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Spatial and temporal temperature and moisture patterns across the Tibetan Plateau are very complex. The onset and magnitude of the Holocene climate optimum in the Asian monsoon realm, in particular, is a subject of considerable debate as this time period is often used as an analogue for recent global warming. In the light of contradictory inferences regarding past climate and environmental change on the Tibetan Plateau, I have attempted to explain mismatches in the timing and magnitude of change. Therefore, I analysed the temporal variation of fossil pollen and diatom spectra and the geochemical record from palaeo-ecological records covering different time scales (late Quaternary and the last 200 years) from two core regions in the NE and SE Tibetan Plateau. For interpretation purposes I combined my data with other available palaeo-ecological data to set up corresponding aquatic and terrestrial proxy data sets of two lake pairs and two sets of sites. I focused on the direct comparison of proxies representing lacustrine response to climate signals (e.g., diatoms, ostracods, geochemical record) and proxies representing changes in the terrestrial environment (i.e., terrestrial pollen), in order to asses whether the lake and its catchments respond at similar times and magnitudes to environmental changes. Therefore, I introduced the established numerical technique procrustes rotation as a new approach in palaeoecology to quantitatively compare raw data of any two sedimentary records of interest in order to assess their degree of concordance. Focusing on the late Quaternary, sediment cores from two lakes (Kuhai Lake 35.3°N; 99.2°E; 4150 m asl; and Koucha Lake 34.0°N; 97.2°E; 4540 m asl) on the semi-arid northeastern Tibetan Plateau were analysed to identify post-glacial vegetation and environmental changes, and to investigate the responses of lake ecosystems to such changes. Based on the pollen record, five major vegetation and climate changes could be identified: (1) A shift from alpine desert to alpine steppe indicates a change from cold, dry conditions to warmer and more moist conditions at 14.8 cal. ka BP, (2) alpine steppe with tundra elements points to conditions of higher effective moisture and a stepwise warming climate at 13.6 cal. ka BP, (3) the appearance of high-alpine meadow vegetation indicates a further change towards increased moisture, but with colder temperatures, at 7.0 cal. ka BP, (4) the reoccurrence of alpine steppe with desert elements suggests a return to a significantly colder and drier phase at 6.3 cal. ka BP, and (5) the establishment of alpine steppe-meadow vegetation indicates a change back to relatively moist conditions at 2.2 cal. ka BP. To place the reconstructed climate inferences from the NE Tibetan Plateau into the context of Holocene moisture evolution across the Tibetan Plateau, I applied a five-scale moisture index and average link clustering to all available continuous pollen and non-pollen palaeoclimate records from the Tibetan Plateau, in an attempt to detect coherent regional and temporal patterns of moisture evolution on the Plateau. However, no common temporal or spatial pattern of moisture evolution during the Holocene could be detected, which can be assigned to the complex responses of different proxies to environmental changes in an already very heterogeneous mountain landscape, where minor differences in elevation can result in marked variations in microenvironments. Focusing on the past 200 years, I analysed the sedimentary records (LC6 Lake 29.5°N, 94.3°E, 4132 m asl; and Wuxu Lake 29.9°N, 101.1°E, 3705 m asl) from the southeastern Tibetan Plateau. I found that despite presumed significant temperature increases over that period, pollen and diatom records from the SE Tibetan Plateau reveal only very subtle changes throughout their profiles. The compositional species turnover investigated over the last 200 years appears relatively low in comparison to the species reorganisations during the Holocene. The results indicate that climatically induced ecological thresholds are not yet crossed, but that human activity has an increasing influence, particularly on the terrestrial ecosystem. Forest clearances and reforestation have not caused forest decline in our study area, but a conversion of natural forests to semi-natural secondary forests. The results from the numerical proxy comparison of the two sets of two pairs of Tibetan lakes indicate that the use of different proxies and the work with palaeo-ecological records from different lake types can cause deviant stories of inferred change. Irrespective of the timescale (Holocene or last 200 years) or region (SE or NE Tibetan Plateau) analysed, the agreement in terms of the direction, timing, and magnitude of change between the corresponding terrestrial data sets is generally better than the match between the corresponding lacustrine data sets, suggesting that lacustrine proxies may partly be influenced by in-lake or local catchment processes whereas the terrestrial proxy reflects a more regional climatic signal. The current disaccord on coherent temporal and spatial climate patterns on the Tibetan Plateau can partly be ascribed to the complexity of proxy response and lake systems on the Tibetan Plateau. Therefore, a multi-proxy, multi-site approach is important in order to gain a reliable climate interpretation for the complex mountain landscape of the Tibetan Plateau.
The East African Rift System (EARS) is a significant example of active tectonics, which provides opportunities to examine the stages of continental faulting and landscape evolution. The southwest extension of the EARS is one of the most significant examples of active tectonics nowadays, however, seismotectonic research in the area has been scarce, despite the fundamental importance of neotectonics. Our first study area is located between the Northern Province of Zambia and the southeastern Katanga Province of the Democratic Republic of Congo. Lakes Mweru and Mweru Wantipa are part of the southwest extension of the EARS. Fault analysis reveals that, since the Miocene, movements along the active Mweru-Mweru Wantipa Fault System (MMFS) have been largely responsible for the reorganization of the landscape and the drainage patterns across the southwestern branch of the EARS. To investigate the spatial and temporal patterns of fluvial-lacustrine landscape development, we determined in-situ cosmogenic 10Be and 26Al in a total of twenty-six quartzitic bedrock samples that were collected from knickpoints across the Mporokoso Plateau (south of Lake Mweru) and the eastern part of the Kundelungu Plateau (north of Lake Mweru). Samples from the Mporokoso Plateau and close to the MMFS provide evidence of temporary burial. By contrast, surfaces located far from the MMFS appear to have remained uncovered since their initial exposure as they show consistent 10Be and 26Al exposure ages ranging up to ~830 ka. Reconciliation of the observed burial patterns with morphotectonic and stratigraphic analysis reveals the existence of an extensive paleo-lake during the Pleistocene. Through hypsometric analyses of the dated knickpoints, the potential maximum water level of the paleo-lake is constrained to ~1200 m asl (present lake lavel: 917 m asl). High denudation rates (up to ~40 mm ka-1) along the eastern Kundelungu Plateau suggest that footwall uplift, resulting from normal faulting, caused river incision, possibly controlling paleo-lake drainage. The lake level was reduced gradually reaching its current level at ~350 ka.
Parallel to the MMFS in the north, the Upemba Fault System (UFS) extends across the southeastern Katanga Province of the Democratic Republic of Congo. This part of our research is focused on the geomorphological behavior of the Kiubo Waterfalls. The waterfalls are the currently active knickpoint of the Lufira River, which flows into the Upemba Depression. Eleven bedrock samples along the Lufira River and its tributary stream, Luvilombo River, were collected. In-situ cosmogenic 10Be and 26Al were used in order to constrain the K constant of the Stream Power Law equation. Constraining the K constant allowed us to calculate the knickpoint retreat rate of the Kiubo Waterfalls at ~0.096 m a-1. Combining the calculated retreat rate of the knickpoint with DNA sequencing from fish populations, we managed to present extrapolation models and estimate the location of the onset of the Kiubo Waterfalls, revealing its connection to the seismicity of the UFS.
In this thesis we mainly generalize two theorems from Mackaay-Picken and Picken (2002, 2004). In the first paper, Mackaay and Picken show that there is a bijective correspondence between Deligne 2-classes $\xi \in \check{H}^2(M,\mathcal{D}^2)$ and holonomy maps from the second thin-homotopy group $\pi_2^2(M)$ to $U(1)$. In the second one, a generalization of this theorem to manifolds with boundaries is given: Picken shows that there is a bijection between Deligne 2-cocycles and a certain variant of 2-dimensional topological quantum field theories. In this thesis we show that these two theorems hold in every dimension. We consider first the holonomy case, and by using simplicial methods we can prove that the group of smooth Deligne $d$-classes is isomorphic to the group of smooth holonomy maps from the $d^{th}$ thin-homotopy group $\pi_d^d(M)$ to $U(1)$, if $M$ is $(d-1)$-connected. We contrast this with a result of Gajer (1999). Gajer showed that Deligne $d$-classes can be reconstructed by a different class of holonomy maps, which not only include holonomies along spheres, but also along general $d$-manifolds in $M$. This approach does not require the manifold $M$ to be $(d-1)$-connected. We show that in the case of flat Deligne $d$-classes, our result differs from Gajers, if $M$ is not $(d-1)$-connected, but only $(d-2)$-connected. Stiefel manifolds do have this property, and if one applies our theorem to these and compare the result with that of Gajers theorem, it is revealed that our theorem reconstructs too many Deligne classes. This means, that our reconstruction theorem cannot live without the extra assumption on the manifold $M$, that is our reconstruction needs less informations about the holonomy of $d$-manifolds in $M$ at the price of assuming $M$ to be $(d-1)$-connected. We continue to show, that also the second theorem can be generalized: By introducing the concept of Picken-type topological quantum field theory in arbitrary dimensions, we can show that every Deligne $d$-cocycle induces such a $d$-dimensional field theory with two special properties, namely thin-invariance and smoothness. We show that any $d$-dimensional topological quantum field theory with these two properties gives rise to a Deligne $d$-cocycle and verify that this construction is surjective and injective, that is both groups are isomorphic.
This paper introduces a novel measure to assess similarity between event hydrographs. It is based on Cross Recurrence Plots and Recurrence Quantification Analysis which have recently gained attention in a range of disciplines when dealing with complex systems. The method attempts to quantify the event runoff dynamics and is based on the time delay embedded phase space representation of discharge hydrographs. A phase space trajectory is reconstructed from the event hydrograph, and pairs of hydrographs are compared to each other based on the distance of their phase space trajectories. Time delay embedding allows considering the multi-dimensional relationships between different points in time within the event. Hence, the temporal succession of discharge values is taken into account, such as the impact of the initial conditions on the runoff event. We provide an introduction to Cross Recurrence Plots and discuss their parameterization. An application example based on flood time series demonstrates how the method can be used to measure the similarity or dissimilarity of events, and how it can be used to detect events with rare runoff dynamics. It is argued that this methods provides a more comprehensive approach to quantify hydrograph similarity compared to conventional hydrological signatures.
Recurrence plots, a rather promising tool of data analysis, have been introduced by Eckman et al. in 1987. They visualise recurrences in phase space and give an overview about the system's dynamics. Two features have made the method rather popular. Firstly they are rather simple to compute and secondly they are putatively easy to interpret. However, the straightforward interpretation of recurrence plots for some systems yields rather surprising results. For example indications of low dimensional chaos have been reported for stock marked data, based on recurrence plots. In this work we exploit recurrences or ``naturally occurring analogues'' as they were termed by E. Lorenz, to obtain three key results. One of which is that the most striking structures which are found in recurrence plots are hinged to the correlation entropy and the correlation dimension of the underlying system. Even though an eventual embedding changes the structures in recurrence plots considerably these dynamical invariants can be estimated independently of the special parameters used for the computation. The second key result is that the attractor can be reconstructed from the recurrence plot. This means that it contains all topological information of the system under question in the limit of long time series. The graphical representation of the recurrences can also help to develop new algorithms and exploit specific structures. This feature has helped to obtain the third key result of this study. Based on recurrences to points which have the same ``recurrence structure'', it is possible to generate surrogates of the system which capture all relevant dynamical characteristics, such as entropies, dimensions and characteristic frequencies of the system. These so generated surrogates are shadowed by a trajectory of the system which starts at different initial conditions than the time series in question. They can be used then to test for complex synchronisation.
Recurrences in past climates
(2023)
Our ability to predict the state of a system relies on its tendency to recur to states it has visited before. Recurrence also pervades common intuitions about the systems we are most familiar with: daily routines, social rituals and the return of the seasons are just a few relatable examples. To this end, recurrence plots (RP) provide a systematic framework to quantify the recurrence of states. Despite their conceptual simplicity, they are a versatile tool in the study of observational data. The global climate is a complex system for which an understanding based on observational data is not only of academical relevance, but vital for the predurance of human societies within the planetary boundaries. Contextualizing current global climate change, however, requires observational data far beyond the instrumental period. The palaeoclimate record offers a valuable archive of proxy data but demands methodological approaches that adequately address its complexities. In this regard, the following dissertation aims at devising novel and further developing existing methods in the framework of recurrence analysis (RA). The proposed research questions focus on using RA to capture scale-dependent properties in nonlinear time series and tailoring recurrence quantification analysis (RQA) to characterize seasonal variability in palaeoclimate records (‘Palaeoseasonality’).
In the first part of this thesis, we focus on the methodological development of novel approaches in RA. The predictability of nonlinear (palaeo)climate time series is limited by abrupt transitions between regimes that exhibit entirely different dynamical complexity (e.g. crossing of ‘tipping points’). These possibly depend on characteristic time scales. RPs are well-established for detecting transitions and capture scale-dependencies, yet few approaches have combined both aspects. We apply existing concepts from the study of self-similar textures to RPs to detect abrupt transitions, considering the most relevant time scales. This combination of methods further results in the definition of a novel recurrence based nonlinear dependence measure. Quantifying lagged interactions between multiple variables is a common problem, especially in the characterization of high-dimensional complex systems. The proposed ‘recurrence flow’ measure of nonlinear dependence offers an elegant way to characterize such couplings. For spatially extended complex systems, the coupled dynamics of local variables result in the emergence of spatial patterns. These patterns tend to recur in time. Based on this observation, we propose a novel method that entails dynamically distinct regimes of atmospheric circulation based on their recurrent spatial patterns. Bridging the two parts of this dissertation, we next turn to methodological advances of RA for the study of Palaeoseasonality. Observational series of palaeoclimate ‘proxy’ records involve inherent limitations, such as irregular temporal sampling. We reveal biases in the RQA of time series with a non-stationary sampling rate and propose a correction scheme.
In the second part of this thesis, we proceed with applications in Palaeoseasonality. A review of common and promising time series analysis methods shows that numerous valuable tools exist, but their sound application requires adaptions to archive-specific limitations and consolidating transdisciplinary knowledge. Next, we study stalagmite proxy records from the Central Pacific as sensitive recorders of mid-Holocene El Niño-Southern Oscillation (ENSO) dynamics. The records’ remarkably high temporal resolution allows to draw links between ENSO and seasonal dynamics, quantified by RA. The final study presented here examines how seasonal predictability could play a role for the stability of agricultural societies. The Classic Maya underwent a period of sociopolitical disintegration that has been linked to drought events. Based on seasonally resolved stable isotope records from Yok Balum cave in Belize, we propose a measure of seasonal predictability. It unveils the potential role declining seasonal predictability could have played in destabilizing agricultural and sociopolitical systems of Classic Maya populations.
The methodological approaches and applications presented in this work reveal multiple exciting future research avenues, both for RA and the study of Palaeoseasonality.
One of the most striking features of ecological systems is their ability to undergo sudden outbreaks in the population numbers of one or a small number of species. The similarity of outbreak characteristics, which is exhibited in totally different and unrelated (ecological) systems naturally leads to the question whether there are universal mechanisms underlying outbreak dynamics in Ecology. It will be shown into two case studies (dynamics of phytoplankton blooms under variable nutrients supply and spread of epidemics in networks of cities) that one explanation for the regular recurrence of outbreaks stems from the interaction of the natural systems with periodical variations of their environment. Natural aquatic systems like lakes offer very good examples for the annual recurrence of outbreaks in Ecology. The idea whether chaos is responsible for the irregular heights of outbreaks is central in the domain of ecological modeling. This question is investigated in the context of phytoplankton blooms. The dynamics of epidemics in networks of cities is a problem which offers many ecological and theoretical aspects. The coupling between the cities is introduced through their sizes and gives rise to a weighted network which topology is generated from the distribution of the city sizes. We examine the dynamics in this network and classified the different possible regimes. It could be shown that a single epidemiological model can be reduced to a one-dimensional map. We analyze in this context the dynamics in networks of weighted maps. The coupling is a saturation function which possess a parameter which can be interpreted as an effective temperature for the network. This parameter allows to vary continously the network topology from global coupling to hierarchical network. We perform bifurcation analysis of the global dynamics and succeed to construct an effective theory explaining very well the behavior of the system.
Redox signalling in plants
(2020)
Once proteins are synthesized, they can additionally be modified by post-translational modifications (PTMs). Proteins containing reactive cysteine thiols, stabilized in their deprotonated form due to their local environment as thiolates (RS-), serve as redox sensors by undergoing a multitude of oxidative PTMs (Ox-PTMs). Ox-PTMs such as S-nitrosylation or formation of inter- or intra-disulfide bridges induce functional changes in these proteins. Proteins containing cysteines, whose thiol oxidation state regulates their functions, belong to the so-called redoxome. Such Ox-PTMs are controlled by site-specific cellular events that play a crucial role in protein regulation, affecting enzyme catalytic sites, ligand binding affinity, protein-protein interactions or protein stability. Reversible protein thiol oxidation is an essential regulatory mechanism of photosynthesis, metabolism, and gene expression in all photosynthetic organisms. Therefore, studying PTMs will remain crucial for understanding plant adaptation to external stimuli like fluctuating light conditions. Optimizing methods suitable for studying plants Ox-PTMs is of high importance for elucidation of the redoxome in plants. This study focusses on thiol modifications occurring in plant and provides novel insight into in vivo redoxome of Arabidopsis thaliana in response to light vs. dark. This was achieved by utilizing a resin-assisted thiol enrichment approach. Furthermore, confirmation of candidates on the single protein level was carried out by a differential labelling approach. The thiols and disulfides were differentially labelled, and the protein levels were detected using immunoblot analysis. Further analysis was focused on light-reduced proteins. By the enrichment approach many well studied redox-regulated proteins were identified. Amongst those were fructose 1,6-bisphosphatase (FBPase) and sedoheptulose-1,7-bisphosphatase (SBPase) which have previously been described as thioredoxin system targeted enzymes. The redox regulated proteins identified in the current study were compared to several published, independent results showing redox regulated proteins in Arabidopsis leaves, root, mitochondria and specifically S-nitrosylated proteins. These proteins were excluded as potential new candidates but remain as a proof-of-concept to the enrichment experiments to be effective. Additionally, CSP41A and CSP41B proteins, which emerged from this study as potential targets of redox-regulation, were analyzed by Ribo-Seq. The active translatome study of csp41a mutant vs. wild-type showed most of the significant changes at end of the night, similarly as csp41b. Yet, in both mutants only several chloroplast-encoded genes were altered. Further studies of CSP41A and CSP41B proteins are needed to reveal their functions and elucidate the role of redox regulation of these proteins.
Post-translational redox-regulation is a well-known mechanism to regulate enzymes of the Calvin cycle, oxidative pentose phosphate cycle, NADPH export and ATP synthesis in response to light. The aim of the present thesis was to investigate whether a similar mechanism is also regulating carbon storage in leaves. Previous studies have shown that the key-regulatory enzyme of starch synthesis, ADPglucose pyrophosphorylase (AGPase) is inactivated by formation of an intermolecular disulfide bridge between the two catalytic subunits (AGPB) of the heterotetrameric holoenzyme in potato tubers, but the relevance of this mechanism to regulate starch synthesis in leaves was not investigated. The work presented in this thesis shows that AGPase is subject to post-translational redox-regulation in leaves of pea, potato and Arabidopsis in response to day night changes. Light was shown to trigger posttranslational redox-regulation of AGPase. AGPB was rapidly converted from a dimer to a monomer when isolated pea chloroplasts were illuminated and from a monomer to a dimer when preilluminated leaves were darkened. Conversion of AGPB from dimer to monomer was accompanied by an increase in activity due to changes in the kinetik properties of the enzyme. Studies with pea chloroplast extracts showed that AGPase redox-activation is mediated by thioredoxins f and m from spinach in-vitro. In a further set of experiments it was shown that sugars provide a second input leading to AGPase redox activation and increased starch synthesis and that they can act as a signal which is independent from light. External feeding of sugars such as sucrose or trehalose to Arabidopsis leaves in the dark led to conversion of AGPB from dimer to monomer and to an increase in the rate of starch synthesis, while there were no significant changes in the level of 3PGA, an allosteric activator of the enyzme, and in the NADPH/NADP+ ratio. Experiments with transgenic Arabidopsis plants with altered levels of trehalose 6-phosphate (T6P), the precursor of trehalose synthesis, provided genetic evidence that T6P rather than trehalose is leading to AGPase redox-activation. Compared to Wt, leaves expressing E.coli trehalose-phosphate synthase (TPS) in the cytosol showed increased activation of AGPase and higher starch level during the day, while trehalose-phosphate phosphatase (TPP) overexpressing leaves showed the opposite. These changes occurred independently of changes in sugar and sugar-phosphate levels and NADPH/NADP+ ratio. External supply of sucrose to Wt and TPS-overexpressing leaves led to monomerisation of AGPB, while this response was attenuated in TPP expressing leaves, indicating that T6P is involved in the sucrose-dependent redox-activation of AGPase. To provide biochemical evidence that T6P promotes redox-activation of AGPase independently of cytosolic elements, T6P was fed to intact isolated chloroplasts for 15 min. incubation with concentrations down to 100 µM of T6P, but not with sucrose 6-phosphate, sucrose, trehalose or Pi as controls, significantly and specifically increased AGPB monomerisation and AGPase activity within 15 minutes, implying T6P as a signal reporting the cytosolic sugar status to the chloroplast. The response to T6P did not involve changes in the NADPH/NADP+ ratio consistent with T6P modulating redox-transfer to AGPase independently of changes in plastidial redox-state. Acetyl-CoA carboxylase (ACCase) is known as key-regulatory enzyme of fatty acid and lipid synthesis in plants. At the start of the present thesis there was mainly in vitro evidence in the literature showing redox-regulation of ACCase by DTT, and thioredoxins f and m. In the present thesis the in-vivo relevance of this mechanism to regulate lipid synthesis in leaves was investigated. ACCase activity measurement in leaf tissue collected at the end of the day and night in Arabidopsis leaves revealed a 3-fold higher activation state of the enzyme in the light than in the dark. Redox-activation was accompanied by change in kinetic properties of ACCase, leading to an increase affinity to its substrate acetyl-CoA . In further experiments, DTT as well as sucrose were fed to leaves, and both treatments led to a stimulation in the rate of lipid synthesis accompanied by redox-activation of ACCase and decrease in acetyl-CoA content. In a final approach, comparison of metabolic and transcript profiling after DTT feeding and after sucrose feeding to leaves provided evidence that redox-modification is an important regulatory mechanism in central metabolic pathways such as TCA cycle and amino acid synthesis, which acts independently of transcript levels.
Text is a ubiquitous entity in our world and daily life. We encounter it nearly everywhere in shops, on the street, or in our flats. Nowadays, more and more text is contained in digital images. These images are either taken using cameras, e.g., smartphone cameras, or taken using scanning devices such as document scanners. The sheer amount of available data, e.g., millions of images taken by Google Streetview, prohibits manual analysis and metadata extraction. Although much progress was made in the area of optical character recognition (OCR) for printed text in documents, broad areas of OCR are still not fully explored and hold many research challenges. With the mainstream usage of machine learning and especially deep learning, one of the most pressing problems is the availability and acquisition of annotated ground truth for the training of machine learning models because obtaining annotated training data using manual annotation mechanisms is time-consuming and costly. In this thesis, we address of how we can reduce the costs of acquiring ground truth annotations for the application of state-of-the-art machine learning methods to optical character recognition pipelines. To this end, we investigate how we can reduce the annotation cost by using only a fraction of the typically required ground truth annotations, e.g., for scene text recognition systems. We also investigate how we can use synthetic data to reduce the need of manual annotation work, e.g., in the area of document analysis for archival material. In the area of scene text recognition, we have developed a novel end-to-end scene text recognition system that can be trained using inexact supervision and shows competitive/state-of-the-art performance on standard benchmark datasets for scene text recognition. Our method consists of two independent neural networks, combined using spatial transformer networks. Both networks learn together to perform text localization and text recognition at the same time while only using annotations for the recognition task. We apply our model to end-to-end scene text recognition (meaning localization and recognition of words) and pure scene text recognition without any changes in the network architecture.
In the second part of this thesis, we introduce novel approaches for using and generating synthetic data to analyze handwriting in archival data. First, we propose a novel preprocessing method to determine whether a given document page contains any handwriting. We propose a novel data synthesis strategy to train a classification model and show that our data synthesis strategy is viable by evaluating the trained model on real images from an archive. Second, we introduce the new analysis task of handwriting classification. Handwriting classification entails classifying a given handwritten word image into classes such as date, word, or number. Such an analysis step allows us to select the best fitting recognition model for subsequent text recognition; it also allows us to reason about the semantic content of a given document page without the need for fine-grained text recognition and further analysis steps, such as Named Entity Recognition. We show that our proposed approaches work well when trained on synthetic data. Further, we propose a flexible metric learning approach to allow zero-shot classification of classes unseen during the network’s training. Last, we propose a novel data synthesis algorithm to train off-the-shelf pixel-wise semantic segmentation networks for documents. Our data synthesis pipeline is based on the famous Style-GAN architecture and can synthesize realistic document images with their corresponding segmentation annotation without the need for any annotated data!
To find out the future of nowadays reef ecosystem turnover under the environmental stresses such as global warming and ocean acidification, analogue studies from the geologic past are needed. As a critical time of reef ecosystem innovation, the Permian-Triassic transition witnessed the most severe demise of Phanerozoic reef builders, and the establishment of modern style symbiotic relationships within the reef-building organisms. Being the initial stage of this transition, the Middle Permian (Capitanian) mass extinction coursed a reef eclipse in the early Late Permian, which lead to a gap of understanding in the post-extinction Wuchiapingian reef ecosystem, shortly before the radiation of Changhsingian reefs. Here, this thesis presents detailed biostratigraphic, sedimentological, and palaeoecological studies of the Wuchiapingian reef recovery following the Middle Permian (Capitanian) mass extinction, on the only recorded Wuchiapingian reef setting, outcropping in South China at the Tieqiao section.
Conodont biostratigraphic zonations were revised from the Early Permian Artinskian to the Late Permian Wuchiapingian in the Tieqiao section. Twenty main and seven subordinate conodont zones are determined at Tieqiao section including two conodont zone below and above the Tieqiao reef complex. The age of Tieqiao reef was constrained as early to middle Wuchiapingian.
After constraining the reef age, detailed two-dimensional outcrop mapping combined with lithofacies study were carried out on the Wuchiapingian Tieqiao Section to investigate the reef growth pattern stratigraphically as well as the lateral changes of reef geometry on the outcrop scale. Semi-quantitative studies of the reef-building organisms were used to find out their evolution pattern within the reef recovery. Six reef growth cycles were determined within six transgressive-regressive cycles in the Tieqiao section. The reefs developed within the upper part of each regressive phase and were dominated by different biotas. The timing of initial reef recovery after the Middle Permian (Capitanian) mass extinction was updated to the Clarkina leveni conodont zone, which is earlier than previous understanding. Metazoans such as sponges were not the major components of the Wuchiapingian reefs until the 5th and 6th cycles. So, the recovery of metazoan reef ecosystem after the Middle Permian (Capitanian) mass extinction was obviously delayed. In addition, although the importance of metazoan reef builders such as sponges did increase following the recovery process, encrusting organisms such as Archaeolithoporella and Tubiphytes, combined with microbial carbonate precipitation, still played significant roles to the reef building process and reef recovery after the mass extinction.
Based on the results from outcrop mapping and sedimentological studies, quantitative composition analysis of the Tieqiao reef complex were applied on selected thin sections to further investigate the functioning of reef building components and the reef evolution after the Middle Permian (Capitanian) mass extinction. Data sets of skeletal grains and whole rock components were analyzed. The results show eleven biocommunity clusters/eight rock composition clusters dominated by different skeletal grains/rock components. Sponges, Archaeolithoporella and Tubiphytes were the most ecologically important components within the Wuchiapingian Tieqiao reef, while the clotted micrites and syndepositional cements are the additional important rock components for reef cores. The sponges were important within the whole reef recovery. Tubiphytes were broadly distributed in different environments and played a key-role in the initial reef communities. Archaeolithoporella concentrated in the shallower part of reef cycles (i.e., the upper part of reef core) and was functionally significant for the enlargement of reef volume.
In general, the reef recovery after the Middle Permian (Capitanian) mass extinction has some similarities with the reef recovery following the end-Permian mass extinction. It shows a delayed recovery of metazoan reefs and a stepwise recovery pattern that was controlled by both ecological and environmental factors. The importance of encrusting organisms and microbial carbonates are also similar to most of the other post-extinction reef ecosystems. These findings can be instructive to extend our understanding of the reef ecosystem evolution under environmental perturbation or stresses.
Polymeric semiconductors are strong contenders for replacing traditional inorganic semiconductors in electronic applications requiring low power, low cost and flexibility, such as biosensors, flexible solar cells and electronic displays. Molecular doping has the potential to enable this revolution by improving the conductivity and charge transport properties of this class of materials. Despite decades of research in this field, gaps in our understanding of the nature of dopant–polymer interactions has resulted in limited commercialization of this technology. This work aims at providing a deeper insight into the underlying mechanisms of molecular p-doping of semiconducting polymers in the solution and solid-state, and thereby bring the scientific community closer to realizing the dream of making organic semiconductors commonplace in the electronics industry. The role of 1) dopant size/shape, 2) polymer chain aggregation and 3) charge delocalization on the doping mechanism and efficiency is addressed using optical (UV-Vis-NIR) and electron paramagnetic resonance (EPR) spectroscopies. By conducting a comprehensive study of the nature and concentration of the doping-induced species in solutions of the polymer poly(3-hexylthiophene) (P3HT) with 3 different dopants, we identify the unique optical signatures of the delocalized polaron, localized polaron and charge-transfer complex, and report their extinction coefficient values. Furthermore, with X-ray diffraction, atomic force microscopy and electrical conductivity measurements, we study the impact of processing technique and doping mechanism on the morphology and thereby, charge transport through the doped films.
This work demonstrates that the doping mechanism and type of doping-induced species formed are strongly influenced by the polymer backbone arrangement rather than dopant shape/size. The ability of the polymer chain to aggregate is found to be crucial for efficient charge transfer (ionization) and polaron delocalization. At the same time, our results suggest that the high ionization efficiency of a dopant–polymer system in solution may subsequently hinder efficient charge transport in the solid-state due to the reduction in the fraction of tie chains, which enable charges to move efficiently between aggregated domains in the films. This study demonstrates the complex multifaceted nature of polymer doping while providing important hints for the future design of dopant-host systems and film fabrication techniques.
Adjustment of empirically derived ground motion prediction equations (GMPEs), from a data- rich region/site where they have been derived to a data-poor region/site, is one of the major challenges associated with the current practice of seismic hazard analysis. Due to the fre- quent use in engineering design practices the GMPEs are often derived for response spectral ordinates (e.g., spectral acceleration) of a single degree of freedom (SDOF) oscillator. The functional forms of such GMPEs are based upon the concepts borrowed from the Fourier spectral representation of ground motion. This assumption regarding the validity of Fourier spectral concepts in the response spectral domain can lead to consequences which cannot be explained physically.
In this thesis, firstly results from an investigation that explores the relationship between Fourier and response spectra, and implications of this relationship on the adjustment issues of GMPEs, are presented. The relationship between the Fourier and response spectra is explored by using random vibration theory (RVT), a framework that has been extensively used in earthquake engineering, for instance within the stochastic simulation framework and in the site response analysis. For a 5% damped SDOF oscillator the RVT perspective of response spectra reveals that no one-to-one correspondence exists between Fourier and response spectral ordinates except in a limited range (i.e., below the peak of the response spectra) of oscillator frequencies. The high oscillator frequency response spectral ordinates are dominated by the contributions from the Fourier spectral ordinates that correspond to the frequencies well below a selected oscillator frequency. The peak ground acceleration (PGA) is found to be related with the integral over the entire Fourier spectrum of ground motion which is in contrast to the popularly held perception that PGA is a high-frequency phenomenon of ground motion.
This thesis presents a new perspective for developing a response spectral GMPE that takes the relationship between Fourier and response spectra into account. Essentially, this frame- work involves a two-step method for deriving a response spectral GMPE: in the first step two empirical models for the FAS and for a predetermined estimate of duration of ground motion are derived, in the next step, predictions from the two models are combined within the same RVT framework to obtain the response spectral ordinates. In addition to that, a stochastic model based scheme for extrapolating the individual acceleration spectra beyond the useable frequency limits is also presented. To that end, recorded acceleration traces were inverted to obtain the stochastic model parameters that allow making consistent extrapola- tion in individual (acceleration) Fourier spectra. Moreover an empirical model, for a dura- tion measure that is consistent within the RVT framework, is derived. As a next step, an oscillator-frequency-dependent empirical duration model is derived that allows obtaining the most reliable estimates of response spectral ordinates. The framework of deriving the response spectral GMPE presented herein becomes a self-adjusting model with the inclusion of stress parameter (∆σ) and kappa (κ0) as the predictor variables in the two empirical models. The entire analysis of developing the response spectral GMPE is performed on recently compiled RESORCE-2012 database that contains recordings made from Europe, the Mediterranean and the Middle East. The presented GMPE for response spectral ordinates should be considered valid in the magnitude range of 4 ≤ MW ≤ 7.6 at distances ≤ 200 km.
STERILE APETALA (SAP) is known to be an essential regulator of flower development for over 20 years. Loss of SAP function in the model plant Arabidopsis thaliana is associated with a reduction of floral organ number, size and fertility. In accordance with the function of SAP during early flower development, its spatial expression in flowers is confined to meristematic stages and to developing ovules. However, to date, despite extensive research, the molecular function of SAP and the regulation of its spatio-temporal expression still remain elusive.
In this work, amino acid sequence analysis and homology modeling revealed that SAP belongs to the rare class of plant F-box proteins with C-terminal WD40 repeats. In opisthokonts, this type of F-box proteins constitutes the substrate binding subunit of SCF complexes, which catalyze the ubiquitination of proteins to initiate their proteasomal degradation. With LC-MS/MS-based protein complex isolation, the interaction of SAP with major SCF complex subunits was confirmed. Additionally, candidate substrate proteins, such as the growth repressor PEAPOD 1 and 2 (PPD1/2), could be revealed during early stages of flower development. Also INDOLE-3-BUTYRIC ACID RESPONSE 5 (IBR5) was identified among putative interactors. Genetic analyses indicated that, different from substrate proteins, IBR5 is required for SAP function. Protein complex isolation together with transcriptome profiling emphasized that the SCFSAP complex integrates multiple biological processes, such as proliferative growth, vascular development, hormonal signaling and reproduction. Phenotypic analysis of sap mutant and SAP overexpressing plants positively correlated SAP function with plant growth during reproductive and vegetative development.
Furthermore, to elaborate on the transcriptional regulation of SAP, publicly available ChIP-seq data of key floral homeotic proteins were reanalyzed. Here, it was shown that the MADS-domain transcription factors APETALA 1 (AP1), APETALA 3 (AP3), PISTILLATA (PI), AGAMOUS (AG) and SEPALLATA 3 (SEP3) bind to the SAP locus, which indicates that SAP is expressed in a floral organ-specific manner. Reporter gene analyses in combination with CRISPR/Cas9-mediated deletion of putative regulatory regions further demonstrated that the intron contains major regulatory elements of SAP in Arabidopsis thaliana.
In conclusion, these data indicate that SAP is a pleiotropic developmental regulator that acts through tissue-specific destabilization of proteins. The presumed transcriptional regulation of SAP by the floral MADS-domain transcription factors could provide a missing link between the specification of floral organ identity and floral organ growth pathways.
The highly conserved protein complex containing the Target of Rapamycin (TOR) kinase is known to integrate intra- and extra-cellular stimuli controlling nutrient allocation and cellular growth. This thesis describes three studies aimed to understand how TOR signaling pathway influences carbon and nitrogen metabolism in Chlamydomonas reinhardtii. The first study presents a time-resolved analysis of the molecular and physiological features across the diurnal cycle. The inhibition of TOR leads to 50% reduction in growth followed by nonlinear delays in the cell cycle progression. The metabolomics analysis showed that the growth repression is mainly driven by differential carbon partitioning between anabolic and catabolic processes. Furthermore, the high accumulation of nitrogen-containing compounds indicated that TOR kinase controls the carbon to nitrogen balance of the cell, which is responsible for biomass accumulation, growth and cell cycle progression. In the second study the cause of the high accumulation of amino acids is explained. For this purpose, the effect of TOR inhibition on Chlamydomonas was examined under different growth regimes using stable 13C- and 15N-isotope labeling. The data clearly showed that an increased nitrogen uptake is induced within minutes after the inhibition of TOR. Interestingly, this increased N-influx is accompanied by increased activities of nitrogen assimilating enzymes. Accordingly, it was concluded that TOR inhibition induces de-novo amino acid synthesis in Chlamydomonas. The recognition of this novel process opened an array of questions regarding potential links between central metabolism and TOR signaling. Therefore a detailed phosphoproteomics study was conducted to identify the potential substrates of TOR pathway regulating central metabolism. Interestingly, some of the key enzymes involved in carbon metabolism as well as amino acid synthesis exhibited significant changes in the phosphosite intensities immediately after TOR inhibition. Altogether, these studies provide a) detailed insights to metabolic response of Chlamydomonas to TOR inhibition, b) identification of a novel process causing rapid upshifts in amino acid levels upon TOR inhibition and c) finally highlight potential targets of TOR signaling regulating changes in central metabolism. Further biochemical and molecular investigations could confirm these observations and advance the understanding of growth signaling in microalgae.
The relationship between nutrition and the development of chronic diseases including metabolic syndrome, diabetes mellitus, cancer and cardiovascular disease has been well studied. On the other hand, changes in the GH-IGF-1 axis in association with nutrition-related diseases have been reported. The interplay between GH, total IGF-1 and different inhibitory and stimulatory kinds of IGF-1 binding proteins (IGFBPs) results in IGF-1 bioactivity, the ability of IGF-1 to induce phosphorylation of its receptor and consequently its signaling. Moreover, IGF-1 bioactivity is sufficient to reflect any change in the GH-IGF-1 system. Accumulating evidence suggests that both of high protein diet, characterized by increased glucagon secretion, and insulin-induced hypoglycemia increase mortality rate and the mechanisms are unclear. However both of glucagon and insulin-induced hypoglycemia are potent stimuli of GH secretion. The aim of the current study was to identify the impact of glucagon and insulin-induced hypoglycemia on IGF-1 bioactivity as possible mechanisms. In a double-blind placebo-controlled study, glucagon was intramuscularly administrated in 13 type 1 diabetic patients (6 males /7 females; [BMI]: 24.8 ± 0.95 kg/m2), 11 obese subjects (OP; 5/ 6; 34.4 ± 1.7 kg/m2), and 13 healthy lean participants (LP; 6/ 7; 21.7 ± 0.6 kg/m2), whereas 12 obese subjects (OP; 6/ 6; 34.4 ± 1.7 kg/m2), and 13 healthy lean participants (LP; 6/ 7; 21.7 ± 0.6 kg/m2) performed insulin tolerance test in another double-blind placebo-controlled study and changes in GH, total IGF-1, IGF binding proteins (IGFBPs) and IGF-1 bioactivity, measured by the cell-based KIRA method, were investigated. In addition, the interaction between the metabolic hormones (glucagon and insulin) and the GH-IGF-1 system on the transcriptional level was studied using mouse primary hepatocytes. In this thesis, glucagon decreased IGF-1 bioactivity in humans independently of endogenous insulin levels, most likely through modulation of IGFBP-1 and-2 levels. The glucagon-induced reduction in IGF-1 bioactivity may represent a novel mechanism underlying the impact of glucagon on GH secretion and may explain the negative effect of high protein diet related to increased cardiovascular risk and mortality rate. In addition, insulin-induced hypoglycemia was correlated with a decrease in IGF-1 bioactivity through up-regulation of IGFBP-2. These results may refer to a possible and poorly explored mechanism explaining the strong association between hypoglycemia and increased cardiovascular mortality among diabetic patients.
Regulation of potassium channels in plants : biophysical mechanisms and physiological implacations
(2011)
The hepatokine FGF21 and the adipokine chemerin have been implicated as metabolic regulators and mediators of inter-tissue crosstalk. While FGF21 is associated with beneficial metabolic effects and is currently being tested as an emerging therapeutic for obesity and diabetes, chemerin is linked to inflammation-mediated insulin resistance. However, dietary regulation of both organokines and their role in tissue interaction needs further investigation.
The LEMBAS nutritional intervention study investigated the effects of two diets differing in their protein content in obese human subjects with non-alcoholic fatty liver disease (NAFLD). The study participants consumed hypocaloric diets containing either low (LP: 10 EN%, n = 10) or high (HP: 30 EN%, n = 9) dietary protein 3 weeks prior to bariatric surgery. Before and after the intervention the participants were anthropometrically assessed, blood samples were drawn, and hepatic fat content was determined by MRS. During bariatric surgery, paired subcutaneous and visceral adipose tissue biopsies as well as liver biopsies were collected. The aim of this thesis was to investigate circulating levels and tissue-specific regulation of (1) FGF21 and (2) chemerin in the LEMBAS cohort. The results were compared to data obtained in 92 metabolically healthy subjects with normal glucose tolerance and normal liver fat content.
(1) Serum FGF21 concentrations were elevated in the obese subjects, and strongly associated with intrahepatic lipids (IHL). In accordance, FGF21 serum concentrations increased with severity of NAFLD as determined histologically in the liver biopsies. Though both diets were successful in reducing IHL, the effect was more pronounced in the HP group. FGF21 serum concentrations and mRNA expression were bi-directionally regulated by dietary protein, independent from metabolic improvements. In accordance, in the healthy study subjects, serum FGF21 concentrations dropped by more than 60% in response to the HP diet. A short-term HP intervention confirmed the acute downregulation of FGF21 within 24 hours. Lastly, experiments in HepG2 cell cultures and primary murine hepatocytes identified nitrogen metabolites (NH4Cl and glutamine) to dose-dependently suppress FGF21 expression.
(2) Circulating chemerin concentrations were considerably elevated in the obese versus lean study participants and differently associated with markers of obesity and NAFLD in the two cohorts. The adipokine decreased in response to the hypocaloric interventions while an unhealthy high-fat diet induced a rise in chemerin serum levels. In the lean subjects, mRNA expression of RARRES2, encoding chemerin, was strongly and positively correlated with expression of several cytokines, including MCP1, TNFα, and IL6, as well as markers of macrophage infiltration in the subcutaneous fat depot. However, RARRES2 was not associated with any cytokine assessed in the obese subjects and the data indicated an involvement of chemerin not only in the onset but also resolution of inflammation. Analyses of the tissue biopsies and experiments in human primary adipocytes point towards a role of chemerin in adipogenesis while discrepancies between the in vivo and in vitro data were detected.
Taken together, the results of this thesis demonstrate that circulating FGF21 and chemerin levels are considerably elevated in obesity and responsive to dietary interventions. FGF21 was acutely and bi-directionally regulated by dietary protein in a hepatocyte-autonomous manner. Given that both, a lack in essential amino acids and excessive nitrogen intake, exert metabolic stress, FGF21 may serve as an endocrine signal for dietary protein balance. Lastly, the data revealed that chemerin is derailed in obesity and associated with obesity-related inflammation. However, future studies on chemerin should consider functional and regulatory differences between secreted and tissue-specific isoforms.
Frailty and sarcopenia share some underlying characteristics like loss of muscle mass, low muscle strength, and low physical performance. Imaging parameters and functional examinations mainly assess frailty and sarcopenia criteria; however, these measures can have limitations in clinical settings. Therefore, finding suitable biomarkers that reflect a catabolic muscle state e.g. an elevated muscle protein turnover as suggested in frailty, are becoming more relevant concerning frailty diagnosis and risk assessment.
3-Methylhistidine (3-MH) and its ratios 3-MH-to-creatinine (3-MH/Crea) and 3 MH-to-estimated glomerular filtration rate (3-MH/eGFR) are under discussion as possible biomarkers for muscle protein turnover and might support the diagnosis of frailty. However, there is some skepticism about the reliability of 3-MH measures since confounders such as meat and fish intake might influence 3-MH plasma concentrations. Therefore, the influence of dietary habits and an intervention with white meat on plasma 3-MH was determined in young and healthy individuals. In another study, the cross-sectional associations of plasma 3-MH, 3-MH/Crea and 3-MH/eGFR with the frailty status (robust, pre-frail and frail) were investigated.
Oxidative stress (OS) is a possible contributor to frailty development, and high OS levels as well as low micronutrient levels are associated with the frailty syndrome. However, data on simultaneous measures of OS biomarkers together with micronutrients are lacking in studies including frail, pre-frail and robust individuals. Therefore, cross-sectional associations of protein carbonyls (PrCarb), 3-nitrotyrosine (3-NT) and several micronutrients with the frailty status were determined.
A validated UPLC-MS/MS (ultra-performance liquid chromatography tandem mass spectrometry) method for the simultaneous quantification of 3-MH and 1-MH (1 methylhistidine, as marker for meat and fish consumption) was presented and used for further analyses. Omnivores showed higher plasma 3-MH and 1-MH concentrations than vegetarians and a white meat intervention resulted in an increase in plasma 3-MH, 3 MH/Crea, 1-MH and 1-MH/Crea in omnivores. Elevated 3-MH and 3-MH/Crea levels declined significantly within 24 hours after this white meat intervention. Thus, 3-MH and 3-MH/Crea might be used as biomarker for muscle protein turnover when subjects did not consume meat 24 hours prior to blood samplings.
Plasma 3-MH, 3-MH/Crea and 3-MH/eGFR were higher in frail individuals than in robust individuals. Additionally, these biomarkers were positively associated with frailty in linear regression models, and higher odds to be frail were found for every increase in 3 MH and 3-MH/eGFR quintile in multivariable logistic regression models adjusted for several confounders. This was the first study using 3-MH/eGFR and it is concluded that plasma 3-MH, 3-MH/Crea and 3-MH/eGFR might be used to identify frail individuals or individuals at higher risk to be frail, and that there might be threshold concentrations or ratios to support these diagnoses.
Higher vitamin D3, lutein/zeaxanthin, γ-tocopherol, α-carotene, β-carotene, lycopene and β-cryptoxanthin concentrations and additionally lower PrCarb concentrations were found in robust compared to frail individuals in multivariate linear models. Frail subjects had higher odds to be in the lowest than in the highest tertile for vitamin D3 α-tocopherol, α-carotene, β-carotene, lycopene, lutein/zeaxanthin, and β cryptoxanthin, and had higher odds to be in the highest than in the lowest tertile for PrCarb than robust individuals in multivariate logistic regression models. Thus, a low micronutrient together with a high PrCarb status is associated with pre-frailty and frailty.
We live in an aging society. The change in demographic structures poses a number of challenges, including an increase in age-associated diseases. Delirium, dementia, and depression are considered to be of particular interest in the field of aging and mental health. A common theory regarding healthy aging and mental health is that the highest satisfaction and best performance is achieved when a person's abilities match the demands of their environment. In this context, the person's environment includes both the physical and the social environment. Based on this assumption, this dissertation focuses on the investigation of non-pharmacological interventions that modify environmental factors in order to facilitate the prevention and treatment of mental disorders in older patients and their caregivers. The first part of this dissertation consists of two publications and deals with the prevention of postoperative delirium in elderly patients. The PAWEL study investigated the use of a multimodal, non-pharmacological intervention in the routine care of patients aged 70 years or older undergoing elective surgery. The intervention included an interdepartmental delirium prevention team, daily use of seven manualized “best practice” procedures, structured staff training on delirium, and the adaptation of the hospital environment to the patients’ needs. The second part of the dissertation used a meta-analysis to investigate whether technology-based interventions are a suitable form of support for informal caregivers of people with dementia. Subgroup analyses were conducted to examine the effect of different types of technology on caregiver burden and depressive symptoms. The following main results were found: The PAWEL study showed that the use of a multimodal, non-pharmacological intervention resulted in a significantly lower incidence rate of postoperative delirium and reduced days with delirium in the intervention group compared to the control group. However, this difference could not be observed in the group of patients undergoing elective cardiac surgery. The results of the meta-analysis showed that technology-based interventions offer a promising alternative to traditional “face-to-face” services. Significant effect sizes could be found in relation to both the burden and the depressive symptoms of caregiving relatives. These results provide further important information on the significant impact of non-pharmacological interventions that modify environmental factors on mental health, and support the consideration of such interventions in the prevention and treatment of mental disorders in both older patients and their caregivers.
Natural extreme events are an integral part of nature on planet earth. Usually these events are only considered hazardous to humans, in case they are exposed. In this case, however, natural hazards can have devastating impacts on human societies. Especially hydro-meteorological hazards have a high damage potential in form of e.g. riverine and pluvial floods, winter storms, hurricanes and tornadoes, which can occur all over the globe. Along with an increasingly warm climate also an increase in extreme weather which potentially triggers natural hazards can be expected. Yet, not only changing natural systems, but also changing societal systems contribute to an increasing risk associated with these hazards. These can comprise increasing exposure and possibly also increasing vulnerability to the impacts of natural events. Thus, appropriate risk management is required to adapt all parts of society to existing and upcoming risks at various spatial scales. One essential part of risk management is the risk assessment including the estimation of the economic impacts. However, reliable methods for the estimation of economic impacts due to hydro-meteorological hazards are still missing. Therefore, this thesis deals with the question of how the reliability of hazard damage estimates can be improved, represented and propagated across all spatial scales. This question is investigated using the specific example of economic impacts to companies as a result of riverine floods in Germany.
Flood damage models aim to describe the damage processes during a given flood event. In other words they describe the vulnerability of a specific object to a flood. The models can be based on empirical data sets collected after flood events. In this thesis tree-based models trained with survey data are used for the estimation of direct economic flood impacts on the objects. It is found that these machine learning models, in conjunction with increasing sizes of data sets used to derive the models, outperform state-of-the-art damage models. However, despite the performance improvements induced by using multiple variables and more data points, large prediction errors remain at the object level. The occurrence of the high errors was explained by a further investigation using distributions derived from tree-based models. The investigation showed that direct economic impacts to individual objects cannot be modeled by a normal distribution. Yet, most state-of-the-art approaches assume a normal distribution and take mean values as point estimators. Subsequently, the predictions are unlikely values within the distributions resulting in high errors. At larger spatial scales more objects are considered for the damage estimation. This leads to a better fit of the damage estimates to a normal distribution. Consequently, also the performance of the point estimators get better, although large errors can still occur due to the variance of the normal distribution. It is recommended to use distributions instead of point estimates in order to represent the reliability of damage estimates.
In addition current approaches also mostly ignore the uncertainty associated with the characteristics of the hazard and the exposed objects. For a given flood event e.g. the estimation of the water level at a certain building is prone to uncertainties. Current approaches define exposed objects mostly by the use of land use data sets. These data sets often show inconsistencies, which introduce additional uncertainties. Furthermore, state-of-the-art approaches also imply problems of missing consistency when predicting the damage at different spatial scales. This is due to the use of different types of exposure data sets for model derivation and application. In order to face these issues a novel object-based method was developed in this thesis. The method enables a seamless estimation of hydro-meteorological hazard damage across spatial scales including uncertainty quantification. The application and validation of the method resulted in plausible estimations at all spatial scales without overestimating the uncertainty.
Mainly newly available data sets containing individual buildings make the application of the method possible as they allow for the identification of flood affected objects by overlaying the data sets with water masks. However, the identification of affected objects with two different water masks revealed huge differences in the number of identified objects. Thus, more effort is needed for their identification, since the number of objects affected determines the order of magnitude of the economic flood impacts to a large extent.
In general the method represents the uncertainties associated with the three components of risk namely hazard, exposure and vulnerability, in form of probability distributions. The object-based approach enables a consistent propagation of these uncertainties in space. Aside from the propagation of damage estimates and their uncertainties across spatial scales, a propagation between models estimating direct and indirect economic impacts was demonstrated. This enables the inclusion of uncertainties associated with the direct economic impacts within the estimation of the indirect economic impacts. Consequently, the modeling procedure facilitates the representation of the reliability of estimated total economic impacts. The representation of the estimates' reliability prevents reasoning based on a false certainty, which might be attributed to point estimates. Therefore, the developed approach facilitates a meaningful flood risk management and adaptation planning.
The successful post-event application and the representation of the uncertainties qualifies the method also for the use for future risk assessments. Thus, the developed method enables the representation of the assumptions made for the future risk assessments, which is crucial information for future risk management. This is an important step forward, since the representation of reliability associated with all components of risk is currently lacking in all state-of-the-art methods assessing future risk.
In conclusion, the use of object-based methods giving results in the form of distributions instead of point estimations is recommended. The improvement of the model performance by the means of multi-variable models and additional data points is possible, but small. Uncertainties associated with all components of damage estimation should be included and represented within the results. Furthermore, the findings of the thesis suggest that, at larger scales, the influence of the uncertainty associated with the vulnerability is smaller than those associated with the hazard and exposure. This leads to the conclusion that for an increased reliability of flood damage estimations and risk assessments, the improvement and active inclusion of hazard and exposure, including their uncertainties, is needed in addition to the improvements of the models describing the vulnerability of the objects.
Remembering the dismembered
(2020)
This thesis – written in co-authorship with Tanzanian activist Mnyaka Sururu Mboro – examines different cases of repatriation of ancestral remains to African countries and communities through the prism of postcolonial memory studies. It follows the theft and displacement of prominent ancestors from East and Southern Africa (Sarah Baartman, Dawid Stuurman, Mtwa Mkwawa, Songea Mbano, King Hintsa and the victims of the Ovaherero and Nama genocides) and argues that efforts made for the repatriation of their remains have contributed to a transnational remembrance of colonial violence.
Drawing from cultural studies theories such as "multidirectional memory", "rehumanisation" and "necropolitics", the thesis argues for a new conceptualisation or "re-membrance" in repatriation, through processes of reunion, empowerment, story-telling and belonging. Besides, the afterlives of the dead ancestors, who stand at the centre of political debates on justice and reparations, remind of their past struggles against colonial oppression. They are therefore "memento vita", fostering counter-discourses that recognize them
as people and stories.
This manuscript is accompanied by a “(web)site of memory” where some of the research findings are made available to a wider audience. This blog also hosts important sound material which appears in the thesis as interventions by external contributors. Through QR codes, both the written and the digital version are linked with each other to problematize the idea of a written monograph and bring a polyphonic perspective to those diverse, yet connected, histories.
Geomorphology seeks to characterize the forms, rates, and magnitudes of sediment and water transport that sculpt landscapes. This is generally referred to as earth surface processes, which incorporates the influence of biologic (e.g., vegetation), climatic (e.g., rainfall), and tectonic (e.g., mountain uplift) factors in dictating the transport of water and eroded material. In mountains, high relief and steep slopes combine with strong gradients in rainfall and vegetation to create dynamic expressions of earth surface processes. This same rugged topography presents challenges in data collection and process measurement, where traditional techniques involving detailed observations or physical sampling are difficult to apply at the scale of entire catchments. Herein lies the utility of remote sensing. Remote sensing is defined as any measurement that does not disturb the natural environment, typically via acquisition of images in the visible- to radio-wavelength range of the electromagnetic spectrum. Remote sensing is an especially attractive option for measuring earth surface processes, because large areal measurements can be acquired at much lower cost and effort than traditional methods. These measurements cover not only topographic form, but also climatic and environmental metrics, which are all intertwined in the study of earth surface processes. This dissertation uses remote sensing data ranging from handheld camera-based photo surveying to spaceborne satellite observations to measure the expressions, rates, and magnitudes of earth surface processes in high-mountain catchments of the Eastern Central Andes in Northwest Argentina. This work probes the limits and caveats of remote sensing data and techniques applied to geomorphic research questions, and presents important progress at this disciplinary intersection.
The Arctic nearshore zone plays a key role in the carbon cycle. Organic-rich sediments get eroded off permafrost affected coastlines and can be directly transferred to the nearshore zone. Permafrost in the Arctic stores a high amount of organic matter and is vulnerable to thermo-erosion, which is expected to increase due to climate change. This will likely result in higher sediment loads in nearshore waters and has the potential to alter local ecosystems by limiting light transmission into the water column, thus limiting primary production to the top-most part of it, and increasing nutrient export from coastal erosion. Greater organic matter input could result in the release of greenhouse gases to the atmosphere. Climate change also acts upon the fluvial system, leading to greater discharge to the nearshore zone. It leads to decreasing sea-ice cover as well, which will both increase wave energy and lengthen the open-water season. Yet, knowledge on these processes and the resulting impact on the nearshore zone is scarce, because access to and instrument deployment in the nearshore zone is challenging.
Remote sensing can alleviate these issues in providing rapid data delivery in otherwise non-accessible areas. However, the waters in the Arctic nearshore zone are optically complex, with multiple influencing factors, such as organic rich suspended sediments, colored dissolved organic matter (cDOM), and phytoplankton. The goal of this dissertation was to use remotely sensed imagery to monitor processes related to turbidity caused by suspended sediments in the Arctic nearshore zone. In-situ measurements of water-leaving reflectance and surface water turbidity were used to calibrate a semi-empirical algorithm which relates turbidity from satellite imagery. Based on this algorithm and ancillary ocean and climate variables, the mechanisms underpinning nearshore turbidity in the Arctic were identified at a resolution not achieved before.
The calibration of the Arctic Nearshore Turbidity Algorithm (ANTA) was based on in-situ measurements from the coastal and inner-shelf waters around Herschel Island Qikiqtaruk (HIQ) in the western Canadian Arctic from the summer seasons 2018 and 2019. It performed better than existing algorithms, developed for global applications, in relating turbidity from remotely sensed imagery. These existing algorithms were lacking validation data from permafrost affected waters, and were thus not able to reflect the complexity of Arctic nearshore waters. The ANTA has a higher sensitivity towards the lowest turbidity values, which is an asset for identifying sediment pathways in the nearshore zone. Its transferability to areas beyond HIQ was successfully demonstrated using turbidity measurements matching satellite image recordings from Adventfjorden, Svalbard. The ANTA is a powerful tool that provides robust turbidity estimations in a variety of Arctic nearshore environments.
Drivers of nearshore turbidity in the Arctic were analyzed by combining ANTA results from the summer season 2019 from HIQ with ocean and climate variables obtained from the weather station at HIQ, the ERA5 reanalysis database, and the Mackenzie River discharge. ERA5 reanalysis data were obtained as domain averages over the Canadian Beaufort Shelf. Nearshore turbidity was linearly correlated to wind speed, significant wave height and wave period. Interestingly, nearshore turbidity was only correlated to wind speed at the shelf, but not to the in-situ measurements from the weather station at HIQ. This shows that nearshore turbidity, albeit being of limited spatial extent, gets influenced by the weather conditions multiple kilometers away, rather than in its direct vicinity. The large influence of wave energy on nearshore turbidity indicates that freshly eroded material off the coast is a major contributor to the nearshore sediment load. This contrasts results from the temperate and tropical oceans, where tides and currents are the major drivers of nearshore turbidity. The Mackenzie River discharge was not identified as a driver of nearshore turbidity in 2019, however, the analysis of 30 years of Landsat archive imagery from 1986 to 2016 suggests a direct link between the prevailing wind direction, which heavily influences the Mackenzie River plume extent, and nearshore turbidity around HIQ. This discrepancy could be caused by the abnormal discharge behavior of the Mackenzie River in 2019.
This dissertation has substantially advanced the understanding of suspended sediment processes in the Arctic nearshore zone and provided new monitoring tools for future studies. The presented results will help to understand the role of the Arctic nearshore zone in the carbon cycle under a changing climate.
Following the principles of green chemistry, a simple and efficient synthesis of functionalised imidazolium zwitterionic compounds from renewable resources was developed based on a modified one-pot Debus-Radziszewski reaction. The combination of different carbohydrate-derived 1,2-dicarbonyl compounds and amino acids is a simple way to modulate the properties and introduce different functionalities. A representative compound was assessed as an acid catalyst, and converted into acidic ionic liquids by reaction with several strong acids. The reactivity of the double carboxylic functionality was explored by esterification with long and short chain alcohols, as well as functionalised amines, which led to the straightforward formation of surfactant-like molecules or bifunctional esters and amides. One of these di-esters is currently being investigated for the synthesis of poly(ionic liquids). The functionalisation of cellulose with one of the bifunctional esters was investigated and preliminary tests employing it for the functionalisation of filter papers were carried out successfully. The imidazolium zwitterions were converted into ionic liquids via hydrothermal decarboxylation in flow, a benign and scalable technique. This method provides access to imidazolium ionic liquids via a simple and sustainable methodology, whilst completely avoiding contamination with halide salts. Different ionic liquids can be generated depending on the functionality contained in the ImZw precursor. Two alanine-derived ionic liquids were assessed for their physicochemical properties and applications as solvents for the dissolution of cellulose and the Heck coupling.
Knowledge graphs are structured repositories of knowledge that store facts
about the general world or a particular domain in terms of entities and
their relationships. Owing to the heterogeneity of use cases that are served
by them, there arises a need for the automated construction of domain-
specific knowledge graphs from texts. While there have been many research
efforts towards open information extraction for automated knowledge graph
construction, these techniques do not perform well in domain-specific settings.
Furthermore, regardless of whether they are constructed automatically from
specific texts or based on real-world facts that are constantly evolving, all
knowledge graphs inherently suffer from incompleteness as well as errors in
the information they hold.
This thesis investigates the challenges encountered during knowledge graph
construction and proposes techniques for their curation (a.k.a. refinement)
including the correction of semantic ambiguities and the completion of missing
facts. Firstly, we leverage existing approaches for the automatic construction
of a knowledge graph in the art domain with open information extraction
techniques and analyse their limitations. In particular, we focus on the
challenging task of named entity recognition for artwork titles and show
empirical evidence of performance improvement with our proposed solution
for the generation of annotated training data.
Towards the curation of existing knowledge graphs, we identify the issue of
polysemous relations that represent different semantics based on the context.
Having concrete semantics for relations is important for downstream appli-
cations (e.g. question answering) that are supported by knowledge graphs.
Therefore, we define the novel task of finding fine-grained relation semantics
in knowledge graphs and propose FineGReS, a data-driven technique that
discovers potential sub-relations with fine-grained meaning from existing pol-
ysemous relations. We leverage knowledge representation learning methods
that generate low-dimensional vectors (or embeddings) for knowledge graphs
to capture their semantics and structure. The efficacy and utility of the
proposed technique are demonstrated by comparing it with several baselines
on the entity classification use case.
Further, we explore the semantic representations in knowledge graph embed-
ding models. In the past decade, these models have shown state-of-the-art
results for the task of link prediction in the context of knowledge graph comple-
tion. In view of the popularity and widespread application of the embedding
techniques not only for link prediction but also for different semantic tasks,
this thesis presents a critical analysis of the embeddings by quantitatively
measuring their semantic capabilities. We investigate and discuss the reasons
for the shortcomings of embeddings in terms of the characteristics of the
underlying knowledge graph datasets and the training techniques used by
popular models.
Following up on this, we propose ReasonKGE, a novel method for generating
semantically enriched knowledge graph embeddings by taking into account the
semantics of the facts that are encapsulated by an ontology accompanying the
knowledge graph. With a targeted, reasoning-based method for generating
negative samples during the training of the models, ReasonKGE is able to
not only enhance the link prediction performance, but also reduce the number
of semantically inconsistent predictions made by the resultant embeddings,
thus improving the quality of knowledge graphs.
Weakly electric mormyrid fish comprise about 200 species. 15 species of the genus Campylomormyrus have been described. These are very diverse concerning the trunk-like snout and the shape and duration of the electric organ discharge (EOD) and the anatomy of the electric organ. In this dissertation data on the reproduction in captivity of four species and on the ontogeny of the EOD and the EO of three species are presented.
Reproduction of the four species C. compressirostris, C. rhynchophorus, C. tshokwe and C. numenius: Cyclical reproduction was provoked by changing only water conductivity (C): decreasing C led to gonadal recrudescence, an increase induced gonad regression. Data on the reproduction and development of three species are presented (in C. numenius gonad development could only be achieved in males). Agonistic behavior in the C. tshokwe pair forced us to divide the breeding tank; therefore, only ovipositions occurred. However, injection of an artificial GnRH hormone allowed us to obtain ripe eggs and sperm and to perform successful artificial reproduction. All three species (C. compressirostris, C. rhynchophorus, C. tshokwe) are indeterminate fractional spawners. Spawnings/ovipositions occurred during the second half of the night; no parental care was observed; no special spawning substrates were necessary. C. compressirostris successfully spawned in breeding groups, C. rhynchophorus as pair. Spawning intervals ranged from 6 to 66 days in C. rhynchophorus, 10–75 days in C. tshokwe, and 18 days in C. compressirostris (calculated values). Fecundities (eggs per fractional spawning) ranged from 70 to 1570 eggs in C. rhynchophorus, 100–1192 in C. tshokwe, and 38–246 in C. compressirostris. All three species produce yolky, slightly sticky eggs. Egg diameter ranges from 2.3–3.0 mm. Hatching occurred on day 3, feeding started on day 11. Transition from larval to juvenile stage occurred at around 20 mm total length (TL). At this size C. rhynchophorus developed a higher body than the two other species and differences between the species in the melanin pigmentation of the unpaired fins occurred. Between 32 and 35 mm TL the upper and lower jaws developed.
C. compressirostris and C. tamandua are similar in morphology and both produce short EODs of ca. 150-200 μs duration. Both species reproduce easily in captivity. We tried to obtain natural hybrids in two breeding groups, 1) four males of C. compressirostris and three females of C. tamandua and 2) six females of C. compressirostris and four males of C. tamandua. In both combinations several times oviposition occurred, however, we never found fertilized eggs. In subsequent experiments, not described here, we obtained hybrids between these two species by means of artificial reproduction.
Ontogeny of the EOD and the EO: The Campylomormyrus species are very diverse both concerning the shape and the duration of their EODs. There are species with very short EODs, e.g. C. compressirostris duration, a species with an EOD length of about 4-8 ms duration (C. tshokwe) and species with very long EODs of about 25 ms duration (e.g. C. rhynchophorus). Due to the successful breeding of the three species in captivity, we were able to investigate in detail the ontogeny of the EOD. Larvae of the three species C. compressirostris, C. tshokwe and C. rhynchophorus first produce a biphasic larval EOD typical for these small larvae. The first activity of the adult electric organ in the caudal peduncle is a biphasic juvenile EOD. Juvenile C. compressirostris and C. tshokwe start out with a short biphasic EOD of about 160 – 200 μs duration at sizes between 25 mm (C. compressirostris) and 37 mm (C. tshokwe). Adult C. compressirostris show an EOD identical to that of the juvenile. In C. tshokwe, the juvenile EOD changes continuously during development both concerning duration, amplitude increase and shape. 18 cm long C. tshokwe still do not yet produce an EOD typical for the adult fish. Juveniles of C. rhynchophorus produce at 33 mm total length a juvenile biphasic EOD, however, of longer duration (about 640 μs) than the two species mentioned above. This juvenile EOD changes continuously both in form, amplitude increase and duration with growth until the adult EOD waveform appears at about 15 cm body length. In juveniles about seven cm long the triphasic feature of the EOD starts to develop due to the appearance of a second head positive phase. Specific EOD stages are produced in relation to size and not to age. Individual differences in the EOD both concerning shape and duration are very small. The basic anatomy of the electrocytes is very similar in all three species: the main stalk which receives the innervation, is located at the caudal face of the electrocyte. Membrane penetrations of the stalks do not occur. However, there are differences in the fine structure of the electrocytes in the three species. Papillae, proliferations of the membrane, which increase the surface area of the electrocyte and are thought to incrase the EOD-duration, are only found in C. tshokwe and C. rhynchophorus. In these two species in addition, holes develop in the electrocytes during ontogeny. This might also have an impact on EOD duration.
Soft actuators have drawn significant attention due to their relevance for applications, such as artificial muscles in devices developed for medicine and robotics. Tuning their performance and expanding their functionality are frequently done by means of chemical modification. The introduction of structural elements rendering non-synthetic modification of the performance possible, as well as control over physical appearance and facilitating their recycling is a subject of a great interest in the field of smart materials. The primary aim of this thesis was to create a shape-memory polymeric actuator, where the capability for non-synthetic tuning of the actuation performance is combined with reprocessability. Physically cross-linked polymeric matrices provide a solid material platform, where the in situ processing methods can be employed for modification of the composition and morphology, resulting in the fine tuning of the related mechanical properties and shape-memory actuation capability.
The morphological features, required for shape-memory polymeric actuators, namely two crystallisable domains and anchoring points for physical cross-links, were embedded into a multiblock copolymer with poly(ε-caprolactone) and poly(L-lactide) segments (PLLA-PCL). Here, the melting transition of PCL was bisected into the actuating and skeleton-forming units, while the cross-linking was introduced via PLA stereocomplexation in blends with oligomeric poly(D-lactide) (ODLA). PLLA segment number average length of 12-15 repeating units was experimentally defined to be capable of the PLA stereocomplexes formation, but not sufficient for the isotactic crystallisation. Multiblock structure and phase dilution broaden the PCL melting transition, facilitating its separation into two conditionally independent crystalline domains. Low molar mass of the PLA stereocomplex components and a multiblock structure enables processing and reprocessing of the PLLA-PCL / ODLA blends with common non-destructive techniques. The modularity of the PLLA-PCL structure and synthetic approach allows for independent tuning of the properties of its components. The designed material establishes a solid platform for non-synthetic tuning of thermomechanical and structural properties of thermoplastic elastomers.
To evaluate the thermomechanical stability of the formed physical network, three criteria were appraised. As physical cross-links, PLA stereocomplexes have to be evenly distributed within the material matrix, their melting temperature shall not overlap with the thermal transitions of the PCL domains and they have to maintain the structural integrity within the strain ε ranges further applied in the shape-memory actuation experiments. Assigning PCL the function of the skeleton-forming and actuating units, and PLA stereocomplexes the role of physical netpoints, shape-memory actuation was realised in the PLLA-PCL / ODLA blends. Reversible strain of shape-memory actuation was found to be a function of PLA stereocomplex crystallinity, i.e. physical cross-linking density, with a maximum of 13.4 ± 1.5% at PLA stereocomplex content of 3.1 ± 0.3 wt%. In this way, shape-memory actuation can be tuned via adjusting the composition of the PLLA-PCL / ODLA blend. This makes the developed material a valuable asset in the production of cost-effective tunable soft polymeric actuators for the applications in medicine and soft robotics.
Polymeric materials, which can perform reversible shape changes after programming, in response to a thermal or electrical stimulation, can serve as (soft) actuating components in devices like artificial muscles, photonics, robotics or sensors. Such polymeric actuators can be realized with hydrogels, liquid crystalline elastomers, electro-active polymers or shape-memory polymers by controlling with stumuli such as heat, light, electrostatic or magnetic field. If the application conditions do not allow the direct heating or electric stimulation of these smart devices, noncontact triggering will be required. Remotely controlled actuation have been reported for liquid crystalline elastomer composites or shape-memory polymer network composites, when a persistent external stress is applied during inductive heating in an alternating magnetic field. However such composites cannot meet the demands of applications requiring remotely controlled free-standing motions of the actuating components.
The current thesis investigates, whether a reprogrammable remotely controlled soft actuator can be realized by magneto-sensitive multiphase shape-memory copolymer network composites containing magnetite nanoparticles as magneto-sensitive multivalent netpoints. A central hypothesis was that a magnetically controlled two-way (reversible bidirectional) shape-memory effect in such nanocomposites can be achieved without application of external stress (freestanding), when the required orientation of the crystallizable actuation domains (ADs) can be ensured by an internal skeleton like structure formed by a second crystallizable phase determing the samples´s geometry, while magneto-sensitive iron oxide nanoparticles covalently integrated in the ADs allow remote temperature control. The polymer matrix of these composites should exhibit a phase-segregated morphology mainly composed of cyrstallizable ADs, whereby a second set of higher melting crystallites can take a skeleton like, geometry determining function (geometry determining domains, GDs) after programming of the composite and in this way the orientation of the ADs is established and maintained during actuation. The working principle for the reversible bidirectional movements in the multiphase shape-memory polymer network composite is related to a melting-induced contraction (MIC) during inductive heating and the crystallization induced elongation (CIE) of the oriented ADs during cooling. Finally, the amount of multivalent magnetosensitive netpoints in such a material should be as low as possible to ensure an adequate overall elasticity of the nanocomposite and at the same time a complete melting of both ADs and GDs via inductive heating, which is mandatory for enabling reprogrammability.
At first, surface decorated iron oxide nanoparticles were synthesized and investigated. The coprecipitation method was applied to synthesize magnetic nanoparticles (mNPs) based on magnetite with size of 12±3 nm and in a next step a ring-opening polymerization (ROP) was utilized for covalent surface modification of such mNPs with oligo(ϵ-caprolactone) (OCL) or oligo(ω-pentadecalactone) (OPDL) via the “grafting from” approach. A successful coating of mNPs with OCL and OPDL was confirmed by differential scanning calorimetry (DSC) experiments showing melting peaks at 52±1 °C for mNP-OCL and 89±1 °C for mNP-OPDL. It was further explored whether two-layered surface decorated mNPs, can be prepared via a second surface-initiated ROP of mNP-OCL or mNP-OPDL with ω-pentadecalactone or ϵ-caprolactone. The observation of two distinct melting transitions in DSC experiments as well as the increase in molecular weight of the detached coatings determined by GPC and 1H-NMR indicated a successful synthesis of the twolayered nanoparticles mNP-OCL-OPDL and mNP-OPDL-OCL. In contrast TEM micrographs revealed a reduction of the thickness of the polymeric coating on the nanoparticles after the second ROP, indicating that the applied synthesis and purification required further optimization.
For evaluating the impact of the dispersion of mNPs within a polymer matrix on the resulting inductive heating capability of composites, plain mNPs as well as OCL coated magnetite nanoparticles (mNP-OCLs) were physically incorporated into crosslinked poly(ε-caprolactone) (PCL) networks. Inductive heating experiments were performed with both networks cPCL/mNP and cPCL/mNP-OCL in an alternating magnetic field (AMF) with a magnetic field strength of H = 30 kA·m-1. Here a bulk temperature of Tbulk = 74±2 °C was achieved for cPCL/mNP-OCL, which was almost 20 °C higher than the melting transition of the PCL-based polymer matrix. In contrast, the composite with plain mNPs could only reach a Tbulk of 48±2 °C, which is not sufficient for a complete melting of all PCL crystallites as required for actuation.
The inductive heating capability of a multiphase copolymer nanocomposite network (designed as soft actuators) containing surface decorated mNPs as covalent netpoints was investigated. Such composite was synthesized from star-shaped OCL and OPDL precursors, as well as mNP-OCLs via reaction with HDI. The weight ratio of OPDL and OCL in the starting reaction mixture was 15/85 (wt%/wt%) and the amount of iron oxide in the nanocomposite was 4 wt%. DSC experiments revealed two well separated melting and crystallization peaks confirming the required phase-segregated morphology in the nanocomposite NC-mNP-OCL. TEM images could illustrate a phase-segregated morphology of the polymer matrix on the microlevel with droplet shaped regions attributed to the OPDL domains dispersed in an OCL matrix. The TEM images could further demonstrate that the nanoparticulate netpoints in NC-mNP-OCL were almost homogeneously dispersed within the OCL domains. The tests of the inductive heating capability of the nanocomposites at a magnetic field strength of Hhigh = 11.2 kA·m-1 revealed a achievable plateau surface temperature of Tsurf = 57±1 °C for NC-mNP-OCL recorded by an infrared video camera. An effective heat generation constant (̅P) can be derived from a multi-scale model for the heat generation, which is proportional to the rate of heat generation per unit volume of the sample. NC-mNP-OCL with homogeneously dispersed mNP-OCLs exhibited a ̅P value of 1.04±0.01 K·s- 1 at Hhigh, while at Hreset = 30.0 kA·m-1 a Tsurf of 88±1 °C (where all OPDL related crystallite are molten) and a ̅P value of 1.93±0.02 K·s-1 was obtained indicating a high magnetic heating capability of the composite.
The free-standing magnetically-controlled reversible shape-memory effect (mrSME) was explored with originally straight nanocomposite samples programmed by bending to an angle of 180°. By switching the magnetic field on and off the composite sample was allowed to repetitively heat to 60 °C and cool to the ambient temperature. A pronounced mrSME, characterized by changes in bending angle of Δϐrev = 20±3° could be obtained for a composite sample programmed by bending when a magnetic field strength of Hhigh = 11.2 kA·m-1 was applied in a multi-cyclic magnetic bending experiment with 600 heating-cooling cycles it could be shown that the actuation performance did not change with increasing number of test cycles, demonstrating the accuracy and reproducibility of this soft actuator. The degree of actuation as well as the kinetics of the shape changes during heating could be tuned by variation of the magnetic filed strength between Hlow and Hhigh or the magnetic field exposure time. When Hreset = 30.0 kA·m-1 was applied the programmed geometry was erased and the composite sample returned to it´s originally straight shape. The reprogrammability of the nanocomposite actuators was demonstrated by one and the same test specimen first exhibiting reversible angle changes when programmed by bending, secondly reprogrammed to a concertina, which expands upon inductive heating and contracts during cooling and finally reprogrammed to a clip like shape, which closes during cooling and opens when Hhigh was applied. In a next step the applicability of the presented remote controllable shape-memory polymer actuators was demonstrated by repetitive opening and closing of a multiring device prepared from NC-mNP-OCL, which repetitively opens and closes when a alternating magnetic field (Hhigh = 11.2 kA·m-1) was switched on and off.
For investigation of the micro- and nanostructural changes related to the actuation of the developed nanocomposite, AFM and WAXS experiments were conducted with programmed nanocomposite samples under cyclic heating and cooling between 25 °C and 60 °C. In AFM experiments the change in the distance (D) between representative droplet-like structures related to the OPDL geometry determining domains was used to calculate the reversible change in D. Here Drev = 3.5±1% was found for NC-mNP-OCL which was in good agreement with the results of the magneto-mechanical actuation experiments. Finally, the analysis of azimuthal (radial) WAXS scattering profiles could support the oriented crystallization of the OCL actuation domains at 25 °C.
In conclusion, the results of this work successfully demonstrated that shape-memory polymer nanocomposites, containing mNPs as magneto-sensitive multifunctional netpoints in a covalently crosslinked multiphase polymer matrix, exhibit magnetically (remotely) controlled actuations upon repetitive exposure to an alternating magnetic field. Furthermore, the (shape) memory of such a nanocomposite can be erased by exposing it to temperatures above the melting temperature of the geometry forming domains, which allows a reprogramming of the actuator. These findings would be relevant for designing novel reprogrammable remotely controllable soft polymeric actuators.
In this thesis the magnetohydrodynamic jet formation and the effects of magnetic diffusion on the formation of axisymmetric protostellar jets have been investigated in three different simulation sets. The time-dependent numerical simulations have been performed, using the magnetohydrodynamic ZEUS-3D code.
Resolute readings of later Wittgenstein and the challenge of avoiding hierarchies in philosophy
(2011)
This dissertation addresses the question: How did later Wittgenstein aim to achieve his goal of putting forward a way of dissolving philosophical problems which centered on asking ourselves what we mean by our words – yet which did not entail any claims about the essence of language and meaning? This question is discussed with reference to “resolute” readings of Wittgenstein. I discuss the readings of James Conant, Oskari Kuusela, and Martin Gustafsson. I follow Oskari Kuusela’s claim that in order to fully appreciate how later Wittgenstein meant to achieve his goal, we need to clearly see how he aimed to do away with hierarchies in philosophy: Not only is the dissolution of philosophical problems via the method of clarifying the grammar of expressions to be taken as independent from any theses about what meaning must be – but furthermore, it is to be taken as independent from the dissolution of any particular problem via this method. As Kuusela stresses, this also holds for the problems involving rule-following and meaning: the clarification of the grammar of “rule” and “meaning” has no foundational status – it is nothing on which the method of clarifying the grammar of expressions as such were meant to in any way rely on. The lead question of this dissertation then is: What does it mean to come to see that the method of dissolving philosophical problems by asking “How is this word actually used?” does not in any way rely on the results of our having investigated the grammar of the particular concepts “rule” and “meaning”? What is the relation of such results – results such as “To follow a rule, [...], to obey an order, [...] are customs (uses, institutions)” or “The meaning of a word is its use in the language” – to this method? From this vantage point, I concern myself with two aspects of the readings of Gustafsson and Kuusela. In Gustafsson, I concern myself with his idea that the dissolution of philosophical problems in general “relies on” the very agreement which – during the dissolution of the rule-following problem – comes out as a presupposition for our talk of “meaning” in terms of rules. In Kuusela, I concern myself with his idea that Wittgenstein, in adopting a way of philosophical clarification which investigates the actual use of expressions, is following the model of “meaning as use” – which model he had previously introduced in order to perspicuously present an aspect of the actual use of the word “meaning”. This dissertation aims to show how these two aspects of Gustafsson’s and Kuusela’s readings still fail to live up to the vision of Wittgenstein as a philosopher who aimed to do away with any hierarchies in philosophy. I base this conclusion on a detailed analysis of which of the occasions where Wittgenstein invokes the notions of “use” and “application” (as also “agreement”) have to do with the dissolution of a specific problem only, and which have to do with the dissolution of philosophical problems in general. I discuss Wittgenstein’s remarks on rule-following, showing how in the dissolution of the rule-following paradox, notions such as “use”, “application”, and “practice” figure on two distinct logical levels. I then discuss an example of what happens when this distinction is not duly heeded: Gordon Baker and Peter Hacker’s idea that the rule-following remarks have a special significance for his project of dissolving philosophical problems as such. I furnish an argument to the effect that their idea that the clarification of the rules of grammar of the particular expression “following a rule” could answer a question about rules of grammar in general rests on a conflation of the two logical levels on which “use” occurs in the rule-following remarks, and that it leads into a regress. I then show that Gustafsson’s view – despite its decisive advance over Baker and Hacker – contains a version of that same idea, and that it likewise leads into a regress. Finally, I show that Kuusela’s idea of a special significance of the model “meaning as use” for the whole of the method of stating rules for the use of words is open to a regress argument of a similar kind as that he himself advances against Baker and Hacker. I conclude that in order to avoid such a regress, we need to reject the idea that the grammatical remark “The meaning of a word is its use in the language” – because of the occurrence of “use” in it – stood in any special relation to the method of dissolving philosophical problems by describing the use of words. Rather, we need to take this method as independent from this outcome of the investigation of the use of the particular word “meaning”.
The problem under consideration in the thesis is a two level atom in a photonic crystal and a pumping laser. The photonic crystal provides an environment for the atom, that modifies the decay of the exited state, especially if the atom frequency is close to the band gap. The population inversion is investigated als well as the emission spectrum. The dynamics is analysed in the context of open quantum systems. Due to the multiple reflections in the photonic crystal, the system has a finite memory that inhibits the Markovian approximation. In the Heisenberg picture the equations of motion for the system variables form a infinite hierarchy of integro-differential equations. To get a closed system, approximations like a weak coupling approximation are needed. The thesis starts with a simple photonic crystal that is amenable to analytic calculations: a one-dimensional photonic crystal, that consists of alternating layers. The Bloch modes inside and the vacuum modes outside a finite crystal are linked with a transformation matrix that is interpreted as a transfer matrix. Formulas for the band structure, the reflection from a semi-infinite crystal, and the local density of states in absorbing crystals are found; defect modes and negative refraction are discussed. The quantum optics section of the work starts with the discussion of three problems, that are related to the full resonance fluorescence problem: a pure dephasing model, the driven atom and resonance fluorescence in free space. In the lowest order of the system-environment coupling, the one-time expectation values for the full problem are calculated analytically and the stationary states are discussed for certain cases. For the calculation of the two time correlation functions and spectra, the additional problem of correlations between the two times appears. In the Markovian case, the quantum regression theorem is valid. In the general case, the fluctuation dissipation theorem can be used instead. The two-time correlation functions are calculated by the two different methods. Within the chosen approximations, both methods deliver the same result. Several plots show the dependence of the spectrum on the parameters. Some examples for squeezing spectra are shown with different approximations. A projection operator method is used to establish two kinds of Markovian expansion with and without time convolution. The lowest order is identical with the lowest order of system environment coupling, but higher orders give different results.
The constantly growing capacity of reconfigurable devices allows simultaneous execution of complex applications on those devices. The mere diversity of applications deems it impossible to design an interconnection network matching the requirements of every possible application perfectly, leading to suboptimal performance in many cases. However, the architecture of the interconnection network is not the only aspect affecting performance of communication. The resource manager places applications on the device and therefore influences latency between communicating partners and overall network load. Communication protocols affect performance by introducing data and processing overhead putting higher load on the network and increasing resource demand. Approaching communication holistically not only considers the architecture of the interconnect, but communication-aware resource management, communication protocols and resource usage just as well. Incorporation of different parts of a reconfigurable system during design- and runtime and optimizing them with respect to communication demand results in more resource efficient communication. Extensive evaluation shows enhanced performance and flexibility, if communication on reconfigurable devices is regarded in a holistic fashion.
Diet is a major force influencing the intestinal microbiota. This is obvious from drastic changes in microbiota composition after a dietary alteration. Due to the complexity of the commensal microbiota and the high inter-individual variability, little is known about the bacterial response at the cellular level. The objective of this work was to identify mechanisms that enable gut bacteria to adapt to dietary factors. For this purpose, germ-free mice monoassociated with the commensal Escherichia coli K-12 strain MG1655 were fed three different diets over three weeks: a diet rich in starch, a diet rich in non-digestible lactose and a diet rich in casein. Two dimensional gel electrophoresis and electrospray tandem mass spectrometry were applied to identify differentially expressed proteins of E. coli recovered from small intestine and caecum of mice fed the lactose or casein diets in comparison with those of mice fed the starch diet. Selected differentially expressed bacterial proteins were characterised in vitro for their possible roles in bacterial adaptation to the various diets. Proteins belonging to the oxidative stress regulon oxyR such as alkyl hydroperoxide reductase subunit F (AhpF), DNA protection during starvation protein (Dps) and ferric uptake regulatory protein (Fur), which are required for E. coli’s oxidative stress response, were upregulated in E. coli of mice fed the lactose-rich diet. Reporter gene analysis revealed that not only oxidative stress but also carbohydrate-induced osmotic stress led to the OxyR-dependent expression of ahpCF and dps. Moreover, the growth of E. coli mutants lacking the ahpCF or oxyR genes was impaired in the presence of non-digestible sucrose. This indicates that some OxyR-dependent proteins are crucial for the adaptation of E. coli to osmotic stress conditions. In addition, the function of two so far poorly characterised E. coli proteins was analysed: 2 deoxy-D gluconate 3 dehydrogenase (KduD) was upregulated in intestinal E. coli of mice fed the lactose-rich diet and this enzyme and 5 keto 4 deoxyuronate isomerase (KduI) were downregulated on the casein-rich diet. Reporter gene analysis identified galacturonate and glucuronate as inducers of the kduD and kduI gene expression. Moreover, KduI was shown to facilitate the breakdown of these hexuronates, which are normally degraded by uronate isomerase (UxaC), altronate oxidoreductase (UxaB), altronate dehydratase (UxaA), mannonate oxidoreductase (UxuB) and mannonate dehydratase (UxuA), whose expression was repressed by osmotic stress. The growth of kduID-deficient E. coli on galacturonate or glucuronate was impaired in the presence of osmotic stress, suggesting KduI and KduD to compensate for the function of the regular hexuronate degrading enzymes under such conditions. This indicates a novel function of KduI and KduD in E. coli’s hexuronate metabolism. Promotion of the intracellular formation of hexuronates by lactose connects these in vitro observations with the induction of KduD on the lactose-rich diet. Taken together, this study demonstrates the crucial influence of osmotic stress on the gene expression of E. coli enzymes involved in stress response and metabolic processes. Therefore, the adaptation to diet-induced osmotic stress is a possible key factor for bacterial colonisation of the intestinal environment.
Modern anthropogenic forcing of atmospheric chemistry poses the question of how the Earth System will respond as thousands of gigatons of greenhouse gas are rapidly added to the atmosphere. A similar, albeit nonanthropogenic, situation occurred during the early Paleogene, when catastrophic release of carbon to the atmosphere triggered abrupt increase in global temperatures. The best documented of these events is the Paleocene-Eocene Thermal Maximum (PETM, ~55 Ma) when the magnitude of carbon addition to the oceans and atmosphere was similar to those expected for the future. This event initiated global warming, changes in hydrological cycles, biotic extinction and migrations. A recently proposed hypothesis concerning changes in marine ecosystems suggests that this global warming strongly influenced the shallow-water biosphere, triggering extinctions and turnover in the Larger Foraminifera (LF) community and the demise of corals. The successions from the Adriatic Carbonate Platform (SW Slovenia) represent an ideal location to test the hypothesis of a possible causal link between the PETM and evolution of shallow-water organisms because they record continuous sedimentation from the Late Paleocene to the Early Eocene and are characterized by a rich biota, especially LF, fundamental for detailed biostratigraphic studies. In order to reconstruct paleoenvironmental conditions during deposition, I focused on sedimentological analysis and paleoecological study of benthic assemblages. During the Late Paleocene-earliest Eocene, sedimentation occurred on a shallow-water carbonate ramp system characterized by enhanced nutrient levels. LF represent the common constituent of the benthic assemblages that thrived in this setting throughout the Late Paleocene to the Early Eocene. With detailed biostratigraphic and chemostratigraphic analyses documenting the most complete record to date available for the PETM event in a shallow-water marine environment, I correlated chemostratigraphically for the first time the evolution of LF with the δ¹³C curves. This correlation demonstrated that no major turnover in the LF communities occurred synchronous with the PETM; thus the evolution of LF was mainly controlled by endogenous biotic forces. The study of Late Thanetian metric-sized microbialite-coral mounds which developed in the middle part of the ramp, documented the first Cenozoic occurrence of microbially-cemented mounds. The development of these mounds, with temporary dominance of microbial communities over corals, suggest environmentally-triggered “phase shifts” related to frequent fluctuations of nutrient/turbidity levels during recurrent wet phases which preceding the extreme greenhouse conditions of the PETM. The paleoecological study of the coral community in the microbialites-coral mounds, the study of corals from Early Eocene platform from SW France, and a critical, extensive literature research of Late Paleocene – Early Eocene coral occurrences from the Tethys, the Atlantic, the Caribbean realms suggested that these corals types, even if not forming extensive reefs, are common in the biofacies as small isolated colonies, piles of rubble or small patch-reefs. These corals might have developed ‘alternative’ life strategies to cope with harsh conditions (high/fluctuating nutrients/turbidity, extreme temperatures, perturbation of aragonite saturation state) during the greenhouse times of the early Paleogene, representing a good fossil analogue to modern corals thriving close to their thresholds for survival. These results demonstrate the complexity of the biological responses to extreme conditions, not only in terms of temperature but also nutrient supply, physical disturbance and their temporal variability and oscillating character.
LCST-type synthetic thermoresponsive polymers can reversibly respond to certain stimuli in aqueous media with a massive change of their physical state. When fluorophores, that are sensitive to such changes, are incorporated into the polymeric structure, the response can be translated into a fluorescence signal. Based on this idea, this thesis presents sensing schemes which transduce the stimuli-induced variations in the solubility of polymer chains with covalently-bound fluorophores into a well-detectable fluorescence output. Benefiting from the principles of different photophysical phenomena, i.e. of fluorescence resonance energy transfer and solvatochromism, such fluorescent copolymers enabled monitoring of stimuli such as the solution temperature and ionic strength, but also of association/disassociation mechanisms with other macromolecules or of biochemical binding events through remarkable changes in their fluorescence properties. For instance, an aqueous ratiometric dual sensor for temperature and salts was developed, relying on the delicate supramolecular assembly of a thermoresponsive copolymer with a thiophene-based conjugated polyelectrolyte. Alternatively, by taking advantage of the sensitivity of solvatochromic fluorophores, an increase in solution temperature or the presence of analytes was signaled as an enhancement of the fluorescence intensity. A simultaneous use of the sensitivity of chains towards the temperature and a specific antibody allowed monitoring of more complex phenomena such as competitive binding of analytes. The use of different thermoresponsive polymers, namely poly(N-isopropylacrylamide) and poly(meth)acrylates bearing oligo(ethylene glycol) side chains, revealed that the responsive polymers differed widely in their ability to perform a particular sensing function. In order to address questions regarding the impact of the chemical structure of the host polymer on the sensing performance, the macromolecular assembly behavior below and above the phase transition temperature was evaluated by a combination of fluorescence and light scattering methods. It was found that although the temperature-triggered changes in the macroscopic absorption characteristics were similar for these polymers, properties such as the degree of hydration or the extent of interchain aggregations differed substantially. Therefore, in addition to the demonstration of strategies for fluorescence-based sensing with thermoresponsive polymers, this work highlights the role of the chemical structure of the two popular thermoresponsive polymers on the fluorescence response. The results are fundamentally important for the rational choice of polymeric materials for a specific sensing strategy.
Restful choreographies
(2019)
Business process management has become a key instrument to organize work as many companies represent their operations in business process models. Recently, business process choreography diagrams have been introduced as part of the Business Process Model and Notation standard to represent interactions between business processes, run by different partners. When it comes to the interactions between services on the Web, Representational State Transfer (REST) is one of the primary architectural styles employed by web services today. Ideally, the RESTful interactions between participants should implement the interactions defined at the business choreography level.
The problem, however, is the conceptual gap between the business process choreography diagrams and RESTful interactions. Choreography diagrams, on the one hand, are modeled from business domain experts with the purpose of capturing, communicating and, ideally, driving the business interactions. RESTful interactions, on the other hand, depend on RESTful interfaces that are designed by web engineers with the purpose of facilitating the interaction between participants on the internet. In most cases however, business domain experts are unaware of the technology behind web service interfaces and web engineers tend to overlook the overall business goals of web services. While there is considerable work on using process models during process implementation, there is little work on using choreography models to implement interactions between business processes. This thesis addresses this research gap by raising the following research question: How to close the conceptual gap between business process choreographies and RESTful interactions? This thesis offers several research contributions that jointly answer the research question.
The main research contribution is the design of a language that captures RESTful interactions between participants---RESTful choreography modeling language. Formal completeness properties (with respect to REST) are introduced to validate its instances, called RESTful choreographies. A systematic semi-automatic method for deriving RESTful choreographies from business process choreographies is proposed. The method employs natural language processing techniques to translate business interactions into RESTful interactions. The effectiveness of the approach is shown by developing a prototypical tool that evaluates the derivation method over a large number of choreography models.
In addition, the thesis proposes solutions towards implementing RESTful choreographies. In particular, two RESTful service specifications are introduced for aiding, respectively, the execution of choreographies' exclusive gateways and the guidance of RESTful interactions.
Earthquakes form by sudden brittle failure of rock mostly as shear ruptures along a rupture plane. Beside this, mechanisms other than pure shearing have been observed for some earthquakes mainly in volcanic areas. Possible explanations include complex rupture geometries and tensile earthquakes. Tensile earthquakes occur by opening or closure of cracks during rupturing. They are likely to be often connected with fluids that cause pressure changes in the pore space of rocks leading to earthquake triggering. Tensile components have been reported for swarm earthquakes in West Bohemia in 2000. The aim and subject of this work is an assessment and the accurate determination of such tensile components for earthquakes in anisotropic media. Currently used standard techniques for the retrieval of earthquake source mechanisms assume isotropic rock properties. By means of moment tensors, equivalent forces acting at the source are used to explain the radiated wavefield. Conversely, seismic anisotropy, i.e. directional dependence of elastic properties, has been observed in the earth's crust and mantle such as in West Bohemia. In comparison to isotropy, anisotropy causes modifications in wave amplitudes and shear-wave splitting. In this work, effects of seismic anisotropy on true or apparent tensile source components of earthquakes are investigated. In addition, earthquake source parameters are determined considering anisotropy. It is shown that moment tensors and radiation patterns due to shear sources in anisotropic media may be similar to those of tensile sources in isotropic media. In contrast, similarities between tensile earthquakes in anisotropic rocks and shear sources in isotropic media may exist. As a consequence, the interpretation of tensile source components is ambiguous. The effects that are due to anisotropy depend on the orientation of the earthquake source and the degree of anisotropy. The moment of an earthquake is also influenced by anisotropy. The orientation of fault planes can be reliably determined even if isotropy instead of anisotropy is assumed and if the spectra of the compressional waves are used. Greater difficulties may arise when the spectra of split shear waves are additionally included. Retrieved moment tensors show systematic artefacts. Observed tensile source components determined for events in West Bohemia in 1997 can only partly be attributed to the effects of moderate anisotropy. Furthermore, moment tensors determined earlier for earthquakes induced at the German Continental Deep Drilling Program (KTB), Bavaria, were reinterpreted under assumptions of anisotropic rock properties near the borehole. The events can be consistently identified as shear sources, although their moment tensors comprise tensile components that are considered to be apparent. These results emphasise the necessity to consider anisotropy to uniquely determine tensile source parameters. Therefore, a new inversion algorithm has been developed, tested, and successfully applied to 112 earthquakes that occurred during the most recent intense swarm episode in West Bohemia in 2000 at the German-Czech border. Their source mechanisms have been retrieved using isotropic and anisotropic velocity models. Determined local magnitudes are in the range between 1.6 and 3.2. Fault-plane solutions are similar to each other and characterised by left-lateral faulting on steeply dipping, roughly North-South oriented rupture planes. Their dip angles decrease above a depth of about 8.4km. Tensile source components indicating positive volume changes are found for more than 60% of the considered earthquakes. Their size depends on source time and location. They are significant at the beginning of the swarm and at depths below 8.4km but they decrease in importance later in the course of the swarm. Determined principle stress axes include P axes striking Northeast and Taxes striking Southeast. They resemble those found earlier in Central Europe. However, depth-dependence in plunge is observed. Plunge angles of the P axes decrease gradually from 50° towards shallow angles with increasing depth. In contrast, the plunge angles of the T axes change rapidly from about 8° above a depth of 8.4km to 21° below this depth. By this thesis, spatial and temporal variations in tensile source components and stress conditions have been reported for the first time for swarm earthquakes in West Bohemia in 2000. They also persist, when anisotropy is assumed and can be explained by intrusion of fluids into the opened cracks during tensile faulting.
As part of our everyday life we consume breaking news and interpret it based on our own viewpoints and beliefs. We have easy access to online social networking platforms and news media websites, where we inform ourselves about current affairs and often post about our own views, such as in news comments or social media posts. The media ecosystem enables opinions and facts to travel from news sources to news readers, from news article commenters to other readers, from social network users to their followers, etc. The views of the world many of us have depend on the information we receive via online news and social media. Hence, it is essential to maintain accurate, reliable and objective online content to ensure democracy and verity on the Web. To this end, we contribute to a trustworthy media ecosystem by analyzing news and social media in the context of politics to ensure that media serves the public interest. In this thesis, we use text mining, natural language processing and machine learning techniques to reveal underlying patterns in political news articles and political discourse in social networks.
Mainstream news sources typically cover a great amount of the same news stories every day, but they often place them in a different context or report them from different perspectives. In this thesis, we are interested in how distinct and predictable newspaper journalists are, in the way they report the news, as a means to understand and identify their different political beliefs. To this end, we propose two models that classify text from news articles to their respective original news source, i.e., reported speech and also news comments. Our goal is to capture systematic quoting and commenting patterns by journalists and news commenters respectively, which can lead us to the newspaper where the quotes and comments are originally published. Predicting news sources can help us understand the potential subjective nature behind news storytelling and the magnitude of this phenomenon. Revealing this hidden knowledge can restore our trust in media by advancing transparency and diversity in the news.
Media bias can be expressed in various subtle ways in the text and it is often challenging to identify these bias manifestations correctly, even for humans. However, media experts, e.g., journalists, are a powerful resource that can help us overcome the vague definition of political media bias and they can also assist automatic learners to find the hidden bias in the text. Due to the enormous technological advances in artificial intelligence, we hypothesize that identifying political bias in the news could be achieved through the combination of sophisticated deep learning modelsxi and domain expertise. Therefore, our second contribution is a high-quality and reliable news dataset annotated by journalists for political bias and a state-of-the-art solution for this task based on curriculum learning. Our aim is to discover whether domain expertise is necessary for this task and to provide an automatic solution for this traditionally manually-solved problem. User generated content is fundamentally different from news articles, e.g., messages are shorter, they are often personal and opinionated, they refer to specific topics and persons, etc. Regarding political and socio-economic news, individuals in online communities make use of social networks to keep their peers up-to-date and to share their own views on ongoing affairs. We believe that social media is also an as powerful instrument for information flow as the news sources are, and we use its unique characteristic of rapid news coverage for two applications. We analyze Twitter messages and debate transcripts during live political presidential debates to automatically predict the topics that Twitter users discuss. Our goal is to discover the favoured topics in online communities on the dates of political events as a way to understand the political subjects of public interest. With the up-to-dateness of microblogs, an additional opportunity emerges, namely to use social media posts and leverage the real-time verity about discussed individuals to find their locations.
That is, given a person of interest that is mentioned in online discussions, we use the wisdom of the crowd to automatically track her physical locations over time. We evaluate our approach in the context of politics, i.e., we predict the locations of US politicians as a proof of concept for important use cases, such as to track people that
are national risks, e.g., warlords and wanted criminals.
In this thesis, I develop a theoretical implementation of prosodic reconstruction and apply it to the empirical domain of German sentences in which part of a focus or contrastive topic is fronted.
Prosodic reconstruction refers to the idea that sentences involving syntactic movement show prosodic parallels with corresponding simpler structures without movement. I propose to model this recurrent observation by ordering syntax-prosody mapping before copy deletion.
In order to account for the partial fronting data, the idea is extended to the mapping between prosody and information structure. This assumption helps to explain why object-initial sentences containing a broad focus or broad contrastive topic show similar prosodic and interpretative restrictions as sentences with canonical word order.
The empirical adequacy of the model is tested against a set of gradient acceptability judgments.
Ribosomes decode mRNA to synthesize proteins. Ribosomes, once considered static, executing machines, are now viewed as dynamic modulators of translation. Increasingly detailed analyses of structural ribosome heterogeneity led to a paradigm shift toward ribosome specialization for selective translation. As sessile organisms, plants cannot escape harmful environments and evolved strategies to withstand. Plant cytosolic ribosomes are in some respects more diverse than those of other metazoans. This diversity may contribute to plant stress acclimation. The goal of this thesis was to determine whether plants use ribosome heterogeneity to regulate protein synthesis through specialized translation. I focused on temperature acclimation, specifically on shifts to low temperatures. During cold acclimation, Arabidopsis ceases growth for seven days while establishing the responses required to resume growth. Earlier results indicate that ribosome biogenesis is essential for cold acclimation. REIL mutants (reil-dkos) lacking a 60S maturation factor do not acclimate successfully and do not resume growth. Using these genotypes, I ascribed cold-induced defects of ribosome biogenesis to the assembly of the polypeptide exit tunnel (PET) by performing spatial statistics of rProtein changes mapped onto the plant 80S structure. I discovered that growth cessation and PET remodeling also occurs in barley, suggesting a general cold response in plants. Cold triggered PET remodeling is consistent with the function of Rei-1, a REIL homolog of yeast, which performs PET quality control. Using seminal data of ribosome specialization, I show that yeast remodels the tRNA entry site of ribosomes upon change of carbon sources and demonstrate that spatially constrained remodeling of ribosomes in metazoans may modulate protein synthesis. I argue that regional remodeling may be a form of ribosome specialization and show that heterogeneous cytosolic polysomes accumulate after cold acclimation, leading to shifts in the translational output that differs between wild-type and reil-dkos. I found that heterogeneous complexes consist of newly synthesized and reused proteins. I propose that tailored ribosome complexes enable free 60S subunits to select specific 48S initiation complexes for translation. Cold acclimated ribosomes through ribosome remodeling synthesize a novel proteome consistent with known mechanisms of cold acclimation. The main hypothesis arising from my thesis is that heterogeneous/ specialized ribosomes alter translation preferences, adjust the proteome and thereby activate plant programs for successful cold acclimation.
Natural hazards pose a threat to human health and life. In Germany, where the research for this thesis was conducted, numerous weather extremes occurred in the recent past that caused high numbers of fatalities and huge financial losses. The focus of this research is centred around two relevant natural hazards: heat stress and flooding. Preventing negative health impacts and deaths, as well as structural and monetary damage is the purpose of risk management and this requires citizens to adapt as well. Risk communication is implemented to foster people’s risk perception and motivate individual adaptation. However, methods of risk and crisis communication are often not evaluated in a structured manner. Much interdisciplinary research exists on both risk perception and adaptation, however, not much is known on the connection between the two. Furthermore, the existing research on risk communication is often not theory-driven and its impact on individual adaptation and risk perception is not thoroughly documented. This dissertation follows three research aims: (1) Compare psychological theories that contribute to natural hazard research. (2) Explore risk perception and adaptive behaviour by applying multiple methods. And (3) evaluate one risk communication method and one crisis communication method in a theory-driven manner to determine their impact on risk perception and adaptive behaviour. First, a literature review is provided on existing psychological theories which aim to explain the behaviour of individuals with regards to natural hazards. The three key theories included are the Protection Motivation Theory (PMT), the Protective Action Decision Model (PADM), and the Risk Information Seeking and Processing Model (RISP). Each of these are described and compared to each other with a focus on their explanatory power and practical significance in interdisciplinary research. Theoretical adaptations and possible extensions for future research are proposed for the presented approaches. Second, a multimethod field study on heat stress at an open-air event is presented. Face-to-face surveys (n = 306) and behavioural observations (n = 2750) were carried out at a horticultural show in Würzburg in summer 2018. The visitors’ risk perception, adaptive behaviour, and activity level were analysed and compared between hot days, summer days, and rainy days, applying correlation analyses, ANOVA, and multiple regression analyses. Heat risk perception was generally high, but most respondents were unaware of heat warnings on the day of their visit. During hot days the highest level of adaptation and lower activity levels were observed. Discrepancies between reported and observed adaptation emerged for different age groups.. Third, a telephone and web-based household survey on heat stress was conducted in the cities of Würzburg, Potsdam, and Remscheid in 2019 (n = 1417). The PADM served as the study’s theoretical framework. In multiple regression analyses the PADM factors of environmental and demographic context, risk communication, and psychological processes explained a substantial share of variance of protection motivation, protective response, and emotion-focused coping. Elements of crisis communication of a heat warning were evaluated experimentally. Results showed that understanding and adaptation intention was significantly higher in individuals that had received action recommendations alongside the heat warning. Fourth, the focus is set on a risk communication method of the flood context. A series of workshops on individual flood protection was carried out in six different settings. The participants (n = 115) answered a pretest-posttest questionnaire. Mixed-model analyses revealed significant increases in self-efficacy, subjective knowledge, and protection motivation. Stronger effects were observed in younger participants and those with lower levels of previous knowledge on flood adaptation as well as no flood experience. The findings of this thesis help to understand individual adaptation, as well as possible impacts of risk and crisis communication on risk perception and adaptation. The scientific background of this work is rooted in the disciplines of psychology and geosciences. The two theories PMT and PADM proved to be useful theoretical frameworks for the presented studies to suggest improvements in risk communication methods. A broad picture of individual adaptation is captured through a variety of methods of self-reports (face-to-face, telephone-based, web-based, and paper-pencil surveys) and behavioural observations, which recorded past and intended behaviour. Alongside with further methodological recommendations, the theory-driven evaluations of risk and crisis communication methods can serve as best-practice examples for future evaluation studies in natural hazard research but also other sciences dealing with risk behaviour to identify and improve effective risk communication pathways.
River floods are among the most devastating natural hazards worldwide. As their generation is highly dependent on climatic conditions, their magnitude and frequency are projected to be affected by future climate change. Therefore, it is crucial to study the ways in which a changing climate will, and already has, influenced flood generation, and thereby flood hazard. Additionally, it is important to understand how other human influences - specifically altered land cover - affect flood hazard at the catchment scale.
The ways in which flood generation is influenced by climatic and land cover conditions differ substantially in different regions. The spatial variability of these effects needs to be taken into account by using consistent datasets across large scales as well as applying methods that can reflect this heterogeneity. Therefore, in the first study of this cumulative thesis a complex network approach is used to find 10 clusters of similar flood behavior among 4390 catchments in the conterminous United States. By using a consistent set of 31 hydro-climatological and land cover variables, and training a separate Random Forest model for each of the clusters, the regional controls on flood magnitude trends between 1960-2010 are detected. It is shown that changes in rainfall are the most important drivers of these trends, while they are regionally controlled by land cover conditions.
While climate change is most commonly associated with flood magnitude trends, it has been shown to also influence flood timing. This can lead to trends in the size of the area across which floods occur simultaneously, the flood synchrony scale. The second study is an analysis of data from 3872 European streamflow gauges and shows that flood synchrony scales have increased in Western Europe and decreased in Eastern Europe. These changes are attributed to changes in flood generation, especially a decreasing relevance of snowmelt. Additionally, the analysis shows that both the absolute values and the trends of flood magnitudes and flood synchrony scales are positively correlated. If these trends persist in the future and are not accounted for, the combined increases of flood magnitudes and flood synchrony scales can exceed the capacities of disaster relief organizations and insurers.
Hazard cascades are an additional way through which climate change can influence different aspects of flood hazard. The 2019/2020 wildfires in Australia, which were preceded by an unprecedented drought and extinguished by extreme rainfall that led to local flooding, present an opportunity to study the effects of multiple preceding hazards on flood hazard. All these hazards are individually affected by climate change, additionally complicating the interactions within the cascade. By estimating and analyzing the burn severity, rainfall magnitude, soil erosion and stream turbidity in differently affected tributaries of the Manning River catchment, the third study shows that even low magnitude floods can pose a substantial hazard within a cascade.
This thesis shows that humanity is affecting flood hazard in multiple ways with spatially and temporarily varying consequences, many of which were previously neglected (e.g. flood synchrony scale, hazard cascades). To allow for informed decision making in risk management and climate change adaptation, it will be crucial to study these aspects across the globe and to project their trajectories into the future. The presented methods can depict the complex interactions of different flood drivers and their spatial variability, providing a basis for the assessment of future flood hazard changes. The role of land cover should be considered more in future flood risk modelling and management studies, while holistic, transferable frameworks for hazard cascade assessment will need to be designed.
Robotic telescopes & Doppler imaging : measuring differential rotation on long-period active stars
(2004)
The sun shows a wide variety of magnetic-activity related phenomena. The magnetic field responsible for this is generated by a dynamo process which is believed to operate in the tachocline, which is located at the bottom of the convection zone. This dynamo is driven in part by differential rotation and in part by magnetic turbulences in the convection zone. The surface differential rotation, one key ingredient of dynamo theory, can be measured by tracing sunspot positions.To extend the parameter space for dynamo theories, one can extend these measurements to other stars than the sun. The primary obstacle in this endeavor is the lack of resolved surface images on other stars. This can be overcome by the Doppler imaging technique, which uses the rotation-induced Doppler-broadening of spectral lines to compute the surface distribution of a physical parameter like temperature. To obtain the surface image of a star, high-resolution spectroscopic observations, evenly distributed over one stellar rotation period are needed. This turns out to be quite complicated for long period stars. The upcoming robotic observatory STELLA addresses this problem with a dedicated scheduling routine, which is tailored for Doppler imaging targets. This will make observations for Doppler imaging not only easier, but also more efficient.As a preview of what can be done with STELLA, we present results of a Doppler imaging study of seven stars, all of which show evidence for differential rotation, but unfortunately the errors are of the same order of magnitude as the measurements due to unsatisfactory data quality, something that will not happen on STELLA. Both, cross-correlation analysis and the sheared image technique where used to double check the results if possible. For four of these stars, weak anti-solar differential rotation was found in a sense that the pole rotates faster than the equator, for the other three stars weak differential rotation in the same direction as on the sun was found.Finally, these new measurements along with other published measurements of differential rotation using Doppler imaging, were analyzed for correlations with stellar evolution, binarity, and rotation period. The total sample of stars show a significant correlation with rotation period, but if separated into antisolar and solar type behavior, only the subsample showing anti-solar differential rotation shows this correlation. Additionally, there is evidence for binary stars showing less differential rotation as single stars, as is suggested by theory. All other parameter combinations fail to deliver any results due to the still small sample of stars available.
In this work we consider statistical learning problems. A learning machine aims to extract information from a set of training examples such that it is able to predict the associated label on unseen examples. We consider the case where the resulting classification or regression rule is a combination of simple rules - also called base hypotheses. The so-called boosting algorithms iteratively find a weighted linear combination of base hypotheses that predict well on unseen data. We address the following issues: o The statistical learning theory framework for analyzing boosting methods. We study learning theoretic guarantees on the prediction performance on unseen examples. Recently, large margin classification techniques emerged as a practical result of the theory of generalization, in particular Boosting and Support Vector Machines. A large margin implies a good generalization performance. Hence, we analyze how large the margins in boosting are and find an improved algorithm that is able to generate the maximum margin solution. o How can boosting methods be related to mathematical optimization techniques? To analyze the properties of the resulting classification or regression rule, it is of high importance to understand whether and under which conditions boosting converges. We show that boosting can be used to solve large scale constrained optimization problems, whose solutions are well characterizable. To show this, we relate boosting methods to methods known from mathematical optimization, and derive convergence guarantees for a quite general family of boosting algorithms. o How to make Boosting noise robust? One of the problems of current boosting techniques is that they are sensitive to noise in the training sample. In order to make boosting robust, we transfer the soft margin idea from support vector learning to boosting. We develop theoretically motivated regularized algorithms that exhibit a high noise robustness. o How to adapt boosting to regression problems? Boosting methods are originally designed for classification problems. To extend the boosting idea to regression problems, we use the previous convergence results and relations to semi-infinite programming to design boosting-like algorithms for regression problems. We show that these leveraging algorithms have desirable theoretical and practical properties. o Can boosting techniques be useful in practice? The presented theoretical results are guided by simulation results either to illustrate properties of the proposed algorithms or to show that they work well in practice. We report on successful applications in a non-intrusive power monitoring system, chaotic time series analysis and a drug discovery process. --- Anmerkung: Der Autor ist Träger des von der Mathematisch-Naturwissenschaftlichen Fakultät der Universität Potsdam vergebenen Michelson-Preises für die beste Promotion des Jahres 2001/2002.
The formation and breaching of natural dammed lakes have formed the landscapes, especially in seismically active high-mountain regions. Dammed lakes pose both, potential water resources, and hazard in case of dam breaching. Central Asia has mostly arid and semi-arid climates. Rock glaciers already store more water than ice-glaciers in some semi-arid regions of the world, but their distribution and advance mechanisms are still under debate in recent research. Their impact on the water availability in Central Asia will likely increase as temperatures rise and glaciers diminish.
This thesis provides insight to the relative age distribution of selected Kyrgyz and Kazakh rock glaciers and their single lobes derived from lichenometric dating. The size of roughly 8000 different lichen specimens was used to approximate an exposure age of the underlying debris surface. We showed that rock-glacier movement differs signifcantly on small scales. This has several implications for climatic inferences from rock glaciers. First, reactivation of their lobes does not necessarily point to climatic changes, or at least at out-of-equilibrium conditions. Second, the elevations of rock-glacier toes can no longer be considered as general indicators of the limit of sporadic mountain permafrost as they have been used traditionally.
In the mountainous and seismically active region of Central Asia, natural dams, besides rock glaciers, also play a key role in controlling water and sediment infux into river valleys. However, rock glaciers advancing into valleys seem to be capable of infuencing the stream network, to dam rivers, or to impound lakes. This influence has not previously been addressed. We quantitatively explored these controls using a new inventory of 1300 Central Asian rock glaciers. Elevation, potential incoming solar radiation, and the size of rock glaciers and their feeder basins played key roles in predicting dam appearance. Bayesian techniques were used to credibly distinguish between lichen sizes on rock glaciers and their lobes, and to find those parameters of a rock-glacier system that are most credibly expressing the potential to build natural dams.
To place these studies in the region's history of natural dams, a combination of dating of former lake levels and outburst flood modelling addresses the history and possible outburst flood hypotheses of the second largest mountain lake of the world, Issyk Kul in Kyrgyzstan. Megafoods from breached earthen or glacial dams were found to be a likely explanation for some of the lake's highly fluctuating water levels. However, our detailed analysis of candidate lake sediments and outburst-flood deposits also showed that more localised dam breaks to the west of Issyk Kul could have left similar geomorphic and sedimentary evidence in this Central Asian mountain landscape. We thus caution against readily invoking megafloods as the main cause of lake-level drops of Issyk Kul. In summary, this thesis addresses some new pathways for studying rock glaciers and natural dams with several practical implications for studies on mountain permafrost and natural hazards.
Role of dietary sulfonates in the stimulation of gut bacteria promoting intestinal inflammation
(2021)
The interplay between intestinal microbiota and host has increasingly been recognized as a major factor impacting health. Studies indicate that diet is the most influential determinant affecting the gut microbiota. A diet rich in saturated fat was shown to stimulate the growth of the colitogenic bacterium Bilophila wadsworthia by enhancing the secretion of the bile acid taurocholate (TC). The sulfonated taurine moiety of TC is utilized as a substrate by B. wadsworthia. The resulting overgrowth of B. wadsworthia was accompanied by an increased incidence and severity of colitis in interleukin (IL)-10-deficient mice, which are genetically prone to develop inflammation.
Based on these findings, the question arose whether the intake of dietary sulfonates also stimulates the growth of B. wadsworthia and thereby promotes intestinal inflammation in genetically susceptible mice. Dietary sources of sulfonates include green vegetables and cyanobacteria, which contain the sulfolipids sulfoquinovosyl diacylglycerols (SQDG) in considerable amounts. Based on literature reports, the gut commensal Escherichia coli is able to release sulfoquinovose (SQ) from SQDG and in further steps, convert SQ to 2,3-dihydroxypropane-1-sulfonate (DHPS) and dihydroxyacetone phosphate. DHPS may then be utilized as a growth substrate by B. wadsworthia, which results in the formation of sulfide. Both, sulfide formation and a high abundance of B. wadsworthia have been associated with intestinal inflammation.
In the present study, conventional IL-10-deficient mice were fed either a diet supplemented with the SQDG-rich cyanobacterium Spirulina (20%, SD) or a control diet. In addition SQ, TC, or water were orally applied to conventional or gnotobiotic IL-10-deficient mice. The gnotobiotic mice harbored a simplified human intestinal microbiota (SIHUMI) either with or without B. wadsworthia. During the intervention period, the body weight of the mice was monitored, the colon permeability was assessed and fecal samples were collected. After the three-week intervention, the animals were examined with regard to inflammatory parameters, microbiota composition and sulfonate concentrations in different intestinal sites.
None of the mice treated with the above-mentioned sulfonates showed weight loss or intestinal inflammation. Solely mice fed SD or gavaged with TC displayed a slight immune response. These mice also displayed an altered microbiota composition, which was not observed in mice gavaged with SQ. The abundance of B. wadsworthia was strongly reduced in mice fed SD, while that of mice treated with SQ or TC was in part slightly increased. The intestinal SQ-concentration was elevated in mice orally treated with SD or SQ, whereas neither TC nor taurine concentrations were consistently elevated in mice gavaged with TC. Additional colonization of SIHUMI mice with B. wadsworthia resulted in a mild inflammatory response, but only in mice treated with TC. In general, TC-mediated effects on the immune system and abundance of B. wadsworthia were not as strong as described in the literature.
In summary, neither the tested dietary sulfonates nor TC led to bacteria-induced intestinal inflammation in the IL-10-deficient mouse model, which was consistently observed in both conventional and gnotobiotic mice. For humans, this means that foods containing SQDG, such as spinach or Spirulina, do not increase the risk of intestinal inflammation.
Over the last decades, interest in the impact of the intestinal microbiota on host health has steadily increased. Diet is a major factor that influences the gut microbiota and thereby indirectly affects human health. For example, a high fat diet rich in saturated fatty acids led to an intestinal proliferation of the colitogenic bacterium Bilophila (B.) wadsworthia by stimulating the release of the bile acid taurocholate (TC). TC contains the sulfonated head group taurine, which undergoes conversion to sulfide (H2S) by B. wadsworthia. In a colitis prone murine animal model (IL10 / mice), the bloom of B. wadsworthia was accompanied by an exacerbation of intestinal inflammation. B. wadsworthia is able to convert taurine and also other sulfonates to H2S, indicating the potential association of sulfonate utilization and the stimulation of colitogenic bacteria.
This potential link raised the question, whether dietary sulfonates or their sulfonated metabolites stimulate the growth of colitogenic bacteria such as B. wadsworthia and whether these bacteria convert sulfonates to H2S. Besides taurine, which is present in meat, fish and life-style beverages, other dietary sulfonates are part of daily human nutrition. Sulfolipids such as sulfoquinovosyldiacylglycerols (SQDG) are highly abundant in salad, parsley and the cyanobacterium Arthrospira platensis (Spirulina). Based on previous findings, Escherichia (E.) coli releases the polar headgroup sulfoquinovose (SQ) from SQDG. Moreover, E. coli is able to convert SQ to 2,3 dihydroxypropane 1 sulfonate (DHPS) under anoxic conditions. DHPS is also converted to H2S by B. wadsworthia or by other potentially harmful gut bacteria such as members of the genus Desulfovibrio. However, only few studies report the conversion of sulfonates to H2S by bacteria directly isolated from the human intestinal tract. Most sulfonate utilizing bacteria were obtained from environmental sources such as soil or lake sediment or from potentially intestinal sources such as sewage.
In the present study, fecal slurries from healthy human subjects were incubated with sulfonates under strictly anoxic conditions, using formate and lactate as electron donors. Fecal slurries that converted sulfonates to H2S, were used as a source for the isolation of H2S forming bacteria. Isolates were identified based on their 16S ribosomal RNA (16S rRNA) gene sequence. In addition, conventional C57BL/6 mice were fed a semisynthetic diet supplemented with the SQDG rich Spirulina (SD) or a Spirulina free control diet (CD). During the intervention, body weight, water and food intake were monitored and fecal samples were collected. After three weeks, mice were killed and organ weight and size were measured, intestinal sulfonate concentrations were quantified, gut microbiota composition was determined and parameters of intestinal and hepatic fat metabolism were analyzed.
Human fecal slurries converted taurine, isethionate, cysteate, 3 sulfolacate, SQ and DHPS to H2S. However, inter individual differences in the degradation of these sulfonates were observed. Taurine, isethionate, and 3 sulfolactate were utilized by fecal microbiota of all donors, while SQ, DHPS and cysteate were converted to H2S only by microbiota from certain individuals. Bacterial isolates from human feces able to convert sulfonates to H2S were identified as taurine-utilizing Desulfovibrio strains, taurine- and isethionate-utilizing B. wadsworthia, or as SQ- and 3-sulfolactate- utilizing E. coli. In addition, a co culture of E. coli and B. wadsworthia led to complete degradation of SQ to H2S, with DHPS as an intermediate. Of the human fecal isolates, B. wadsworthia and Desulfovibrio are potentially harmful. E. coli strains might be also pathogenic, but isolated E. coli strains from human feces were identified as commensal gut bacteria.
Feeding SD to mice increased the cecal and fecal SQ concentration and altered the microbiota composition, but the relative abundance of SQDG or SQ converting bacteria and colitogenic bacteria was not enriched in mice fed SD for 21 days. SD did not affect the relative abundance of Enterobacteriaceae, to which the SQDG- and SQ-utilizing E. coli strain belong to. Furthermore, the abundance of B. wadsworthia decreased from day 2 to day 9 in feces, but recovered afterwards in the same mice. In cecum, the family Desulfovibrionaceae, to which B. wadsworthia and Desulfovibrio belong to, were reduced. No changes in the number of B. wadsworthia in cecal contents or of Desulfovibrionaceae in feces were observed. SD led to a mild activation of the immune system, which was not observed in control mice fed CD. Mice fed SD had an increased body weight, a higher adipose tissue weight, and a decreased liver weight compared to the control mice, suggesting an impact of Spirulina supplementation on fat metabolism. However, expression levels of genes involved in intestinal and hepatic intracellular lipid uptake and availability were reduced. Further investigations on the lipid metabolism at protein level could help to clarify these discrepancies.
In summary, humans differ in the ability of their fecal microbiota to utilize dietary sulfonates. While sulfonates stimulated the proliferation of potentially colitogenic isolates from human fecal slurries, the increased availability of SQ in Spirulina fed conventional mice did not lead to an enrichment of such bacteria. Presence or absence of these bacteria may explain the inter individual differences in sulfonate conversion observed for fecal slurries. This work provides new insights in the ability of intestinal bacteria to utilize sulfonates and thus, contributes to a better understanding of microbiota-mediated effects on dietary sulfonate utilization. Interestingly, feeding of the Spirulina-supplemented diet led to body-weight gain in mice in the first two days of intervention, the reasons for which are unknown.
Scope: Several studies show that excessive lipid intake can cause hepatic steatosis. To investigate lipotoxicity on cellular level, palmitate (PA) is often used to highly increase lipid droplets (LDs). One way to remove LDs is autophagy, while it is controversially discussed if autophagy is also affected by PA. It is aimed to investigate whether PA-induced LD accumulation can impair autophagy and punicalagin, a natural autophagy inducer from pomegranate, can improve it.
Methods and results: To verify the role of autophagy in LD degradation, HepG2 cells are treated with PA and analyzed for LD and perilipin 2 content in presence of autophagy inducer Torin 1 and inhibitor 3-Methyladenine. PA alone seems to initially induce autophagy-related proteins but impairs autophagic-flux in a time-dependent manner, considering 6 and 24 h PA. To examine whether punicalagin can prevent autophagy impairment, cells are cotreated for 24 h with PA and punicalagin. Results show that punicalagin preserves expression of autophagy-related proteins and autophagic flux, while simultaneously decreasing LDs and perilipin 2.
Conclusion: Data provide new insights into the role of PA-induced excessive LD content on autophagy and suggest autophagy-inducing properties of punicalagin, indicating that punicalagin can be a health-beneficial compound for future research on lipotoxicity in liver.
The morphogenesis of sessile plants is mainly driven by directional cell growth and cell division. The organization of their cytoskeleton and the mechanical properties of the cell wall greatly influence morphogenetic events in plants. It is well known that cortical microtubules (CMTs) contribute to directional growth by regulating the deposition of the cellulose microfibrils, as major cell wall fortifying elements. More recent findings demonstrate that mechanical stresses existing in cells and tissues influence microtubule organization. Also, in dividing cells, mechanical stress directions contribute to the orientation of the new cell wall. In comparison to the microtubule cytoskeleton, the role of the actin cytoskeleton in regulating shoot meristem morphogenesis has not been extensively studied.
This thesis focuses on the functional relevance of the actin cytoskeleton during cell and tissue scale morphogenesis in the shoot apical meristem (SAM) of Arabidopsis thaliana. Visualization of transcriptional reporters indicates that ACTIN2 and ACTIN7 are two highly expressed actin genes in the SAM. A link between the actin cytoskeleton and SAM development derives from the observation that the act2-1 act7-1 double mutant has abnormal cell shape and perturbed phyllotactic patterns. Live-cell imaging of the actin cytoskeleton further shows that its organization correlates with cell shape, which indicates a potential role of actin in influencing cellular morphogenesis.
In this thesis, a detailed characterization of the act2-1 act7-1 mutant reveals that perturbation of actin leads to more rectangular cellular geometries with more 90° cell internal angles, and higher incidences of four-way junctions (four cell boundaries intersecting together). This observation deviates from the conventional tricellular junctions found in epidermal cells. Quantitative cellular-level growth data indicates that such differences in the act2-1 act7-1 mutant arise due to the reduced accuracy in the placement of the new cell wall, as well as its mechanical maturation. Changes in cellular morphology observed in the act2-1 act7-1 mutant result in cell packing defects that subsequently compromise the flow of information among cells in the SAM.
Growth differentiation factor 15 (GDF15) is a stress-induced cytokine secreted into the circulation by a number of tissues under different pathological conditions such as cardiovascular disease, cancer or mitochondrial dysfunction, among others. While GDF15 signaling through its recently identified hindbrain-specific receptor GDNF family receptor alpha-like (GFRAL) has been proposed to be involved in the metabolic stress response, its endocrine role under chronic stress conditions is still poorly understood. Mitochondrial dysfunction is characterized by the impairment of oxidative phosphorylation (OXPHOS), leading to inefficient functioning of mitochondria and consequently, to mitochondrial stress. Importantly, mitochondrial dysfunction is among the pathologies to most robustly induce GDF15 as a cytokine in the circulation.
The overall aim of this thesis was to elucidate the role of the GDF15-GFRAL pathway under mitochondrial stress conditions. For this purpose, a mouse model of skeletal muscle-specific mitochondrial stress achieved by ectopic expression of uncoupling protein 1 (UCP1), the HSA-Ucp1-transgenic (TG) mouse, was employed. As a consequence of mitochondrial stress, TG mice display a metabolic remodeling consisting of a lean phenotype, an improved glucose metabolism, an increased metabolic flexibility and a metabolic activation of white adipose tissue.
Making use of TG mice crossed with whole body Gdf15-knockout (GdKO) and Gfral-knockout (GfKO) mouse models, this thesis demonstrates that skeletal muscle mitochondrial stress induces the integrated stress response (ISR) and GDF15 in skeletal muscle, which is released into the circulation as a myokine (muscle-induced cytokine) in a circadian manner. Further, this work identifies GDF15-GFRAL signaling to be responsible for the systemic metabolic remodeling elicited by mitochondrial stress in TG mice. Moreover, this study reveals a daytime-restricted anorexia induced by the GDF15-GFRAL axis under muscle mitochondrial stress, which is, mechanistically, mediated through the induction of hypothalamic corticotropin releasing hormone (CRH). Finally, this work elucidates a so far unknown physiological outcome of the GDF15-GFRAL pathway: the induction of anxiety-like behavior.
In conclusion, this study uncovers a muscle-brain crosstalk under skeletal muscle mitochondrial stress conditions through the induction of GDF15 as a myokine that signals through the hindbrain-specific GFRAL receptor to elicit a stress response leading to metabolic remodeling and modulation of ingestive- and anxiety-like behavior.
Sulfur is essential for the functionality of some important biomolecules in humans. Biomolecules like the Iron-sulfur clusters, tRNAs, Molybdenum cofactor, and some vitamins. The trafficking of sulfur involves proteins collectively called sulfurtransferase. Among these are TUM1, MOCS3, and NFS1.
This research investigated the role of TUM1 for molybdenum cofactor biosynthesis and cytosolic tRNA thiolation in humans. The rhodanese-like protein MOCS3 and the L-cysteine desulfurase (NFS1) have been previously demonstrated to interact with TUM1. These interactions suggested a dual function of TUM1 in sulfur transfer for Moco biosynthesis and cytosolic tRNA thiolation. TUM1 deficiency has been implicated to be responsible for a rare inheritable disorder known as mercaptolactate cysteine disulfiduria (MCDU), which is associated with a mental disorder. This mental disorder is similar to the symptoms of sulfite oxidase deficiency which is characterised by neurological disorders. Therefore, the role of TUM1 as a sulfurtransferase in humans was investigated, in CRISPR/Cas9 generated TUM1 knockout HEK 293T cell lines.
For the first time, TUM1 was implicated in Moco biosynthesis in humans by quantifying the intermediate product cPMP and Moco using HPLC. Comparing the TUM1 knockout cell lines to the wild-type, accumulation and reduction of cPMP and Moco were observed respectively. The effect of TUM1 knockout on the activity of a Moco-dependent enzyme, Sulfite oxidase, was also investigated. Sulfite oxidase is essential for the detoxification of sulfite to sulfate. Sulfite oxidase activity and protein abundance were reduced due to less availability of Moco. This shows that TUM1 is essential for efficient sulfur transfer for Moco biosynthesis. Reduction in cystathionin -lyase in TUM1 knockout cells was quantified, a possible coping mechanism of the cell against sulfite production through cysteine catabolism.
Secondly, the involvement of TUM1 in tRNA thio-modification at the wobble Uridine-34 was reported by quantifying the amount of mcm5s2U and mcm5U via HPLC. The reduction and accumulation of mcm5s2U and mcm5U in TUM1 knockout cells were observed in the nucleoside analysis. Herein, exogenous treatment with NaHS, a hydrogen sulfide donor, rescued the Moco biosynthesis, cytosolic tRNA thiolation, and cell proliferation deficits in TUM1 knockout cells.
Further, TUM1 was shown to impact mitochondria bioenergetics through the measurement of the oxygen consumption rate and extracellular acidification rate (ECAR) via the seahorse cell Mito stress analyzer. Reduction in total ATP production was also measured. This reveals how important TUM1 is for H2S biosynthesis in the mitochondria of HEK 293T.
Finally, the inhibition of NFS1 in HEK 293T and purified NFS1 protein by 2-methylene 3-quinuclidinone was demonstrated via spectrophotometric and radioactivity quantification. Inhibition of NFS1 by MQ further affected the iron-sulfur cluster-dependent enzyme aconitase activity.
Romance and Irony
(2017)
Aldehyde oxidases (AOXs) (E.C. 1.2.3.1) are molybdoflavo-enzymes belonging to the xanthine oxidase (XO) family. AOXs in mammals contain one molybdenum cofactor (Moco), one flavin adenine dinucleotide (FAD) and two [2Fe-2S] clusters, the presence of which is essential for the activity of the enzyme. Human aldehyde oxidase (hAOX1) is a cytosolic enzyme mainly expressed in the liver. hAOX1is involved in the metabolism of xenobiotics. It oxidizes aldehydes to their corresponding carboxylic acids and hydroxylates N-heterocyclic compounds. Since these functional groups are widely present in therapeutics, understanding the behaviour of hAOX1 has important implications in medicine. During the catalytic cycle of hAOX1, the substrate is oxidized at Moco and electrons are internally transferred to FAD via the FeS clusters. An electron acceptor juxtaposed to the FAD receives the electrons and re-oxidizes the enzyme for the next catalytic cycle. Molecular oxygen is the endogenous electron acceptor of hAOX1 and in doing so it is reduced and produces reactive oxygen species (ROS) including hydrogen peroxide (H2O2) and superoxide (O2.-). The production of ROS has patho-physiological importance, as ROS can have a wide range of effects on cell components including the enzyme itself.
In this thesis, we have shown that hAOX1 loses its activity over multiple cycles of catalysis due to endogenous ROS production and have identified a cysteine rich motif that protects hAOX1 from the ROS damaging effects. We have also shown that a sulfido ligand, which is bound at Moco and is essential for the catalytic activity of the enzyme, is vulnerable during turnover. The ROS produced during the course of the reaction are also able to remove this sulfido ligand from Moco. ROS, in addition, oxidize particular cysteine residues. The combined effects of ROS on the sulfido ligand and on specific cysteine residues in the enzyme result in its inactivation. Furthermore, we report that small reducing agents containing reactive sulfhydryl groups, in a selective manner, inactivate some of the mammalian AOXs by modifying the sulfido ligand at Moco. The mechanism of ROS production by hAOX1 is another scope that has been investigated as part of the work in this thesis. We have shown that the ratio of type of ROS, i.e. hydrogen peroxide (H2O2) and superoxide (O2.-), produced by hAOX1 is determined by a particular position on a flexible loop that locates in close proximity of FAD. The size of the cavity at the ROS producing site, i.e. the N5 position of the FAD isoalloxazine ring, kinetically affects the amount of each type of ROS generated by hAOX1. Taken together, hAOX1 is an enzyme with emerging importance in pharmacological and medical studies, not only due to its involvement in drug metabolism, but also due to ROS production which has physiological and pathological implications.
ROS transcriptional networks controlling cell expansion during leaf growth in Arabidopsis thaliana
(2012)
Extreme weather events like heatwaves and floods severely affect societies with impacts ranging from economic damages to losses in human lifes. Global warming caused by anthropogenic greenhouse gas emissions is expected to increase their frequency and intensity, particularly in the warm season. Next to these thermodynamic changes, climate change might also impact the large scale atmospheric circulation.Such dynamic changes might additionally act on the occurence of extreme weather events, but involved mechanisms are often highly non-linear. Therefore, large uncertainty exists on the exact nature of these changes and the related risks to society. Particularly in the densely populated mid-latitudes weather patterns are governed by the large scale circulation like the jet-streams and storm tracks. Extreme weather in this region is often related to persistent weather systems associated with a strongly meandering jet-stream. Such meanders are called Rossby waves. Under specific conditions they can become slow moving, stretched around the entire hemisphere and generate simultaneaous heat- and rainfall extremes in far-away regions.
This thesis aims at enhancing the understanding of synoptic-scale, circumglobal Rossby waves and the associated risks of dynamical changes to society. More specific, the analyses investigate their relation to extreme weather, regions at risk, under which conditions they are generated, and the influence of anthropogenic climate change on those conditions now, in the past and in the future.
I find that circumglobal Rossby waves promoted simultaneous occuring weather extremes across the northern hemisphere in several recent summers. Further, I present evidence that they are often linked to quasiresonant-amplification of planetary waves. These events include the 2003 European heatwave and the Moscow heatwave of 2010. This non-linear mechanism acts on the upper level flow through trapping and amplification of stationary synoptic scale waves. I show that this resonance mechanism acts in both hemispheres and is related to extreme weather. A main finding is that circumglobal Rossby waves primarily occur as two specific teleconnection patterns associated with a wave 5 and wave 7 pattern in the northern hemisphere, likely due to the favourable longitudinal distance of prominent mountain ridges here. Furthermore, I identify those regions which are particularly at risk: The central United States, western Europe and the Ukraine/Russian region. Moreover, I present evidence that the wave 7 pattern has and extreme weather in these regions. My results suggest that the increase in frequency can be linked to favourable changes in large scale temperature gradients, which I show to be largely underestimated by model simulations. Using surface temperature fingerprint as proxy for investigating historic and future model ensembles, evidence is presented that anthropogenic warming has likely increased the probability for the occurence of circumglobal Rossby waves. Further it is shown that this might lead to a doubling of such events until the end of the century under a high-emission scenario.
Overall, this thesis establishes several atmosphere-dynamical pathways by which changes in large scale temperature gradients might link to persistent boreal summer weather. It highlights the societal risks associated with the increasing occurence of a newly discovered Rossby wave teleconnection pattern, which has the potential to cause simultaneaous heat-extremes in the mid-latitudinal bread-basket regions. In addition, it provides further evidence that the traditional picture by which quasi-stationary Rossby waves occur only in the low wavenumber regime, should be reconsidered.
In this thesis entitled “Saccharide Recognition - Boronic acids as Receptors in Polymeric Networks” different aspects of boronic acid synthesis, their analysis and incorporation or attachment to different polymeric networks and characterisation thereof were investigated. The following key aspects were considered: • Provision of a variety of different characterised arylboronic acids and benzoboroxoles • Attachment of certain derivatives to nanoparticles and the characterisation of saccharide binding by means of isothermal titration calorimetry and displacement assay (ARS) to enhance the association constant to saccharides at pH 7.4 • Enhancement of selectivity in polymeric systems by means of molecular imprinting using fructose as template and a polymerisable benzoboroxole as functional monomer for the recognition at pH 7.4 (Joined by a diploma thesis of F. Grüneberger) • Development of biomimetic saccharide structures and the development of saccharide (especially glucose and fructose) binding MIPs by using these structures as template molecules. In the first part of the thesis different arylboronic acid derivatives were synthesised and their binding to glucose or fructose was investigated by means of isothermal titration calorimetry (ITC). It could be derived, which is in parallel to the literature, that derivatives bearing a methylhydroxyl-group in ortho-position to the boron (benzoboroxole) exhibit in most cases a two-fold higher association constant compared to the corresponding phenylboronic acid derivative. To gain a deeper understanding NMR spectroscopy and mass spectrometry with the benzoboroxole and glucose or fructose was performed. It could be shown that the exchange rate in terms of NMR time scale is quite slow since in titration experiments new peaks appeared. Via mass spectrometry of a mixture between benzoboroxole and glucose or fructose, different binding stoichiometries could be detected showing that the binding of saccharides is comparable with their binding to phenylboronic acid. In addition, the use of Alizarin Red S as an electrochemical reporter was described for the first time to monitor the saccharide binding to arylboronic acids not only with spectroscopy. Here, the redox behaviour and the displacement were recorded by cyclic voltammograms. In the second part different applications of boronic acids in polymeric networks were investigated. The attachment of benzoboroxoles to nanoparticles was investigated and monitored by means of isothermal titration calorimetry and a colourimetric assay with Alizarin Red S as the report dye. The investigations by isothermal titration calorimetry compared the fructose binding of arylboronic acids and benzoboroxoles coupled to these nanoparticles and “free” in solution. It could be shown that the attached derivatives showed a higher binding constant due to an increasing entropy term. This states for possible multivalent binding combined with a higher water release. Since ITC could not characterise the binding of glucose to these nanoparticles due to experimental restrictions the glucose binding at pH 7.4 was shown with ARS. Here, the displacement of ARS by fructose and also glucose could be followed and consequently these nanoparticles can be used for saccharide determination. Within this investigation also the temperature stability of these nanoparticles was examined and after normal sterilisation procedures (121°C, 20 min.) the binding behaviour was still unchanged. To target the selectivity of the used polymeric networks, molecular imprinting was used as a technique for creating artificial binding pockets on a molecular scale. As functional monomer 3-methacrylamidobenzoboroxole was introduced for the recognition of fructose. In comparison to polymers prepared with vinylphenylboronic acid the benzoboroxole containing polymer had a stronger binding at pH 7.4 which was shown for the first time. In addition, another imprinted polymer was synthesised especially for the recognition of glucose and fructose employing biomimetic saccharide analogues as template molecule. The advantage to use the saccharide analogues is the defined template-functional monomer complex during the polymerisation which is not the case, for example, for glucose-boronic acid interaction. The biomimetic character was proven through structural superimposition of crystal structures of the analogues with already described crystal structures of boronic acid esters of glucose and fructose. A molecularly imprinted polymer was synthesised with vinylphenylboronic acid as the functional monomer to show that both glucose and fructose are able to bind to the polymer which was predicted by the structural similarity of the analogues. The major scientific contributions of this thesis are • the determination of binding constants for some, not yet reported saccharide – boronic acid / benzoboroxole pairs, • the use of ARS as electrochemical reporter for saccharide detection, • the thermodynamic characterisation of a saccharide binding nanoparticle system containing benzoboroxole and functioning at pH 7.4, • the use of a polymerisable benzoboroxole as functional monomer for saccharide recognition in neutral, aqueous environments • and the synthesis and utilisation of biomimetic saccharide analogues as template molecules especially for the development of a glucose binding MIP.
The present thesis is to be brought into line with the current need for alternative and sustainable approaches toward energy management and materials design. In this context, carbon in particular has become the material of choice in many fields such as energy conversion and storage. Herein, three main topics are covered: 1)An alternative synthesis strategy toward highly porous functional carbons with tunable porosity using ordinary salts as porogen (denoted as “salt templating”) 2)The one-pot synthesis of porous metal nitride containing functional carbon composites 3)The combination of both approaches, enabling the generation of highly porous composites with finely tunable properties All approaches have in common that they are based on the utilization of ionic liquids, salts which are liquid below 100 °C, as precursors. Just recently, ionic liquids were shown to be versatile precursors for the generation of heteroatom-doped carbons since the liquid state and a negligible vapor pressure are highly advantageous properties. However, in most cases the products do not possess any porosity which is essential for many applications. In the first part, “salt templating”, the utilization of salts as diverse and sustainable porogens, is introduced. Exemplarily shown for ionic liquid derived nitrogen- and nitrogen-boron-co-doped carbons, the control of the porosity and morphology on the nanometer scale by salt templating is presented. The studies within this thesis were conducted with the ionic liquids 1-Butyl-3-methyl-pyridinium dicyanamide (Bmp-dca), 1-Ethyl-3-methyl-imidazolium dicyanamide (Emim-dca) and 1 Ethyl 3-methyl-imidazolium tetracyanoborate (Emim-tcb). The materials are generated through thermal treatment of precursor mixtures containing one of the ionic liquids and a porogen salt. By simple removal of the non-carbonizable template salt with water, functional graphitic carbons with pore sizes ranging from micro- to mesoporous and surface areas up to 2000 m2g-1 are obtained. The carbon morphologies, which presumably originate from different onsets of demixing, mainly depend on the nature of the porogen salt whereas the nature of the ionic liquid plays a minor role. Thus, a structural effect of the porogen salt rather than activation can be assumed. This offers an alternative to conventional activation and templating methods, enabling to avoid multiple-step and energy-consuming synthesis pathways as well as employment of hazardous chemicals for the template removal. The composition of the carbons can be altered via the heat-treatment procedure, thus at lower synthesis temperatures rather polymeric carbonaceous materials with a high degree of functional groups and high surface areas are accessible. First results suggest the suitability of the materials for CO2 utilization. In order to further illustrate the potential of ionic liquids as carbon precursors and to expand the class of carbons which can be obtained, the ionic liquid 1-Ethyl-3-methyl-imidazolium thiocyanate (Emim-scn) is introduced for the generation of nitrogen-sulfur-co-doped carbons in combination with the already studied ionic liquids Bmp-dca and Emim-dca. Here, the salt templating approach should also be applicable eventually further illustrating the potential of salt templating, too. In the second part, a one-pot and template-free synthesis approach toward inherently porous metal nitride nanoparticle containing nitrogen-doped carbon composites is presented. Since ionic liquids also offer outstanding solubility properties, the materials can be generated through the carbonization of homogeneous solutions of an ionic liquid acting as nitrogen as well as carbon source and the respective metal precursor. The metal content and surface area are easily tunable via the initial metal precursor amount. Furthermore, it is also possible to synthesize composites with ternary nitride nanoparticles whose composition is adjustable by the metal ratio in the precursor solution. Finally, both approaches are combined into salt templating of the one-pot composites. This opens the way to the one-step synthesis of composites with tunable composition, particle size as well as precisely controllable porosity and morphology. Thereby, common synthesis strategies where the product composition is often negatively affected by the template removal procedure can be avoided. The composites are further shown to be suitable as electrodes for supercapacitors. Here, different properties such as porosity, metal content and particle size are investigated and discussed with respect to their influence on the energy storage performance. Because a variety of ionic liquids, metal precursors and salts can be combined and a simple closed-loop process including salt recycling is imaginable, the approaches present a promising platform toward sustainable materials design.
Samarium hexaboride
(2018)
Although the basic structure of biological membranes is provided by the lipid bilayer, most of the specific functions are carried out by membrane proteins (MPs) such as channels, ion-pumps and receptors. Additionally, it is known, that mutations in MPs are directly or indirectly involved in many diseases. Thus, structure determination of MPs is of major interest not only in structural biology but also in pharmacology, especially for drug development. Advances in structural biology of membrane proteins (MPs) have been strongly supported by the success of three leading techniques: X-ray crystallography, electron microscopy and solution NMR spectroscopy. However, X-ray crystallography and electron microscopy, require highly diffracting 3D or 2D crystals, respectively. Today, structure determination of non-crystalline solid protein preparations has been made possible through rapid progress of solid-state MAS NMR methodology for biological systems. Castellani et. al. solved and refined the first structure of a microcrystalline protein using only solid-state MAS NMR spectroscopy. These successful application open up perspectives to access systems that are difficult to crystallise or that form large heterogeneous complexes and insoluble aggregates, for example ligands bound to a MP-receptor, protein fibrils and heterogeneous proteins aggregates. Solid-state MAS NMR spectroscopy is in principle well suited to study MP at atomic resolution. In this thesis, different types of MP preparations were tested for their suitability to be studied by solid-state MAS NMR. Proteoliposomes, poorly diffracting 2D crystals and a PEG precipitate of the outer membrane protein G (OmpG) were prepared as a model system for large MPs. Results from this work, combined with data found in the literature, show that highly diffracting crystalline material is not a prerequirement for structural analysis of MPs by solid-state MAS NMR. Instead, it is possible to use non-diffracting 3D crystals, MP precipitates, poorly diffracting 2D crystals and proteoliposomes. For the latter two types of preparations, the MP is reconstituted into a lipid bilayer, which thus allows the structural investigation in a quasi-native environment. In addition, to prepare a MP sample for solid-state MAS NMR it is possible to use screening methods, that are well established for 3D and 2D crystallisation of MPs. Hopefully, these findings will open a fourth method for structural investigation of MP. The prerequisite for structural studies by NMR in general, and the most time consuming step, is always the assignment of resonances to specific nuclei within the protein. Since the last few years an ever-increasing number of assignments from solid-state MAS NMR of uniformly carbon and nitrogen labelled samples is being reported, mostly for small proteins of up to around 150 amino acids in length. However, the complexity of the spectra increases with increasing molecular weight of the protein. Thus the conventional assignment strategies developed for small proteins do not yield a sufficiently high degree of assignment for the large MP OmpG (281 amino acids). Therefore, a new assignment strategy to find starting points for large MPs was devised. The assignment procedure is based on a sample with [2,3-13C, 15N]-labelled Tyr and Phe and uniformly labelled alanine and glycine. This labelling pattern reduces the spectral overlap as well as the number of assignment possibilities. In order to extend the assignment, four other specifically labelled OmpG samples were used. The assignment procedure starts with the identification of the spin systems of each labelled amino acid using 2D 13C-13C and 3D NCACX correlation experiments. In a second step, 2D and 3D NCOCX type experiments are used for the sequential assignment of the observed resonances to specific nuclei in the OmpG amino acid sequence. Additionally, it was shown in this work, that biosynthetically site directed labelled samples, which are normally used to observe long-range correlations, were helpful to confirm the assignment. Another approach to find assignment starting points in large protein systems, is the use of spectroscopic filtering techniques. A filtering block that selects methyl resonances was used to find further assignment starting points for OmpG. Combining all these techniques, it was possible to assign nearly 50 % of the observed signals to the OmpG sequence. Using this information, a prediction of the secondary structure elements of OmpG was possible. Most of the calculated motifs were in good aggreement with the crystal structures of OmpG. The approaches presented here should be applicable to a wide variety of MPs and MP-complexes and should thus open a new avenue for the structural biology of MPs.
This thesis presents new approaches of SAR methods and their application to tectonically active systems and related surface deformation. With 3 publications two case studies are presented:
(1) The coseismic deformation related to the Nura earthquake (5th October 2008, magnitude Mw 6.6) at the eastern termination of the intramontane Alai valley. Located between the southern Tien Shan and the northern Pamir the coseismic surface displacements are analysed using SAR (Synthetic Aperture RADAR) data. The results show clear gradients in the vertical and horizontal directions along a complex pattern of surface ruptures and active faults. To integrate and to interpret these observations in the context of the regional active tectonics a SAR data analysis is complemented with seismological data and geological field observations. The main moment release of the Nura earthquake appears to be on the Pamir Frontal thrust, while the main surface displacements and surface rupture occurred in the footwall and along of the NE–SW striking Irkeshtam fault. With InSAR data from ascending and descending satellite tracks along with pixel offset measurements the Nura earthquake source is modelled as a segmented rupture. One fault segment corresponds to high-angle brittle faulting at the Pamir Frontal thrust and two more fault segments show moderate-angle and low-friction thrusting at the Irkeshtam fault. The integrated analysis of the coseismic deformation argues for a rupture segmentation and strain partitioning associated to the earthquake. It possibly activated an orogenic wedge in the easternmost segment of the Pamir-Alai collision zone. Further, the style of the segmentation may be associated with the presence of Paleogene evaporites.
(2) The second focus is put on slope instabilities and consequent landslides in the area of prominent topographic transition between the Fergana basin and high-relief Alai range. The Alai range constitutes an active orogenic wedge of the Pamir – Tien Shan collision zone that described as a progressively northward propagating fold-and-thrust belt. The interferometric analysis of ALOS/PALSAR radar data integrates a period of 4 years (2007-2010) based on the Small Baseline Subset (SBAS) time-series technique to assess surface deformation with millimeter surface change accuracy. 118 interferograms are analyzed to observe spatially-continuous movements with downslope velocities up to 71 mm/yr. The obtained rates indicate slow movement of the deep-seated landslides during the observation time. We correlated these movements with precipitation and seismic records. The results suggest that the deformation peaks correlate with rainfall in the 3 preceding months and with one earthquake event. In the next step, to understand the spatial pattern of landslide processes, the tectonic morphologic and lithologic settings are combined with the patterns of surface deformation. We demonstrate that the lithological and tectonic structural patterns are the main controlling factors for landslide occurrence and surface deformation magnitudes. Furthermore active contractional deformation in the front of the orogenic wedge is the main mechanism to sustain relief. Some of the slower but continuously moving slope instabilities are directly related to tectonically active faults and unconsolidated young Quaternary syn-orogenic sedimentary sequences. The InSAR observed slow moving landslides represent active deep-seated gravitational slope deformation phenomena which is first time observed in the Tien Shan mountains. Our approach offers a new combination of InSAR techniques and tectonic aspects to localize and understand enhanced slope instabilities in tectonically active mountain fronts in the Kyrgyz Tien Shan.
Boolean Satisfiability (SAT) is one of the problems at the core of theoretical computer science. It was the first problem proven to be NP-complete by Cook and, independently, by Levin. Nowadays it is conjectured that SAT cannot be solved in sub-exponential time. Thus, it is generally assumed that SAT and its restricted version k-SAT are hard to solve. However, state-of-the-art SAT solvers can solve even huge practical instances of these problems in a reasonable amount of time.
Why is SAT hard in theory, but easy in practice? One approach to answering this question is investigating the average runtime of SAT. In order to analyze this average runtime the random k-SAT model was introduced. The model generates all k-SAT instances with n variables and m clauses with uniform probability. Researching random k-SAT led to a multitude of insights and tools for analyzing random structures in general. One major observation was the emergence of the so-called satisfiability threshold: A phase transition point in the number of clauses at which the generated formulas go from asymptotically almost surely satisfiable to asymptotically almost surely unsatisfiable. Additionally, instances around the threshold seem to be particularly hard to solve.
In this thesis we analyze a more general model of random k-SAT that we call non-uniform random k-SAT. In contrast to the classical model each of the n Boolean variables now has a distinct probability of being drawn. For each of the m clauses we draw k variables according to the variable distribution and choose their signs uniformly at random. Non-uniform random k-SAT gives us more control over the distribution of Boolean variables in the resulting formulas. This allows us to tailor distributions to the ones observed in practice. Notably, non-uniform random k-SAT contains the previously proposed models random k-SAT, power-law random k-SAT and geometric random k-SAT as special cases.
We analyze the satisfiability threshold in non-uniform random k-SAT depending on the variable probability distribution. Our goal is to derive conditions on this distribution under which an equivalent of the satisfiability threshold conjecture holds. We start with the arguably simpler case of non-uniform random 2-SAT. For this model we show under which conditions a threshold exists, if it is sharp or coarse, and what the leading constant of the threshold function is. These are exactly the three ingredients one needs in order to prove or disprove the satisfiability threshold conjecture. For non-uniform random k-SAT with k=3 we only prove sufficient conditions under which a threshold exists. We also show some properties of the variable probabilities under which the threshold is sharp in this case. These are the first results on the threshold behavior of non-uniform random k-SAT.
Large areas in the humid tropics are currently undergoing land-use change. The decrease of tropical rainforest, which is felled for land clearing and timber production, is countered by increasing areas of tree plantations and secondary forests. These changes are known to affect the regional water cycle as a result of plant-specific water demand and by influencing key soil properties which determine hydrological flow paths. One of these key properties sensitive to land-use change is the saturated hydraulic conductivity (Ks) as it governs vertical percolation of water within the soil profile. Low values of Ks in a certain soil depth can form an impeding layer and lead to perched water tables and the development of predominantly lateral flow paths such as overland flow. These processes can induce nutrient redistribution, erosion and soil degradation and thus affect ecosystem services and human livelihoods. Due to its sensitivity to land-use change, Ks is commonly used to assess the associated changes in hydrological flow paths. The objective of this dissertation was to assess the effect of land-use change on hydrological flow paths by analysing Ks as indicator variable. Sources of Ks variability, their implications for Ks monitoring and the relationship between Ks and near-surface hydrological flow paths in the context of land-use change were studied. The research area was located in central Panama, a country widely experiencing the abovementioned changes in land use. Ks is dependent on both static, soil-inherent properties such as particle size and clay mineralogy and dynamic, land use-dependent properties such as organic carbon content. By conducting a pair of studies with one of these influences held constant in each, the importance of static and dynamic properties for Ks was assessed. Applying a space-for-time approach to sample Ks under secondary forests of different age classes on comparable soils, a recovery of Ks from the former pasture use was shown to require more than eight years. The process was limited to the 0−6 cm sampling depth and showed large variability among replicates. A wavelet analysis of a Ks transect crossing different soil map units under comparable land cover, old-growth tropical rainforest, showed large small-scale variability, which was attributed to biotic influences, as well as a possible but non-conclusive influence of soil types. The two results highlight the importance of dynamic, land use-dependent influences on Ks. Monitoring studies can help to quantify land use-induced change of Ks, but there is a variety of sampling designs which differ in efficiency of estimating mean Ks. A comparative study of four designs and their suitability for Ks monitoring is used to give recommendations about designing a Ks monitoring scheme. Quantifying changes in spatial means of Ks for small catchments with a rotational stratified sampling design did not prove to be more efficient than Simple Random Sampling. The lack of large-scale spatial structure prevented benefits of stratification, and large small-scale variability resulting from local biotic processes and artificial effects of destructive sampling caused a lack of temporal consistency in the re-sampling of locations, which is part of the rotational design. The relationship between Ks and near-surface hydrological flow paths is of critical importance when assessing the consequences of land-use change in the humid tropics. The last part of this dissertation aimed at disclosing spatial relationships between Ks and overland flow as influenced by different land cover types. The effects of Ks on overland-flow generation were spatially variable, different between planar plots and incised flowlines and strongly influenced by land-cover characteristics. A simple comparison of Ks values and rainfall intensities was insufficient to describe the observed pattern of overland flow. Likewise, event flow in the stream was apparently not directly related to overland flow response patterns within the catchments. The study emphasises the importance of combining pedological, hydrological, meteorological and botanical measurements to comprehensively understand the land use-driven change in hydrological flow paths. In summary, Ks proved to be a suitable parameter for assessing the influence of land-use change on soils and hydrological processes. The results illustrated the importance of land cover and spatial variability of Ks for decisions on sampling designs and for interpreting overland-flow generation. As relationships between Ks and overland flow were shown to be complex and dependent on land cover, an interdisciplinary approach is required to comprehensively understand the effects of land-use change on soils and near-surface hydrological flow paths in the humid tropics.
Savannas cover a broad geographical range across continents and are a biome best described by a mix of herbaceous and woody plants. The former create a more or less continuous layer while the latter should be sparse enough to leave an open canopy. What has long intrigued ecologists is how these two competing plant life forms of vegetation coexist.
Initially attributed to resource competition, coexistence was considered the stable outcome of a root niche differentiation between trees and grasses. The importance of environmental factors became evident later, when data from moister environments demonstrated that tree cover was often lower than what the rainfall conditions would allow for. Our current understanding relies on the interaction of competition and disturbances in space and time. Hence, the influence of grazing and fire and the corresponding feedbacks they generate have been keenly investigated. Grazing removes grass cover, initiating a self-reinforcing process propagating tree cover expansion. This is known as the encroachment phenomenon. Fire, on the other hand, imposes a bottleneck on the tree population by halting the recruitment of young trees into adulthood. Since grasses fuel fires, a feedback linking grazing, grass cover, fire, and tree cover is created. In African savannas, which are the focus of this dissertation, these feedbacks play a major role in the dynamics.
The importance of these feedbacks came into sharp focus when the notion of alternative states began to be applied to savannas. Alternative states in ecology arise when different states of an ecosystem can occur under the same conditions. According to this an open savanna and a tree-dominated savanna can be classified as alternative states, since they can both occur under the same climatic conditions. The aforementioned feedbacks are critical in the creation of alternative states. The grass-fire feedback can preserve an open canopy as long as fire intensity and frequency remain above a certain threshold. Conversely, crossing a grazing threshold can force an open savanna to shift to a tree-dominated state. Critically, transitions between such alternative states can produce hysteresis, where a return to pre-transition conditions will not suffice to restore the ecosystem to its original state.
In the chapters that follow, I will cover aspects relating to the coexistence mechanisms and the role of feedbacks in tree-grass interactions. Coming back to the coexistence question, due to the overwhelming focus on competition and disturbance another important ecological process was neglected: facilitation. Therefore, in the first study within this dissertation I examine how facilitation can expand the tree-grass coexistence range into drier conditions. For the second study I focus on another aspect of savanna dynamics which remains underrepresented in the literature: the impacts of inter-annual rainfall variability upon savanna trees and the resilience of the savanna state. In the third and final study within this dissertation I approach the well-researched encroachment phenomenon from a new perspective: I search for an early warning indicator of the process to be used as a prevention tool for savanna conservation. In order to perform all this work I developed a mathematical ecohydrological model of Ordinary Differential Equations (ODEs) with three variables: soil moisture content, grass cover and tree cover.
Facilitation: Results showed that the removal of grass cover through grazing was detrimental to trees under arid conditions, contrary to expectation based on resource competition. The reason was that grasses preserved moisture in the soil through infiltration and shading, thus ameliorating the harsh conditions for trees in accordance with the Stress Gradient Hypothesis. The exclusion of grasses from the model further demonstrated this: tree cover was lower in the absence of grasses, indicating that the benefits of grass facilitation outweighed the costs of grass competition for trees. Thus, facilitation expanded the climatic range where savannas persisted into drier conditions.
Rainfall variability: By adjusting the model to current rainfall patterns in East Africa, I simulated conditions of increasing inter-annual rainfall variability for two distinct mean rainfall scenarios: semi-arid and mesic. Alternative states of tree-less grassland and tree-dominated savanna emerged in both cases. Increasing variability reduced semi-arid savanna tree cover to the point that at high variability the savanna state was eliminated, because variability intensified resource competition and strengthened the fire disturbance during high rainfall years. Mesic savannas, on the other hand, became more resilient along the variability gradient: increasing rainfall variability created more opportunities for the rapid growth of trees to overcome the fire disturbance, boosting the chances of savannas persisting and thus increasing mesic savanna resilience.
Preventing encroachment: The breakdown in the grass-fire feedback caused by heavy grazing promoted the expansion of woody cover. This could be irreversible due to the presence of alternative states of encroached and open savanna, which I found along a simulated grazing gradient. When I simulated different short term heavy grazing treatments followed by a reduction to the original grazing conditions, certain cases converged to the encroached state. Utilising woody cover changes only during the heavy grazing treatment, I developed an early warning indicator which identified these cases with a high risk of such hysteresis and successfully distinguished them from those with a low risk. Furthermore, after validating the indicator on encroachment data, I demonstrated that it appeared early enough for encroachment to be prevented through realistic grazing-reduction treatments.
Though this dissertation is rooted in the theory of savanna dynamics, its results can have significant applications in savanna conservation. Facilitation has only recently become a topic of interest within savanna literature. Given the threat of increasing droughts and a general anticipation of drier conditions in parts of Africa, insights stemming from this research may provide clues for preserving arid savannas. The impacts of rainfall variability on savannas have not yet been thoroughly studied, either. Conflicting results appear as a result of the lack of a robust theoretical understanding of plant interactions under variable conditions. . My work and other recent studies argue that such conditions may increase the importance of fast resource acquisition creating a ‘temporal niche’. Woody encroachment has been extensively studied as phenomenon, though not from the perspective of its early identification and prevention. The development of an encroachment forecasting tool, as the one presented in this work, could protect both the savanna biome and societies dependent upon it for (economic) survival. All studies which follow are bound by the attempt to broaden the horizons of savanna-related research in order to deal with extreme conditions and phenomena; be it through the enhancement of the coexistence debate or the study of an imminent external threat or the development of a management-oriented tool for the conservation of savannas.
Cloud computing is a model for enabling on-demand access to a shared pool of computing resources. With virtually limitless on-demand resources, a cloud environment enables the hosted Internet application to quickly cope when there is an increase in the workload. However, the overhead of provisioning resources exposes the Internet application to periods of under-provisioning and performance degradation. Moreover, the performance interference, due to the consolidation in the cloud environment, complicates the performance management of the Internet applications. In this dissertation, we propose two approaches to mitigate the impact of the resources provisioning overhead. The first approach employs control theory to scale resources vertically and cope fast with workload. This approach assumes that the provider has knowledge and control over the platform running in the virtual machines (VMs), which limits it to Platform as a Service (PaaS) and Software as a Service (SaaS) providers. The second approach is a customer-side one that deals with the horizontal scalability in an Infrastructure as a Service (IaaS) model. It addresses the trade-off problem between cost and performance with a multi-goal optimization solution. This approach finds the scale thresholds that achieve the highest performance with the lowest increase in the cost. Moreover, the second approach employs a proposed time series forecasting algorithm to scale the application proactively and avoid under-utilization periods. Furthermore, to mitigate the interference impact on the Internet application performance, we developed a system which finds and eliminates the VMs suffering from performance interference. The developed system is a light-weight solution which does not imply provider involvement. To evaluate our approaches and the designed algorithms at large-scale level, we developed a simulator called (ScaleSim). In the simulator, we implemented scalability components acting as the scalability components of Amazon EC2. The current scalability implementation in Amazon EC2 is used as a reference point for evaluating the improvement in the scalable application performance. ScaleSim is fed with realistic models of the RUBiS benchmark extracted from the real environment. The workload is generated from the access logs of the 1998 world cup website. The results show that optimizing the scalability thresholds and adopting proactive scalability can mitigate 88% of the resources provisioning overhead impact with only a 9% increase in the cost.
Scalable data profiling
(2018)
Data profiling is the act of extracting structural metadata from datasets. Structural metadata, such as data dependencies and statistics, can support data management operations, such as data integration and data cleaning. Data management often is the most time-consuming activity in any data-related project. Its support is extremely valuable in our data-driven world, so that more time can be spent on the actual utilization of the data, e. g., building analytical models. In most scenarios, however, structural metadata is not given and must be extracted first. Therefore, efficient data profiling methods are highly desirable.
Data profiling is a computationally expensive problem; in fact, most dependency discovery problems entail search spaces that grow exponentially in the number of attributes. To this end, this thesis introduces novel discovery algorithms for various types of data dependencies – namely inclusion dependencies, conditional inclusion dependencies, partial functional dependencies, and partial unique column combinations – that considerably improve over state-of-the-art algorithms in terms of efficiency and that scale to datasets that cannot be processed by existing algorithms. The key to those improvements are not only algorithmic innovations, such as novel pruning rules or traversal strategies, but also algorithm designs tailored for distributed execution. While distributed data profiling has been mostly neglected by previous works, it is a logical consequence on the face of recent hardware trends and the computational hardness of dependency discovery.
To demonstrate the utility of data profiling for data management, this thesis furthermore presents Metacrate, a database for structural metadata. Its salient features are its flexible data model, the capability to integrate various kinds of structural metadata, and its rich metadata analytics library. We show how to perform a data anamnesis of unknown, complex datasets based on this technology. In particular, we describe in detail how to reconstruct the schemata and assess their quality as part of the data anamnesis.
The data profiling algorithms and Metacrate have been carefully implemented, integrated with the Metanome data profiling tool, and are available as free software. In that way, we intend to allow for easy repeatability of our research results and also provide them for actual usage in real-world data-related projects.
This study investigates spatial patterns of Ks and tests the hypothesis of whether structural variance emerges from noise with increasing sampling precision. We analyzed point measurements of Ks along independent transects at sampling intervals of 25, 10, 1 and 0.25 m. The field area is a tropical rainforest catena (i.e. toposequence) characterized by systematic downslope changes in soil properties including color (red to yellow), mineralogy (kaolinite- illite to kaolinite) and texture (sandy clay to sand). Independent tramsects spanning the entire catena at lag intervals of 25 and 10 in reveal little to no spatial patterns in Ks; i.e. scatter plots are noisy and lack apparent spatial trends, and semivariograms suggest little to no autocorrelation in Ks. As sampling precision is increased (h = 1 and 0.25 m), spatial patterns emerge in Ks for the downslope areas, in which distinctive hydraulic boundaries in Ks correlate with relatively small-scale, topography-controlled soils with coarse textures (greater than or equal to 80% sand). For these areas, semivariograms of Ks and those of %sand and %clay exhibit similar spatial structure characterized by small nugget variances and large ranges, and nugget variance is reduced as sampling precision increases from 1 to 0.25 m. In the upslope, clay-rich locations along this toposequence, Ks exhibits few spatial patterns, irrespective of sampling scale. For these locations, scatter plots are noisy without apparent spatial trends, and semivariograms show almost complete nugget variance, suggesting little to no correlation in this hydraulic parameter at any scale. This study suggests that in the absence of coarse textures (greater than or equal to 80% sand), there is little predictability in Ks, even at sampling intervals of 0.25 m. We believe this lack of spatial structure is due to a predominance of small-scale processes such as biological activity that largely control Ks in this forested setting. (C) 2003 Elsevier B.V. All rights reserved
Subject of this work is the investigation of universal scaling laws which are observed in coupled chaotic systems. Progress is made by replacing the chaotic fluctuations in the perturbation dynamics by stochastic processes. First, a continuous-time stochastic model for weakly coupled chaotic systems is introduced to study the scaling of the Lyapunov exponents with the coupling strength (coupling sensitivity of chaos). By means of the the Fokker-Planck equation scaling relations are derived, which are confirmed by results of numerical simulations. Next, the new effect of avoided crossing of Lyapunov exponents of weakly coupled disordered chaotic systems is described, which is qualitatively similar to the energy level repulsion in quantum systems. Using the scaling relations obtained for the coupling sensitivity of chaos, an asymptotic expression for the distribution function of small spacings between Lyapunov exponents is derived and compared with results of numerical simulations. Finally, the synchronization transition in strongly coupled spatially extended chaotic systems is shown to resemble a continuous phase transition, with the coupling strength and the synchronization error as control and order parameter, respectively. Using results of numerical simulations and theoretical considerations in terms of a multiplicative noise partial differential equation, the universality classes of the observed two types of transition are determined (Kardar-Parisi-Zhang equation with saturating term, directed percolation).