/classification/ddc/000
ddc:000
Simulation, Metabolische Netwerke, Robustheit, Evolution
Comnputer simulation, metabolic networks, evolution, robustness
Ullrich, Alexander
Stadler, Peter
Universität Leipzig
2012-02-27
2011-11-07
2011-10-10
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11359
https://ul.qucosa.de/api/qucosa%3A11359/attachment/ATT-0/
oai:qucosa:de:qucosa:11384
2021-03-29T08:19:26Z
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Natural optimization: An analysis of self-organization principles found in social insects and their application for optimization
urn:nbn:de:bsz:15-qucosa-86174
eng
Das Forschungsfeld Schwarmintelligenz, also die Anwendung des Verhaltens dezentraler selbstorganisierender Tierkollektive, im Kontext der Informatik hat eine Reihe von state-of-the-art Kontroll- und Optimierungsmechanismen hervorgebracht. Die Untersuchung selbstorganisierender biologischer Systeme fördert zum einen das Design neuer robuster und adaptiver Algorithmen. Zum anderen kann sie das Verständnis der Funktionalität von selbstorganisierenden Prinzipien, welche in der Natur auftreten, unterstützen.
Diese Arbeit deckt beide zuvor beschriebenen Aspekte ab. Unter Verwendung von Modellen und Simulation werden offene Fragen bezüglich der Organisation und des Verhaltens von sozialen Insekten beleuchtet. Weiter werden Abstraktionen von selbstorganisierenden Konzepten, welche man bei sozialen Insekten findet, genutzt, um neue Methoden zur Optimierung zu entwickeln.
Der erste Teil dieser Arbeit untersucht allgemeine Aspekte der Arbeitsteilung sozialer Insekten. Zuerst wird die Anpassungsfähigkeit von unterschiedlich großen Kolonien, bezüglich dynamischer Veränderungen in der Umwelt untersucht. Die Ergebnisse zeigen, dass die Fähigkeit einer Kolonie, auf Veränderung in der Umwelt zu reagieren, von der Koloniegröße beeinflusst wird. Ein weiterer Aspekt der Arbeitsteilung, welcher in dieser Arbeit untersucht wird, ist, inwieweit eine räumliche Verteilung von Aufgaben und Individuen einen Einfluss auf die Arbeitsteilung hat. Die Ergebnisse deuten an, dass soziale Insekten von einer räumlichen Trennung, der zu bewerkstelligenden Aufgaben profitieren, da eine solche Trennung die Produktivität der Kolonie erhöht. Das könnte erklären, warum eine räumliche getrennte Anordnung von Aufgaben und Individuen häufig in realen Kolonien sozialer Insekten beobachtet werden kann.
Der zweite Teil dieser Arbeit untersucht verschiedene Aspekte von Selbstorganisation bei Honigbienen. Zunächst wird der Einfluss der räumlichen Verteilung von Nestplätzen auf die Nestplatzsuche der europäischen Honigbiene Apis mellifera untersucht. Die Ergebnisse legen nahe, dass die Nestplatzsuche eines Schwarms aktiv durch die Anordnung der Nestplätze in der Umwelt beeinflusst wird. Eine nestplatzreiche Umgebung kann den Prozess eines Schwarms, sich für einen Nestplatz zu entscheiden, stark behindern. Das könnte erklären, warum Honigbienenarten, die geringe Anforderungen an Nestplätze haben, was die Anzahl von potenziellen Nestplätzen natürlich erhöht, eine sehr ungenaue Form der Nestplatzsuche aufweisen.
Ein zweiter Aspekt der Honigbienen, welcher untersucht wird, sind die Steuerungsmechanismen, die dem kollektiven Flug eines Bienenschwarms unterliegen. Zwei mögliche Führungsmechanismen, aktive und passive Führung, werden hinsichtlich ihrer Fähigkeit verglichen, die Flugeigenschaften eines echten Honigbienenschwarms zu reproduzieren. Die Simulationsergebnisse bestätigen aktuelle empirische Befunde und zeigen, dass aktive Führung in der Lage ist, Charakteristika fliegender Schwärme widerzuspiegeln. Bei passiver Führung ist das nicht der Fall.
Eine Anwendung biologischer Konzepte im Bereich der Informatik wird anhand der Nestplatzsuche demonstriert. Diese ist ein natürlicher Optimierungsprozess, basierend auf einfachen Regeln. Erzielt wird eine lokale Optimierung, die es einem Schwarm ermöglicht, Nestplätze in einer bisher unbekannten Umgebung zu finden und aus diesen den besten Nestplatz zu wählen. Das ist die Motivation, Nestplatzsuche im Bereich der Optimierung anzuwenden. Hierfür wird zuerst das Optimierungspotenzial der biologischen Nestplatzsuche mit Hilfe eines biologischen Modells untersucht. Basierend auf der Nestplatzsuche wird ein abstrahiertes algorithmisches Schema, das so genannte „Bee Nest-Site Selection Scheme“ (BNSSS) entworfen. Basierend auf dem Schema wird der erste Nestplatzsuche inspirierte Optimierungsalgorithmus „Bee-Nest\\\''\\\'' für die Anwendung im Bereich von molekular Docking entwickelt. Im Vergleich zu anderen Optimierungsalgorithmen erzielt „Bee-Nest“ eine sehr gute Leistung.
The application in computer science of the behaviour found in decentralized self-organizing animal collectives -- also known as swarm intelligence -- has brought forward a number of state-of-the art control and optimization mechanisms. Further
study of such self-organizing biological systems can foster the design of new robust and adaptive algorithms, as well as aid in the understanding of self-organizing processes found in nature.
This thesis covers both of the aspects described above, namely the use of computational models to investigate open questions regarding the organization and behaviour of social insects, as well as using the abstraction of concepts found in social insects to generate new optimization methods.
In the first part of this work, general aspects of division of labour in social insects are investigated. First the adaptiveness of different-sized colonies to dynamic changes in the environment is analysed. The findings show that a colony\\\''s ability to react to changes in the environment scales with its size. Another aspect of division of labour which is investigated is the extent to which different spatial distributions of tasks and individuals influence division of labour. The results suggest that social insects can benefit from a spatial separation of tasks within their environment, as this increases the colony\\\''s productivity. This could explain why a spatial organization of tasks and individuals is often observed in real social insect colonies.
The second part of this work investigates several aspects of self-organization found in honeybees. First the influence of spatial nest-site distribution on the ability of the European honeybee Apis mellifera to select a new nest-site is studied. The results suggest that a swarm\\\''s habitat can influence its decision-making process. Nest-site rich habitats can obstruct a swarm\\\''s ability to choose a single site if all sites are of equal quality. This could explain why in nature honeybee species which have less requirements regarding a new nest-site have evolved a more imprecise form of nest-site selection than cavity-nesting species.
Another aspect of honeybees which is investigated is the guidance behaviour in migrating swarms. Two potential guidance mechanisms, active and passive guidance, are compared regarding their ability to reproduce real honeybee swarm flight characteristics. The simulation results confirm previous empirical findings, as they show that active guidance is able to reflect a number of characteristics which can be observed in real moving honeybee swarms, while this is not the case for passive guidance.
Nest-site selection in honeybees can be regarded as a natural optimization process. It is based on simple rules and achieves local optimization as it enables a swarm to decide between several potential nest-sites in a previously unknown dynamic environment. These factors motivate the application of the nest-site selection process to the problem domain of function optimization. First, the optimization potential of the biological nest-site selection process is studied. Then a general algorithmic scheme called ``Bee Nest-Site Selection Scheme\\\''\\\'' (BNSSS) is introduced. Based on the scheme the first nest-site inspired optimization algorithm ``Bee-Nest\\\''\\\'' is introduced and successfully applied to the domain of molecular docking.
info:eu-repo/classification/ddc/500
ddc:500
info:eu-repo/classification/ddc/000
ddc:000
Schwarmintelligenz
swarm intelligence, self-organization
Diwold, Konrad
Middendorf, Martin
Meyer, Bernd
Universität Leipzig
2012-07-31
2011-07-09
2012-09-02
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11384
https://ul.qucosa.de/api/qucosa%3A11384/attachment/ATT-0/
oai:qucosa:de:qucosa:11382
2021-05-25T08:48:23Z
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Technik und Gesellschaft. Rudolf Rochhausen zum Gedenken.: Texte und Erinnerungen zur Dahlener Tagung 2012
urn:nbn:de:bsz:15-qucosa-86158
ger
urn:nbn:de:bsz:15-qucosa2-748423
qucosa:74842
Band zum Gedenken an den Technikphilosophen Rudolf Rochhausen (1919-2012), der lange Jahre an der Leipziger Universität wirkte, dort u.a. seit 1975 für die Konzeption der Marxistischen Abendschule in Rohrbach (Thüringen) verantwortlich zeichnete und nach der Wende mit dem 'Rohrbacher Kreis' einen Diskursort initiierte, an dem sich Natur- und Geisteswissenschaftler auf Augenhöhe begegnen konnten.:Hans-Gert Gräbe: Vorwort
Rudolf Rochhausen -- Leben und Werk
Rudolf Rochhausen: Freiheit – ein Wert der Linken
Michael Franzke: Ökonomisierung, Ethik und Identität der Sozialen Arbeit
Kerstin Popp: Der historische Wandel der Rolle von Menschen mit Behinderung in der Gesellschaft und der Beitrag der Sonderpädagogik dazu
Siegfried Bönisch, Horst Pickert: Anmerkungen zu Problemen eines marxistischen Menschenbildes
Hans-Gert Gräbe: Arbeiterklasse und Intelligenz. Unabgegoltenes im \'Sozialismus des 20. Jahrhunderts\
Technik, Gesellschaft, Arbeiterklasse, Intelligenz, soziale Arbeit, Ökonomisierung, Menschen mit Behinderung,Sonderpädagogik, Menschenbild
technics, society, manpower, brainpower, social labour, economization, handicaped people, idea of man
info:eu-repo/classification/ddc/000
ddc:000
Gräbe, Hans-Gert
Rochhausen, Rudolf
Hans-Gert Gräbe
info:eu-repo/semantics/publishedVersion
2012-04-18
Rohrbacher Manuskripte
info:eu-repo/semantics/openAccess
doc-type:book
info:eu-repo/semantics/book
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11382
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oai:qucosa:de:qucosa:11446
2021-03-29T08:20:08Z
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Jahresspiegel / Universität Leipzig
urn:nbn:de:bsz:15-qucosa-144454
ger
urn:nbn:de:bsz:15-qucosa-148573
qucosa:12743
Der in diesem Jahr erstmals erscheinende „Jahresspiegel“ ersetzt den Statistikteil des bisherigen Jahresberichts der Universität Leipzig. Mit diesem neuen Berichtsformat soll in kompakter Form gegenüber den Mitgliedern und Angehörigen der Universität, ihren Förderern und Freunden sowie einer breiten Öffentlichkeit Rechenschaft über die im Jahr 2011 erreichten Ziele und Ergebnisse der Universität abgelegt werden. Aus der Vielzahl der Aufgaben, Ergebnisse und Ereignisse sollen hier nur schlaglichtartig einige wesentliche und prägende genannt werden.:Vorwort; Organigramm; Studium; Forschung; Haushalt; Personal; Organe und Gremien; Ehrungen; Internationale Kooperationen; Chronik
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ddc:000
Universität, Jahresbericht
University, Annual report
Universität Leipzig
2014-06-02
2012
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EDV in Medizin und Biologie
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0300-8282
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-26
1976
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1983
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EDV in Medizin und Biologie
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-07-01
1988
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Innovationsmanagement im Service Center: Anforderungen, Konzeption und Realisierung einer informationstechnischen Unterstützungslösung
urn:nbn:de:bsz:15-qucosa-94810
ger
Aus Sicht der Innovationsforschung besteht der Kern eines erfolgreichen Unternehmens aus folgender Formel: Innovative Ideen + Gute Umsetzung = Unternehmenserfolg. Hierbei spielten Service Center in der allgemeinen Managementwahrnehmung bislang eine untergeordnete Rolle. Damit wird ihnen Unrecht getan. Denn im Innovationsprozess stehen die Service Center am Ende des Produktzyklus. Was übersehen wird, ist, dass sie zugleich den Anfang eines neuen Produktzyklus bilden können. Insbesondere da in den Service Centern alle Erfahrungen zusammen laufen - vor allem die der Kunden.
Um dieses Missverhältnis zwischen allgemeiner Wahrnehmung und effektiver Bedeutung von Service Centern für den Innovationsprozess herauszuarbeiten und Korrekturmöglichkeiten aufzuzeigen, wurden im Rahmen der Dissertation informationstechnische Methoden und Werkzeuge entworfen, entwickelt und eingesetzt. Am Ende entstand daraus sogar ein eigenes Produkt, das in Kundensituationen eingesetzt werden kann.:1 Einleitung
1.1 Ausgangssituation
1.2 Methodischer Bedarf
1.3 Zielsetzung und Forschungsfrage
1.4 Forschungsansatz
1.5 Iteratives Vorgehen bei der Entwicklung der IT-Lösung
2 Kundenzentriertes Innovationsmanagement im Service Center als Entwicklungsobjekt
2.1 Begriffsbildung
2.1.1 Definition von Innovationsmanagement
2.1.2 Open Innovation
2.1.3 Kundenzentriertes Innovationsmanagement
2.1.4 Service Center
2.1.5 IT-gestütztes kundenzentriertes Innovationsmanagement im Service Center
2.2 Einbettung der Begrifflichkeit in das aktuelle Forschungsumfeld
2.2.1 Kundenmanagement
2.2.2 Innovationsmanagement
2.2.3 Open Innovation
2.2.4 Kundenintegration in Innovationsmanagementaktivitäten
2.2.5 Service Center
2.2.6 IT-Lösungen für Kundeneinbindung in Innovationsmanagement
2.2.7 IT-Lösungen im Service Center Umfeld
2.2.8 Qualitätsmanagement
2.2.9 Wissensmanagement
2.2.10 Marktforschung
2.2.11 Zusammenfassung relevanter, quantitativer, empirischer Studien
2.3 Empirische Untersuchung
2.3.1 Begründung und Grundlagen der empirischen Untersuchung
2.3.2 Konzeption der qualitativen Datenerhebung durch Experteninterviews
2.4 Analyse der Nachteile und Restriktionen
2.4.1 Restriktion auf Kundenseite
2.4.2 Restriktion auf Unternehmensseite
2.4.3 Zusammenfassung
2.5 Analyse der Vorteile
2.5.1 Unterstützung des gesamten Innovationsprozesses
2.5.2 Vielfalt an Kundeninformationen
2.5.3 Repräsentativität
2.5.4 Vorhandene Informationsfülle
2.5.5 Informationstiefe
2.5.6 Direkte Aufnahme von Kundenbedürfnissen
2.5.7 Einblick in Nutzungsverhalten
2.5.8 Geringe Verarbeitungszeit von Informationen
2.5.9 Iterationsmöglichkeit
2.5.10 Unterstützungsmöglichkeit bei allen Innovationstypen
2.5.11 Zusammenfassung
3 Anforderungen für kundenzentriertes Innovationsmanagement im Service Center
3.1 Einzelanforderungen und Anforderungsrahmenkonzept
3.2 Grundvoraussetzungen
3.2.1 Einbindung in bestehende Strukturen
3.2.2 Minimale Auswirkung auf den Service Center Betrieb
3.2.3 Reporting
3.3 Anforderungen hoher Priorität
3.3.1 Adaptierbarkeit auf Unternehmensziele
3.3.2 Modulare Struktur der Lösung
3.3.3 Bidirektionale Ausrichtung der Lösung
3.3.4 Berücksichtigung der besonderen Kundeneigenschaften
3.4 Anforderungen mittlerer Priorität
3.4.1 Anpassung auf Kundeneigenschaften
3.4.2 Anpassung auf Mitarbeitereigenschaften
3.4.3 Bewertung und Verifikation durch Kunden
3.5 Anforderungen niedriger Priorität
3.5.1 Einstellung auf individuelle Unternehmensstrukturen
3.5.2 Optimierte Lösung für Informationsaufnahme
3.5.3 Vereinfachte Implementierung
4 Spezifikation des Unterstützungssystems für Innovationsmanagement im Service Center
4.1 Funktionalitätsentwicklung
4.1.1 Übersetzung der Anforderungen in Funktionalitäten
4.1.2 Zusammenfassung zu Services und Servicegruppen
4.1.3 Identifikation der Kernfunktionalitäten
4.2 Servicegruppe 1: Aufnahme der Kundeninformation
4.2.1 Einbeziehung bestehender Datenquellen
4.2.2 Vorqualifizierung
4.2.3 Informationserfassung
4.3 Servicegruppe 2: Informationsaufbereitung
4.3.1 Analyse der Kundeninformation
4.3.2 Detaillierung der Information
4.4 Servicegruppe 3: Entwicklung der Innovationsidee
4.4.1 Analyse Innovationspotential
4.4.2 Erfassung der Innovationsidee
4.4.3 Bewertung der Innovationsidee
4.4.4 Analyse des Anpassungsbedarfs
4.5 Servicegruppe 4: Verifikation und Bewertung der Innovationsidee
4.5.1 Anfrage nach weiterem Feedback
4.5.2 Verwaltung Feedback
4.6 Servicegruppe 5: Verwaltung und Management
4.6.1 Managementunterstützung
4.6.2 Berichtswesen
4.7 Prozess- und Produktmodell
4.7.1 Aufnahme Kundeninformation
4.7.2 Informationsaufbereitung
4.7.3 Entwicklung von Innovationsideen
4.7.4 Verifikation und Bewertung
4.7.5 Verwaltung und Management
4.8 Diskussion der optionalen Funktionalitäten
4.8.1 Aufnahme der Kundeninformation
4.8.2 Informationsaufbereitung
4.8.3 Verifikation und Bewertung der Innovationsidee
4.8.4 Aufnahme der Kundeninformation
4.8.5 Verwaltung und Management
5 Technologische Umsetzung des Lösungsmodells
5.1 Vorgehensbeschreibung
5.2 Ausgangssituation im Referenzunternehmen
5.2.1 Unternehmenskontext
5.2.2 Strukturelle Rahmenbedingungen
5.2.3 Systemtechnische Gegebenheiten
5.3 Design der technischen Lösung
5.3.1 Prozessmodell
5.3.2 Datenmodell
5.3.3 Konzeption der grafischen Nutzeroberfläche
5.4 Prototypische IT-Lösung
5.4.1 Vorgehen zur Softwareimplementierung
5.4.2 Generelle Aspekte der technischen Unterstützungslösung
5.4.3 Technische Unterstützungslösung für die Aufnahme der Kundeninformation
5.4.4 Technische Unterstützungslösung für die Detaillierung der Kundeninformation
5.4.5 Technische Unterstützungslösung für die Aufnahme von Innovationsideen
5.4.6 Technische Unterstützungslösung zur Bewertung und Verifikation
5.4.7 Technische Unterstützungslösung für Verwaltung und Management
5.5 Evaluation der Unterstützungslösung
5.5.1 Bewertung, basierend auf Anforderungsrahmenkonzept
5.5.2 Besonderheiten und kritische Aspekte beim Betrieb der Lösung
5.5.3 Diskussion von Implikationen und möglichen Modifizierungen
5.5.4 Konklusion der Evaluationsergebnisse
5.6 Skizzierung der nächsten Erweiterungsschritte
5.6.1 Stärken und Einsatzbereiche von Semantic Web Technologien
5.6.2 Verwendung zu Requirements Engineering mit großen Stakeholdergruppen
5.6.3 Einsatz semantischer Technologien zur Suche im Unternehmenskontext
5.6.4 Konzeption der nächsten Erweiterungsstufe als Semantic Web Lösung
5.6.5 Möglichkeiten der Einbindung unstrukturierter Daten mittels NLP
6 Zusammenfassung
6.1 Zusammenfassung der Ergebnisse
6.1.1 Vor- und Nachteile bestehender Kundenkontakte
6.1.2 Anforderungen an Innovationsmanagement im Service Center
6.1.3 Gesamtmodell einer informationstechnischen Unterstützungslösung
6.1.4 IT-Unterstützung für Innovationsmanagement im Service Center
6.2 Reflexion des gewählten Forschungsansatzes
6.3 Ansatzpunkte für weitere Forschung
6.4 Fazit und abschließende Bemerkung
Literaturverzeichnis
A Untersuchungsdesign der Experteninterviews
B Ergebnisse der Experteninterviews
C Modell zum kundenzentrierten Innovationsmanagement im Service Center
D Technische Umsetzung
E Analysen und Diskussionen zu weiteren relevanten Inhalten aus Forschung und Praxis
F Selbstständigkeitserklärung
info:eu-repo/classification/ddc/000
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Innovationsmanagement, Service Center, Call Center, Open Innovation, Requierments Engineering, customer-driven innovation, Innovation, Produktentwicklung,
innovation management, service center, call center, open innovation, requierments engineering, customer-driven innovation, innovation, product development, product engineering
Strehl, Benjamin
Meyer, Kyrill
Fähnrich, Klaus-Peter
Spath, Dieter
Universität Leipzig
2012-08-23
2012-02-01
2012-07-04
info:eu-repo/semantics/openAccess
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2021-03-29T08:22:16Z
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EDV in Medizin und Biologie
urn:nbn:de:bsz:15-qucosa-146802
0300-8282
ger
urn:nbn:de:bsz:15-qucosa-145292
qucosa:12541
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-24
1972
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Smart Services and Service Science: Proceedings of the 4th Internaional Symposium on Services Science, Leipzig (Germany), September 25, 2012
urn:nbn:de:bsz:15-qucosa-95475
978-3-941608-23-8
ger
eng
urn:nbn:de:bsz:15-qucosa-155763
qucosa:13006
Services Science is a new research discipline that has received, over the last years, a growing attention from academia and practice. It combines research from various fields which have evolved more or less independently and is concerned with the development and management of service products. Whereas theories from organizational and marketing science usually capture the nature of
these products, engineering disciplines focus on shaping and developing these information goods, and the information systems field on integrating services as encapsulated application functionalities
by using standardized (XML) interfaces. All these research streams converge in the new interdisciplinary area of Services Science which integrates the principles, design, and management of economic and technical services.
For the fourth time, the \\\\\\\'International Symposium on Services Science (ISSS)\\\\\\\' offered an outstanding platform for the advancement and discussion of research in Service Science. In 2012, the ISSS focused on knowledge-intensive business services, also known as Smart Services, and their application in theory and practice. The ISSS was part of the Multi-Conference SABRE (Software, Agents and Services for Business, Research and E-Sciences, 24th-25th September 2012) and was held in Leipzig, Germany as a one-day event on the 25th September, 2012.
The symposium was organized by the Information Systems Institute and the Department of Computer Science at the University of Leipzig as well as the Institute for Applied Informatics (InfAI), Fraunhofer MOEZ and the Leipziger Informatik-Verbund (LIV). As reflected in the conference proceedings, the sessions included in the agenda dealt with Smart Services from different perspectives: Smart Services in Theory and Practice, Smart Services in Management and Application,
and Smart Services in High-Tech-Sectors. Although the official language of the conference is English, the authors had the opportunity to write their research contributions in English or German.
Dienstleistungsinformatik, ISSS 2012
Service Science, Smart Services, ISSS 2012
info:eu-repo/classification/ddc/000
ddc:000
Meyer, Kyrill
Abdelkafi, Nizar
Institut für Angewandte Informatik
Fraunhofer - Zentrum für Mittel- und Osteuropa (MOEZ)
Institut für Angewandte Informatik (InfAI) e.V.
Universität Leipzig
2012
info:eu-repo/semantics/publishedVersion
2012-09-13
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2021-03-29T08:22:33Z
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High-Tech-Services, Clustermanagement und Dienstleistungsengineering: Potentiale, Trends und Perspektiven
urn:nbn:de:bsz:15-qucosa-95623
978-3-941608-22-1
ger
urn:nbn:de:bsz:15-qucosa-155763
qucosa:13006
Das Buch widmet sich dem Potential von Dienstleistungen in Hochtechnologiefeldern und versucht, Potentiale für eine Verknüpfung von Forschung im Bereich von Dienstleistungen und Hochtechnologie aufzuzeigen. Einen Ansatzpunkt hierfür bilden Clusterstrukturen. Eine stärkere „Servifizierung“ in den Strukturen dieser High-Tech-Cluster bietet hohe Potentiale zur Generierung von integrierten Smart-Services, die adaptiv, wissensintensiv, verteilt, unter Kundeneinbeziehung und mit Einsatz von entsprechender Hochtechnologie Lösungen in Märkte tragen. Dazu sind Strategien zu suchen, wie unter Nutzung existierender Erkenntnisse der Dienstleistungsforschung High-Tech-Cluster Smart Services gezielt entwickeln und in den Markt tragen können.
Cluster, Smart Services, Dienstleistungen, Service Engineering, Dienstleistungsentwicklung
Service Science, Cluster, Service Engineering
info:eu-repo/classification/ddc/000
ddc:000
Meyer, Kyrill
Thieme, Michael
Institut für Angewandte Informatik
Fraunhofer MOEZ
Leipziger Informatik Verbund
2012
info:eu-repo/semantics/publishedVersion
2012-09-13
Leipziger Beiträge zur Informatik
Leipziger Beiträge zur Informatik
info:eu-repo/semantics/openAccess
doc-type:book
info:eu-repo/semantics/book
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2021-03-29T08:22:47Z
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Informatik, Biometrie und Epidemiologie in Medizin und Biologie: offizielles Organ der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS) e.V.
urn:nbn:de:bsz:15-qucosa-147845
0943-5581
ger
urn:nbn:de:bsz:15-qucosa-145588
qucosa:12568
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/570
ddc:570
info:eu-repo/classification/ddc/610
ddc:610
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Urban & Fischer
Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie
2014-07-07
1995
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
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2021-03-29T08:22:53Z
qucosa:ubl
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open_access
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openaire
Zukunft der Produktivität von Dienstleistungssystemen
urn:nbn:de:bsz:15-qucosa-97041
978-3-941608-18-4
ger
urn:nbn:de:bsz:15-qucosa-155763
qucosa:13006
Das Thema 'Produktivität von Dienstleistungssystemen' besitzt eine hohe Relevanz für die Dienstleistungswirtschaft. Die Produktivitätsbetrachtung adressiert einen Bereich der Dienstleistungsdomäne, welcher bislang nur unzureichend betrachtet
wurde. Darüber hinaus stellt die zunehmende Komplexität, wie sie in Dienstleistungssystemen zu diagnostizieren ist, besondere Herausforderungen an die Dienstleistungswirtschaft im Allgemeinen und die Produktivitätsbetrachtung im Speziellen. Aus diesem Grund wurde die strategische Partnerschaft „Produktivität von Dienstleistungen“ etabliert, in deren Rahmen verschiedene Arbeitskreise interdisziplinär vielfältige Aspekte von Produktivität bei Dienstleistungen bearbeiten. Innerhalb dieser gliedert sich
der Arbeitskreis „Produktivität von Dienstleistungssystemen“
ein, welcher unter der Leitung der Universität Leipzig durchgeführt wurde. Innerhalb des Arbeitskreis „Produktivität von Dienstleistungssystemen“ wurden aktuelle Entwicklungen, zukünftige Herausforderungen, Best Practices sowie Forschungs- und Entwicklungsfragen aus der Sicht von Wirtschaft und Wissenschaft identifiziert und diskutiert. Die Ergebnisse sind in der vorliegenden Broschüre präsentiert.
Dienstleistungen, Produktivität, Service Engineering, Dienstleistungssysteme
Service Productivity
info:eu-repo/classification/ddc/000
ddc:000
Böttcher, Martin
Klingner, Stephan
Becker, Michael
Schumann, Kathleen
Universität Leipzig
2012
info:eu-repo/semantics/publishedVersion
2012-10-11
Leipziger Beiträge zur Informatik
Leipziger Beiträge zur Informatik
info:eu-repo/semantics/openAccess
doc-type:book
info:eu-repo/semantics/book
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2021-03-29T08:23:55Z
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Hierarchische Integration und der Strahlungstransport in streuenden Medien
urn:nbn:de:bsz:15-qucosa-98584
ger
Der Strahlungstransport stellt eine von drei Arten des Wärmetransports zwischen Gebieten unterschiedlicher Temperatur dar. Eine der einfachsten Formen bildet der Strahlungstransport im Vakuum, ein Vorgang, der im kosmischen Umfeld, beispielsweise bei der Energieübertragung von einem Stern auf seine Planeten, beobachtbar ist. Hierbei ist es hinreichend, sich auf die Betrachtung von Oberflächen zu beschränken. Strahlungstransport kann jedoch auch in semitransparenten Medien, wie biologischem Gewebe oder Glas, beobachtet werden. Das Medium, in dem der Strahlungstransport erfolgt, wirkt sich durch Vorgänge wie Absorption, Emission, Reflexion oder Streuung auf den Strahlungstransport aus. Für die Modellierung des Strahlungstransports in einem solchen Umfeld können verschiedene Modelle, darunter das Strahlenmodell, genutzt werden. Dieses Modell beschreibt den Wärmetransport anhand einer skalaren Größe, die Strahlungsintensität genannt wird. Betrachtet wird die Strahlungsintensität in diesem Modell entlang eines Strahls in eine vorgegebene Richtung. Die mathematische Darstellung des Strahlenmodells des Strahlungstransports in partizipierenden Medien führt auf eine richtungsabhängige Integro-Differentialgleichung. Ist die Richtungsabhängigkeit nicht von Interesse, so kann der Übergang zu einer winkelintegrierten Form erfolgen. Dieser Übergang führt schließlich auf ein System schwach singulärer fredholmscher Integralgleichungen zweiter Art. Dieses charakterisiert nun nicht mehr die erwähnte Strahlungsintensität, sondern beschreibt die sogenannte Einstrahlung sowie den Strahlungsfluss.
Das System singulärer Integralgleichungen kann mittels eines Galerkin-Ansatzes numerisch gelöst werden. Geht man von einer hinreichenden Glattheit des Randes aus, kann die Kompaktheit des Operators der Integralgleichungen gezeigt werden. Dies wiederum erlaubt Rückschlüsse auf die Existenz und Eindeutigkeit einer Lösung.
Ein Augenmerk bei der Ermittlung der Galerkin-Näherung ist auf die Bestimmung der singulären Integrale der Galerkin-Diskretisierung zu richten. Für die Bestimmung multidimensionaler, singulärer Integrale stellt die Arbeit das Verfahren der hierarchischen Integration vor. Basierend auf einer Zerlegung des Integrationsgebietes, erfolgt die Beschreibung singulärer Integrale durch ein Gleichungssystem, dessen rechte Seite nur von regulären Integralen abhängig ist. Können diese regulären Integrale sowie die Lösung des Gleichungssystems exakt bestimmt werden, so sind auch die singulären Integrale exakt bestimmt. Bei einer numerischen Bestimmung der regulären Integrale ist die Fehlerordnung ausschlaggebend für den Fehler der singulären Integrale. Als Integrationsgebiete werden Hyperwürfel beliebiger Dimension sowie Simplizes bis einschließlich Dimension 3 als Integrationsgebiete betrachtet. Als Voraussetzungen an den Kern des Doppelintegrals sind nur die Eigenschaften der Translationsinvarianz sowie der Homogenität zu richten. Kann ein nicht translationsinvarianter oder nicht homogener Kern eines Integrals in Summanden zerlegt werden, die selbst translationsinvariant und homogen sind, ist auch die Bestimmung solcher Integrale möglich. Darüber hinaus stellt die Arbeit Verbindungen zu dem Begriff des Hadamard partie finie her. Auf diese Weise lässt sich das Verfahren der hierarchischen Integration für beliebige Dimensionen und beliebige Singularitätsordnungen anwenden.
Die Strahlungstransportgleichung ist im Allgemeinen mittels eines Galerkin-Ansatzes lösbar, führt jedoch auf eine voll besetzte Systemmatrix. Numerische Beispiele beleuchten daher Methoden der Matrixkompression mittels hierarchischer Matrizen sowie der direkten Erzeugung schwach besetzter Matrizen über regulären Gittern und Gittern mit hängenden Knoten und skizziert Ansätze zur Parallelisierung auf entsprechenden Computersystemen.
info:eu-repo/classification/ddc/510
ddc:510
info:eu-repo/classification/ddc/000
ddc:000
Strahlungstransport; numerische Integration; singuläres Integral; mehrdimensionales Integral; mehrfaches Integral; Finite-Elemente-Methode; schwachsinguläre Fredholm-Integralgleichung
Strahlungstransport in streuenden Medien, numerische Integration, singuläre Integrale, fredholmsche Integralgleichung zweiter Art
Radiative heat transfer in participating media, numerical integration, singular integrals, Fredholm integral equation of the second kind
Meszmer, Peter
Hackbusch, Wolfgang
Bebendorf, Mario
Universität Leipzig
Max-Planck-Institut für Mathematik in den Naturwissenschaften
2012-11-07
2012-05-02
2012-10-10
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11754
https://ul.qucosa.de/api/qucosa%3A11754/attachment/ATT-0/
oai:qucosa:de:qucosa:11796
2021-03-29T08:24:25Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Evolutionary Analysis of the Protein Domain Distribution in Eukaryotes
urn:nbn:de:bsz:15-qucosa-100869
eng
Investigations into the origin and evolution of regulatory mechanisms require quantitative estimates of the abundance and co-occurrence of functional protein domains among distantly related genomes. The metabolic and regulatory capabilities of an organism are implicit in its protein content. Currently available methods suffer for strong ascertainment biases, requiring methods for unbiased approaches to protein domain contents at genome-wide scales. The discussion will be highlighted on large scale patterns of similarities and differences of domain contains between phylum-level or even higher level taxonomic groups. This provides
insights into large-scale evolutionary trends. The complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Transcription factors (TF) typically cooperate to activate or repress the expression of genes. They play a critical role in developmental processes. While Chromatin Regulation (CR) facilitates DNA organization and prevent DNA aggregation and tangling which is important for replication, segregation, and gene expression. To compare the set of TFs and CRs between species, the genome annotation of equal quality was employed. However, the existing annotation suffers from bias in model organism. The similar count of transcripts are expected to be similar in mammals, but model organism such as human has more annotated transcripts than non model such as gorilla. Moreover, closely related species (e.g, dolphin and human) show a dramatically different distribution of TFs and CRs. Within vertebrates, this is unreasonable and contradicts phylogenetic knowledge. To overcome this problem, performing gene prediction followed by the detection of functional domains via HMM-based annotation of SCOP domains were proposed. This methods was demonstrated to lead toward consistent estimates for quantitative comparison. To emphasize the applicability, the protein domain distribution of putative TFs and CRs by quantitative and boolean means were analyzed. In particular, systematic studies of protein domain occurrences and co-occurrences to study avoidance or preferential co-occurrence of certain protein domains within TFs and CRs were utilized. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. it was shown for 18 diverse representatives from all eukaryotic kingdoms that a pooled analysis of the tendencies for co-occurrence or avoidance of protein domains is indeed feasible. This type of analysis can reveal general large-scale patterns in the domain co-occurrence and helps to identify lineage-specific variations in the evolution of protein domains. Somewhat surprisingly, strong ubiquitous patterns governing the evolutionary behavior of specific functional classes were not found. Instead, there are strong variations between the major
groups of Eukaryotes, pointing at systematic differences in their evolutionary constraints. Species-specific training is required, however, to account for the genomic peculiarities in many lineages. In contrast to earlier studies wide-spread statistically significant avoidance of protein domains associated with distinct functional high-level gene-ontology terms were found.
info:eu-repo/classification/ddc/000
ddc:000
Proteindomänen, HMM-Modelle GO Klassifizierung, funktionellen Genom-Annotation, Eukarya
protein domains, HMM models, GO classification, functional genome annotation, Eukarya
Parikesit, Arli Aditya
Prohaska, Sonja J.
Bornberg-Bauer, Erich
Universität Leipzig
2012-12-11
2012-06-09
2012-04-12
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11796
https://ul.qucosa.de/api/qucosa%3A11796/attachment/ATT-0/
oai:qucosa:de:qucosa:11801
2021-03-29T08:24:29Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
A Multivariate Framework for Variable Selection and Identification of Biomarkers in High-Dimensional Omics Data
urn:nbn:de:bsz:15-qucosa-101223
978-3-8439-0731-6
eng
In this thesis, we address the identification of biomarkers in high-dimensional omics data. The identification of valid biomarkers is especially relevant for personalized medicine that depends on accurate prediction rules. Moreover, biomarkers elucidate the provenance of disease, or molecular changes related to disease. From a statistical point of view the identification of biomarkers is best cast as variable selection. In particular, we refer to variables as the molecular attributes under investigation, e.g. genes, genetic variation, or metabolites; and we refer to observations as the specific samples whose attributes we investigate, e.g. patients and controls. Variable selection in high-dimensional omics data is a complicated challenge due to the characteristic structure of omics data. For one, omics data is high-dimensional, comprising cellular information in unprecedented details. Moreover, there is an intricate correlation structure among the variables due to e.g internal cellular regulation, or external, latent factors. Variable selection for uncorrelated data is well established. In contrast, there is no consensus on how to approach variable selection under correlation.
Here, we introduce a multivariate framework for variable selection that explicitly accounts for the correlation among markers. In particular, we present two novel quantities for variable importance: the correlation-adjusted t (CAT) score for classification, and the correlation-adjusted (marginal) correlation (CAR) score for regression. The CAT score is defined as the Mahalanobis-decorrelated t-score vector, and the CAR score as the Mahalanobis-decorrelated correlation between the predictor variables and the outcome. We derive the CAT and CAR score from a predictive point of view in linear discriminant analysis and regression; both quantities assess the weight of a decorrelated and standardized variable on the prediction rule. Furthermore, we discuss properties of both scores and relations to established quantities. Above all, the CAT score decomposes Hotelling’s T 2 and the CAR score the proportion of variance explained. Notably, the decomposition of total variance into explained and unexplained variance in the linear model can be rewritten in terms of CAR scores.
To render our approach applicable on high-dimensional omics data we devise an efficient algorithm for shrinkage estimates of the CAT and CAR score. Subsequently, we conduct extensive simulation studies to investigate the performance of our novel approaches in ranking and prediction under correlation. Here, CAT and CAR scores consistently improve over marginal approaches in terms of more true positives selected and a lower model error. Finally, we illustrate the application of CAT and CAR score on real omics data. In particular, we analyze genomics, transcriptomics, and metabolomics data. We ascertain that CAT and CAR score are competitive or outperform state of the art techniques in terms of true positives detected and prediction error.
info:eu-repo/classification/ddc/000
ddc:000
Biomarker Identifikation, Variablen Selektion, Lineare Regression, Klassifikation
Biomarker Identification, Variable Selection, Linear Regression, Classification
Zuber, Verena
Strimmer, Korbinian
Stadler, Peter
Rahnenenführer, Jörg
Universität Leipzig
2012-12-17
2012-04-05
2012-06-27
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11801
https://ul.qucosa.de/api/qucosa%3A11801/attachment/ATT-0/
oai:qucosa:de:qucosa:11798
2021-03-29T08:24:27Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Hierarchical Matrix Techniques on Massively Parallel Computers
urn:nbn:de:bsz:15-qucosa-101164
eng
Hierarchical matrix (H-matrix) techniques can be used to efficiently treat dense matrices. With an H-matrix, the storage
requirements and performing all fundamental operations, namely matrix-vector multiplication, matrix-matrix multiplication and matrix inversion
can be done in almost linear complexity.
In this work, we tried to gain even further
speedup for the H-matrix arithmetic by utilizing multiple processors. Our approach towards an H-matrix distribution
relies on the splitting of the index set.
The main results achieved in this work based on the index-wise H-distribution are: A highly scalable algorithm for the H-matrix truncation and matrix-vector multiplication, a scalable algorithm for the H-matrix matrix multiplication, a limited scalable algorithm for the H-matrix inversion for a large number of processors.
info:eu-repo/classification/ddc/000
ddc:000
Hierarchische Matrizen, parallelen Algorithmus,Distributed-Memory-Systeme
Hierarchical matrices, parallel algorithm, Distributed-Memory-System
Izadi, Mohammad
Hackbusch, Wolfgang
Zumbusch, Gerhard
Max Planck Institute for Mathematics in the Sciences (MIS)
2012-12-11
2012-07-16
2012-04-12
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11798
https://ul.qucosa.de/api/qucosa%3A11798/attachment/ATT-0/
oai:qucosa:de:qucosa:11802
2021-03-29T08:24:30Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Analysis of large-scale molecular biological data using self-organizing maps
urn:nbn:de:bsz:15-qucosa-101298
eng
Modern high-throughput technologies such as microarrays, next generation sequencing and mass spectrometry provide huge amounts of data per measurement and challenge traditional analyses. New strategies of data processing, visualization and functional analysis are inevitable. This thesis presents an approach which applies a machine learning technique known as self organizing maps (SOMs). SOMs enable the parallel sample- and feature-centered view of molecular phenotypes combined with strong visualization and second-level analysis capabilities.
We developed a comprehensive analysis and visualization pipeline based on SOMs. The unsupervised SOM mapping projects the initially high number of features, such as gene expression profiles, to meta-feature clusters of similar and hence potentially co-regulated single features. This reduction of dimension is attained by the re-weighting of primary information and does not entail a loss of primary information in contrast to simple filtering approaches. The meta-data provided by the SOM algorithm is visualized in terms of intuitive mosaic portraits. Sample-specific and common properties shared between samples emerge as a handful of localized spots in the portraits collecting groups of co-regulated and co-expressed meta-features. This characteristic color patterns reflect the data landscape of each sample and promote immediate identification of (meta-)features of interest. It will be demonstrated that SOM portraits transform large and heterogeneous sets of molecular biological data into an atlas of sample-specific texture maps which can be directly compared in terms of similarities and dissimilarities. Spot-clusters of correlated meta-features can be extracted from the SOM portraits in a subsequent step of aggregation. This spot-clustering effectively enables reduction of the dimensionality of the data in two subsequent steps towards a handful of signature modules in an unsupervised fashion.
Furthermore we demonstrate that analysis techniques provide enhanced resolution if applied to the meta-features. The improved discrimination power of meta-features in downstream analyses such as hierarchical clustering, independent component analysis or pairwise correlation analysis is ascribed to essentially two facts: Firstly, the set of meta-features better represents the diversity of patterns and modes inherent in the data and secondly, it also possesses the better signal-to-noise characteristics as a comparable collection of single features.
Additionally to the pattern-driven feature selection in the SOM portraits, we apply statistical measures to detect significantly differential features between sample classes. Implementation of scoring measurements supplements the basal SOM algorithm. Further, two variants of functional enrichment analyses are introduced which link sample specific patterns of the meta-feature landscape with biological knowledge and support functional interpretation of the data based on the ‘guilt by association’ principle.
Finally, case studies selected from different ‘OMIC’ realms are presented in this thesis. In particular, molecular phenotype data derived from expression microarrays (mRNA, miRNA), sequencing (DNA methylation, histone modification patterns) or mass spectrometry (proteome), and also genotype data (SNP-microarrays) is analyzed. It is shown that the SOM analysis pipeline implies strong application
capabilities and covers a broad range of potential purposes ranging from time series and treatment-vs.-control experiments to discrimination of samples according to genotypic, phenotypic or taxonomic classifications.
info:eu-repo/classification/ddc/000
ddc:000
analysis of molecular-biological data, self-organizing maps
Wirth, Henry
Binder, Hans
Stadler, Peter F.
Kreil, David
Universität Leipzig
2012-12-19
2012-05-22
2012-12-06
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11802
https://ul.qucosa.de/api/qucosa%3A11802/attachment/ATT-0/
oai:qucosa:de:qucosa:11822
2021-03-29T08:24:44Z
qucosa:ubl
doc-type:Text
doc-type:workingPaper
open_access
ddc:000
status-type:submittedVersion
openaire
Approximating Operators and Semantics for Abstract Dialectical Frameworks
urn:nbn:de:bsz:15-qucosa-102943
1430-3701
eng
urn:nbn:de:bsz:15-qucosa-154857
qucosa:11933
We provide a systematic in-depth study of the semantics of abstract dialectical frameworks (ADFs), a recent generalisation of Dung\''s abstract argumentation frameworks. This is done by associating with an ADF its characteristic one-step consequence operator and defining various semantics for ADFs as different fixpoints of this operator. We first show that several existing semantical notions are faithfully captured by our definition, then proceed to define new ADF semantics and show that they are proper generalisations of existing argumentation semantics from the literature. Most remarkably, this operator-based approach allows us to compare ADFs to related nonmonotonic formalisms like Dung argumentation frameworks and propositional logic programs. We use polynomial, faithful and modular translations to relate the formalisms, and our results show that both abstract argumentation frameworks and abstract dialectical frameworks are at most as expressive as propositional normal logic programs.
Wissensrepräsentation, Nichtmonotones Schließen, Argumentation
knowledge representation, nonmonotonic reasoning, argumentation
info:eu-repo/classification/ddc/000
ddc:000
Strass, Hannes
Universität Leipzig
2013
info:eu-repo/semantics/submittedVersion
2013-01-31
info:eu-repo/semantics/openAccess
doc-type:workingPaper
info:eu-repo/semantics/workingPaper
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11822
https://ul.qucosa.de/api/qucosa%3A11822/attachment/ATT-0/
oai:qucosa:de:qucosa:11825
2021-03-29T08:24:46Z
qucosa:ubl
doc-type:book
doc-type:Text
open_access
ddc:000
status-type:publishedVersion
openaire
Produktivitätsorientiertes Service Engineering
urn:nbn:de:bsz:15-qucosa-103786
978-3-941608-26-9
ger
urn:nbn:de:bsz:15-qucosa-155763
qucosa:13006
Der 39. Band der Leipziger Beiträge zur Informatik setzt sich mit den Herausforderungen im Zusammenhang mit der zunehmenden Industrialisierung der Dienstleistungswirtschaft auseinander. Eine hohe Komplexität der Dienstleistungsportfolios sowie eine zunehmende
Dienstleistungsorientierung ehemals rein produktionswirtschaftlich ausgerichteter Unternehmen bedürfen leistungsfähiger und angepasster Methoden und Werkzeuge. Voraussetzung dafür ist die präzise und umfassende Modellierung von Dienstleistungen,
die Berücksichtigung von Aspekten der Produktivität sowie die Entwicklung geeigneter Softwarewerkzeuge. Das vorliegende Buch beschäftigt sich mit diesen Herausforderungen und Fragestellungen und schlägt verschiedene Lösungsansätze vor.:Stephan Klingner
Produktivitätssteigerung durch komponentenbasierte Dienstleistungen – Ergebnisse eines Forschungsprojekts
Thomas Meiren, Sabrina Lamberth
Beschreibung und Strukturierung von Dienstleistungsan
geboten
Sabrina Lamberth
Dienstleistungsproduktivität – Grundlagen und Kennzahlen für die komponentenbasierte Produktivitätsbetrachtung von Dienstleistungen.
Stephan Klingner, Martin Böttcher
Der Begriff der Komponente als Grundlage von Konfigurationen in der Dienstleistungsdomäne
Michael Becker, Stephan Klingner
Metamodell zur komponentenbasierten Modellierung komplexer Dienstleistungen.
Michael Becker, Stephan Klingner
Abhängigkeitsbeziehungen zwischen Elementen von
Dienstleistungsportfolios
Michael Becker, Stephan Klingner, Frank Schumacher
Werkzeug zur komponentenbasierten Modellierung und Konfiguration von Dienstleistungen
Sabrina Lamberth, Thomas Meiren
Methodik zur produktivitätsorientierten Granularitätsoptimierung bei komponentenbasierten Dienstleistungen
Sabrina Lamberth
Methodik zur Analyse und Optimierung der Dienstleistungsproduktivität unter Berücksichtigung qualitativer Faktoren
Mike Freitag, Franz Pauthner, Stefan Ochs, Mathias Mayer
Entwicklung eines Frameworks zum Change Management für ECM-Lösungen
Ronni Swialkowski, Arndt Döhler
Komponentisierung des Full-Services E-Commerce Angebots bei Intershop
Till Post, Wilhelm Taurel
Aus der Praxis der Produktivität internationaler Hightech-Dienstleistungssysteme
Service Engineering, Komponenten, Dienstleistungsmodellierung, Dienstleistungen, Kennzahlen, Produktivität, Konfiguration, Orchestrierung, Module
Service Engineering, Components, Service modelling, Key performance indicators, Productivity
info:eu-repo/classification/ddc/000
ddc:000
Dienstleistung; Produktivität
Klingner, Stephan
Meiren, Thomas
Becker, Michael
LIV
Universtität Leipzig
2013
info:eu-repo/semantics/publishedVersion
2013-01-31
Leipziger Beiträge zur Informatik
Leipziger Beiträge zur Informatik
info:eu-repo/semantics/openAccess
doc-type:book
info:eu-repo/semantics/book
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A11825
https://ul.qucosa.de/api/qucosa%3A11825/attachment/ATT-0/
oai:qucosa:de:qucosa:11877
2021-03-29T08:25:23Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Informationstechnische Aspekte des Historical Text Re-use: Computational Aspects of Historical Text Re-use
urn:nbn:de:bsz:15-qucosa-108515
ger
Gegenstand der Arbeit
-----------------------
Was ist Text Re-use? Text Re-use beschreibt die mit unterschiedlichen Absichten mündliche und schriftliche Wiedergabe von Textinhalten. Diese können im Sinne einer Definition das Anerkennen einer Autorität aber auch das Wiedergeben einer besonders interessanten Information sein. Während der Fokus dieser Arbeit auf dem Erstellen eines Hypertextes durch eine Text Re-use Analysis liegt, sind die PageRanking-Technik oder auch bibliometrische Analysen weiterführende Anwendungen. Im Kontext derartiger Einsatzmöglichkeiten kann auf historischen Dokumenten, die dieser Arbeit zugrunde liegen, durch eine automatische Analyse eine noch nie zuvor erstellte Breite von Zitierabhängigkeiten erstellt werden, welche heutzutage Aufschluss darüber geben, was in früheren Zeiten als wichtig erachtet worden ist, auch wenn es in der Gegenwart für Sprachen, wie dem Altgriechischen oder dem Latein, keine Muttersprachler mehr gibt.
Stand der Forschung
-------------------
In der Plagiarismuserkennung, einer modernen Anwendung von Text Re-use, werden meist einfache Ngramm-Ansätze eingesetzt. Diese Form einer Abtastung eines Textes bietet in erster Linie den Vorteil, dass die benötigte Rechenzeit relativ klein bleibt. Ferner genügt dieser Ansatz, um ein einfaches Copy & Paste zu erkennen.
Außerhalb des Plagiarismus stellt sich der Forschungsstand so dar, dass nahezu beliebig Daten und Algorithmen kombiniert werden. Die Ergebnisse geben datenspezifische Charakteristika wieder und sind somit oft nicht auf andere Daten reproduzierbar. Der Forschungsstand reflektiert somit mehr Insellösungen als eine ganzheitliche Sicht auf das Thema.
Ganzheitliche Sicht auf Text Re-use
-----------------------------------
In Kapitel 2 wird die derzeit vollständigste Systematisierung des Text Re-use vorgenommen. Dies umfasst zwei wesentliche Aspekte:
- Es werden insgesamt 45 verschiedene Typisierungen von Textstellen, nachfolgend auch Meme im Sinne eines Gedanken oder Gedankensplitters genannt, eingeführt, welche in der Regel wiederverwendet werden. Entsprechende typisierte Meme reichen nur beispielhaft von Sprichwort, über Schlachtruf und Vers bis hin zur Legende.
- Es wird eine Systematik zu verschiedenen Re-use Styles definiert, welche beschreibt, wie ein entsprechendes Meme wiederverwendet wird. Das kann zum Beispiel ein wortwörtliches Zitat aber auch eine Paraphrase oder Allusion sein.
Das Ziel dieser ganzheitlichen Sicht besteht darin, grundlegende Eigenschaften der Meme sowie der Re-use Styles zu definieren. Während ein Meme, wie z. B. eine Redewendung, eher kurz und syntaktisch fest verwendet wird, ist es beim größeren Meme Legende üblich, dieses mündlich und damit wesentlich freier wiederzugeben.
Während die Typisierung der verschiedenen Meme die Frage aufwirft, warum bestimmte Textinhalte wiederverwendet werden, gibt die zweite Systematik des Re-use Styles Aufschluss darüber, wie jeder persönlich andere Inhalte wiedergibt.
Sowohl die Typisierung der verschiedenen Meme mit ihren unterschiedlichen Charakteristika als auch die Systematik der Re-use Styles reflektieren eine Data Diversity, welche eine Herausforderung sowohl für die Text Re-use Analysis aber auch für deren Evaluation aus ganzheitlicher Sicht bedeutet, da es keinen Gold Standard gibt, welcher sowohl alle möglichen Meme als auch die verschiedenen Re-use Styles adäquat repräsentiert.
Forschungsfragen
----------------
Aus ganzheitlicher Sicht ergeben sich somit für diese Arbeit die folgenden Forschungsfragen:
- Im Kontext der verschiedenen Re-use Styles muss die Frage danach gestellt werden, bis zu welchem Grad der Veränderung ein Text Re-use automatisch noch erkannt werden kann.
- Wie kann eine Text Re-use Analysis so gestaltet werden, dass sie auch für unterschiedliche Meme mit verschiedenen Charakteristika gleich gut funktioniert?
- Wie können Veränderungen eines wiederverwendenden Autors systematisch bestimmt und extrahiert werden?
- Wie kann das Ergebnis einer Text Re-use Analysis in einer Digital Library in Anbetracht der Data Diversity ganzheitlich evaluiert werden?
Untersuchungsmethodik und Lösungsansatz
---------------------------------------
Da die Data Diversity aus informationstechnischer Sicht nicht mit einem einzelnen Algorithmus bzw. einer kleinen Menge von Ansätzen abgedeckt werden kann, wird in Kapitel 3 die 7-Level-Architektur des Historical Text Re-use vorgestellt. Diese Architektur kann als ein modulares Konzept verstanden werden, um die Text Re-use Analysis auf die verschiedenen Bedürfnisse, bedingt durch spezielle Eigenschaften von Meme, unterschiedlichen Re-use Styles aber auch verschiedenen Sprachvarianten, entsprechend anzupassen. Die einzelnen Level entsprechen den sieben Unteraufgaben Segmentation, Preprocessing, Featuring, Selection, Linking, Scoring und Postprocessing. In Kapitel 3 werden zu jedem Level in einem separaten Abschnitt entsprechende Implementierungen sowohl ausführlich vorgestellt als auch systematisiert. Zur Abgabe dieser Dissertation stehen in der TRACER-Implementierung, welche die 7-Level-Architektur umsetzt, insgesamt über eine Million Kombinationsmöglichkeiten der verschiedenen Ansätze der einzelnen Level zur Verfügung.
Sowohl die drei genannten Forschungsfragen als auch die aufgezeigte Data Diversity des Historical Text Re-use werden im Rahmen der Dissertation als hinreichende Motivation verstanden, den Historical Text Re-use in Shannon\''s Noisy Channel Theorem einzubetten. In diesem Kontext kann ein Original- bzw. zitierter Autor als Source und ein wiederverwendender Autor als Target verstanden werden. Der Noisy Channel stellt ein unbekanntes Modell von Modifikationen, den äußeren Einflüssen, dar.
In Kapitel 4 wird das Noisy Channel Model dazu eingesetzt, ein zufälliges und rein künstliches Störsignal zum Noisy Channel hinzuzufügen, so dass eine Randomised Digital Library entsteht. Es werden insgesamt fünf Klassen von Randomisierungstechniken, die künstlichen Störsignale, im Sinne eines Turingtests vorgestellt, welche unterschiedliche Schwierigkeitsgrade einer rein quantitativen Evaluierung mit sich bringen. Für diese quantitative Evaluierung, die Noisy Channel Evaluation, wird der neuartige Score der Mining Ability eingeführt. Die Mining Ability setzt hierbei das Ergebnis einer Text Re-use Analysis auf einer Digital Library mit dem Resultat einer durch ein künstliches Störsignal veränderten Randomised Digital Library ins Verhältnis, wodurch nicht nur Parameter optimiert sondern auch verschiedene Sprachmodelle vollautomatisch und bzgl. des Ergebnisses ganzheitlich sowie ohne Gold Standard evaluiert
werden können.
In Kapitel 5 wird der Noisy Channel als Modell eingesetzt, um historisch paradigmatische Relationen systematisch zu bestimmen. Das ist insbesondere unter Berücksichtigung der großen Zeitfenster von geisteswissenschaftlichen Texten von Interesse, da sich semantische Beziehungen von Konzepten im Laufe der Zeit verändert haben.
Ergebnisse
----------
Die Ergebnisse dieser Arbeit sind sehr vielschichtig und umfassen neben Ergebnissen von Evaluierungen, auch Erfahrungen innerhalb der eHumanities sowie der entsprechenden Grundlagenarbeit. Im Detail können die Ergebnisse wie folgt zusammengefasst werden:
Es wird im einführenden Kapitel der Dissertation das Paradigma ACID for the eHumanities vorgestellt. ACID ist hierbei eine Abkürzung für Acceptance, Complexity, Interoperability und Diversity. Diese vier Säulen werden als Aspekte vorgestellt, denen sich die Informatik in der Zusammenarbeit mit den Geisteswissenschaften stellen muss. Der Fokus der Arbeit liegt auf der Diversity aber auch Aspekte der Acceptance und Complexity werden ausführlich verdeutlicht.
In Kapitel 4 wird neben der Einführung der Noisy Channel Evaluation auch aufgezeigt, welche statistischen Probleme probabilistische Sprachmodelle begleiten. Während probabilistische Sprachmodelle das Gesetz der großen Zahlen und somit eine hinreichend große Auftretenswahrscheinlichkeit voraussetzen, folgen verschiedene Charakteristika natürlicher Sprache einem Power Law, wie dem Zipfschen Gesetz, so dass für den Long Tail dieser Verteilung eine geringe Frequenz zugrunde liegt, woraus letztlich ein statistisches Problem resultiert. Im Detail kann so gezeigt werden, dass der eingeführte Score der Mining Ability bei zunehmender Größe einer Digital Library nach Erreichen eines Maximums wieder sinkt. Das resultiert daraus, dass mit zunehmender Größe der Digital Library vermehrt aus Rauschen als Neuem ``gelernt\''\'' wird. Auch wenn Kapitel 4 das auf den Text Re-use einschränkt, so sind die Ergebnisse einfach auf andere probabilistische
Sprachmodelle adaptierbar. Insbesondere wird der Widerspruch des Gesetzes der großen Zahlen, welches den auf Wahrscheinlichkeiten aufsetzenden Sprachmodellen implizit zugrunde liegt, und den oftmals sehr seltenen Ereignissen beim Umgang mit natürlichsprachlichen Texten deutlich.
In Kapitel 5 wird weiterhin gezeigt, dass es kein Text Re-use Model gibt, welches in jedem Szenario optimale Ergebnisse liefert. Basierend auf sieben Bibelversionen mit unterschiedlichen Bezügen untereinander, wird verdeutlicht, dass sich nicht nur die Algorithmen der 7-Level-Architektur unterscheiden können, sondern auch entsprechende Schwellwerte.
Im Rahmen der Arbeit werden zwei rein quantitative Evaluierungsgrößen, die Text Re-use Compression sowie die Noisy Channel Evaluation, eingeführt. In Kapitel 5 wird gezeigt, dass es eine signifikante Korrelation zu existierenden Evaluierungsgrößen gibt, welche jedoch einen Gold Standard oder zumindest eine Evaluierungsgrundlage benötigen. Einerseits gibt es eine nach Pearson sehr starke Korrelation zwischen dem Recall und der Text Re-use Compression. Andererseits wird auch gezeigt, dass das F-Measure sowie die im Rahmen dieser Arbeit eingeführte Noisy Channel Evaluation sehr vergleichbare Evaluierungsergebnisse erzeugen. Das wird im Rahmen einer System Evaluation in Kapitel 5 anhand der sieben Bibelversionen in insgesamt 504 verschiedenen Experimenten dargestellt.
Beitrag zur Forschung
---------------------
Neben den aufgezeigten Ergebnissen stellt diese Arbeit Grundlagenforschung sowohl in der Systematisierung des Text Re-use aber auch bei der Evaluierung von Ergebnissen dar. Wie eingangs zum Forschungsstand umrissen wurde, verlieren sich derzeit viele Arbeiten in der nahezu beliebigen Kombination aus Daten und Algorithmen. Mit dieser Arbeit wird ein Evaluierungsszenario vorgestellt, welches es ermöglicht, auch ohne Gold Standard das Ergebnis zu bewerten. Somit wird das Resultat nicht mehr durch unterschiedliche Überlappungsgrade zwischen Digital Library und Gold Standard verfälscht.
Des Weiteren geht mit dieser Arbeit ein Paradigmenwechsel einher. Während in der Automatischen Sprachverarbeitung Text Re-use bisher aus einer ``1-Algorithmus-Sicht\''\'' betrachtet wird, zeigen die Ergebnisse aus Kapitel 5 auf, dass zukünftig stärker der paarweise Vergleich zweier Werke im Forschungsvordergrund stehen sollte. Das geht damit einher, dass jeder Mensch einen eigenen Re-use Style besitzt, so dass durch das paarweise Vergleichen die menschlichen Individualitäten im Fokus der Text Re-use Analysis stehen. Deshalb wird vorgeschlagen, die Einzelergebnisse der werkweisen Vergleiche anschließend zu einem Hybrid Text Re-use Graph zusammenzusetzen. Mit der Noisy Channel Evaluation sowie der Text Re-use Compression stehen nun weiterführend auch vollautomatische Evaluierungstechniken zur Verfügung, so dass eine wesentlich präzisere Text Re-use Analysis möglich ist.
Perspektive
-----------
Entgegen modernen Anwendungen des Text Re-use, wie dem Plagiarismus, kann der Historical Text Re-use als ein nützliches Instrument verstanden werden, welches nicht nur Evidenzen von Transferwegen, sondern vielmehr auch einen fundamentalen Teil des sprachlich-kulturellen Erbes der Menschheit darstellt. Aus der Vielfalt des Historical Text Re-use ergeben sich für die Informatik im Rahmen der eHumanities vielschichtige Herausforderungen, die Gegenstand dieser Arbeit sind. Im Detail bedeutet das einen Paradigmenwechsel vom Pragmatismus im Vergleich von Sprachmodellen hin zur bestmöglichen Vollständigkeit.
info:eu-repo/classification/ddc/000
ddc:000
Text Re-use, Cultural Heritage, Bibel, Noisy Channel Model, Intertextualität
Text Re-use, Cultural Heritage, Bibel, Noisy Channel Model, Intertextuality
BÜCHLER, Marco
HEYER, Gerhard
SCHULZ, Klaus
Universität Leipzig
2013-04-29
2013-06-02
2013-03-19
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SKIL 2012 - Dritte Studentenkonferenz Informatik Leipzig: Dritte Studentenkonferenz Informatik Leipzig 2012Leipzig, Deutschland, 25. September 2012Tagungsband
urn:nbn:de:bsz:15-qucosa-112891
978-3-941608-21-4
ger
eng
urn:nbn:de:bsz:15-qucosa-155763
qucosa:13006
Die Studentenkonferenz des Instituts für Informatik der Universität Leipzig richtet sich an alle Studierende der Informatik sowie angrenzender Disziplinen mit Schwerpunkt Informatik. Die Konferenz setzt sich zum Ziel, Studierenden eine Plattform zu bieten, ihre Projekte und Forschungsvorhaben vorzustellen. Im Mittelpunkt der Tagung stehen studentische Projekte aus Seminaren, Praktika, Abschlussarbeiten oder extracurricularen Aktivitäten.
Die SKIL bietet den Studierenden die Möglichkeit, vor einem akademischen Publikum Ideen, Pläne und Ergebnisse zu präsentieren und zu diskutieren. Die Organisation der Konferenz unterscheidet sich nur wenig von wissenschaftlichen Fachkonferenzen. Die Einreichung der Beiträge erfolgte mit Hilfe eines Conference Systems; anschließend wurden alle Einreichungen durch das Programmkomitee bewertet. Angenommene Beiträge wurden am Konferenztag vorgestellt und in dem hier vorliegendem Tagungsband publiziert.
Die dritte Studentenkonferenz Informatik Leipzig 2012 fand im Rahmen der SABRE am 25.09.2012 statt. Die
SABRE ist eine internationale integrative Multikonferenz auf dem Gebiet zukunftsweisender Technologien der
Softwareentwicklung, Agententechnologien und Servicecomputing für Wirtschaft, Entwicklung und Wissenschaft. Die SKIL 2012 wurde am Institut für Angewandte Informatik (InfAI) e.V. organisiert. Initiiert und maßgeblich realisiert wurde die SKIL 2012 von den Forschungsgruppen Agile Knowledge Engineering and Semantic Web (AKSW) und Service Science and Technology (SeSaT) der Universität Leipzig.
Studentenkonferenz, Informatik, Studierende, Konferenz, Leipzig
Student Conference Leipzig
info:eu-repo/classification/ddc/000
ddc:000
Schmidt, Johannes
Riechert, Thomas
Auer, Sören
Institut für Angewandte Informatik (InfAI) e. V. an der Universität Leipzig
Leipziger Informatik-Verbund (LIV) an der Universit¨at Leipzig
Universität Leipzig
2012
info:eu-repo/semantics/publishedVersion
2013-04-29
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Proceedings of the 11th International Conference on Wirtschaftsinformatik (WI2013) - Volume 1: Feb 27 – Mar 01 2013 / University Leipzig, Germany
Proceedings der 11. Internationalen Tagung Wirtschaftsinformatik (WI2013) - Band 1
urn:nbn:de:bsz:15-qucosa-113389
978-3-00-041359-9
ger
eng
The two volumes represent the proceedings of the 11th International Conference on Wirtschaftsinformatik WI2013 (Business Information Systems). They include 118 papers from ten research tracks, a general track and the Student Consortium. The selection of all submissions was subject to a double blind procedure with three reviews for each paper and an overall acceptance rate of 25 percent. The WI2013 was organized at the University of Leipzig between February 27th and March 1st, 2013 and followed the main themes Innovation, Integration and Individualization.:Track 1: Individualization and Consumerization
Track 2: Integrated Systems in Manufacturing Industries
Track 3: Integrated Systems in Service Industries
Track 4: Innovations and Business Models
Track 5: Information and Knowledge Management
Die zweibändigen Tagungsbände zur 11. Internationalen Tagung Wirtschaftsinformatik (WI2013) enthalten 118 Forschungsbeiträge aus zehn thematischen Tracks der Wirtschaftsinformatik, einem General Track sowie einem Student Consortium. Die Selektion der Artikel erfolgte nach einem Double-Blind-Verfahren mit jeweils drei Gutachten und führte zu einer Annahmequote von 25%. Die WI2013 hat vom 27.02. - 01.03.2013 unter den Leitthemen Innovation, Integration und Individualisierung an der Universität Leipzig stattgefunden.:Track 1: Individualization and Consumerization
Track 2: Integrated Systems in Manufacturing Industries
Track 3: Integrated Systems in Service Industries
Track 4: Innovations and Business Models
Track 5: Information and Knowledge Management
info:eu-repo/classification/ddc/000
ddc:000
Wirtschaftsinformatik, WI2013, Konferenz, Proceedings, Innovation, Integration, Individualisierung
Business Information Systems, WI2013, Conference, Proceedings, Innovation, Integration, Individualization
Alt, Rainer
Franczyk, Bogdan
Universität Leipzig
2013-05-23
2013
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Proceedings of the 11th International Conference on Wirtschaftsinformatik (WI2013) - Volume 2: Feb 27 – Mar 01 2013 / University Leipzig, Germany
Proceedings der 11. Internationalen Tagung Wirtschaftsinformatik (WI2013) - Band 2
urn:nbn:de:bsz:15-qucosa-113401
978-3-00-041360-5
ger
eng
The two volumes represent the proceedings of the 11th International Conference on Wirtschaftsinformatik WI2013 (Business Information Systems). They include 118 papers from ten research tracks, a general track and the Student Consortium. The selection of all submissions was subject to a double blind procedure with three reviews for each paper and an overall acceptance rate of 25 percent. The WI2013 was organized at the University of Leipzig between February 27th and March 1st, 2013 and followed the main themes Innovation, Integration and Individualization.:Track 6: Business Process and Service Management
Track 7: Sustainability and Security
Track 8: Modeling and Development Methods
Track 9: Integration and Architectures
Track 10: Research Methods and Philosophy
Track 11: General Track - Visionary and Cross-Disciplinary Issues
Student Consortium
Die zweibändigen Tagungsbände zur 11. Internationalen Tagung Wirtschaftsinformatik (WI2013) enthalten 118 Forschungsbeiträge aus zehn thematischen Tracks der Wirtschaftsinformatik, einem General Track sowie einem Student Consortium. Die Selektion der Artikel erfolgte nach einem Double-Blind-Verfahren mit jeweils drei Gutachten und führte zu einer Annahmequote von 25%. Die WI2013 hat vom 27.02. - 01.03.2013 unter den Leitthemen Innovation, Integration und Individualisierung an der Universität Leipzig stattgefunden.:Track 6: Business Process and Service Management
Track 7: Sustainability and Security
Track 8: Modeling and Development Methods
Track 9: Integration and Architectures
Track 10: Research Methods and Philosophy
Track 11: General Track - Visionary and Cross-Disciplinary Issues
Student Consortium
info:eu-repo/classification/ddc/000
ddc:000
Wirtschaftsinformatik, WI2013, Konferenz, Proceedings, Innovation, Integration, Individualisierung
Business Information Systems, WI2013, Conference, Proceedings, Innovation, Integration, Individualization
Alt, Rainer
Franczyk, Bogdan
Universität Leipzig
2013-05-23
2013
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Variability Modeling in the Real: An Empirical Journey from Software Product Lines to Software Ecosystems
urn:nbn:de:bsz:15-qucosa-113623
eng
Variability modeling is one of the key disciplines to cope with complex variability in large software product lines. It aims at creating, evolving, and configuring variability models, which describe the common and variable characteristics, also known as features, of products in a product line. Since the introduction of feature models more than twenty years ago, many variability modeling languages and notations have been proposed both in academia and industry, followed by hundreds of publications on variability modeling techniques that have built upon these theoretical foundations.
Surprisingly, there are relatively few empirical studies that aim at understanding the use of such languages. What variability modeling concepts are actually used in practice? Do variability models applied in real-world look similar to those published in literature? In what technical and organizational contexts are variability models applicable?
We present an empirical study that addresses this research gap. Our goals are i) to verify existing theoretical research, and ii) to explore real-world variability modeling languages and models expressed in them. We study concepts and semantics of variability modeling languages conceived by practitioners, and the usage of these concepts in real, large-scale models. Our aim is to support variability modeling research by providing empirical data about the use of its core modeling concepts, by identifying and characterizing further concepts that have not been as widely addressed, and by providing realistic assumptions about scale, structure, content, and complexity of real-world variability models. We believe that our findings are of relevance to variability modeling researchers and tool designers, for example, those working on interactive product configurators or feature dependency checkers. Our extracted models provide realistic benchmarks that can be used to evaluate new techniques.
Recognizing the recent trend in software engineering to open up software platforms to facilitate inter-organizational reuse of software, we extend our empirical discourse to the emerging field of software ecosystems. As natural successors of successful product lines, ecosystems manage huge variability among and within their software assets, thus, represent a highly interesting class of systems to study variability modeling concepts and mechanisms. Our studied systems comprise eleven highly configurable software systems, two ecosystems with closed platforms, and three ecosystems relying on open platforms. Some of our subjects are among the largest successful systems in existence today. Results from a survey on industrial variability modeling complement these subjects.
Our overall results provide empirical evidence that the well-researched concepts of feature modeling are used in practice, but also that more advanced concepts are needed. We observe that assumptions about variability models in the literature do not hold. Our study also reveals that variability models work best in centralized variability management scenarios, and that they are fragile and have to be controlled by a small team. We also identify a particular type of dependencies that is increasingly used in open platforms and helps sustain the growth of ecosystems. Interestingly, while enabling distributed variability, these dependencies rely on a centralized and stable vocabulary. Finally, we formulate new hypotheses and research questions that provide direction for future research.
info:eu-repo/classification/ddc/000
ddc:000
Empirische Softwaretechnick, Variabilitätsmodellierung, Software-Produktlinien, Software-Ökosysteme
empirical software engineering, variability modeling, software product lines, software ecosystems
Berger, Thorsten
Fähnrich, Klaus-Peter
Grünbacher, Paul
Universität Leipzig
2013-05-15
2012-10-04
2013-04-16
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The Dynamic Epigenome: Analysis of the Distribution of Histone Modifications
urn:nbn:de:bsz:15-qucosa-119746
eng
There is a genome in a cell, as everyone knows, but there is also an epigenome. The epigenome regulates the transcription of the underlying genome. In the last decade, it was discovered that the epigenome state and its regulation are important for differentiation and
development. Correlation studies with aging samples had led to the hypothesis that misregulation of the epigenome causes aging and cancer. Furthermore, diseases were identified which are caused by
errors in the epigenome state and its regulation.
Identification of erroneous epigenome states and misregulation requires the prior knowledge of the common state. Several studies
aim at measuring epigenome states in different organisms and cell
types and thus, provide a huge amount of data.
In this dissertation, a pipeline is developed to analyze and characterize histone modifications with respect to different cell types. Application of this pipeline is shown for a published data set of mouse consisting of data for H3K4me3, H3K27me3, and H3K9me3 measured in embryonic stem cells, embryonic fibroblasts and neuronal progenitors.
Furthermore, methods for the detection of the epigenetic patterns are
presented in this dissertation. Therefore, a segmentation method is developed to segment the genome guided by the data sets. Based on this segmentation, the epigenome states as well as epigenetic variation can be studied. Different visualization methods are developed to highlight the epigenetic patterns in the segmentation data. Application of the segmentation AND visualization methods to the mouse data set had resulted in not only colorful squares but also in biological conclusions! It demonstrate the power of the developed methods.
Although the studied data set in this dissertation contains only ordinary tissue cells, the methods are not restricted to study the reference epigenome state. Comparison of normal and disease cells as well as comparison with aged cells are possible with all of the methods.
Finally, the methods are compared based on the obtained results. It shows that all methods highlight different aspects of the data. Thus, applying all methods to the same data sets, deep insights into the epigenome in murine embryonic stem cells, embryonic fibroblasts and
neuronal progenitor cells are gained. For example, it had been found
that several mechanisms exist setting H3K4me3 marks. Furthermore, not all mechanisms are found in all cell types. Strong evidence had been
found that catalysis of H3K4me3 and H3K27me3 is coupled.
info:eu-repo/classification/ddc/000
ddc:000
Epigenetik, Histonmodifikationen, Visualsierung
epigenetic, histone modifications, visualization
Steiner, Lydia
Prohaska, Sonja J.
Torda, Andrew
Universität Leipzig
2013-08-05
2013-01-18
2013-06-27
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Tätigkeitsbericht / Universitätsbibliothek Leipzig
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Die UB unterstützt die Studierenden, Lehrenden und Forschenden der Universität mit wissenschaftlicher Literatur und mit elektronischen Medien, mit verlässlichen Katalogen und geordneten Freihandbereichen, mit technisch modernisierten Lesesälen und mit aktueller Reproduktionstechnologie. Dazu wurde 2006 eine ganze Reihe von Maßnahmen angestoßen: Verbesserung der fachspezifischen Informationsvermittlung, Retrokatalogisierung, besser strukturierte Homepage, W-LAN in allen größeren Zweigbibliotheken. Zur Stärkung ihres Dienstleistungsangebots kooperiert die UB Leipzig auch mit Bibliotheken in Sachsen und deutschlandweit.
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Bibliothek
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Für die Universitätsbibliothek Leipzig war 2007 ein "normales" Jahr, d. h. ein Jahr mit den üblichen Herausforderungen. Studierende und Lehrende wollen unkomplizierten, schnellen, umfassenden und dauerhaft verlässlichen Service. Die Verwaltungen der Universität und des Landes drängen auf Effektivität und Sparpotenziale. Technische Innovationen, neue Software und Hardware erzwingen Anpassungen und Schulungen für das Personal. Die Bibliothek der Zukunft wird pausenlos getestet.
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Im System der Universitätsbibliothek Leipzig, zu dem augenblicklich 26 Einrichtungen gehören, stehen weitere Veränderungen an, die 2008 in Planung und Umsetzung vorangetrieben wurden und eine Konzentration der Bestände an zentralen Standorten befördern: Eröffnung der Campus-Bibliothek (für Wirtschaftswissenschaften, Mathematik, Informatik, das Sondersammelgebiet Kommunikations- und Medienwissenschaften und die Lehrbuchsammlung) im Herbst 2009, Einrichtung einer Bibliothek für die räumlich benachbarten Fächer Sport und Erziehungswissenschaften (Standort Jahnallee, vermutlich 2010), Zentralbibliothek Medizin/Life Sciences ca. 2011. In allen neuen Zweigbibliotheken sollen nach Möglichkeit die Öffnungszeiten ausgedehnt werden, was Bau- und Personalplanung voraussetzt – besonders im Fall der Campus-Bibliothek, die als 24-Stunden-Bibliothek
funktionieren soll.
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Das Jahr 2011 war durch umfangreiche Planungen, Konzeptentwicklungen und den Beginn langfristiger Vorhaben gekennzeichnet, die in den kommenden Jahren zu sichtbaren Verbesserungen im Service und zu schlankeren Strukturen führen werden. Das betrifft eine ganze Reihe von Arbeitsbereichen hinter den Kulissen (s. II), alle Bauvorhaben (s. III) und bereitet auch die Forschungsbibliothek vor (s. IV).
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2012
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qucosa:12744
Das Jubiläumsjahr der Universität war ereignisreich auch für die Universitätsbibliothek. In diesem Tätigkeitsbericht sollen nur die wichtigsten Geschehnisse kurz angesprochen werden. Vier Dinge ragen heraus: die Eröffnung der Campus-Bibliothek als 24-Stunden-
Bibliothek, die Ausstellungen in den USA, die Eröffnung eines neuen Ausstellungsraums und die Förder-ung durch die Carl Friedrich von Siemens Stiftung. Zentrale Stichpunkte im Zusammenhang mit diesen Höhepunkten sind: Serviceverbesserung, wissenschaftliche Vernetzung, Bestandspflege und Entwicklung der Forschungsbibliothek.
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Tätigkeitsbericht / Universitätsbibliothek Leipzig
urn:nbn:de:bsz:15-qucosa-131998
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Seit Jahren fördert der Freistaat Sachsen durch Mittel des europäischen Strukturfonds (EFRE) die Modernisierung sächsischer Hochschulbibliotheken. Die UB Leipzig hat durch die EFRE-Finanzierung die 24-Stunden-Öffnung der Campus-Bibliothek mit Einführung der Funkchip-Technologie RFID realisiert. Sie profitiert weiterhin von einem durch die Landesbibliothek in Dresden (SLUB) geleiteten Projekt der Retrokatalogisierung: Seit zwei Jahren kommen jeden Tag bis zu 1.000 Titel neu in den elektronischen Katalog, die zuvor nur in Papierform verzeichnet waren. Nun gibt es ein neues EFRE-Projekt, federführend vorbereitet durch die UB Leipzig, zur Entwicklung einer neuen Nutzeroberfläche.
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Mit dem Einzug der Zweigbibliothek Theologie und des Magazinbestands der Zweigbibliothek Musik in die Bibliotheca Albertina konnten erste Schritte auf dem 2011 begonnenen Weg der Standortkonsolidierung gegangen werden. Die Aufnahme der Theologiebestände in die Bibliotheca Albertina stellt eine deutliche Bereicherung des interdisziplinären Arbeitens in den Geisteswissenschaften dar. Es waren größere Umräumarbeiten notwendig, um alle Bestände im Historischen Lesesaal und den angrenzenden Lesebereichen aufnehmen zu können.
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Jahresbericht / Universität Leipzig
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The Eukaryotic Chromatin Computer: Components, Mode of Action, Properties, Tasks, Computational Power, and Disease Relevance
urn:nbn:de:bsz:15-qucosa-137584
eng
Eukaryotic genomes are typically organized as chromatin, the complex of DNA and proteins that forms chromosomes within the cell\\\''s nucleus. Chromatin has pivotal roles for a multitude of functions, most of which are carried out by a complex system of covalent chemical modifications of histone proteins.
The propagation of patterns of these histone post-translational modifications across cell divisions is particularly important for maintenance of the cell state in general and the transcriptional program in particular. The discovery of epigenetic inheritance phenomena - mitotically and/or meiotically heritable changes in gene function resulting from changes in a chromosome without alterations in the DNA sequence - was remarkable because it disproved the assumption that information is passed to daughter cells exclusively through DNA.
However, DNA replication constitutes a dramatic disruption of the chromatin state that effectively amounts to partial erasure of stored information. To preserve its epigenetic state the cell reconstructs (at least part of) the histone post-translational modifications by means of processes that are still very poorly understood. A plausible hypothesis is that the different combinations of reader and writer domains in histone-modifying enzymes implement local rewriting rules that are capable of \\\"recomputing\\\" the desired parental patterns of histone post-translational modifications on the basis of the partial information contained in that half of the nucleosomes that predate replication.
It is becoming increasingly clear that both information processing and computation are omnipresent and of fundamental importance in many fields of the natural sciences and the cell in particular. The latter is exemplified by the increasingly popular research areas that focus on computing with DNA and membranes.
Recent work suggests that during evolution, chromatin has been converted into a powerful cellular memory device capable of storing and processing large amounts of information. Eukaryotic chromatin may therefore also act as a cellular computational device capable of performing actual computations in a biological context. A recent theoretical study indeed demonstrated that even relatively simple models of chromatin computation are computationally universal and hence conceptually more powerful than gene regulatory networks.
In the first part of this thesis, I establish a deeper understanding of the computational capacities and limits of chromatin, which have remained largely unexplored.
I analyze selected biological building blocks of the chromatin computer and compare it to system components of general purpose computers, particularly focusing on memory and the logical and arithmetical operations. I argue that it has a massively parallel architecture, a set of read-write rules that operate non-deterministically on chromatin, the capability of self-modification, and more generally striking analogies to amorphous computing. I therefore propose a cellular automata-like 1-D string as its computational paradigm on which sets of local rewriting rules are applied asynchronously with time-dependent probabilities. Its mode of operation is therefore conceptually similar to well-known concepts from the complex systems theory. Furthermore, the chromatin computer provides volatile memory with a massive information content that can be exploited by the cell. I estimate that its memory size lies in the realms of several hundred megabytes of writable information per cell, a value that I compare with DNA itself and cis-regulatory modules. I furthermore show that it has the potential to not only perform computations in a biological context but also in a strict informatics sense. At least theoretically it may therefore be used to calculate any computable function or algorithm more generally. Chromatin is therefore another representative of the growing number of non-standard computing examples.
As an example for a biological challenge that may be solved by the \\\"chromatin computer\\\", I formulate epigenetic inheritance as a computational problem and develop a flexible stochastic simulation system for the study of recomputation-based epigenetic inheritance of individual histone post-translational modifications. The implementation uses Gillespie\\\''s stochastic simulation algorithm for exactly simulating the time evolution of the chemical master equation of the underlying stochastic process. Furthermore, it is efficient enough to use an evolutionary algorithm to find a system of enzymes that can stably maintain a particular chromatin state across multiple cell divisions. I find that it is easy to evolve such a system of enzymes even without explicit boundary elements separating differentially modified chromatin domains. However, the success of this task depends on several previously unanticipated factors such as the length of the initial state, the specific pattern that should be maintained, the time between replications, and various chemical parameters. All these factors also influence the accumulation of errors in the wake of cell divisions.
Chromatin-regulatory processes and epigenetic (inheritance) mechanisms constitute an intricate and sensitive system, and any misregulation may contribute significantly to various diseases such as Alzheimer\\\''s disease. Intriguingly, the role of epigenetics and chromatin-based processes as well as non-coding RNAs in the etiology of Alzheimer\\\''s disease is increasingly being recognized.
In the second part of this thesis, I explicitly and systematically address the two hypotheses that (i) a dysregulated chromatin computer plays important roles in Alzheimer\\\''s disease and (ii) Alzheimer\\\''s disease may be considered as an evolutionarily young disease. In summary, I found support for both hypotheses although for hypothesis 1, it is very difficult to establish causalities due to the complexity of the disease. However, I identify numerous chromatin-associated, differentially expressed loci for histone proteins, chromatin-modifying enzymes or integral parts thereof, non-coding RNAs with guiding functions for chromatin-modifying complexes, and proteins that directly or indirectly influence epigenetic stability (e.g., by altering cell cycle regulation and therefore potentially also the stability of epigenetic states). %Notably, we generally observed enrichment of probes located in non-coding regions, particularly antisense to known annotations (e.g., introns).
For the identification of differentially expressed loci in Alzheimer\\\''s disease, I use a custom expression microarray that was constructed with a novel bioinformatics pipeline. Despite the emergence of more advanced high-throughput methods such as RNA-seq, microarrays still offer some advantages and will remain a useful and accurate tool for transcriptome profiling and expression studies.
However, it is non-trivial to establish an appropriate probe design strategy for custom expression microarrays because alternative splicing and transcription from non-coding regions are much more pervasive than previously appreciated. To obtain an accurate and complete expression atlas of genomic loci of interest in the post-ENCODE era, this additional transcriptional complexity must be considered during microarray design and requires well-considered probe design strategies that are often neglected. This encompasses, for example, adequate preparation of a set of target sequences and accurate estimation of probe specificity. With the help of this pipeline, two custom-tailored microarrays have been constructed that include a comprehensive collection of non-coding RNAs. Additionally, a user-friendly web server has been set up that makes the developed pipeline publicly available for other researchers.
Eukaryotische Genome sind typischerweise in Form von Chromatin organisiert, dem Komplex aus DNA und Proteinen, aus dem die Chromosomen im Zellkern bestehen. Chromatin hat lebenswichtige Funktionen in einer Vielzahl von Prozessen, von denen die meisten durch ein komplexes System von kovalenten Modifikationen an Histon-Proteinen ablaufen.
Muster dieser Modifikationen sind wichtige Informationsträger, deren Weitergabe über die Zellteilung hinaus an beide Tochterzellen besonders wichtig für die Aufrechterhaltung des Zellzustandes im Allgemeinen und des Transkriptionsprogrammes im Speziellen ist. Die Entdeckung von epigenetischen Vererbungsphänomenen - mitotisch und/oder meiotisch vererbbare Veränderungen von Genfunktionen, hervorgerufen durch Veränderungen an Chromosomen, die nicht auf Modifikationen der DNA-Sequenz zurückzuführen sind - war bemerkenswert, weil es die Hypothese widerlegt hat, dass Informationen an Tochterzellen ausschließlich durch DNA übertragen werden.
Die Replikation der DNA erzeugt eine dramatische Störung des Chromatinzustandes, welche letztendlich ein partielles Löschen der gespeicherten Informationen zur Folge hat. Um den epigenetischen Zustand zu erhalten, muss die Zelle Teile der parentalen Muster der Histonmodifikationen durch Prozesse rekonstruieren, die noch immer sehr wenig verstanden sind. Eine plausible Hypothese postuliert, dass die verschiedenen Kombinationen der Lese- und Schreibdomänen innerhalb von Histon-modifizierenden Enzymen lokale Umschreibregeln implementieren, die letztendlich das parentale Modifikationsmuster der Histone neu errechnen. Dies geschieht auf Basis der partiellen Informationen, die in der Hälfte der vererbten Histone gespeichert sind.
Es wird zunehmend klarer, dass sowohl Informationsverarbeitung als auch computerähnliche Berechnungen omnipräsent und in vielen Bereichen der Naturwissenschaften von fundamentaler Bedeutung sind, insbesondere in der Zelle. Dies wird exemplarisch durch die zunehmend populärer werdenden Forschungsbereiche belegt, die sich auf computerähnliche Berechnungen mithilfe von DNA und Membranen konzentrieren. Jüngste Forschungen suggerieren, dass sich Chromatin während der Evolution in eine mächtige zelluläre Speichereinheit entwickelt hat und in der Lage ist, eine große Menge an Informationen zu speichern und zu prozessieren. Eukaryotisches Chromatin könnte also als ein zellulärer Computer agieren, der in der Lage ist, computerähnliche Berechnungen in einem biologischen Kontext auszuführen. Eine theoretische Studie hat kürzlich demonstriert, dass bereits relativ simple Modelle eines Chromatincomputers berechnungsuniversell und damit mächtiger als reine genregulatorische Netzwerke sind.
Im ersten Teil meiner Dissertation stelle ich ein tieferes Verständnis des Leistungsvermögens und der Beschränkungen des Chromatincomputers her, welche bisher größtenteils unerforscht waren. Ich analysiere ausgewählte Grundbestandteile des Chromatincomputers und vergleiche sie mit den Komponenten eines klassischen Computers, mit besonderem Fokus auf Speicher sowie logische und arithmetische Operationen. Ich argumentiere, dass Chromatin eine massiv parallele Architektur, eine Menge von Lese-Schreib-Regeln, die nicht-deterministisch auf Chromatin operieren, die Fähigkeit zur Selbstmodifikation, und allgemeine verblüffende Ähnlichkeiten mit amorphen Berechnungsmodellen besitzt. Ich schlage deswegen eine Zellularautomaten-ähnliche eindimensionale Kette als Berechnungsparadigma vor, auf dem lokale Lese-Schreib-Regeln auf asynchrone Weise mit zeitabhängigen Wahrscheinlichkeiten ausgeführt werden. Seine Wirkungsweise ist demzufolge konzeptionell ähnlich zu den wohlbekannten Theorien von komplexen Systemen. Zudem hat der Chromatincomputer volatilen Speicher mit einem massiven Informationsgehalt, der von der Zelle benutzt werden kann. Ich schätze ab, dass die Speicherkapazität im Bereich von mehreren Hundert Megabytes von schreibbarer Information pro Zelle liegt, was ich zudem mit DNA und cis-regulatorischen Modulen vergleiche.
Ich zeige weiterhin, dass ein Chromatincomputer nicht nur Berechnungen in einem biologischen Kontext ausführen kann, sondern auch in einem strikt informatischen Sinn. Zumindest theoretisch kann er deswegen für jede berechenbare Funktion benutzt werden. Chromatin ist demzufolge ein weiteres Beispiel für die steigende Anzahl von unkonventionellen Berechnungsmodellen.
Als Beispiel für eine biologische Herausforderung, die vom Chromatincomputer gelöst werden kann, formuliere ich die epigenetische Vererbung als rechnergestütztes Problem. Ich entwickle ein flexibles Simulationssystem zur Untersuchung der epigenetische Vererbung von individuellen Histonmodifikationen, welches auf der Neuberechnung der partiell verlorengegangenen Informationen der Histonmodifikationen beruht. Die Implementierung benutzt Gillespies stochastischen Simulationsalgorithmus, um die chemische Mastergleichung der zugrundeliegenden stochastischen Prozesse über die Zeit auf exakte Art und Weise zu modellieren. Der Algorithmus ist zudem effizient genug, um in einen evolutionären Algorithmus eingebettet zu werden. Diese Kombination erlaubt es ein System von Enzymen zu finden, dass einen bestimmten Chromatinstatus über mehrere Zellteilungen hinweg stabil vererben kann. Dabei habe ich festgestellt, dass es relativ einfach ist, ein solches System von Enzymen zu evolvieren, auch ohne explizite Einbindung von Randelementen zur Separierung differentiell modifizierter Chromatindomänen. Dennoch ängt der Erfolg dieser Aufgabe von mehreren bisher unbeachteten Faktoren ab, wie zum Beispiel der Länge der Domäne, dem bestimmten zu vererbenden Muster, der Zeit zwischen Replikationen sowie verschiedenen chemischen Parametern. Alle diese Faktoren beeinflussen die Anhäufung von Fehlern als Folge von Zellteilungen.
Chromatin-regulatorische Prozesse und epigenetische Vererbungsmechanismen stellen ein komplexes und sensitives System dar und jede Fehlregulation kann bedeutend zu verschiedenen Krankheiten, wie zum Beispiel der Alzheimerschen Krankheit, beitragen. In der Ätiologie der Alzheimerschen Krankheit wird die Bedeutung von epigenetischen und Chromatin-basierten Prozessen sowie nicht-kodierenden RNAs zunehmend erkannt.
Im zweiten Teil der Dissertation adressiere ich explizit und auf systematische Art und Weise die zwei Hypothesen, dass (i) ein fehlregulierter Chromatincomputer eine wichtige Rolle in der Alzheimerschen Krankheit spielt und (ii) die Alzheimersche Krankheit eine evolutionär junge Krankheit darstellt. Zusammenfassend finde ich Belege für beide Hypothesen, obwohl es für erstere schwierig ist, aufgrund der Komplexität der Krankheit Kausalitäten zu etablieren. Dennoch identifiziere ich zahlreiche differentiell exprimierte, Chromatin-assoziierte Bereiche, wie zum Beispiel Histone, Chromatin-modifizierende Enzyme oder deren integrale Bestandteile, nicht-kodierende RNAs mit Führungsfunktionen für Chromatin-modifizierende Komplexe oder Proteine, die direkt oder indirekt epigenetische Stabilität durch veränderte Zellzyklus-Regulation beeinflussen.
Zur Identifikation von differentiell exprimierten Bereichen in der Alzheimerschen Krankheit benutze ich einen maßgeschneiderten Expressions-Microarray, der mit Hilfe einer neuartigen Bioinformatik-Pipeline erstellt wurde. Trotz des Aufkommens von weiter fortgeschrittenen Hochdurchsatzmethoden, wie zum Beispiel RNA-seq, haben Microarrays immer noch einige Vorteile und werden ein nützliches und akkurates Werkzeug für Expressionsstudien und Transkriptom-Profiling bleiben.
Es ist jedoch nicht trivial eine geeignete Strategie für das Sondendesign von maßgeschneiderten Expressions-Microarrays zu finden, weil alternatives Spleißen und Transkription von nicht-kodierenden Bereichen viel verbreiteter sind als ursprünglich angenommen. Um ein akkurates und vollständiges Bild der Expression von genomischen Bereichen in der Zeit nach dem ENCODE-Projekt zu bekommen, muss diese zusätzliche transkriptionelle Komplexität schon während des Designs eines Microarrays berücksichtigt werden und erfordert daher wohlüberlegte und oft ignorierte Strategien für das Sondendesign. Dies umfasst zum Beispiel eine adäquate Vorbereitung der Zielsequenzen und eine genaue Abschätzung der Sondenspezifität. Mit Hilfe der Pipeline wurden zwei maßgeschneiderte Expressions-Microarrays produziert, die beide eine umfangreiche Sammlung von nicht-kodierenden RNAs beinhalten. Zusätzlich wurde ein nutzerfreundlicher Webserver programmiert, der die entwickelte Pipeline für jeden öffentlich zur Verfügung stellt.
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ddc:000
Histon-Modifikation, Epigenetik, Chromatin, biologischer Computer, Alzheimer, Gillespie, stochastische Simulation
histone modification, epigenetics, chromatin, biological computer, Alzheimer, Gillespie, stochastic simulation
Arnold, Christian
Prohaska, Sonja
Stadler, Peter F.
Laubichler, Manfred D.
Universität Leipzig
2016-11-01
2013-05-11
2014-02-14
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Jahresbericht / Universität Leipzig
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ger
urn:nbn:de:bsz:15-qucosa-148557
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Die Universität Leipzig verändert ihr Antlitz. Sichtbar wird dies nicht nur auf dem Campus am Augustusplatz, sondern auch am Jahresbericht. Nach der durchweg günstigen Aufnahme der inhaltlich und gestalterisch neuen Form der Ausgabe für das Jahr 2006/2007, freue ich mich, Ihnen mit diesem Bericht auch die Arbeitsergebnisse der Universität für das Akademische Jahr 2007/2008 in Wort und Bild präsentieren zu können. Es war wieder ein sehr spannendes und aufregendes Jahr für uns. Zum einen sind es die Probleme und Herausforderungen, die sich aus der Umsetzung der komplexen Studienreform und ihrer Überlagerung mit dem Hochschulpakt 2020 ergeben, und zum anderen die rasch aufeinander folgenden Exzellenzinitiativen in der Forschung von Bund und Ländern sowie des Freistaates. Hinzu kommen die Vorbereitung des 600. Jubiläums unserer Universität im Jahr 2009 und das Neu- und Umbauvorhaben am Augustusplatz.:Vor 500 Jahren: Ein Student als Rektor Heinrich Stromer von Auerbach; Vorwort des Rektors; Die Entwicklung unserer Universität; Forschung; Studium; Universität und Öffentlichkeit; Chronik; Rektoratskollegium; Organigramm; Zahlen – Daten – Fakten; In memoriam; Register
info:eu-repo/classification/ddc/000
ddc:000
Universität, Jahresbericht
University, Annual report
Universität Leipzig
2014-06-02
2008
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Das zurückliegende Jahr 2009 war für die Universität Leipzig ein ganz besonderes, seit langem geplant und sorgfältig vorbereitet: Die Universität Leipzig erinnerte an ihre Gründung vor 600 Jahren. Parallel zu den zentralen Veranstaltungen wurden rund 300 Ausstellungen, Tagungen, Fachkongresse, studentische Projekte der Initiative „Studierende 2009“ und Konzerte durchgeführt. Lehre und Forschung ruhten im Jubiläumsjahr 2009 jedoch nicht. Diskussionspunkte der Studienreform waren die Beseitigung der Überlastsituation und die Reform des Wahlbereiches in den geistes- und sozialwissenschaftlichen Studiengängen, die Reduzierung der Prüfungslast und die Akkreditierung neuer Studiengänge.:Student und Magister an der Universität Leipzig:
Paul Fleming; Vorwort des Rektors; Die Entwicklung unserer Universität; Forschung; Studium; Sechs Jahrhunderte Leipziger Universitätsgeschichte; Wir feiern unser Jubiläum; Chronik; Das Rektorat; Organigramm; Zahlen – Daten – Fakten; In memoriam; Register
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ddc:000
Universität, Jahresbericht
University, Annual report
Universität Leipzig
2014-06-02
2010
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Nach 2011 erscheint nun die 2. Ausgabe des "Jahresspiegels". Damit soll – wie es das Sächsische Hochschulgesetz vorsieht – insbesondere über wesentliche Daten der entwicklung der Universität und ergebnisse
der leistungsprozesse in Forschung und Lehre informiert werden.:Vorwort der Rektorin; Organigramm; Studium; Forschung; Haushalt; Personal; Organe und Gremien; Ehrungen; Internationale Kooperationen; Chronik
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ddc:000
Leipzig, Universität
Leipzig, university
Universität Leipzig
2014-06-13
2013
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EDV in Medizin und Biologie: EDP in medicine und biology: Versuchsplanung, Datensammlung und biometrische Auswertung in Biologie, klinischer und experimenteller Medizin, Veterinärmedizin und Agrarwissenschaften
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie
Urban & Fischer
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-20
1970
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
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Ulmer
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1970
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-20
1971
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-20
1971
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-20
1971
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-20
1973
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-20
1971
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
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1974
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Electronic data processing, EDP, medicine, biology
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Ulmer
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1973
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1974
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1974
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1974
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1975
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1977
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1976
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1977
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1976
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1977
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1976
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Ulmer
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1977
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Ulmer
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1979
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Ulmer
2014-06-26
1978
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Ulmer
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1978
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Ulmer
2014-06-26
1979
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Ulmer
2014-06-26
1979
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Ulmer
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1979
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Ulmer
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1980
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Ulmer
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1980
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Electronic data processing, EDP, medicine, biology
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Ulmer
2014-06-30
1981
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0300-8282
ger
urn:nbn:de:bsz:15-qucosa-145292
qucosa:12541
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
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Ulmer
2014-06-27
1980
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ger
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
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Ulmer
2014-06-30
1981
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ger
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
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Ulmer
2014-06-27
1980
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ger
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
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Ulmer
2014-06-30
1982
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ger
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qucosa:12541
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ddc:000
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ddc:570
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
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2014-06-30
1981
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0300-8282
ger
urn:nbn:de:bsz:15-qucosa-145292
qucosa:12541
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ddc:610
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ddc:570
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1981
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ger
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ddc:610
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ddc:570
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1982
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ger
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ddc:610
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ddc:570
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1982
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ger
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1984
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ger
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ddc:610
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1982
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ger
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1985
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ger
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ddc:570
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1983
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ger
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ddc:570
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1985
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ger
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1985
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ger
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Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-06-30
1984
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ger
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Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-07-01
1985
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ger
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Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-07-01
1987
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Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-07-01
1986
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-07-01
1986
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ger
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Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-07-01
1986
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ger
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Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-07-01
1987
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ger
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ddc:570
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Fischer
Ulmer
2014-07-01
1988
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0300-8282
ger
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1992
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1992
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2014-07-11
2003
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12734
https://ul.qucosa.de/api/qucosa%3A12734/attachment/ATT-0/
oai:qucosa:de:qucosa:12737
2021-03-29T08:36:08Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
ddc:570
ddc:610
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Informatik, Biometrie und Epidemiologie in Medizin und Biologie: offizielles Organ der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS) e.V.
urn:nbn:de:bsz:15-qucosa-148384
0943-5581
ger
urn:nbn:de:bsz:15-qucosa-145588
qucosa:12568
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/570
ddc:570
info:eu-repo/classification/ddc/610
ddc:610
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Urban & Fischer
Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie
2014-07-11
2001
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12737
https://ul.qucosa.de/api/qucosa%3A12737/attachment/ATT-0/
oai:qucosa:de:qucosa:12738
2021-03-29T08:36:09Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
ddc:570
ddc:610
openaire
Informatik, Biometrie und Epidemiologie in Medizin und Biologie: offizielles Organ der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS) e.V.
urn:nbn:de:bsz:15-qucosa-148397
0943-5581
ger
urn:nbn:de:bsz:15-qucosa-145588
qucosa:12568
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/570
ddc:570
info:eu-repo/classification/ddc/610
ddc:610
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Urban & Fischer
Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie
2014-07-11
2001
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12738
https://ul.qucosa.de/api/qucosa%3A12738/attachment/ATT-0/
oai:qucosa:de:qucosa:12741
2021-03-29T08:36:11Z
qucosa:ubl
doc-type:Periodical
open_access
ddc:000
ddc:060
openaire
Bericht des Rektoratskollegiums der Universität Leipzig:
urn:nbn:de:bsz:15-qucosa-148544
ger
qucosa:12313
qucosa:12318
qucosa:12317
qucosa:12295
qucosa:12296
qucosa:12321
qucosa:12312
qucosa:12742
nicht vorhanden
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/060
ddc:060
Universität, Leipzig, Jahresbericht
University, Leipzig, Annual report
Universität Leipzig
2014-07-11
info:eu-repo/semantics/openAccess
doc-type:Periodical
info:eu-repo/semantics/Periodical
doc-type:Collection
https://ul.qucosa.de/id/qucosa%3A12741
oai:qucosa:de:qucosa:12742
2021-03-29T08:36:12Z
qucosa:ubl
doc-type:Periodical
open_access
ddc:000
ddc:060
openaire
Jahresbericht / Universität Leipzig
urn:nbn:de:bsz:15-qucosa-148557
ger
urn:nbn:de:bsz:15-qucosa-148544
qucosa:12741
qucosa:12493
qucosa:12495
qucosa:12494
qucosa:12322
qucosa:12743
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/060
ddc:060
Leipzig, Universität, Jahresbericht
Leipzig, university, annual report
Universität Leipzig
2014-07-11
info:eu-repo/semantics/openAccess
doc-type:Periodical
info:eu-repo/semantics/Periodical
doc-type:Collection
https://ul.qucosa.de/id/qucosa%3A12742
oai:qucosa:de:qucosa:12744
2021-03-29T08:36:13Z
qucosa:ubl
doc-type:Periodical
open_access
ddc:000
ddc:020
openaire
Tätigkeitsbericht / Universitätsbibliothek Leipzig
urn:nbn:de:bsz:15-qucosa-148591
ger
qucosa:71313
qucosa:12271
qucosa:21194
qucosa:12270
qucosa:13413
qucosa:78560
qucosa:12803
qucosa:12273
qucosa:14782
qucosa:15662
qucosa:12272
qucosa:12275
qucosa:12274
qucosa:12276
qucosa:33975
qucosa:74923
...
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/020
ddc:020
Universitätsbibliothek, Leipzig, Jahresbericht
University library, Leipzig, annual report
Universität Leipzig
2014-07-14
info:eu-repo/semantics/openAccess
doc-type:Periodical
info:eu-repo/semantics/Periodical
doc-type:Collection
https://ul.qucosa.de/id/qucosa%3A12744
oai:qucosa:de:qucosa:12743
2021-03-29T08:36:12Z
qucosa:ubl
doc-type:Periodical
open_access
ddc:000
ddc:060
openaire
Jahresspiegel / Universität Leipzig: Zahlen, Daten, Fakten
urn:nbn:de:bsz:15-qucosa-148573
ger
urn:nbn:de:bsz:15-qucosa-148557
qucosa:12742
qucosa:12522
qucosa:11446
qucosa:12802
qucosa:15151
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/060
ddc:060
Leipzig, Universität, Jahresbericht
Leipzig, University, Annual report
Universität Leipzig
2014-07-11
info:eu-repo/semantics/openAccess
doc-type:Periodical
info:eu-repo/semantics/Periodical
doc-type:Collection
https://ul.qucosa.de/id/qucosa%3A12743
oai:qucosa:de:qucosa:12752
2022-02-07T10:25:48Z
qucosa:ubl
doc-type:article
doc-type:Text
open_access
ddc:000
ddc:100
status-type:publishedVersion
openaire
Situation der Philosophie, Kultur der Philosophen: über die neudeutsche Universitätsphilosophie
urn:nbn:de:bsz:15-qucosa-148897
ger
urn:nbn:de:bsz:15-qucosa2-776112
qucosa:77611
Seit 1990 sind westdeutsche Verhältnisse auch im Osten der erweiterten BRD anzutreffen: Für wenige Bereiche trifft das so allgemein zu wie für die Universitäten, die in den neuen Bundesländern strukturell denen der alten Bundesländer gleichgemacht wurden. Die Inhalte haben gewechselt, je nach Disziplin. Aber ist damit alles gesagt? Was heißt das zum Beispiel für die Philosophie, nachdem die Universitäten das westdeutsche Muster adaptiert haben, und zugleich Inhalte und Personen fast völlig ausgetauscht wurden?
DDR, Philosophie, Universität, Bundesrepublik, Deutschland
GDR, philosophy, university, Federal Republic of Germany, Germany
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/100
ddc:100
Schneider, Ulrich Johannes
de Gruyter
1996
info:eu-repo/semantics/publishedVersion
2014-07-16
Deutsche Zeitschrift für Philosophie 44 (1996), 1, S. 149-159 ISSN 0012-1045
info:eu-repo/semantics/openAccess
doc-type:article
info:eu-repo/semantics/article
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12752
https://ul.qucosa.de/api/qucosa%3A12752/attachment/ATT-0/
oai:qucosa:de:qucosa:12763
2022-02-07T10:38:03Z
qucosa:ubl
doc-type:bookPart
doc-type:Text
open_access
ddc:000
ddc:030
status-type:publishedVersion
openaire
Enzyklopädien des 18. Jahrhunderts digital: Einführung
urn:nbn:de:bsz:15-qucosa-149028
ger
urn:nbn:de:bsz:15-qucosa2-776112
qucosa:77611
Durch Digitalisierung und Bereitstellung im Internet rücken jetzt die Nachschlagewerke näher an die Leser und Schreiber heran. Orientierung beim Schreiben geben neben den gedruckten Werken längst auch Online-Dienste wie Wikipedia, während die Lektüre zugleich von Fachportalen und einschlägigen Hypertexten gesteuert wird, die immer weniger dazu auffordern, den Schreibtischstuhl zu verlassen. Die Kultur des wissenschaftlichen Arbeitens mag gleich bleiben, ihre Medien ändern sich entscheidend, wenn sie digital werden.
Enzyklopädie, 18. Jahrhundert, Digitalisierung
Encyclopedia, 18. century, digitization
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/030
ddc:030
Schneider, Ulrich Johannes
de Gruyter
2008
info:eu-repo/semantics/publishedVersion
2014-07-17
Kulturen des Wissens im 18. Jahrhundert / hrsg. von Ulrich Johannes Schneider. Berlin [u.a.] : de Gruyter, 2008, S.159-162 ISBN 978-3-11-019822-5
info:eu-repo/semantics/openAccess
doc-type:bookPart
info:eu-repo/semantics/bookPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12763
https://ul.qucosa.de/api/qucosa%3A12763/attachment/ATT-0/
oai:qucosa:de:qucosa:12760
2022-02-07T15:09:45Z
qucosa:ubl
doc-type:bookPart
doc-type:Text
open_access
ddc:000
status-type:publishedVersion
openaire
Der Ort der Bücher in der Bibliothek und im Katalog am Beispiel von Herzog Augusts Wolfenbütteler Büchersammlung
urn:nbn:de:bsz:15-qucosa-148995
ger
urn:nbn:de:bsz:15-qucosa2-776112
qucosa:77611
Jedes Buch begehrt viele Plätze und kann doch nur einen haben, jedenfalls im Regal. Das ist das zentrale Problem der Bibliothek: Ordnung heißt für sie Verortung. Bücher werden im Regal abgestellt, und wo immer sie stehen, verletzt und beschränkt das die Ordnungen, die sie entwerfen, in die sie sich selbst entworfen haben, in denen
sie entworfen werden. Die Frage WAS? wird in der
Bibliothek gekoppelt an die Frage WO?, und diese Koppelung war und ist sowohl ein Problem der Erkenntnis wie eines der Praxis des Umgangs mit Büchern, der sich durch die Bibliothek und mit der Bibliothek realisiert.
Bibliothek, Wolfenbüttel, Herzog-August-Bibliothek, Auffstellung, Katalog, Ordnung
Library, Wolfenbüttel, Herzog, August-Bibliothek, shelving, catalogue, arrangement of books
info:eu-repo/classification/ddc/000
ddc:000
Schneider, Ulrich Johannes
de Gruyter
2005
info:eu-repo/semantics/publishedVersion
2014-07-17
Archiv für Geschichte des Buchwesens / hrsg. von Monika Estermann ... Berlin [u.a.] : de Gruyter 59 (2005), S. 91-104 ISBN 3-598-24855-5
info:eu-repo/semantics/openAccess
doc-type:bookPart
info:eu-repo/semantics/bookPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12760
https://ul.qucosa.de/api/qucosa%3A12760/attachment/ATT-0/
oai:qucosa:de:qucosa:12765
2022-02-07T15:10:56Z
qucosa:ubl
doc-type:bookPart
doc-type:Text
open_access
ddc:000
ddc:030
status-type:publishedVersion
openaire
Die Konstruktion des allgemeinen Wissens in Zedlers 'Universal-Lexicon
urn:nbn:de:bsz:15-qucosa-149051
ger
urn:nbn:de:bsz:15-qucosa2-776112
qucosa:77611
Das 'Universal-Lexicon', das ab 1732 von Johann Heinrich Zedler herausgegeben wurde und bis 1754 auf 68 Folianten und damit zum größten Lexikon des 18. Jahrhunderts anwuchs, ist ein Lexikon ohne Programm. Das macht moderne Leser ratlos im Hinblick auf die verfolgten Ziele. Man sucht ergebnislos eine Ideologie wie bei der französischen 'Encyclopedie', ein Bekenntnis zum Wie und Warum,
das im bürgerlichen 18. Jahrhundert ein Datum darstellte. Das 'Universal-Lexicon' wirkt ohne Programm schwach und scheint verteidigt werden zu müssen, etwa wie ein Zedler-Forscher 1969 formulierte: „Das Universallexikon blieb allein ein alphabetisches Nachschlagewerk. Aber auch so wurde es dem Anspruch, der Wissenschaft zu dienen, gerecht.' Welcher Wissenschaft hat das
'Universal-Lexicon' gedient? Und vor allem: wie eigentlich? Das sind bis heute offene Fragen.
Zedler, Johann Heinrich, Universal-Lexicon, Wissen
Zedler, Johann Heinrich, Universal-Lexicon, knowledge
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/030
ddc:030
Schneider, Ulrich Johannes
Akad.-Verl.
2004
info:eu-repo/semantics/publishedVersion
2014-07-17
Wissenssicherung, Wissensordnung und Wissensverarbeitung : das europäische Modell der Enzyklopädien / hrsg. von Theo Stammen ... Berlin : Akad.-Verl., 2004, S. 81-101 ISBN 3-05-003776-8
info:eu-repo/semantics/openAccess
doc-type:bookPart
info:eu-repo/semantics/bookPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12765
https://ul.qucosa.de/api/qucosa%3A12765/attachment/ATT-0/
oai:qucosa:de:qucosa:12762
2021-03-29T08:36:26Z
qucosa:ubl
doc-type:bookPart
doc-type:Text
open_access
ddc:000
ddc:030
openaire
Der Aufbau der Wissenswelt: eine phänotypische Beschreibung enzyklopädischer Literatur
urn:nbn:de:bsz:15-qucosa-149015
ger
Im Spannungsfeld zwischen der gültigen Repräsentation des aktuellen Wissensstandes und der allgemeinen Verständlichkeit für den nichtakademischen Leser stellt die enzyklopädische Literatur des 18. Jahrhunderts eine Praxis der Wissenserstellung und Wissensvermittlung dar, die an ihren Formen selbst studiert werden muss. Nach einer kurzen Erläuterung
des Ansatzes (1.) werden nachfolgend diese Wissensformen als gattungsgenerierend (2.) und, am Beispiel von Zedlers Universal-Lexicon (3.), als textgenerierend für das allgemeine Wissen beschrieben.
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/030
ddc:030
Wissen, 18. Jahrhundert, Lexikon, Enzyklopädie
Knowledge, 18. century, lexicon, encyclopedia
Schneider, Ulrich Johannes
de Gruyter
2014-07-17
2008
Kulturen des Wissens im 18. Jahrhundert / hrsg. von Ulrich Johannes Schneider. Berlin [u.a.] : de Gruyter, 2008, S. 81-100 ISBN 978-3-11-019822-5
info:eu-repo/semantics/openAccess
doc-type:bookPart
info:eu-repo/semantics/bookPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12762
https://ul.qucosa.de/api/qucosa%3A12762/attachment/ATT-0/
oai:qucosa:de:qucosa:12785
2022-02-07T10:49:37Z
qucosa:ubl
doc-type:conferenceObject
doc-type:Text
open_access
ddc:000
openaire
Bibliothekarischer Exhibitionismus?: Handschriften im Internet
urn:nbn:de:bsz:15-qucosa-149393
ger
urn:nbn:de:bsz:15-qucosa2-776112
qucosa:77611
Jeder sieht, dass auf dem mit unserer Veröffentlichungskultur wesentlich verbundenen Buchmarkt viel in Bewegung isr. Klar ist zugleich, dass das Rad der Geschichte nicht zurückgedreht werden kann. Moderne Kommunikationstechniken setzen sich durch und drängen juristische Schutzregelungen wie kulturelle Gewohnheiten in die Defensive, auch und gerade bei der Digitalisierung des Buchbestandes. Vor diesem knapp skizzierten Hinrergrund der sich wandelnden Texrkulrur lässt sich die Fragestellung verschärfen und fragen, welchen Sinn es hat, Handschrifren digital ins Nerz zu stellen, also solche Texte, die bis eben noch als exrrem schurzbedürftig und erklärungswürdig eingestuft wurden. Der gesamte kulrurelle Apparat,
der sich um Handschriften herum entwickelt hat, geht nicht ohne Grund von der Annahme aus, dass nur Spezialisten Handschriften in der Rohform des historischen Dokumentes begreifen können, und dass eine Begegnung mir Handschriften nicht voraussetzungslos geschehen kann. Was also bringt deren Veröffentlichung online?
Handschrift, Digitalisierung, Internet,
Manuscript, digitization, Internet
info:eu-repo/classification/ddc/000
ddc:000
Schneider, Ulrich Johannes
Olms
2010
2014-07-21
98. Deutscher Bibliothekartag in Erfurt 2009 : ein neuer Blick auf Bibliotheken / hrsg. von Ulrich Hohoff ... Hildesheim [u.a.] : Olms, 2010, S. 239-245 ISBN 978-3-487-14334-7
info:eu-repo/semantics/openAccess
doc-type:conferenceObject
info:eu-repo/semantics/conferenceObject
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12785
https://ul.qucosa.de/api/qucosa%3A12785/attachment/ATT-0/
oai:qucosa:de:qucosa:12791
2022-02-08T08:53:11Z
qucosa:ubl
doc-type:bookPart
doc-type:Text
open_access
ddc:000
status-type:publishedVersion
openaire
Wo die Geschichte in Büchern sitzt
urn:nbn:de:bsz:15-qucosa-149489
ger
urn:nbn:de:bsz:15-qucosa2-776112
qucosa:77611
Bücher, die bewegen, liest man mit dem Bleistift in der Hand, man knickt
die Ecken wichtiger Seiten ab, legt Zettel ein und klebt Zeitungsausschnitte in die vorderen oder hinteren Buchspiegel, kurz: Man eignet sie sich an wie selbst geschriebene Texte. Die Geschichte sitzt hier am Rand des Satzspiegels in Anmerkungen, sie sitzt in Unterstreichungen und Kommentaren ebenso wie in Frage- und
Ausrufungszeichen. Die Leser mögen so tot sein wie die Autoren: Immer
aber sagen diese Zeichen der aufmerksamen Lektüre früherer Epochen,
dass Bücher beweglich sind, dass sie den Text vom Autor zum Leser bringen und dort auf autorähnliche Heftigkeit stoßen, die in manchen Fällen zu einem eigenen Text führt, meist aber zu Anmerkungen und Kommentaren, für die es keinen besseren Ort gibt als eben jene Stellen, zu denen sie Anmerkungen und Kommentare sind. Die folgenden Beobachtungen sind die eines Lesers, der den schreibenden
Eingriff in gedruckte Texte oft genug geübt hat und nun um Verständnis
bittet, dass er nur persönlich sprechen kann und eigene Erlebnisse beim
Umgang mit Büchern ausstellt. Im Aufbrechen solcher Intimität zeigen sich Spuren einer oft vernachlässigten Geschichte, die in Büchern sitzt und daraus von Fall zu Fall befreit werden muss.
Text, Leser, Anstreichung, Bemerkung, Annotation
text, reader, mark, comment, annotation
info:eu-repo/classification/ddc/000
ddc:000
Schneider, Ulrich Johannes
Wallstein-Verl.
2009
info:eu-repo/semantics/publishedVersion
2014-07-22
Zeichen, Bücher, Wissensnetze : 125 Jahre Deutsches Buch- und Schriftmuseum der Deutschen Nationalbibliothek / hg. von Stefanie Jacobs. Göttingen : Wallstein-Verl., 2009, S. 137-144 ISBN 978-3-8353-0583-0
info:eu-repo/semantics/openAccess
doc-type:bookPart
info:eu-repo/semantics/bookPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12791
https://ul.qucosa.de/api/qucosa%3A12791/attachment/ATT-0/
oai:qucosa:de:qucosa:12802
2021-03-29T08:36:55Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
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Jahresspiegel / Universität Leipzig
urn:nbn:de:bsz:15-qucosa-149708
ger
urn:nbn:de:bsz:15-qucosa-148573
qucosa:12743
Mit dem nun im dritten Jahr erscheinenden "Jahresspiegel" informiert die Universitätsleitung über Eckdaten der Entwicklung der Universität und Ergebnisse der Leistungsprozesse in Forschung, Lehre und Verwaltung des abgelaufenen Jahres 2013.
info:eu-repo/classification/ddc/000
ddc:000
Leipzig, Universität
Leipzig, university
Universität Leipzig
2014-07-24
2014
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12802
https://ul.qucosa.de/api/qucosa%3A12802/attachment/ATT-0/
oai:qucosa:de:qucosa:12803
2021-03-29T08:36:56Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
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Tätigkeitsbericht / Universitätsbibliothek Leipzig
urn:nbn:de:bsz:15-qucosa-149711
ger
urn:nbn:de:bsz:15-qucosa-148591
qucosa:12744
Das Jahr 2013 brachte eine ganze Reihe von erfreulichen Neuerungen, auch wenn es nicht frei von Sorgen war. Was im letzten Tätigkeitsbericht angesprochen wurde, trat ein: Eine Krise bei den Erwerbungsmitteln, die sich seit längerem ankündigte (s. Tabelle unter IV ). Eine Reihe von Online‐Lizenzen konnte nicht mehr verlängert werden. Im Verein mit dem Rektorat und den Fakultäten bemüht sich die Universitätsbibliothek um Verbesserungen in der angespannten Situation.
info:eu-repo/classification/ddc/000
ddc:000
Bibliothek, Universitätsbibliothek, Leipzig, Jahresbericht
library, university library, Leipzig, annual report
Universität Leipzig
2014-07-24
2014
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12803
https://ul.qucosa.de/api/qucosa%3A12803/attachment/ATT-0/
oai:qucosa:de:qucosa:12864
2021-03-29T08:37:41Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
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Informatik, Biometrie und Epidemiologie in Medizin und Biologie: offizielles Organ der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS) e.V.
urn:nbn:de:bsz:15-qucosa-151188
0943-5581
ger
urn:nbn:de:bsz:15-qucosa-145588
qucosa:12568
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/610
ddc:610
info:eu-repo/classification/ddc/570
ddc:570
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie
Urban & Fischer
2014-08-28
2001
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12864
https://ul.qucosa.de/api/qucosa%3A12864/attachment/ATT-0/
oai:qucosa:de:qucosa:12865
2021-03-29T08:37:42Z
qucosa:ubl
doc-type:PeriodicalPart
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open_access
ddc:000
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ddc:610
openaire
Informatik, Biometrie und Epidemiologie in Medizin und Biologie: offizielles Organ der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS) e.V.
urn:nbn:de:bsz:15-qucosa-151196
0943-5581
ger
urn:nbn:de:bsz:15-qucosa-145588
qucosa:12568
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/610
ddc:610
info:eu-repo/classification/ddc/570
ddc:570
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie
Urban & Fischer
2014-08-28
2002
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12865
https://ul.qucosa.de/api/qucosa%3A12865/attachment/ATT-0/
oai:qucosa:de:qucosa:12866
2021-03-29T08:37:43Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
ddc:570
ddc:610
openaire
Informatik, Biometrie und Epidemiologie in Medizin und Biologie: offizielles Organ der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS) e.V.
urn:nbn:de:bsz:15-qucosa-151205
0943-5581
ger
urn:nbn:de:bsz:15-qucosa-145588
qucosa:12568
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/570
ddc:570
info:eu-repo/classification/ddc/610
ddc:610
Elektronische Datenverarbeitung, EDV, Medizin, Biologie
Electronic data processing, EDP, medicine, biology
Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie
Urban & Fischer
2014-08-28
2003
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12866
https://ul.qucosa.de/api/qucosa%3A12866/attachment/ATT-0/
oai:qucosa:de:qucosa:12983
2021-03-29T08:39:00Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Distributed Semantic Social Networks: Architecture, Protocols and Applications
urn:nbn:de:bsz:15-qucosa-154844
eng
Online social networking has become one of the most popular services on the Web. Especially Facebook with its 845Mio+ monthly active users and 100Mrd+ friendship relations creates a Web inside the Web. Drawing on the metaphor of islands, Facebook is becoming more like a continent. However, users are locked up on this continent with hardly any opportunity to communicate easily with users on other islands and continents or even to relocate trans-continentally. In addition to that, privacy, data ownership and freedom of communication issues are problematically in centralized environments. The idea of distributed social networking enables users to overcome the drawbacks of centralized social networks. The goal of this thesis is to provide an architecture for distributed social networking based on semantic technologies. This architecture consists of semantic artifacts, protocols and services which enable social network applications to work in a distributed environment and with semantic interoperability. Furthermore, this thesis presents applications for distributed semantic social networking and discusses user interfaces, architecture and communication strategies for this application category.
Soziale Netzwerke gehören zu den beliebtesten Online Diensten im World Wide Web. Insbesondere Facebook mit seinen mehr als 845 Mio. aktiven Nutzern im Monat und mehr als 100 Mrd. Nutzer- Beziehungen erzeugt ein eigenständiges Web im Web. Den Nutzern dieser Sozialen Netzwerke ist es jedoch schwer möglich mit Nutzern in anderen Sozialen Netzwerken zu kommunizieren oder aber mit ihren Daten in ein anderes Netzwerk zu ziehen. Zusätzlich dazu werden u.a. Privatsphäre, Eigentumsrechte an den eigenen Daten und uneingeschränkte Freiheit in der Kommunikation als problematisch empfunden. Die Idee verteilter Soziale Netzwerke ermöglicht es, diese Probleme zentralisierter Sozialer Netzwerke zu überwinden. Das Ziel dieser Arbeit ist die Darstellung einer Architektur verteilter Soziale Netzwerke welche auf semantischen Technologien basiert. Diese Architektur besteht aus semantischen Artefakten, Protokollen und Diensten und ermöglicht die Kommunikation von Sozialen Anwendungen in einer verteilten Infrastruktur. Darüber hinaus präsentiert diese Arbeit mehrere Applikationen für verteilte semantische Soziale Netzwerke und diskutiert deren Nutzer-Schnittstellen, Architektur und Kommunikationsstrategien.

info:eu-repo/classification/ddc/000
ddc:000
Verteilte Soziale Netzwerke, Architektur, Evaluation, WebID, Semantic Pingback, xOperator, MSSW
Distributed Social Networks, Social Semantic Web, Architecture, Evaluation, WebID, Semantic Pingback, xOperator, MSSW
Tramp, Sebastian
Fähnrich, Klaus-Peter
Auer, Sören
García, Roberto
Universität Leipzig
2014-11-04
2014-04-22
2014-10-27
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12983
https://ul.qucosa.de/api/qucosa%3A12983/attachment/ATT-0/
oai:qucosa:de:qucosa:12991
2021-03-29T08:39:05Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
ddc:004
ddc:330
ddc:650
openaire
Supply Chain Event Management – Bedarf, Systemarchitektur und Nutzen aus Perspektive fokaler Unternehmen der Modeindustrie
urn:nbn:de:bsz:15-qucosa-155014
ger
Supply Chain Event Management (SCEM) bezeichnet eine Teildisziplin des Supply Chain Management und ist für Unternehmen ein Ansatzpunkt, durch frühzeitige Reaktion auf kritische Ausnahmeereignisse in der Wertschöpfungskette Logistikleistung und -kosten zu optimieren.
Durch Rahmenbedingungen wie bspw. globale Logistikstrukturen, eine hohe Artikelvielfalt und volatile Geschäftsbeziehungen zählt die Modeindustrie zu den Branchen, die für kritische Störereignisse besonders anfällig ist. In diesem Sinne untersucht die vorliegende Dissertation nach einer Beleuchtung der wesentlichen Grundlagen zunächst, inwiefern es in der Modeindustrie tatsächlich einen Bedarf an SCEM-Systemen gibt.
Anknüpfend daran zeigt sie nach einer Darstellung bisheriger SCEM-Architekturkonzepte Gestaltungsmöglichkeiten für eine Systemarchitektur auf, die auf den Designprinzipien der Serviceorientierung beruht. In diesem Rahmen erfolgt u. a. auch die Identifikation SCEM-relevanter Business Services. Die Vorzüge einer serviceorientierten Gestaltung werden detailliert anhand der EPCIS (EPC Information Services)-Spezifikation illustriert.
Abgerundet wird die Arbeit durch eine Betrachtung der Nutzenpotenziale von SCEM-Systemen. Nach einer Darstellung von Ansätzen, welche zur Nutzenbestimmung infrage kommen, wird der Nutzen anhand eines Praxisbeispiels aufgezeigt und fließt zusammen mit den Ergebnissen einer Literaturrecherche in eine Konsolidierung von SCEM-Nutzeffekten. Hierbei wird auch beleuchtet, welche zusätzlichen Vorteile sich für Unternehmen durch eine serviceorientierte Architekturgestaltung bieten.
In der Schlussbetrachtung werden die wesentlichen Erkenntnisse der Arbeit zusammengefasst und in einem Ausblick sowohl beleuchtet, welche Relevanz die Ergebnisse der Arbeit für die Bewältigung künftiger Herausforderungen innehaben als auch welche Anknüpfungspunkte sich für anschließende Forschungsarbeiten ergeben.
info:eu-repo/classification/ddc/330
ddc:330
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/004
ddc:004
info:eu-repo/classification/ddc/650
ddc:650
SCEM, Supply Chain Event Management, SOA, Serviceorientierte Architektur, EPCIS, EPC Information Services, Modeindustrie, Bedarf, Architektur, Systemarchitektur, Nutzen, SCEM-System, Business Services, Geschäftsorientierte Services, Supply Chain Management, SCM, Logistik, Fokale Unternehmen, Bekleidungsindustrie, Textilindustrie, Logistikleistung, Logistikkosten, Simulation, Service Science, Service Design, Event, Kritisches Ausnahmeereignis, Störung, Störereignis, Lieferkette, Wertschöpfungskette, Fallstudie, EPC, Electronic Product Code, Cloud Computing, Cloud-Infrastruktur, Cloud-ERP, Service-Identifikation, Service-Beschreibung, Gerry Weber, van Laack, Gardeur, Seidensticker, ThyssenKrupp, Deutsche Post, DHL, fTRACE, GS1, GS1 Germany, René Lezard, März München, Kybernetischer Regelkreis, Management by Exception, Supply Chain Risk Management, Supply Network Event Management, SNEM, Service-Repository, Service-Registry, Original Brand Manufacturer, OBM, SaaS, Software as a Service, RFID, Radio Frequency Identification, Komplexität, Störungsanfälligkeit, Nutzenpotenzial, SCEM-Lösung, Value Chain Integrator, Transaktionskostentheorie, Ressourcenbasierter Ansatz, Theorie der informatorischen Kaskaden, Systemtheorie, Prinzipal-Agent-Theorie, Theorien zur Informationsverarbeitung, Nutzenquantifizierung, Auto-ID, Automatische Identifikation, EDI, Electronic Data Interchange, Event-Typisierung, SCEM-Funktionen, SCEM-Funktionalitäten, Geschäftsprozesse, Servicekatalog, Servicekandidat, Servicespezifikation, Standard, Schnittstelle, Überwachen, Melden, Steuern, Messen, Simulieren, FMEA, Fehlermöglichkeits- und Einflussanalyse, SCEM-FMEA, Ereignisorientierte Simulation, Konfiguration
SCEM, Supply chain event management, SOA, Service-oriented architecture, EPCIS, EPC information services, Fashion industry, Need, Business need, Architecture, System architecture, Benefit, SCEM system, Business services, Business-oriented services, Supply chain management, SCM, Logistics, Apparel industry, Textile industry, Logistics performance, Logistics costs, Simulation, Service science, Service design, Event, Critical exception, Deviation, Disruption, Disruptive event, Supply chain, Value chain, Case study, EPC, Electronic product code, Cloud computing, Cloud infrastructure, Cloud ERP, Service identification, Service description, Gerry Weber, van Laack, Gardeur, Seidensticker, ThyssenKrupp, Deutsche Post, DHL, fTRACE, GS1, GS1 Germany, René Lezard, März München, Control system, Management by exception, Supply chain risk management, Supply network event management, SNEM, Service repository, Service registry, Original brand manufacturer, OBM, SaaS, Software as a Service, RFID, Radio Frequency Identification, Complexity, Vulnerability to disruptions, Potential, SCEM solution, Value chain integrator, Transaction cost theory, Resource-based view, Information cascades, System theory, Principal-agent theory, Information processing, AIDC, Automatic identification and data capture, EDI, Electronic data interchange, Event classification, SCEM functions, SCEM functionalities, Business processes, Service catalogue, Service candidate, Service specification, Standard, Interface, Monitor, Notify, Simulate, Control, Measure, FMEA, Failure mode and effects analysis, SCEM FMEA, Discrete event simulation, Configuration
Tröger, Ralph
Alt, Rainer
Stölzle, Wolfgang
Universität Leipzig
2014-11-10
2014-05-31
2014-10-17
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A12991
https://ul.qucosa.de/api/qucosa%3A12991/attachment/ATT-0/
oai:qucosa:de:qucosa:13006
2021-03-29T08:39:17Z
qucosa:ubl
doc-type:Periodical
open_access
ddc:000
ddc:004
openaire
Leipziger Beiträge zur Informatik
urn:nbn:de:bsz:15-qucosa-155763
ger
qucosa:11904
qucosa:12897
qucosa:11642
qucosa:11634
qucosa:11305
qucosa:11349
qucosa:11825
qucosa:11381
qucosa:12682
qucosa:11670
qucosa:12683
qucosa:12213
qucosa:11333
In der Buchreihe "Leipziger Beiträge zur Informatik" erscheinen Berichte aus Forschungsvorhaben, Herausgeberbände im Bereich innovativer und sich etablierender Forschungsgebiete, Habilitationsschriften und Dissertationen sowie Konferenz-Proceedings und herausragende studentische Arbeiten. Der Wert dieser durch den „Leipziger Informatik Verbund“ (LIV) als Zusammenschluss und Interessenverbund verschiedener Informatik-Einrichtungen im Jahr 2003 begründeten Reihe liegt darin, zeitnah und umfassend über abgeschlossene oder laufende wissenschaftliche Arbeiten sowie über neu entstehende Forschungsfelder zu berichten. Die Reihe stellt die innovative Themenvielfalt in den Herausgeberbänden neben die hohe wissenschaftliche Durchdringung in Habilitationen und Dissertationen. Zudem ergänzt sie forschungsrelevante Bereiche mit praxisorientierten technischen Beiträgen und Dokumentationen.
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/004
ddc:004
Informatik, Angewandte Informatik, Wirtschaftsinformatik
computer science, applied computer science, business informatics
Fähnrich, Klaus-Peter
Universität Leipzig
2014-11-20
info:eu-repo/semantics/openAccess
doc-type:Periodical
info:eu-repo/semantics/Periodical
doc-type:Collection
https://ul.qucosa.de/id/qucosa%3A13006
oai:qucosa:de:qucosa:13122
2021-03-29T08:40:44Z
qucosa:ubl
doc-type:article
doc-type:Text
open_access
ddc:000
ddc:570
openaire
ExpaRNA-P : simultaneous exact pattern matching and folding of RNAs
urn:nbn:de:bsz:15-qucosa-159847
eng
Background: Identifying sequence-structure motifs common to two RNAs can speed up the comparison of structural RNAs substantially. The core algorithm of the existent approach ExpaRNA solves this problem for a priori known input structures. However, such structures are rarely known; moreover, predicting them computationally is no rescue, since single sequence structure prediction is highly unreliable. Results: The novel algorithm ExpaRNA-P computes exactly matching sequence-structure motifs in entire Boltzmann-distributed structure ensembles of two RNAs; thereby we match and fold RNAs simultaneously, analogous to the well-known “simultaneous alignment and folding” of RNAs. While this implies much higher flexibility compared to ExpaRNA, ExpaRNA-P has the same very low complexity (quadratic in time and space), which is enabled by its novel structure ensemble-based sparsification. Furthermore, we devise a generalized chaining algorithm to compute compatible subsets of ExpaRNA-P’s sequence-structure motifs. Resulting in the very fast RNA alignment approach ExpLoc-P, we utilize the best chain as anchor constraints for the sequence-structure alignment tool LocARNA. ExpLoc-P is benchmarked in several variants and versus state-of-the-art approaches. In particular, we formally introduce and evaluate strict and relaxed variants of the problem; the latter makes the approach sensitive to compensatory mutations. Across a benchmark set of typical non-coding RNAs, ExpLoc-P has similar accuracy to LocARNA but is four times faster (in both variants), while it achieves a speed-up over 30-fold for the longest benchmark sequences (≈400nt). Finally, different ExpLoc-P variants enable tailoring of the method to specific application scenarios. ExpaRNA-P and ExpLoc-P are distributed as part of the LocARNA package. The source code is freely available at http://www.bioinf.uni-freiburg.de/Software/ExpaRNA-P webcite. Conclusions: ExpaRNA-P’s novel ensemble-based sparsification reduces its complexity to quadratic time and space. Thereby, ExpaRNA-P significantly speeds up sequence-structure alignment while maintaining the alignment quality. Different ExpaRNA-P variants support a wide range of applications.
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/570
ddc:570
RNA, Bioinformatik, Struktur, RNA, Vergleich, Vereinfachung
RNA bioinformatics; Structure-based comparison of RNA
Otto, Christina
Möhl, Mathias
Heyne, Steffen
Amit, Mika
Landau, Gad M.
Backofen, Rolf
Will, Sebastian
Universität Freiburg
Universität Leipzig
Max-Planck-Institut für Immunbiologie und Epigenetik
University of Haifa
New York University-Poly
University of Copenhagen
BioMed Central
2014-01-22
2014
BMC Bioinformatics 2014, 15:404 doi:10.1186/s12859-014-0404-0
info:eu-repo/semantics/openAccess
doc-type:article
info:eu-repo/semantics/article
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A13122
https://ul.qucosa.de/api/qucosa%3A13122/attachment/ATT-0/
oai:qucosa:de:qucosa:13152
2021-03-29T08:41:06Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Subgraph Covers- An Information Theoretic Approach to Motif Analysis in Networks
urn:nbn:de:bsz:15-qucosa-160888
eng
A large number of complex systems can be modelled as networks of interacting units. From a mathematical point of view the topology of such systems can be represented as graphs of which the nodes represent individual elements of the system and the edges interactions or relations between them. In recent years networks have become a principal tool for analyzing complex systems in many different fields.
This thesis introduces an information theoretic approach for finding characteristic connectivity patterns of networks, also called network motifs. Network motifs are sometimes also referred to as basic building blocks of complex networks. Many real world networks contain a statistically surprising number of certain subgraph patterns called network motifs. In biological and technological networks motifs are thought to contribute to the overall function of the network by performing modular tasks such as information processing. Therefore, methods for identifying network motifs are of great scientific interest.
In the prevalent approach to motif analysis network motifs are defined to be subgraphs that occur significantly more often in a network when compared to a null model that preserves certain features of the network. However, defining appropriate null models and sampling these has proven to be challenging. This thesis introduces an alternative approach to motif analysis which looks at motifs as regularities of a network that can be exploited to obtain a more efficient representation of the network. The approach is based on finding a subgraph cover that represents the network using minimal total information. Here, a subgraph cover is a set of subgraphs such that every edge of the graph is contained in at least one subgraph in the cover while the total information of a subgraph cover is the information required to specify the connectivity patterns occurring in the cover together with their position in the graph.
The thesis also studies the connection between motif analysis and random graph models for networks. Developing random graph models that incorporate high densities of triangles and other motifs has long been a goal of network research. In recent years, two such model have been proposed . However, their applications have remained limited because of the lack of a method for fitting such models to networks. In this thesis, we address this problem by showing that these models can be formulated as ensembles of subgraph covers and that the total information optimal subgraph covers can be used to match networks with such models. Moreover, these models can be solved analytically for many of their properties allowing for more accurate modelling of networks in general.
Finally, the thesis also analyzes the problem of finding a total information optimal subgraph cover with respect to its computational complexity. The problem turns out to be NP-hard hence, we propose a greedy heuristic for it. Empirical results for several real world networks from different fields are presented. In order to test the presented algorithm we also consider some synthetic networks with predetermined motif structure.
info:eu-repo/classification/ddc/000
ddc:000
Netzwerkanalyse, Komplexe Netzwerke, Motivanalyse, Graph, Netzwerk, Informationstheorie
Network analysis, Complex networks, Motif analysis, Grpah, Network Information theory
Wegner, Anatol Eugen
Jost, Jürgen
Bornholdt, Stefan
Universität Leipzig
2015-02-16
2014-06-10
2015-04-02
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A13152
https://ul.qucosa.de/api/qucosa%3A13152/attachment/ATT-0/
oai:qucosa:de:qucosa:13192
2021-03-29T08:41:37Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Cooperation in self-organized heterogeneous swarms
urn:nbn:de:bsz:15-qucosa-161633
eng
Cooperation in self-organized heterogeneous swarms is a phenomenon from nature with many applications in autonomous robots. I specifically analyzed the problem of auto-regulated team formation in multi-agent systems and several strategies to learn socially how to make multi-objective decisions. To this end I proposed new multi-objective ranking relations and analyzed their properties theoretically and within multi-objective metaheuristics. The results showed that simple decision mechanism suffice to build effective teams of heterogeneous agents and that diversity in groups is not a problem but can increase the efficiency of multi-agent systems.
info:eu-repo/classification/ddc/000
ddc:000
Multi-agent systeme, multi-kriterielle Optimierung, k[ünstliche Intelligenz, Schwarmintelligenz
Multi-agent.systems, multi-objective optimization, artificial intelligence, swarm intelligence
Moritz, Ruby Louisa Viktoria
Middendorf, Martin
Mostaghim, Sanaz
Universität Leipzig
2015-03-23
2015-01-12
2015-02-26
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A13192
https://ul.qucosa.de/api/qucosa%3A13192/attachment/ATT-0/
oai:qucosa:de:qucosa:13263
2021-03-29T08:42:29Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
ddc:600
openaire
Softwareframework zur universellen Methodenentwicklung für ein fMRT- BCI: Adaptive Paradigmen und Echtzeitdatenanalyse: Softwareframework zur universellen Methodenentwicklung für ein fMRT- BCI: Adaptive Paradigmen und Echtzeitdatenanalyse
urn:nbn:de:bsz:15-qucosa-165443
ger
Die funktionelle Magnetresonanztomographie (fMRT) ist ein nicht-invasives Bildgebungsverfahren, mit dem Veränderungen der neuronalen Aktivität im Gehirn mit hoher räumlicher Auflösung erfasst werden können. Mit der fMRT-Bildgebung bei neurowissenschaftlichen Experimenten wurden in den letzten beiden Jahrzehnten bedeutende Erkenntnisse für die Hirnforschung und Medizin gewonnen. Mit Hilfe dieser Methode werden neuronale Aktivitätsunterschiede bei der Durchführung einer bestimmten Aufgabe, z. B. dem Betrachten von Bildern mit emotionalen Inhalten, erfasst und die Daten unabhängig von der Messung zu einem späteren Zeitpunkt statistisch ausgewertet. Mit Hilfe des technischen Fortschritts im letzten Jahrzehnt
ist es darüber hinaus möglich geworden, fMRT-Daten direkt zur Aufnahmezeit zu verarbeiten und auszuwerten. Dies wird als Echtzeit-fMRT bezeichnet, wenn die Datenverarbeitung schneller erfolgt als die Aufnahme eines Hirnvolumens (aktuell ca. zwei Sekunden). Die Ergebnisse der Echtzeitdatenverarbeitung können dann wiederum als Steuerbefehle für verschiedene Anwendungen verwendet werden. Daher wird dies auch als Hirn-Computer-Schnittstelle (Brain Computer Interface, BCI) mittels fMRT bezeichnet. Die Echtzeitverarbeitung von fMRT-Daten ermöglicht mehrere neue Anwendungen. Dazu gehören unter anderem die Qualitätskontrolle
zur Laufzeit von fMRT-Experimenten, die schnelle funktionelle Lokalisierung von Hirnarealen entweder für neurowissenschaftliche Experimente oder intraoperativ, die Kontrolle des Experimentes mittels des Probandenverhaltens und insbesondere die Möglichkeit, sogenannte fMRT-Neurofeedbackexperimente durchzuführen. Bei diesen Experimenten lernen Probanden, die Aktivität von definierten Hirnarealen willentlich zu beeinflussen. Das Ziel dabei ist, Veränderungen in ihrem Verhalten zu generieren. Die Umsetzung eines BCIs mittels Echtzeit-fMRT ist eine
interdisziplinäre Aufgabenstellung von MR-Physik, Informatik und Neurowissenschaften um das Verständnis des menschlichen Gehirns zu verbessern und neue Therapieansätze zu gestalten. Für diese hard- und softwaretechnisch anspruchsvolle Aufgabe gibt es einen enormen Bedarf an
neuen Algorithmen zur Datenverarbeitung und Ansätzen zur verbesserten Datenakquise.
In diesem Zusammenhang präsentiert die vorliegende Arbeit ein neues Softwareframework, das einerseits eine integrierte Gesamtlösung für die Echtzeit-fMRT darstellt und in seinen Teilmodulen eine abstrakte Basis für eine universelle Methodenentwicklung anbietet. Diese Arbeit beschreibt die grundlegenden abstrakten Konzepte und die Implementierung in ein neues Softwarepaket namens ’Brain Analysis in Real-Time’ (BART). Der Fokus der Arbeit liegt auf zwei Kernmodulen, die für universelle Gestaltung von sogenannten adaptiven Paradigmen und die Einbindung von Echtzeit-fMRT-Datenverarbeitungsalgorithmen konzipiert sind. Bei adaptiven Paradigmen werden zur Laufzeit eines Experiments physiologische Parameter (z. B. Herzrate) oder Verhaltensdaten (z. B. Augenbewegungen) simultan zu den fMRT-Daten erfasst und analysiert, um die Stimulation eines Probanden entsprechend zu adaptieren. Damit kann die Zuverlässigkeit der Daten, die zur Auswertung zur Verfügung stehen, optimiert werden. Die vorliegende
Arbeit präsentiert das dazu notwendige abstrakte Grundkonzept des neuen Softwareframeworks und die ersten konkreten Implementierungen für die Datenverarbeitung und adaptive Paradigmen. Das Framework kann zukünftig mit neuen methodischen Ideen erweitert werden. Dazu gehören
die Einbindung neuer Datenverarbeitungsalgorithmen, wie z. B. Konnektivitätsanalysen und die Adaption von Paradigmen durch weitere physiologische Parameter. Dabei ist insbesondere die Kombination mit EEG-Signalen von großem Interesse. Außerdem bietet das System eine universelle Grundlage für die zukünftige Arbeit an Neurofeedbackexperimenten. Das in dieser Arbeit entwickelte Framework bietet im Vergleich zu bisher vorgestellten Lösungsansätzen ein Ein-Computer-Setup mit einem erweiterbaren Methodenspektrum. Damit wird die Komplexität des notwendigen technischen Setups reduziert und ist nicht auf einzelne Anwendungsfälle beschränkt. Es können flexibel neue Datenverarbeitungsalgorithmen für ein fMRT-BCI eingebunden und vielgestaltige Anwendungsfälle von adaptiven Paradigmen konzipiert
werden. Eine Abstraktion der Stimulation und die Kombination mit der Echtzeitauswertung ist bisher einzigartig für neurowissenschaftliche Experimente.
Zusätzlich zu den theoretischen und technischen Erläuterungen werden im empirischen Teil der vorliegenden Arbeit neurowissenschaftliche Experimente, die mit dem Softwarepaket BART durchgeführt wurden, vorgestellt und deren Ergebnisse erläutert. Dabei wird die Zuverlässigkeit und Funktionsweise der Implementierung in allen Teilschritten der Datenerfassung und -verarbeitung validiert. Die Ergebnisse verifizieren die Implementierung einer parallelisierten fMRT-Analyse.Weiterhin wird eine erste konkrete Umsetzung für ein adaptives Paradigma vorgestellt, bei dem zur Laufzeit die Blickrichtung der Probanden berücksichtigt wird. Die Ergebnisse zeigen die signifikanten Verbesserungen der Reliabilität der fMRT-Ergebnisse aufgrund der optimierten Datenqualität durch die Adaption des Paradigmas.
Zusammengefasst umfasst die vorliegende Arbeit eine interdisziplinäre Aufgabe, die sich aus der Verarbeitung von MR-Daten in Echtzeit, einem neuen abstraktes Softwarekonzept für Entwicklung neuer methodischer Ansätze und der Durchführung von neurowissenschaftlichen Experimenten zusammensetzt.
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/600
ddc:600
Echtzeit-fMRT, Hirn-Computer-Schnittstelle, Neurofeedback, adaptive Paradigmen
real-time fMRI, Brain Computer Interface, adaptive paradigms, neurofeedback
Hellrung, Lydia
Villringer, Arno
Bogdan, Martin
Müller, Klaus-Robert
Mathematik und Informatik
2015-05-04
2014-06-30
2015-01-28
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A13263
https://ul.qucosa.de/api/qucosa%3A13263/attachment/ATT-0/
oai:qucosa:de:qucosa:13283
2021-03-29T08:42:44Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Ontological Semantics: An Attempt at Foundations of Ontology Representation
urn:nbn:de:bsz:15-qucosa-166326
eng
The original and still a major purpose of ontologies in computer and information sciences is to serve for the semantic integration of represented content, facilitating information system interoperability. Content can be data, information, and knowledge, and it can be distributed within or across these categories. A myriad of languages is available for representation. Ontologies themselves are artifacts which are expressed in various languages. Different such languages are utilized today, including, as well-known representatives, predicate logic, subsuming first-order (predicate) logic (FOL), in particular, and higher-order (predicate) logic (HOL); the Web Ontology Language (OWL) on the basis of description logics (DL); and the Unified Modeling Language (UML). We focus primarily on languages with formally defined syntax and semantics.
This overall picture immediately suggests questions of the following kinds: What is the relationship between an ontology and the language in which it is formalized? Especially, what is the impact of the formal semantics of the language on the formalized ontology? How well understood is the role of ontologies in semantic integration? Can the same ontology be represented in multiple languages and/or in distinct ways within one language? Is there an adequate understanding of whether two expressions are intensionally/conceptually equivalent and whether two ontologies furnish the same ontological commitments?
One may assume that these questions are resolved. Indeed, the development and adoption of ontologies is widespread today. Ontologies are authored in a broad range of different languages, including offering equally named ontologies in distinct languages. Much research is devoted to techniques and technologies that orbit ontologies, for example, ontology matching, modularization, learning, and evolution, to name a few. Ontologies have found numerous beneficial applications, and hundreds of ontologies have been created, considering solely the context of biomedical research. For us, these observations increase the relevance of the stated questions and close relatives thereof, and raise the desire for solid theoretical underpinnings. In the literature of computer and information sciences, we have found only few approaches that tackle the foundations of ontologies and their representation to allow for answering such questions or that actually answer them.
We elaborate an analysis of the subject as the first item of central contributions within this thesis. It mainly results in the identification of a vicious circularity in (i) the intended use of ontologies to mediate between formal representations and (ii) solely exploiting formal semantic notions in representing ontologies and defining ontology-based equivalence as a form of intensional/conceptual equivalence. On this basis and in order to overcome its identified limitations, we contribute a general model-theoretic semantic account, named \\\"ontological semantics\\\". This kind of semantics takes the approach of assigning arbitrary entities as referents of atomic symbols and to link syntactic constructions with corresponding ontological claims and commitments. In particular, ontological semantics targets the avoidance of encoding effects in its definition. Therefore we argue that this semantic account is well suited for interpreting formalized ontologies and for defining languages for the representation of ontologies. It is further proposed as a fundament for envisioned novel definitions of the intensional equivalence of expressions, in potential deviation from only being formally equivalent under set-theoretic semantics. The thesis is defended that a particular usage of a formalism and its respective vocabulary should be accompanied by establishing an ontological semantics that is tailored to that use of the formalism, in parallel to the formal semantics of the language, in order to capture the ontological content of the formal representation for adequate reuse in other formalisms. Accordingly, we advocate ontological semantics as a useful framework for justifying translations on an intensional basis. Despite all deviations of ontological semantics from its set-theoretic blueprint, close relationships between the two can be shown, which allow for using established FOL and DL reasoners while assuming ontological semantics.:* Preface
** Abstract
** Contents
** Acknowledgments
** Foreword
1 Introduction
1.1 Background
1.2 Motivations
1.3 Theses, Objectives and Scope
1.4 Outline and Contributions
1.5 Formal Preliminaries
2 Foundations on Languages, Semantics, and Ontology
2.1 Formal Syntax and Formal Semantics
2.2 The Role of Ontologies in Semantic Integration
2.3 Ontological Analysis and Meta-Ontological Architecture
2.4 Conceptualization of Categories and Relations - CR
2.5 Summary of the Analysis and Next Steps
3 Views on Set-Theoretic Semantics of Classical Predicate Logics
3.1 Tarskian Model Theory and Set-Theoretic Superstructure
3.2 Formal Semantics and Choices for Entity Postulation
3.3 Theory View of Semantics
3.4 Aims for an Ontologically Neutral Semantic Account
4 Ontological Semantics
4.1 Definition of Ontological Structures by Analogy to the Set-Theoretic Approach
4.2 Properties and Further Background for Ontological Structures in General
4.3 Ontological Models & Signature Aspects
4.4 Semantics of Predication
4.5 Semantics of Connectives and Quantifiers & Semantic Notions
4.6 Relations between Ontological and Set-Theoretic Semantics
4.7 Ontological Neutrality
5 Ontological Engineering and Applications
5.1 Formalization Method for Ontology Representation in FOL
5.2 Ontological Usage Schemes
5.3 Glimpse on Characterizing Modular Representation
5.4 Applications in the Biomedical Domain
6 Contributions to Ontologies
6.1 Formalizations of Categories and Relations - CR
6.2 Remarks on Further Contributions
6.3 Ontologies of Time
7 Conclusion and Continuation
7.1 Resume
7.2 Related Work
7.3 Conclusions
7.4 Beginnings of Future Work
Appendix
A Additional Preliminaries
A.1 Logical Notions
A.2 Axiomatic Systems of Set and Number Theory
B Axioms of the CR Taxonomy in OWL
B.1 Asserted OWL Class Axioms
B.2 Asserted OWL Object Property Axioms
C Lists of Figures and Tables
C.1 List of Figures
C.2 List of Tables
D Abbreviations, Acronyms and Names
D.1 Abbreviations
D.2 Acronyms and Names
E References
E.1 Literature References
E.2 Web References/List of URLs
F Work and Author Information
** Selbständigkeitserklärung (Declaration of Authorship)
** Bibliographic Data
** Scientific Record
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/160
ddc:160
Ontologie; Formale Ontologie; Semantik; Formale Semantik; Logik; Prädikatenlogik
Ontologie, Formale Ontologie, Angewandte Ontologie, Ontologierepräsentation, Logik, Prädikatenlogik, Semantik, Ontologische Semantik, Top-Level Ontologie, Formale Ontologie der Zeit, Bio-Ontologie
ontology, formal ontology, applied ontology, ontology representation, logic, predicate logic, semantics, ontological semantics, top-level ontology, formal ontology of time, bio-ontology
Loebe, Frank
Herre, Heinrich
Grüninger, Michael
Universität Leipzig
2015-05-06
2015-02-09
2015-03-26
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A13283
https://ul.qucosa.de/api/qucosa%3A13283/attachment/ATT-0/
oai:qucosa:de:qucosa:13413
2021-03-29T08:44:19Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
openaire
Tätigkeitsbericht / Universitätsbibliothek Leipzig
urn:nbn:de:bsz:15-qucosa-175465
ger
urn:nbn:de:bsz:15-qucosa-148591
qucosa:12744
Das Jahr 2014 war ein Jahr der Weichenstellungen: Bauten wurden geplant und begonnen (s. I), ein neues Serviceportfolio in Sachen Katalog inauguriert (s. II), sowie Open Access an der Universität etabliert (s. III). Drittmittelstark ist die Universitätsbibliothek Leipzig mit über 40 Projektvorhaben, davon allein knapp 30 in den Bereichen Erschließung und Erforschung (s. V). Mit jedem Fortschritt öffnen sich neue Horizonte: Wo ein Erschließungsprojekt endet, knüpft ein Forschungsprojekt an. Wo ein Bauvorhaben geplant oder realisiert wird, wird die Ausstattung zur Herausforderung. Die Universitätsbibliothek arbeitet in allen Bereichen und Abteilungen daran, sich planmäßig und zielstrebig als ein zentraler Dienstleister der Universität und als Forschungsbibliothek zu profilieren. Der hier vorgelegte Tätigkeitsbericht dokumentiert Leistungen auf diesem Weg.
info:eu-repo/classification/ddc/000
ddc:000
Bibliothek, Universitätsbibliothek, Leipzig, Jahresbericht
library, university library, Leipzig, annual report
Universität Leipzig
2015-07-24
2015
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A13413
https://ul.qucosa.de/api/qucosa%3A13413/attachment/ATT-0/
oai:qucosa:de:qucosa:13485
2021-03-29T08:45:15Z
qucosa:ubl
doc-type:bachelorThesis
doc-type:Text
open_access
ddc:000
ddc:330
openaire
Generative und modellgetriebene Softwarevisualisierung am Beispiel der Stadtmetapher
urn:nbn:de:bsz:15-qucosa-178702
ger
Für den Visualisierungsgenerator der Forschungsgruppe „Softwarevisualisierung in drei Dimensionen und virtueller Realität“ soll eine Stadtmetapher zur Darstellung von Software implementiert werden. Als Vorlage dient „CodeCity“, dessen Umsetzung der Stadtmetapher auf den Generator übertragen werden soll. Die Anforderungsermittlung basiert auf der Analyse beider Bestandteile, um ein strukturiertes Vorgehen zu gewährleisten. Die Implementierung der Generatorartefakte erfolgt mittels Xtext zur Erstellung eines Metamodells, das die Entitäten der neuen Metapher beschreibt, und Xtend, das genutzt wird um die Datenmodelle zu modifizieren und in Quelltext umzuwandeln. Darauf aufbauend folgt abschließend die Abstraktion zu einem Prozessmodell für die generative und modellgetriebene Softwarevisualisierung, das als Leitfaden für zukünftige Implementierungen dienen soll.:Gliederung
Abbildungsverzeichnis
Tabellenverzeichnis
Verzeichnis der Listings
Abkürzungsverzeichnis
1 Einleitung
1.1 Motivation und Problemstellung
1.2 Zielstellung der Arbeit
1.3 Aufbau der Arbeit
2 Grundlagen des Visualisierungsgenerator
2.1 Generative und modellgetriebene Softwareentwicklung
2.2 FAMIX
2.3 Xtext und Xtend
2.4 X3D
3 Implementierung des Prototyps
3.1 Analyse der Zielmetapher
3.1.1 Grundlagen von „CodeCity“
3.1.2 Anforderungen
3.1.3 Analyseergebnisse
3.2 Auswahl und Analyse der Referenzmetapher
3.2.1 Grundlagen der Referenzmetapher
3.2.2 Erweiterung der Anforderungen
3.3 Das Metamodell
3.4 Der Workflow
3.5 Modell-zu-Modell-Transformation
3.6 Modellmodifikation
3.7 Modell-zu-Text-Transformation
3.8 Anpassungen und Ergänzungen
4 Abstrahiertes Prozessmodell
5 Zusammenfassung und Ausblick
Anhang A – Metamodell Recursive Disk-Metapher
Anhang B – Hilfestellung für Eclipse-Konfigurationen
Anhang C – Konzepte zur Durchführung der Modellmodifikation
Anhang D – Entwicklungsstadien der Stadtmetapher
Quellen- und Literaturverzeichnis
Ehrenwörtliche Erklärung
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/330
ddc:330
Prozessmodell ; Modellgetriebene Entwicklung ; Softwareentwicklung
Stadtmetapher, generative und modellgetriebene Softwareentwicklung, „CodeCity“, Prozessmodell
city metaphor, generative and model-driven software development, \\\"Code City\\\", process model
Zilch, Denise
Müller, Richard
Universität Leipzig
2015-09-17
2015-02-03
2015-02-03
info:eu-repo/semantics/openAccess
doc-type:bachelorThesis
info:eu-repo/semantics/bachelorThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A13485
https://ul.qucosa.de/api/qucosa%3A13485/attachment/ATT-0/
oai:qucosa:de:qucosa:13790
2021-03-29T08:49:04Z
qucosa:ubl
doc-type:article
doc-type:Text
open_access
ddc:000
ddc:570
openaire
Processed small RNAs in Archaea and BHB elements
urn:nbn:de:bsz:15-qucosa-185322
eng
Bulge-helix-bulge (BHB) elements guide the enzymatic splicing machinery that in Archaea excises introns from tRNAs, rRNAs from their primary precursor, and accounts for the assembly of piece-wise encoded tRNAs. This processing pathway renders the intronic sequences as circularized RNA species. Although archaeal transcriptomes harbor a large number of circular small RNAs, it remains unknown whether most or all of them are produced through BHB-dependent splicing. We therefore conduct a genome-wide survey of BHB elements of a phylogenetically diverse set of archaeal species and complement this approach by searching for BHB-like structures in the vicinity of circularized transcripts. We find that besides tRNA introns, the majority of box C/D snoRNAs is associated with BHB elements. Not all circularized sRNAs, however, can be explained by BHB elements, suggesting that there is at least one other mechanism of RNA circularization at work in Archaea. Pattern search methods were unable, however, to identify common sequence and/or secondary structure features that could be characteristic for such a mechanism.
info:eu-repo/classification/ddc/570
ddc:570
info:eu-repo/classification/ddc/000
ddc:000
ringförmig geschlossene RNA-Moleküle, Archaea, Spleißen, struktur-basiert
Circular RNA; Archaea; splicing; structure-based
Berkemer, Sarah J.
Höner zu Siederdissen, Christian
Amman, Fabian
Wintsche, Axel
Will, Sebastian
Hofacker, Ivo L.
Prohaska, Sonja J.
Stadler, Peter F.
Universität Leipzig
Universität Wien
University of Copenhagen
Max-Planck-Institut für Mathematik
Fraunhofer-Institut für Zelltherapie und Immunologie IZI
Santa Fe Institute
Kernel Press UG
2015-10-27
2015
Genomics and computational biology Vol. 1, No. 1 (2015): e18
info:eu-repo/semantics/openAccess
doc-type:article
info:eu-repo/semantics/article
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A13790
https://ul.qucosa.de/api/qucosa%3A13790/attachment/ATT-0/
oai:qucosa:de:qucosa:13820
2021-03-29T08:49:26Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Close and Distant Reading Visualizations for the Comparative Analysis of Digital Humanities Data
urn:nbn:de:bsz:15-qucosa-207418
eng
Traditionally, humanities scholars carrying out research on a specific or on multiple literary work(s) are interested in the analysis of related texts or text passages. But the digital age has opened possibilities for scholars to enhance their traditional workflows. Enabled by digitization projects, humanities scholars can nowadays reach a large number of digitized texts through web portals such as Google Books or Internet Archive. Digital editions exist also for ancient texts; notable examples are PHI Latin Texts and the Perseus Digital Library.
This shift from reading a single book “on paper” to the possibility of browsing many digital texts is one of the origins and principal pillars of the digital humanities domain, which helps developing solutions to handle vast amounts of cultural heritage data – text being the main data type. In contrast to the traditional methods, the digital humanities allow to pose new research questions on cultural heritage datasets. Some of these questions can be answered with existent algorithms and tools provided by the computer science domain, but for other humanities questions scholars need to formulate new methods in collaboration with computer scientists.
Developed in the late 1980s, the digital humanities primarily focused on designing standards to represent cultural heritage data such as the Text Encoding Initiative (TEI) for texts, and to aggregate, digitize and deliver data. In the last years, visualization techniques have gained more and more importance when it comes to analyzing data. For example, Saito introduced her 2010 digital humanities conference paper with: “In recent years, people have tended to be overwhelmed by a vast amount of information in various contexts. Therefore, arguments about ’Information Visualization’ as a method to make information easy to comprehend are more than understandable.” A major impulse for this trend was given by Franco Moretti. In 2005, he published the book “Graphs, Maps, Trees”, in which he proposes so-called distant reading approaches for textual data that steer the traditional way of approaching literature towards a completely new direction. Instead of reading texts in the traditional way – so-called close reading –, he invites to count, to graph and to map them. In other words, to visualize them.
This dissertation presents novel close and distant reading visualization techniques for hitherto unsolved problems. Appropriate visualization techniques have been applied to support basic tasks, e.g., visualizing geospatial metadata to analyze the geographical distribution of cultural heritage data items or using tag clouds to illustrate textual statistics of a historical corpus. In contrast, this dissertation focuses on developing information visualization and visual analytics methods that support investigating research questions that require the comparative analysis of various digital humanities datasets. We first take a look at the state-of-the-art of existing close and distant reading visualizations that have been developed to support humanities scholars working with literary texts. We thereby provide a taxonomy of visualization methods applied to show various aspects of the underlying digital humanities data. We point out open challenges and we present our visualizations designed to support humanities scholars in comparatively analyzing historical datasets. In short, we present (1) GeoTemCo for the comparative visualization of geospatial-temporal data, (2) the two tag cloud designs TagPies and TagSpheres that comparatively visualize faceted textual summaries, (3) TextReuseGrid and TextReuseBrowser to explore re-used text passages among the texts of a corpus, (4) TRAViz for the visualization of textual variation between multiple text editions, and (5) the visual analytics system MusikerProfiling to detect similar musicians to a given musician of interest. Finally, we summarize our and the collaboration experiences of other visualization researchers to emphasize the ingredients required for a successful project in the digital humanities, and we take a look at future challenges in that research field.
info:eu-repo/classification/ddc/000
ddc:000
Close Reading, Distant Reading, Visualisierung, Digitale Geisteswissenschaften, Visual Analytics, Textvisualisierung
Close Reading, Distant Reading, Visualization, Digital Humanities, Visual Analytics, Textvisualization
Jänicke, Stefan
Scheuermann, Gerik
Hagen, Hans
Universität Leipzig
2016-07-19
2016-02-11
2016-07-06
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A13820
https://ul.qucosa.de/api/qucosa%3A13820/attachment/ATT-0/
oai:qucosa:de:qucosa:14663
2021-03-29T09:00:33Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Inter-InnoLab Collaboration: Conceptualization, Assessment, and Technological Supportive Artifact of the Interconnection among Innovation Laboratories
urn:nbn:de:bsz:15-qucosa-225342
eng
Over the recent years, the paradigm of Innovation Laboratories (abr. InnoLabs) is gaining an increasing attention among business organizations as a potential source of assistance in the process of the development of new or the improvement of their existing products and/or services. Business organizations approach the InnoLabs in the search for assistance in dealing with the challenges of the often times complex and uncertain innovation process, and ultimately become successful in their innovation projects. Although the overall goal of the existing InnoLabs is to support the systematic, effective, and efficient innovation development, they target different innovation challenges and thereby vary in their focus and service offerings. As a consequence, all the innovation support that might be needed in the course of an innovation process remains dispersed among different InnoLabs. In this esteem, this thesis aims to centralize all the mediated support offered by the existing InnoLabs by bringing them into a collaborative network. In pursuance of this, initially, the diversity among the existing InnoLabs in terms of their structural and functional manifestations is explored by employing a triangulation of online survey and in-depth expert interviews with the InnoLab facilitators. Subsequently, based on the diversity observed herein, the incentives, approaches, and possibilities of interconnection among InnoLabs are determined.
Having conceptualized the framework for inter-InnoLab collaboration, the next part of this thesis deals with facilitating such collaborations in an online space. The internet, since its inception, has drastically altered the practices of intra- and inter-organizational connectivity. Recently, one could observe a growing interest among all types of organizations towards the social networking sites (abr. SNSs) as an effective medium for reaching out to a global audience. As a result, a significant amount of business related information is already available and continuously accumulating on SNSs. However, the SNSs fall inadequate in supporting the inter-InnoLab collaboration because of the missing dedicated functionalities, isolated platform boundaries, platform dependencies, lack of support for domain-specific features, privacy concerns, and issues of data transparency. In response to this, this thesis advocates the designing of dedicated inter-organizational collaboration platforms with seamless integration of SNS data. Successively, employing a design science research approach, a dedicated, domain specific, and SNS integrated web-based collaboration platform (the InnoLab_Net) is designed for supporting inter-InnoLab collaborative activities.
info:eu-repo/classification/ddc/000
ddc:000
Innovationslabor, Vernetzung der Innovationslabore, Web-basierte interorganisationale Kooperationsplattformen, Online Kollaborationswerkzeuge, Integration Sozialer Netzwerke
Innovation Laboratory, Innovation Laboratories interconnection, Web-based inter-organizational collaboration platforms, Online collaboration tools, Integration of Social Networking Sites
Memon, Atia Bano
Fähnrich, Klaus-Peter
Franczyk, Bogdan
University of Leipzig
2017-05-29
2016-01-11
2017-12-05
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A14663
https://ul.qucosa.de/api/qucosa%3A14663/attachment/ATT-0/
oai:qucosa:de:qucosa:14753
2021-03-29T09:01:44Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Adding Threshold Concepts to the Description Logic EL
urn:nbn:de:bsz:15-qucosa-204523
eng
We introduce a family of logics extending the lightweight Description Logic EL, that allows us to define concepts in an approximate way. The main idea is to use a graded membership function m, which for each individual and concept yields a number in the interval [0,1] expressing the degree to which the individual belongs to the concept. Threshold concepts C~t for ~ in {<,<=,>,>=} then collect all the individuals that belong to C with degree ~t. We further study this framework in two particular directions. First, we define a specific graded membership function deg and investigate the complexity of reasoning in the resulting Description Logic tEL(deg) w.r.t. both the empty terminology and acyclic TBoxes. Second, we show how to turn concept similarity measures into membership degree functions. It turns out that under certain conditions such functions are well-defined, and therefore induce a wide range of threshold logics. Last, we present preliminary results on the computational complexity landscape of reasoning in such a big family of threshold logics.
info:eu-repo/classification/ddc/000
ddc:000
Description Logics, approximate reasoning, computational complexity
Fernández Gil, Oliver
Baader, Franz
Brewka, Gerhard
Wolter, Frank
Universität Leipzig
2016-06-14
2016-01-29
2016-05-18
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A14753
https://ul.qucosa.de/api/qucosa%3A14753/attachment/ATT-0/
oai:qucosa:de:qucosa:14754
2021-03-29T09:01:45Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Probabilistic models of natural language semantics
urn:nbn:de:bsz:15-qucosa-204503
eng
This thesis tackles the problem of modeling the semantics of natural language. Neural Network models are reviewed and a new Bayesian approach is developed and evaluated. As the performance of standard Monte Carlo algorithms proofed to be unsatisfactory for the developed models, the main focus lies on a new adaptive algorithm from the Sequential Monte Carlo (SMC) family. The Gradient Importance Sampling (GRIS) algorithm developed in the thesis is shown to give very good performance as compared to many adaptive Markov Chain Monte Carlo (MCMC) algorithms on a range of complex target distributions. Another advantage as compared to MCMC is that GRIS provides a straight forward estimate of model evidence. Finally, Sample Inflation is introduced as a means to reduce variance and speed up mode finding in Importance Sampling and SMC algorithms. Sample Inflation provides provably consistent estimates and is empirically found to improve convergence of integral estimates.
Diese Dissertation befasst sich mit der Modellierung der Semantik natürlicher Sprache. Eine Übersicht von Neuronalen Netzwerkmodellen wird gegeben und ein eigener Bayesscher Ansatz wird entwickelt und evaluiert. Da die Leistungsfähigkeit von Standardalgorithmen aus der Monte-Carlo-Familie auf dem entwickelten Model unbefriedigend ist, liegt der Hauptfokus der Arbeit auf neuen adaptiven Algorithmen im Rahmen von Sequential Monte Carlo (SMC). Es wird gezeigt, dass der in der Dissertation entwickelte Gradient Importance Sampling (GRIS) Algorithmus sehr leistungsfähig ist im Vergleich zu vielen Algorithmen des adaptiven Markov Chain Monte Carlo (MCMC), wobei komplexe und hochdimensionale Integrationsprobleme herangezogen werden. Ein weiterer Vorteil im Vergleich mit MCMC ist, dass GRIS einen Schätzer der Modelevidenz liefert. Schließlich wird Sample Inflation eingeführt als Ansatz zur Reduktion von Varianz und schnellerem auffinden von Modi in einer Verteilung, wenn Importance Sampling oder SMC verwendet werden. Sample Inflation ist beweisbar konsistent und es wird empirisch gezeigt, dass seine Anwendung die Konvergenz von Integralschätzern verbessert.
info:eu-repo/classification/ddc/000
ddc:000
natürliche Sprache, semantik,Monte Carlo
natural language, semantics,Monte Carlo
Schuster, Ingmar
Heyer, Gerhard
Robert, Christian
Universität Leipzig
2016-06-14
2015-11-06
2016-06-01
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A14754
https://ul.qucosa.de/api/qucosa%3A14754/attachment/ATT-0/
https://ul.qucosa.de/api/qucosa%3A14754/attachment/ATT-1/
oai:qucosa:de:qucosa:14782
2021-03-29T09:02:07Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
openaire
Tätigkeitsbericht / Universitätsbibliothek Leipzig
urn:nbn:de:bsz:15-qucosa-205457
ger
urn:nbn:de:bsz:15-qucosa-148591
qucosa:12744
Im Jahr 2015 konnten lange währende Baumaßnahmen in der Bibliotheca Albertina abgeschlossen werden – das versetzt die UB Leipzig in einen glücklichen Zustand. Ebenfalls seit 2015 gibt es eine feste Perspektive für die Neubauten der künftigen Fachbibliotheken Medizin/Naturwissenschaften in der Liebigstraße und den Bildungscampus in der Jahnallee – das macht uns hoffnungsfroh, den Service auch
in diesen Bereichen grundlegend verbessern zu können. Wir nutzen die Gelegenheit dieses Tätigkeitsberichts und danken dem Rektorat für dauerhafte Unterstützung bei all diesen Vorhaben, dem Baudezernat der Universität ebenso wie dem Staatsbetrieb Sächsisches Immobilien- und Baumanagement – Leipzig II und nicht zuletzt den
für die Gestaltung verantwortlichen Architekturbüros (Architekturbüro Weis&Volkmann in der Bibliotheca Albertina, Architekturbüro agn für den Bildungscampus und h.e.i.z.Haus für die Medizin/Naturwissenschaften). Im Jahr 2015 hat die Universitätsbibliothek eine Reihe weiterer Neuerungen einführen oder umsetzen können, worüber wir in diesem Bericht gern Auskunft geben.
Bibliothek, Universitätsbibliothek, Leipzig, Jahresbericht
library, university library, Leipzig, annual report
info:eu-repo/classification/ddc/000
ddc:000
Universität Leipzig
2016
2016-06-21
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A14782
https://ul.qucosa.de/api/qucosa%3A14782/attachment/ATT-0/
oai:qucosa:de:qucosa:14873
2021-03-29T09:03:09Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Efficient Source Selection For SPARQL Endpoint Query Federation
urn:nbn:de:bsz:15-qucosa-207662
eng
The Web of Data has grown enormously over the last years. Currently, it comprises a large compendium of linked and distributed datasets from multiple domains. Due to the decentralised architecture of the Web of Data, several of these datasets contain complementary data. Running complex queries on this compendium thus often requires accessing data from different data sources within one query. The abundance of datasets and the need for running complex query has thus motivated a considerable body of work on SPARQL query federation systems, the dedicated means to access data distributed over the Web of Data.
This thesis addresses two key areas of federated SPARQL query processing: (1) efficient source selection, and (2) comprehensive SPARQL benchmarks to test and ranked federated SPARQL engines as well as triple stores.
Efficient Source Selection: Efficient source selection is one of the most important optimization steps in federated SPARQL query processing. An overestimation of query relevant data sources increases the network traffic, result in irrelevant intermediate results, and can significantly affect the overall query processing time. Previous works have focused on generating optimized query execution plans for fast result retrieval. However, devising source selection approaches beyond triple pattern-wise source selection has not received much attention. Similarly, only little attention has been paid to the effect of duplicated data on federated querying. This thesis presents HiBISCuS and TBSS, novel hypergraph-based source selection approaches, and DAW, a duplicate-aware source selection approach to federated querying over the Web of Data. Each of these approaches can be combined directly with existing SPARQL query federation engines to achieve the same recall while querying fewer data sources. We combined the three (HiBISCuS, DAW, and TBSS) source selections approaches with query rewriting to form a complete SPARQL query federation engine named Quetsal. Furthermore, we present TopFed, a Cancer Genome Atlas (TCGA) tailored federated query processing engine that exploits the data distribution to perform intelligent source selection while querying over large TCGA SPARQL endpoints. Finally, we address the issue of rights managements and privacy while accessing sensitive resources. To this end, we present SAFE: a global source selection approach that enables decentralised, policy-aware access to sensitive clinical information represented as distributed RDF Data Cubes.
Comprehensive SPARQL Benchmarks: Benchmarking is indispensable when aiming to assess technologies with respect to their suitability for given tasks. While several benchmarks and benchmark generation frameworks have been developed to evaluate federated SPARQL engines and triple stores, they mostly provide a one-fits-all solution to the benchmarking problem. This approach to benchmarking is however unsuitable to evaluate the performance of a triple store for a given application with particular requirements. The fitness of current SPARQL query federation approaches for real applications is difficult to evaluate with current benchmarks as current benchmarks are either synthetic or too small in size and complexity. Furthermore, state-of-the-art federated SPARQL benchmarks mostly focused on a single performance criterion, i.e., the overall query runtime. Thus, they cannot provide a fine-grained evaluation of the systems. We address these drawbacks by presenting FEASIBLE, an automatic approach for the generation of benchmarks out of the query history of applications, i.e., query logs and LargeRDFBench, a billion-triple benchmark for SPARQL query federation which encompasses real data as well as real queries pertaining to real bio-medical use cases.
Our evaluation results show that HiBISCuS, TBSS, TopFed, DAW, and SAFE all can significantly reduce the total number of sources selected and thus improve the overall query performance. In particular, TBSS is the first source selection approach to remain under 5% overall relevant sources overestimation. Quetsal has reduced the number of sources selected (without losing recall), the source selection time as well as the overall query runtime as compared to state-of-the-art federation engines. The LargeRDFBench evaluation results suggests that the performance of current SPARQL query federation systems on simple queries does not reflect the systems\\\'' performance on more complex queries. Moreover, current federation systems seem unable to deal with many of the challenges that await them in the age of Big Data. Finally, the FEASIBLE\\\''s evaluation results shows that it generates better sample queries than the state-of-the-art. In addition, the better query selection and the larger set of query types used lead to triple store rankings which partly differ from the rankings generated by previous works.
info:eu-repo/classification/ddc/000
ddc:000
SPARQL, RDF, Federation, Benchmarks
SPARQL, RDF, Federation, Benchmarks
Saleem, Muhammad
Fähnrich, Klaus-Peter
Molli, Pascal
Universität Leipzig
2016-10-28
2015-10-27
2016-05-13
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A14873
https://ul.qucosa.de/api/qucosa%3A14873/attachment/ATT-0/
oai:qucosa:de:qucosa:14951
2021-03-29T09:04:12Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
The Systematic Design and Application of Robust DNA Barcodes
urn:nbn:de:bsz:15-qucosa-209812
eng
High-throughput sequencing technologies are improving in quality, capacity, and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag, index, or barcode that is attached to the sequencing or amplification primer and hence accompanies every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.
Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and codes based on the Levenshtein distance.
Levenshtein-based codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this thesis we demonstrate the decreased error correction capability of Levenshtein-based codes in a DNA context and suggest an adaptation of Levenshtein-based codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaptation, we take any DNA context into account and impose more strict rules for the selection of barcode sets. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors.
We present an adaptation of Levenshtein-based codes to DNA contexts capable of guaranteed correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of correcting on average more random mutations than traditional Levenshtein-based or Hamming codes. As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance.
However, not every platform is susceptible to a large number of both indel and substitution errors. The Illumina “Sequencing by Synthesis” platform shows a very large number of substitution errors as well as a very specific shift of the read that results in inserted and deleted bases at the 5’-end and the 3’-end (which we call phaseshifts). We argue in this scenario that the application of Sequence-Levenshtein-based codes is not efficient because it aims for a category of errors that barely occurs on this platform, which reduces the code size needlessly. As a solution, we propose the “Phaseshift distance” that exclusively supports the correction of substitutions and phaseshifts. Additionally, we enable the correction of arbitrary combinations of substitution and phaseshift errors. Thus, we address the lopsided number of substitutions compared to phaseshifts on the Illumina platform.
To compare codes based on the Phaseshift distance to Hamming Codes as well as codes based on the Sequence-Levenshtein distance, we simulated an experimental scenario based on the error pattern we identified on the Illumina platform. Furthermore, we generated a large number of different sets of DNA barcodes using the Phaseshift distance and compared codes of different lengths and error correction capabilities. We found that codes based on the Phaseshift distance can correct a number of errors comparable to codes based on the Sequence-Levenshtein distance while offering the number of DNA barcodes comparable to Hamming codes. Thus, codes based on the Phaseshift distance show a higher efficiency in the targeted scenario. In some cases (e.g., with PacBio SMRT in Continuous Long Read mode), the position of the barcode and DNA context is not well defined. Many reads start inside the genomic insert so that adjacent primers might be missed. The matter is further complicated by coincidental similarities between barcode sequences and reference DNA. Therefore, a robust strategy is required in order to detect barcoded reads and avoid a large number of false positives or negatives.
For mass inference problems such as this one, false discovery rate (FDR) methods are powerful and balanced solutions. Since existing FDR methods cannot be applied to this particular problem, we present an adapted FDR method that is suitable for the detection of barcoded reads as well as suggest possible improvements.
info:eu-repo/classification/ddc/000
ddc:000
DNA Barcodes, sample tags, SMRT, single molecule real time sequencing, Fehlerkorrektur, false discovery rate, next generation sequencing, Hochdurchsatzsequenzierung, deep sequencing, multiplexing, clonal analysis
DNA Barcodes, sample tags, SMRT, single molecule real time sequencing, error correction, false discovery rate, next generation sequencing, high throughput sequencing, deep sequencing, multiplexing, clonal analysis
Buschmann, Tilo
Bystrykh, Leonid V.
Große, Ivo
Stadler, Peter
Universität Leipzig
2016-09-19
2015-10-15
2016-09-02
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A14951
https://ul.qucosa.de/api/qucosa%3A14951/attachment/ATT-0/
oai:qucosa:de:qucosa:14996
2021-03-29T09:04:47Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Gene regulatory factors in the evolutionary history of humans: Gene Regulatory Factors, key genes in the evolutionary history of modern humans: Positive selection on GRF genes as source for regulatory diversity in human populations: Human lineage‐specific transcriptional regulation through GA binding protein transcription factor alpha (GABPa)
urn:nbn:de:bsz:15-qucosa-211743
eng
Changes in cis- and trans-regulatory elements are among the prime sources of genetic and phenotypical variation at species level. The introduction of cis- and trans- regulatory variation has played important roles in driving diversity, phenotypical differentiation, and evolution of humans. Therefore, variation that occurs on cis- and trans- regulatory elements becomes imperative to better understanding of human genetic diversity and its evolution.
In this research, around 3360 gene regulatory factors (GRF) from the human genome were catalogued. This catalog includes genes that code for proteins that perform gene regulatory activities such DNA-depending transcription, RNA polymerase II transcription cofactor and co-repressor activity, chromatin binding and remodeling, among other 218 regulatory functions. This GRF catalog allowed us to initially explore how some GRF genes have evolved in humans, archaic humans (Neandertal and Denisovan) and non-human primate species. We discussed the likely phenotypical and medical effects that evolutionary changes in GRF genes may have introduced into the human genome; for instance, traits associated to speech and language capabilities, genomic recombination hotspots, diseases, among others.
By using genome-wide datasets, we additionally looked for GRFs likely to be candidates for positive selection in three human populations: Utah Residents with Northern and Western Ancestry (CEU), Han Chinese in Beijing (CHB), and Yoruba in Ibadan (YRI). As result, we produced a set of candidates that gathers genes that may have contributed in shaping the phenotypical diversity currently observed in these populations; for instance, by introducing regulatory diversity at population-specific level. We additionally identified six GRF classes enriched for genes located in regions that are likely candidates for positive selection at population specific level. We found that out of the 41 DNA-binding GRF classes classified so far, six groups exhibited enrichment for genes located on regions that may have been under positive selection: C2H2 zinc finger, KRAB-ZNF zinc finger, Homeo domain, Tryptophan cluster, Fork head/winged helix and, and High-mobility HMG domain. We additionally identified three KRAB-ZNF gene clusters, in the chromosomes one, three, and 16, for the Asian population that exhibit regions with extended haplotype homozygosity EHH (larger than 100 kb). This EHH suggests that these regions have undergone positive selection in CHB population.
Finally, considering that a representative fraction of the phenotypic diversity observed between humans and its closely related species are likely explained by changes in cis-regulatory elements (CREs), we investigated putative binding sites for the transcription factor GABPa. Using ChIP-Seq data generated from a human cell line (HEK293T), 11,619 putative GABPa CREs were found, Out of which 224 are putative human-specific. To experimentally validate the transcriptional activity of these human-specific CREs, reporter gene essays and knock-down experiments were performed. Our results supported the functionality of these human-specific GABPa CREs and suggest that at least 1,215 genes are primary targets of GABPa. Finally, further analyses depict scenarios that put together transcriptional regulation by GABPa and the evolution of particular human traits; for instance, cognitive abilities, breast morphology, lipids and glucose metabolic pathways, among others.
info:eu-repo/classification/ddc/000
ddc:000
Human regulatorische Evolution, Genregulatorische Faktoren, positive Selektion, Cis-regulatorische Elemente, GABPa
Human regulatory evolution, gene regulatory factors, positive selection, Cis-regulatory elements, GABPa
Perdomo-Sabogal, Alvaro
Stadler, Peter F.
Torda, Andrew
Universität Leipzig
2016-10-13
2016-10-05
2016-08-24
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A14996
https://ul.qucosa.de/api/qucosa%3A14996/attachment/ATT-0/
oai:qucosa:de:qucosa:15151
2021-03-29T09:06:46Z
qucosa:ubl
doc-type:Periodical
open_access
ddc:000
ddc:060
openaire
Jahresbericht ... / Universität Leipzig
urn:nbn:de:bsz:15-qucosa-215393
ger
urn:nbn:de:bsz:15-qucosa-148573
qucosa:12743
qucosa:15152
qucosa:15336
qucosa:31433
qucosa:31686
Der bisher jährlich veröffentlichte Jahresspiegel der Universität Leipzig wird ab diesem Jahr [2014] durch einen "Jahresbericht" abgelöst, der so gestaltet ist, dass er auch ein Bericht zur fachlichen, strukturellen,
personellen und finanziellen Entwicklung und zu den Ergebnissen der wesentlichen Leistungsprozesse im Sinne der Vorgaben des Sächsischen Hochschulfreiheitsgesetzes ist. Gleichzeitig soll mit dem neuen Jahresbericht auch der Rechenschaftspflicht der Universität gegenüber Ministerien, Drittmittelgebern und Öffentlichkeit nach gekommen werden.
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/060
ddc:060
Leipzig, Universität, Jahresbericht
Leipzig, university, annual report
Universität Leipzig
2016-12-02
2015
info:eu-repo/semantics/openAccess
doc-type:Periodical
info:eu-repo/semantics/Periodical
doc-type:Collection
https://ul.qucosa.de/id/qucosa%3A15151
oai:qucosa:de:qucosa:15152
2021-03-29T09:06:46Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
ddc:060
openaire
Jahresbericht ... / Universität Leipzig
urn:nbn:de:bsz:15-qucosa-215402
ger
urn:nbn:de:bsz:15-qucosa-215393
qucosa:15151
Der bisher jährlich veröffentlichte Jahresspiegel der Universität Leipzig wird ab diesem Jahr durch einen "Jahresbericht" abgelöst, der so gestaltet ist, dass er auch ein Bericht zur fachlichen, strukturellen,
personellen und finanziellen Entwicklung und zu den Ergebnissen der wesentlichen Leistungsprozesse im Sinne der Vorgaben des Sächsischen Hochschulfreiheitsgesetzes ist. Gleichzeitig soll mit dem neuen Jahresbericht auch der Rechenschaftspflicht der Universität
gegenüber Ministerien, Drittmittelgebern und Öffentlichkeit nach gekommen werden.
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/060
ddc:060
Leipzig, Universität, Jahresbericht
Leipzig, university, annual report
Universität Leipzig
2016-12-02
2015
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15152
https://ul.qucosa.de/api/qucosa%3A15152/attachment/ATT-0/
oai:qucosa:de:qucosa:15177
2021-03-29T09:07:06Z
qucosa:ubl
doc-type:article
doc-type:Text
open_access
ddc:000
ddc:570
openaire
Phylogenetic distribution of plant snoRNA families
urn:nbn:de:bsz:15-qucosa-215736
eng
Background: Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention. Results: In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. Conclusions: The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation.
info:eu-repo/classification/ddc/570
ddc:570
info:eu-repo/classification/ddc/000
ddc:000
snoRNA, kleine nukleoläre Ribonukleinsäure, Evolution,Zielmolekül
snoRNAs, evolution, small RNAs, snoRNA targets
Bhattacharya, Deblina Patra
Canzler, Sebastian
Kehr, Stephanie
Hertel, Jana
Grosse, Ivo
Stadler, Peter F.
Universität Leipzig
Martin-Luther-Universität
Max-Planck-Institut für Mathematik in den Naturwissenschaften
Fraunhofer-Institut für Zelltherapie und Immunologie
Universität Wien
Univ. Copenhagen
Santa Fe Institute
Helmholtz Centre for Environmental Research - UFZ
BioMed Central
2016-12-08
2016
BMC Genomics (2016) 17:969 DOI 10.1186/s12864-016-3301-2
info:eu-repo/semantics/openAccess
doc-type:article
info:eu-repo/semantics/article
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15177
https://ul.qucosa.de/api/qucosa%3A15177/attachment/ATT-0/
oai:qucosa:de:qucosa:15175
2021-03-29T09:07:05Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Automating Geospatial RDF Dataset Integration and Enrichment
urn:nbn:de:bsz:15-qucosa-215708
eng
Over the last years, the Linked Open Data (LOD) has evolved from a mere 12 to more than 10,000 knowledge bases. These knowledge bases come from diverse domains including (but not limited to) publications, life sciences, social networking, government, media, linguistics. Moreover, the LOD cloud also contains a large number of crossdomain knowledge bases such as DBpedia and Yago2. These knowledge bases are commonly managed in a decentralized fashion and contain partly verlapping information. This architectural choice has led to knowledge pertaining to the same domain being published by independent entities in the LOD cloud. For example, information on drugs can be found in Diseasome as well as DBpedia and Drugbank. Furthermore, certain knowledge bases such as DBLP have been published by several bodies, which in turn has lead to duplicated content in the LOD . In addition, large amounts of geo-spatial information have been made available with the growth of heterogeneous Web of Data.
The concurrent publication of knowledge bases containing related information promises to become a phenomenon of increasing importance with the growth of the number of independent data providers. Enabling the joint use of the knowledge bases published by these providers for tasks such as federated queries, cross-ontology question answering and data integration is most commonly tackled by creating links between the resources described within these knowledge bases. Within this thesis, we spur the transition from isolated knowledge bases to enriched Linked Data sets where information can be easily integrated and processed. To achieve this goal, we provide concepts, approaches and use cases that facilitate the integration and enrichment of information with other data types that are already present on the Linked Data Web with a focus on geo-spatial data.
The first challenge that motivates our work is the lack of measures that use the geographic data for linking geo-spatial knowledge bases. This is partly due to the geo-spatial resources being described by the means of vector geometry. In particular, discrepancies in granularity and error measurements across knowledge bases render the selection of appropriate distance measures for geo-spatial resources difficult. We address this challenge by evaluating existing literature for point set measures that can be used to measure the similarity of vector geometries. Then, we present and evaluate the ten measures that we derived from the literature on samples of three real knowledge bases.
The second challenge we address in this thesis is the lack of automatic Link Discovery (LD) approaches capable of dealing with geospatial knowledge bases with missing and erroneous data. To this end, we present Colibri, an unsupervised approach that allows discovering links between knowledge bases while improving the quality of the instance data in these knowledge bases. A Colibri iteration begins by generating links between knowledge bases. Then, the approach makes use of these links to detect resources with probably erroneous or missing information. This erroneous or missing information detected by the approach is finally corrected or added.
The third challenge we address is the lack of scalable LD approaches for tackling big geo-spatial knowledge bases. Thus, we present Deterministic Particle-Swarm Optimization (DPSO), a novel load balancing technique for LD on parallel hardware based on particle-swarm optimization. We combine this approach with the Orchid algorithm for geo-spatial linking and evaluate it on real and artificial data sets. The lack of approaches for automatic updating of links of an evolving knowledge base is our fourth challenge. This challenge is addressed in this thesis by the Wombat algorithm. Wombat is a novel approach for the discovery of links between knowledge bases that relies exclusively on positive examples. Wombat is based on generalisation via an upward refinement operator to traverse the space of Link Specifications (LS). We study the theoretical characteristics of Wombat and evaluate it on different benchmark data sets.
The last challenge addressed herein is the lack of automatic approaches for geo-spatial knowledge base enrichment. Thus, we propose Deer, a supervised learning approach based on a refinement operator for enriching Resource Description Framework (RDF) data sets. We show how we can use exemplary descriptions of enriched resources to generate accurate enrichment pipelines. We evaluate our approach against manually defined enrichment pipelines and show that our approach can learn accurate pipelines even when provided with a small number of training examples.
Each of the proposed approaches is implemented and evaluated against state-of-the-art approaches on real and/or artificial data sets. Moreover, all approaches are peer-reviewed and published in a conference or a journal paper. Throughout this thesis, we detail the ideas, implementation and the evaluation of each of the approaches. Moreover, we discuss each approach and present lessons learned. Finally, we conclude this thesis by presenting a set of possible future extensions and use cases for each of the proposed approaches.
info:eu-repo/classification/ddc/000
ddc:000
Linked Data ; Open Data ; Maschinelles Lernen
Linkentdeckung, maschinelles Lernen, geographische Daten, Lastverteilung, Verfeinerungsoperator, Linked Data, offene Daten, RDF
Link Discovery, Machine Learning, Geographic data, Load balancing, refinement operator, Linked Data, Open data, RDF, Big Data
Sherif, Mohamed Ahmed Mohamed
Fähnrich, Klaus-Peter
Lehmann, Jens
Ngonga Ngomo, Axel-Cyrille
Auer, Sören
Mirankar, Daniel
Universität Leipzig
2016-12-12
2016-02-25
2016-05-12
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15175
https://ul.qucosa.de/api/qucosa%3A15175/attachment/ATT-0/
oai:qucosa:de:qucosa:15187
2021-03-29T09:07:14Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Expanding the SnoRNA Interaction Network: Conservation of Guiding Function in Vertebrates
urn:nbn:de:bsz:15-qucosa-216221
eng
Small nucleolar RNAs (snoRNAs) are one of the most abundant and evolutionary ancient group of small non-coding RNAs. Their main function is to target chemical modifications of ribosomal RNAs (rRNAs) and small nuclear (snRNAs). They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of modification that they govern.
The box H/ACA snoRNAs are responsible for targeting pseudouridylation sites and the box C/D snoRNAs for directing 2’-O-methylation of ribonucleotides. A subclass that localize to the Cajal bodies, termed scaRNAs, are responsible for methylation and pseudouridylation of snRNAs. In addition an amazing diversity of non-canonical functions of individual snoRNAs arose. The modification patterns in rRNAs and snRNAs are retained during evolution making it even possible to project them from yeast onto human. The stringent conservation of modification sites and the slow evolution of rRNAs and snRNAs contradicts the rapid evolution of snoRNA sequences.
Recent studies that incorporate high-throughput sequencing experiments still identify undetected snoRNAs even in well studied organisms as human. The snoRNAbase, which has been the standard database for human snoRNAs has not been updated ince 2006 and misses these new data. Along with the lack of a centralized data collection across species, which incorporates also snoRNA class specific characteristics the need to integrate distributed data from literature and databases into a comprehensive snoRNA set arose. Although several snoRNA studies included pro forma target predictions in individual species and more and more studies focus on non-canonical functions of subclasses a systematic survey on the guiding function and especially functional homologies of snoRNAs was not available.
To establish a sound set of snoRNAs a computational snoRNA annotation pipeline, named snoStrip that identifies homologous snoRNAs in related species was employed.
For large scale investigation of the snoRNA function, state-of-the-art target pedictions were performed with our software RNAsnoop and PLEXY. Further, a new measure the Interaction Conservation Index (ICI) was developed to evaluate the conservation of snoRNA function.
The snoStrip pipeline was applied to vertebrate species, where the genome sequence has been available. In addition, it was used in several ncRNA annotation studies (48 avian, spotted gar) of newly assembled genomes to contribute the snoRNA genes.
Detailed target analysis of the new vertebrate snoRNA set revealed that in general functions of homologous snoRNAs are evolutionarily stable, thus, members of the same snoRNA family guide equivalent modifications. The conservation of snoRNA sequences is high at target binding regions while the remaining sequence varies significantly. In addition to elucidating principles of correlated evolution it was possible, with the help of the ICI measure, to assign functions to previously orphan snoRNAs and to associate snoRNAs as partners to known but so far unexplained chemical modifications. As further pattern redundant guiding became apparent. For many modification sites more than one snoRNA encodes the appropriate antisense element (ASE), which could ensure constant modification through snoRNAs that have different expression patterns. Furthermore, predictions of snoRNA functions in conjunction with sequence conservation could identify distant homologies. Due to the high overall entropy of snoRNA sequences, such relationships are hard to detect by means of sequence homology search methods alone.
The snoRNA interaction network was further expanded through novel snoRNAs that were detected in data from high-throughput experiments in human and mouse. Through subsequent target analysis the new snoRNAs could immediately explain known modifications that had no appropriate snoRNA guide assigned before. In a further study a full catalog of expressed snoRNAs in human was provided. Beside canonical snoRNAs also recent findings like AluACAs, sno-lncRNAs and extraordinary short SNORD-like transcripts were taken into account. Again the target analysis workflow identified undetected connections between snoRNA guides and modifications. Especially some species/clade specific interactions of SNORD-like genes emerged that seem to act as bona fide snoRNA guides for rRNA and snRNA modifications. For all high confident new snoRNA genes identified during this work official gene names were requested from the HUGO Gene Nomenclature Committee (HGNC) avoiding further naming confusion.
info:eu-repo/classification/ddc/000
ddc:000
snoRNA, Bioinformatik, ncRNA
snoRNA, target prediction, rRNA modification, ncRNA, bioinformatics, comparative genomics
Kehr, Stephanie
Hertel, Jana
Stadler, Peter F.
Gautheret, Daniel
Universität Leipzig
2016-12-19
2016-04-08
2016-12-12
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15187
https://ul.qucosa.de/api/qucosa%3A15187/attachment/ATT-0/
oai:qucosa:de:qucosa:15255
2021-03-29T09:08:07Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Insights into the Evolution of small nucleolar RNAs: Prediction, Comparison, Annotation
urn:nbn:de:bsz:15-qucosa-217924
eng
Over the last decades, the formerly irrevocable believe that proteins are the only key-factors in the complex regulatory machinery of a cell was crushed by a plethora of findings in all major eukaryotic lineages. These suggested a rugged landscape in the eukaryotic genome consist- ing of sequential, overlapping, or even bi-directional transcripts and myriads of regulatory elements. The vast part of the genome is indeed transcribed into an RNA intermediate, but solely a small fraction is finally translated into functional proteins. The sweeping majority, however, is either degraded or functions as a non-protein coding RNA (ncRNA).
Due to continuous developments in experimental and computational research, the variety of ncRNA classes grew larger and larger, ranging from key-processes in the cellular lifespan to regulatory processes that are driven and guided by ncRNAs. The bioinformatical part pri- marily concentrates on the prediction, annotation, and extraction of characteristic properties of novel ncRNAs. Due to conservation of sequence and/or structure, this task is often deter- mined by an homology-search that utilizes information about functional, and hence conserved regions, as an indicator.
This thesis focuses mainly on a special class of ncRNAs, small nucleolar RNAs (snoRNAs). These abundant molecules are mainly responsible for the guidance of 2’-O-ribose-methylations and pseudouridylations in different types of RNAs, such as ribosomal and spliceosomal RNAs. Although the relevance of single modifications is still rather unclear, the elimination of a bunch of modifications is shown to cause severe effects, including lethality.
Several de novo prediction programs have been published over the last years and a substantial amount of publicly available snoRNA databases has originated. Normally, these are restricted to a small amount of species and a collection of experimentally extracted snoRNA. The detection of snoRNAs by means of wet lab experiments and/or de novo prediction tools is generally time consuming (wet lab) and a quite tedious task (identification of snoRNA-specific characteristics).
The snoRNA annotation pipeline snoStrip was developed with the intention to circumvent these obstacles. It therefore utilizes a homology-based search procedure to reliably predict snoRNA genes in genomic sequences. In a subsequent step, all candidates are filtered with respect to specific sequence motifs and secondary structures. In a functional analysis, poten- tial target sites are predicted in ribosomal and spliceosomal RNA sequences. In contrast to de novo prediction tools, snoStrip focuses on the extension of the known snoRNA world to uncharted organisms and the mapping and unification of the existing diversity of snoRNAs into functional, homologous families.
The pipeline is properly suited to analyze a manifold set of organisms in search for their snoRNAome in short timescales. This offers the opportunity to generate large scale analyses over whole eukaryotic kingdoms to gain insights into the evolutionary history of these spe- cial ncRNA molecules. A set of experimentally validated snoRNA genes in Deuterostomia and Fungi were starting points for highly comprehensive surveys searching and analyzing the snoRNA repertoire in these two major eukaryotic clades. In both cases, the snoStrip pipeline proved itself as a fast and reliable tool and collected thousands of snoRNA genes in nearly 200 organisms. Additionally, the Interaction Conservation Index (ICI), which is am- plified to additionally work on single lineages, provides a convenient measure to analyze and evaluate the conservation of snoRNA-targetRNA interactions across different species. The massive amount of data and the possibility to score the conservation of predicted interactions constitute the main pillars to gain an extraordinary insight into the evolutionary history of snoRNAs on both the sequence and the functional level. A substantial part of the snoR- NAome is traceable down to the root of both eukaryotic lineages and might indicate an even more ancient origin of these snoRNAs. However, a plenitude of lineage specific innovation and deletion events are also discernible. Due to its automated detection of homologous and functionally related snoRNA sequences, snoStrip identified extraordinary target switches in fungi. These unveiled a coupled evolutionary history of several snoRNA families that were previously thought to be independent. Although these findings are exceedingly interesting, the broad majority of snoRNA families is found to show remarkable conservation of the se- quence and the predicted target interactions.
On two occasions, this thesis will shift its focus from a genuine snoRNA inspection to an analysis of introns. Both investigations, however, are still conducted under an evolutionary viewpoint. In case of the ubiquitously present U3 snoRNA, functional genes in a notable amount of fungi are found to be disrupted by U2-dependent introns. The set of previously known U3 genes is considerably enlarged by an adapted snoStrip-search procedure. Intron- disrupted genes are found in several fungal lineages, while their precise insertion points within the snoRNA-precursor are located in a small and homologous region. A potential targetRNA of snoRNA genes, U6 snRNA, is also found to contain intronic sequences. Within this work, U6 genes are detected and annotated in nearly all fungal organisms. Although a few U6 intron- carrying genes have been known before, the widespread of these findings and the diversity regarding the particular insertion points are surprising. Those U6 genes are commonly found to contain more than just one intron. In both cases of intron-disrupted non-coding RNA genes, the detected RNA molecules seem to be functional and the intronic sequences show remarkable sequence conservation for both their splice sites and the branch site.
In summary, the snoStrip pipeline is shown to be a reliable and fast prediction tool that works on homology-based search principles. Large scale analyses on whole eukaryotic lineages become feasible on short notice. Furthermore, the automated detection of functionally related but not yet mapped snoRNA families adds a new layer of information. Based on surveys covering the evolutionary history of Fungi and Deuterostomia, profound insights into the evolutionary history of this ncRNA class are revealed suggesting ancient origin for a main part of the snoRNAome. Lineage specific innovation and deletion events are also found to occur at a large number of distinct timepoints.
info:eu-repo/classification/ddc/000
ddc:000
snoRNA,Bioinformatik,Genomik,RNA
snoRNA,Bioinformatics,RNA,Genomics
Canzler, Sebastian
Stadler, Peter F.
Huang, Hsien-Da
Universität Leipzig
2017-01-26
2016-08-03
2017-01-16
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15255
https://ul.qucosa.de/api/qucosa%3A15255/attachment/ATT-0/
oai:qucosa:de:qucosa:1531
2021-09-29T06:08:27Z
qucosa:slub
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
ddc:500
ddc:600
openaire
Tagungszeitschrift der 127. Versammlung der Gesellschaft Deutscher Naturforscher und Ärzte e.V. (GDNÄ)
urn:nbn:de:bsz:14-qucosa-97309
ger
Gesellschaft braucht Wissenschaft - Mobilität, Kommunikation, Interaktion, lautete das Generalthema der 127. GDNÄ-Versammlung vom 14. bis 18. September 2012 in Göttingen.
info:eu-repo/classification/ddc/500
ddc:500
info:eu-repo/classification/ddc/600
ddc:600
info:eu-repo/classification/ddc/000
ddc:000
Mobilität; Kommunikation; Interaktion; Göttingen / Universität Göttingen
GDNÄ, Naturforscher, Ärzte, Kommunikation, Mobilität, Interaktion, Göttingen, Versammlung
Gesellschaft Deutscher Naturforscher und Ärzte e.V. (GDNÄ)
2012-12-13
2012
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://slub.qucosa.de/id/qucosa%3A1531
https://slub.qucosa.de/api/qucosa%3A1531/attachment/ATT-0/
oai:qucosa:de:qucosa:15336
2021-03-29T09:09:10Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
ddc:060
openaire
Jahresbericht ... / Universität Leipzig
urn:nbn:de:bsz:15-qucosa-219218
ger
urn:nbn:de:bsz:15-qucosa-215393
qucosa:15151
Zum fünften Mal in Folge haben mehr als 7000 junge Menschen ihr Studium an unserer Universität aufgenommen. Mit 44 550 erreichte die Zahl der Bewerbungen den zweithöchsten Wert in der Geschichte der Universität. Auch in der Forschung erzielte die Universität Leipzig beachtliche Erfolge, neue Sonderforschungsbereiche wurden eingeworben, die strategische Ausrichtung der Forschungsprofilbereiche wurde verbessert und die Förderung durch die Deutsche Forschungsgemeinschaft (DFG) erhöht. Die Universitätsmedizin konnte ihre Krebs-, Adipositas- und Herzforschung mit Fördermitteln vom Freistaat Sachsen und der Bundesregierung weiterentwickeln.
info:eu-repo/classification/ddc/000
ddc:000
info:eu-repo/classification/ddc/060
ddc:060
Leipzig, Universität, Jahresbericht
Leipzig, university, annual report
Universität Leipzig
2017-02-14
2016
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15336
https://ul.qucosa.de/api/qucosa%3A15336/attachment/ATT-0/
oai:qucosa:de:qucosa:15442
2021-03-29T09:10:32Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Weighted Unranked Tree Automata over Tree Valuation Monoids
urn:nbn:de:bsz:15-qucosa-221154
eng
Quantitative aspects of systems, like the maximal consumption of resources, can be modeled by weighted automata. The usual approach is to weight transitions with elements of a semiring and to define the behavior of the weighted automaton by mul- tiplying the transition weights along a run. In this thesis, we define and investigate a new class of weighted automata over unranked trees which are defined over valuation monoids. By turning to valuation monoids we use a more general cost model: the weight of a run is now determined by a global valuation function. Besides the binary cost functions implementable via semirings, valuation functions enable us to cope with average and discounting. We first investigate the supports of weighted unranked tree automata over valuation monoids, i.e., the languages of all words which are evalu- ated to a non-zero value. We will furthermore consider the support of several other weighted automata models over different structures, like words and ranked trees. Next we prove a Nivat-like theorem for the new weighted unranked tree automata. More- over, we give a logical characterization for them. We show that weighted unranked tree automata are expressively equivalent to a weighted MSO logic for unranked trees. This solves an open problem posed by Droste and Vogler. Finally, we present a Kleene- type result for weighted ranked tree automata over valuation monoids.
info:eu-repo/classification/ddc/000
ddc:000
Gewichtete Baumautomaten, Gewichtete MSO Logik, Gewichtete rationale Ausdrücke, Bäume ohne Rang, Bäume mit Rang, Baumbewertungmonoide
weighted tree automata, weighed MSO logic, weighted rational expressions, unranked trees, ranked trees, valuation monoids
Götze, Doreen
Droste, Manfred
Rahonis, George
Universität Leipzig
2017-03-16
2016-12-06
2017-03-14
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15442
https://ul.qucosa.de/api/qucosa%3A15442/attachment/ATT-0/
oai:qucosa:de:qucosa:15443
2021-03-29T09:10:32Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Quantitative Automata and Logic for Pictures and Data Words
urn:nbn:de:bsz:15-qucosa-221165
eng
Mathematical logic and automata theory are two scientific disciplines with a close relationship that is not only fundamental for many theoretical results but also forms the basis of a coherent methodology for the verification and synthesis of computing systems. This connection goes back to a much longer history in the 1960s, through the fundamental work of Büchi-Elgot-Trakhtenbrot, which shows the expressive equivalence of automata and logical systems such as monadic second-order logic on finite and infinite words. This allowed the handling of specifications (where global system properties are stated), and implementations (which involve the definition of the local steps in order to satisfy the global goals laid out in the specifications) in a single framework. This connection has been extended to and well-investigated for many other structures such as trees, finite pictures, timed words and data words.
For many computer science applications, however, quantitative phenomena need to be modelled, as well. Examples are vagueness and uncertainty of a statement, length of time periods, spatial information, and resource consumption. Weighted automata, introduced by Schützenberger, are prominent models for quantitative aspects of systems. The framework of weighted monadic second-order logic over words was first introduced by Droste and Gastin. They gave a characterization of quantitative behavior of weighted finite automata, as semantics of monadic second-order sentences within their logic. Meanwhile, the idea of weighted logics was also applied to devices recognizing more general structures such as weighted tree automata, weighted automata on infinite words or traces. The main goal of this thesis is to give logical characterizations for weighted automata models on pictures and data words as well as for Büchi-tiling systems in the spirit of the classical Büchi-Elgot theorem. As the second goal, we deal with synchronizing problem for data words. Below, we briefly summarize the contents of this thesis.
Informally, a two-dimensional string is called a picture and is defined as a rectangular array of symbols taken from a finite alphabet. A two-dimensional language (or picture language) is a set of pictures. Picture languages have been intensively investigated by several research groups. In Chapter 1, we define weighted two-dimensional on-line tessellation automata (W2OTA) taking weights from a new weight structure called picture valuation monoid. This new weighted picture automaton model can be used to model several applications, e.g. the average density of a picture. Such aspects could not be modelled by semiring weighted picture automaton model. The behavior of this automaton model is a picture series mapping pictures over an alphabet to elements of a picture valuation monoid. As one of our main results, we prove a Nivat theorem for W2OTA. It shows that recognizable picture series can be obtained precisely as projections of particularly simple unambiguously recognizable series restricted to unambiguous recognizable picture languages. In addition, we introduce a weighted monadic second-order logic (WMSO) which can model average density of pictures. As the other main result, we show that W2OTA and a suitable fragment of our weighted MSO logic are expressively equivalent.
In Chapter 2, we generalize the notion of finite pictures to +ω-pictures, i.e., pictures which have finite number of rows and infinite number of columns. We extend conventional tiling systems with a Büchi acceptance condition in order to define the class of Büchi-tiling recognizable +ω-picture languages. The class of recognizable +ω-picture languages is indeed, a natural generalization of ω-regular languages. We show that the class of all Büchi-tiling recognizable +ω-picture languages has the similar closure properties as the class of tiling recognizable languages of finite pictures: it is closed under projection, union, and intersection, but not under complementation. While for languages of finite pictures, tiling recognizability and EMSO-definability coincide, the situation is quite different for languages of +ω-pictures. In this setting, the notion of tiling recognizability does not even cover the language of all
+ω -pictures over Σ = {a, b} in which the letter a occurs at least once – a picture language that can easily be defined in first-order logic. As a consequence, EMSO is too strong for being captured by the class of tiling recognizable +ω-picture languages. On the other hand, EMSO is too weak for being captured by the class of all Büchi-tiling
recognizable +ω-picture languages. To obtain a logical characterization of this class, we introduce the logic EMSO∞, which extends EMSO with existential quantification of infinite sets. Additionally, using combinatorial arguments, we show that the Büchi characterization theorem for ω-regular languges does not carry over to the Büchi-tiling recognizable +ω-picture languages.
In Chapter 3, we consider the connection between weighted register automata and weighted logic on data words. Data words are sequences of pairs where the first element is taken from a finite alphabet (as in classical words) and the second element is taken from an infinite data domain. Register automata, introduced by Francez and Kaminski, provide a widely studied model for reasoning on data words. These automata can be considered as classical nondeterministic finite automata equipped with a finite set of registers which are used to store data in order to compare them with some data in the future. In this chapter, for quantitative reasoning on data words, we introduce weighted register automata over commutative data semirings equipped with a collection of binary data functions in the spirit of the classical theory of weighted automata. Whereas in the models of register automata known from the literature data are usually compared with respect to equality or a linear order, here we allow data comparison by means of an arbitrary collection of binary data relations. This approach permits easily to incorporate timed automata and weighted timed automata into our framework. Motivated by the seminal Büchi-Elgot-Trakhtenbrot theorem about the expressive equivalence of finite automata and monadic second-order (MSO) logic and by the weighted MSO logic of Droste and Gastin, we introduce weighted MSO logic on data words and give a logical characterization of weighted register automata.
In Chapter 4, we study the concept of synchronizing data words in register automata. The synchronizing problem for data words asks whether there exists a data word that sends all states of the register automaton to a single state. The class of register automata that we consider here has a decidable non-emptiness problem, and the subclass of nondeterministic register automata with a single register has a decidable non-universality problem. We provide the complexity bounds of the synchronizing problem in the family of deterministic register automata with k registers (k-DRA), and in the family of nondeterministic register automata with single register (1-NRA), and in general undecidability of the problem in the family of k-NRA. To this end, we prove that, for k-DRA, inputting data words with only 2k + 1 distinct data values, from the infinite data domain, is sufficient to synchronize. Then, we show that the synchronizing problem for k-DRA is in general PSPACE-complete, and it is in NLOGSPACE for 1-DRA. For nondeterministic register automata (NRA), we show that Ackermann(n) distinct data, where n is the number of states of the register automaton, might be necessary to synchronize. Then, by means of a construction, proving that the synchronizing problem and the non-universality problem in 1-NRA are interreducible, we show the Ackermann-completeness of the problem for 1-NRA. However, for k-NRA, in general, we prove that this problem is undecidable due to the unbounded length of synchronizing data words.
info:eu-repo/classification/ddc/000
ddc:000
Quantitative Automata
Quantitative Logics
Babari, Parvaneh
Droste, Manfred
Bollig, Benedikt
Universität Leipzig
2017-03-20
2016-09-09
2017-03-03
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15443
https://ul.qucosa.de/api/qucosa%3A15443/attachment/ATT-0/
oai:qucosa:de:qucosa:15647
2021-03-29T09:13:08Z
qucosa:ubl
doc-type:doctoralThesis
doc-type:Text
open_access
ddc:000
openaire
Knowledge Extraction for Hybrid Question Answering
urn:nbn:de:bsz:15-qucosa-225097
eng
Since the proposal of hypertext by Tim Berners-Lee to his employer CERN on March 12, 1989 the World Wide Web has grown to more than one billion Web pages and still grows.
With the later proposed Semantic Web vision,Berners-Lee et al. suggested an extension of the existing (Document) Web to allow better reuse, sharing and understanding of data.
Both the Document Web and the Web of Data (which is the current implementation of the Semantic Web) grow continuously. This is a mixed blessing, as the two forms of the Web grow concurrently and most commonly contain different pieces of information. Modern information systems must thus bridge a Semantic Gap to allow a holistic and unified access to information about a particular information independent of the representation of the data.
One way to bridge the gap between the two forms of the Web is the extraction of structured data, i.e., RDF, from the growing amount of unstructured and semi-structured information (e.g., tables and XML) on the Document Web. Note, that unstructured data stands for any type of textual information like news, blogs or tweets.
While extracting structured data from unstructured data allows the development of powerful information system, it requires high-quality and scalable knowledge extraction frameworks to lead to useful results. The dire need for such approaches has led to the development of a multitude of annotation frameworks and tools. However, most of these approaches are not evaluated on the same datasets or using the same measures. The resulting Evaluation Gap needs to be tackled by a concise evaluation framework to foster fine-grained and uniform evaluations of annotation tools and frameworks over any knowledge bases.
Moreover, with the constant growth of data and the ongoing decentralization of knowledge, intuitive ways for non-experts to access the generated data are required. Humans adapted their search behavior to current Web data by access paradigms such as keyword search so as to retrieve high-quality results. Hence, most Web users only expect Web documents in return. However, humans think and most commonly express their information needs in their natural language rather than using keyword phrases. Answering complex information needs often requires the combination of knowledge from various, differently structured data sources. Thus, we observe an Information Gap between natural-language questions and current keyword-based search paradigms, which in addition do not make use of the available structured and unstructured data sources. Question Answering (QA) systems provide an easy and efficient way to bridge this gap by allowing to query data via natural language, thus reducing (1) a possible loss of precision and (2) potential loss of time while reformulating the search intention to transform it into a machine-readable way. Furthermore, QA systems enable answering natural language queries with concise results instead of links to verbose Web documents. Additionally, they allow as well as encourage the access to and the combination of knowledge from heterogeneous knowledge bases (KBs) within one answer.
Consequently, three main research gaps are considered and addressed in this work:
First, addressing the Semantic Gap between the unstructured Document Web and the Semantic Gap requires the development of scalable and accurate approaches for the extraction of structured data in RDF. This research challenge is addressed by several approaches within this thesis. This thesis presents CETUS, an approach for recognizing entity types to populate RDF KBs. Furthermore, our knowledge base-agnostic disambiguation framework AGDISTIS can efficiently detect the correct URIs for a given set of named entities. Additionally, we introduce REX, a Web-scale framework for RDF extraction from semi-structured (i.e., templated) websites which makes use of the semantics of the reference knowledge based to check the extracted data.
The ongoing research on closing the Semantic Gap has already yielded a large number of annotation tools and frameworks. However, these approaches are currently still hard to compare since the published evaluation results are calculated on diverse datasets and evaluated based on different measures. On the other hand, the issue of comparability of results is not to be regarded as being intrinsic to the annotation task. Indeed, it is now well established that scientists spend between 60% and 80% of their time preparing data for experiments. Data preparation being such a tedious problem in the annotation domain is mostly due to the different formats of the gold standards as well as the different data representations across reference datasets.
We tackle the resulting Evaluation Gap in two ways: First, we introduce a collection of three novel datasets, dubbed N3, to leverage the possibility of optimizing NER and NED algorithms via Linked Data and to ensure a maximal interoperability to overcome the need for corpus-specific parsers. Second, we present GERBIL, an evaluation framework for semantic entity annotation. The rationale behind our framework is to provide developers, end users and researchers with easy-to-use interfaces that allow for the agile, fine-grained and uniform evaluation of annotation tools and frameworks on multiple datasets.
The decentral architecture behind the Web has led to pieces of information being distributed across data sources with varying structure. Moreover, the increasing the demand for natural-language interfaces as depicted by current mobile applications requires systems to deeply understand the underlying user information need. In conclusion, the natural language interface for asking questions requires a hybrid approach to data usage, i.e., simultaneously performing a search on full-texts and semantic knowledge bases.
To close the Information Gap, this thesis presents HAWK, a novel entity search approach developed for hybrid QA based on combining structured RDF and unstructured full-text data sources.
info:eu-repo/classification/ddc/000
ddc:000
Named Entity Disambiguierung, Benchmarking, Hybrid Question Answering, Web of Data, Web of Documents, RDF, Semantic Annotation
Named Entity Disambiguation, Benchmarking, Hybrid Question Answering, Web of Data, Web of Documents, RDF
Usbeck, Ricardo
Fähnrich, Klaus-Peter
Ngonga Ngomo, Axel-Cyrille
Both, Andreas
Cimiano, Philipp
Universität Leipzig
2017-05-22
2016-12-04
2017-05-18
info:eu-repo/semantics/openAccess
doc-type:doctoralThesis
info:eu-repo/semantics/doctoralThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15647
https://ul.qucosa.de/api/qucosa%3A15647/attachment/ATT-0/
oai:qucosa:de:qucosa:15662
2021-03-29T09:13:17Z
qucosa:ubl
doc-type:PeriodicalPart
doc-type:Text
open_access
ddc:000
openaire
Tätigkeitsbericht / Universitätsbibliothek Leipzig
urn:nbn:de:bsz:15-qucosa-225300
ger
urn:nbn:de:bsz:15-qucosa-148591
qucosa:12744
Bericht über Strukturveränderungen, Personal, Projekte, Öffentlichkeitsarbeit, Ausstellungen, Vorträge u.a. der Universitätsbibliothek Leipzig und Ihre MitarbeiterInnen im Jahr 2016
Leipzig, Universitätsbibliothek, Jahresbericht
Leipzig, university library, annual report
info:eu-repo/classification/ddc/000
ddc:000
Universitätsbibliothek Leipzig
2017
2017-05-22
info:eu-repo/semantics/openAccess
doc-type:PeriodicalPart
info:eu-repo/semantics/PeriodicalPart
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15662
https://ul.qucosa.de/api/qucosa%3A15662/attachment/ATT-0/
oai:qucosa:de:qucosa:15771
2022-02-10T08:51:38Z
qucosa:ubl
doc-type:masterThesis
doc-type:Text
open_access
ddc:000
status-type:acceptedVersion
openaire
Entwicklung und Evaluation von Feedbacktechniken in der Softwarevisualisierung
urn:nbn:de:bsz:15-qucosa2-157716
ger
ger
Innovative und komplexe Informationssysteme erfordern zur Erfassung neuartige
Analysewerkzeuge. Dazu dienen in der Softwarevisualisierung Modelle zur Darstellung und Interaktionstechniken zur Steuerung. Ein Teilgebiet der Interaktionstechniken sind Feedbacktechniken, die dem Benutzer Rückmeldungen auf Interaktionen liefern. In der vorliegenden Arbeit werden bestehende Feedbacktechniken eingeordnet und neue entwickelt. Anhand von drei Prototypen werden unterschiedliche Feedbacktechniken vorgestellt und implementiert. Abschließend werden die Techniken auf ihre Nützlichkeit getestet. Dazu wird eine explorative Evaluation konzipiert, durchgeführt und ausgewertet.:Gliederung
Abbildungsverzeichnis
Listings
Tabellenverzeichnis
Abkürzungsverzeichnis
1 Einleitung
1.1 Motivation und Problemstellung
1.2 Zielstellung
1.3 Aufbau der Arbeit
2 Interaktionstechniken in der Softwarevisualisierung
2.1 Softwarevisualisierung
2.2 Interaktionstechniken
2.3 Bewertung von User-Interfaces
2.4 Stand der Forschung
3 Entwicklung von Feedbacktechnologie für SV
3.1 Taxonomien für ITecs
3.2 Vorhandene ITecs in SV
3.3 Konzeption neuer Feedbacktechniken für SV
3.4 Implementierung und Funktionsweise
4 Erhebung zur Messung des Nutzens von ITecs
4.1 Theoretische Grundlagen und Methodik der Erhebung
4.1.1 Methoden zur Evaluation von Software
4.1.2 Wahl einer Evaluationsmethode
4.2 Konzeption und Versuchsaufbau
4.3 Durchführung
5 Evaluation des Nutzens von ITecs
5.1 Stichprobenbeschreibung
5.2 Auswertung, Priorisierung und Klassifikation der Ergebnisse
5.3 Interpretation
5.4 Diskussion
6 Fazit und Ausblick
Informationsvisualisierung, Evaluation, Softwarevisualisierung, Interaktionstechnik, Feedbacktechnik, Softwareevaluation
info:eu-repo/classification/ddc/000
ddc:000
Buch, Jonas
Universität Leipzig
2016-10-10
2016
info:eu-repo/semantics/acceptedVersion
2017-06-19
info:eu-repo/semantics/openAccess
doc-type:masterThesis
info:eu-repo/semantics/masterThesis
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15771
https://ul.qucosa.de/api/qucosa%3A15771/attachment/ATT-0/
oai:qucosa:de:qucosa:15774
2021-03-29T09:14:42Z
qucosa:ubl
doc-type:article
doc-type:Text
open_access
ddc:000
status-type:acceptedVersion
openaire
Creating Linked Data morphological language resources with MMoOn: the Hebrew Morpheme Inventory
urn:nbn:de:bsz:15-qucosa2-157741
eng
978-2-9517408-9-1
The development of standard models for describing general lexical resources has led to the emergence of numerous lexical datasets of various languages in the Semantic Web. However, there are no models that describe the domain of Morphology in a similar manner.
As a result, there are hardly any language resources of morphemic data available in RDF to date. This paper presents the creation of the Hebrew Morpheme Inventory from a manually compiled tabular dataset comprising around 52.000 entries. It is an ongoing effort of representing the lexemes, word-forms and morphologigal patterns together with their underlying relations based on the newly created Multilingual
Morpheme Ontology (MMoOn). It will be shown how segmented Hebrew language data can be granularly described in a Linked Data format, thus, serving as an exemplary case for creating morpheme inventories of any inflectional language with MMoOn. The resulting dataset is described a) according to the structure of the underlying data format, b) with respect to the Hebrew language characteristic of building word-forms directly from roots, c) by exemplifying how inflectional information is realized and d) with regard to its enrichment with external links to sense resources.
morpheme ontology, Hebrew, language data, morphology, linguistic linked open data, MMoOn
info:eu-repo/classification/ddc/000
ddc:000
Klimek, Bettina
Arndt, Natanael
Krause, Sebastian
Arndt, Timotheus
Universität Leipzig
2016
info:eu-repo/semantics/acceptedVersion
2017-06-22
info:eu-repo/semantics/openAccess
doc-type:article
info:eu-repo/semantics/article
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15774
https://ul.qucosa.de/api/qucosa%3A15774/attachment/ATT-0/
oai:qucosa:de:qucosa:15779
2021-03-29T09:14:45Z
qucosa:ubl
doc-type:article
doc-type:Text
open_access
ddc:000
status-type:acceptedVersion
openaire
Structured feedback: a distributed protocol for feedback and patches on the Web of Data
urn:nbn:de:bsz:15-qucosa2-157796
eng
The World Wide Web is an infrastructure to publish and retrieve information through web resources. It evolved from a static Web 1.0 to a multimodal and interactive communication and information space which is used to collaboratively contribute and discuss web resources, which is better known as Web 2.0. The evolution into a Semantic Web (Web 3.0) proceeds. One of its remarkable advantages is the decentralized and interlinked data composition. Hence, in contrast to its data distribution, workflows and technologies for decentralized collaborative contribution are missing. In this paper we propose the Structured Feedback protocol as an interactive addition to the Web of Data. It offers support for users to contribute to the evolution of web resources, by providing structured data artifacts as patches for web resources, as well as simple plain text comments. Based on this approach it enables crowd-supported quality assessment and web data cleansing processes in an ad-hoc fashion most web users are familiar with.
linked data, dssn, semantic pingback, pubsubhubub, feedback, distributed semantic services, quality, crowd sourcing
info:eu-repo/classification/ddc/000
ddc:000
Arndt, Natanael
Junghanns, Kurt
Meissner, Roy
Frischmuth, Philipp
Radtke, Norman
Frommhold, Marvin
Martin, Michael
Universität Leipzig
2016
info:eu-repo/semantics/acceptedVersion
2017-06-23
info:eu-repo/semantics/openAccess
doc-type:article
info:eu-repo/semantics/article
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15779
https://ul.qucosa.de/api/qucosa%3A15779/attachment/ATT-0/
oai:qucosa:de:qucosa:15777
2021-03-29T09:14:45Z
qucosa:ubl
doc-type:article
doc-type:Text
open_access
ddc:000
status-type:acceptedVersion
openaire
Towards versioning of arbitrary RDF data
urn:nbn:de:bsz:15-qucosa2-157779
eng
78-1-4503-4752-5/16/09
10.1145/2993318.2993327
Coherent and consistent tracking of provenance data and in particular update history information is a crucial building block for any serious information system architecture. Version Control Systems can be a part of such an architecture enabling users to query and manipulate versioning information as well as content revisions. In this paper, we introduce an RDF versioning approach as a foundation for a full featured RDF Version Control System. We argue that such a system needs support for all concepts of the RDF specification including support for RDF datasets and blank nodes. Furthermore, we placed special emphasis on the protection against unperceived history manipulation by hashing the resulting patches. In addition to the conceptual analysis and an RDF vocabulary for representing versioning information, we present a mature implementation which captures versioning information for changes to arbitrary RDF datasets.
RDF, versioning, blank node, RDF quad, hashing
info:eu-repo/classification/ddc/000
ddc:000
Frommhold, Marvin
Navarro Piris, Rubén
Arndt, Natanael
Tramp, Sebastian
Petersen, Niklas
Martin, Michael
Universität Leipzig
2016
info:eu-repo/semantics/acceptedVersion
2017-06-23
info:eu-repo/semantics/openAccess
doc-type:article
info:eu-repo/semantics/article
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15777
https://ul.qucosa.de/api/qucosa%3A15777/attachment/ATT-0/
oai:qucosa:de:qucosa:15780
2021-03-29T09:14:46Z
qucosa:ubl
doc-type:article
doc-type:Text
open_access
ddc:000
status-type:acceptedVersion
openaire
Quit diff: calculating the delta between RDF datasets under version control
urn:nbn:de:bsz:15-qucosa2-157802
eng
978-1-4503-4752-5
10.1145/2993318.2993349
Distributed actors working on a common RDF dataset regularly encounter the issue to compare the status of one graph with another or generally to synchronize copies of a dataset. A versioning system helps to synchronize the copies of a dataset, combined with a difference calculation system it is also possible to compare versions in a log and to determine, in which version a certain statement was introduced or removed. In this demo we present Quit Diff 1, a tool to compare versions of a Git versioned quad store, while it is also applicable to simple unversioned RDF datasets. We are following an approach to abstract from differences on a syntactical level to differences on the level of the RDF data model, while we leave further semantic interpretation on the schema and instance level to specialized applications. Quit Diff can generate patches in various output formats and can be directly integrated in the distributed version control system Git which provides a foundation for a comprehensive co-evolution work flow on RDF datasets.
RDF, dataset, data model
info:eu-repo/classification/ddc/000
ddc:000
Arndt, Natanael
Radtke, Norman
Universität Leipzig
2016
info:eu-repo/semantics/acceptedVersion
2017-06-23
info:eu-repo/semantics/openAccess
doc-type:article
info:eu-repo/semantics/article
doc-type:Text
https://ul.qucosa.de/id/qucosa%3A15780
https://ul.qucosa.de/api/qucosa%3A15780/attachment/ATT-0/
X259765491/1