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Schriftenreihe
Sonstige beteiligte Institutionen
- IZKF Nachwuchsgruppe Geweberegeneration für muskuloskelettale Erkrankungen (5)
- Bernhard-Heine-Centrum für Bewegungsforschung (4)
- Zentraleinheit Klinische Massenspektrometrie (3)
- Fraunhofer-Institut für Silicatforschung ISC (2)
- Helmholtz Institute for RNA-based Infection Research (HIRI) (2)
- Krankenhaushygiene und Antimicrobial Stewardship (Universitätsklinikum) (2)
- Wilhelm-Conrad-Röntgen-Forschungszentrum für komplexe Materialsysteme (2)
- ALPARC - The Alpine Network of Protected Areas (1)
- Albert-Ludwigs-Universität Freiburg (1)
- Arizona State University, Tempe, Arizona, USA (1)
The interaction between circadian clocks and metabolism is of increasing interest, since clock dysfunction often correlates with metabolic pathologies. Many research articles have been published analysing the impact of factors such as circadian clock, light, feeding time and diet-type on energy homeostasis in various tissues/organs of organisms with most of the findings done in mammals. Little is known about the impact of circadian clock and the above-mentioned factors on circulating lipids, especially the transport form of lipids - diacylglycerol (DG) and membrane lipids such as phosphatidylethanolamine (PE) and phosphatidylcholine (PC) in the Drosophila hemolymph. The fruit fly Drosophila is a prime model organism in circadian, behaviour and metabolism research.
To study the role of circadian clock and behaviour in metabolism, we performed an extensive comparative hemolymph lipid (diacylglycerol: DG, phosphatidylethanolamine: PE, phosphatidylcholine: PC) analysis using ultra performance liquid chromatography coupled to time-of-flight mass spectrometry (UPLC-MS) between wild-type flies (WTCS) and clock disrupted mutants (per01). In addition, clock controlled food intake– feeding behaviour was investigated. Time-dependent variation of transport (DG) and membrane lipids (PE and PC) were not rhythmic in WTCS under constant darkness and in per01 under LD, suggesting an impact of light and clock genes on daily lipid oscillations. Day-time and night-time restriction of food led to comparable lipid profiles, suggesting that lipid oscillations are not exclusively entrained by feeding but rather are endogenously regulated. Ultradian oscillations in lipid levels in WTCS under LD were masked by digested fatty acids since lipid levels peaked more robustly at the beginning and end of light phase when flies were fed a lipid- and protein-free diet. These results suggest that metabolite (DG, PE and PC) oscillation is influenced by complex interactions between nutrient-type, photic conditions, circadian clock and feeding time.
In conclusion, the results of this thesis suggest that circadian clocks determine transport and membrane lipid oscillation in Drosophila hemolymph in complex interactions between nutrient-type, photic conditions and feeding behaviour.
In today's world, circumstances, processes, and requirements for systems in general-in this thesis a special focus is given to the context of Cyber-Physical Systems (CPS)-are becoming increasingly complex and dynamic.
In order to operate properly in such dynamic environments, systems must adapt to dynamic changes, which has led to the research area of Self-Adaptive Systems (SAS).
These systems can deal with changes in their environment and the system itself.
In our daily lives, we come into contact with many different self-adaptive systems that are designed to support and improve our way of life.
In this work we focus on the two domains Intelligent Transportation Systems (ITS) and logistics as both domains provide complex and adaptable use cases to prototypical apply the contributions of this thesis.
However, the contributions are not limited to these areas and can be generalized also to other domains such as the general area of CPS and Internet of Things including smart grids or even intelligent computer networks.
In ITS, real-time traffic control is an example adaptive system that monitors the environment, analyzes observations, and plans and executes adaptation actions.
Another example is platooning, which is the ability of vehicles to drive with close inter-vehicle distances.
This technology enables an increase in road throughput and safety, which directly addresses the increased infrastructure needs due to increased traffic on the roads.
In logistics, the Vehicle Routing Problem (VRP) deals with the planning of road freight transport tours.
To cope with the ever-increasing transport volume due to the rise of just-in-time production and online shopping, efficient and correct route planning for transports is important.
Further, warehouses play a central role in any company's supply chain and contribute to the logistical success.
The processes of storage assignment and order picking are the two main tasks in mezzanine warehouses highly affected by a dynamic environment.
Usually, optimization algorithms are applied to find solutions in reasonable computation time.
SASes can help address these dynamics by allowing systems to deal with changing demands and constraints.
For the application of SASes in the two areas ITS and logistics, the definition of adaptation planning strategies is the key success factor.
A wide range of adaptation planning strategies for different domains can be found in the literature, and the operator must select the most promising strategy for the problem at hand.
However, the No-Free-Lunch theorem states that the performance of one strategy is not necessarily transferable to other problems.
Accordingly, the algorithm selection problem, first defined in 1976, aims to find the best performing algorithm for the current problem.
Since then, this problem has been explored more and more, and the machine learning community, for example, considers it a learning problem.
The ideas surrounding the algorithm selection problem have been applied in various use cases, but little research has been done to generalize the approaches.
Moreover, especially in the field of SASes, the selection of the most appropriate strategy depends on the current situation of the system.
Techniques for identifying the situation of a system can be found in the literature, such as the use of rules or clustering techniques.
This knowledge can then be used to improve the algorithm selection, or in the scope of this thesis, to improve the selection of adaptation planning strategies.
In addition, knowledge about the current situation and the performance of strategies in similar previously observed situations provides another opportunity for improvements.
This ongoing learning and reasoning about the system and its environment is found in the research area Self-Aware Computing (SeAC).
In this thesis, we explore common characteristics of adaptation planning strategies in the domain of ITS and logistics presenting a self-aware optimization framework for adaptation planning strategies.
We consider platooning coordination strategies from ITS and optimization techniques from logistics as adaptation planning strategies that can be exchanged during operation to better reflect the current situation.
Further, we propose to integrate fairness and uncertainty handling mechanisms directly into the adaptation planning strategies.
We then examine the complex structure of the logistics use cases VRP and mezzanine warehouses and identify their systems-of-systems structure.
We propose a two-stage approach for vertical or nested systems and propose to consider the impact of intertwining horizontal or coexisting systems.
More specifically, we summarize the six main contributions of this thesis as follows:
First, we analyze specific characteristics of adaptation planning strategies with a particular focus on ITS and logistics.
We use platooning and route planning in highly dynamic environments as representatives of ITS and we use the rich Vehicle Routing Problem (rVRP) and mezzanine warehouses as representatives of the logistics domain.
Using these case studies, we derive the need for situation-aware optimization of adaptation planning strategies and argue that fairness is an important consideration when applying these strategies in ITS.
In logistics, we discuss that these complex systems can be considered as systems-of-systems and this structure affects each subsystem.
Hence, we argue that the consideration of these characteristics is a crucial factor for the success of the system.
Second, we design a self-aware optimization framework for adaptation planning strategies.
The optimization framework is abstracted into a third layer above the application and its adaptation planning system, which allows the concept to be applied to a diverse set of use cases.
Further, the Domain Data Model (DDM) used to configure the framework enables the operator to easily apply it by defining the available adaptation planning strategies, parameters to be optimized, and performance measures.
The framework consists of four components: (i) Coordination, (ii) Situation Detection, (iii) Strategy Selection, and (iv) Parameter Optimization.
While the coordination component receives observations and triggers the other components, the situation detection applies rules or clustering techniques to identify the current situation.
The strategy selection uses this knowledge to select the most promising strategy for the current situation, and the parameter optimization applies optimization algorithms to tune the parameters of the strategy.
Moreover, we apply the concepts of the SeAC domain and integrate learning and reasoning processes to enable ongoing advancement of the framework.
We evaluate our framework using the platooning use case and consider platooning coordination strategies as the adaptation planning strategies to be selected and optimized.
Our evaluation shows that the framework is able to select the most appropriate adaptation strategy and learn the situational behavior of the system.
Third, we argue that fairness aspects, previously identified as an important characteristic of adaptation planning strategies, are best addressed directly as part of the strategies.
Hence, focusing on platooning as an example use case, we propose a set of fairness mechanisms to balance positive and negative effects of platooning among all participants in a platoon.
We design six vehicle sequence rotation mechanisms that continuously change the leader position among all participants, as this is the position with the least positive effects.
We analyze these strategies on roads of different sizes and with different traffic volumes, and show that these mechanisms should also be chosen wisely.
Fourth, we address the uncertainty characteristic of adaptation planning strategies and propose a methodology to account for uncertainty and also address it directly as part of the adaptation planning strategies.
We address the use case of fueling planning along a route associated with highly dynamic fuel prices and develop six utility functions that account for different aspects of route planning.
Further, we incorporate uncertainty measures for dynamic fuel prices by adding penalties for longer travel times or greater distance to the next gas station.
Through this approach, we are able to reduce the uncertainty at planning time and obtain a more robust route planning.
Fifth, we analyze optimization of nested systems-of-systems for the use case rVRP.
Before proposing an approach to deal with the complex structure of the problem, we analyze important constraints and objectives that need to be considered when formulating a real-world rVRP.
Then, we propose a two-stage workflow to optimize both systems individually, flexibly, and interchangeably.
We apply Genetic Algorithms and Ant Colony Optimization (ACO) to both nested systems and compare the performance of our workflow with state-of-the-art optimization algorithms for this use case.
In our evaluation, we show that the proposed two-stage workflow is able to handle the complex structure of the problem and consider all real-world constraints and objectives.
Finally, we study coexisting systems-of-systems by optimizing typical processes in mezzanine warehouses.
We first define which ergonomic and economic constraints and objectives must be considered when addressing a real-world problem.
Then, we analyze the interrelatedness of the storage assignment and order picking problems; we identify opportunities to design optimization approaches that optimize all objectives and aim for a good overall system performance, taking into account the interdependence of both systems.
We use the NSGA-II for storage assignment and Ant Colony Optimization (ACO) for order picking and adapt them to the specific requirements of horizontal systems-of-systems.
In our evaluation, we compare our approaches to state-of-the-art approaches in mezzanine warehouses and show that our proposed approaches increase the system performance.
Our proposed approaches provide important contributions to both academic research and practical applications.
To the best of our knowledge, we are the first to design a self-aware optimization framework for adaptation planning strategies that integrates situation-awareness, algorithm selection, parameter tuning, as well as learning and reasoning.
Our evaluation of platooning coordination shows promising results for the application of the framework.
Moreover, our proposed strategies to compensate for negative effects of platooning represent an important milestone, which could lead to higher acceptance of this technology in society and support its future adoption in the real world.
The proposed methodology and utility functions that address uncertainty are an important step to improving the capabilities of SAS in an increasingly turbulent environment.
Similarly, our contributions to systems-of-systems optimization are major contributions to the state of logistics and systems-of-systems research.
Finally, we select real-world use cases for the application of our approaches and cooperate with industrial partners, which highlights the practical relevance of our contributions.
The reduction of manual effort and required expert knowledge in our self-aware optimization framework is a milestone in bridging the gap between academia and practice.
One of our partners integrated the two-stage approach to tackling the rVRP into its software system, improving both time to solution and solution quality.
In conclusion, the contributions of this thesis have spawned several research projects such as a long-term industrial project on optimizing tours and routes in parcel delivery funded by Bayerisches Verbundforschungsprogramm (BayVFP) – Digitalisierung and further collaborations, opening up many promising avenues for future research.
Microbial rhodopsins are abundant membrane proteins often capable of ion transport and are found in all three domains of life. Thus, many fungi, especially phyto-associated or phyto-pathogenic ones, contain these green-light-sensing photoreceptors. Proteins that perceive other wavelengths are often well characterized in terms of their impact on fungal biology whereas little is known about the function of fungal rhodopsins. In this work, five fungal rhodopsins, UmOps1 and UmOps2 from the corn smut Ustilago maydis as well as ApOps1, ApOps2 and ApOps3 from the black yeast Aureobasidium pullulans, were characterized electrophysiologically using mammalian expression systems and the patch-clamp technique to explore their ion transport properties. The latter three were modified using a membrane trafficking cassette, termed “2.0” that consists of the lucy rho motif, two Kir2.1 Golgi apparatus trafficking signals and a Kir2.1 endoplasmic reticulum export signal, what resulted in better plasma membrane localization. Rhodopsin mutants were created to identify amino acid residues that are key players in the ion transport process. Current enhancement in the presence of weak organic acids, that was already described before for the fungal rhodopsin CarO from Fusarium fujikuroi (García-Martínez et al., 2015; Adam et al., 2018), was investigated for the U. maydis rhodopsins as well as for ApOps2 by supplementing acetate in the patch-clamp electrolyte solutions. All five rhodopsins were found to be proton pumps unidirectionally transporting protons out of the cytosol upon green-light exposure with every rhodopsin exhibiting special features or unique characteristics in terms of the photocurrents. To name just a few, UmOps1, for example, showed a striking pH-dependency with massive enhancement of pump currents in the presence of extracellular acidic pH. Moreover, especially ApOps2 and ApOps3 showed very high current densities, however, the ones of ApOps3 were impaired when exchanging intracellular sodium to cesium. Concerning the mutations, it was found, that the electron releasing group in UmOps1 seems to be involved in the striking pH effect and that the mutation of the proton donor site resulted in almost unfunctional proteins. Moreover, a conserved arginine inside ApOps2 was mutated to turn the proton pump into a channel. Regarding the effect of weak organic acids, acetate was able to induce enhanced pump currents in UmOps1 and ApOps2, but not in UmOps2. Due to the capability of current production upon light illumination, microbial rhodopsins are used in the research field of optogenetics that aims to control neuronal activity by light. ApOps2 was used to test its functionality in differentiated NG108-15 cells addressing the question whether it is a promising candidate that can be used as an optogenetic tool. Indeed, this rhodopsin could be functionally expressed in this experimental system. Furthermore, microscopic studies were done to elucidate the localization of selected rhodopsins in fungal cells. Therefore, conventional (confocal laser scanning or structured illumination microscopy) as well as novel super-resolution techniques (expansion or correlated light and electron microscopy) were used. This was done on U. maydis sporidia, the yeast-like form of this fungus, via eGFP-tagged UmOps1 or UmOps2 expressing strains. Moreover, CarO-eYFP expressing F. fujikuroi was imaged microscopically to confirm the plasma membrane and tonoplast localization (García-Martínez et al., 2015) with the help of counterstaining experiments. UmOps1 was found to reside in the plasma membrane, UmOps2 localized to the tonoplast and CarO was indeed found in both of these localizations. This work gains further insight into rhodopsin functions and paves the way for further research in terms of the biological role of rhodopsins in fungal life cycles.
In this work, the influence of aromatic structures on drug encapsulation, self-assembly and hydrogel formation was investigated. The physically crosslinked gelling systems were characterized and optimized for the use in biofabrication and applied in initial (bio)printing experiments.
Chapter I: The cytocompatible (first in vitro and in vivo studies) amphiphile PMeOx-b-PBzOx-b- PMeOx (A-PBzOx-A) was used for the solubilization of PTX, schizandrin A (SchA), curcumin (CUR), niraparib and HS-173.
Chapter II: Compared to the polymers A-PPheOx-A, A-PBzOx-A and A-PBzOzi-A, only the polymer A-PPheOzi-A showed a reversible temperature- and concentration-dependent inverse thermogelation, which is accompanied by a morphology change from long wormlike micelles in the gel to small spherical micelles in solution. The worm formation results from novel interactions between the hydrophilic and hydrophobic aromatic polymer blocks. Changes in the hydrophilic block significantly alter the gel system. Rheological properties can be optimized by concentration and temperature, which is why the hydrogel was used to significantly improve the printability and stability of Alg in a blend system.
Chapter III: By extending the side chain of the aromatic hydrophobic block, the inverse thermogelling polymer A-poly(2-phenethyl-2-oxazoline)-A (A-PPhenEtOx-A) is obtained. Rapid gelation upon cooling is achieved by inter-correlating spherical micelles. Based on ideal rheological properties, first cytocompatible bioprinting experiments were performed in combination with Alg. The polymers A- poly(2-benzhydryl-2-oxazoline)-A (A-PBhOx-A) and A-poly(2-benzhydryl-2-oxazine) (A-PBhOzi-A) are characterized by two aromatic benzyl units per hydrophobic repeating unit. Only the polymer A- PBhOzi-A exhibited inverse thermogelling behavior. Merging micelles could be observed by electron microscopy. The system was rheologically characterized and discussed with respect to an application in 3D printing.
Chapter IV: The thermogelling POx/POzi system, in particular the block copolymer PMeOx-b- PnPrOzi, was used in different applications in the field of biofabrication. The introduction of maleimide and furan units along the hydrophilic polymer part ensured additional stabilization by Diels-Alder crosslinking after the printing process.
∆Np63 is a master regulator of squamous cell identity and regulates several signaling pathways that crucially
contribute to the development of squamous cell carcinoma (SCC) tumors. Its contribution to coordinating the
expression of genes involved in oncogenesis, epithelial identity, DNA repair, and genome stability has been
extensively studied and characterized. For SCC, the expression of ∆Np63 is an essential requirement to
maintain the malignant phenotype. Additionally, ∆Np63 functionally contributes to the development of cancer
resistance toward therapies inducing DNA damage.
SCC patients are currently treated with the same conventional Cisplatin therapy as they would have been
treated 30 years ago. In contrast to patients with other tumor entities, the survival of SCC patients is limited,
and the efficacy of the current therapies is rather low. Considering the rising incidences of these tumor entities,
the development of novel SCC therapies is urgently required. Targeting ∆Np63, the transcription factor, is a
potential alternative to improve the therapeutic response and clinical outcomes of SCC patients.
However, ∆Np63 is considered “undruggable.” As is commonly observed in transcription factors, ∆Np63 does
not provide any suitable domains for the binding of small molecule inhibitors. ∆Np63 regulates a plethora of
different pathways and cellular processes, making it difficult to counteract its function by targeting
downstream effectors. As ∆Np63 is strongly regulated by the ubiquitin–proteasome system (UPS), the
development of deubiquitinating enzyme inhibitors has emerged as a promising therapeutic strategy to target
∆Np63 in SCC treatment.
This work involved identifying the first deubiquitinating enzyme that regulates ∆Np63 protein stability. Stateof-the-art SCC models were used to prove that USP28 deubiquitinates ∆Np63, regulates its protein stability,
and affects squamous transcriptional profiles in vivo and ex vivo. Accordingly, SCC depends on USP28 to
maintain essential levels of ∆Np63 protein abundance in tumor formation and maintenance. For the first time,
∆Np63, the transcription factor, was targeted in vivo using a small molecule inhibitor targeting the activity of
USP28. The pharmacological inhibition of USP28 was sufficient to hinder the growth of SCC tumors in
preclinical mouse models.
Finally, this work demonstrated that the combination of Cisplatin with USP28 inhibitors as a novel therapeutic
alternative could expand the limited available portfolio of SCC therapeutics. Collectively, the data presented
within this dissertation demonstrates that the inhibition of USP28 in SCC decreases ∆Np63 protein abundance,
thus downregulating the Fanconi anemia (FA) pathway and recombinational DNA repair. Accordingly, USP28
inhibition reduces the DNA damage response, thereby sensitizing SCC tumors to DNA damage therapies, such
as Cisplatin.
Our current data demonstrate that besides the known risk factors, including apical aneurysm, reduced left ventricular longitudinal systolic function (MAPSE) and advanced diastolic dysfunction, Right ventricular dysfunction as determined by reduced tricuspid annular plane systolic excursion (TAPSE) or right ventricular fractional area change (RV_FAC) is independently associated with left ventricular thrombus formation in acute anterior myocardial infarction patients, especially in the setting of anterior myocardial infarction without the formation of an apical aneurysm. This study suggests that besides left ventricular abnormalities, right ventricular dysfunction likewise contributes LVT formation in patients with acute anterior myocardial infarction.
Cancer is one of the major causes of mortality in developed countries. In 2020, there were more than 19.3 million new cases of tumor malignancies worldwide, with more than 10 million deaths. The high rates of cancer cases and mortality necessitate extensive research and the development of novel cancer treatments and antitumor agents. In most cases, conventional treatment strategies for tumor therapy are based on chemotherapeutic treatment, which is supplemented with radiotherapy and/or surgical resection of solid tumors [1]. The use of chemotherapy for the treatment of cancer has significant side effects, the most dangerous of which is toxicity [2] [3].
Modern methods of treating tumors focus on specific drug delivery to the tumor site, actively targeting the tumor cells, as well as the reduction of side effects. One of the most promising current approaches is based on oncolytic viruses. Antitumor properties of viruses were documented at the beginning of the 20th century when some cancer patients recovered after acute viral infections, particularly influenza [4]. Vaccinia virus (VACV) is a member of the Poxviridae family, has natural antitumor properties, and provides a good basis for generating efficient recombinant oncolytic strains. Furthermore, VACV has never been shown to integrate into the host genome [5]. VACV is likely one of the safest and well-studied viruses due to extensive research being done in molecular biology and pathophysiology to investigate its potential as a vaccine for smallpox eradication programs. It has been administered to over 200 million people worldwide. VACV antitumor therapeutic effectiveness has been established in xenograft models with a variety of tumor types for human and canine cancers. Furthermore, recombinant oncolytic VACVs expressing genes encoding light-emitting proteins are a big improvement in a treatment strategy that combines tumor-specific therapies and diagnostics.
Oncolytic virus treatments are effective in xenograft cancer models in mice, however, the significant improvements found in mice do not always translate to human cancer patients. These therapies should be tested in dogs with spontaneous cancer not only to offer well translatable information regarding the possible efficiency of viral therapy for human cancers but also to improve the health of our household pets as well. Spontaneous canine tumors are starting to be regarded as an essential model of human cancers that can reproduce the tumor microenvironment and immune response of cancer patients [6]. Just as data obtained in dog experiments can improve cancer therapy for human patients, these findings can also be used to improve treatment protocols in canine patients.
Hundreds of studies and dozens of reviews have been published regarding the antitumor effects of various recombinants of VACV, but information on the anticancer features of initial, genetically-unmodified “naïve” VACV is still limited. In the first studies, we compared different wild-type, non-modified strains of VACV and tested their oncolytic properties on a panel of various cancer cells derived from different organs. In addition, we also tested a protection system based on the “Trojan horse” concept - using a combination of human Adipose tissue-derived Stem Cells (hADSC) and three different wild-type single plaque purified Vaccinia virus strains: W1, L1, and T1. We showed that all tested human cell lines (FaDu, MDA MB 231, HNT-13, HNT-35, and PC-3) are permissive to L0, W0, T0, L1, W1, and L1 infection. Furthermore, we tested the cytotoxicity of VACV in different cancer cell lines (A549, PC-3, MDA-MB 231, FaDu, HNT-13, HNT-25, and HNT-35). All strains lysed the cells, which was most visible at 96 hpi. We also showed that all tested strains could efficiently infect and multiply in hADSC at a high level. In our in vivo study, we tested the therapeutic efficacy of the wild-type Vaccinia viruses L1, W1, and T1 alone or in combination with hADSC. Wild-type VACV strains were tested for their oncolytic efficiency in human lung adenocarcinoma (A549) in a xenograft model. Treatment of A549 tumors with different doses of L1 and W1 as well as with a L1/ADSC or W1/ADSC combination led to significant tumor regression compared to the PBS control. Additionally, the treatment with L1 and W1 and the combination of L1/ADSC and W1/ADSC was well tolerated by the animals. In the case of the wild-type Tian Tan strain, results were not obtained due to the high cytotoxicity of this strain. Therefore, it should be attenuated for further studies.
In the second part of the current study, we investigated the oncolytic effect of C1-opt1, W1 opt1, and L3-opt1 strains based on the wild-type Copenhagen, Wyeth, and Lister vaccines with additional expression of turboFP635. Replication and cytotoxicity assays demonstrated that all 3 viruses were able to infect, replicate in and kill canine tumor cell lines STSA-1 and CT1258 in a virus dose- and time- dependent fashion. Cytotoxicity and replication assays were also performed on cultured canine Adipose-derived Mesenchymal Stem Cells (cAdMSC). The results showed that the cells were lysed much slower than the tumor cells. It suggests that these cells can harbour the virus for a long-term period, allowing the virus to spread into the body and there is enough time to reach the primary tumor or metastases before the cell carrier is destroyed. The viral replication in cAdMSC in our study was lower than in canine cancer cells (STSA-1 and CT1258) at the same MOI. After being studied in cell culture, C1 opt1 and their combination with cAdMSC (C1-opt1/cAdMSC) were used in canine STSA 1 tumor bearing nude mice. We tested the oncolytic effect of the C1-opt1 virus alone and in combination with cAdMSC in the canine STSA-1 xenograft mouse model. Altogether, our findings have shown that both C1-opt1 and cAdMSC/C1-opt1 significantly reduced tumor size or eliminated the tumor. There was no significant difference between C1-opt1 alone and cAdMSC/C1-opt1. The virus particles were mostly found within the tumor after 24 dpi, some amount of virus particles were found in the lungs of mice injected with a combination of cAdMSC/C1-opt1 but not in the group injected with virus alone (cAdMSC might get stuck in the lungs and cause virus propagation there).
Taken together, this study provided a proof-of-concept that hADSC/cAdMSC can be used as a carrier system for the “Trojan horse” concept. However, it should be confirmed in another experimental model system, such as canine patients. Moreover, these findings suggest that wild-type, non-modified strains of Vaccinia virus isolates can be considered promising candidates for oncolytic virotherapy, especially in combination with mesenchymal stem cells.
For a large fraction of the proteins expressed in the human brain only the primary
structure is known from the genome project. Proteins conserved in evolution can
be studied in genetic models such as Drosophila. In this doctoral thesis monoclonal
antibodies (mAbs) from the Wuerzburg Hybridoma library are produced and
characterized with the aim to identify the target antigen. The mAb ab52 was found
to be an IgM which recognized a cytosolic protein of Mr ~110 kDa on Western
blots. The antigen was resolved by two-dimensional gel electrophoresis (2DE) as a
single distinct spot. Mass spectrometric analysis of this spot revealed EPS-15
(epidermal growth factor receptor pathway substrate clone 15) to be a strong
candidate. Another mAb from the library, aa2, was already found to recognize
EPS-15, and comparison of the signal of both mAbs on Western blots of 1D and
2D electrophoretic separations revealed similar patterns, hence indicating that both
antigens could represent the same protein. Finally absence of the wild-type signal
in homozygous Eps15 mutants in a Western blot with ab52 confirmed the ab52
antigen to be EPS-15. Thus both the mAbs aa2 and ab52 recognize the Drosophila
homologue of EPS-15. The mAb aa2, being an IgG, is more suitable for
applications like immunoprecipitation (IP). It has already been submitted to the
Developmental Studies Hybridoma Bank (DSHB) to be easily available for the
entire research community.
The mAb na21 was also found to be an IgM. It recognizes a membrane associated
antigen of Mr ~10 kDa on Western blots. Due to the membrane associated nature
of the protein, it was not possible to resolve it by 2DE and due to the IgM nature of
the mAb it was not possible to enrich the antigen by IP. Preliminary attempts to
biochemically purify the endogenously expressed protein from the tissue, gave
99
promising results but could not be completed due to lack of time. Thus
biochemical purification of the protein seems possible in order to facilitate its
identification by mass spectrometry. Several other mAbs were studied for their
staining pattern on cryosections and whole mounts of Drosophila brains. However,
many of these mAbs stained very few structures in the brain, which indicated that
only a very limited amount of protein would be available as starting material.
Because these antibodies did not produce signals on Western blots, which made it
impossible to enrich the antigens by electrophoretic methods, we did not attempt
their purification. However, the specific localization of these proteins makes them
highly interesting and calls for their further characterization, as they may play a
highly specialized role in the development and/or function of the neural circuits
they are present in. The purification and identification of such low expression
proteins would need novel methods of enrichment of the stained structures.
During natural behavior, cognitive processes constantly coincide with body movements such as head or eye movements or blinks. However, during experimental investigations of cognitive processes, movements are often highly restricted which is rather unnatural. In order to improve our understanding of natural behavior, this thesis investigates the interaction between cognition and movements by focusing on spontaneous blinks, which naturally interact with other body movements.
Spontaneous blinks are inevitably connected to vision as they shut out incoming visual information. Both sensory-based and cognitive factors, for example, stimulus occurrence and evaluation, were reported to influence blink behavior. Our first study investigated if such influences are comparable for visual and non-visual input. The chosen experimental design allowed dissociating sensory-driven and cognitive influences, which then could be compared between the visual and auditory domain. Our results show that blinks are more strongly modulated during passive observation of visual input compared to auditory input. This modulation is however enhanced for both input modalities by an increased attentional demand. In addition, the cognitively defined meaning of a stimulus changes blink latency independent of the sensory domain. Overall, our findings show that spontaneous blinks and cognitive processes are linked beyond vision. Moreover, the underlying cognitive processes that influence blinks are largely the same across different sensory input indicating that blinks are profoundly integrated into our system.
When investigating natural behavior, it is important to consider that movements rarely occur in isolation, but are executed side by side. As these movements interact and have a link to cognitive processes, the complexity of our system increases. In order to take this complexity into account, the second part of the experimental research focused on movement interactions, more specifically on the interactions between blinks, pupil size and speaking. Our results reveal that speech-related motor activity increases blink rate and pupil size as well as modulates blink timing. This is in line with previous research that described a relation between different body and eye movements. Importantly, each bodily-induced change in eye movements affects visual information intake. Therefore, different movements can be tightly linked to perceptual processes through complex interactions.
Altogether, the work of this thesis provides rich evidence that movements and cognitive processes are deeply intertwined. Therefore, movements should be seen as an integral part of our system. Taking the relevance of movements and their interactions into account during experimental investigations is necessary in order to reveal a more realistic and complete picture of human natural behavior.
Aims
There is an ongoing discussion whether the categorization of patients with heart failure according to left ventricular ejection fraction (LVEF) is scientifically justified and clinically relevant. Major efforts are directed towards the identification of appropriate cut-off values to correctly allocate heart failure-specific pharmacotherapy. Alternatively, an LVEF continuum without definite subgroups is discussed. This study aimed to evaluate the natural distribution of LVEF in patients presenting with acutely decompensated heart failure and to identify potential subgroups of LVEF in male and female patients.
Methods and results
We identified 470 patients (mean age 75 ± 11 years, n = 137 female) hospitalized for acute heart failure in whom LVEF could be quantified by Simpson's method in an in-hospital echocardiogram. Non-parametric modelling revealed a bimodal shape of the LVEF distribution. Parametric modelling identified two clusters suggesting two LVEF peaks with mean (variance) of 61% (9%) and 31% (10%), respectively. Sub-differentiation by sex revealed a sex-specific bimodal clustering of LVEF. The respective threshold differentiating between ‘high’ and ‘low’ LVEF was 45% in men and 52% in women.
Conclusions
In patients presenting with acute heart failure, LVEF clustered in two subgroups and exhibited profound sex-specific distributional differences. These findings might enrich the scientific process to identify distinct subgroups of heart failure patients, which might each benefit from respectively tailored (pharmaco)therapies.
Background
Influenza virus infections in immunologically naïve children (primary infection) may be more severe than in children with re-infections who are already immunologically primed. We compared frequency and severity of influenza virus primary and re-infections in pre-school children requiring outpatient treatment.
Methods
Influenza-unvaccinated children 1–5 years of age presenting at pediatric practices with febrile acute respiratory infection < 48 h after symptom onset were enrolled in a prospective, cross-sectional, multicenter surveillance study (2013–2015). Influenza types/subtypes were PCR-confirmed from oropharyngeal swabs. Influenza type/subtype-specific IgG antibodies serving as surrogate markers for immunological priming were determined using ELISA/hemagglutination inhibition assays. The acute influenza disease was defined as primary infection/re-infection by the absence/presence of influenza type-specific immunoglobulin G (IgG) and, in a second approach, by the absence/presence of subtype-specific IgG. Socio-demographic and clinical data were also recorded.
Results
Of 217 influenza infections, 178 were due to influenza A (87 [49%] primary infections, 91 [51%] re-infections) and 39 were due to influenza B (38 [97%] primary infections, one [3%] re-infection). Children with “influenza A primary infections” showed fever with respiratory symptoms for a shorter period than children with “influenza A re-infections” (median 3 vs. 4 days; age-adjusted p = 0.03); other disease characteristics were similar. If primary infections and re-infections were defined based on influenza A subtypes, 122 (87%) primary infections (78 “A(H3N2) primary infections”, 44 “A(H1N1)pdm09 primary infections”) and 18 (13%) re-infections could be classified (14 “A(H3N2) re-infections” and 4 “A(H1N1)pdm09 re-infections”). Per subtype, primary infections and re-infections were of similar disease severity. Children with re-infections defined on the subtype level usually had non-protective IgG titers against the subtype of their acute infection (16 of 18; 89%). Some patients infected by one of the influenza A subtypes showed protective IgG titers (≥ 1:40) against the other influenza A subtype (32/140; 23%).
Conclusions
Pre-school children with acute influenza A primary infections and re-infections presented with similar frequency in pediatric practices. Contrary to expectation, severity of acute “influenza A primary infections” and “influenza A re-infections” were similar. Most “influenza A re-infections” defined on the type level turned out to be primary infections when defined based on the subtype. On the subtype level, re-infections were rare and of similar disease severity as primary infections of the same subtype. Subtype level re-infections were usually associated with low IgG levels for the specific subtype of the acute infection, suggesting only short-time humoral immunity induced by previous infection by this subtype. Overall, the results indicated recurring influenza virus infections in this age group and no or only limited heterosubtypic antibody-mediated cross-protection.
Motives motivate human behavior. Most behaviors are driven by more than one motive, yet it is unclear how different motives interact and how such motive combinations affect the neural computation of the behaviors they drive. To answer this question, we induced two prosocial motives simultaneously (multi-motive condition) and separately (single motive conditions). After the different motive inductions, participants performed the same choice task in which they allocated points in favor of the other person (prosocial choice) or in favor of themselves (egoistic choice). We used fMRI to assess prosocial choice-related brain responses and drift diffusion modeling to specify how motive combinations affect individual components of the choice process. Our results showed that the combination of the two motives in the multi-motive condition increased participants' choice biases prior to the behavior itself. On the neural level, these changes in initial prosocial bias were associated with neural responses in the bilateral dorsal striatum. In contrast, the efficiency of the prosocial decision process was comparable between the multi-motive and the single-motive conditions. These findings provide insights into the computation of prosocial choices in complex motivational states, the motivational setting that drives most human behaviors .
Chorioamnionitis is associated with an increased risk of preterm birth and aggravates adverse outcomes such as BPD. Development of BPD is associated with chronic inflammatory reactions and oxidative stress in the airways which may be antenatally initiated by chorioamnionitis. A20 is an immunomodulatory protein involved in the negative feedback regulation of inflammatory reactions and is a possible regulator protein in oxidative stress reactions. The influence of chorioamnionitis on A20 gene regulation in the fetal lung is unknown. We characterized the influence of LPS and proinflammatory cytokines on A20 expression in human lung endothelial (HPMEC-ST1.6R) and epithelial (A549) cells in vitro by real-time PCR and/or western blotting and used a sheep model of LPS-induced chorioamnionitis for in vivo studies. To study the functional role of A20, endogenous A20 was overexpressed in HPMEC-ST1.6R and A549 cells. LPS induced proinflammatory cytokines in HPMEC-ST1.6R and A549 cells. Both LPS and/or proinflammatory cytokines elevated A20 at transcriptional and translational levels. Intra-amniotic LPS transiently increased IL-1β, IL-6, IL-8, and TNF-α mRNA levels in fetal lamb lungs, associated with an increase in A20 mRNA and protein levels. Overexpression of A20 reduced proinflammatory cytokines in vitro. Repeated LPS exposure induced LPS tolerance for proinflammatory cytokines and A20 in vitro and in vivo. Antenatal inflammation induced a transient increase in proinflammatory cytokines in the preterm fetal lung. The expression of proinflammatory cytokines increased expression of A20. Elevated A20 may have a protective role by downregulating chorioamnionitis-triggered fetal lung inflammation. A20 may be a novel target for pharmacological interventions to prevent chorioamnionitis-induced airway inflammation and lung damage, which can result in BPD later in life.
Background
Non-suicidal self-injury (NSSI) has become a substantial public health problem. NSSI is a high-risk marker for the development and persistence of mental health problems, shows high rates of morbidity and mortality, and causes substantial health care costs. Thus, there is an urgent need for action to develop universal prevention programs for NSSI before adolescents begin to show this dangerous behavior. Currently, however, universal prevention programs are lacking.
Methods
The main objective of the present study is to evaluate a newly developed universal prevention program (“DUDE – Du und deine Emotionen / You and your emotions”), based on a skills-based approach in schools, in 3200 young adolescents (age 11–14 years). The effectiveness of DUDE will be investigated in a cluster-randomized controlled trial (RCT) in schools (N = 16). All groups will receive a minimal intervention called “Stress-free through the school day” as a mental health literacy program to prevent burnout in school. The treatment group (N = 1600; 8 schools) will additionally undergo the universal prevention program DUDE and will be divided into treatment group 1 (DUDE conducted by trained clinical psychologists; N = 800; 4 schools) and treatment group 2 (DUDE conducted by trained teachers; N = 800; 4 schools). The active control group (N = 1600; 8 schools) will only receive the mental health literacy prevention. Besides baseline assessment (T0), measurements will occur at the end of the treatment (T1) and at 6- (T2) and 12-month (T3) follow-up evaluations. The main outcome is the occurrence of NSSI within the last 6 months assessed by a short version of the Deliberate Self-Harm Inventory (DSHI-9) at the 1-year follow-up (primary endpoint; T3). Secondary outcomes are emotion regulation, suicidality, health-related quality of life, self-esteem, and comorbid psychopathology and willingness to change.
Discussion
DUDE is tailored to diminish the incidence of NSSI and to prevent its possible long-term consequences (e.g., suicidality) in adolescents. It is easy to access in the school environment. Furthermore, DUDE is a comprehensive approach to improve mental health via improved emotion regulation.
In ischemic stroke (IS) impairment of the blood-brain barrier (BBB) has an important role in the secondary deterioration of neurological function. BBB disruption is associated with ischemia-induced inflammation, brain edema formation, and hemorrhagic infarct transformation, but the underlying mechanisms are incompletely understood. Dysfunction of endothelial cells (EC) may play a central role in this process. Although neuronal NLR-family pyrin domain-containing protein 3 (NLRP3) inflammasome upregulation is an established trigger of inflammation in IS, the contribution of its expression in EC is unclear. We here used brain EC, exposed them to oxygen and glucose deprivation (OGD) in vitro, and analyzed their survival depending on inflammasome inhibition with the NLRP3-specific drug MCC950. During OGD, EC death could significantly be reduced when targeting NLRP3, concomitant with diminished endothelial NLRP3 expression. Furthermore, MCC950 led to reduced levels of Caspase 1 (p20) and activated Gasdermin D as markers for pyroptosis. Moreover, inflammasome inhibition reduced the secretion of pro-inflammatory chemokines, cytokines, and matrix metalloproteinase-9 (MMP9) in EC. In a translational approach, IS was induced in C57Bl/6 mice by 60 mins transient middle cerebral artery occlusion and 23 hours of reperfusion. Stroke volume, functional outcome, the BBB integrity, and-in good agreement with the in vitro results-MMP9 secretion as well as EC survival improved significantly in MCC950-treated mice. In conclusion, our results establish the NLRP3 inflammasome as a critical pathogenic effector of stroke-induced BBB disruption by activating inflammatory signaling cascades and pyroptosis in brain EC.
Bacteria thrive and survive in many different environments, and as a result, they have developed robust mechanisms to adapt rapidly to alterations in their surroundings. The protection against osmotic forces is provided by mechanosensitive channels: their primary function is to maintain the integrity of the cell upon a hypoosmotic shock. The mechanosensitive channel of small conductance (MscS) is not only the smallest common structural unit of a diverse family that allows for a tailored response in osmoregulation; it is also the most intensively studied homologue. Mechanosensitive channels directly sense elevated membrane tension levels generated by increased pressure within the cell and open transiently. Escherichia coli has six paralogues that differ in their gating properties and the number of additional transmembrane (TM) helices. These TM helices, termed sensor paddles, are essential for sensing, as they directly contact the surrounding membrane; however, the role of the additional TM helices is still unclear. Furthermore, lipids occupy hydrophobic pockets far away from the membrane plane. A recent gating model for MscS states that increased membrane tension triggers the expulsion of lipids out of those pockets, modulating different conformational states of MscS. This model focuses on bound lipids, but it is still unclear to what extent the direct interaction with the membrane influences sensing and how relevant it is for the larger paralogues.
In the herein described work, structural studies on two larger paralogues, the medium-sized channel YnaI and the large channel YbiO were realised using electron cryomicroscopy (cryo-EM). Lipids were identified in YnaI in the pockets in a similar position and orientation as in MscS, suggesting a conserved sensing mechanism. Moreover, the copolymer diisobutylene/maleic acid (DIBMA) allowed the extraction of artificially activated YnaI from plasma membranes, leading to an open-like form of this channel. This novel conformation indicated that the pore helices bend at a GGxGG motif during gating, which is unique among the Escherichia coli paralogues, concomitant with a structural reorganisation of the sensor paddles. Thus, despite a high similarity of their closed states, the gating mechanisms of MscS and YnaI are surprisingly different. Furthermore, the comparison of MscS, YnaI, and YbiO accentuates variations and similarities between the differently sized family members, implying fine-tuning of channel properties in the pore regions and the cytosolic lateral entry sides into the channel. Structural analyses of MscS reconstituted into different systems showed the advantages and disadvantages of certain polymers and detergents. The novel DIBMA copolymer and the more conventional amphiphilic polymers, so-called Amphipols, perturb contacting transmembrane helices or lead to their denaturation. Due to this observation, the obtained structures of YnaI must also be cautiously considered. The structures obtained in detergents resulted in unaffected channels; however, the applicability of detergents for MscS-like channels is limited by the increased required sample concentration.
The role of lipids for gating MscS in the absence of a membrane was examined by deliberately removing coordinated lipid molecules from MscS using different amounts and kinds of detergent. The effects on the channel were inspected by cryo-EM. These experiments showed that closed MscS adopts the open conformation when it is enough delipidated by incubation with the detergent n-dodecyl-β-D-maltoside, and adding lipids to the open channel reverses this process. The results agree with the state-of-the-art model that the amount of lipid molecules in the pockets and grooves is responsible for the conformational state of MscS. Furthermore, incubation with the detergent lauryl maltose neopentyl glycol, which has stabilising and delipidating characteristics, resulted in a high-resolution structure of open MscS exhibiting an intricate network of ligands. Based on this structure, an updated gating model is proposed, which states that upon opening, lipids from the pockets migrate into the cytosolic membrane leaflet, while lipids from the periplasmic leaflet enter the grooves that arise between the sensor paddles.
To date, no consensus exists regarding the best surgical management of isolated, micro-traumatic long thoracic nerve (LTN) paresis. Our hypothesis was that a combined decompression of the LTN at two potential locations for entrapment would be effective in the management of dynamic LTN paresis. We report on twelve patients with isolated LTN parersis, with tenderness at two entrapment sites, who underwent bifocal LTN decompression after undergoing unsuccessful conservative treatment for at least 6 months; all patients had preoperative electrodiagnostic studies that confirmed the paresis and ruled out peripheral neuritis. Clinical and electrical improvements were observed in eight patients (67%) regarding shoulder flexion, shoulder abduction, and Quick-DASH scores. Four patients (33%) did not improve after surgery. The results corroborate our hypothesis that a bifocal LTN decompression can be an effective and reliable therapeutic option in more than half of a very selective patient population suffering from serratus anterior muscle deficiency.
Introduction
Detailed and up-to-date data on the epidemiology and healthcare costs of Influenza are fundamental for public health decision-making. We analyzed inpatient data on Influenza-associated hospitalizations (IAH), selected complications and risk factors, and their related direct costs for Germany during ten consecutive years.
Methods
We conducted a retrospective cost-of-illness study on patients with laboratory-confirmed IAH (ICD-10-GM code J09/J10 as primary diagnosis) by ICD-10-GM-based remote data query using the Hospital Statistics database of the German Federal Statistical Office. Clinical data and associated direct costs of hospital treatment are presented stratified by demographic and clinical variables.
Results
Between January 2010 to December 2019, 156,097 persons were hospitalized due to laboratory-confirmed Influenza (J09/J10 primary diagnosis). The annual cumulative incidence was low in 2010, 2012 and 2014 (1.3 to 3.1 hospitalizations per 100,000 persons) and high in 2013 and 2015-2019 (12.6 to 60.3). Overall direct per patient hospitalization costs were mean (SD) 3521 EUR (± 8896) and median (IQR) 1805 EUR (1502; 2694), with the highest mean costs in 2010 (mean 8965 EUR ± 26,538) and the lowest costs in 2012 (mean 2588 EUR ± 6153). Mean costs were highest in 60-69 year olds, and in 50-59, 70-79 and 40-49 year olds; they were lowest in 10-19 year olds. Increased costs were associated with conditions such as diabetes (frequency 15.0%; 3.45-fold increase compared to those without diabetes), adiposity (3.3%; 2.09-fold increase) or immune disorders (5.6%; 1.88-fold increase) and with Influenza-associated complications such as Influenza pneumonia (24.3%; 1.95-fold), bacterial pneumonia (6.3%; 3.86-fold), ARDS (1.2%; 10.90-fold increase) or sepsis (2.3%; 8.30-fold). Estimated overall costs reported for the 10-year period were 549.6 Million euros (95% CI 542.7-556.4 million euros).
Conclusion
We found that the economic burden of IAH in Germany is substantial, even when considering solely laboratory-confirmed IAH reported as primary diagnosis. The highest costs were found in the elderly, patients with certain underlying risk factors and patients who required advanced life support treatment, and median and mean costs showed considerable variations between single years. Furthermore, there was a relevant burden of disease in middle-aged adults, who are not covered by the current vaccination recommendations in Germany.
Protein kinase D2 drives chylomicron-mediate lipid transport in the intestine and promotes obesity
(2022)
Obesity and associated metabolic syndrome are growing concerns in modern society due to the negative consequences for human health and well-being. Cardiovascular diseases and type 2 diabetes are only some of the pathologies associated to overweight. Among the main causes are decreased physical activity and food availability and composition. Diets with high content of fat are energy-dense and their overconsumption leads to an energy imbalance, which ultimately promotes energy storage as fat and obesity. Aberrant activation of signalling cascades and hormonal imbalances are characteristic of this disease and members of the Protein Kinase D (PKD) family have been found to be involved in several mechanisms mediating metabolic homeostasis. Therefore, we aimed to investigate the role of Protein Kinase D2 (PKD2) in the regulation of metabolism. Our investigation initiated with a mice model for global PKD2 inactivation, which allowed us to prove a direct involvement of this kinase in lipids homeostasis and obesity. Inactivation of PKD2 protected the mice from high-fat diet-induced obesity and improved their response to glucose, insulin and lipids. Furthermore, the results indicated that, even though there were no changes in energy intake or expenditure, inactivation of PKD2 limited the absorption of fat from the intestine and promoted energy excretion in feces. These results were verified in a mice model for specific deletion of intestinal PKD2. These mice not only displayed an improved metabolic fitness but also a healthier gut microbiome profile. In addition, we made use of a small-molecule inhibitor of PKD in order to prove that local inhibition of PKD2 in the intestine was sufficient to inhibit lipid absorption. The usage of the inhibitor not only protected the mice from obesity but also was efficient in avoiding additional body-weight gain after obesity was pre-established in mice. Mechanistically, we determined that PKD2 regulates lipids uptake in enterocytes by phosphorylation of Apolipoprotein A4 (APOA4) and regulation of chylomicron-mediated triglyceride absorption. PKD2 deletion or inactivation increased abundance of APOA4 and decreased the size of chylomicrons and therefore lipids absorption from the diet. Moreover, intestinal activation of PKD2 in human obese patients correlated with higher levels of triglycerides in circulation and a detrimental blood profile. In conclusion, we demonstrated that PKD2 is a key regulator of dietary fat absorption in murine and human context, and its inhibition might contribute to the treatment of obesity.
RNA represents one of the most abundant macromolecules in both eukaryotic and prokaryotic cells. Since the discovery that RNA could play important gene regulatory functions in the physiology of a cell, small regulatory RNAs (sRNAs) have been at the center of molecular biology studies. Functional sRNAs can be independently transcribed or derived from processing of mRNAs and other non-coding regions and they often associate with RNA-binding proteins (RBPs). Ever since the two major bacterial RBPs, Hfq and ProQ, were identified, the way we approach the identification and characterization of sRNAs has drastically changed. Initially, a single sRNA was annotated and its function studied with the use of low-throughput biochemical techniques. However, the development of RNA-seq techniques over the last decades allowed for a broader identification of sRNAs and their functions. The process of studying a sRNA mainly focuses on the characterization of its interacting RNA partner(s) and the consequences of this binding. By using RNA interaction by ligation and sequencing (RIL-seq), the present thesis aimed at a high-throughput mapping of the Hfq-mediated RNA-RNA network in the major human pathogen Salmonella enterica.
RIL-seq was at first performed in early stationary phase growing bacteria, which enabled the identification of ~1,800 unique interactions. In- depth analysis of such complex network was performed with the aid of a newly implemented RIL-seq browser. The interactome revealed known and new interactions involving sRNAs and genes part of the envelope regulon. A deeper investigation led to the identification of a new RNA sponge of the MicF sRNA, namely OppX, involved in establishing a cross-talk between the permeability at the outer membrane and the transport capacity at the periplasm and the inner membrane. Additionally, RIL-seq was applied to Salmonella enterica grown in SPI-2 medium, a condition that mimicks the intracellular lifestyle of this pathogen, and finally extended to in vivo conditions during macrophage infection. Collectively, the results obtained in the present thesis helped unveiling the complexity of such RNA networks.
This work set the basis for the discovery of new mechanisms of RNA-based regulation, for the identification of a new physiological role of RNA sponges and finally provided the first resource of RNA interactions during infection conditions in a major human pathogen.
The propounded thesis investigated fear learning including fear conditioning, its generalization as well as its extinction in 133 healthy children and adolescents aged 8 to 17 years. The main goal was to analyze these processes also in the course of childhood and adolescence due to far less research in this age span compared to adults. Of note, childhood is the typical period for the onset of anxiety disorders. To achieve this, an aversive discriminative fear conditioning, generalization and extinction paradigm, which based on the “screaming lady paradigm” from Lau et al. (2008) and was adapted by Schiele & Reinhard et al. (2016), was applied. All probands traversed the pre-acquisition (4 x CS-, 4 x CS+, no US), the acquisition (12 x CS-, 12 x CS+, reinforcement rate: 83%), the generalization (12 x CS-, 12 x GS4, 12 x GS3, 12 x GS2, 12 x GS1, 12 x CS+, reinforcement rate: 50%) and the extinction (18 x CS-, 18 x CS+, no US). The generalization stimuli, i.e. GS1-GS4, were built out of CS- and CS+ in different mixtures on a percentage basis in steps of 20% from CS- to CS+. Pictures of faces of two actresses with a neutral expression were used for the discriminative conditioning, whereby the CS+ was paired with a 95-dB loud female scream at the same time together with a fearful facial expression (US). CS- and GS1-GS4 were never followed by the US. Subjective ratings (arousal, valence and US expectancy) were collected and further the psychophysiological measure of the skin conductance response (SCR). The hypotheses were 1) that underage probands show a negative correlation between age and overgeneralization and 2) that anxiety is positively correlated with overgeneralization in the same sample. ANOVAs with repeated measures were conducted for all four dependent variables with phase (pre-acquisition phase, 1. + 2. acquisition phase, 1. + 2. generalization phase, 1. - 3. extinction phase) and stimulus type
(CS-, CS+, GS1-GS4) as within-subject factors. For the analyses of the modulatory effects of age and anxiety in additional separate ANCOVAs were conducted including a) age, b) the STAIC score for trait anxiety and c) the CASI score for anxiety sensitivity as covariates. Sex was always included as covariate of no interest. On the one hand, findings indicated that the general extent of the reactions (arousal, valence and US expectancy ratings and the SCR) decreased with growing age, i.e. the older the probands the lower their reactions towards the stimuli regardless of the type of dependent variable. On the other hand, ratings of US expectancy, i.e. the likelihood that a stimulus is followed by a US (here: female scream coupled with a fearful facial expression), showed better discrimination skills the older the probands were, resulting in a smaller overgeneralization within older probands. It must be emphasized very clearly that no causality can be derived. Thus, it was only an association revealed between
15
age and generalization of conditioned fear, which is negative. Furthermore, no obvious impact of trait anxiety could be detected on the different processes of fear learning. Especially, no overgeneralization was expressed by the probands linked to higher trait anxiety. In contrast to trait anxiety, for anxiety sensitivity there was an association between its extent and the level of fear reactions. This could be described best with a kind of parallel shifts: the higher the anxiety sensitivity, the stronger the fear reactions. Likewise, for anxiety sensitivity no overgeneralization due to a stronger extent of anxiety sensitivity could be observed.
Longitudinal follow-up examinations and, furthermore, neurobiological investigations are needed for replication purposes and purposes of gaining more supporting or opposing insights, but also for the profound exploration of the impact of hormonal changes during puberty and of the maturation processes of different brain structures. Finally, the question whether enhanced generalization of conditioned fear facilitates the development of anxiety disorders or vice versa remains unsolved yet.
Avocado (Persea americana Mill.) is a major horticultural crop that relies on insect mediated pollination. In avocado production, a knowledge gap exists as to the importance of insect pollination, especially in East African smallholder farms. Although it is evident that pollination improves the yield of avocado fruits, it is still unclear if pollination has benefits on fruit quality and the nutritional profile, particularly oils. Prior studies have shown that honey bees increase avocado’s fruit set and yield. However, an avocado flower is being visited by various insect species. Therefore, determining pollination efficiency will allow a comparison of the relative importance of the different insect species to optimize crop pollination for increased fruit set and crop yield and pollinator conservation. This study was conducted in a leading smallholder avocado production region in Kenya, first I assessed the dependence of avocado fruit set on insect pollination and whether current smallholder production systems suffer from a deficit in pollination services. Furthermore, I assessed if supplementation with colonies of the Western honey bee (Apis mellifera L.) to farms mitigated potential pollination deficits. The results revealed a very high reliance of avocado on insect pollinators, with a significantly lower fruit set observed for self- and wind-pollinated (17.4%) or self-pollinated flowers (6.4%) in comparison with insect-pollinated flowers (89.5%). I found a significant pollination deficit across farms, with hand-pollinated flowers on average producing 20.7% more fruits than non-treated open flowers prior to fruit abortion. This pollination deficit could be compensated by the supplementation of farms with A. mellifera colonies. These findings suggest that pollination is limiting fruit set in avocado and that A. mellifera supplementation on farms is a potential option to increase fruit yield. Secondly, I investigated the contribution of insect pollination to fruit and seed weight, oil, protein, carbohydrate, and phytochemicals contents (flavonoids and phenolics), and whether supplementation with pollinators (honey bee) could improve these fruit parameters was assessed. This was through pollinator-manipulative pollination treatments: hand, open, pollinator exclusion experiments. The results showed that avocado fruit weight was significantly higher in open and hand-pollinated than pollinator exclusion treatments, indicating that flower visitors/pollinators contribute to avocado yields and enhance marketability. Furthermore, insect pollination resulted in heavier seeds and higher oil contents, indicating that insect pollination is beneficial for the fruit’s high seed yield and quantity of oil. Honey bee supplementation also enhanced the avocado fruit weight by 18% more than in control farms and slightly increased the avocado oil content (3.6%). Contrarily, insect pollination did not influence other assayed fruit quality parameters (protein, carbohydrates, and phytochemicals). These results indicate that insect pollinators are essential for optimizing avocado yields, nutritional quality (oils), and thus marketability, underscoring the value of beehive supplementation to achieve high-quality avocado fruits and improved food security. Thirdly, pollinator efficiency based on pollen deposition after single visits by different pollinator species in avocado flowers was tested, and their frequency was recorded. The estimated pollination efficiency was highest in honey bees (Apis mellifera), followed by the hoverfly species (Phytomia incisa). These two species had the highest pollen deposition and more pollen grains on their bodies. In addition, honey bees were the most frequent avocado flower visitors, followed by flies. The findings from this study highlight the higher pollination efficiency of honey bees and Phytomia incisa. Hence, management practices supporting these species will promote increased avocado fruit yield. Additionally, these results imply that managed honey bees can be maintained to improve avocado pollination, particularly in areas lacking sufficient wild pollinators.
Mesenchymal stem/stromal cells (MSCs) are a rare subpopulation of cells first identified in bone marrow with the potential to proliferate in plastic-adherent colonies and to generate de novo bone marrow stroma and its environment upon serial transplantation to heterotopic anatomical sites. Given their multipotency and self renewal competence, MSCs are prime prospective candidates for most modern musculoskeletal-tissue engineering and regenerative medicine approaches. Still, their envisioned therapeutic use is being questioned with concerns regarding their definition, characterization and integrative functions in vivo. It is well established that microenvironmental cues such as the extracellular matrix (ECM)-chemistry, the mechanical environment and local cellular and/or paracrine interactions critically control MSCs behavior. Yet, most of the scientific knowledge regarding the biology and therapeutic effect of MSCs originates from mechanistic in vitro studies where microenvironmental cues are hardly addressed. Therefore, manifestable changes in cell proliferation behavior and multilineage differentiation potential might be triggered that eventually compromise the translation of results to clinics. This thesis aims to address the complexity of MSCs interactions within the skeletal niche microenvironment in order to provide alternative methods to bypass the current MSCs in vitro culture limitations. Firstly, the influence of ECM-chemistry on MSCs behavior in vitro was explored by means of decellularized human bone models here established. Basal or osteogenic tailored cell-derived decellularized 2D matrices (dECM), proved to be suitable culture substrates for MSCs expansion by providing close-to-native cell-ECM interactions. Moreover, quantified morphological shape changes suggested a material osteo supportive potential, further functionally validated by observable spontaneous mineralization of MSCs. Aiming to identify novel intrinsic ECM regulatory features specific to the skeletal niche, 3D decellularized human trabecular bone scaffolds (dBone) were additionally developed and comprehensively characterized. Remarkably, the MSCs cultured on dBone scaffolds exhibit upregulation of genes associated with stemness as well as niche-related protein expression advocating for the conservation of the naïve MSCs phenotype. vi On the other hand, the effect of biomimetic mineralization on MSCs osteogenic lineage differentiation potential was further addressed by hydroxyapatite functionalization of type-I collagen in presence of magnesium. Mineralized scaffolds exhibited higher cell viability and a clear trend of osteogenic genes upregulation comparing with non-mineralized scaffolds. Lastly, in order to mimic the complexity of the native MSCs environment, a dynamic culture system was applied to the 3D decellularized bone constructs, previously studied in single static conditions. Mechanical stimuli generated by (1) continuous perfusion of cell culture medium at 1.7 mL/min and (2) compressive stress from 10% uniaxial load at 1 Hz, resulted in an improved cell repopulation within the scaffold and boosting of de novo ECM production. The stress-induced gene expression pattern suggested early MSCs commitment towards the osteogenic lineage mediated by integrin matrix adhesion, therefore further corroborating the recapitulation of a reliable in vitro bone niche model in dBone scaffolds. To conclude, the here developed in vitro models provide a progressive increased biomimicking complexity through which significant insights regarding MSC interactions with microenvironmental features in the skeletal niche can be obtained, thus surely paving the way for a better understanding of the role of MSCs in bone homeostasis and regeneration.
RNA sequencing (RNA-seq) has become a transformative method to profile genome-wide gene expression and whole transcriptome analysis over the last decade. In recent years, with the development of new technologies, it has become possible to study gene expression at single-cell level. This new advances in single-cell RNA-sequencing has revolutionized the way scientists study biological processes. Single-cell RNA-sequencing has been used in different areas to better understand the underlying mechanisms of biological processes.
In particular, single-RNA-sequencing is a suitable method to study infectious diseases. Infection is composed of heterogeneous mechanisms on either the host or pathogen side and the best way to understand the heterogeneity of these mechanisms and how they interact with each other is to study infectious diseases at the single-cell level. Studying infection processes at the single-cell level can reveal not only the heterogeneity but also the dynamics of infection and the interplay between the host and pathogen at the molecular level.
In this thesis, we implemented and applied different single-cell RNA-seq technologies to better understand infectious diseases. In the present work, we conducted four independent but related research works to shed light on different aspects of infection biology:
● We took advantage of this novel technology to study the consequences of RSV infection on primary human epithelial cells. The primary human epithelial cells were collected from six donors and cultured in air liquid interface (ALI) cell culture inoculated with respiratory syncytial virus (RSV). In this project, we discovered ciliated cells as the susceptible cell types in RSV infection. We applied viral load as an indicator of infection progression and used it to reconstruct the dynamics of host response to RSV infection. Reconstruction of the dynamics of infection revealed many host genes and pathways that were suppressed or induced as a result of RSV infection. Pathways related to innate immune response and interferon response were suppressed during the progression of infection and on the other hand pathways like protein targeting to endoplasmic reticulum and apoptosis were induced.
● We developed a new method which is capable of sequencing the transcriptome of a bacterium at the single-cell level and potentially can help us to characterize the bacterial heterogeneity during the course of infection. In this research project, bacteria were cultured in three different culture conditions namely Late stationary phase, Anaerobic shock and NaCl shock and we used a poly(A)-independent single-cell RNA-sequencing protocol to sequence bacteria at the single-cell level. In this work, we report the faithful capture of growth-dependent gene expression patterns in individual Salmonella and Pseudomonas bacteria. The results of our analysis showed that not only we could capture transcripts across different RNA classes but also our method is capable of discerning the transcriptome of bacteria across different culture conditions.
● We used single-cell RNA-sequencing technology to characterize the immune cells landscape over the course of atherosclerosis. Atherosclerosis is considered a cardiac disease which is highly related to infections and previous infections with bacteria or viruses is considered as a risk factor for atherosclerosis. We performed single-cell RNA sequencing of aortic CD45+ cells extracted from healthy and atherosclerotic aorta of mice. We managed to find certain cell populations which were specifically present in atherosclerotic mice. One of the atheroschelorotic populations was previously undescribed TREM2high macrophages showing enrichment in Trem2 gene expression. This population of macrophages seemed to be involved in functions like lipid metabolism and catabolism and lesion calcification. This work revealed the phenotypic heterogeneity and immune cells landscape of different immune cell populations at different stages of atherosclerosis. Our work paves the way to better describe the relation between different infectious diseases and cardiovascular diseases.
● We developed a web-based platform called Infection Atlas to browse and visualize single-cell RNA-sequencing data. Infection Atlas platform provides a user-friendly interface to study different aspects of infectious diseases at the single-cell level and can potentially promote targeted approaches to intervene in infectious diseases. This platform which is available at infection-atlas.org in the short term provides a user-friendly interface to browse and visualize different aspects of infectious diseases and in the long-term is expected to be a comprehensive atlas of infection in human and mouse across different tissues and different pathogens.
Overall, in this thesis we provide a framework to study infectious diseases at the single cell level with providing novel data analysis methods and this thesis paves the way for future studies to study host-pathogen encounters at the single-cell level.
The small intestine represents a strong barrier separating the lumen from blood circulation thereby playing a major role in the absorption and the transport of pharmacological agents prior to their arrival on the respective target site. In order to gain more knowledge about specialized uptake mechanisms and risk assessment for the patient after oral admission of drugs, intestinal in vitro models demonstrating a close similarity to the in vivo situation are needed.
In the past, cell line-based in vitro models composed of Caco-2 cells cultured on synthetic cell carriers represented the “gold standard” in the field of intestinal tissue engineering. Expressive advantages of these models are a reproducible, cost-efficient and standardized model set up, but cell function can be negatively influenced by the low porosity or unwanted molecular adhesion effects of the artificial scaffold material. Natural extracellular matrices (ECM) such as the porcine decellularized small intestinal submucosa (SIS) are used as alternative to overcome some common drawbacks; however, the fabrication of these scaffolds is time- and cost-intensive, less well standardized and the 3Rs (replacement, reduction, refinement) principle is not entirely fulfilled. Nowadays, biopolymer-based scaffolds such as the bacterial nanocellulose (BNC) suggest an interesting option of novel intestinal tissue engineered models, as the BNC shows comparable features to the native ECM regarding fiber arrangement and hydrophilic properties. Furthermore, the BNC is of non-animal origin and the manufacturing process is faster as well as well standardized at low costs.
In this context, the first part of this thesis analyzed the BNC as alternative scaffold to derive standardized and functional organ models in vitro. Therefore, Caco-2 cells were cultured on two versions of BNC with respect to their surface topography, the unmodified BNC as rather smooth surface and the surface-structured BNC presenting an aligned fiber arrangement. As controls, Caco-2 in vitro models were set up on PET and SIS matrices. In this study, the BNC-based models demonstrated organ-specific properties comprising typical cellular morphologies, a characteristic tight junction protein expression profile, representative ultrastructural features and the formation of a tight epithelial barrier together with a corresponding transport activity. In summary, these results validated the high quality of the BNC-based Caco-2 models under cost-efficient conditions and their suitability for pre-clinical research purposes. However, the full functional diversity of the human intestine cannot be presented by Caco-2 cells due to their tumorigenic background and their exclusive representation of mature enterocytes.
Next to the scaffold used for the setup of in vitro models, the cellular unit mainly drives functional performance, which demonstrates the crucial importance of mimicking the cellular diversity of the small intestine in vitro. In this context, intestinal primary organoids are of high interest, as they show a close similarity to the native epithelium regarding their cellular diversity comprising enterocytes, goblet cells, enteroendocrine cells, paneth cells, transit amplifying cells and stem cells. In general, such primary organoids grow in a 3D Matrigel® based environment and a medium formulation supplemented with a variety of growth factors to maintain stemness, to inhibit differentiation and to stimulate cell migration supporting long term in vitro culture.
Intestinal primary spheroid/organoid cultures were set up as Transwell®-like models on both BNC variants, which resulted in a fragmentary cell layer and thereby unfavorable properties of these scaffold materials under the applied circumstances. As the BNC manufacturing process is highly flexible, surface properties could be adapted in future studies to enable a good cell adherence and barrier formation for primary intestinal cells, too. However, the application of these organoid cultures in pre-clinical research represents an enormous challenge, as the in vitro culture is complex and additionally time- and cost-intensive.
With regard to the high potential of primary intestinal spheroids/organoids and the necessity of a simplified but predictive model in pre-clinical research purposes, the second part of this thesis addressed the establishment of a primary-derived immortalized intestinal cell line, which enables a standardized and cost-efficient culture (including in 2D), while maintaining the cellular diversity of the organoid in vitro cultures. In this study, immortalization of murine and human intestinal primary organoids was induced by ectopic expression of a 10- (murine) or 12 component (human) pool of genes regulating stemness and the cell cycle, which was performed in cooperation with the InSCREENeX GmbH in a 2D- and 3D-based transduction strategy. In first line, the established cell lines (cell clones) were investigated for their cell culture prerequisites to grow under simplified and cost-efficient conditions. While murine cell clones grew on uncoated plastic in a medium formulation supplemented with EGF, Noggin, Y-27632 and 10% FCS, the human cell clones demonstrated the necessity of a Col I pre coating together with the need for a medium composition commonly used for primary human spheroid/organoid cultures. Furthermore, the preceding analyses resulted in only one human cell clone and three murine cell clones for ongoing characterization. Studies regarding the proliferative properties and the specific gene as well as protein expression profile of the remaining cell clones have shown, that it is likely that transient amplifying cells (TACs) were immortalized instead of the differentiated cell types localized in primary organoids, as 2D, 3D or Transwell®-based cultures resulted in slightly different gene expression profiles and in a dramatically reduced mRNA transcript level for the analyzed marker genes representative for the differentiated cell types of the native epithelium. Further, 3D cultures demonstrated the formation of spheroid-like structures; however without forming organoid-like structures due to prolonged culture, indicating that these cell populations have lost their ability to differentiate into specific intestinal cell types. The Transwell®-based models set up of each clone exhibit organ-specific properties comprising an epithelial-like morphology, a characteristic protein expression profile with an apical mucus-layer covering the villin-1 positive cell layer, thereby representing goblet cells and enterocytes, together with representative tight junction complexes indicating an integer epithelial barrier. The proof of a functional as well as tight epithelial barrier in TEER measurements and in vivo-like transport activities qualified the established cell clones as alternative cell sources for tissue engineered models representing the small intestine to some extent. Additionally, the easy handling and cell expansion under more cost-efficient conditions compared to primary organoid cultures favors the use of these newly generated cell clones in bioavailability studies.
Altogether, this work demonstrated new components, structural and cellular, for the establishment of alternative in vitro models of the small intestinal epithelium, which could be used in pre-clinical screenings for reproducible drug delivery studies.
The transcription factor MYC is a onco-protein, found to be deregulated in many human cancers. High MYC levels correlate with an aggressive tumor outcome and poor survival rates. Despite MYC being discovered as an oncogene already in the 1970s, how MYC regulates transcription of its target genes, which are involved in cellular growth and proliferation, is not fully understood yet.
In this study, the question how MYC influences factors interacting with the RNA polymerase II ensuring productive transcription of its target genes was addressed using quantitative mass spectrometry. By comparing the interactome of RNA polymerase II under varying MYC levels, several potential factors involved in transcriptional elongation were identified. Furthermore, the question which of those factors interact with MYC was answered by employing quantitative mass spectrometry of MYC itself. Thereby, the direct interaction of MYC with the transcription elongation factor SPT5, a subunit of the DRB-sensitivity inducing factor, was discovered and analyzed in greater detail. SPT5 was shown to be recruited to chromatin by MYC. In addition, the interaction site of MYC on SPT5 was narrowed down to its evolutionary conserved NGN-domain, which is the known binding site for SPT4, the earlier characterized second subunit of the DRB-sensitivity inducing factor. This finding suggests a model in which MYC and SPT4 compete for binding the NGN-domain of SPT5.
Investigations of the SPT5-interacting region on MYC showed binding of SPT5 to MYC’s N-terminus including MYC-boxes 0, I and II.
In order to analyze proteins interacting specifically with the N-terminal region of MYC, a truncated MYC-mutant was used for quantitative mass spectrometric analysis uncovering reduced binding for several proteins including the well-known interactor TRRAP and TRRAP-associated complexes.
Summarized, ...
Laser spectroscopic gas sensing has been applied for decades for several applications
as atmospheric monitoring, industrial combustion gas analysis or fundamental research.
The availability of new laser sources in the mid-infrared opens the spectral fingerprint
range to the technology where multiple molecules possess their fundamental ro-vibrational
absorption features that allow very sensitive detection and accurate discrimination of
the species. The increasing maturity of quantum cascade lasers that cover this highly
interesting spectral range motivated this research to gain fundamental knowledge about
the spectra of hydrocarbon gases in pure composition and in complex mixtures as they
occur in the petro-chemical industry. The long-term target of developing accurate and fast
hydrocarbon gas analyzers, capable of real-time operation while enabling feedback-loops,
would lead to a paradigm change in this industry.
This thesis aims to contribute to a higher accuracy and more comprehensive understanding
of the sensing of hydrocarbon gas mixtures. This includes the acquisition of yet
unavailable high resolution and high accuracy reference spectra of the respective gases,
the investigation of their spectral behavior in mixtures due to collisional broadening of
their transitions and the verification of the feasibility to quantitatively discriminate the
spectra when several overlapping species are simultaneously measured in gas mixtures.
To achieve this knowledge a new laboratory environment was planned and built up to
allow for the supply of the individual gases and their arbitrary mixing. The main element
was the development of a broadly tunable external-cavity quantum cascade laser based
spectrometer to record the required spectra. This also included the development of a new
measurement method to obtain highly resolved and nearly gap-less spectral coverage as
well as a sophisticated signal post-processing that was crucial to achieve the high accuracy
of the measurements. The spectroscopic setup was used for a thorough investigation of
the spectra of the first seven alkanes as of their mixtures. Measurements were realized
that achieved a spectral resolution of 0.001 cm-1 in the range of 6-11 µm while ensuring an
accuracy of 0.001 cm-1 of the spectra and attaining a transmission sensitivity of 2.5 x 10-4
for long-time averaging of the acquired spectra.
These spectral measurements accomplish a quality that compares to state-of-the art
spectral databases and revealed so far undocumented details of several of the investigated
gases that have not been measured with this high resolution before at the chosen measurement
conditions. The results demonstrate the first laser spectroscopic discrimination of a
seven component gas mixture with absolute accuracies below 0.5 vol.% in the mid-infrared
provided that a sufficiently broad spectral range is covered in the measurements. Remaining
challenges for obtaining improved spectral models of the gases and limitations of the
measurement accuracy and technology are discussed.
The fate and behavior of bone marrow mesenchymal stem/stromal cells (BM-MSC) is bidirectionally influenced by their microenvironment, the stem cell niche, where a magnitude of biochemical and physical cues communicate in an extremely orchestrated way. It is known that simplified 2D in vitro systems for BM-MSC culture do not represent their naïve physiological environment. Here, we developed four different 2D cell-based decellularized matrices (dECM) and a 3D decellularized human trabecular-bone scaffold (dBone) to evaluate BM-MSC behavior. The obtained cell-derived matrices provided a reliable tool for cell shape-based analyses of typical features associated with osteogenic differentiation at high-throughput level. On the other hand, exploratory proteomics analysis identified native bone-specific proteins selectively expressed in dBone but not in dECM models. Together with its architectural complexity, the physico-chemical properties of dBone triggered the upregulation of stemness associated genes and niche-related protein expression, proving in vitro conservation of the naïve features of BM-MSC.
Continued reports over the past decades of unknown aerial phenomena (short UAP) have given high relevance to the investigation and research of these. Especially reports by US Navy pilots and official investigations by the US Office of the director of national intelligence have emphasized the value of such efforts. Due to the inherently limited scope of earth based observations, a satellite based instrument for detection of such phenomena may prove especially useful. This paper as such investigates the possible viability of such an instrument on a nano satellite mission.
Purpose
The goal of our study was to conduct an online survey that highlights patterns of practice during total hip arthroplasty (THA).
Methods
The survey was conducted in June and August 2020. Three hundred thirteen members of the German Society for Endoprosthesis participated in the survey.
Results
The anterolateral approach is by far the most popular approach used for primary total hip arthroplasty, followed by the anterior approach during minimally invasive (55% for the anterolateral and 29% for the anterior) and regular surgery (52% for the anterolateral and 20% for the anterior). Two-thirds of the orthopaedic surgeons do not use drainages during THA. Moreover, 80% of the survey participants routinely apply tranexamic acid during surgery. Surgeons who perform minimally invasive surgery for THA use more frequently fast-track-concepts for post-operative rehabilitation. According to the interviewees, the application of fast-track-concepts leads to reduced periods of hospital stay after THA.
Conclusion
Our data demonstrate that patterns of practice during THA in Germany are in line with the evidence provided by current literature. This study can be seen as a stimulus to conduct similar surveys in other countries in order to promote minimally invasive surgery for THA.
In this view point we do not change cosmology after the hot fireball starts (hence agrees well with observation), but the changed start suggested and resulting later implications lead to an even better fit with current observations (voids, supercluster and galaxy formation; matter and no antimatter) than the standard model with big bang and inflation: In an eternal ocean of qubits, a cluster of qubits crystallizes to defined bits. The universe does not jump into existence (“big bang”) but rather you have an eternal ocean of qubits in free super-position of all their quantum states (of any dimension, force field and particle type) as permanent basis. The undefined, boiling vacuum is the real “outside”, once you leave our everyday universe. A set of n Qubits in the ocean are “liquid”, in very undefined state, they have all their m possibilities for quantum states in free superposition. However, under certain conditions the qubits interact, become defined, and freeze out, crystals form and give rise to a defined, real world with all possible time series and world lines. GR holds only within the crystal. In our universe all n**m quantum possibilities are nicely separated and crystallized out to defined bit states: A toy example with 6 qubits each having 2 states illustrates, this is completely sufficient to encode space using 3 bits for x,y and z, 1 bit for particle type and 2 bits for its state. Just by crystallization, space, particles and their properties emerge from the ocean of qubits, and following the arrow of entropy, time emerges, following an arrow of time and expansion from one corner of the toy universe to everywhere else. This perspective provides time as emergent feature considering entropy: crystallization of each world line leads to defined world lines over their whole existence, while entropy ensures direction of time and higher representation of high entropy states considering the whole crystal and all slices of world lines. The crystal perspective is also economic compared to the Everett-type multiverse, each qubit has its m quantum states and n qubits interacting forming a crystal and hence turning into defined bit states has only n**m states and not more states. There is no Everett-type world splitting with every decision but rather individual world trajectories reside in individual world layers of the crystal. Finally, bit-separated crystals come and go in the qubit ocean, selecting for the ability to lay seeds for new crystals. This self-organizing reproduction selects over generations also for life-friendliness. Mathematical treatment introduces quantum action theory as a framework for a general lattice field theory extending quantum chromo dynamics where scalar fields for color interaction and gravity have to be derived from the permeating qubit-interaction field. Vacuum energy should get appropriately low by the binding properties of the qubit crystal. Connections to loop quantum gravity, string theory and emergent gravity are discussed. Standard physics (quantum computing; crystallization, solid state physics) allow validation tests of this perspective and will extend current results.
In this paper we study properties of the Laplace approximation of the posterior distribution arising in nonlinear Bayesian inverse problems. Our work is motivated by Schillings et al. (Numer Math 145:915–971, 2020. https://doi.org/10.1007/s00211-020-01131-1), where it is shown that in such a setting the Laplace approximation error in Hellinger distance converges to zero in the order of the noise level. Here, we prove novel error estimates for a given noise level that also quantify the effect due to the nonlinearity of the forward mapping and the dimension of the problem. In particular, we are interested in settings in which a linear forward mapping is perturbed by a small nonlinear mapping. Our results indicate that in this case, the Laplace approximation error is of the size of the perturbation. The paper provides insight into Bayesian inference in nonlinear inverse problems, where linearization of the forward mapping has suitable approximation properties.
T lymphocytes (T cells) represent one of the major cell populations of the immune system. Named by the place of their development, the thymus, several types can be distinguished as the αβ T cells, the γδ T cells, the mucosa-associated invariant T cells (MAIT), and the natural killer T (NKT) cells. The αβ lineages of CD4+ THelper and the CD8+ T cytotoxic cells with the T cell receptor (TCR) composed of α- and β-chain are major players of the adaptive immune system. In the thymus, CD4+ and CD8+ single positive (SP) αβ cells represent the ultimate result of positive and negative selection of CD4+CD8+ double positive (DP) thymocytes. The DP population derives from the double negative (DN) thymocytes that develop from bone marrow-derived progenitors through different stages (DN1-DN4) that are characterized by CD25 and CD44 surface expression.
NFATc1, a member of the Nuclear Factor of Activated T cells (NFAT) transcription factors family, is critically involved in the differentiation and function of T cells. During thymocyte development, the nuclear expression of NFATc1 reaches the highest level at the DN3 (CD44-CD25+) stage. The hematopoietic cell-specific ablation of NFATc1 activity results in an arrest of thymocyte differentiation at the DN1 (CD44+CD25-) stage. On the other hand, over-expression of a constitutively active version of NFATc1 results in an impaired transition of DN3 cells to the DN4 (CD44-CD25-) stage, suggesting that a certain threshold level of NFATc1 activity is critical at this point.
ChIP-seq and RNA-seq analysis allowed us the identification of NFATc1/A target genes involved in lineage development as the Tcra and Tcrb gene loci. Furthermore, we identified multiple NFATc1-regulated genes that are involved in γδ T cell development. In the mouse models, Rag1Cre-Nfatc1fl/fl and Rag1Cre-E2fl/fl, in which the activity of NFATc1 or inducible NFATc1 in the latter is impaired during the early stages of thymocyte development, we observed increased numbers of γδ T cells. These γδ T cells showed an unusual overexpression of CD4, a lack of CD24 expression, and overexpression of the anti-apoptotic gene Bcl2a1a.
We hypothesize that during the DN stages NFATc1 plays an important role in regulating crucial steps of αβ thymocyte development and when NFATc1 activity is missing this may disturb αβ development resulting in alternative cell fates like γδ T cells.
Purpose
The present study determined the postoperative phenotypes after unrestricted calipered kinematically aligned (KA) total knee arthroplasty (TKA), whether any phenotypes were associated with reoperation, implant revision, and lower outcome scores at 4 years, and whether the proportion of TKAs within each phenotype was comparable to those of the nonarthritic contralateral limb.
Methods
From 1117 consecutive primary TKAs treated by one surgeon with unrestricted calipered KA, an observer identified all patients (N = 198) that otherwise had normal paired femora and tibiae on a long-leg CT scanogram. In both legs, the distal femur–mechanical axis angle (FMA), proximal tibia–mechanical axis angle (TMA), and the hip–knee–ankle angle (HKA) were measured. Each alignment angle was assigned to one of Hirschmann’s five FMA, five TMA, and seven HKA phenotype categories.
Results
Three TKAs (1.5%) underwent reoperation for anterior knee pain or patellofemoral instability in the subgroup of patients with the more valgus phenotypes. There were no implant revisions for component loosening, wear, or tibiofemoral instability. The median Forgotten Joint Score (FJS) was similar between phenotypes. The median Oxford Knee Score (OKS) was similar between the TMA and HKA phenotypes and greatest in the most varus FMA phenotype. The phenotype proportions after calipered KA TKA were comparable to the contralateral leg.
Conclusion
Unrestricted calipered KA’s restoration of the wide range of phenotypes did not result in implant revision or poor FJS and OKS scores at a mean follow-up of 4 years. The few reoperated patients had a more valgus setting of the prosthetic trochlea than recommended for mechanical alignment. Designing a femoral component specifically for KA that restores patellofemoral kinematics with all phenotypes, especially the more valgus ones, is a strategy for reducing reoperation risk.
In this doctoral thesis we cover the performance evaluation of next generation data plane architectures, comprised of complex software as well as programmable hardware components that allow fine granular configuration. In the scope of the thesis we propose mechanisms to monitor the performance of singular components and model key performance indicators of software based packet processing solutions. We present novel approaches towards network abstraction that allow the integration of heterogeneous data plane technologies into a singular network while maintaining total transparency between control and data plane. Finally, we investigate a full, complex system consisting of multiple software-based solutions and perform a detailed performance analysis. We employ simulative approaches to investigate overload control mechanisms that allow efficient operation under adversary conditions. The contributions of this work build the foundation for future research in the areas of network softwarization and network function virtualization.
Background
It is unknown whether technological advancement of stent-retriever devices influences typical observational indicators of safety or effectiveness.
Methods
Observational retrospective study of APERIO® (AP) vs. new generation APERIO® Hybrid (APH) (Acandis®, Pforzheim, Germany) stent-retriever device (01/2019–09/2020) for mechanical thrombectomy (MT) in large vessel occlusion (LVO) stroke. Primary effectiveness endpoint was successful recanalization eTICI (expanded Thrombolysis In Cerebral Ischemia) ≥ 2b67, primary safety endpoint was occurrence of hemorrhagic complications after MT. Secondary outcome measures were time from groin puncture to first pass and successful reperfusion, and the total number of passes needed to achieve the final recanalization result.
Results
A total of 298 patients with LVO stroke who were treated by MT matched the inclusion criteria: 148 patients (49.7%) treated with AP vs. 150 patients (50.3%) treated with new generation APH. Successful recanalization was not statistically different between both groups: 75.7% for AP vs. 79.3% for APH; p = 0.450. Postinterventional hemorrhagic complications and particularly subarachnoid hemorrhage as the entity possibly associated with stent-retriever device type was significantly less frequent in the group treated with the APH: 29.7% for AP and 16.0% for APH; p = 0.005; however, rates of symptomatic hemorrhage with clinical deterioration and in domo mortality were not statistically different. Neither the median number of stent-retriever passages needed to achieve final recanalization, time from groin puncture to first pass, time from groin puncture to final recanalization nor the number of cases in which successful recanalization could only be achieved by using a different stent-retriever as bail-out device differed between both groups.
Conclusion
In the specific example of the APERIO® stent-retriever device, we observed that further technological developments of the new generation device were not associated with disadvantages with respect to typical observational indicators of safety or effectiveness.
Central European forests experience a substantial loss of open-forest organisms due to forest management and increasing nitrogen deposition. However, management strategies, removing different levels of nitrogen, have been rarely evaluated simultaneously.
We tested the additive effects of coppicing and topsoil removal on communities of dung-inhabiting beetles compared to closed forests. We sampled 57 021 beetles, using baited pitfall traps exposed on 27 plots.
Experimental treatments resulted in significantly different communities by promoting open-habitat species. While alpha diversity did not differ among treatments, gamma diversity of Geotrupidae and Scarabaeidae and beta diversity of Staphylinidae were higher in coppice than in forest. Functional diversity of rove beetles was higher in both, coppice and topsoil-removed plots, compared to control plots. This was likely driven by higher habitat heterogeneity in established forest openings. Five dung beetle species and four rove beetle species benefitted from coppicing, one red-listed dung beetle and two rove beetle species benefitted from topsoil removal.
Our results demonstrate that dung-inhabiting beetles related to open forest patches can be promoted by both, coppicing and additional topsoil removal. A mosaic of coppice and bare-soil-rich patches can hence promote landscape-level gamma diversity of dung and rove beetles within forests.
Background and Objectives
Immunoadsorptions (IA) are used to remove autoantibodies from the plasma in autoimmune disorders. In this study, we evaluated the effects of a single-use, recombinant staphylococcal protein A-based immunoadsorber on blood composition of the patient.
Materials and Methods
In a cohort of patients with myasthenia gravis or stiff-person syndrome, essential parameters of blood cell count, coagulation, clinical chemistry or plasma proteins and immunoglobulins (Ig) were measured before and after IA (n = 11).
Results
In average, IA reduced the levels of total IgG, IgG1, IgG2 and IgG4 by approximately 60%, the acetylcholine receptor autoantibody levels by more than 70%. IgG3, IgA or IgM were diminished to a lower extent. In contrast to fibrinogen or other coagulation factors, the column markedly removed vitamin K-dependent coagulation factors II, VII, IX and X by approximately 40%–70%. Accordingly, international normalized ratio and activated partial thromboplastin time were increased after IA by 59.1% and 32.7%, respectively. Coagulation tests almost returned to baseline values within 24 h. Blood cell count, electrolytes, total protein or albumin were not essentially affected. No clinical events occurred.
Conclusion
The single-use, multiple-pass protein A adsorber column is highly efficient to remove IgG1, IgG2 and IgG4 or specific acetylcholine receptor autoantibodies from the plasma. Coagulation parameters should be monitored, since the column has the capacity to largely reduce vitamin K-dependent factors.
Patterns of resource use by animals can clarify how ecological communities have assembled in the past, how they currently function and how they are likely to respond to future perturbations. Bumble bees (Hymentoptera: Bombus spp.) and their floral hosts provide a diverse yet tractable system in which to explore resource selection in the context of plant–pollinator networks. Under conditions of resource limitation, the ability of bumble bees species to coexist should depend on dietary niche overlap. In this study, we report patterns and dynamics of floral morphotype preferences in a mountain bumble bee community based on ~13 000 observations of bumble bee floral visits recorded along a 1400 m elevation gradient. We found that bumble bees are highly selective generalists, rarely visiting floral morphotypes at the rates predicted by their relative abundances. Preferences also differed markedly across bumble bee species, and these differences were well-explained by variation in bumble bee tongue length, generating patterns of preference similarity that should be expected to predict competition under conditions of resource limitation. Within species, though, morphotype preferences varied by elevation and season, possibly representing adaptive flexibility in response to the high elevational and seasonal turnover of mountain floral communities. Patterns of resource partitioning among bumble bee communities may determine which species can coexist under the altered distributions of bumble bees and their floral hosts caused by climate and land use change.
Objective
At high altitude (HA), acute mountain sickness (AMS) is accompanied by neurologic and upper gastrointestinal symptoms (UGS). The primary aim of this study was to test the hypothesis that delayed gastric emptying (GE), assessed by \(^{13}\)C-octanoate breath testing (OBT), causes UGS in AMS. The secondary aim was to assess post-gastric mechanisms of OBT, which could confound results under these conditions, by determination of intermediary metabolites, gastrointestinal peptides, and basal metabolic rate.
Methods
A prospective trial was performed in 25 healthy participants (15 male) at 4559 m (HA) and at 490 m (Zurich). GE was assessed by OBT (428 kcal solid meal) and UGS by visual analogue scales (VAS). Blood sampling of metabolites (glucose, free fatty acids (FFA), triglycerides (TG), beta-hydroxyl butyrate (BHB), L-lactate) and gastrointestinal peptides (insulin, amylin, PYY, etc.) was performed as well as blood gas analysis and spirometry. Statistical analysis: variance analyses, bivariate correlation, and multilinear regression analysis.
Results
After 24 h under hypoxic conditions at HA, participants developed AMS (p < 0.001). \(^{13}\)CO\(_{2}\) exhalation kinetics increased (p < 0.05) resulting in reduced estimates of gastric half-emptying times (p < 0.01). However, median resting respiratory quotients and plasma profiles of TG indicated that augmented beta-oxidation was the main predictor of accelerated \(^{13}\)CO\(_{2}\)-generation under these conditions.
Conclusion
Quantification of \(^{13}\)C-octanoate oxidation by a breath test is sensitive to variation in metabolic (liver) function under hypoxic conditions. \(^{13}\)C-breath testing using short-chain fatty acids is not reliable for measurement of gastric function at HA and should be considered critically in other severe hypoxic conditions, like sepsis or chronic lung disease.
Background
Student performance is a mirror of teaching quality. The pre-/post-test design allows a pragmatic approach to comparing the effects of interventions. However, the calculation of current knowledge gain scores introduces varying degrees of distortion. Here we present a new metric employing a linear weighting coefficient to reduce skewness on outcome interpretation.
Methods
We compared and contrasted a number of common scores (raw and relative gain scores) with our new method on two datasets, one simulated and the other empirical from a previous intervention study (n = 180) employing a pre-/post-test design.
Results
The outcomes of the common scores were clearly different, demonstrating a significant dependency on pre-test scores. Only the new metric revealed a linear relationship to the knowledge baseline, was less skewed on the upper or lower extremes, and proved well suited to allow the calculation of negative learning gains. Employing the empirical dataset, the new method also confirmed the interaction effect of teaching formats with specific subgroups of learner characteristics.
Conclusion
This work introduces a new weighted metric enabling meaningful comparisons between interventions based on a linear transformation. This method will form the basis to intertwine the calculation of test performance closely with the outcome of learning as an important factor reflecting teaching quality and efficacy. Its regular use can improve the transparency of teaching activities and outcomes, contribute to forming rounded judgements of students' acquisition of knowledge and skills and enable valuable feedforward to develop and enhance curricular concepts.
This paper shows that labor demand plays an important role in the labor market reactions to a pension reform in Germany. Employers with a high share of older worker inflow compared with their younger worker inflow, employers in sectors with few investments in research and development, and employers in sectors with a high share of collective bargaining agreements allow their employees to stay employed longer after the reform. These employers offer their older employees partial retirement instead of forcing them into unemployment before early retirement because the older employees incur low substitution costs and high dismissal costs.
Gifted underachievers perform worse in school than would be expected based on their high intelligence. Possible causes for underachievement are low motivational dispositions (need for cognition) and metacognitive competences. This study tested the interplay of these variables longitudinally with gifted and non-gifted students from Germany (N = 341, 137 females) in Grades 6 (M = 12.02 years at t1) and 8 (M = 14.07 years). Declarative and procedural metacognitive competences were assessed in the domain of reading comprehension. Path analyses showed incremental effects of procedural metacognition over and above intelligence on the development of school achievement in gifted students (β = .139). Moreover, declarative metacognition and need for cognition interactively predicted procedural metacognition (β = .169), which mediated their effect on school achievement.
Quantifying tree defoliation by insects over large areas is a major challenge in forest management, but it is essential in ecosystem assessments of disturbance and resistance against herbivory. However, the trajectory from leaf-flush to insect defoliation to refoliation in broadleaf trees is highly variable. Its tracking requires high temporal- and spatial-resolution data, particularly in fragmented forests.
In a unique replicated field experiment manipulating gypsy moth Lymantria dispar densities in mixed-oak forests, we examined the utility of publicly accessible satellite-borne radar (Sentinel-1) to track the fine-scale temporal trajectory of defoliation. The ratio of backscatter intensity between two polarizations from radar data of the growing season constituted a canopy development index (CDI) and a normalized CDI (NCDI), which were validated by optical (Sentinel-2) and terrestrial laser scanning (TLS) data as well by intensive caterpillar sampling from canopy fogging.
The CDI and NCDI strongly correlated with optical and TLS data (Spearman's ρ = 0.79 and 0.84, respectively). The ΔNCDII\(_{Defoliation(A−C)}\) significantly explained caterpillar abundance (R\(^{2}\) = 0.52). The NCDI at critical timesteps and ΔNCDI related to defoliation and refoliation well discriminated between heavily and lightly defoliated forests.
We demonstrate that the high spatial and temporal resolution and the cloud independence of Sentinel-1 radar potentially enable spatially unrestricted measurements of the highly dynamic canopy herbivory. This can help monitor insect pests, improve the prediction of outbreaks and facilitate the monitoring of forest disturbance, one of the high priority Essential Biodiversity Variables, in the near future.
Within the Spessart low mountain range in central Germany, numerous castle ruins of the 13th century ce exist. Their construction and destruction were often determined by the struggle for political and economic supremacy in the region and for control over the Spessart's natural resources. Wahlmich Castle is located in a relatively uncommon strategic and geomorphological position, characterized by a fairly remote position and atypical rough relief. In order to reconstruct the local relief development and possible human impact, a multi-method approach was applied combining two-dimensional geoelectrical measurements, geomorphological mapping and stratigraphic-sedimentological investigations. This provides new insights into the influence of landscape characteristics on choices of castle locations.
The combined geoelectrical, geomorphological and stratigraphic-sedimentological data show that the rough relief is of natural origin and influenced by regional faulting, which triggered sliding and slumping as well as weathering and dissection of the surface deposits. The rough relief and the lithology permitted intensive land use and building activities. However, the location of the castle offered access to and possibly control over important medieval traffic routes and also represented certain ownership claims in the Aschaff River valley.
The economic situation combined with rivalry between different elites led to the castle being built in a geomorphological challenging and strategically less valuable location. Focusing on castles located in rare and challenging geomorphological positions may therefore lead to a better understanding of castle siting in the future.
The capacity to develop immunological memory is a hallmark of the adaptive immune system. To investigate the role of Samd3 for cellular immune responses and memory development, we generated a conditional knock-out mouse including a fluorescent reporter and a huDTR cassette for conditional depletion of Samd3-expressing cells. Samd3 expression was observed in NK cells and CD8 T cells, which are known for their specific function against intracellular pathogens like viruses. After acute viral infections, Samd3 expression was enriched within memory precursor cells and the frequency of Samd3-expressing cells increased during the progression into the memory phase. Similarly, during chronic viral infections, Samd3 expression was predominantly detected within precursors of exhausted CD8 T cells that are critical for viral control. At the functional level however, Samd3-deficient CD8 T cells were not compromised in the context of acute infection with Vaccinia virus or chronic infection with Lymphocytic choriomeningitis virus. Taken together, we describe a novel multifunctional mouse model to study the role of Samd3 and Samd3-expressing cells. We found that Samd3 is specifically expressed in NK cells, memory CD8 T cells, and precursor exhausted T cells during viral infections, while the molecular function of this enigmatic gene remains further unresolved.
High programmed cell death 1 ligand 1 (PD-L1) protein expression and copy number alterations (CNAs) of the corresponding genomic locus 9p24.1 in Hodgkin- and Reed–Sternberg cells (HRSC) have been shown to be associated with favourable response to anti-PD-1 checkpoint inhibition in relapsed/refractory (r/r) classical Hodgkin lymphoma (cHL). In the present study, we investigated baseline 9p24.1 status as well as PD-L1 and major histocompatibility complex (MHC) class I and II protein expression in 82 biopsies from patients with early stage unfavourable cHL treated with anti-PD-1-based first-line treatment in the German Hodgkin Study Group (GHSG) NIVAHL trial (ClinicalTrials.gov Identifier: NCT03004833). All evaluated specimens showed 9p24.1 CNA in HRSC to some extent, but with high intratumoral heterogeneity and an overall smaller range of alterations than reported in advanced-stage or r/r cHL. All but two cases (97%) showed PD-L1 expression by the tumour cells in variable amounts. While MHC-I was rarely expressed in >50% of HRSC, MHC-II expression in >50% of HRSC was found more frequently. No obvious impact of 9p24.1 CNA or PD-L1 and MHC-I/II expression on early response to the highly effective anti-PD-1-based NIVAHL first-line treatment was observed. Further studies evaluating an expanded panel of potential biomarkers are needed to optimally stratify anti-PD-1 first-line cHL treatment.
The US National Research Council (NRC) report "Toxicity Testing in the 21st Century: A Vision and a strategy (Tox21)", published in 2007, calls for a complete paradigm shift in tox-icity testing. A central aspect of the proposed strategy includes the transition from apical end-points in in vivo studies to more mechanistically based in vitro tests. To support and facilitate the transition and paradigm shift in toxicity testing, the Adverse Outcome Pathway (AOP) concept is widely recognized as a pragmatic tool. As case studies, the AOP concept was ap-plied in this work to develop AOPs for proximal tubule injuries initiated by Receptor-mediated endocytosis and lysosomal overload and Inhibition of mtDNA polymerase-. These AOPs were used as a mechanistic basis for the development of in vitro assays for each key event (KE). To experimentally support the developed in vitro assays, proximal tubule cells from rat (NRK-52E) and human (RPTEC/TERT1) were treated with model compounds. To measure the dis-turbance of lysosomal function in the AOP – Receptor-mediated endocytosis and lysosomal overload, polymyxin antibiotics (polymyxin B, colistin, polymyxin B nonapeptide) were used as model compounds. Altered expression of lysosomal associated membrane protein 1/2 (LAMP-1/2) (KE1) and cathepsin D release from lysosomes (KE2) were determined by im-munofluorescence, while cytotoxicity (KE3) was measured using the CellTiter-Glo® cell via-bility assay. Importantly, significant differences in polymyxin uptake and susceptibility be-tween cell lines were observed, underlining the importance of in vitro biokinetics to determine an appropriate in vitro point of departure (PoD) for risk assessment. Compared to the in vivo situation, distinct expression of relevant transporters such as megalin and cubilin on mRNA and protein level in the used cell lines (RPTEC/TERT1 and NRK-52E) could not be con-firmed, making integration of quantitative in vitro to in vivo extrapolations (QIVIVE) neces-sary. Integration of QIVIVE by project partners of the University of Utrecht showed an im-provement in the modelled biokinetic data for polymyxin B. To assess the first key event, (KE1) Depletion of mitochondrial DNA, in the AOP – Inhibition of mtDNA polymerase-, a RT-qPCR method was used to determine the mtDNA copy number in cells treated with mod-el compounds (adefovir, cidofovir, tenofovir, adefovir dipivoxil, tenofovir disoproxil fumarate). Mitochondrial toxicity (KE2) was measured by project partners using the high-content imaging technique and MitoTracker® whereas cytotoxicity (KE3) was determined by CellTiter-Glo® cell viability assay. In contrast to the mechanistic hypothesis underlying the AOP – Inhibition of mtDNA polymerase-, treatment with model compounds for 24 h resulted in an increase rather than a decrease in mtDNA copy number (KE1). Only minor effects on mitochondrial toxicity (KE2) and cytotoxicity (KE3) were observed. Treatment of RPT-EC/TERT1 cells for 14 days showed only a slight decrease in mtDNA copy number after treatment with adefovir dipivoxil and tenofovir disoproxil fumarate, underscoring some of the limitations of short-term in vitro systems. To obtain a first estimation for risk assessment based on in vitro data, potential points of departure (PoD) for each KE were calculated from the obtained in vitro data. The most common PoDs were calculated such as the effect concentra-tion at which 10 % or 20_% effect was measured (EC10, EC20), the highest no observed effect concentration (NOEC), the lowest observed effect concentration (LOEC), the benchmark 10 % (lower / upper) concentrations (BMC10, BMCL10, BMCU10) and a modelled non-toxic con-centration (NtC). These PoDs were then compared with serum and tissue concentrations de-termined from in vivo studies after treatment with therapeutic / supratherapeutic doses of the respective drugs in order to obtain a first estimate of risk based on in vitro data. In addition, AOPs were used to test whether the quantitative key event relationships between key events allow prediction of downstream effects and effects on the adverse outcome (AO) based on measurements of an early key event. Predictions of cytotoxicity from the mathematical rela-tionships showed good concordance with measured cytotoxicity after treatment with colistin and polymyxin b nonapeptide. The work also revealed uncertainties and limitations of the ap-plied strategy, which have a significant impact on the prediction and on a risk assessment based on in vitro results.
Paclitaxel (PTX) is one of the leading drugs against breast and ovarian cancer. Due to its low solubility, treatment of the patients with this drug requires a very well-suited combination with a soluble pharmaceutical excipient to increase the bioavailability and reduce the strong side ef-fects. One efficient way to achieve this in the future could be the incorporation of PTX into pol-ymeric micelles composed of poly(2-oxazoline) based triblock copolymers (POL) which ena-bles PTX loadings of up to 50 wt.%. However, structural information at an atomic level and thus the knowledge of interaction sites within these promising but complex PTX-POL formula-tions were not yet available. Such results could support the future development of improved excipients for PTX and suitable excipients for other pharmaceutical drugs. Therefore, a solid-state MAS NMR investigation of these amorphous formulations with different POL-PTX com-positions was performed in this thesis as this gives insights of the local structure at an atomic level in its solid state. NMR in solution showed very broad 13C signals of PTX for this system due to the reduced mobility of the incorporated drug which exclude this as an analytical meth-od.
In a first study, crystalline PTX was structurally characterized by solid-state NMR as no com-plete 13C spectrum assignment and no 1H NMR data existed for the solid state. In addition, the asymmetric unit of the PTX crystal structure consists of two molecules (Z'=2) that can only be investigated in its solid state. As crystalline PTX in total has about 100 different 13C and 1H chemical shifts with very small differences due to Z’=2, and furthermore, its unit cell consisting of more than 900 atoms, accompanying GIPAW (CASTEP) calculations were required for NMR signal assignments. These calculations were performed using the first three available purely hydrous and anhydrous PTX structures, which were determined by XRD and published by Vel-la-Zarb et al. in 2013. Within this thesis, is was discovered that two investigated batches of commercially available PTX from the same supplier both contained an identical and so far un-known PTX phase that was elucidated by PXRD as well as solid-state NMR data. One of the two batches consists of an additional phase that was shown to be very similar to a known hy-drated phase published in 2013.[1] By heating the batch with the mixture of the two phases un-der vacuum, it is transformed completely to the new dry phase occurring in both PTX batches. Since the drying conditions to obtain anhydrous PTX in-situ on the PXRD setup described by Vella-Zarb et. al.[1] were much softer than ours, we identify our dry phase as a relaxed version of their published anhydrate structure. The PXRD data of the new anhydrate phase was trans-ferred into a new structural model, which currently undergoes geometry optimization. Based on solid-state NMR data at MAS spinning frequencies up to 100 kHz, a 13C and a partial 1H signal assignment for the new anhydrous structure were achieved. These results provided sufficient structural information for further investigations of the micellar POL-PTX system.
In a second study, the applicability and benefit of two-dimensional solid-state 14N-1H HMQC MAS NMR spectra for the characterization of amorphous POL-PTX formulations was investi-gated. The mentioned technique has never been applied to a system of similar complexity be-fore and was chosen because around 84% of the small-molecule drugs contain at least one nitrogen atom. In addition, the number of nitrogen atoms in both POL and PTX is much smaller than the number of carbons or hydrogens, which significantly reduces the spectral complexity. 14N has a natural abundance of 99.6% but leads to quadrupolar broadening due to its nuclear spin quantum number I = 1. While this is usually undesirable due to broadening in the resulting 1D 14N NMR spectra, this effect is explicitly used in the 2D 14N-1H HMQC MAS experiment. The indirect 14N measurement can avoid the broadening while maintaining the advantage of the high natural abundance and making use of the much more dispersed signals due to the additional quadrupolar shifts as compared to 15N.
This measurement method could be successfully applied to the complex amorphous POL-PTX mixtures. With increasing PTX loading of the formulations, additional peaks arise as spatial proximities of the amide nitrogens of POL to NH or OH groups of PTX. In addition, the 14N quadrupolar shift of these amide nitrogens decreases with increasing PTX content indicating a more symmetric nitrogen environment. The latter can be explained by a transformation of the trigonal planar coordination of the tertiary amide nitrogen atoms in pure POL towards a more tetrahedral environment upon PTX loading induced by the formation of hydrogen bonds with NH/OH groups of PTX.
In the third and last project, the results of the two abovementioned studies were used and ex-tended by solid state 13C and two-dimensional 1H-13C as well as 1H-1H MAS NMR data with the aim to derive a structural model of the POL-PTX formulations at an atomic level. The knowledge of the NMR signal assignments for crystalline PTX was transferred to amorphous PTX (present in the micelles of the formulations). The 13C solid-state NMR signals were evalu-ated concerning changes in chemical shifts and full widths of half maximum (FWHM) for the different PTX loadings. In this way, the required information about possible interaction sites at an atomic level becomes available. Due to the complexity of these systems, such proximities often cannot be assigned to special atoms, but more to groups of atoms, as the individual de-velopments of line widths and line shifts are mutually dependent. An advantageous aspect for this analysis was that pure POL already forms unloaded micelles. The evaluation of the data showed that the terminal phenyl groups of PTX seem to be most involved in the interaction by the establishment of the micelle for lowest drug loading and that they are likely to react to the change in the amount of PTX molecules as well. For the incorporation of PTX in the micelles, the following model could be obtained: For lowest drug loading, PTX is mainly located in the inner part of the micelles. Upon further increasing of the loading, it progressively extends to-ward the micellar shell. This could be well shown by the increasing interactions of the hydro-phobic butyl chain of POL and PTX, proceeding in the direction of the polymer backbone with rising drug load. Furthermore, due to the size of PTX and the hydrodynamic radius of the mi-celles, even at the lowest loading, the PTX molecules partially reach the core-shell interface of the micelle. Upon increasing the drug loading, the surface coverage with PTX clusters increas-es based on the obtained model approach. The latter result is supported by DLS and SANS data of this system. The abovementioned results of the 14N-1H HMQC MAS investigation of the POL-PTX formulations support the outlined model.
As an outlook, the currently running geometry optimization and subsequently scheduled calcu-lation of the chemical shieldings of the newly obtained anhydrous PTX crystal structure can further improve the solid-state NMR characterization through determination of further spatial proximities among protons using the existing 2D 1H(DQ)-1H(SQ) solid-state MAS NMR spec-trum at 100 kHz rotor spinning frequency. The 2D 14N-1H HMQC MAS NMR experiments were shown to have great potential as a technique for the analysis of other disordered and amor-phous drug delivery systems as well. The results of this thesis should be subsequently applied to other micellar systems with varying pharmaceutical excipients or active ingredients with the goal of systematically achieving higher drug loadings (e.g., for the investigated PTX, the similar drug docetaxel or even different natural products). Additionally, it is planned to transfer the knowledge to another complex polymer system containing poly(amino acids) which offers hy-drogen bonding donor sites for additional intermolecular interactions. Currently, the POL-PTX system is investigated by further SANS studies that may provide another puzzle piece to the model as complementary measurement method in the future. In addition, the use of MD simu-lations might be considered in the future. This would allow a computerized linking of the differ-ent pieces of information with the aim to determine the most likely model.
Spin- and \(k\)-resolved hard X-ray photoelectron spectroscopy (HAXPES) is a powerful tool to probe bulk electronic properties of complex metal oxides. Due to the low efficiency of common spin detectors of about \(10^{-4}\), such experiments have been rarely performed within the hard X-ray regime since the notoriously low photoionization cross sections further lower the performance tremendously. This thesis is about a new type of spin detector, which employs an imaging spin-filter with multichannel electron recording. This increases the efficiency by a factor of \(10^4\) and makes spin- and \(k\)-resolved photoemission at high excitation energies possible. Two different technical approaches were pursued in this thesis: One using a hemispherical deflection analyzer (HDA) and a separate external spin detector chamber, the other one resorting to a momentum- or \(k\)-space microscope with time-of-flight (TOF) energy recording and an integrated spin-filter crystal. The latter exhibits significantly higher count rates and - since it was designed for this purpose from scratch - the integrated spin-filter option found out to be more viable than the subsequent upgrade of an existing setup with an HDA. This instrumental development is followed by the investigation of the complex metal oxides (CMOs) KTaO\(_3\) by angle-resolved HAXPES (HARPES) and Fe\(_3\)O\(_4\) by spin-resolved HAXPES (spin-HAXPES), respectively.
KTaO\(_3\) (KTO) is a band insulator with a valence-electron configuration of Ta 5\(d^0\). By angle- and spin-integrated HAXPES it is shown that at the buried interface of LaAlO\(_3\)/KTO - by the generation of oxygen vacancies and hence effective electron doping - a conducting electron system forms in KTO. Further investigations using the momentum-resolution of the \(k\)-space TOF microscope show that these states are confined to the surface in KTO and intensity is only obtained from the center or the Gamma-point of each Brillouin zone (BZ). These BZs are furthermore square-like arranged reflecting the three-dimensional cubic crystal structure of KTO. However, from a comparison to calculations it is found that the band structure deviates from that of electron-doped bulk KTaO\(_3\) due to the confinement to the interface.
There is broad consensus that Fe\(_3\)O\(_4\) is a promising material for spintronics applications due to its high degree of spin polarization at the Fermi level. However, previous attempts to measure the spin polarization by spin-resolved photoemission spectroscopy have been hampered by the use of low photon energies resulting in high surface sensitivity. The surfaces of magnetite, though, tend to reconstruct due to their polar nature, and thus their magnetic and electronic properties may strongly deviate from each other and from the bulk, dependent on their orientation and specific preparation. In this work, the intrinsic bulk spin polarization of magnetite at the Fermi level (\(E_F\)) by spin-resolved photoelectron spectroscopy, is determined by spin-HAXPES on (111)-oriented thin films, epitaxially grown on ZnO(0001) to be \(P(E_F) = -80^{+10}_{-20}\) %.
Bacterial small RNAs (sRNAs) are widespread post-transcriptional regulators that control bacterial stress responses and virulence. Nevertheless, little is known about how they arise and evolve. Homologs can be difficult to identify beyond the strain level using sequence-based approaches, and similar functionalities can arise by convergent evolution. Here, we found that the virulence-associated CJnc190 sRNA of the foodborne pathogen Campylobacter jejuni resembles the RepG sRNA from the gastric pathogen Helicobacter pylori. However, while both sRNAs bind G-rich sites in their target mRNAs using a C/U-rich loop, they largely differ in their biogenesis. RepG is transcribed from a stand-alone gene and does not require processing, whereas CJnc190 is transcribed from two promoters as precursors that are processed by RNase III and also has a cis-encoded antagonist, CJnc180. By comparing CJnc190 homologs in diverse Campylobacter species, we show that RNase III-dependent processing of CJnc190 appears to be a conserved feature even outside of C. jejuni. We also demonstrate the CJnc180 antisense partner is expressed in C. coli, yet here might be derived from the 3’UTR (untranslated region) of an upstream flagella-related gene. Our analysis of G-tract targeting sRNAs in Epsilonproteobacteria demonstrates that similar sRNAs can have markedly different biogenesis pathways.
Comparative genomics provides structural and functional insights into Bacteroides RNA biology
(2022)
Bacteria employ noncoding RNA molecules for a wide range of biological processes, including scaffolding large molecular complexes, catalyzing chemical reactions, defending against phages, and controlling gene expression. Secondary structures, binding partners, and molecular mechanisms have been determined for numerous small noncoding RNAs (sRNAs) in model aerobic bacteria. However, technical hurdles have largely prevented analogous analyses in the anaerobic gut microbiota. While experimental techniques are being developed to investigate the sRNAs of gut commensals, computational tools and comparative genomics can provide immediate functional insight. Here, using Bacteroides thetaiotaomicron as a representative microbiota member, we illustrate how comparative genomics improves our understanding of RNA biology in an understudied gut bacterium. We investigate putative RNA-binding proteins and predict a Bacteroides cold-shock protein homolog to have an RNA-related function. We apply an in silico protocol incorporating both sequence and structural analysis to determine the consensus structures and conservation of nine Bacteroides noncoding RNA families. Using structure probing, we validate and refine these predictions and deposit them in the Rfam database. Through synteny analyses, we illustrate how genomic coconservation can serve as a predictor of sRNA function. Altogether, this work showcases the power of RNA informatics for investigating the RNA biology of anaerobic microbiota members.
In this thesis, I study entanglement in quantum field theory, using methods from operator algebra theory. More precisely, the thesis covers original research on the entanglement properties of the free fermionic field. After giving a pedagogical introduction to algebraic methods in quantum field theory, as well as the modular theory of Tomita-Takesaki and its relation to entanglement, I present a coherent framework that allows to solve Tomita-Takesaki theory for free fermionic fields in any number of dimensions. Subsequently, I use the derived machinery on the free massless fermion in two dimensions, where the formulae can be evaluated analytically. In particular, this entails the derivation of the resolvent of restrictions of the propagator, by means of solving singular integral equations. In this way, I derive the modular flow, modular Hamiltonian, modular correlation function, R\'enyi entanglement entropy, von-Neumann entanglement entropy, relative entanglement entropy, and mutual information for multi-component regions. All of this is done for the vacuum and thermal states, both on the infinite line and the circle with (anti-)periodic boundary conditions. Some of these results confirm previous results from the literature, such as the modular Hamiltonian and entanglement entropy in the vacuum state. The non-universal solutions for modular flow, modular correlation function, and R\'enyi entropy, however are new, in particular at finite temperature on the circle. Additionally, I show how boundaries of spacetime affect entanglement, as well as how one can define relative (entanglement) entropy and mutual information in theories with superselection rules. The findings regarding modular flow in multi-component regions can be summarised as follows: In the non-degenerate vacuum state, modular flow is multi-local, in the sense that it mixes the field operators along multiple trajectories, with one trajectory per component. This was already known from previous literature but is presented here in a more explicit form. In particular, I present the exact solution for the dynamics of the mixing process. What was not previously known at all, is that the modular flow of the thermal state on the circle is infinitely multi-local even for a connected region, in the sense that it mixes the field along an infinite, discretely distributed set, of trajectories. In the limit of high temperatures, all trajectories but the local one are pushed towards the boundary of the region, where their amplitude is damped exponentially, leaving only the local result. At low temperatures, on the other hand, these trajectories distribute densely in the region to either---for anti-periodic boundary conditions---cancel, or---for periodic boundary conditions---recover the non-local contribution due to the degenerate vacuum state. Proceeding to spacetimes with boundaries, I show explicitly how the presence of a boundary implies entanglement between the two components of the Dirac spinor. By computing the mutual information between the components inside a connected region, I show quantitatively that this entanglement decreases as an inverse square law at large distances from the boundary. In addition, full conformal symmetry (which is explicitly broken due to the presence of a boundary) is recovered from the exact solution for modular flow, far away from the boundary. As far as I know, all of these results are new, although related results were published by another group during the final stage of this thesis. Finally, regarding relative entanglement entropy in theories with superselection sectors, I introduce charge and flux resolved relative entropies, which are novel measures for the distinguishability of states, incorporating a charge operator, central to the algebra of observables. While charge resolved relative entropy has the interpretation of being a ``distinguishability per charge sector'', I argue that it is physically meaningless without placing a cutoff, due to infinite short-distance entanglement. Flux resolved relative entropy, on the other hand, overcomes this problem by inserting an Aharonov-Bohm flux and thus passing to a variant of the grand canonical ensemble. It takes a well defined value, even without putting a cutoff, and I compute its value between various states of the free massless fermion on the line, the charge operator being the total fermion number.
One consequence of the recent coronavirus pandemic is increased demand and use of online services around the globe. At the same time, performance requirements for modern technologies are becoming more stringent as users become accustomed to higher standards. These increased performance and availability requirements, coupled with the unpredictable usage growth, are driving an increasing proportion of applications to run on public cloud platforms as they promise better scalability and reliability.
With data centers already responsible for about one percent of the world's power consumption, optimizing resource usage is of paramount importance. Simultaneously, meeting the increasing and changing resource and performance requirements is only possible by optimizing resource management without introducing additional overhead. This requires the research and development of new modeling approaches to understand the behavior of running applications with minimal information.
However, the emergence of modern software paradigms makes it increasingly difficult to derive such models and renders previous performance modeling techniques infeasible. Modern cloud applications are often deployed as a collection of fine-grained and interconnected components called microservices. Microservice architectures offer massive benefits but also have broad implications for the performance characteristics of the respective systems. In addition, the microservices paradigm is typically paired with a DevOps culture, resulting in frequent application and deployment changes. Such applications are often referred to as cloud-native applications. In summary, the increasing use of ever-changing cloud-hosted microservice applications introduces a number of unique challenges for modeling the performance of modern applications. These include the amount, type, and structure of monitoring data, frequent behavioral changes, or infrastructure variabilities. This violates common assumptions of the state of the art and opens a research gap for our work.
In this thesis, we present five techniques for automated learning of performance models for cloud-native software systems. We achieve this by combining machine learning with traditional performance modeling techniques. Unlike previous work, our focus is on cloud-hosted and continuously evolving microservice architectures, so-called cloud-native applications. Therefore, our contributions aim to solve the above challenges to deliver automated performance models with minimal computational overhead and no manual intervention. Depending on the cloud computing model, privacy agreements, or monitoring capabilities of each platform, we identify different scenarios where performance modeling, prediction, and optimization techniques can provide great benefits. Specifically, the contributions of this thesis are as follows:
Monitorless: Application-agnostic prediction of performance degradations.
To manage application performance with only platform-level monitoring, we propose Monitorless, the first truly application-independent approach to detecting performance degradation. We use machine learning to bridge the gap between platform-level monitoring and application-specific measurements, eliminating the need for application-level monitoring. Monitorless creates a single and holistic resource saturation model that can be used for heterogeneous and untrained applications. Results show that Monitorless infers resource-based performance degradation with 97% accuracy. Moreover, it can achieve similar performance to typical autoscaling solutions, despite using less monitoring information.
SuanMing: Predicting performance degradation using tracing.
We introduce SuanMing to mitigate performance issues before they impact the user experience. This contribution is applied in scenarios where tracing tools enable application-level monitoring. SuanMing predicts explainable causes of expected performance degradations and prevents performance degradations before they occur. Evaluation results show that SuanMing can predict and pinpoint future performance degradations with an accuracy of over 90%.
SARDE: Continuous and autonomous estimation of resource demands.
We present SARDE to learn application models for highly variable application deployments. This contribution focuses on the continuous estimation of application resource demands, a key parameter of performance models. SARDE represents an autonomous ensemble estimation technique. It dynamically and continuously optimizes, selects, and executes an ensemble of approaches to estimate resource demands in response to changes in the application or its environment. Through continuous online adaptation, SARDE efficiently achieves an average resource demand estimation error of 15.96% in our evaluation.
DepIC: Learning parametric dependencies from monitoring data.
DepIC utilizes feature selection techniques in combination with an ensemble regression approach to automatically identify and characterize parametric dependencies. Although parametric dependencies can massively improve the accuracy of performance models, DepIC is the first approach to automatically learn such parametric dependencies from passive monitoring data streams. Our evaluation shows that DepIC achieves 91.7% precision in identifying dependencies and reduces the characterization prediction error by 30% compared to the best individual approach.
Baloo: Modeling the configuration space of databases.
To study the impact of different configurations within distributed DBMSs, we introduce Baloo. Our last contribution models the configuration space of databases considering measurement variabilities in the cloud. More specifically, Baloo dynamically estimates the required benchmarking measurements and automatically builds a configuration space model of a given DBMS. Our evaluation of Baloo on a dataset consisting of 900 configuration points shows that the framework achieves a prediction error of less than 11% while saving up to 80% of the measurement effort.
Although the contributions themselves are orthogonally aligned, taken together they provide a holistic approach to performance management of modern cloud-native microservice applications.
Our contributions are a significant step forward as they specifically target novel and cloud-native software development and operation paradigms, surpassing the capabilities and limitations of previous approaches.
In addition, the research presented in this paper also has a significant impact on the industry, as the contributions were developed in collaboration with research teams from Nokia Bell Labs, Huawei, and Google.
Overall, our solutions open up new possibilities for managing and optimizing cloud applications and improve cost and energy efficiency.
Efficacy of transcranial direct current stimulation in people with multiple sclerosis: a review
(2022)
Background and purpose
Multiple sclerosis (MS) is a chronic inflammatory disease causing a wide range of symptoms including motor and cognitive impairment, fatigue and pain. Over the last two decades, non-invasive brain stimulation, especially transcranial direct current stimulation (tDCS), has increasingly been used to modulate brain function in various physiological and pathological conditions. However, its experimental applications for people with MS were noted only as recently as 2010 and have been growing since then. The efficacy for use in people with MS remains questionable with the results of existing studies being largely conflicting. Hence, the aim of this review is to paint a picture of the current state of tDCS in MS research grounded on studies applying tDCS that have been done to date.
Methods
A keyword search was performed to retrieve articles from the earliest article identified until 14 February 2021 using a combination of the groups (1) ‘multiple sclerosis’, ‘MS’ and ‘encephalomyelitis’ and (2) ‘tDCS’ and ‘transcranial direct current stimulation’.
Results
The analysis of the 30 articles included in this review underlined inconsistent effects of tDCS on the motor symptoms of MS based on small sample sizes. However, tDCS showed promising benefits in ameliorating fatigue, pain and cognitive symptoms.
Conclusion
Transcranial direct current stimulation is attractive as a non-drug approach in ameliorating MS symptoms, where other treatment options remain limited. The development of protocols tailored to the individual's own neuroanatomy using high definition tDCS and the introduction of network mapping in the experimental designs might help to overcome the variability between studies.
The genetic modification of T cells for the expression a chimeric antigen receptor (CAR) endows them with a new specificity for an antigen. Adoptive immunotherapy with CD19-CAR T cells has achieved high rates of sustained complete remissions in B cell malignancies. However, the downregulation or loss of the targeted antigen after mono-specific CAR T cell therapy, e.g. against CD19 or CD22, has been reported. Targeting multiple antigens on tumour cells, sequentially or simultaneously, could overcome this limitation. Additionally, targeting multiple antigens with CAR T cells could drive the translation from hematologic malignancies to prevalent solid cancers, which often express tumour-associated antigens heterogeneously. We hypothesised that expression of a universal CAR, which can be programmed with hapten-like molecules, could endow T cells with specificities for multiple antigens.
In this study we introduce a novel chemically programmable CAR (cpCAR) based on monoclonal antibody h38C2. Our data show, that cpCARs form a reversible chemical bond to molecules containing a diketone-group and therefore can be programmed to acquire multiple specificities. We programmed cpCAR T cells with hapten-like compounds against integrins αvβ3 and α4β1 as well as the folate receptor. We observed tumour cell lysis, IFN ɣ and IL-2 production and proliferation of programmed cpCAR T cells against tumour cells expressing the respective target antigen in vitro.
As a reference to cpCARs programmed against αvβ3, we further introduced novel conventional αvβ3-CARs. These CARs, based on humanised variants of monoclonal antibody LM609 (hLM609), directly bind to integrin αvβ3 via their scFv. The four αvβ3-CAR constructs comprised either an scFv with higher affinity (hLM609v7) or lower affinity (hLM609v11) against αvβ3 integrin and either a long (IgG4 hinge, CH2, CH3) or short (IgG4 hinge) extracellular spacer. We selected the hLM609v7-CAR with short spacer, which showed potent anti-tumour reactivity both in vitro and in a murine xenograft model, for comparison with the cpCAR programmed against αvβ3. Our data show specific lysis of αvβ3-positive tumour cells, cytokine production and proliferation of both hLM609-CAR T cells and cpCAR T cells in vitro. However, conventional hLM609-CAR T cells mediated stronger anti-tumour effects compared to cpCAR T cells in the same amount of time. In line with the in vitro data, complete destruction of tumour lesions in a murine melanoma xenograft model was only observed for mice treated with conventional αvβ3-CAR T cells.
Collectively, we introduce a cpCAR, which can be programmed against multiple tumour antigens, and hLM609-CARs specific for the integrin αvβ3. The cpCAR technology bears the potential to counteract current limitations, e.g. antigen loss, of current monospecific CAR T cell therapy. Targeting αvβ3 integrin with CAR T cells could have clinical applications in the treatment of solid malignancies, because αvβ3 is not only expressed on a variety of solid malignancies, but also on tumour-associated vasculature and fibroblast.
DNA damage occurs frequently during normal cellular progresses or by environmental factors. To preserve the genome integrity, DNA damage response (DDR) has evolved to repair DNA and the non-properly repaired DNA induces human diseases like immune deficiency and cancer. Since a large number of proteins involved in DDR are enzymes of ubiquitin system, it is critical to investigate how the ubiquitin system regulates cellular response to DNA damage. Hereby, we reveal a novel mechanism for DDR regulation via activation of SCF ubiquitin ligase upon DNA damage.
As an essential step for DNA damage-induced inhibition of DNA replication, Cdc25A degradation by the E3 ligase β-TrCP upon DNA damage requires the deubiquitinase Usp28. Usp28 deubiquitinates β-TrCP in response to DNA damage, thereby promotes its dimerization, which is required for its activity in substrate ubiquitination and degradation. Particularly, ubiquitination at a specific lysine on β-TrCP suppresses dimerization.
The key mediator protein of DDR, 53BP1, forms oligomers and associates with β-TrCP to inhibit its activity in unstressed cells. Upon DNA damage, 53BP1 is degraded in the nucleoplasm, which requires oligomerization and is promoted by Usp28 in a β-TrCP-dependent manner. Consequently, 53BP1 destruction releases and activates β-TrCP during DNA damage response.
Moreover, 53BP1 deletion and DNA damage promote β-TrCP dimerization and recruitment to chromatin sites that locate in the vicinity of putative replication origins. Subsequently, the chromatin-associated Cdc25A is degraded by β-TrCP at the origins. The stimulation of β-TrCP binding to the origins upon DNA damage is accompanied by unloading of Cdc45, a crucial component of pre-initiation complexes for replication. Loading of Cdc45 to origins is a key Cdk2-dependent step for DNA replication initiation, indicating that localized Cdc25A degradation by β-TrCP at origins inactivates Cdk2, thereby inhibits the initiation of DNA replication.
Collectively, this study suggests a novel mechanism for the regulation of DNA replication upon DNA damage, which involves 53BP1- and Usp28-dependent activation of the SCF(β-TrCP) ligase in Cdc25A degradation.
Articular cartilage is a highly specialized tissue which provides a lubricated gliding surface in joints and thereby enables low-friction movement. If damaged once it has a very low intrinsic healing capacity and there is still no treatment in the clinic which can restore healthy cartilage tissue. 3D biofabrication presents a promising perspective in the field by combining healthy cells and bioactive ink materials. Thereby, the composition of the applied bioink is crucial for defect restoration, as it needs to have the physical properties for the fabrication process and also suitable chemical cues to provide a supportive environment for embedded cells. In the last years, ink compositions with high polymer contents and crosslink densities were frequently used to provide 3D printability and construct stability. But these dense polymeric networks were often associated with restricted bioactivity and impaired cell processes like differentiation and the distribution of newly produced extracellular matrix (ECM), which is especially important in the field of cartilage engineering. Therefore, the aim of this thesis was the development of hyaluronic acid (HA)-based bioinks with a reduced polymer content which are 3D printable and additionally facilitate chondrogenic differentiation of mesenchymal stromal cells (MSCs) and the homogeneous distribution of newly produced ECM. Starting from not-printable hydrogels with high polymer contents and restricted bioactivity, distinct stepwise improvements were achieved regarding stand-alone 3D printability as well as MSC differentiation and homogeneous ECM distribution. All newly developed inks in this thesis made a valuable contribution in the field of cartilage regeneration and represent promising approaches for potential clinical applications. The underlying mechanisms and established ink design criteria can further be applied to other biofabricated tissues, emphasizing their importance also in a more general research setting.
Lack of acid sphingomyelinase (ASM) activity, either through genetic deficiency or through pharmacological inhibition, is linked with increased activity and frequency of Foxp3+ regulatory T cells (Treg) among cluster of differentiation (CD) 4+ T cells in mice in vivo and in vitro1. Thus, pharmacological blockade of ASM activity, which catalyzes the cleavage of sphingomyelin to ceramide and phosphocholine, might be used as a new therapeutic mechanism to correct numeric and/ or functional Treg de-ficiencies in diseases like multiple sclerosis or major depression.
In the present study, the effect of pharmacological inhibition of ASM in humans, in vitro and in vivo, was analyzed. In the in vitro experiments, peripheral blood mono-nuclear cells (PBMC) of healthy human blood donors were treated with two widely prescribed antidepressants with high (sertraline, Ser) or low (citalopram, Cit) capaci-ty to inhibit ASM activity. Similar to the findings in mice an increase in the frequency of Treg among human CD4+ T cells upon inhibition of ASM activity was observed. For the analysis in vivo, a prospective study of the composition of the CD4+ T cell com-partment of patients treated for major depression was done. The data show that pharmacological inhibition of ASM activity was superior to antidepressants with little or no ASM-inhibitory activity in increasing CD45RA- CD25high effector Treg (efTreg) frequencies among CD4+ T cells to normal levels. Independently of ASM inhibition, correlating the data with the clinical response, i.e. improvement of the Hamilton rat-ing scale for depression (HAMD) by at least 50 per cent (%) after four weeks of treatment, it was found that an increase in efTreg frequencies among CD4+ cells dur-ing the first week of treatment identified patients with a clinical response.
Regarding the underlying mechanism, it could be found that the positive effect of ASM inhibition on Treg required CD28 co-stimulation suggesting that enhanced CD28 co-stimulation was the driver of the observed increase in the frequency of Treg among human CD4+ T cells. Inhibition of ASM activity was further associated with changes in the expression and shuttling of CTLA-4, a key inhibitory molecule ex-pressed by Treg, between cellular compartments but the suppressive activity of CTLA-4 through its transendocytosis activity was unaffected by the inhibition of ASM activity.
In summary, the frequency of (effector) Treg among CD4+ T cells in mice and in hu-mans is increased after inhibition of ASM activity suggesting that ASM blockade might beneficially modulate autoimmune diseases and depression-promoting in-flammation.
Wilms tumor (WT) or nephroblastoma is the most common kidney tumor in childhood. Several genetic alterations have been identified in WT over the past years. However, a clear-cut underlying genetic defect has remained elusive. Growing evidence suggests that miRNA processing genes play a major role in the formation of pediatric tumors, including WT.
We and others have identified the microprocessor genes DROSHA and DGCR8 as key players in Wilms tumorigenesis. Exome sequence analysis of a cohort of blastemal-type WTs revealed the recurrent hotspot mutations DROSHA E1147K and DGCR8 E518K mapping to regions important for catalyic activity and RNA-binding. These alterations were expected to affect processing of miRNA precursors, ultimately leading to altered miRNA expression. Indeed, mutated tumor samples were characterized by distinct miRNA patterns. Notably, these mutations have been observed almost exclusively in WT, suggesting that they play a specific role in WT formation.
The aim of the present work was to first examine the mutation frequency of DROSHA E1147K and DGCR8 E518K in a larger cohort of WTs, and to further characterize these microprocessor gene mutations as potential oncogenic drivers for WT formation.
Screening of additional 700 WT samples by allele-specific PCR revealed a high frequency of DROSHA E1147K and DGCR8 E518K mutations, with the highest incidence found in tumors of high-risk histology. DROSHA E1147K was heterozygously expressed in all cases, which strongly implies a dominant negative effect. In contrast, DGCR8 E518K exclusively exhibited homozygous expression, suggestive for the mutation to act recessive.
To functionally assess the mutations of the microprocessor complex in vitro, I generated stable HEK293T cell lines with inducible overexpression of DROSHA E1147K, and stable mouse embryonic stem cell (mESC) lines with inducible overexpression of DGCR8 E518K. To mimic the homozygous expression observed in WT, DGCR8 mESC lines were generated on a DGCR8 knockout background. Inducible overexpression of wild-type or mutant DROSHA in HEK293T cells showed that DROSHA E1147K leads to a global downregulation of miRNA expression. It has previously been shown that the knockout of DGCR8 in mESCs also results in a significant downregulation of canonical miRNAs. Inducible overexpression of wild type DGCR8 rescued this processing defect. DGCR8 E518K on the other hand, only led to a partial rescue. Differentially expressed miRNAs comprised members of the ESC cell cycle (ESCC) and let-7 miRNA families whose antagonism is known to play a pivotal role in the regulation of stem cell properties. Along with altered miRNA expression, DGCR8-E518K mESCs exhibited alterations in target gene expression potentially affecting various biological processes.
We could observe decreased proliferation rates, most likely due to reduced cell viability. DGCR8-E518K seemed to be able to overcome the block of G1-S transition and to rescue the cell cycle defect in DGCR8-KO mESCs, albeit not to the full extent like DGCR8-wild-type. Moreover, DGCR8-E518K appeared to be unable to completely block epithelial-to-mesenchymal transition (EMT). Embryoid bodies (EBs) with the E518K mutation, however, were still able to silence the self-renewal program rescuing the differentiation defect in DGCR8-KO mESCs.
Taken together, I could show that DROSHA E1147K and DGCR8 E518K are frequent events in WT with the highest incidence in high-risk tumor entities. Either mutation led to altered miRNA expression in vitro confirming our previous findings in tumor samples. While the DROSHA E1147K mutation resulted in a global downregulation of canonical miRNAs, DGCR8 E518K was able to retain significant activity of the microprocessor complex, suggesting that partial reduction of activity or altered specificity may be critical in Wilms tumorigenesis.
Despite the significant differences found in the miRNA and mRNA profiles of DGCR8 E518K and DGCR8-wild-type mESCs, functional analysis showed that DGCR8 E518K could mostly restore important cellular functions in the knockout and only slightly differed from the wild-type situation. Further studies in a rather physiological environment, such as in a WT blastemal model system, may additionally help to better assess the subtle differences between DGCR8 E518K and DGCR8 wild-type observed in our mESC lines. Together with our findings, these model systems may thus contribute to better understand the role of these microprocessor mutations in the formation of WT.
Background
Epithelioid haemangioma (EH) arising from the skin is a benign vascular tumour with marked inflammatory cell infiltration, which exhibits a high tendency to persist and frequently recurs after resection. So far, the underlying pathogenesis is largely elusive.
Objectives
To identify genetic alterations by next-generation sequencing and/or droplet digital polymerase chain reaction (ddPCR) in cutaneous EH.
Methods
DNA and RNA from an EH lesion of an index patient were subjected to whole-genome and RNA sequencing. Multiplex PCR-based panel sequencing of genomic DNA isolated from archival formalin-fixed paraffin-embedded tissue of 18 patients with cutaneous EH was performed. ddPCR was used to confirm mutations.
Results
We identified somatic mutations in genes of the mitogen-activated protein kinase (MAPK) pathway (MAP2K1 and KRAS) in cutaneous EH biopsies. By ddPCR we could confirm the recurrent presence of activating, low-frequency mutations affecting MAP2K1. In total, nine out of 18 patients analysed showed activating MAPK pathway mutations, which were mutually exclusive. Comparative analysis of tissue areas enriched for lymphatic infiltrate or aberrant endothelial cells, respectively, revealed an association of these mutations with the presence of endothelial cells.
Conclusions
Taken together, our data suggest that EH shows somatic mutations in genes of the MAPK pathway which might contribute to the formation of this benign tumour.
Background
Pemphigus vulgaris and pemphigus foliaceus are potentially life-threatening autoimmune disorders triggered by IgG autoantibodies against mucosal and epidermal desmogleins. There is an unmet need for fast-acting drugs that enable patients to achieve early sustained remission with reduced corticosteroid reliance.
Objectives
To investigate efgartigimod, an engineered Fc fragment that inhibits the activity of the neonatal Fc receptor, thereby reducing serum IgG levels, for treating pemphigus.
Methods
Thirty-four patients with mild-to-moderate pemphigus vulgaris or foliaceus were enrolled in an open-label phase II adaptive trial. In sequential cohorts, efgartigimod was dosed at 10 or 25 mg kg\(^{-1}\) intravenously with various dosing frequencies, as monotherapy or as add-on therapy to low-dose oral prednisone. Safety endpoints comprised the primary outcome. The study is registered at ClinicalTrials.gov (identifier NCT03334058).
Results
Adverse events were mostly mild and were reported by 16 of 19 (84%) patients receiving efgartigimod 10 mg kg\(^{-1}\) and 13 of 15 (87%) patients receiving 25 mg kg−1, with similar adverse event profiles between dose groups. A major decrease in serum total IgG and anti-desmoglein autoantibodies was observed and correlated with improved Pemphigus Disease Area Index scores. Efgartigimod, as monotherapy or combined with prednisone, demonstrated early disease control in 28 of 31 (90%) patients after a median of 17 days. Optimized, prolonged treatment with efgartigimod in combination with a median dose of prednisone 0·26 mg \(^{-1}\) per day (range 0·06–0·48) led to complete clinical remission in 14 of 22 (64%) patients within 2–41 weeks.
Conclusions
Efgartigimod was well tolerated and exhibited an early effect on disease activity and outcome parameters, providing support for further evaluation as a therapy for pemphigus.
Climate and land-use change are key drivers of environmental degradation in the Anthropocene, but too little is known about their interactive effects on biodiversity and ecosystem services. Long-term data on biodiversity trends are currently lacking. Furthermore, previous ecological studies have rarely considered climate and land use in a joint design, did not achieve variable independence or lost statistical power by not covering the full range of environmental gradients.
Here, we introduce a multi-scale space-for-time study design to disentangle effects of climate and land use on biodiversity and ecosystem services. The site selection approach coupled extensive GIS-based exploration (i.e. using a Geographic information system) and correlation heatmaps with a crossed and nested design covering regional, landscape and local scales. Its implementation in Bavaria (Germany) resulted in a set of study plots that maximise the potential range and independence of environmental variables at different spatial scales.
Stratifying the state of Bavaria into five climate zones (reference period 1981–2010) and three prevailing land-use types, that is, near-natural, agriculture and urban, resulted in 60 study regions (5.8 × 5.8 km quadrants) covering a mean annual temperature gradient of 5.6–9.8°C and a spatial extent of ~310 × 310 km. Within these regions, we nested 180 study plots located in contrasting local land-use types, that is, forests, grasslands, arable land or settlement (local climate gradient 4.5–10°C). This approach achieved low correlations between climate and land use (proportional cover) at the regional and landscape scale with |r ≤ 0.33| and |r ≤ 0.29| respectively. Furthermore, using correlation heatmaps for local plot selection reduced potentially confounding relationships between landscape composition and configuration for plots located in forests, arable land and settlements.
The suggested design expands upon previous research in covering a significant range of environmental gradients and including a diversity of dominant land-use types at different scales within different climatic contexts. It allows independent assessment of the relative contribution of multi-scale climate and land use on biodiversity and ecosystem services. Understanding potential interdependencies among global change drivers is essential to develop effective restoration and mitigation strategies against biodiversity decline, especially in expectation of future climatic changes. Importantly, this study also provides a baseline for long-term ecological monitoring programs.
Gazes are of central relevance for people. They are crucial for navigating the world and communicating with others. Nevertheless, research in recent years shows that many findings from experimental research on gaze behavior cannot be transferred from the laboratory to everyday behavior. For example, the frequency with which conspecifics are looked at is considerably higher in experimental contexts than what can be observed in daily behavior. In short: findings from laboratories cannot be generalized into general statements. This thesis is dedicated to this matter. The dissertation describes and documents the current state of research on social attention through a literature review, including a meta-analysis on the /gaze cueing/ paradigm and an empirical study on the robustness of gaze following behavior. In addition, virtual reality was used in one of the first studies in this research field. Virtual reality has the potential to significantly improve the transferability of experimental laboratory studies to everyday behavior. This is because the technology enables a high degree of experimental control in naturalistic research designs. As such, it has the potential to transform empirical research in the same way that the introduction of computers to psychological research did some 50 years ago. The general literature review on social attention is extended to the classic /gaze cueing/ paradigm through a systematic review of publications and a meta-analytic evaluation (Study 1). The cumulative evidence supported the findings of primary studies: Covert spatial attention is directed by faces. However, the experimental factors included do not explain the surprisingly large variance in the published results. Thus, there seem to be further, not well-understood variables influencing these social processes. Moreover, classic /gaze cueing/ studies have limited ecological validity. This is discussed as a central reason for the lack of generalisability. Ecological validity describes the correspondence between experimental factors and realistic situations. A stimulus or an experimental design can have high and low ecological validity on different dimensions and have different influences on behavior. Empirical research on gaze following behavior showed that the /gaze cueing/ effect also occurs with contextually embedded stimuli (Study 2). The contextual integration of the directional cue contrasted classical /gaze cueing/ studies, which usually show heads in isolation. The research results can thus be transferred /within/ laboratory studies to higher ecologically valid research paradigms. However, research shows that the lack of ecological validity in experimental designs significantly limits the transferability of experimental findings to complex situations /outside/ the laboratory. This seems to be particularly the case when social interactions and norms are investigated. However, ecological validity is also often limited in these studies for other factors, such as contextual embedding /of participants/, free exploration behavior (and, thus, attentional control), or multimodality. In a first study, such high ecological validity was achieved for these factors with virtual reality, which could not be achieved in the laboratory so far (Study 3). Notably, the observed fixation patterns showed differences even under /most similar/ conditions in the laboratory and natural environments. Interestingly, these were similar to findings also derived from comparisons of eye movement in the laboratory and field investigations. These findings, which previously came from hardly comparable groups, were thus confirmed by the present Study 3 (which did not have this limitation). Overall, /virtual reality/ is a new technical approach to contemporary social attention research that pushes the boundaries of previous experimental research. The traditional trade-off between ecological validity and experimental control thus becomes obsolete, and laboratory studies can closely inherit an excellent approximation of reality. Finally, the present work describes and discusses the possibilities of this technology and its practical implementation. Within this context, the extent to which this development can still guarantee a constructive classification of different laboratory tests in the future is examined.
Motoneurons are highly compartmentalized cells with very long extensions that separate their nerve terminals from cell bodies. To maintain their extensive morphological complexity and protect their cellular integrity from neurotoxic stresses, neurons rely on the functions of RNA-binding proteins. One such protein is hnRNP R, a multifunctional protein with a plethora of roles related to RNA metabolism that comes into play in the nervous system. hnRNP R is localized mainly in the nucleus but also exists in the cytoplasm and axons of motoneurons. Increasing in vitro evidence indicates a potential function of hnRNP R in the development and maintenance of motoneurons by regulating axon growth and axonal RNA transport. Additionally, hnRNP R interacts with several proteins involved in motoneuron diseases. Hnrnpr pre-mRNA undergoes alternative splicing to produce transcripts encoding two protein isoforms: a full-length protein (hnRNP R-FL) and a shorter form lacking the N-terminal acidic domain (hnRNP R-ΔN). While the neuronal defects produced by total hnRNP R depletion have been investigated before, the contribution of individual isoforms towards such functions has remained mostly unknown.
In this study, we showed that while both isoforms are expressed across multiple tissues, the full-length isoform is particularly abundant in the nervous system. We generated a mouse model for selective knockout of the full-length hnRNP R isoform (Hnrnprtm1a/tm1a) and found that the hnRNP R-∆N isoform remains expressed in these mice and is upregulated in a compensatory post-transcriptional process. We found that the truncated isoform is sufficient to support subcellular RNA transport related to axon growth in primary motoneurons. However, Hnrnprtm1a/tm1a mice show defects in DNA damage repair after exposure to γ-irradiation and etoposide. Knock down of both hnRNP R isoforms showed a similar extent of DNA damage as for motoneurons depleted of just full-length hnRNP R. Rescue experiments showed that expression of full-length hnRNP R but not of hnRNP R-ΔN can restore DNA damage repair when endogenous hnRNP R is depleted. By performing subcellular fractionation, we found that hnRNP R associates with chromatin independently from its association with pre-mRNA. Interestingly, we show that hnRNP R interacts with phosphorylated histone H2AX (γ-H2AX), following DNA damage. Proteomics analysis identifies the multifunctional protein Y-box binding protein 1 (Yb1) as one of the top interacting partners of hnRNP R. Similar to loss of full-length hnRNP R, DNA damage repair was impaired upon knockdown of Yb1 in motoneurons. Finally, we show that following exposure to γ-irradiation, Yb1 is recruited to the chromatin where it interacts with γ-H2AX, a mechanism that is dependent on the full-length hnRNP R.
Taken together, this study describes a novel function of the full-length isoform of hnRNP R in maintaining the genomic integrity of motoneurons and provides new mechanistic insights into its function in DNA damage response.
Pollen beetles (Brassicogethes spp.) are the main pests of oilseed rape (OSR, Brassica napus) in Europe and responsible for massive yield losses. Upcoming pesticide resistances highlight the need for other means of crop protection, such as natural pest control. Sown flower fields aim to counteract the decrease of insect biodiversity in agricultural landscapes by providing resources to ecosystem service providers. However, the optimal age and size of flower fields to increase natural pest control is still unclear.
We conducted experiments on 31 OSR fields located along a gradient of landscape-scale semi-natural habitat (SNH). OSR fields were located adjacent to flower fields which differed in age, continuity and size, or adjacent to crop fields or calcareous grasslands. Pesticide-free areas were established to examine interactive effects of pesticide use and flower field characteristics. The abundance of pollen beetle adults and larvae, parasitism and superparasitism rates in OSR were recorded at increasing distances to the adjacent sites.
Flower fields and calcareous grasslands increased pollen beetle parasitism when compared to OSR fields neighbouring crop fields. The threshold for effective natural pest control of 35% could be reached in the pesticide-free areas of OSR fields adjacent to calcareous grasslands and flower fields maintained continuously for at least 6 years. In pesticide-sprayed areas, pollen beetle parasitism and superparasitism declined with increasing distance to the adjacent field. Furthermore, flower fields larger than 1.5 ha were able to improve pollen beetle parasitism more than smaller fields.
Synthesis and applications. To promote natural pest control in oilseed rape (OSR), large flower fields should be maintained for several years, to create stable habitats for natural enemies. The continuous maintenance of flower fields should be preferred, as ploughing and resowing after 5–6 years decreased the positive effects of the flower fields on natural pest control in adjacent OSR fields. However, pesticide use can abrogate positive effects of flower fields on pollen beetle parasitism. This study highlights that sown flower fields have the potential to increase natural pest control in OSR, but this potential is depending on its age, continuity and size and can be hindered by pesticide use.
The Multiweek Thermal Stability of Medical-Grade Poly(ε-caprolactone) During Melt Electrowriting
(2022)
Melt electrowriting (MEW) is a high-resolution additive manufacturing technology that places unique constraints on the processing of thermally degradable polymers. With a single nozzle, MEW operates at low throughput and in this study, medical-grade poly(ε-caprolactone) (PCL) is heated for 25 d at three different temperatures (75, 85, and 95 °C), collecting daily samples. There is an initial increase in the fiber diameter and decrease in the jet speed over the first 5 d, then the MEW process remains stable for the 75 and 85 °C groups. When the collector speed is fixed to a value at least 10% above the jet speed, the diameter remains constant for 25 d at 75 °C and only increases with time for 85 and 95 °C. Fiber fusion at increased layer height is observed for 85 and 95 °C, while the surface morphology of single fibers remain similar for all temperatures. The properties of the prints are assessed with no observable changes in the degree of crystallinity or the Young's modulus, while the yield strength decreases in later phases only for 95 °C. After the initial 5-d period, the MEW processing of PCL at 75 °C is extraordinarily stable with overall fiber diameters averaging 13.5 ± 1.0 µm over the entire 25-d period.
Purpose
Image acquisition and subsequent manual analysis of cardiac cine MRI is time-consuming. The purpose of this study was to train and evaluate a 3D artificial neural network for semantic segmentation of radially undersampled cardiac MRI to accelerate both scan time and postprocessing.
Methods
A database of Cartesian short-axis MR images of the heart (148,500 images, 484 examinations) was assembled from an openly accessible database and radial undersampling was simulated. A 3D U-Net architecture was pretrained for segmentation of undersampled spatiotemporal cine MRI. Transfer learning was then performed using samples from a second database, comprising 108 non-Cartesian radial cine series of the midventricular myocardium to optimize the performance for authentic data. The performance was evaluated for different levels of undersampling by the Dice similarity coefficient (DSC) with respect to reference labels, as well as by deriving ventricular volumes and myocardial masses.
Results
Without transfer learning, the pretrained model performed moderately on true radial data [maximum number of projections tested, P = 196; DSC = 0.87 (left ventricle), DSC = 0.76 (myocardium), and DSC =0.64 (right ventricle)]. After transfer learning with authentic data, the predictions achieved human level even for high undersampling rates (P = 33, DSC = 0.95, 0.87, and 0.93) without significant difference compared with segmentations derived from fully sampled data.
Conclusion
A 3D U-Net architecture can be used for semantic segmentation of radially undersampled cine acquisitions, achieving a performance comparable with human experts in fully sampled data. This approach can jointly accelerate time-consuming cine image acquisition and cumbersome manual image analysis.
Here, a postpolymerization modification method for an α-terminal functionalized poly-(N-methyl-glycine), also known as polysarcosine, is introduced. 4-(Methylthio)phenyl piperidine-4-carboxylate as an initiator for the ring-opening polymerization of N-methyl-glycine-N-carboxyanhydride followed by oxidation of the thioester group to yield an α-terminal reactive 4-(methylsulfonyl)phenyl piperidine-4-carboxylate polymer is utilized. This represents an activated carboxylic acid terminus, allowing straightforward modification with nucleophiles under mild reaction conditions and provides the possibility to introduce a wide variety of nucleophiles as exemplified using small molecules, fluorescent dyes, and model proteins. The new initiator yielded polymers with well-defined molar mass, low dispersity, and high end-group fidelity, as observed by gel permeation chromatography, nuclear magnetic resonance spectroscopy, and matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy. The introduced method can be of great interest for bioconjugation, but requires optimization, especially for protein conjugation.
3D bioprinting often involves application of highly concentrated polymeric bioinks to enable fabrication of stable cell-hydrogel constructs, although poor cell survival, compromised stem cell differentiation, and an inhomogeneous distribution of newly produced extracellular matrix (ECM) are frequently observed. Therefore, this study presents a bioink platform using a new versatile dual-stage crosslinking approach based on thiolated hyaluronic acid (HA-SH), which not only provides stand-alone 3D printability but also facilitates effective chondrogenic differentiation of mesenchymal stromal cells. A range of HA-SH with different molecular weights is synthesized and crosslinked with acrylated (PEG-diacryl) and allylated (PEG-diallyl) polyethylene glycol in a two-step reaction scheme. The initial Michael addition is used to achieve ink printability, followed by UV-mediated thiol–ene reaction to stabilize the printed bioink for long-term cell culture. Bioinks with high molecular weight HA-SH (>200 kDa) require comparably low polymer content to facilitate bioprinting. This leads to superior quality of cartilaginous constructs which possess a coherent ECM and a strongly increased stiffness of long-term cultured constructs. The dual-stage system may serve as an example to design platforms using two independent crosslinking reactions at one functional group, which allows adjusting printability as well as material and biological properties of bioinks.
Energy-demanding organs like the heart are strongly dependent on oxidative phosphorylation in mitochondria. Oxidative phosphorylation is governed by the respiratory chain located in the inner mitochondrial membrane. The inner mitochondrial membrane is the only cellular membrane with significant amounts of the phospholipid cardiolipin, and cardiolipin was found to directly interact with a number of essential protein complexes, including respiratory chain complexes I to V. An inherited defect in the biogenesis of cardiolipin causes Barth syndrome, which is associated with cardiomyopathy, skeletal myopathy, neutropenia and growth retardation. Energy conversion is dependent on reducing equivalents, which are replenished by oxidative metabolism in the Krebs cycle. Cardiolipin deficiency in Barth syndrome also affects Krebs cycle activity, metabolite transport and mitochondrial morphology. During excitation-contraction coupling, calcium (Ca\(^{2+}\)) released from the sarcoplasmic reticulum drives sarcomeric contraction. At the same time, Ca\(^{2+}\) influx into mitochondria drives the activation of Krebs cycle dehydrogenases and the regeneration of reducing equivalents. Reducing equivalents are essential not only for energy conversion, but also for maintaining a redox buffer, which is required to detoxify reactive oxygen species (ROS). Defects in CL may also affect Ca\(^{2+}\) uptake into mitochondria and thereby hamper energy supply and demand matching, but also detoxification of ROS. Here, we review the impact of cardiolipin deficiency on mitochondrial function in Barth syndrome and discuss potential therapeutic strategies.
The diorgano(bismuth)alcoholate [Bi((C\(_{6}\)H\(_{4}\)CH\(_{2}\))\(_{2}\)S)OPh] (1-OPh) has been synthesized and fully characterized. Stoichiometric reactions, UV/Vis spectroscopy, and (TD-)DFT calculations suggest its susceptibility to homolytic and heterolytic Bi−O bond cleavage under given reaction conditions. Using the dehydrocoupling of silanes with either TEMPO or phenol as model reactions, the catalytic competency of 1-OPh has been investigated (TEMPO=(tetramethyl-piperidin-1-yl)-oxyl). Different reaction pathways can deliberately be addressed by applying photochemical or thermal reaction conditions and by choosing radical or closed-shell substrates (TEMPO vs. phenol). Applied analytical techniques include NMR, UV/Vis, and EPR spectroscopy, mass spectrometry, single-crystal X-ray diffraction analysis, and (TD)-DFT calculations.
Mineralocorticoid-receptor antagonism and its metabolic consequences in haemodialysis patients
(2022)
Patients on haemodialysis are highly susceptible to different forms of heart failure. To date, the benefit of Mineralocorticoid-receptor antagonist (MRA) administration in haemodialysis patients remains subject to discussion. Biomarkers play an important role in therapy guidance and pose a promising tool to detect pathological processes of heart failure in an earlier stage. The randomised-controlled Mineralocorticoid-Receptor Antagonists in End-Stage Renal Disease (MiREnDa) trial was set up to investigate the effect of 50 mg of spironolactone once daily on left ventricular mass index in haemodialysis patients and several secondary endpoints. This dissertation reports findings from the MiREnDa trial on (a) the efficacy of spironolactone to influence serum levels of biomarkers of heart failure, fibrosis and inflammation and electrolytes and (b) the ability of N-terminal pro-B-type natriuretic peptide (NT-proBNP), Galectin-3 and soluble source of tumorigenicity 2 (sST2) to reflect left ventricular hypertrophy and diastolic dysfunction assessed by imaging characteristics. Treatment of spironolactone over a 40-week period did not alter serum levels of biomarkers of heart failure, fibrosis and inflammation including NT-proBNP, Galectin-3 and sST2. A small but significant effect on serum sodium but not potassium was observed. NT-proBNP was significantly different in the presence or absence of left ventricular hypertrophy (LVH) (normal vs. LVH (median [IQR]): 2,120 [810; 5,040] vs. 6,340 [2,410; 15,360] pg/ml, p<0.01) or moderate and severe diastolic dysfunction (DD) (normal diastolic function and DD grade I vs. DD grade II and DD grade III: 2,300 [850; 6,050] vs. 12,260 [3,340; 34,830] pg/ml, p=0.02). NT-proBNP further showed a significant correlation at baseline with LVMi (Spearman’s rho=0.41, p<0.001), LAVi (Spearman’s rho=0.55, p<0.001) and septal E/e’ (Spearman’s rho=0.45, p<0.001). No correlation was observed between Galectin-3 and the investigated functional and morphological parameters. sST2 was mildly correlated to LVMi at baseline (Spearman’s rho=0.21, p=0.05) and NT-proBNP at baseline (Spearman’s rho=0.37, p<0.001). In conclusion, spironolactone did not affect the investigated parameters but NT-proBNP proved to be significantly correlated to cardiac imaging measurements.
In modern medicine hip and knee joint replacement are common surgical procedures. However, about 11 % of hip implants and about 7 % of knee implants need re-operations. The comparison of implant registers revealed two major indications for re-operations: aseptic loosening and implant infections, that both severely impact the patients’ health and are an economic burden for the health care system. To address these problems, a calcium hydroxide coating on titanium was investigated in this thesis. Calcium hydroxide is a well-known antibacterial agent and used with success in dentistry. The coatings were applied with electrochemically assisted deposition, a versatile tool that combines easiness of process with the ability to coat complex geometries homogeneously. The pH-gradient during coating was investigated and showed the surface confinement of the coating process. Surface pre-treatment altered the surface morphology and chemistry of the titanium substrates and was shown to affect the morphology of the calcium hydroxide coatings. The influence of the coating parameters stirring speed and current pulsing were examined in various configurations and combinations and could also affect the surface morphology. A change in surface morphology results in a changed adhesion and behavior of cells and bacteria. Thus, the parameters surface pre-treatment, stirring speed and current pulsing presented a toolset for tailoring cellular response and antibacterial properties. Microbiological tests with S. aureus and S. epidermidis were performed to test the time-dependent antibacterial activity of the calcium hydroxide coatings. A reduction of both strains could be achieved for 13 h, which makes calcium hydroxide a promising antibacterial coating. To give insight into biofilm growth, a protocol for biofilm staining was investigated on titanium disks with S. aureus and S. epidermidis. Biofilm growth could be detected after 5 days of bacterial incubation, which was much earlier than the 3 weeks that are currently assumed in medical treatment. Thus, it should be considered to treat infections as if a biofilm were present from day 5 on. The ephemeral antibacterial properties of calcium hydroxide were further enhanced and prolonged with the addition of silver and copper ions. Both ionic modifications significantly enhanced the bactericidal potential. The copper modification showed higher antibacterial effects than the silver modification and had a higher cytocompatibility which was comparable to the pure calcium hydroxide coating. Thus, copper ions are an auspicious option to enhance the antibacterial properties. Calcium hydroxide coatings presented in this thesis have promising antibacterial properties and can easily be applied to complex geometries, thus they are a step in fighting aseptic loosening and implant infections.
Persistent room temperature phosphorescent (RTP) luminophores have gained remarkable interest recently for a number of applications in security printing, OLEDs, optical storage, time-gated biological imaging and oxygen sensors. We report the first persistent RTP with lifetimes up to 0.5 s from simple triarylboranes which have no lone pairs. We also have prepared 3 isomeric (o, m, p-bromophenyl)-bis(2,6-dimethylphenyl)boranes. Among the 3 isomers (o-, m- and p-BrTAB) synthesized, the ortho-one is the only one which shows dual phosphorescence, with a short lifetime of 0.8 ms and a long lifetime of 234 ms in the crystalline state at room temperature. At last, we checked the RTP properties from the boric acid. We found that the pure boric acid does not show RTP in the solid state.
Visual perception of surfaces is of utmost importance in everyday life. Therefore, it comes naturally, that different surface structures evoke different visual impressions in the viewer even if the material underlying these surface structures is the same. This topic is especially virulent for manufacturing processes in which more than one stakeholder is involved, but where the final product needs to meet certain criteria. A common practice to address such slight but perceivable differences in the visual appearance of structured surfaces is that trained evaluators assess the samples and assign a pass or fail. However, this process is both time consuming and cost intensive. Thus, we conducted two studies to analyze the relationship between physical surface structure parameters and participants visual assessment of the samples. With the first experiment, we aimed at uncovering a relationship between physical roughness parameters and visual lightness perception while the second experiment was designed to test participants' discrimination sensitivity across the range of stimuli. Perceived lightness and the measured surface roughness were nonlinearly related to the surface structure. Additionally, we found a linear relationship between the engraving parameter and physical brightness. Surface structure was an ideal predictor for perceived lightness and participants discriminated equally well across the entire range of surface structures.
Realization and Spectroscopy of the Quantum Spin Hall Insulator Bismuthene on Silicon Carbide
(2022)
Topological matter is one of the most vibrant research fields of contemporary solid state physics since the theoretical prediction of the quantum spin Hall effect in graphene in 2005. Quantum spin Hall insulators possess a vanishing bulk conductivity but symmetry-protected, helical edge states that give rise to dissipationless charge transport.
The experimental verification of this exotic state of matter in 2007 lead to a boost of research activity in this field, inspired by possible ground-breaking future applications.
However, the use of the quantum spin Hall materials available to date is limited to cryogenic temperatures owing to their comparably small bulk band gaps.
In this thesis, we follow a novel approach to realize a quantum spin Hall material with a large energy gap and epitaxially grow bismuthene, i.e., Bi atoms adopting a honeycomb lattice, in a \((\sqrt{3}\times\sqrt{3})\) reconstruction on the semiconductor SiC(0001). In this way, we profit both from the honeycomb symmetry as well as the large spin-orbit coupling of Bi, which, in combination, give rise to a topologically non-trivial band gap on the order of one electronvolt.
An in-depth theoretical analysis demonstrates that the covalent bond between the Si and Bi atoms is not only stabilizing the Bi film but is pivotal to attain the quantum spin Hall phase.
The preparation of high-quality, unreconstructed SiC(0001) substrates sets the basis for the formation of bismuthene and requires an extensive procedure in ultra-pure dry H\(_2\) gas. Scanning tunneling microscopy measurements unveil the (\(1\times1\)) surface periodicity and smooth terrace planes, which are suitable for the growth of single Bi layers by means of molecular beam epitaxy. The chemical configuration of the resulting Bi film and its oxidation upon exposure to ambient atmosphere are inspected with X-ray photoelectron spectroscopy.
Angle-resolved photoelectron spectroscopy reveals the excellent agreement of probed and calculated band structure. In particular, it evidences a characteristic Rashba-splitting of the valence bands at the K point. Scanning tunneling spectroscopy probes signatures of this splitting, as well, and allows to determine the full band gap with a magnitude of \(E_\text{gap}\approx0.8\,\text{eV}\).
Constant-current images and local-density-of-state maps confirm the presence of a planar honeycomb lattice, which forms several domains due to different, yet equivalent, nucleation sites of the (\(\sqrt{3}\times\sqrt{3}\))-Bi reconstruction.
Differential conductivity measurements demonstrate that bismuthene edge states evolve at atomic steps of the SiC substrate. The probed, metallic local density of states is in agreement with the density of states expected from the edge state's energy dispersion found in density functional theory calculations - besides a pronounced dip at the Fermi level.
By means of temperature- and energy-dependent tunneling spectroscopy it is shown that the spectral properties of this suppressed density of states are successfully captured in the framework of the Tomonaga-Luttinger liquid theory and most likely originate from enhanced electronic correlations in the edge channel.
Cardiovascular diseases (CVD), subsuming atherosclerosis of the coronary arteries and subsequent myocardial infarction, are the leading cause of death in the European Union (over 4 million deaths annually), with devastating individual and economic consequences.
Recent studies revealed that T cells play a crucial role in post-MI inflammation, healing and remodelling processes. Nevertheless, the specificity profile of adaptive immune responses in the infarcted myocardium has not yet been differentiated. The experiments portrayed in this thesis sought to assess whether post-MI CD4+ T cell responses in mice are triggered by heart specific antigens, and eventually identify relevant epitopes.
We were able to create a murine antigen atlas including a list of 206 epitopes for I-Ab and 193 epitopes for I-Ad presented on MHC-II in the context of MI. We sought to consecutively test this panel by in vitro T cell proliferation and antigen recall assays ex vivo. The elispot assay was used as a readout for antigen-specific stimulation by measurement of IL-2 and IFN-γ production, currently the most sensitive approach available to detect even small counts of antigen producing cells. Splenocytes as well as lymphocytes from mediastinal lymph nodes were purified from animals 7 days or 56 days after EMI conducted by ligation of the left anterior descending artery.
We were able to provide evidence that post-MI T cell responses in Balb/c mice are triggered by heart-specific antigens and that MYHCA, especially MYHCA614-628, is relevant for that response. Moreover, a significant specific T cell response after MI in C57BL/6J mice was observed for α actin, cardiac muscle 1 [ACTC1], myosin-binding protein C3 [MYBPC3] and myosin heavy chain α [MYHCA] derived heart specific antigens.
Generally, the epitopes of interest for Balb/c as well as C57BL/6J could be further investigated and may eventually be modulated in the future.
This dissertation focuses on the construct and criterion validity of integrity tests and aims to enhance both. To accomplish this goal, three approaches were adopted: First, an overview and systematic comparison of integrity tests was conducted with reference to the construction and application of the tests. Second, the nomological network of integrity tests was expanded with reference to honesty-humility and organizational citizenship behavior at their factor and facet level. Third, two promising methods to reduce faking on integrity tests were tested: the double rating method (Hui, 2001) and the indirect questioning technique. In line with previous research, the results of the overview and comparison of integrity measures confirmed that integrity tests are multidimensional and heterogenous. A clear definition of integrity is urgently needed. The personality trait of honesty-humility and its facets of fairness, and modesty revealed the most significant relationships to integrity. Moreover, organizational citizenship behavior and its facets of altruism, conscientiousness, and sportsmanship were found to significantly relate to integrity. Furthermore, integrity tests were able not only to predict organizational citizenship behavior but also to incrementally predict job performance and organizational citizenship behavior beyond the factor and facet level of the personality traits of conscientiousness and honesty-humility. In contrast to the indirect questioning technique, the double rating method, which includes an other rating and a self rating, was shown to be able to significantly reduce faking on integrity tests in an anonymous survey setting. This dissertation makes an important contribution to better explain the construct and nomological network of integrity, provide a more detailed view on integrity tests and their protection against faking, and expand the predictive and incremental validity of these tests. The implications for future research and practice are further discussed.
In the last decade continuous-time quantum Monte Carlo in the hybridization expansion (CTHYB) was one of the most successful Monte Carlo techniques to describe correlated quantum phenomena in conjunction with dynamical mean field theory (DMFT). The first part of the thesis consists of algorithmical developments regarding CTHYB and DMFT. I provide a complete derivation and an extensive discussion of the expansion formula. We generalized it to treat spin-orbit coupling, and invented the superstate sampling algorithm to make it efficient enough for describing systems with general interactions, crystal fields and spin-orbit coupling at low temperatures. But CTHYB is known to fail in the standard implementation for equal-time correlators, certain higher-order Green’s functions and the atomic limit; we discovered that its estimator for the Greens function is also inconsistent for Anderson impurities with finite, discrete baths. I focus then on further improvements of CTHYB that we have conceived and worked on, in particular for f-orbitals and for taking physical symmetries into account in the calculation of the Monte Carlo observables. The second part of the thesis presents selected physical applications of these methods. I show DMFT calculations of highest accuracy for elemental iron and nickel and discover a new mechanism of magnetic ordering in nickel: the ordering of band structure-induced local moments. Then we analyze the stability of this phenomenon under pressure and temperatures, that characterize in the Earth’s core. We find, that the mechanism survives these conditions and may give a significant contribution to the generation of the Earth’s magnetic field. The next topic is the stability of double Dirac fermions against electronic correlations. We find, that the Coulomb interaction in the corresponding material Bi2 CuO4 are strong enough to destroy the double Dirac cone, and substantial uniform pressure is necessary to restore them. In the last chapter I derive the properties of Higgs and Goldstone bosons from Ginzburg-Landau theory, and identify these excitations in a model of an excitonic magnet.
In terms of the need of environmentally benign renewable and storable energy sources, splitting of water into hydrogen and oxygen by using sunlight is a promising approach. Hereby, water oxidation catalysts (WOCs) are required to perform the water oxidation comprising the transfer of four electrons to provide the reducing equivalents for producing hydrogen. The class of Ru(bda) (bda = 2,2'-bipyridine-6,6'-dicarboxylate) catalysts has proven to be efficient for this reaction.
In this thesis, ligand exchange processes in Ru(bda) complexes have been analyzed and the formation of multinuclear macrocyclic WOCs was studied. Based on the knowledge acquired by these studies, new multinuclear cyclic Ru(bda) complexes have been synthesized and their catalytic efficiencies in homogeneous water oxidation have been investigated. Going one step further for setting up functional devices, molecular WOCs have been immobilized on conducting or semiconducting supporting materials. Direct anchoring on carbon nanotubes generated a promising materials for further applications.
In the heart the β\(_1\)-adrenergic receptor (AR) and the β\(_2\)-AR, two prototypical G protein-coupled receptors (GPCRs), are both activated by the same hormones, namely adrenaline and noradrenaline. Both receptors couple to stimulatory G\(_s\) proteins, mediate an increase in cyclic adenosine monophosphate (cAMP) and influence the contractility and frequency of the heart upon stimulation. However, activation of the β\(_1\)-AR, not the β\(_2\)-AR, lead to other additional effects, such as changes in gene transcription resulting in cardiac hypertrophy, leading to speculations on how distinct effects can arise from receptors coupled to the same downstream signaling pathway.
In this thesis the question of whether this distinct behavior may originate from a differential localization of these two receptors in adult cardiomyocytes is addressed. Therefore, fluorescence spectroscopy tools are developed and implemented in order to elucidate the presence and dynamics of these endogenous receptors at the outer plasma membrane as well as on the T-tubular network of intact adult cardiomyocytes. This allows the visualization of confined localization and diffusion of the β\(_2\)-AR to the T-tubular network at endogenous expression. In contrast, the β\(_1\)-AR is found diffusing at both the outer plasma membrane and the T-tubules. Upon overexpression of the β\(_2\)-AR in adult transgenic cardiomyocytes, the receptors experience a loss of this compartmentalization and are also found at the cell surface. These data suggest that distinct signaling and functional effects can be controlled by specific cell surface targeting of the receptor subtypes.
The tools at the basis of this thesis work are a fluorescent adrenergic antagonist in combination of fluorescence fluctuation spectroscopy to monitor the localization and dynamics of the lowly expressed adrenergic receptors. Along the way to optimizing these approaches, I worked on combining widefield and confocal imaging in one setup, as well as implementing a stable autofocus mechanism using electrically tunable lenses.
Purpose
Definitive fascial closure is an essential treatment objective after open abdomen treatment and mitigates morbidity and mortality. There is a paucity of evidence on factors that promote or prevent definitive fascial closure.
Methods
A multi-center multivariable analysis of data from the Open Abdomen Route of the European Hernia Society included all cases between 1 May 2015 and 31 December 2019. Different treatment elements, i.e. the use of a visceral protective layer, negative-pressure wound therapy and dynamic closure techniques, as well as patient characteristics were included in the multivariable analysis. The study was registered in the International Clinical Trials Registry Platform via the German Registry for Clinical Trials (DRK00021719).
Results
Data were included from 630 patients from eleven surgical departments in six European countries. Indications for OAT were peritonitis (46%), abdominal compartment syndrome (20.5%), burst abdomen (11.3%), abdominal trauma (9%), and other conditions (13.2%). The overall definitive fascial closure rate was 57.5% in the intention-to-treat analysis and 71% in the per-protocol analysis. The multivariable analysis showed a positive correlation of negative-pressure wound therapy (odds ratio: 2.496, p < 0.001) and dynamic closure techniques (odds ratio: 2.687, p < 0.001) with fascial closure and a negative correlation of intra-abdominal contamination (odds ratio: 0.630, p = 0.029) and the number of surgical procedures before OAT (odds ratio: 0.740, p = 0.005) with DFC.
Conclusion
The clinical course and prognosis of open abdomen treatment can significantly be improved by the use of treatment elements such as negative-pressure wound therapy and dynamic closure techniques, which are associated with definitive fascial closure.
Religion and social support along with trait emotional intelligence (EI) help individuals to reduce stress caused by difficult situations. Their implications may vary across cultures in reference to predicting health-related quality of life (HRQoL). A convenience sample of N = 200 chronic heart failure (CHF) patients was recruited at cardiology centers in Germany (n = 100) and Pakistan (n = 100). Results indicated that trait-EI predicted better mental component of HRQoL in Pakistani and German CHF patients. Friends as social support appeared relevant for German patients only. Qualitative data indicate an internal locus of control in German as compared to Pakistani patients. Strengthening the beneficial role of social support in Pakistani patients is one example of how the current findings may inspire culture-specific treatment to empower patients dealing with the detrimental effects of CHF.
Nucleic acids are not only one of the most important classes of macromolecules in biochemistry but also a promising platform for the defined arrangement of chromophores. Thanks to their precise organization by directional polar and hydrophobic interactions, oligonucleotides can be exploited as suitable templates for multichromophore assemblies with predictable properties. To expand the toolbox of emissive, base pairing nucleobase analogs several barbituric acid merocyanine (BAM) chromophores with tunable spectroscopic properties were synthesized and incorporated into RNA, DNA and glycol nucleic acid (GNA) oligonucleotides. A multitude of duplexes containing up to ten BAM chromophores was obtained and analysis by spectroscopic methods revealed the presence of dipolarly coupled merocyanine aggregates with properties
strongly dependent on the chromophore orientation toward each other and the backbone conformation. These characteristics were exploited for various applications such as FRET pair formation and polymerase chain reaction (PCR) experiments. The observed formation of higher-order aggregates implies future applications of these new oligonucleotide-chromophore systems as light-harvesting DNA nanomaterials. Besides oligonucleotide templated covalent assembly of chromophores also non-covalent nucleic acid-chromophore complexes are a broad field of research. Among these, fluorogenic RNA aptamers are of special interest with the most versatile ones based on derivatives of the GFP chromophore hydroxybenzylidene imidazolone (HBI). Therefore, new HBI-derived chromophores with an expanded conjugated system and an additional exocyclic amino group for an enhanced binding affinity were synthesized and analyzed in complex with the Chili aptamer. Among these, structurally new fluorogenes with strong fluorescence activation upon binding to Chili were identified which are promising for further derivatization and application as color-switching sensor devices for example.
A practical and direct method was developed for the production of versatile alkyl boronate esters via transition metal-free borylation of primary and secondary alkyl sulfones. The key to the success of the strategy is the use of bis(neopentyl glycolato) diboron (B\(_{2}\)neop\(_{2}\)), with a stoichiometric amount of base as a promoter. The practicality and industrial potential of this protocol are highlighted by its wide functional group tolerance, the late-stage modification of complex compounds, no need for further transesterification, and operational simplicity. Radical clock, radical trap experiments, and EPR studies were conducted which show that the borylation process involves radical intermediates.
The thesis at hand is concerned with improving our understanding of and our control over transport properties of the three-dimensional topological insulator HgTe. Topological insulators are characterized by an insulating bulk and symmetry-protected metallic surface states. These topological surface states hold great promise for research and technology; at the same time, many properties of experimentally accessible topological insulator materials still need to be explored thoroughly. The overall aim of this thesis was to experimentally investigate micrometer-sized HgTe transport devices to observe the ballistic transport regime as well as intercarrier scattering and possibly identify special properties of the topological surface states.
Part I of the thesis presents lithographic developments concerned with etching small HgTe devices. The aim was to replace existing processes which relied on dry etching with high-energy \(\text{Ar}^+\) ions and an organic etch mask. This etching method is known to degrade the HgTe crystal quality. In addition, the etch mask turned out to be not durable for long etching processes and difficult to remove completely after etching. First, \(\text{BaF}_2\) was introduced as a new etch mask for dry etching to replace the organic etch mask. With common surface characterization techniques like SEM and XPS it was shown that \(\text{BaF}_2\) etch masks are easy to deposit, highly durable in common dry etching processes for \(\text{Hg}_{1-x}\text{Cd}_x\text{Te}\), and easy to remove in deionized water. Transport results of HgTe devices fabricated with the new etch mask are comparable to results obtained with the old process. At the same time, the new etch mask can withstand longer etching times and does not cause problems due to incomplete removal. Second, a new inductively coupled plasma dry etching process based on \(\text{CH}_4\) and Ar was introduced. This etching process is compatible with \(\text{BaF}_2\) etch masks and yields highly reproducible results. Transport results indicate that the new etching process does not degrade the crystal quality and is suitable to produce high-quality transport devices even in the micrometer range. A comparison with wet-etched samples shows that inductively coupled plasma etching introduces a pronounced edge roughness. This - usually undesirable - property is actually beneficial for some of the experiments in this study and mostly irrelevant for others. Therefore, most samples appearing in this thesis were fabricated with the new process.
Part II of the thesis details the advancements made in identifying topological and trivial states which contribute to transport in HgTe three-dimensional topological insulators. To this end, macroscopic Hall bar samples were fabricated from high-quality tensilely strained HgTe layers by means of the improved lithographic processes. All samples were equipped with a top gate electrode, and some also with a modulation doping layer or a back gate electrode to modify the carrier density of the surface states on both sides of the HgTe layer. Due to the high sample quality, Landau levels could be well-resolved in standard transport measurements down to magnetic fields of less than 0.5T. High-resolution measurements of the Landau level dispersion with gate voltage and magnetic field allowed disentangling different transport channels. The main result here is that the upper (electron) branches of the two topological surface states contribute to transport in all experimentally relevant density regimes, while the hole branch is not accessible. Far in n-regime bulk conduction band states give a minor contribution to transport. More importantly, trivial bulk valence band holes come into play close to the charge neutrality point. Further in p-regime, the strong applied gate voltage leads to the formation of two-dimensional, massive hole states at the HgTe surface. The interplay of different states gives rise to rich physics: Top gate-back gate maps revealed that an anticrossing of Landau levels from the two topological surface states occurs at equal filling. A possible explanation for this effect is a weak hybridization of the surface states; however, future studies need to further clarify this point. Furthermore, the superposition of n-type topological and p-type trivial surface states leads to an intriguing Landau level dispersion. The good quantization of the Hall conductance in this situation indicates that the counterpropagating edge states interact with each other. The nature of this interaction will be the topic of further research.
Part III of the thesis is focused on HgTe microstructures. These "channel samples" have a typical width of 0.5 to 4µm and a typical length of 5 to 80µm. The quality of these devices benefits particularly from the improved lithographic processes. As a result, the impurity mean free path of the topological surface state electrons is on the order of the device width and transport becomes semiballistic. This was verified by measuring the channel resistance in small magnetic fields in n-regime. The deflection of carriers towards the dissipative channel walls results in a pronounced peak in the magnetoresistance, which scales in a predictable manner with the channel width. To investigate transport effects due to mutual scattering of charge carriers, the differential resistance of channel samples was measured as a function of carrier temperature. Selective heating of the charge carriers - but not the lattice - was achieved by passing a heating current through the channel. Increasing the carrier temperature has two pronounced effects when the Fermi level is situated in proximity to the bulk valence band maximum where the density of states is large. First, when both topological surface state electrons and bulk holes are present, electron-hole scattering leads to a pronounced increase in resistance with increasing carrier temperature. Second, a thermally induced increase of the electron and hole carrier densities reduces the resistance again at higher temperatures. A model considering these two effects was developed, which can well reproduce the experimental results. Current heating experiments in zero-gap HgTe quantum wells and compressively strained HgTe layers are consistent with this model. These observations raise the question as to how electron-hole scattering may affect other transport properties of HgTe-based three-dimensional topological insulators, which is briefly discussed in the outlook.
Microorganisms that colonize the human body face large fluctuations in their surroundings. Therefore, those microbes developed sophisticated mechanisms that allow them to adapt their cell biology and maintain cellular homeostasis. One organelle vital to preserve cell physiology is the vacuole. The vacuole exhibits a wide range of functions and is able to adjust itself in response to both external and internal stimuli. Moreover, it plays an important role in host interaction and virulence in fungi such as Candida albicans. Despite this connection, only a few regulatory proteins have been described to modulate vacuolar biology in fungal pathogens. Furthermore, whether such regulation alters fungus-host interplay remains largely unknown.
This thesis focuses on the characterization of ZCF8, a fungus-specific transcription regulator in the human-associated yeast C. albicans. To this end, I combined genome-wide protein-DNA interaction assays and gene expression analysis that identified genes regulated by Zcf8p. Fluorescence microscopy uncovered that several top targets of Zcf8p localize to the fungal vacuole. Moreover, deletion and overexpression of ZCF8 resulted in alterations in vacuolar morphology and in luminal pH and rendered the fungus resistant or susceptible to a vacuole-disturbing drug. Finally, in vitro adherence assays showed that Zcf8p modulates the attachment of C. albicans to human epithelial cells in a vacuole-dependent manner.
Given those findings, I posit that the previously uncharacterized transcription regulator Zcf8p modulates fungal attachment to epithelial cells in a manner that depends on the status of the fungal vacuole. Furthermore, the results highlight that vacuolar physiology is a substantial factor influencing the physical interaction between Candida cells and mammalian mucosal surfaces.
Photosynthetic plants have a remarkable ability to modify their metabolism and development according to ever changing environmental conditions. The root system displays continuous growth of the primary root and formation of lateral roots enabling efficient water and nutrient uptake and anchorage of the plant in soil. With regard to lateral roots, development is post-embryonic, originating from the pericycle of the primary root. Coordinated activity of several molecular signalling pathways controlled by the hormone auxin is important throughout all stages of lateral root development.At first, two adjacent Xylem Pole Pericycle (XPP) cells are activated and the nuclei of these cells migrate towards a common cell wall.This is followed by XPP cells acquiring volume thus swelling up.The XPP cells then undergo anticlinal cell division, followed by a series of periclinal and anticlinal divisions,leading to lateral root primordia.These break through the radial cell layers and emerge out the primary root.
Although root system plasticity is well-described in response to environmental cues such as ion nutrition in the soil, little is known on how root development is shaped according to the endogenous energy status of the plant.In this study, we were able to connect limited perturbations in photosynthetic energy supply to lateral root development.We established two experimental systems – treatment with low light and unexpected darkness which led to short-term energy imbalance in the plant.These short perturbations administered, showed an increase in the emerged lateral root density and decrease in root hexose availability and activation of the low energy marker gene ASN1 (ASPARAGINE SYNTHETASE 1).Although not demonstrated, presumably, these disturbances in the plant energy homeo-stasis activates SnRK1 (SNF1 RELATED KINASE 1),an evolutionary conserved kinase mediat-ing metabolic and transcriptional responses towards low energy conditions. In A. thaliana, two catalytic α-subunits of this kinase (SnRK1.α1 and SnRK1.α2) are functionally active and form ternary complexes with the regulatory β- and γ- subunits. Whereas unexpected darkness results in an increase in emerged lateral root density, the snrk1.α1 loss-of-function mutant displayed decrease in emerged lateral root density. As this effect is not that pronounced in the snrk1.α2 loss-of-function mutant, the α1 catalytic subunit is important for the observed lateral root phenotype under short-term energy perturbations. Moreover, root expression patterns of SnRK1.α1:GFP supports a role of this catalytic subunit in lateral root development. Furthermore, the lateral root response during short-term perturbations requires the SnRK1 downstream transcriptional regulator bZIP63 (BASIC LEU-CINE ZIPPER 63), as demonstrated here by a loss-of-function approach. Phenotypic studies showed that in comparison to wild-type, bzip63 mutants displayed decreased lateral root density upon low-light and unexpected darkness conditions. Previous work has demonstrat-ed that SnRK1 directly phosphorylates bZIP63 at three serine residues. Alanine-exchange mutants of the SnRK1 dependent bZIP63 phosphorylation sites behave similarly to bzip63 loss-of-function mutants and do not display increased lateral root density upon short-term unexpected darkness. This data strongly supports an impact of SnRK1-bZIP63 signalling in mediating the observed lateral root density phenotype. Plants expressing a bZIP63:YFP fu-sion protein showed specific localization patterns in primary root and in all developmental stages of the lateral root. bzip63 loss-of-function mutant lines displayed reduced early stage lateral root initiation events under unexpected darkness as demonstrated by Differen-tial Interference Contrast microscopy (DIC) and the use of a GATA23 reporter line. This data supports a role of bZIP63 in early lateral root initiation.
Next, by employing Chromatin Immunoprecitation (ChIP) sequencing, we were able to iden-tify global binding targets of bZIP63, including the auxin-regulated transcription factor (TF) ARF19 (AUXIN RESPONSE FACTOR 19), a well-described central regulator of lateral root development. Additional ChIP experiments confirmed direct binding of bZIP63 to an ARF19 promoter region harboring a G-Box cis-element, a well-established bZIP63 binding site. We also observed that short-term energy perturbation upon unexpected darkness induced tran-scription of ARF19, which was impaired in the bzip63 loss-of-function mutant. These results propose that bZIP63 mediates lateral root development under short-term energy perturba-tion via ARF19.
In conclusion, this study provides a novel mechanistic link between energy homeostasis and plant development. By employing reverse genetics, confocal imaging and high-throughput sequencing strategies, we were able to propose a SnRK1-bZIP63-ARF19 signalling module in integrating energy signalling into lateral root developmental programs.
Overview of the Organolead Trihalide Perovskite Crystal Area
Studies of perovskite single crystals with high crystallographic quality is an important technological area of the perovskite research, which enables to estimate their full optoelectronic potential, and thus to boost their future applications [26]. It was therefore essential to grow high-quality single crystals with lowest structural as well as chemical defect densities and with a stoichiometry relevant for their thin-film counterparts [26]. Optoelectronic devices, e.g. solar cells, are highly complex systems in which the properties of the active layer (absorber) are strongly influenced by the adjacent layers, so it is not always easy to define the targeted properties and elaborate the design rules for the active layer. Currently, organolead trihalide perovskite (OLTP) single crystals with the structure ABX3 are one of the most studied crystalline systems. These hybrid crystals are solids composed of an organic cation such as methylammonium (A = MA+) or formamidinium (A = FA+) to form a three-dimensional periodic lattice together with the lead cation (B = Pb2+) and a halogen anion such as chloride, bromide or iodide (X = Cl-, Br- or I-) [23]. Among them are methylammonium lead tribromide (MAPbBr3), methylammonium lead triiodide (MAPbI3), as well as methylammonium lead trichloride (MAPbCl3) [62, 63]. Important representatives with the larger cation FA+ are formamidinium lead tribromide (FAPbBr3) and formamidinium lead triiodide (FAPbI3) [23, 64]. Besides the exchange of cations as well as anions, it was possible to grow crystals containing two halogens to obtain mixed crystals with different proportions of chlorine to bromine and bromine to iodine, as it is shown in Figure 70. By varying the mixing ratio of the halogens, it was therefore possible to vary the colour and thus the absorption properties of the crystals [85], as it can be done with thin polycrystalline perovskite films. In addition, since a few years it is also doable to grow complex crystals that contain several cations as well as anions [26, 80, 81]. These include the perovskites double cation – double halide formamidinium lead triiodide – methylammonium lead tribromide (FAPbI3)0.9(MAPbBr3)0.1 (FAMA) [26, 80] and formamidinium lead triiodide – methylammonium lead tribromide – caesium lead tribromide (FAPbI3)0.9(MAPbBr3)0.05(CsPbBr3)0.05 (CsFAMA) [81], which have made a significant contribution to increase the power conversion efficiency (PCE) in thin-film photovoltaics [47, 79, 182]. The growth of crystals to this day is performed exclusively from solution [23, 26, 56, 62]. Important preparation methods are the cooling acid-based precursor solution crystallisation [22], the inverse temperature crystallisation (ITC) [62], and the antisolvent vapour-assistant crystallisation (AVC) [137]. In the cooling crystallisation, the precursor salts AX and PbX2 are dissolved in an aqueous halogen-containing acid at high temperatures [56]. Controlled and slow cooling finally results in a supersaturated precursor solution, which leads to spontaneous nucleation of crystal nuclei, followed by subsequent crystal growth. The ITC method is based on the inverse or retrograde solubility of a dissociated perovskite in an organic solvent [23, 64]. With increasing temperature, the solubility of the perovskite decreases and mm-sized crystals can be grown within a few hours [23]. In the AVC method, the precursors are also dissolved in an organic solvent as well [137]. By slow evaporation of a so-called antisolvent [137], the solubility of the perovskite in the now present solvent mixture decreases and it finally precipitates. In addition, there are many other methods with the goal of growing high quality and large crystals in a short period of
time [60, 61, 233, 310].
Innovative possibilities for data collection, networking, and evaluation are unleashing previously untapped potential for industrial production. However, harnessing this potential also requires a change in the way we work. In addition to expanded automation, human-machine cooperation is becoming more important: The machine achieves a reduction in complexity for humans through artificial intelligence. In fractions of a second large amounts of data of high decision quality are analyzed and suggestions are offered. The human being, for this part, usually makes the ultimate decision. He validates the machine’s suggestions and, if necessary, (physically) executes them.
Both entities are highly dependent on each other to accomplish the task in the best possible way. Therefore, it seems particularly important to understand to what extent such cooperation can be effective. Current developments in the field of artificial intelligence show that research in this area is particularly focused on neural network approaches. These are considered to be highly powerful but have the disadvantage of lacking transparency. Their inherent computational processes and the respective result reasoning remain opaque to humans. Some researchers assume that human users might therefore reject the system’s suggestions. The research domain of explainable artificial intelligence (XAI) addresses this problem and tries to develop methods to realize systems that are highly efficient and explainable.
This work is intended to provide further insights relevant to the defined goal of XAI. For this purpose, artifacts are developed that represent research achievements regarding the systematization, perception, and adoption of artificially intelligent decision support systems from a user perspective. The focus is on socio-technical insights with the aim to better understand which factors are important for effective human-machine cooperation. The elaborations predominantly represent extended grounded research. Thus, the artifacts imply an extension of knowledge in order to develop and/ or test effective XAI methods and techniques based on this knowledge. Industry 4.0, with a focus on maintenance, is used as the context for this development.
Impacts of climate variability and change on Maize (\(Zea\) \(mays\)) production in tropical Africa
(2022)
Climate change is undeniable and constitutes one of the major threats of the 21st century. It impacts sectors of our society, usually negatively, and is likely to worsen towards the middle and end of the century. The agricultural sector is of particular concern, for it is the primary source of food and is strongly dependent on the weather. Considerable attention has been given to the impact of climate change on African agriculture because of the continent’s high vulnerability, which is mainly due to its low adaptation capac- ity. Several studies have been implemented to evaluate the impact of climate change on this continent. The results are sometimes controversial since the studies are based on different approaches, climate models and crop yield datasets. This study attempts to contribute substantially to this large topic by suggesting specific types of climate pre- dictors. The study focuses on tropical Africa and its maize yield. Maize is considered to be the most important crop in this region. To estimate the effect of climate change on maize yield, the study began by developing a robust cross-validated multiple linear regression model, which related climate predictors and maize yield. This statistical trans- fer function is reputed to be less prone to overfitting and multicollinearity problems. It is capable of selecting robust predictors, which have a physical meaning. Therefore, the study combined: large-scale predictors, which were derived from the principal component analysis of the monthly precipitation and temperature; traditional local-scale predictors, mainly, the mean precipitation, mean temperature, maximum temperature and minimum temperature; and the Water Requirement Satisfaction Index (WRSI), derived from the specific crop (maize) water balance model. The projected maize-yield change is forced by a regional climate model (RCM) REMO under two emission scenarios: high emission scenario (RCP8.5) and mid-range emission scenario (RCP4.5). The different effects of these groups of predictors in projecting the future maize-yield changes were also assessed. Furthermore, the study analysed the impact of climate change on the global WRSI. The results indicate that almost 27 % of the interannual variability of maize production of the entire region is explained by climate variables. The influence of climate predictors on maize-yield production is more pronounced in West Africa, reaching 55 % in some areas. The model projection indicates that the maize yield in the entire region is expected to decrease by the middle of the century under an RCP8.5 emission scenario, and from the middle of the century to the end of the century, the production will slightly recover but will remain negative (around -10 %). However, in some regions of East Africa, a slight increase in maize yield is expected. The maize-yield projection under RCP4.5 remains relatively unchanged compared to the baseline period (1982-2016). The results further indicate that large-scale predictors are the most critical drivers of the global year-to-year maize-yield variability, and ENSO – which is highly correlated with the most important predictor (PC2) – seems to be the physical process underlying this variability. The effects of local predictors are more pronounced in the eastern parts of the region. The impact of the future climate change on WRSI reveals that the availability of maize water is expected to decrease everywhere, except in some parts of eastern Africa.
The fascination of microcavity exciton-polaritons (polaritons) rests upon the combination of advanced technological control over both the III-V semiconductor material platform as well as the precise spectroscopic access to polaritonic states, which provide access to the investigation of open questions and complex phenomena due to the inherent nonlinearity and direct spectroscopic observables such as energy-resolved real and Fourier space information, pseudospin and coherence. The focus of this work was to advance the research area of polariton lattice simulators with a particular emphasis on their lasing properties. Following the brief introduction into the fundamental physics of polariton lattices in chapter 2, important aspects of the sample fabrication as well as the Fourier spectroscopy techniques used to investigate various features of these lattices were summarized in chapter 3. Here, the implementation of a spatial light modulator for advanced excitation schemes was presented.
At the foundation of this work is the capability to confine polaritons into micropillars or microtraps resulting in discrete energy levels. By arranging these pillars or traps into various lattice geometries and ensuring coupling between neighbouring sites, polaritonic band structures were engineered. In chapter 4, the formation of a band structure was visualised in detail by investigating ribbons of honeycomb lattices. Here, the transition of the discrete energy levels of a single chain of microtraps to the fully developed band structure of a honeycomb lattice was observed. This study allows to design the size of individual domains in more complicated lattice geometries such that a description using band structures becomes feasible, as it revealed that a width of just six unit cells is sufficient to reproduce all characteristic features of the S band of a honeycomb lattice. In particular in the context of potential technological applications in the realms of lasing, the laser-like, coherent emission from polariton microcavities that can be achieved through the excitation of polariton condensates is intriguing. The condensation process is significantly altered in a lattice potential environment when compared to a planar microcavity. Therefore, an investigation of the polariton condensation process in a lattice with respect to the characteristics of the excitation laser, the exciton-photon detuning as well as the reduced trap distance that represents a key design parameter for polaritonic lattices was performed. Based on the demonstration of polariton condensation into multiple bands, the preferred condensation into a desired band was achieved by selecting the appropriate detuning. Additionally, a decreased condensation threshold in confined systems compared to a planar microcavity was revealed.
In chapter 5, the influence of the peculiar feature of flatbands arising in certain lattice geometries, such as the Lieb and Kagome lattices, on polaritons and polariton condensates was investigated. Deviations from a lattice simulator described by a tight binding model that is solely based on nearest neighbour coupling cause a remaining dispersiveness of the flatbands along certain directions of the Brillouin zone. Therefore, the influence of the reduced trap distance on the dispersiveness of the flatbands was investigated and precise technological control over the flatbands was demonstrated. As next-nearest neighbour coupling is reduced drastically by increasing the distance between the corresponding traps, increasing the reduced trap distance enables to tune the S flatbands of both Lieb and Kagome lattices from dispersive bands to flatbands with a bandwidth on the order of the polariton linewidth. Additionally to technological control over the band structures, the controlled excitation of large condensates, single compact localized state (CLS) condensates as well as the resonant excitation of polaritons in a Lieb flatband were demonstrated. Furthermore, selective condensation into flatbands was realised. This combination of technological and spectroscopic control illustrates the capabilities of polariton lattice simulators and was used to study the coherence of flatband polariton condensates. Here, the ability to tune the dispersiveness from a dispersive band to an almost perfect flatband in combination with the selectivity of the excitation is particularly valuable. By exciting large flatband condensates, the increasing degree of localisation to a CLS with decreasing dispersiveness was demonstrated by measurements of first order spatial coherence. Furthermore, the first order temporal coherence of CLS condensates was increased from τ = 68 ps for a dispersive flatband, a value typically achieved in high-quality microcavity samples, to a remarkable τ = 459 ps in a flatband with a dispersiveness below the polarion linewidth. Corresponding to this drastic increase of the first order coherence time, a decrease of the second order temporal coherence function from g(2)(τ =0) = 1.062 to g(2)(0) = 1.035 was observed. Next to laser-like, coherent emission, polariton condensates can form vortex lattices. In this work, two distinct vortex lattices that can form in polariton condensates in Kagome flatbands were revealed. Furthermore, chiral, superfluid edge transport was realised by breaking the spatial symmetry through a localised excitation spot. This chirality was related to a change in the vortex orientation at the edge of the lattice and thus opens the path towards further investigations of symmetry breaking and chiral superfluid transport in Kagome lattices.
Arguably the most influential concept in solid-state physics of the recent decades is the idea of topological order that has also provided a new degree of freedom to control the propagation of light. Therefore, in chapter 6, the interplay of topologically non-trivial band structures with polaritons, polariton condensates and lasing was emphasised. Firstly, a two-dimensional exciton-polariton topological insulator based on a honeycomb lattice was realised. Here, a topologically non-trivial band gap was opened at the Dirac points through a combination of TE-TM splitting of the photonic mode and Zeeman splitting of the excitonic mode. While the band gap is too small compared to the linewidth to be observed in the linear regime, the excitation of polariton condensates allowed to observe the characteristic, topologically protected, chiral edge modes that are robust against scattering at defects as well as lattice corners. This result represents a valuable step towards the investigation of non-linear and non-Hermitian topological physics, based on the inherent gain and loss of microcavities as well as the ability of polaritons to interact with each other. Apart from fundamental interest, the field of topological photonics is driven by the search of potential technological applications, where one direction is to advance the development of lasers. In this work, the starting point towards studying topological lasing was the Su-Schrieffer-Heeger (SSH) model, since it combines a simple and well-understood geometry with a large topological gap. The coherence properties of the topological edge defect of an SSH chain was studied in detail, revealing a promising degree of second order temporal coherence of g(2)(0) = 1.07 for a microlaser with a diameter of only d = 3.5 µm. In the context of topological lasing, the idea of using a propagating, topologically protected mode to ensure coherent coupling of laser arrays is particularly promising. Here, a topologically non-trivial interface mode between the two distinct domains of the crystalline topological insulator (CTI) was realised. After establishing selective lasing from this mode, the coherence properties were studied and coherence of a full, hexagonal interface comprised of 30 vertical-cavity surface-emitting lasers (VCSELs) was demonstrated. This result thus represents the first demonstration of a topological insulator VCSEL array, combining the compact size and convenient light collection of vertically emitting lasers with an in-plane topological protection.
Finally, in chapter 7, an approach towards engineering the band structures of Lieb and honeycomb lattices by unbalancing the eigenenergies of the sites within each unit cell was presented. For Lieb lattices, this technique opens up a path towards controlling the coupling of a flatband to dispersive bands and could enable a detailed study of the influence of this coupling on the polariton flatband states. In an unbalanced honeycomb lattice, a quantum valley Hall boundary mode between two distinct, unbalanced honeycomb domains with permuted sites in the unit cells was demonstrated. This boundary mode could serve as the foundation for the realisation of a polariton quantum valley Hall effect with a truly topologically protected spin based on vortex charges. Modifying polariton lattices by unbalancing the eigenenergies of the sites that comprise a unit cell was thus identified as an additional, promising path for the future development of polariton lattice simulators.
Thermoplastic polymers have a history of decades of safe and effective use in the clinic as implantable medical devices. In recent years additive manufacturing (AM) saw increased clinical interest for the fabrication of customizable and implantable medical devices and training models using the patients’ own radiological data. However, approval from the various regulatory bodies remains a significant hurdle. A possible solution is to fabricate the AM scaffolds using materials and techniques with a clinical safety record, e.g. melt processing of polymers. Melt Electrowriting (MEW) is a novel, high resolution AM technique which uses thermoplastic polymers. MEW produces scaffolds with microscale fibers and precise fiber placement, allowing the control of the scaffold microarchitecture. Additionally, MEW can process medical-grade thermoplastic polymers, without the use of solvents paving the way for the production of medical devices for clinical applications. This pathway is investigated in this thesis, where the layout is designed to resemble the journey of a medical device produced via MEW from conception to early in vivo experiments. To do so, first, a brief history of the development of medical implants and the regenerative capability of the human body is given in Chapter 1. In Chapter 2, a review of the use of thermoplastic polymers in medicine, with a focus on poly(ε-caprolactone) (PCL), is illustrated, as this is the polymer used in the rest of the thesis. This review is followed by a comparison of the state of the art, regarding in vivo and clinical experiments, of three polymer melt AM technologies: melt-extrusion, selective laser sintering and MEW. The first two techniques already saw successful translation to the bedside, producing patient-specific, regulatory-approved AM implants. To follow in the footsteps of these two technologies, the MEW device parameters need to be optimized. The MEW process parameters and their interplay are further discussed in Chapter 3 focusing on the importance of a steady mass flow rate of the polymer during printing. MEW reaches a balance between polymer flow, the stabilizing electric field and moving collector to produce reproducible, high-resolution scaffolds. An imbalance creates phenomena like fiber pulsing or arcing which result in defective scaffolds and potential printer damage. Chapter 4 shows the use of X-ray microtomography (µCT) as a non-destructive method to characterize the pore-related features: total porosity and the pore size distribution. MEW scaffolds are three-dimensional (3D) constructs but have long been treated in the literature as two-dimensional (2D) ones and characterized mainly by microscopy, including stereo- and scanning electron microscopy, where pore size was simply reported as the distance between the fibers in a single layer. These methods, together with the trend of producing scaffolds with symmetrical pores in the 0/90° and 0/60/120° laydown patterns, disregarded the lateral connections between pores and the potential of MEW to be used for more complex 3D structures, mimicking the extracellular matrix. Here we characterized scaffolds in the aforementioned symmetrical laydown patterns, along with the more complex 0/45/90/135° and 0/30/60/90/120/150° ones. A 2D pore size estimation was done first using stereomicroscopy, followed by and compared to µCT scanning. The scaffolds with symmetrical laydown patterns resulted in the predominance of one pore size, while those with more complex patterns had a broader distribution, which could be better shown by µCT scans. Moreover, in the symmetrical scaffolds, the size of 3D pores was not able to reach the value of the fiber spacing due to a flattening effect of the scaffold, where the thickness of the scaffold was less than the fiber spacing, further restricting the pore size distribution in such scaffolds. This method could be used for quality assurance of fabricated scaffolds prior to use in in vitro or in vivo experiments and would be important for a clinical translation. Chapter 5 illustrates a proof of principle subcutaneous implantation in vivo experiment. MEW scaffolds were already featured in small animal in vivo experiments, but to date, no analysis of the foreign body reaction (FBR) to such implants was performed. FBR is an immune reaction to implanted foreign materials, including medical devices, aimed at protecting the host from potential adverse effects and can interfere with the function of some medical implants. Medical-grade PCL was used to melt electrowrite scaffolds with 50 and 60 µm fiber spacing for the 0/90° and 0/60/120° laydown patterns, respectively. These implants were implanted subcutaneously in immunocompetent, outbred mice, with appropriate controls, and explanted after 2, 4, 7 and 14 days. A thorough characterization of the scaffolds before implantation was done, followed by a full histopathological analysis of the FBR to the implants after excision. The scaffolds, irrespective of their pore geometry, induced an extensive FBR in the form of accumulation of foreign body giant cells around the fiber walls, in a manner that almost occluded available pore spaces with little to no neovascularization. This reaction was not induced by the material itself, as the same reaction failed to develop in the PCL solid film controls. A discussion of the results was given with special regard to the literature available on flat surgical meshes, as well as other hydrogel-based porous scaffolds with similar pore sizes. Finally, a general summary of the thesis in Chapter 6 recapitulates the most important points with a focus on future directions for MEW.
While the field of electrochromic (EC) materials and devices (ECDs) continues to advance in terms of color palette and understanding the underlying mechanism, several scientific and technological challenges need to be addressed by optimizing the materials and understanding the electrochemical interplay of these materials in full cells. The main issue here is to further improve the EC profile for color neutrality and cycling stability in order to commercialize dimmable EC products. The transparent conductive substrates used in this work (FTO and ultra-thin ITO glass) have high visible light transmittance (τv > 85%) and low sheet resistance (< 25 Ω·sq-1). In addition, the Li+-containing gel electrolyte has sufficient ionic conductivity (2.8·10-4 S·cm-1 at 25 °C), so the investigated ECDs could achieve a fast response (required ionic conductivity is between 10−3 and 10−7 S·cm-1).
This work shows that the combination of cathodically-coloring Fe-MEPE with anodically-coloring non-stoichiometric nickel oxide (Ni1-xO) electrodes (prepared by the National Institute of Chemistry in Ljubljana, Slovenia) can be used in neutral-coloring type III ECDs. The Fe-MEPE/Ni1-xO ECD with the underbalanced CE (ECD1-1, 2: 1) and the balanced configuration (ECD1-2, 1: 1) are both nearly neutrally-colored (ECD1-1: a* = -6.7, b* = 8.8; ECD1-2: a* = -9.0, b* = 10.1) in the bright state with a τv of almost 70%. Due to the overbalancing of the CE (ECD1-3, 1:3), a deviation (a* = -2.8, b* = 19.9) from the neutral coloration occurred here. The balanced as well as the overbalanced ECD configurations show high electrochemical cycling stability (over 1,000 potentiostatic switching cycles). In general, the overbalanced configuration offers the advantage of a smaller operating voltage range (-1 V ↔ 2.5 V to -1 V ↔ 1.5 V), i.e., avoiding possible electrochemical degradation of the EC materials, electrolyte, or conductive layers. By using a Li RE in the full cell, insights into the optimal matching of electrochemical and optical properties between the two electrodes are obtained to achieve more stable ECDs. Thereby, the redox potentials of both EC electrodes (Fe-MEPE and Ni1-xO) can be measured during operation. The incomplete decolorization of ECD1-1 can be explained by the measured electrode potentials (below the required 4 V vs. Li/Li+), excluding side reactions and degradation at both electrodes. The results demonstrate the importance of using balanced and (slightly) overbalanced ECD configurations with complementary-coloring EC electrodes to achieve high cycling stability and fast switching at low operating voltages. Therefore, this three-electrode configuration provides an excellent method for in situ electrochemical characterization of the individual EC electrodes to better understand the redox processes during device operation and to further improve the optical contrast and cycle stability of ECDs.
The Fe-MEPE/Ni1-xO combination was tested on flexible ultrathin ITO glass (ECD1-4). Here, by applying a low voltage of -1 V ↔ 2.5 V, the MEPE/Ni1-xO ECDs can be reversibly switched from a colored (L* = 35.6, a* = 19.4, b* = -26.7) to a nearly colorless (L* = 78.5, a* = -14.0, b* = 21.3) state. This is accompanied by a change in τv from 6% to 53%. The ECDs exhibit fast response and good cycling stability (5% loss of optical contrast over 100 switching cycles).
To further improve color neutrality and cycling stability, ECDs combining Fe-MEPE and mixed metal oxides as ion storage layers were investigated. Titanium manganese oxide (TMO, Fraunhofer IST) and titanium vanadium oxide (TiVOx, EControl-Glas GmbH & Co. KG) electrodes are compared for use as optically-passive ion storage layers. TiVOx with a maximum charge density of approx. 27 mC·cm-2 and a coloration efficiency of η = 2 cm·C-1 at 584 nm shows a color change from yellow to light gray at 2 V vs. Ag/AgCl, while the slightly anodically-coloring Ti-rich TMO (10.5 mC·cm-², η584 nm = -4 cm·C-1) switches from light yellow to colorless at -2.5 V vs. Ag/AgCl. These materials show only a slight change in τv value from 85% to 75% and from 72% to 81%, respectively, thus reaching the requirements for highly transmissive optical-passive ion storage layers. The ECDs with Fe-MEPE in combination with TiVOx (ECD2-1) and TMO-1 (ECD2-2) are blue-purple in the dark state (0 V) and turn colorless by applying a voltage of 1.5 V, changing the τv value from 28% to 69% and from 21% to 57% in 3 s and 13 s, respectively. The ECDs show fast responses and high cyclability over more than 100 cycles.
In the last section, the simplification of cell architecture by using redox mediators shows that different redox mediators (KHCF(III), Fc-PF6, Fc-BF4, and TMTU) can be used in type II ECDs (4 instead of 5 layers) consisting of Fe-MEPE or Ni1-xO thin film electrodes. The combination of KHCF(III) with Fe-MEPE has a low cycling stability due to the electrochemical formation of Prussian blue (PB). This side reaction is undesirable as it decreases the optical contrast. It can be avoided by using Fc+- (ECD3-5/6) or TMTU-based (ECD3-7) redox mediators, which exhibit reversible redox behavior. A high τv value of 72% is obtained for the use of TMTU. Low concentrations (<0.1 M) of redox mediators decrease the cell voltage for complete switching without affecting the optical properties of the ECDs. The redox couple TMTU/TMFDS2+ (molar ratio of 1:0.1 in 1 M LiClO4/PC as electrolyte) works well in combination with
Ni1-xO electrodes (ECD3-10), with a change in τv value from 38% (colored at 2 V, L* = 67.1, a* = 3.9, b* = 17.2) to 70% at (decolored at -2 V, L* = 86.6, a* = -0.6, b* = 17.2). This result implies that incorporating redox mediators into the electrolyte is an effective means to simplify the cell assembly and color neutrality can be obtained with one optically active WE and a color-neutral redox mediator. Moreover, the combination of Ni1-xO and the colorless TMTU/TMFDS2+ redox mediator is a potential candidate to obtain neutrally colored ECDs.
It is shown that the lab-sized FTO- and ultra-thin ITO-glass-based ECDs are very attractive for energy-efficient EC applications, e.g., in architectural or automotive glazing, aircraft, ships, home appliances and displays. To monitor the EC performance and to prevent diverging electrode potentials during the switching process, the studied three-electrode configuration can help to extend the cycle stability as well as to improve the charge balancing of dimmable applications. The studied ECDs display a route towards neutral tint, e.g., EC active Ni1-xO, optically-inactive mixed metal oxides, and colorless redox mediators. Nevertheless, color neutrality should be further improved to meet the requirements for industrial applications. For future work, a scale-up process from lab-sized (few cm²) to prototype (few m²) ECDs will be necessary.
RNA-cleaving deoxyribozymes have found broad application as useful tools for RNA biochemistry. However, tedious in vitro selection procedures combined with laborious characterization of individual candidate catalysts hinder the discovery of novel catalytic motifs. Here, we present a new high-throughput sequencing method, DZ-seq, which directly measures activity and localizes cleavage sites of thousands of deoxyribozymes. DZ-seq exploits A-tailing followed by reverse transcription with an oligo-dT primer to capture the cleavage status and sequences of both deoxyribozyme and RNA substrate. We validated DZ-seq by conventional analytical methods and demonstrated its utility by discovery of novel deoxyribozymes that allow for cleaving challenging RNA targets or the analysis of RNA modification states.
Human-computer interfaces have the potential to support mental health practitioners in alleviating mental distress.
Adaption of this technology in practice is, however, slow.
We provide means to extend the design space of human-computer interfaces for mitigating mental distress.
To this end, we suggest three complementary approaches: using presentation technology, using virtual environments, and using communication technology to facilitate social interaction.
We provide new evidence that elementary aspects of presentation technology affect the emotional processing of virtual stimuli, that perception of our environment affects the way we assess our environment, and that communication technologies affect social bonding between users.
By showing how interfaces modify emotional reactions and facilitate social interaction, we provide converging evidence that human-computer interfaces can help alleviate mental distress.
These findings may advance the goal of adapting technological means to the requirements of mental health practitioners.
This thesis deals with the first part of a larger project that follows the ultimate goal of implementing a software tool that creates a Mission Control Room in Virtual Reality. The software is to be used for the operation of spacecrafts and is specially developed for the unique real-time requirements of unmanned satellite missions. Beginning from launch, throughout the whole mission up to the recovery or disposal of the satellite, all systems need to be monitored and controlled in continuous intervals, to ensure the mission’s success. Mission Operation is an essential part of every space mission and has been undertaken for decades. Recent technological advancements in the realm of immersive technologies pave the way for innovative methods to operate spacecrafts. Virtual Reality has the capability to resolve the physical constraints set by traditional Mission Control Rooms and thereby delivers novel opportunities. The paper highlights underlying theoretical aspects of Virtual Reality, Mission Control and IP Communication. However, the focus lies upon the practical part of this thesis which revolves around the first steps of the implementation of the virtual Mission Control Room in the Unity Game Engine. Overall, this paper serves as a demonstration of Virtual Reality technology and shows its possibilities with respect to the operation of spacecrafts.
One of the pronounced global challenges facing ecologists is how to feed the current growing human population while sustaining biodiversity and ecosystem services. To shed light on this, I investigated the impact of human land use on bee diversity and plant-pollinator interactions in Tanzania Savannah ecosystems. The thesis comprises the following chapters:
Chapter I: General Introduction
This chapter provides the background information including the study objectives and hypotheses. It highlights the ecological importance of bees and the main threats facing bee pollinators with a focus on two land-use practices namely livestock grazing and agriculture. It also highlights the diversity and global distribution of bees. It further introduces the tropical savannah ecosystem, its climate, and vegetation characteristics and explains spectacular megafauna species of the system that form centers of wildlife tourism and inadequacy knowledge on pollinators diversity of the system. Finally, this chapter describes the study methodology including, the description of the study area, study design, and data collection.
Chapter II: Positive effects of low livestock grazing intensity on East African bee assemblages mediated by increases in floral resources
The impact of livestock grazing intensity on bee assemblage has been subjected to research over decades. Moreover, most of these studies have been conducted in temperate Europe and America leaving the huge tropical savannah of East Africa less studied. Using sweep netting and pan traps, a total of 183 species (from 2,691 individuals) representing 55 genera and five families were collected from 24 study sites representing three levels of livestock grazing intensity in savannah ecosystem of northern Tanzania. Results have shown that moderate livestock grazing slightly increased bee species richness. However, high livestock grazing intensity led to a strong decline. Besides, results revealed a unimodal distribution pattern of bee species richness and mean annual temperature. It was also found that the effect of livestock grazing and environmental temperature on bee species richness was mediated by a positive effect of moderate grazing on floral resource richness. The study, therefore, reveals that bee communities of the African savannah zone may benefit from low levels of livestock grazing as this favors the growth of flowering plant species. A high level of livestock grazing intensity will cause significant species losses, an effect that may increase with climatic warming.
Chapter III: Agricultural intensification with seasonal fallow land promotes high bee diversity in Afrotropical drylands
This study investigated the impact of local agriculture intensification on bee diversity in the Afro tropical drylands of northern Tanzania. Using sweep netting and pan traps, a total of 219 species (from 3,428 individuals) representing 58 genera and six families were collected from 24 study sites (distributed from 702 to 1708 m. asl) representing three levels of agriculture intensity spanning an extensive gradient of mean annual temperature. Results showed that bee species richness increased with agricultural intensity and with increasing temperature. However, the effects of agriculture intensity and temperature on bee species richness were mediated by the positive effects of agriculture and temperature on floral resource richness used by bee pollinators. Moreover, results showed that variation of bee body sizes increases with agricultural intensification, “that effect”, however, diminished in environments with higher temperatures. This study reveals that bee assemblages in Afrotropical drylands benefit from agriculture intensification in the way it is currently practiced. Further intensification, including year-round irrigated crop monocultures and extensive use of agrochemicals, is likely to exert a negative impact on bee diversity and pollination services, as reported in temperate regions. Moreover, several bee species were restricted to natural savannah habitats. Therefore, to conserve bee communities in Afro tropical drylands and guarantee pollination services, a mixture of savannah and agriculture, with long periods of fallow land should be maintained.
Chapter IV: Impact of land use intensification and local features on plants and pollinators in Sub-Saharan smallholder farms
For the first time in the region, this study explores the impact of land-use intensification on plants and pollinators in Sub-Saharan smallholder farms. The study complemented field surveys of bees with a modern DNA metabarcoding approach to characterize the foraged plants and thus built networks describing plant-pollinator interactions at the individual insect level. This information was coupled with quantitative traits of landscape composition and floral availability surrounding each farm. The study found that pollinator richness decreased with increasing impervious and agricultural cover in the landscape, whereas the flower density at each farm correlated with pollinator richness. The intensification of agricultural land use and urbanization correlated with a higher foraging niche overlap among pollinators due to the convergence of individuals' flower-visiting strategies. Furthermore, within farms, the higher availability of floral resources drove lower niche overlap among individuals, greater abundance of flower visitors shaped higher generalization at the networks level (H2I), possibly due to increased competition. These mechanistic understandings leading to individuals’ foraging niche overlap and generalism at the network level, could imply stability of interactions and the pollination ecosystem service. The integrative survey proved that plant-pollinator systems are largely affected by land use intensification and by local factors in smallholder farms of Sub-Saharan Africa. Thus, policies promoting nature-based solutions, among which the introduction of more pollinator-friendly practices by smallholder farmers, could be effective in mitigating the intensification of both urban and rural landscapes in this region, as well as in similar Sub-Saharan contexts.
Chapter V: A synopsis of the Bee occurrence data of northern Tanzania
This study represents a synopsis of the bee occurrence data of northern Tanzania obtained from a survey in the Kilimanjaro, Arusha, and Manyara regions. Bees were sampled using two standardized methods, sweep netting and colored pan traps. The study summed up 953 species occurrences of 45 species belonging to 20 genera and four families (Halictidae, Apidae, Megachilidae, and andrenidae) A. This study serves as the baseline information in understanding the diversity and distribution of bees in the northern parts of the country. Understanding the richness and distribution of bees is a critical step in devising robust conservation and monitoring strategies for their populations since limited taxonomic information of the existing and unidentified bee species makes their conservation haphazard.
Chapter VI: General discussion
In general, findings obtained in these studies suggest that livestock grazing and agriculture intensification affects bee assemblages and floral resources used by bee pollinators. Results have shown that moderate livestock grazing intensity may be important in preserving bee diversity. However, high level of livestock grazing intensity may result in a strong decline in bee species richness and abundance. Moreover, findings indicate that agriculture intensification with seasonal fallow lands supports high floral resource richness promoting high bee diversity in Afrotropical drylands. Nonetheless, natural savannahs were found to contain unique bee species. Therefore, agriculture intensification with seasonal fallow should go in hand with conserving remnant savannah in the landscapes to increase bee diversity and ensure pollination services. Likewise, findings suggest that increasing urbanization and agriculture cover at the landscape level reduce plant and pollinator biodiversity with negative impacts on their complex interactions with plants. Conversely, local scale availability of floral resources has shown the positive effects in buffering pollinators decline and mitigating all detrimental effects induced by land-use intensification. Moreover, findings suggest that the impact of human land use (livestock grazing and agriculture) do not act in isolation but synergistically interacts with climatic factors such as mean annual temperature, MAT. The impact of MAT on bee species richness in grazing gradient showed to be more detrimental than in agriculture habitats. This could probably be explained by the remaining vegetation cover following anthropogenic disturbance. Meaning that the remaining vegetation cover in the agricultural gradient probably absorbs the solar radiations hence reducing detrimental effect of mean annual temperature on bee species richness. This one is not the case in grazing gradient since the impact of livestock grazing is severe, leaving the bare land with no vegetation cover. Finally, our findings conclude that understanding the interplay of multiple anthropogenic activities and their interaction with MAT as a consequence of ongoing climate change is necessary for mitigating their potential consequences on bee assemblages and the provision of ecosystem services. Morever, future increases in livestock grazing and agriculture intensification (including year-round crop irrigated monocultures and excessive use of agrochemicals) may lead to undesirable consequences such as species loss and impair provision of pollination services.