Bianchi models are posited by the BKL picture to be essential building blocks towards an understanding of generic cosmological singularities. We study the behaviour of spatially homogeneous anisotropic vacuum spacetimes of Bianchi type VIII and IX, as they approach the big bang singularity. It is known since 2001 that generic Bianchi IX spacetimes converge towards the so-called Mixmaster attractor as time goes towards the singularity. We extend this result to the case of Bianchi VIII vacuum. The BKL picture suggests that particle horizons should form, i.e. spatially separate regions should causally decouple. We prove that this decoupling indeed occurs, for Lebesgue almost every Bianchi VIII and IX vacuum spacetime.
View lessWithin the body, every cell contains the same genetic blueprint, the DNA, which is wrapped around histones and densely packed in the nucleus. Given the same genome, the identity of each cell is in part defined by modifications to the histones but also the genomic sequence itself, such as DNA methylation, that define active and inactive parts of the DNA. In somatic cells, DNA methylation levels are largely bimodal, with a high genome-wide methylation average that predominantly excludes CpG islands (CGIs), features often found near gene promoters that remain free of methylation. These patterns change across the majority of human cancer types, which exhibit global loss of methylation accompanied by a gain of methylation at select CGIs. To date, bisulfite sequencing represents the gold-standard method to profile DNA methylation at single-base resolution and has been widely used to characterize and understand DNA methylation landscapes in healthy and tumor cells. This thesis presents advancements in the computational analysis of bisulfite sequencing data sets, as well as applications to large-scale studies of DNA methylation in cancer. It showcases the adaptation of a local alignment tool to enable homology search for bisulfite-converted sequences, which outperforms established semi-global alignment tools when applied to the search of metagenomic data sets. Additionally, this thesis describes the development of a new application that provides fast and simplified extraction of DNA methylation heterogeneity metrics from single reads of bisulfite sequencing data. The importance of such metrics is demonstrated in the context of two studies that focus on DNA methylation changes within primary tumors and cancer cell lines. Single-read metrics and single-cell methylome profiling show that primary tumors are mainly characterized by heterogeneous, intermediate global and CGI DNA methylation that is intrinsic to the underlying single tumor cells. In contrast, cancer cell lines mostly assume one of two different states, where global DNA methylation levels are either drastically decreased or comparable to healthy tissues, while CGIs become almost fully methylated in both scenarios. Although rarely seen in solid tumors, extremely high genome-wide methylation levels can also be observed in an exceptional primary tumor type, acute lymphoblastic leukemia, where this landscape is influenced by specific epigenetic regulators. Together, the findings of this thesis advance our ability to analyze bisulfite sequencing data sets as well as to apply these more nuanced measurements to understand DNA methylation changes during tumorigenesis and in culture.
View lessIm Jahr 2018 wurden 844 Augenabstriche von 785 verschiedenen Pferden bakteriologisch untersucht. Die Keimidentifizierung erfolgte neben Beurteilung der Kulturmorphologie und biochemischen Methoden mittels MALDI-TOF. Die Resistenztestung wurde im Mikrodilutionsverfahren nach den Standards des CLSI als Breakpoint-Methode durchgeführt. 8% (n=65/844) aller Augentupfer waren bakteriologisch negativ. Bei 31% (n=264/844) zeigte sich nur grampositives, bei 25% (n=207/844) ausschließlich gramnegatives Wachstum. Mischkulturen grampositiver und -negativer Keimspezies zeigten sich bei 36% (n=308/844) der Proben. Unterschiede in der Art des Keimwachstums ergaben sich im jahreszeitlichen Vergleich. Insgesamt konnten 1510 Bakterien isoliert werden. Die meisten Isolate gehörten zu den Familien der Enterobacteriaceae, Staphylococcaceae und Bacillaceae. Weiterhin kamen die Familien Streptococcaceae, Moraxellaceae und Pseudomonadaceae häufig vor. Größte Gattungen waren (in absteigender Reihenfolge): Pantoea, Staphylococcus, Bacillus, Streptococcus, Pseudomonas und Acinetobacter. Das gramnegative Keimspektrum setzt sich größtenteils aus den drei Familien Enterobacteriaceae (n=359/678), Moraxellaceae (n=141/678) und Pseudomonadaceae (n=137/678) zusammen. Weder das Alter der beprobten Pferde noch lokale antibiotische Vorbehandlung hatten einen signifikanten Einfluss auf die Nachweishäufigkeit gramnegativer Keimspezies. Auch konnten bei Schädigung der Hornhaut nicht vermehrt gramnegative Bakterien isoliert werden. Moraxella bovoculi war innerhalb der Jahresverlaufs im Herbst am häufigsten vertreten. Die klinische Relevanz der nachgewiesenen gramnegativen Bakteriengattungen muss individuell beurteilt werden.
Von 1421 Bakterienisolaten wurden Antibiogramme angefertigt. Getestet wurden die antibiotischen Wirkstoffe Oxacillin, Gentamicin, Neomycin, Kanamycin, Enrofloxacin, Tetracyclin, Florfenicol und Polymyxin. Gegenüber den gramnegativen Isolaten (n=654) zeigte sich Enrofloxacin in vitro als am wirksamsten (n= 625/654), gefolgt von Gentamicin (n=620/654) und Neomycin (n=618/654). Die meisten Isolate der grampositiven Keime waren in vitro sensibel gegenüber Florfenicol (n=713/767), Enrofloxacin (n=710/767) und Tetracyclin (n=679/767). Lokale antibiotische Vorbehandlungen hatten keinen besonderen Einfluss auf die Resistenzlage.
Das große aerobe Keimspektrum der Augenoberfläche des Pferdes und die Unterschiede in der Resistenzlage machen eine bakteriologische Untersuchung mit anschließender Antibiogrammerstellung notwendig.
View lessStaff training for persons handling animals intended for slaughter is necessary and its relevance is undisputed. Despite this, there is no legal basis that describes the need of repetitive training for persons with a certificate of competence in this field. Within the meat industry, there is a need for well-developed, easily understandable training materials translated in correspondingly necessary languages, containing descriptive photos and videos which provide ongoing training to the heterogeneous group of employees. Any lack of knowledge could lead to animal welfare violations by employees. Regardless of whether these violations are caused by a lack of knowledge or another cause, there must not be any handling of pigs that is in violation of animal welfare.
Through the survey and data collection of the first publication, it became clear that animal welfare training for employees is usually carried out once a year. Smaller abattoirs were comparatively less satisfied with their training concepts, materials and content. The need for descriptive videos, photos and different target languages became clear, as well as a need for adapted and specific modules depending on the area of work. The desire for practical sessions was also mentioned. It was also stated that online access or carrying out the animal welfare training online-only could be problematic.
The relevance of human-animal interactions, and the management of transport and slaughter, was confirmed by the systematic literature review and potentially training-relevant topics were identified. Mistakes in handling pigs can only be identified and corrected if they are known and recognized by staff. Appropriately prepared and repetitive training courses can help to form this recognition. Existing handouts and after publication the materials from the project "eSchulTS2" (access via https://tetfolio.fu-berlin.de/web/eschults2) are good bases for complex training and, if necessary, management adjustments.
The knowledge testing of the additional, unpublished work showed that participants answered more questions correctly as a percentage after completing the pilot modules "Handling of pigs" and "Electrical stunning". The increase in knowledge, however, varied depending on the topic and previous experience, even for individual questions. Participants with a lower level of education were more likely to have a certificate of competence and thus to work in areas relevant to animal welfare. The influence of language selection remains unclear. Romanian speaking participants had worse results than German speaking participants. We posit that the reason for the worse results in the tests is not the country of origin per se, but rather the factor of the career changing of people from other countries. An increase in knowledge was also observed among participants with a certificate of competence, which confirms the need for repetitive training for all staff.
Overall, the increase in knowledge of the participants in the pre-evaluation showed that the underlying didactic concept for the created E-learning pilot modules in the area of animal welfare training for employees of pig abattoirs is suitable. The transfer and increase in knowledge represent an added value for the protection and animal welfare of pigs intended for slaughter.
View lessThe emergence of a European public sphere as a shared communication space for European citizens in different countries and its importance for the democratic legitimacy of the European Union have long been subject to scholarly debate. The existence of a European public sphere is usually discussed in terms of the Europeanization of national public spheres, which includes the synchronicity of issue agendas in various countries and the degree of communicative interactions between actors from the European and the national level (vertical Europeanization) as well as in different member states (horizontal Europeanization). Over time, two key developments have contributed to increasing Europeanization of national public spheres. First, political and economic crises have served as catalysts for politicization and consequently the visibility of European issues in recent years. Second, digitalization has led to the emergence of networked public spheres as interconnection of different platforms and issue publics online. Specifically, the advent of the internet and the rise of social media platforms have fostered new communication infrastructures that allow direct communication between different actor groups and across national borders. Europeanization can thus be conceptualized as increasing density of communicative interactions between various actors in communication networks. These developments lead to a more diverse set of voices in online debates, because actors formerly dependent on journalists as gatekeepers can now directly address others online. More diverse actor constellations might in turn increase the variation of (European) issues discussed in networked public spheres, which would provide the possibility for (communicative) input to the European level from citizens and civil society actors as an important precondition for the Europeanization of networked public spheres as well as for the democratic legitimacy of the EU on the input and the output level. Problems related to the legitimacy of the EU and European institutions such as missing accountability and growing Euroscepticism have been addressed by the institutions and scholars alike. Overall, favourable context conditions regarding the communication environment on the one hand (i.e. easy direct and transnational communication) are met by unfavorable context conditions for Europeanization and democratic legitimacy (i.e. growing Euroscepticism, crises) on the other hand. Furthermore, when different actor groups can communicate directly on social media platforms, strategic decisions and communication contexts of these actor groups need to be taken into consideration. It is assumed that actors use the different communication options of social media platforms (e.g. addressing other users, sharing and forwarding contents, replying to others) for different strategic purposes. The actual outplay of communicative interactions and the resulting network structures are a result of actor-specific strategies. Consequently, an actor-centered approach to Europeanization, democratic legitimacy, as well as the salience of conflict lines is necessary when social media platforms are at the center of attention. These contemporary developments raise the question in how far networked public spheres and social media platforms with their potential for direct and transnational communication may lead to increasing Europeanization of communicative interactions and new (European) issues being discussed by diverse actors online. Specifically, this dissertation focusses on three concepts related to the scholarly debate about European public spheres and the impact of contemporary communication infrastructures and networked public spheres on these concepts. First, vertical and horizontal Europeanization are discussed against the background of changing communication environments and actor-specific communication strategies. Second, the potential of direct communication between citizens and (European) politicians as precondition for increasing democratic legitimacy of the EU is discussed. Third, the salience of Eurosceptic voices and consequent calls for newly emerging political conflict lines on the European level will be addressed. Conceptualizing communication flows in networked public spheres as communication networks with the communicating actors as nodes and communicative interactions between these actors as edges, all three concepts can be investigated using network analytical measures. To analyze Europeanization, direct communication as a precondition for democratic legitimacy as well as the salience of European level conflict lines, a combination of different methods from computational communication science (i.e. Exponential Random Graph Modelling, Structural Topic Modelling) is combined with a manual content analysis. The debate about the 2019 European Parliament elections on Twitter as discussed under the official election hashtag (#EP2019) in April and May 2019 is used as a case study for several reasons. First, European Parliament elections are times of increased importance of European actors and issues. Second, Twitter is a particularly important platform for political communication. Third, hashtag-based data sampling via Twitter’s Rest API allows to analyze the corresponding debate without prior selection of countries, issues, or actors that should be included in the analysis. The results provide optimistic outlooks for the Europeanization of networked public spheres and the inclusion of different voices in political online debates, but they also leave room for improvement when it comes to direct communication between politicians and citizens as a precondition for increasing democratic legitimacy of the EU. It also become apparent that different actor groups play different roles when it comes to the Europeanization of networked public spheres and political as well as media actors are still the most important receivers of attention in terms of incoming communicative interactions. First indicators for European level conflict lines do emerge in the network structures of the debate regarding, for example, European integration and environmental protection. However, it remains to be seen in how far these conflict lines may turn into fully-fledged cleavages in the future. The dissertation provides a detailed discussion of these results and their impact for further scholarly debates as well as practical implication for Europeanization, democratic legitimacy, and conflict lines.
View lessSince its launch in 2012, Wikidata has grown to become the largest open knowledge base (KB), containing more than 100 million data items and over 6 million registered users. Wikidata serves as the structured data backbone of Wikipedia, addressing data inconsistencies, and adhering to the motto of “serving anyone anywhere in the world,” a vision realized through the diversity of knowledge. Despite being a collaboratively contributed platform, the Wikidata community heavily relies on bots, automated accounts with batch, and speedy editing rights, for a majority of edits. As Wikidata approaches its first decade, the question arises: How close is Wikidata to achieving its vision of becoming a global KB and how diverse is it in serving the global population? This dissertation investigates the current status of Wikidata’s diversity, the role of bot interventions on diversity, and how bots can be leveraged to improve diversity within the context of Wikidata. The methodologies used in this study are mapping study and content analysis, which led to the development of three datasets: 1) Wikidata Research Articles Dataset, covering the literature on Wikidata from its first decade of existence sourced from online databases to inspect its current status; 2) Wikidata Requests-for-Permissions Dataset, based on the pages requesting bot rights on the Wikidata website to explore bots from a community perspective; and 3) Wikidata Revision History Dataset, compiled from the edit history of Wikidata to investigate bot editing behavior and its impact on diversity, all of which are freely available online. The insights gained from the mapping study reveal the growing popularity of Wikidata in the research community and its various application areas, indicative of its progress toward the ultimate goal of reaching the global community. However, there is currently no research addressing the topic of diversity in Wikidata, which could shed light on its capacity to serve a diverse global population. To address this gap, this dissertation proposes a diversity measurement concept that defines diversity in a KB context in terms of variety, balance, and disparity and is capable of assessing diversity in a KB from two main angles: user and data. The application of this concept on the domains and classes of the Wikidata Revision History Dataset exposes imbalanced content distribution across Wikidata domains, which indicates low data diversity in Wikidata domains. Further analysis discloses that bots have been active since the inception of Wikidata, and the community embraces their involvement in content editing tasks, often importing data from Wikipedia, which shows a low diversity of sources in bot edits. Bots and human users engage in similar editing tasks but exhibit distinct editing patterns. The findings of this thesis confirm that bots possess the potential to influence diversity within Wikidata by contributing substantial amounts of data to specific classes and domains, leading to an imbalance. However, this potential can also be harnessed to enhance coverage in classes with limited content and restore balance, thus improving diversity. Hence, this study proposes to enhance diversity through automation and demonstrate the practical implementation of the recommendations using a specific use case. In essence, this research enhances our understanding of diversity in relation to a KB, elucidates the influence of automation on data diversity, and sheds light on diversity improvement within a KB context through the usage of automation.
View lessMore and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, and even some types of cancer. Advances in high-throughput omics technologies have made it possible to directly analyze the human microbiome and its impact on human health and physiology. Microbial composition is usually observed over long periods of time and the interactions between their members are explored. Numerous studies have used microbiome data to accurately differentiate disease states and understand the differences in microbiome profiles between healthy and ill individuals. However, most of them mainly focus on various statistical approaches, omitting microbe-microbe interactions among a large number of microbiome species that, in principle, drive microbiome dynamics. Constructing and analyzing time-evolving graphs is needed to understand how microbial ecosystems respond to a range of distinct perturbations, such as antibiotic exposure, diseases, or other general dynamic properties. This becomes especially challenging due to dozens of complex interactions among microbes and metastable dynamics.
The key to addressing this challenge lies in representing time-evolving graphs constructed from microbiome data as fixed-length, low-dimensional feature vectors that preserve the original dynamics. Therefore, we propose two unsupervised approaches that map the time-evolving graph constructed from microbiome data into a low-dimensional space where the initial dynamic, such as the number of metastable states and their locations, is preserved. The first method relies on the spectral analysis of transfer operators, such as the Perron--Frobenius or Koopman operator, and graph kernels. These components enable us to extract topological information such as complex interactions of species from the time-evolving graph and take into account the dynamic changes in the human microbiome composition. Further, we study how deep learning techniques can contribute to the study of a complex network of microbial species. The method consists of two key components: 1) the Transformer, the state-of-the-art architecture used in the sequential data, that learns both structural patterns of the time-evolving graph and temporal changes of the microbiome system and 2) contrastive learning that allows the model to learn the low-dimensional representation while maintaining metastability in a low-dimensional space.
Finally, this thesis will address an important challenge in microbiome data, specifically identifying which species or interactions of species are responsible for or affected by the changes that the microbiome undergoes from one state (healthy) to another state (diseased or antibiotic exposure). Using interpretability techniques of deep learning models, which, at the outset, have been used as methods to prove the trustworthiness of a deep learning model, we can extract structural information of the time-evolving graph pertaining to particular metastable states.
View lessDer "Masterstudiengang für das Lehramt an Integrierten Sekundarschulen und Gymnasien mit dem Profil Quereinstieg" (Q-Master) stellt einen alternativen Weg in das Lehramt dar. Es ist wenig darüber bekannt, ob ein solcher Qualifikationsweg in adäquater Weise auf die beruflichen Herausforderungen vorbereitet.
Mit der vorliegenden Arbeit wurde die Ausprägung und Entwicklung fachspezifischer professioneller Kompetenzen der Studierenden des Q-Masterstudiengangs (N=14) im Fach Physik längsschnittlich erhoben und mit den Studierenden des regulären Lehramtsmasterstudiengangs (N=30) verglichen. Ergänzend wurden Interviews zu den motivationalen Eingangsbedingungen der Q-Masterstudierenden sowie Aspekten der individuellen Nutzung der Lernangebote des Lehramtstudiums durchgeführt.
Als Ergebnis zeigt sich ein großer Zuwachs des fachdidaktischen Wissens der Q-Masterstudierenden im Verlauf des Q-Masterstudiums. Im Vergleich zu den regulären Lehramtsmasterstudieren werden keine Unterschiede in der Kompetenzausprägung und -entwicklung nachgewiesen. Die motivationalen Eingangsbedingungen der Q-Masterstudierenden scheinen günstig für die professionelle Entwicklung zu sein und die Lerngelegenheiten des Studiums werden als überwiegend nützlich erlebt. Damit scheint der Modellstudiengang geeignet zu sein, um einen qualitätsgesicherten Wechsel in das Lehramt innerhalb eines überschaubaren Zeitraums zu ermöglichen.
View lessThe present research was inspired by the chance encounter of an important dissonance between the Basic Principles and Guidelines on the Right to a Remedy and Reparation for Victims of Gross Violations of International Human Rights Law and Serious Violations of International Humanitarian Law and Uganda’s nascent transitional justice policy. The latter foresaw reparations for all victims of Uganda’s civil wars while the former stated that customary international law merely encouraged but did not oblige States to repair victims of non-State actors, the victims of others. Was Uganda’s policy gratuitous? Or has public international law evolved beyond the economy of the Basic Principles and Guidelines? It is the purpose of the present text to answer these questions. The thesis is divided into three substantive chapters that are preceded by an Introduction and tied together by a brief Conclusion.
The Introduction articulates the hypothesis and highlights that if correct, i.e., if there exists a rule of public international law obliging States to repair victims not their own, there exist two candidates for the content of that rule. The candidates are explored in Chapters 1 and 2. Before turning to them, the Introduction demonstrates that avenues typically proposed today are insufficient juxtaposed with the aim of making reparations a reality for victims of non-State actors. It thereby underlines that the hypothesis is not just thought-provoking but also of immense practical value.
Chapter 1 first investigates the nature of the States’ obligation to protect economic, social and cultural rights, and concludes that the existing consensus as it is contained in the Basic Principles and Guidelines is that the obligation is a qualified obligation of result. It then examines the historical origins of the rule, demonstrates why it is inappropriate to apply it to the situation at hand and proposes that the obligation to protect be understood as an unqualified obligation of result instead, meaning that the State would find itself in a position of wrongfulness at the exact moment a non-State actor committed a violation. This would ipso facto create the State’s secondary obligation to repair. Lacking a conventional articulation to that effect, such a rule would have to exist in the sphere of customary international law.
Chapter 2 takes under the magnifying glass the International Covenant on Economic, Social and Cultural Rights and explores the potential of the obligation of progressive realisation, the prohibition against discrimination and studies the work of the Committee on Economic, Social and Cultural Rights, substantiating the argument that the obligation to repair could be understood as a primary obligation.
What we do not yet know at this point in the thesis is whether either proposition corresponds to the States’ understanding of the law. Chapter 3 therefore examines a dozen countries that have experienced a non-international armed conflict in their more or less recent past. It looks at their practice in regard to reparations, paying particular attention to whether States discriminate between victims of the State and those not of the State. As far as it can be discerned, it also analyses their understanding of public international law.
The Conclusion suggests an affirmation of the hypothesis.
View lessRepresenting molecules in a computer-interpretable way plays a crucial role in enabling the application of computational method to the field of chemistry and pharmaceutical drug development in particular. Recently, there has been a surge of interest in using machine learning to predict molecular properties such as the binding affinity to protein targets of interest or to generate molecular structures with desirable properties. However, as chemical entities are challenging to represent in an expressive and computer-interpretable way, much work in the field of cheminformatics has concerned itself with defining clever feature extractors, which encode the chemical graph structure in a uniform, fixed-sized, numerical manner. Recently Deep Neural Networks have shown great success in learning to extract meaningful features directly from raw data representations, outperforming hand-crafted feature extraction protocols and revolutionizing fields such as image analysis or natural language processing. Deep Neural Networks have also been directly applied on raw data representations of molecules such as their structural graph. However, the capabilities of this method in pharmaceutical drug development are usually limited by the scarcity of labeled data as their collection usually involves running expensive wet lab experiments. Unsupervised Learning, on the other hand, is a powerful machine learning strategy that enables the training of Deep Neural Networks without the need of labeled training data. In this thesis we discuss how Unsupervised Learning can be used to train powerful feature extractors on unlabeled chemical structures. We propose for different input representations of molecules (such as line notations, graphs and point clouds) novel methods to extract expressive representations. We show how those representations can efficiently be used as input for downstream molecular property prediction models or to generate novel molecules with desirable properties. Moreover, we discuss how certain symmetries of molecular representations are crucial to respect (e.g. permutation invariance of molecular graphs or rotation and translation invariance of molecular conformations) and develop novel methods particularly designed to extract invariant representations.
View lessBacteria mostly prefer to live as biofilms on surfaces rather than in flowing environments. However, biofilms are mostly unwanted by humans and preventing possibilities besides biocides and antibiotics are urgently needed. One strategy is to prevent the bacteria directly from attaching to the substrate. This study aims to investigate the effect of nano- and microstructures on bacterial attachment and pursues two approaches whether such surfaces reduce bacterial attachment under flow conditions. The first approach involves ZnO nanorods to design surfaces with varying topographies in the nano- and micrometer range, while the second uses 3D printed microstructures to induce microflows that repel bacteria from the surface. The tailored substrates were integrated into a specially developed flow chamber and exposed to a flowing suspension of P. fluorescens under in-situ conditions. Additionally, the attached bacteria were subjected to higher shear forces by increased flow velocities. For evaluation, the attached bacteria were imaged using fluorescence microscopy and automated counted on a single-cell level. The cell counts were compared between different substrates and a control surface to assess the effectiveness of the surfaces in preventing bacterial attachment. Lower cell numbers indicated a surface that better prevented bacterial attachment. However, it was found that none of the investigated surfaces reduced the attachment of P. fluorescens. These findings and additionally made observations have the potential to alter the current perspective of the believed capability of nano and microstructures for preventing microbial attachment. Remarkably, it was found that although accompanying computational fluid dynamic simulations predicted uniform flows in the channels, anomalies in the flows occurred, resulting in uneven distribution of the bacteria. Furthermore, P. fluorescens revealed the ability to attach to any surface studied and rapidly establish irreversible attachment there. Thus, this study also suggests using those microorganism types that perform best in attachment for benchmarking surfaces that are intended to have a bacteria-repellent effect in the future. During the project, a method for a lipopolysaccharide encapsulated polystyrene (LPS-PS) microparticle system was developed as a further approach. The easy-to-use method was developed to mimic bacteria for attachment studies. A variety of analytical techniques were used to detect the LPS on the polystyrene microparticles. Among others, a procedure for labeling the particles for fluorescence microscopy is presented. The data from the analyses offers a reference for future applications of the LPS-PS microparticles, whose use goes far beyond bacterial attachment studies; they are attractive for vaccine research and serological tests.
View lessAprès l’énonciation en 1993 de conditions d’adhésion à l’Union européenne (UE), la politique d’élargissement à l’Est a été qualifiée d’asymétrique et unilatérale. A la suite de la réforme de 1997, la littérature a identifié l’introduction d’un nouveau mode de gouvernance. Qu’en est-il exactement ? Les éléments empiriques réunis entre 2000 et 2004 nous ont permis de formuler l’hypothèse selon laquelle l’UE a transféré une méthode de gouvernance interne fondée sur l’interaction – la méthode ouverte de coordination (MOC) – pour résoudre les difficultés rencontrées au niveau externe. Lors des élargissements précédents, la Communauté européenne s’est toujours inspirée des modes d’intégration interne – intergouvernementalisme, régulation économique, méthode communautaire – pour dépasser ses contradictions. Ainsi, dans quelle mesure la conditionnalité de l’adhésion à l’UE a-t-elle représenté à partir de 1997 un cadre d’apprentissages et de socialisation mutuelle entre acteurs de l’élargissement ? L’approche constructiviste par les cadres normatif et d’action nous a permis de déconstruire trois vertus de la gouvernance par les connaissances : la cohérence et la légitimité interne de la politique d’élargissement sont restées inaccomplies ; dans les pays candidats, la mise en oeuvre des réformes est restée limitée par les héritages du passé ; enfin, les mécanismes d’apprentissages et de socialisation mutuelle ont certes ouvert des possibilités de définition communes des cadres cognitif et d’action des politiques internes et externes à l’UE. Néanmoins, la convergence sur des valeurs partagées n’empêche pas l’existence de tensions internes relatives au sens à donner à l’Europe à Vingt-Cinq.
View lessPredicting the behavior of foldamer assemblies with all-α-peptides in higher-ordered arrangements remains a challenge. However, there is a strong interest and need to develop a deeper and more thorough knowledge to access foldamer designs that undergo interactions with natural peptide motifs. In this dissertation, the endeavors of investigating higher-ordered interactions between foldamers and all-α-peptides were continued in a well-defined tetrameric coiled-coil model system. First, two Cys/Phe-motifs identified in previous work as complementary binding partners of an α/β/γ-chimera were compared using CD-spectroscopy and cryogenic transmission electron microscopy (cryo-TEM). Systematic substitutions were performed on cysteine and analyzed by CD-spectroscopy to determine differences between the two different Cys/Phe-motif-containing complementary sequences in the formation of helical bundles with the α/β/γ-chimeric sequence. High-resolution structural data were obtained using a variety of analytical methods to investigate the favored side chain packing in the higher-ordered helical fold. The analytical techniques applied are NMR spectroscopy, vibrational sum-frequency generation (SFG) spectroscopy, Fourier-transform infrared (FT-IR) spectroscopy, and X-ray crystallography. In the course of this thesis, the thiol region was examined for the first time by vibrational SFG-spectroscopy at the air/water interface for shifts due to H-bonding. In addition, the first crystal structure of a heterotypic coiled-coil assembly of an α/β/γ-chimera with an all-α-peptide was generated, providing the first high-resolution packing information of the heterotypic helical bundle in a solid state. Another part of this work deals with the construction of a library of chimeric peptides with iterative substitutions that increase the number of β/γ-modules. These chimeras were then evaluated for stability when complemented with corresponding all- α-peptide sequences involving the Cys/Phe-motifs. This investigation revealed a restriction of intermolecular interactions sensitive to a variation in the number of backbone residues. Finally, a β/γ-peptide consisting of five β/γ-modules was analyzed for structural features by CD-spectroscopy.
View lessIn the arid and semi-arid region in northern Namibia, there are three main catchment areas the Kunene, the Kavango, and the Cuvelai-Etosha Basin (CEB). The Kunene and the Kavango Rivers are perennial and provide the northwestern and northeastern regions with water. In central northern Namibia, the transboundary CEB consists of an ephemeral and endorheic drainage system with channels and depressions, known as the Iishana system. High temperatures, high evaporation rates, and low rainfall increase the risk of polluting these waters. Groundwater resources near the surface are heavily salinized and can hardly serve as an adequate water source. Deeper groundwater reservoirs are difficult to access. The high population density in the Iishana system area increases the demand upon the surface waters. The geomorphology and surface hydrology of the Iishana system favors very slow surface runoff and low infiltration rates. An extreme change in dry and rainy seasons results in an erratic freshwater supply, which can decrease water quantity and water quality and is thus a major challenge. Since there were no data on the quality of the surface waters in this area, the state of the ecosystem and the health risk for the population are completely unclear; therefore, the regional surface waters were examined to determine their suitability as potable water. The aim is to better understand the hydrological systems in northern Namibia. In four field campaigns between 2017 and 2021, the surface waters, suspended solids, and sediments of the three systems (Kunene, Kavango, and CEB) and the local water supply system, the Calueque-Oshakati Canal, were sampled at more than 30 sites. Relevant hydrochemical parameters were analyzed, microplastics were investigated, and bioassays were conducted to gain insights into the status of aquatic ecosystems and the ecological impacts of pollutants. Spatial differences in the water quality relative to the decreasing precipitation gradient from east to west were noticed. Furthermore, metals such as aluminum and iron accumulate around the densely populated region in the eastern part of the study area. These waters were more polluted during the drought events in 2018 and 2019 than in 2017. Microplastics were found in different quantities, in particular PE and PP fragments. Three different trophic levels (algae, daphnia, and zebrafish embryos) were tested for acute toxicity. Mechanism-specific effects, such as estrogenicity (YES), cytochrome potential (micro-EROD), and mutagenicity (AMES) were investigated using in vitro assays. Acute toxicity could be detected for all three systems; in particular, the fish embryos showed several effects. Estrogenic and mutagenic effects were identified for several sampling sites. The different methodological approaches facilitate a holistic monitoring. This work is the first study to provide a comprehensive statement on water quality. The ecosystems of the Iishana, the Kunene, and Kavango Rivers are severely stressed and differ significantly. They show several signs of anthropogenic pollution that can affect human health. The use of water as potable water is not possible without prior treatment. Further investigation of the exact influencing factors, such as pesticides, is necessary to find suitable treatment measures for water use.
View lessCarbohydrates represent the most diverse and prevalent class of biomolecules in nature and are essential in a wide variety of biological processes. Antigenic glycans at the surface of microbes have the potential to be developed into glycoconjugate vaccines. The Automated Glycan Assembly (AGA) approach can provide those glycans rapidly in a solid-supported synthesis. Challenges in the synthesis of glycans by AGA arise from their complex structures, which require both strict regio- and stereocontrol, but also from technical limitations of the current AGA synthesizer. The goal of my research was to expand capabilities of AGA by introducing new orthogonal protecting groups and developing new strategies for 1,2-cis stereoselective glycosylations to give access to materials for research on infectious diseases. The first part of this dissertation focuses on orthogonality and the expansion of the protecting group portfolio in AGA (Chapter 3). The introduction of microwave-assistance to the AGA synthesizer enabled a larger temperature range (-40 to 100 °C) and the development of a mannose building block with four orthogonal protecting groups. When utilized in the microwave-assisted platform, this building block allowed 1) on-resin global deprotection and 2) the synthesis of glycan structures with up to four branches. In parallel, photo-labile 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) protecting groups were developed. A BODIPY protecting group bearing a boron difluoride unit provided the optimal compromise between glycosylation-stability and photo-lability by green light irradiation. This protecting group enabled a solution-phase consecutive glycan assembly without intermediate purification up to a trisaccharide. The second part of this dissertation describes studies on factors that influence the stereoselectivity for 1,2-cis glycosylations (Chapter 4). The influence of positional and electronic effects in acyl and ether groups on the efficacy for remote participation were investigated. An array of uniquely substituted building blocks was synthesized followed by the evaluation in model glycosylations and cold-ion IR spectroscopy. The obtained mechanistic insights helped to design building blocks for the formation of α-(1→3)-galactosidic linkages. In Chapter 5, the new knowledge and developed methods were utilized to synthesize a conjugation-ready glycan library of the Porphorymonas gingivalis lipopolysaccharide (LPS). P. gingivalis has an immense social and medical impact as it is the major cause of chronical periodontitis and is associated with several systemic diseases. The improvement of our basic understanding of interactions between human immune system and LPS may allow for treatment and prevention strategies. Twelve LPS fragments of P. gingivalis were screened for IgG and IgA binding in human saliva and serum using glycan microarray studies, which enabled the identification of 5-amino-pentyl α-D-Galp-(1→6)-α-D-Glcp-(1→4)-α-L-Rhap-(1→3)-2-β-D-GalNAc as a potential glycoconjugate vaccine candidate against P. gingivalis.
View lessThe project’s objective is to gain knowledge about the interconnection between cell growth and metabolism in the colon cancer cells HCT116 and RKO that rely on glutamine’s nitrogen. The non-cancerous HEK293 cells were tested in parallel to understand the specific metabolic settings and differences in glutamine-independent proliferation. A proteome analysis via liquid chromatography coupled to mass spectrometry (MS) was performed and revealed compartment specific protein expression in HCT116 and RKO cells. Interestingly, the enzyme glutamine synthetase (GLUL) was highly expressed in HEK293 cells under normal growth conditions. We wanted to know if HCT116 and RKO cells can grow independently from glutamine and starved the cells upon glutamine for a longer period. Surprisingly, HCT116 cells survived and persisted, while RKO cells did not. We suspected small molecules or residual glutamine in the growth medium and replaced the cell culture medium composition by dialyzed fetal bovine serum (FBS). Interestingly, in this case neither HCT116 nor HEK293 cells were able to proliferate when glutamine was deprived. Thus, glutamine was also essential for these cells when using dialyzed FBS. Based on these results, we assumed that HCT116 and HEK293 cells synthesize glutamine in the absence of external glutamine. Therefore, a supplementation growth experiment with substrates of the glutamine-centric metabolic network was performed. HCT116 and HEK293 cells showed highest proliferation rates in Glu + NH4 +, while RKO cells revealed an irreplaceable dependence on glutamine supplemented medium. Treatment with a competitive inhibitor of glutamine synthetase, methionine sulfoximine (MSO), blocked proliferation. Thus, glutamine synthetase was confirmed to be the survival factor in glutamine-depleted conditions, if substrates are provided. In order to examine the metabolic fate of glutamine, newly synthesized via GLUL, we have developed an isotope tracing technique using ultra high resolution MS, which allows us to distinguish between simultaneous labeling of carbon- 13 and nitrogen-15 isotopic patterns and that allows new insights into biological reactions in glutamine-deprived HCT116, RKO and HEK293 cells. With this new technique we were able to observe 13C and 15N incorporation in purine nucleotides. Additionally, we investigated the glutamine-analogue 6-Diazo-5-oxo-l-norleucine (DON) as it inhibits all glutamine-utilizing enzymes with focus on amidotransferases. An inital DON-inhibition experiment was performed to examine the interconnection of nucleotide synthesis and glutamine. We revealed an accumulation of nucleotide intermediates in HCT116 and HEK293 cells. To gain a clearer understanding, we traced glutamine‘s nitrogen flow in de novo nucleotide biosynthesis and where it is interfered by DON. Therefore, in the Kempa laboratory a new technique and method based on direct-infusion MS was developed that facilitates dynamic tracing of nitrogen with applied drugs on nucleotide substrates (Rayman (2022)). Finally, we observed decreased nitrogen incorporation into FGAR and the nucleotides of the purine pathway upon DON treatment in HCT116 cells. In conclusion, we demonstrated the inability of RKO cells to synthesize glutamine or to compensate glutamine-deficiency perhaps because of missing functionality of the enzyme GLUL. However, HCT116 and HEK293 cells have proven survivability. Furthermore, we were able to show DON targets in the purine nucleotide biosynthesis.
View lessHigh-alpine landscapes are exposed to pronounced temperature rise due to climate change. In particular, glacial and periglacial dynamics such as glacier retreat and permafrost thaw are accelerating, affecting the stability of rockwalls and posing hazards to the alpine environment. With recent deglaciation, rockfall activity and the production of debris are observed to increase. As the erosion of so-called headwalls above glaciers and associated debris deposition onto the ice surface increase, a thick supraglacial debris cover can form, modifying glacial mass balance and potentially delaying glacier retreat. Yet, debris supply rates and their changes vary spatially. To predict the evolution of glacial landscapes with climate change therefore requires to temporally and spatially examine rockwall erosion and potential temperature-related patterns. However, in situ measurements of rockwall erosion rates, specifically at headwalls, are rare as they are potentially dangerous in the difficult-to-access terrain, and the few existing records are often based on short-term monitoring from the last few decades. This thesis examines spatiotemporal records of headwall erosion in the Swiss Alps on longer terms to study glacial landscape dynamics with climate change. Headwall erosion rates were quantified by concentrations of the in situ-produced cosmogenic nuclide 10Be in medial moraine debris, obtained by interval-sampling along longitudinal moraine profiles. In a first small-scale case study, the archive function of medial moraines and temporal evolution of headwall erosion are studied in detail. Two medial moraine records were combined with a simple glacier transport model to account for the additional accumulation of 10Be during post-depositional downglacier debris transport and to assess the time of headwall erosion. Systematically varying 10Be concentrations over approximately the last 200 years indicate an increase in headwall erosion from the end of the Little Ice Age towards the following deglaciation period. This trend is reflected by different debris grain size fractions, implying that the records are unaffected by episodic large-scale erosion. In a follow-up study on a small mountain massif, temporal and spatial patterns of rockwall erosion are examined for five nearby glaciers and in relation to spatially distinct rockwall morphology. As an extension of the first study, ice cover changes across each debris source area were quantified to assess the potential contribution of recently deglaciated bedrock of possibly low 10Be concentrations, which seems to be low at most sites. Compared to the data from the first study, temporally constant 10Be concentrations over the last 100 years imply more stable rockwall erosion throughout the deglaciation period. At the same time, rockwall erosion rates are higher at steeper north faces in the massif. In a final, still ongoing study on a large-scale glacier catchment, two high-resolution medial moraine records are combined for the first time with paired in situ 14C/10Be analysis to resolve erosional landscape transience in more detail. Preliminary analyses suggest that conditions that caused an apparent pulse in erosion in one of two major debris source areas may be minor in the other due to differing headwall deglaciation histories. Yet, such rapid changes in transient landscapes, debris supply from long-time exposed or recently deglaciated surfaces, and post-depositional 10Be accumulation pose methodological challenges to derive rockwall erosion rates directly from measured medial moraine 10Be concentrations and require debris particle tracing in glacial landscapes and future research. Eventually, the studies of this thesis demonstrate that 10Be concentrations along medial moraines provide systematic results in landscapes that typically erode stochastically. Headwall erosion seems to be controlled by slope and temperature, and to accelerate at the transition of the Little Ice Age to deglaciation before stabilizing again - both observations that ultimately highlight the climate sensitivity of glacial landscapes.
View lessIn response to the climate crisis, there is a need for technological innovations to reduce the escalating CO2 emissions. Two promising semiconductor technologies in this regard, perovskite-based solar cells and memristive devices based on two-dimensional layered transition metal dichalcogenide (TMDC), can potentially contribute to the expansion of renewable energy sources and the development of energy-efficient computing hardware.
Within perovskite and TMDC materials, ions dislocate from their ideal position in the semiconductor crystal and leave void spaces. So far, the precise influence of these vacancies and their dynamics on device performance remain underexplored. Therefore, this thesis is dedicated to comprehensively examining the impact of vacancy-assisted charge transport in innovative semiconductor devices through a theoretical approach by modeling and simulating systems of partial differential equations. We start by deriving drift-diffusion equations using thermodynamic principles, including Maxwell-Stefan diffusion and the grand canonical ensemble of an ideal lattice gas. Particular attention is directed towards accurately limiting vacancy accumulation. Furthermore, we formulate drift-diffusion models to describe charge transport in perovskite solar cells and TMDC memristors. We discretize the transport equations via the finite volume method and establish the existence of discrete solutions using the entropy method. Our study concludes with simulations conducted with ChargeTransport.jl, an open source software tool developed in the programming language Julia. These simulations investigate the large time behavior of discrete solutions for both transport models. Additionally, we explore the influence of volume exclusion effects on charge transport in perovskite solar cells and compare our simulation results with experimental measurements found in literature for TMDC-based memristive devices.
View lessEinleitung Das Zervixkarzinom tritt mit hoher Inzidenz auf, wobei das mittlere Alter der Erstdiagnose stetig sinkt. Durch die Standardtherapie, die radikale Hysterektomie, wird die Familienplanung vieler Frauen beeinträchtigt. Die radikale vaginale Tachelektomie ermöglicht es, das Zervixkarzinom bis zum Stadium FIGO Ib2 stadiengerecht und zugleich fertilitätserhaltend zu therapieren. Unser Ziel war es, die Effekte der prophylaktischen, quadrivalenten HPV-Impfung bei Applikation post-Trachelektomie zu quantifizieren und die Stimulation einer Immunreaktion nachzuweisen. Methoden Den 75 zwischen 2002 und 2008 in unserer Klinik trachelektomierten Frauen wurde die quadrivalente HPV-Impfung empfohlen. 19 Patientinnen lehnten die Studienteilnahme ab, 37 entschieden sich für, 16 gegen die Impfung (Kontrollgruppe). Um die Titerentwicklung der Impf- und Kontrollgruppe beurteilen zu können, wurden die Antikörpertiter (L1-, E6- und E7-Antikörper der HPV-Typen 6, 11, 16, 18, 31 und 45) im Plasma der Patientinnen vor und gegebenenfalls nach Impfung an mehreren, longitudinal verteilten Zeitpunkten, durch GST-Luminex bestimmt (Anzahl der Messungen pro Patientin: 1-13, Median=5). Die Titer wurden deskriptiv dargestellt und zwischen den Messzeitpunkten durch den Wilcoxon-Vorzeichen-Rang-Test verglichen. Unter Miteinbeziehung der Daten zum HPV-Typ im Primärtumor und dem Blutabnahmezeitpunkt bildeten wir gemischte lineare Modelle zur Testung der Titerveränderungen nach Impfung bzw. in der Kontrollgruppe. Ergebnisse Wir konnten nachweisen, dass die L1-Antikörper aller geimpfter HPV-Typen sowie der Typen 31 und 45 als Folge der Impfung stark anstiegen. Der aggregierte Median der Titer der gegen die im Impfstoff enthaltenen L1-Antigene gerichte-ten Antikörper stieg von 162,3 MFI vor der ersten Impfung auf 3218 MFI nach mindestens einer Impfung (p<0,001). Auf die serologische Antwort gegen die jeweils untersuchten HPV-Typen hatte die zweite Impfung den stärksten Effekt (Range: 3,3- [HPV 18] bis 9,6-fach [HPV 11] des L1- Baseline-Titers) (Tab. 13-24). Die dritte Impfung hatte einen schwächeren Effekt (Range 1,8 [HPV 45] – 8,1-fach [HPV 11] im Vergleich zu vor der Impfung), gefolgt von der ersten Impfung (Range 1,4 [HPV 45] – 6,6-fach [HPV 11] im Vergleich zu vor der Impfung). Dieser Effekt konnte, wenngleich deutlich schwächer, auch für die E6- und E7-Antikörper der HPV-Typen 6, 11, 18 und 45 sowie die E6-Antikörper des HPV-Typ 31 nachgewiesen werden. Ebenso zeigten wir, dass der Effekt der Impfung auf den Titeranstieg bei Patientinnen, bei denen HPV-16, -18 oder -31 im Primärtumor nachgewiesen werden konnte, schwächer war als bei Probandinnen mit anderen HPV-Typen im Primärtumor. Begründet ist dies durch den vorhergehenden Antigenkontakt – und die dadurch bereits erhöhten Baseline- Antikörpertiter. Die L1-Antikörpertiter stiegen im Verlauf auf ein letztendlich hohes Niveau. Diskussion Wir konnten einen zuverlässig starken Anstieg der L1-Antikörpertiter der HPV-Typen 6,11,16,18,31 und 45 um mehr als das 10-Fache im Vergleich zu den Werten vor der Impfung signifikant nachweisen. Dieser Effekt ist der Impfung zuzuschreiben, in der Kontrollgruppe war er nicht nachweisbar. Dieser Nachweis wurde hier erstmalig bei Patientinnen nach Behandlung eines Karzinoms erbracht. Die Immunogenität der Impfung post-Trachelektomie ist gegeben. Ein leichter, aber dennoch signifikanter Anstieg der E6- und E7-Antikörper der HPV-Typen 18, 45, 6 und 11 sowie den E6-Antikörper des HPV-Typs 31 konnte ebenso nachgewiesen werden, die Bedeutung dieser indirekt stimulierten Reaktion, insbesondere der Langzeitauswirkungen, bedarf weiterer Forschung.
View lessThe process of bone fracture healing relies on a tight regulation of cellular and molecular events. However, obesity can disrupt the healing cascade, leading to defective repair. A heightened inflammatory state, primarily regulated by the adaptive immunity, is believed to contribute to the pathophysiology of obesity linked to bone healing defects. Despite the high obesity prevalence, limited research has explored this relationship. Herein, the underlying hypothesis of this work is that increased pro-inflammation associated with obesity may be causative for delayed bone repair. The specific aims were to understand the impact of different degrees of obesity, as encountered in clinical settings, on the modulation of immunity and its effects on bone fracture healing. To investigate this, a high-fat diet (HFD)-induced obesity model was used in conjunction with femoral osteotomy. Based on metabolic measurements, two obese subtypes were included in this study: a group with low glucose intolerance and a group with high glucose intolerance that indicates a possible developing type 2 diabetes mellitus (T2DM). The findings provided evidence that the early onset of obesity induced by a short-term HFD resulted in a pro-inflammatory state that caused impaired healing of femoral fractures with an altered microarchitecture in both obese groups. Remarkably, obese mice with high glucose intolerance showed signs of adapting to the metabolic conditions in terms of pro-inflammatory responses and bone healing capacity. Consistently, a long-term HFD resulted in reduced pro-inflammation in both groups. Surprisingly, along with increased weight gain, callus adiposity and bone mineralization, the previously observed healing defects associated with obesity were repealed regarding the mineralization process. However, abnormal extracellular matrix (ECM) remodeling and formation were observed during initial bone fracture healing, with more pronounced effects seen in mice with high glucose intolerance, hinting at a T2DM manifestation. This finding poses a potential risk for the development of fibrosis. Neutralization of potentially detrimental CD8+ T cells during the early healing phase reversed the disturbance in the formation of ECM in the obese group with high glucose intolerance. This finding highlights the critical role of CD8+ T cells in regeneration and offers a potential therapeutic approach to improve bone formation in specific patients. The microbiome's role in obesity and its connection to adaptive immunity and metabolic inflammation is well established. The analysis of feces and cecal samples revealed that long-term obesity altered the gut microbiome structure, while bacterial diversity remained unchanged. Interestingly, obese mice with high glucose intolerance exhibited a distinct microbial signature associated with metabolic rather than immunological alterations. Importantly, these obesity-related changes were partially reversible through the neutralization of CD8+ T cells. Overall, this work emphasizes that aberrant bone formation occurs early in the progression of obesity, before the development of obesity-associated T2DM. The activation of the immune system is even enhanced at the onset of obesity, leading to impaired bone formation. Although the skeletal system adapts to the immunological and metabolic imbalance associated with persistent obesity, this still results in an altered ECM. The data increase our comprehension and awareness of obesity progression in clinical contexts, providing potential therapeutic avenues. Addressing obesity becomes crucial to making right and timely decisions for susceptible fracture patients.
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