Stuttgart, Univ., Habil.-Schr., 2005.

Stuttgart, Univ., Diplomarb., 2005.

Als Kopf der Hypothalamus-Hypophysen-Nebennierenrinden-Achse spielt der Hypothalamus eine Schlüsselrolle für die depressive Symptomatik und bei pathogenetischen Modellen affektiver Störungen. Für nahezu alle Ebenen dieser Hormonachse lassen sich Funktions- und Strukturveränderungen, insbesondere Volumenveränderungen bei uni- oder bipolaren affektiven Störungen nachweisen. Zum Hypothalamus existiert hingegen, neben histochemischen Analysen, nur ein explorativer post mortem Befund einer Volumenreduktion von bis zu 15.5% bei uni- oder bipolar affektiv Erkrankten. Die vorliegende Arbeit verfolgt das Ziel, Volumenveränderungen des Hypothalamus bei uni- und bipolaren affektiven Störungen in vivo nachzuweisen. Mittels der Hochfeld-MRT lässt sich der Hypothalamus seit einigen Jahren mit einer Auflösung von weniger als 1 mm detailgetreu abbil-den. Zur Beurteilung, ob diese Genauigkeit dem Studienziel gerecht wird, wird eingangs in einem vorab publizierten Literaturüberblick der aktuelle Forschungstand zu Strukturveränderungen des Hypothalamus bei uni- und bipolaren affektiven Störungen zusammengefasst und diskutiert. Die Überblicksarbeit kommt zu dem Urteil, dass auch in vivo Volumenreduktionen des Hypothalamus solcher Größenordnungen zu erwarten sind, dass sie mittels Hochfeldbildgebung nachgewiesen werden können. Zur präzisen Vermessung des Hypothalamusvolumens stellen anschließend zwei ebenfalls publizierte Methodenstudien die Entwicklung und Evaluation einer geeigneten Messmethodik anhand hochaufgelöster, T1-gewichteter 7 Tesla MRT-Aufnahmen vor. Sie umfasst eine Intensitätsstandardisierung sowie einen falschfarbengestützten Segmentierungsalgorithmus. Aufbauend auf diesen theoretischen und methodischen Vorarbeiten präsentiert die vierte publizierte Arbeit die weltweit ersten in vivo Daten zu Volumenveränderungen des Hypothalamus bei uni- und bipolaren affektiven Störungen. Im querschnittlichen Vergleich mit gesunden Probanden und unter Kontrolle des intrakraniellen Volumens und psychotroper Medikation konnten bei beiden Störungsbildern linksseitige Volumenvergrößerungen des Hypothalamus nachgewiesen werden. Diese sind möglicherweise ein strukturelles Korrelat histochemisch nachweisbarer Aktivitätssteigerungen hypothalamischer Kerngebiete. Alternativ können sie eine Aktivierung und Vermehrung der Gliazellen anzeigen. Schließlich kann eine Volumenzunahme des Hypothalamus auch auf eine Vergrößerung der Zellzwischenräume zurückgehen. Der relative Mangel an Gerüststrukturen könnte, infolge mechanischer Krafteinwirkungen bei der histologischen Gewebeaufbereitung, zu einer verstärkten Stauchung bei den Patienten führen und so den früheren, gegenteiligen post mortem Befund erklären. Zur Untersuchung der mikrostrukturellen Gewebeeigenschaften des Hypothalamus bei uni- und bipolaren affektiven Störungen soll daher in der Folge diffusionsgewichtete Bildgebung zum Einsatz kommen.:Kapitel 1 1.1 Der Hypothalamus als Vermittler zwischen Gehirn und Körper 1.2 Theoretische Einordnung und empirischer Kenntnisstand 1.2.1 Die HPA-Achse als Bindeglied zwischen Diathese und Stress. 1.2.2 Hirnstrukturelle und -funktionelle Korrelate affektiver Störungen. 1.3 Forschungsthema 1.3.1 Problemstellung. 1.3.2 Forschungsziele. 1.4 Fragestellungen und Hypothesen 1.4.1 In vivo Strukturveränderungen des Hypothalamus bei affektiven Störungen. 1.4.2 Wie gestaltet sich eine reliable Messmethode? 1.4.3 Welche Intensitätsstandardisierung optimiert die Bilddatenqualität? 1.4.4 Verringertes in vivo Hypothalamusvolumen bei affektiven Störungen. Kapitel 2 2.1 Review Artikel 2.2 Segmentierungsalgorithmus 2.3 Intensitätsstandardisierung 2.4 Patientenstudie Kapitel 3 3.1 Hauptergebnisse 3.1.1 Theoretische und methodische Vorarbeiten. 3.1.2 Patientenstudie. 3.2 Wissenschaftliche Bewertung und Einordnung der Hauptergebnisse 3.2.1 Fundierung der Hypothesen. 3.2.2 Stärken und Schwächen der Patientenstudie. 3.2.3 Bewertung der Messmethodik. 3.2.4 Inhaltliche Interpretation des explorativen Befunds. 3.2.5 Ausblick. Anhang 4.1 Literaturverzeichnis 4.2 Abkürzungsverzeichnis 4.3 Zusammenfassung 4.4 Summary 4.5 Publikationsverzeichnis 4.6 Selbsständigkeitserklärung 4.7 Nachweise über Anteile der Co-Autoren

In the recent years, a rapidly increasing amount of experimental data has been generated by high-throughput technologies. Despite of these large quantities of protein-related data and the development of computational prediction methods, the function of many proteins is still unknown. In the human proteome, at least 20% of the annotated proteins are not characterized. Thus, the question, how to predict protein function from its amino acid sequence, remains to be answered for many proteins. Classical bioinformatics approaches for function prediction are based on inferring function from well-characterized homologs, which are identified based on sequence similarity. However, these methods fail to identify distant homologs with low sequence similarity. As protein structure is more conserved than sequence in protein families, structure-based methods (e.g. fold recognition) may recognize possible structural similarities even at low sequence similarity and therefore provide information for function inference. These fold recognition methods have already been proven to be successful for individual proteins, but their automation for high-throughput application is difficult due to intrinsic challenges of these techniques, mainly caused by a high false positive rate. Automated identification of remote homologs based on fold recognition methods would allow a signi cant improvement in functional annotation of proteins. My approach was to combine structure-based computational prediction methods with experimental data from genome-wide RNAi screens to support the establishment of functional hypotheses by improving the analysis of protein structure prediction results. In the first part of my thesis, I characterized proteins from the Ska complex by computational methods. I showed the benefit of including experimental information to identify remote homologs: Integration of functional data helped to reduce the number of false positives in fold recognition results and made it possible to establish interesting functional hypotheses based on high con dence structural predictions. Based on the structural hypothesis of a GLEBS motif in c13orf3 (Ska3), I could derive a potential molecular mechanism that could explain the observed phenotype. In the second part of my thesis, my goal was to develop computational tools and automated analysis techniques to be able to perform structure-based functional annotation in a high-throughput way. I designed and implemented key tools that were successfully integrated into a computational platform, called StrAnno, which I set up together with my colleagues. These novel computational modules include a domain prediction algorithm and a graphical overview that facilitates and accelerates the analysis of results. StrAnno can be seen as a first step towards automatic functional annotation of proteins by structure-based methods. First, the analysis of long hit lists to identify promising candidates for further analysis is substantially facilitated by integration and combination of various sequence-based computational tools and data from functional databases. Second, the developed post-processing tools accelerate the evaluation of structural and functional hypotheses. False positives from the threading result lists are removed by various filters, and analysis of the possible true positives is greatly enhanced by the graphical overview. With these two essential benefits, fold recognition techniques are applicable to large-scale approaches. By applying this developed methodology to hits from a genome-wide cell cycle RNAi screen and evaluating structural hypotheses by molecular modeling techniques, I aimed to associate biological functions to human proteins and link the RNAi phenotype to a molecular function. For two selected human proteins, c20orf43 and HJURP, I could establish interesting structural and functional hypotheses. These predictions were based on templates with low sequence identity (10-20%). The uncharacterized human protein c20orf43 might be a E3 SUMO-ligase that could be involved either in DNA repair or rRNA regulatory processes. Based on the structural hypotheses of two domains of HJURP, I predicted a potential link to ubiquitylation processes and direct DNA binding. In addition, I substantiated the cell cycle arrest phenotype of these two genes upon RNAi knockdown. Fold recognition methods are a promising alternative for functional annotation of proteins that escape sequence-based annotation due to their low sequence identity to well-characterized protein families. The structural and functional hypotheses I established in my thesis open the door to investigate the molecular mechanisms of previously uncharacterized proteins, which may provide new insights into cellular mechanisms.

In a previous ICFCA paper we have shown that, in the Description Logics EL and ELgfp, the set of general concept inclusions holding in a finite model always has a finite basis. In this paper, we address the problem of how to compute this basis efficiently, by adapting methods from formal concept analysis.

Graphene nanoplatelets have been introduced into the interphase between electrically insulating glass fibre and polymer matrix to functionalize the traditional composite. Owing to the distribution of network structure of GNPs, the interphase can transfer the signals about various internal change of material. Consequently, due to the novel bio-inspired overlapping structure, our GNPs-glass fibre shows a unique opportunity as a micro-scale multifunctional sensor. The following conclusions can be drawn from present research: • We prepared GNPs solution via a scalable and highly effective liquid-phase exfoliation method. This method produces high-quality, unoxidized graphene flakes from flake graphite. We control the thickness and size of GNPs by varying the centrifugation rate. • A simple fibre oriented capillary flow which can suppress ‘coffee ring’ effect to deposit GNPs onto the curved glass fibre surface. The GNPs form continuous fish scales like overlapping structure. • The electrical conductivity of our GNPs-glass fibre shows semiconductive property. The electrical resistance value scattering and the advancing contact angle value scattering indicate a uniform deposit structure. The uniform overlapping structure is a key factor for higher electrical conductivity compared with our previous work with CNTs. • The contact angles of our GNPs-glass fibre with water indicate that the GNPs are almost unoxidized, so the inert GNPs coating decreases the interfacial shears strength. • A micro scale GNPs-glass fibre sensor for gas sensing is achieved by deposit GNPs onto glass fibre surface. This sensor can be used to detect solvents vapours, such as water, ethanol and acetone. All these vapours work as electron acceptor when reacting with GNPs. The acetone shows the highest sensitivity (45000%) compared with water and ethanol. • The doping-dedoping of GNPs-glass fibres during adsorption-desorption cycles of acetone result in the efficient “break-junction” (GNPs lost electron carrier concentration) mechanism, which provides the possibility to fabricate the electrochemical “switch” in a simple and unique way. • The resistance of our GNPs-glass fibre shows exponential relationship with RH. This is attributed to two points. Firstly, the water vapours show similar exponential adsorption on carbon surface; secondly, the bandgap of GNPs increases with the increase of adsorbed water vapour concentration. • Due to the weak van der Waals interaction when water molecules are adsorbed on GNPs surface, our GNPs-glass fibre shows extreme fast response and recovery time with RH. It is potential for our GNPs-glass fibre being used to monitor the breath frequency. • Utilizing the negative temperature coefficient of GNPs, our GNPs-glass fibre can be used as temperature sensor with a sensing region of -150 to 30 °C. • Through the observed abnormal resistance change at a temperature of about – 18 °C, we discovered a phase change of the trance confined water in graphene layers. Based on the resistance change, we can study the interaction of water and carbon nanoparticles. • The bio-inspired novel overlapped multilayer structure of GNPs coating shows structural colours. Even more, our GNPs-glass fibre can be used to monitor the loading force in the interphase when it is embedded into epoxy resin. • Our GNPs-glass fibre shows an excellent piezoresistive property, the single GNPs-glass fibre shows a larger gauge factor than the commercial strains sensor. • The semiconductive interphase was formed when the GNPs-glass fibre was embedded in polymer matrix. This semiconductive interphase is very sensitive to the deformation of material, therefore, an in-situ strain sensor was manufactured to real-time monitor the microcracks in a composite instead of external sensors. The area of resistance ‘jump’ increase can be seen as the feature area for damage’s early warning. • Monitoring the resistance variation of the single fibre composite was conducted under cyclic loading with progressively increasing the strain peaks in order to further investigate the response of in-situ sensor to the interphase damage process. The deviation of resistance/strain when the stress is larger than 2 % highlights the accumulation of damage, which gives insight into the mechanism of resistance change.

Wir betrachten die Detektion und Lokalisation von plötzlichen Änderungen in der Kovarianzstruktur hochdimensionaler zufälliger Daten. Diese Arbeit schlägt zwei neuartige Ansätze für dieses Problem vor. Die Vorgehensweise beinhaltet im Wesentlichen Verfahren zum Test von Hypothesen, welche ihrerseits die Wahl geeigneter kritischer Werte erfordern. Dafür werden Kalibrierungsschemata vorgeschlagen, die auf unterschiedlichen Nichtstandard-Bootstrap-Verfahren beruhen. Der eine der beiden Ansätze verwendet Techniken zum Schätzen inverser Kovarianzmatrizen und ist durch Anwendungen in der neurowissenschaftlichen Bildgebung motiviert. Eine Beschränkung dieses Ansatzes besteht in der für die Schätzung der „Precision matrix“ wesentlichen Voraussetzung ihrer schwachen Besetztheit. Diese Bedingung ist im zweiten Ansatz nicht erforderlich. Die Beschreibung beider Ansätze wird gefolgt durch ihre theoretische Untersuchung, welche unter schwachen Voraussetzungen die vorgeschlagenen Kalibrierungsschemata rechtfertigt und die Detektion von Änderungen der Kovarianzstruktur gewährleistet. Die theoretischen Resultate für den ersten Ansatz basieren auf den Eigenschaften der Verfahren zum Schätzen der Präzisionsmatrix. Wir können daher die adaptiven Schätzverfahren für die Präzisionsmatrix streng rechtfertigen. Alle Resultate beziehen sich auf eine echt hochdimensionale Situation (Dimensionalität p >> n) mit endlichem Stichprobenumfang. Die theoretischen Ergebnisse werden durch Simulationsstudien untermauert, die durch reale Daten aus den Neurowissenschaften oder dem Finanzwesen inspiriert sind. / We consider the detection and localization of an abrupt break in the covariance structure of high-dimensional random data. The study proposes two novel approaches for this problem. The approaches are essentially hypothesis testing procedures which requires a proper choice of a critical level. In that regard calibration schemes, which are in turn different non-standard bootstrap procedures, are proposed. One of the approaches relies on techniques of inverse covariance matrix estimation, which is motivated by applications in neuroimaging. A limitation of the approach is a sparsity assumption crucial for precision matrix estimation which the second approach does not rely on. The description of the approaches are followed by a formal theoretical study justifying the proposed calibration schemes under mild assumptions and providing the guaranties for the break detection. Theoretical results for the first approach rely on the guaranties for inference of precision matrix procedures. Therefore, we rigorously justify adaptive inference procedures for precision matrices. All the results are obtained in a truly high-dimensional (dimensionality p >> n) finite-sample setting. The theoretical results are supported by simulation studies, most of which are inspired by either real-world neuroimaging or financial data.

Deutsch: Die vorliegende Arbeit beinhaltet die kombinatorische Synthese sowie biomedizinische Aspekte von neuen, lipophilisierten Nucleosiden (Nucleolipiden) als small molecules. Für die Synthesen wurden sowohl Nucleosid-Metabolite als auch -Antimetabolite lipophilisiert. Als Lipidreste wurden natürlich vorkommende Verbindungen, wie azyklische Terpene und (a)symmetrische Ketone verwendet. Diese wurden am O-2‘,3‘-cis-glycosidischen Rest oder an der N(3)-Position von β-D-Pyrimidinen oder an der N(1)-Position von β-D-Purinen eingeführt. Die Einführung der Reste erfolgte durch Ketalisierung der glyconischen Hydroxylgruppen oder durch direkte Alkylierung sowie durch Dimroth-Umlagerung des Aglycons. Zusätzlich wurden in weiteren Reaktionen ausgewählte Nucleolipide in 2-(Cyanoethyl)phosphoramidit für die automatische DNA-Festphasensynthese von Oligo-nucleotiden umgewandelt. Diese wurden für eine Reihe von Penetrationsversuchen hinsichtlich ihres Einlagerungs-und Penetrationsverhaltens in eine künstliche Lipidmembran untersucht und untereinander verglichen. Die synthetisierten Nucleolipide wurden NMR-spektroskopisch im Hinblick auf die strukturellen Parameter (1) Zuckerpucker (3’T2‘⇌3’T2‘) und (2) die Konformation um die exozyklische C(4‘)-C(5‘)-Bindung (γ+(g)⇌γt⇌γ-(g)) charakterisiert. Außerdem wurden die Nucleolipide hinsichtlich ihrer biologischen Aktivität in in vitro-Tests auf humane, differenzierte THP-1-Makrophagen bezüglich des Immunoeffekts und auf eine Rattengliom- sowie einer humanen Gliom-Zellline bezüglich der Antitumoraktivität getestet. English: The thesis comprises the combinatorial synthesis and biomedicinal aspects of novel lipophilized nucleosides (Nucleolipids) as small molecules. Nucleoside-metabolites, as well as -antimetabolites, were used for the lipophilization. The chemical structure of the lipid residues resembles naturally-occurring compounds, namely acyclic terpenes, and (a)symmetric ketones. They are positioned either at the O-2’,3’-cis-glyconic moiety or at the N(3) of β-D-pyrimidines or N(1) of β-D-purines. The introduction of the lipophilic residues was performed either by ketalization of the glyconic hydroxyls or by direct alkylation as well as by Dimroth rearrangement at the N-alkylated aglycone. Additionally, selected nucleolipids were further converted to 2-(cyanoethyl) phosphoramidites as building blocks for automated solid phase nucleic acid synthesis. The latters were used for the preparation of a series of lipo-oligonucleotides which were studied with respect to their immobilization within artificial lipid bilayers and compared concerning immobilization rate and stability. The resulting nucleolipids were characterized with respect to the structural parameters (1) the sugar pucker (3’T2‘⇌3’T2‘) as well as (2) the conformation around the exocyclic C(4’)-C(5’)-bond (γ+(g)⇌γt⇌γ-(g)) by 1H-NMR-spectroscopy. Moreover, the biological activity of the nucleolipids was tested in-vitro on human, differentiated THP-1-macrophages for the immunoeffect and towards the rat gliom cell line BT4Ca as well as a human gliom (GOS-3) for anticancer activity.

Aus der Einleitung: „In this paper, we reuse the representation formalism `description graph' in order to characterize subsumption of ALN-concepts. The description logic ALN allows for conjunction, valuerestrictions, number restrictions, and primitive negation. Since Classic allows for more constructors than ALN, e.g., equality restrictions an attribute chains by the constructor SAME-AS,we can confine the notion of description graphs from [BP94]. On the other hand, ALN explicitly allows for primitive negation which yields another possibility { besides conflicting number restrictions { to express inconsistency. Thus, we have to modify the notion of canonical description graphs in order to cope with inconsistent concepts in the structural characterization of subsumption. It turns out that the description graphs obtained from ALN-concepts are in fact trees. A canonical graph is a deterministic tree. The conditions required by the structural characterization of subsumption on these trees can be tested by an eficient algorithm, i.e., we obtain an algorithm deciding subsumption of C and D in time polynomial in the size of C and D. The report is structured as follows. In the preliminaries, we define syntax and semantics of the description logic ALN as well as the inference problem of subsumption. In Section 3, we introduce description graphs, the data structure our structural subsumption algorithm is working on. Besides syntax and semantics also an algorithm for translating ALN-concepts into description graphs is given. Thereafter, we present the main result of this report in Section 6, a characterization of subsumption of ALN-concepts by a structural comparison of corresponding description graphs. Furthermore, a structural subsumption algorithm can be found in Section 6.2. In the last section we summarize our results and give an outlook to further applications of structural subsumption in terminological knowledge representation systems.

Aus der Einleitung: „Equational unification is a generalization of syntactic unification in which semantic properties of function symbols are taken into account. For example, assume that the function symbol '+' is known to be commutative. Given the unication problem x + y ≐ a + b (where x and y are variables, and a and b are constants), an algorithm for syntactic unification would return the substitution {x ↦ a; y ↦ b} as the only (and most general) unifier: to make x + y and a + b syntactically equal, one must replace the variable x by a and y by b. However, commutativity of '+' implies that {x ↦ b; y ↦ b} also is a unifier in the sense that the terms obtained by its application, namely b + a and a + b, are equal modulo commutativity of '+'. More generally, equational unification is concerned with the problem of how to make terms equal modulo a given equational theory, which specifies semantic properties of the function symbols that occur in the terms to be unified.”