We investigate the computational complexity of axiom pinpointing in Description Logics, which is the task of finding minimal subsets of a knowledge base that have a given consequence. We consider the problems of enumerating such subsets with and without order, and show hardness results that already hold for the propositional Horn fragment, or for the Description Logic EL. We show complexity results for several other related decision and enumeration problems for these fragments that extend to more expressive logics. In particular we show that hardness of these problems depends not only on expressivity of the fragment but also on the shape of the axioms used.

Prostate cancer is one of the most common human malignancies and, consequently it is critical to develop appropriate diagnostic and therapeutic tools. Glutamate carboxypeptidase II (GCPII) is currently being considered one of the most important prostate cancer markers due to its tissue- specific expression. Whereas in healthy prostatic tissue the expression levels of GCPII are low, the transformation into the tumor is associated with the substantial increase of GCPII expression, with the highest levels observed in androgen-independent metastatic tumors. GCPII is thus considered a promising marker for early phase as well as advanced metastatic stages of prostate cancer. Current research is focused on the development of highly sensitive and specific reagents that allow detection of small amounts of GCPII, for example in early stages of cancer. Antibody derivatives are promising molecules for this purpose because they have high affinity and specificity and minimum negative side effects. Protein engineering is a prefered approach for preparation of various antibody molecules that differ in size, binding properties, stability, solubility, and production means. Different types of derivatives are being developed for medical needs such as in vitro diagnosis, therapy, and in vivo imagingSmall molecular...

Mittelalterliche Pergamentkodizes sind äußerst kostbar und werden selten im Antiquariatshandel angeboten. Spektakuläre Erwerbungen wie die Nibelungen-Handschrift C (Badische Landesbibliothek, Karlsruhe) oder die Ottheinrich-Bibel (Bayerische Staatsbibliothek, München) sind große Ausnahmen, möglich nur unter Aufwendung außerplanmäßiger Mittel undmit finanzieller Unterstützung von Sponsoren und Stiftungen. Heute gilt jede mittelalterliche Handschrift als einzigartiges Zeugnis – sei es für die durch sie überlieferten Texte und Bilder, sei es für ihr historisch-kulturelles Umfeld. Diese Wertschätzung erfuhren mittelalterliche Handschriften nicht zu allen Zeiten. Mit zunehmender Verbreitung gedruckter Bücher verloren sie in der frühen Neuzeit ihre Funktion als Informationsträger und wurden oft nur noch ihres Beschreibstoffes, des Pergaments wegen geschätzt, das vor allem die Buchbinder gut gebrauchen konnten. Auf diese Weise sind unzählige Fragmente entstanden, die mitunter ebenso wertvoll sein können wie vollständig erhaltene Kodizes, vor allem dann, wenn es sich um singuläre Text- / Bildzeugen handelt oder wenn dadurch andere Fragmente ergänzt werden können.

Mittelalterliche Pergamentkodizes sind äußerst kostbar und werden selten im Antiquariatshandel angeboten. Spektakuläre Erwerbungen wie die Nibelungen-Handschrift C (Badische Landesbibliothek, Karlsruhe) oder die Ottheinrich-Bibel (Bayerische Staatsbibliothek, München) sind große Ausnahmen, möglich nur unter Aufwendung außerplanmäßiger Mittel undmit finanzieller Unterstützung von Sponsoren und Stiftungen. Heute gilt jede mittelalterliche Handschrift als einzigartiges Zeugnis – sei es für die durch sie überlieferten Texte und Bilder, sei es für ihr historisch-kulturelles Umfeld. Diese Wertschätzung erfuhren mittelalterliche Handschriften nicht zu allen Zeiten. Mit zunehmender Verbreitung gedruckter Bücher verloren sie in der frühen Neuzeit ihre Funktion als Informationsträger und wurden oft nur noch ihres Beschreibstoffes, des Pergaments wegen geschätzt, das vor allem die Buchbinder gut gebrauchen konnten. Auf diese Weise sind unzählige Fragmente entstanden, die mitunter ebenso wertvoll sein können wie vollständig erhaltene Kodizes, vor allem dann, wenn es sich um singuläre Text- / Bildzeugen handelt oder wenn dadurch andere Fragmente ergänzt werden können.

Fragment-based drug discovery is an emerging process that has gained popularity in recent years. The process starts from small molecules called fragments. One major step in fragment-based drug discovery is fragment screening, which is a strategy to screen libraries of small molecules to find hits. The strategy in theory is more efficient than traditional high-throughput screening that works with larger molecules. As fragments intrinsically possess weak affinity to a target, detection techniques of high sensitivity to affinity are required for fragment screening. Furthermore, the use of different screening methods is necessary to improve the likelihood of success in finding suitable fragments. Since no single method can work for all types of screening, there is a demand for new techniques. The aim of this thesis is to introduce weak affinity chromatography (WAC) as a novel technique for fragment screening. WAC is, as the name suggests, an affinity-based liquid chromatographic technique that separates compounds based on their different weak affinities to an immobilized target. The higher affinity a compound has towards the target, the longer it remains in the separation unit, and this will be expressed as a longer retention time. The affinity measure and ranking of affinity can be achieved by processing the obtained retention times of analyzed compounds. In this thesis, WAC is studied for fragment screening on two platforms. The first system comprised a 24-channel affinity cartridge that works in cooperation with an eight-needle autosampler and 24 parallel UV detector units. The second system was a standard analytical LC-MS platform that is connected to an affinity column, generally called WAC-MS or affinity LC-MS. The evaluation criteria in studying WAC for fragment screening using these platforms were throughput, affinity determination and ranking, specificity, operational platform characteristics and consumption of target protein and sample. The model target proteins were bovine serum albumin for the first platform, thrombin and trypsin for the latter. Screened fragments were either small molecule drugs, a thrombin-directed collection of compounds, or a general-purpose fragment library. To evaluate WAC for early stages of fragment elaboration, diastereomeric mixtures from a thrombin-directed synthesis project were screened. Although both analytical platforms can be used for fragment screening, WAC-MS shows more useful features due to easy access to the screening platform, higher throughput and ability to analyze mixtures. Affinity data from WAC are in good correlation with IC50 values from enzyme assay experiments. The possibility to distinguish specific from non- specific interactions plays an important role in the interpretation of WAC results. In this thesis, this was achieved by inhibiting the active site of the target protein to measure off-site interactions. WAC proves to be a sensitive, robust, moderate in cost and easy to access technique for fragment screening, and can also be useful in the early stages of fragment evolution. In conclusion, this thesis has demonstrated the proof of principle of using WAC as a new tool to monitor affinity and to select hits in fragment-based drug discovery. This thesis has indicated the primary possibilities, advantages as well as the limitations of WAC in fragment screening procedures.  In the future, WAC should be evaluated on other targets and fragment libraries in order to realize more fully the potential of the technology.

Advantages of cache cooperation on edge cache networks serving dynamic web content were studied. Design of cooperative edge cache grid a large-scale cooperative edge cache network for delivering highly dynamic web content with varying server update frequencies was presented. A cache clouds-based architecture was proposed to promote low-cost cache cooperation in cooperative edge cache grid. An Internet landmarks-based scheme, called selective landmarks-based server-distance sensitive clustering scheme, for grouping edge caches into cooperative clouds was presented. Dynamic hashing technique for efficient, load-balanced, and reliable documents lookups and updates was presented. Utility-based scheme for cooperative document placement in cache clouds was proposed. The proposed architecture and techniques were evaluated through trace-based simulations using both real-world and synthetic traces. Results showed that the proposed techniques provide significant performance benefits. A framework for automatically detecting cache-effective fragments in dynamic web pages was presented. Two types of fragments in web pages, namely, shared fragments and lifetime-personalization fragments were identified and formally defined. A hierarchical fragment-aware web page model called the augmented-fragment tree model was proposed. An efficient algorithm to detect maximal fragments that are shared among multiple documents was proposed. A practical algorithm for detecting fragments based on their lifetime and personalization characteristics was designed. The proposed framework and algorithms were evaluated through experiments on real web sites. The effect of adopting the detected fragments on web-caches and origin-servers is experimentally studied.

Crystallization is often a major bottleneck to macromolecular structure determination. This is particularly true for membrane proteins, which have hydrophobic surfaces that cannot readily form crystal contacts. Of the roughly 109,000 protein structures in the PDB, only about 539 represent unique membrane proteins, despite immense interest in membrane proteins from both a biological and therapeutic standpoint. Membrane protein crystallization has been facilitated by the development of new detergents, lipidic cubic phase methods, soluble protein chimeras, and non-covalent protein complexes. The design process of protein fusion constructs and non-covalent antibody fragments specific for each target membrane protein, however, is costly and time-consuming. An improved, more general method of membrane protein co-crystallization is needed. This dissertation details the development of two approaches for cost-effective non-covalent crystallization chaperones: (1) Engineered hypercrystallizable Fab antibody fragment with high affinity for EYMPME (EE epitope), which form complexes with EE-tagged soluble and membrane proteins. (2) Engineered monomeric streptavidin (mSA2) for complexation with biotinylated membrane proteins. Both methods are generalizable through insertion of a short epitope into a surface-exposed loop of a membrane protein by site directed mutagenesis. Crystallization trials of representative chaperone-membrane protein complexes and possible difficulties with the approach are discussed.

Zugl.: Mainz, Universiẗat, Diss.

Cette thèse a pour but de développer le pendant in silico des étapes clés du Fragment-Based Drug Design (FBDD), et ce dans le cadre plus général du développement de l'outil S4MPLE. Le FBDD génère des ligands drug-like à partir de petites molécules (fragments). Après une étape de validation de S4MPLE et de sa fonction d’énergie, un recentrage autour du FBDD est réalisé, à travers le docking puis l'optimisation virtuelle de fragments par growing ou linking (G/L). Cette stratégie reposesur 1) la création d’une chimiothèque focalisée en connectant un ou deux fragment(s) avec des linkers pré-générés, et 2) l’échantillonnage avec S4MPLE des composés chimères dans le site avec des contraintes. Des simulations de G/L plus ou moins ambitieuses (site flexible, ajout de H2O libres) permettent de valider cette approche avec des études rétrospectives basées sur des données expérimentales. La dernière phase de la thèse a consisté à appliquer ce protocole in silico à un projet de l’entreprise. / This work aims to develop in silico methods targeting the key stages of Fragment-Based Drug Design (FBDD), participating to the development of the molecular modeling tool S4MPLE. Briefly, FBDD generates ıdrug-likeı ligands from small organic molecules called fragments. After a validation step of S4MPLE and its energy function, the work focused on FBDD: molecular docking of fragments and their subsequent virtual optimization. The latter mimics standard evolution strategies in FBDD(growing and linking). This in silico approach involves among other two key stages 1) building of a focused library by plugging in pre-generated linkers into reference fragments using rules and 2) sampling of these new compounds under atomic and binding site constraints. Validation simulations, relying on known experimental data, included ıclassicalı growing / linking and more challenging ones (site flexibility, free waters). Finally, this strategy is applied to one project of the company.

Ami intime de Chateaubriand et de Pauline de Beaumont, témoin de la Révolution française qui a, dit-il, « chassé [s]on esprit du monde réel », Joseph Joubert rédige toute sa vie des notes consignées dans deux-cent cinq cahiers et dans des feuillets épars. Ces notes, qu’il ne publiera pas, sont éditées par André Beaunier dans leur quasi totalité en 1938 sous l’appellation de Carnets. Ce texte protéiforme ressortissant à la poétique du brouillon est envisagé dans cet ouvrage sous l’angle d’une notion héritée d’Yves Bonnefoy. La désécriture englobe l’ensemble des mouvements venant faire obstacle à l’élaboration de l’œuvre : les phénomènes de réticences, d’auto-censure, d’hésitations, de déconstruction, de minage, de pudeur qui viennent manifestement gêner l’expression, et plus encore toute possibilité d’édification d’une « œuvre » achevée. La poétique de Joubert naît de ces mouvements contradictoires entre un idéal littéraire nettement défini par des critères étiquetés comme classiques (clarté, ordre, achèvement) et une pratique littéraire qui tient cet idéal en échec, mais ce faisant trouve dans le fragmentaire et le provisoire une éthique aussi bien qu’une poétique. La désécriture est en effet aussi une expérience de la positivité : contre toutes les impuissances, l’effacement des mots se révèle comme puissance d’affirmation. / Joseph Joubert was a close friend of Chateaubriand and Pauline de Beaumont and a witness of the French Revolution, which has « chased away [his] mind from the real world », as he stated. He wrote during his whole life a set of notes in 205 notebooks and loose sheets of papers, but never published them. In 1938, André Beaunier edited most part of them under the name of Carnets. This multifaceted text, belonging to the draft poetry, is here considered through the angle of a notion coming from Yves Bonnefoy. The désécriture includes all the movements that prevent from creating a finished book : reluctance, self-censorship, hesitations, modesty, literary deconstruction and mining which impede the writing, and his achievement as a piece of work. Joubert’s poetry arises from this conflicting movements between a literary ideal characterized by the classical way (clarity, order, achievement) and Joubert’s style compromising this ideal. Nonetheless, the author finds his ethic and poetic way thanks to a fragmented and temporary style. The désécriture is in fact a positive experience : the vanishing words become an affirmative power of saying, opposite to all forms of impotence.