With the advent of high­throughput sequencing (HTS), profiling immunoglobulin (IG) repertoires has become an essential part of immunological research. The dissection of IG repertoires promises to transform our understanding of the adaptive immune system dynamics. Advances in sequencing technology now also allow the use of the Ion Torrent Personal Genome Machine (PGM) to cover the full length of IG mRNA transcripts. The applications of this bench­top scale HTS platform range from identification of new therapeutic antibodies to the deconvolution of malignant B cell tumors. In the context of this thesis, the usability of the PGM is assessed to investigate the IG heavy chain (IGH) repertoires of animal models. First, an innovate bioinformatics approach is presented to identify antigendriven IGH sequences from bulk sequenced bone marrow samples of transgenic humanized rats, expressing a human IG repertoire (OmniRatTM). We show, that these rats mount a convergent IGH CDR3 response towards measles virus hemagglutinin protein and tetanus toxoid, with high similarity to human counterparts. In the future, databases could contain all IGH CDR3 sequences with known specificity to mine IG repertoire datasets for past antigen exposures, ultimately reconstructing the immunological history of an individual. Second, a unique molecular identifier (UID) based HTS approach and network property analysis is used to characterize the CLL­like CD5+ B cell expansion of A20BKO mice overexpressing a natural short splice variant of the CYLD gene (A20BKOsCYLDBOE). We could determine, that in these mice, overexpression of sCYLD leads to unmutated subvariant of CLL (U­CLL). Furthermore, we found that this short splice variant is also seen in human CLL patients highlighting it as important target for future investigations. Third, the UID based HTS approach is improved by adapting it to the PGM sequencing technology and applying a custom­made data processing pipeline including the ImMunoGeneTics (IMGT) database error detection. Like this, we were able to obtain correct IGH sequences with over 99.5% confidence and correct CDR3 sequences with over 99.9% confidence. Taken together, the results, protocols and sample processing strategies described in this thesis will improve the usability of animal models and the Ion Torrent PGM HTS platform in the field if IG repertoire research.

Digital libraries have become a central aspect of our live. They provide us with an immediate access to an amount of data which has been unthinkable in the past. Support of computers and the ability to aggregate data from different libraries enables small projects to maintain large digital collections on various topics. A central aspect of digital libraries is the metadata -- the information that describes the objects in the collection. Metadata are digital and can be processed and studied automatically. In recent years, several studies considered different aspects of metadata. Many studies focus on finding defects in the data. Specifically, locating errors related to the handling of personal names has drawn attention. In most cases the studies concentrate on the most recent metadata of a collection. For example, they look for errors in the collection at day X. This is a reasonable approach for many applications. However, to answer questions such as when the errors were added to the collection we need to consider the history of the metadata itself. In this work, we study how the history of metadata can be used to improve the understanding of a digital library. To this goal, we consider how digital libraries handle and store their metadata. Based in this information we develop a taxonomy to describe available historical data which means data on how the metadata records changed over time. We develop a system that identifies changes to metadata over time and groups them in semantically related blocks. We found that historical meta data is often unavailable. However, we were able to apply our system on a set of large real-world collections. A central part of this work is the identification and analysis of changes to metadata which corrected a defect in the collection. These corrections are the accumulated effort to ensure data quality of a digital library. In this work, we present a system that automatically extracts corrections of defects from the set of all modifications. We present test collections containing more than 100,000 test cases which we created by extracting defects and their corrections from DBLP. This collections can be used to evaluate automatic approaches for error detection. Furthermore, we use these collections to study properties of defects. We will concentrate on defects related to the person name problem. We show that many defects occur in situations where very little context information is available. This has major implications for automatic defect detection. We also show that properties of defects depend on the digital library in which they occur. We also discuss briefly how corrected defects can be used to detect hidden or future defects. Besides the study of defects, we show that historical metadata can be used to study the development of a digital library over time. In this work, we present different studies as example how historical metadata can be used. At first we describe the development of the DBLP collection over a period of 15 years. Specifically, we study how the coverage of different computer science sub fields changed over time. We show that DBLP evolved from a specialized project to a collection that encompasses most parts of computer science. In another study we analyze the impact of user emails to defect corrections in DBLP. We show that these emails trigger a significant amount of error corrections. Based on these data we can draw conclusions on why users report a defective entry in DBLP.

This paper describes a system, which helps to interact with E-learning platforms via speech recognition. The system observes the presentation of a speaker and helps the listeners to orientate in the presented material by highlighting text passages, which correspond to the currently referred topics.

We are living in a connected world, surrounded by interwoven technical systems. Since they pervade more and more aspects of our everyday lives, a thorough understanding of the structure and dynamics of these systems is becoming increasingly important. However - rather than being blueprinted and constructed at the drawing board - many technical infrastructures like for example the Internet's global router network, the World Wide Web, large scale Peer-to-Peer systems or the power grid - evolve in a distributed fashion, beyond the control of a central instance and influenced by various surrounding conditions and interdependencies. Hence, due to this increase in complexity, making statements about the structure and behavior of tomorrow's networked systems is becoming increasingly complicated. A number of failures has shown that complex structures can emerge unintentionally that resemble those which can be observed in biological, physical and social systems. In this dissertation, we investigate how such complex phenomena can be controlled and actively used. For this, we review methodologies stemming from the field of random and complex networks, which are being used for the study of natural, social and technical systems, thus delivering insights into their structure and dynamics. A particularly interesting finding is the fact that the efficiency, dependability and adaptivity of natural systems can be related to rather simple local interactions between a large number of elements. We review a number of interesting findings about the formation of complex structures and collective dynamics and investigate how these are applicable in the design and operation of large scale networked computing systems. A particular focus of this dissertation are applications of principles and methods stemming from the study of complex networks in distributed computing systems that are based on overlay networks. Here we argue how the fact that the (virtual) connectivity in such systems is alterable and widely independent from physical limitations facilitates a design that is based on analogies between complex network structures and phenomena studied in statistical physics. Based on results about the properties of scale-free networks, we present a simple membership protocol by which scale-free overlay networks with adjustable degree distribution exponent can be created in a distributed fashion. With this protocol we further exemplify how phase transition phenomena - as occurring frequently in the domain of statistical physics - can actively be used to quickly adapt macroscopic statistical network parameters which are known to massively influence the stability and performance of networked systems. In the case considered in this dissertation, the adaptation of the degree distribution exponent of a random, scale-free overlay allows - within critical regions - a change of relevant structural and dynamical properties. As such, the proposed scheme allows to make sound statements about the relation between the local behavior of individual nodes and large scale properties of the resulting complex network structures. For systems in which the degree distribution exponent cannot easily be derived for example from local protocol parameters, we further present a distributed, probabilistic mechanism which can be used to monitor a network's degree distribution exponent and thus to reason about important structural qualities. Finally, the dissertation shifts its focus towards the study of complex, non-linear dynamics in networked systems. We consider a message-based protocol which - based on the Kuramoto model for coupled oscillators - achieves a stable, global synchronization of periodic heartbeat events. The protocol's performance and stability is evaluated in different network topologies. We further argue that - based on existing findings about the interrelation between spectral network properties and the dynamics of coupled oscillators - the proposed protocol allows to monitor structural properties of networked computing systems. An important aspect of this dissertation is its interdisciplinary approach towards a sensible and constructive handling of complex structures and collective dynamics in networked systems. The associated investigation of distributed systems from the perspective of non-linear dynamics and statistical physics highlights interesting parallels both to biological and physical systems. This foreshadows systems whose structures and dynamics can be analyzed and understood in the conceptual frameworks of statistical physics and complex systems.

This work is concerned with two kinds of objects: regular expressions and finite automata. These formalisms describe regular languages, i.e., sets of strings that share a comparatively simple structure. Such languages - and, in turn, expressions and automata - are used in the description of textual patterns, workflow and dependence modeling, or formal verification. Testing words for membership in any given such language can be implemented using a fixed - i.e., finite - amount of memory, which is conveyed by the phrasing finite-automaton. In this aspect they differ from more general classes, which require potentially unbound memory, but have the potential to model less regular, i.e., more involved, objects. Other than expressions and automata, there are several further formalisms to describe regular languages. These formalisms are all equivalent and conversions among them are well-known.However, expressions and automata are arguably the notions which are used most frequently: regular expressions come natural to humans in order to express patterns, while finite automata translate immediately to efficient data structures. This raises the interest in methods to translate among the two notions efficiently. In particular,the direction from expressions to automata, or from human input to machine representation, is of great practical relevance. Probably the most frequent application that involves regular expressions and finite automata is pattern matching in static text and streaming data. Common tools to locate instances of a pattern in a text are the grep application or its (many) derivatives, as well as awk, sed and lex. Notice that these programs accept slightly more general patterns, namely ''POSIX expressions''. Concerning streaming data, regular expressions are nowadays used to specify filter rules in routing hardware.These applications have in common that an input pattern is specified in form a regular expression while the execution applies a regular automaton. As it turns out, the effort that is necessary to describe a regular language, i.e., the size of the descriptor,varies with the chosen representation. For example, in the case of regular expressions and finite automata, it is rather easy to see that any regular expression can be converted to a finite automaton whose size is linear in that of the expression. For the converse direction, however, it is known that there are regular languages for which the size of the smallest describing expression is exponential in the size of the smallest describing automaton.This brings us to the subject at the core of the present work: we investigate conversions between expressions and automata and take a closer look at the properties that exert an influence on the relative sizes of these objects.We refer to the aspects involved with these consideration under the titular term of Relative Descriptional Complexity.