@phdthesis{Brachs2015,
  author    = {Brachs, Maria},
  title     = {Genome wide expression analysis and metabolic mechanisms predicting body weight maintenance},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-100767},
  school      = {Universit{\"a}t Potsdam},
  pages     = {106},
  year      = {2015},
  abstract  = {Obesity is a major health problem for many developing and industrial countries. Increasing rates reach almost 50 \% of the population in some countries and related metabolic diseases including cardiovascular events and T2DM are challenging the health systems. Adiposity, an increase in body fat mass, is a major hallmark of obesity. Adipose tissue is long known not only to store lipids but also to influence whole-body metabolism including food intake, energy expenditure and insulin sensitivity. Adipocytes can store lipids and thereby protect other tissue from lipotoxic damage. However, if the energy intake is higher than the energy expenditure over a sustained time period, adipose tissue will expand. This can lead to an impaired adipose tissue function resulting in higher levels of plasma lipids, which can affect other tissue like skeletal muscle, finally leading to metabolic complications. Several studies showed beneficial metabolic effects of weight reduction in obese subjects immediately after weight loss. However, weight regain is frequently observed along with potential negative effects on cardiovascular risk factors and a high intra-individual response. We performed a body weight maintenance study investigating the mechanisms of weight maintenance after intended WR. Therefore we used a low caloric diet followed by a 12-month life-style intervention. Comprehensive phenotyping including fat and muscle biopsies was conducted to investigate hormonal as well as metabolic influences on body weight regulation. In this study, we showed that weight reduction has numerous potentially beneficial effects on metabolic parameters. After 3-month WR subjects showed significant weight and fat mass reduction, lower TG levels as well as higher insulin sensitivity. Using RNA-Seq to analyse whole fat and muscle transcriptome a strong impact of weight reduction on adipose tissue gene expression was observed. Gene expression alterations over weight reduction included several cellular metabolic genes involved in lipid and glucose metabolism as well as insulin signalling and regulatory pathways. These changes were also associated with anthropometric parameters assigning body composition. Our data indicated that weight reduction leads to a decreased expression of several lipid catabolic as well as anabolic genes. Long-term body weight maintenance might be influenced by several parameters including hormones, metabolic intermediates as well as the transcriptional landscape of metabolic active tissues. Our data showed that genes involved in biosynthesis of unsaturated fatty acids might influence the BMI 18-month after a weight reduction phase. This was further supported by analysing metabolic parameters including RQ and FFA levels. We could show that subjects maintaining their lost body weight had a higher RQ and lower FFA levels, indicating increased metabolic flexibility in subjects. Using this transcriptomic approach we hypothesize that low expression levels of lipid synthetic genes in adipose tissue together with a higher mitochondrial activity in skeletal muscle tissue might be beneficial in terms of body weight maintenance.},
  language  = {en}
}
@phdthesis{Bourgonje2021,
  author    = {Bourgonje, Peter},
  title     = {Shallow discourse parsing for German},
  doi       = {10.25932/publishup-50663},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-506632},
  school      = {Universit{\"a}t Potsdam},
  pages     = {vii, 140},
  year      = {2021},
  abstract  = {While the last few decades have seen impressive improvements in several areas in Natural Language Processing, asking a computer to make sense of the discourse of utterances in a text remains challenging. There are several different theories that aim to describe and analyse the coherent structure that a well-written text inhibits. These theories have varying degrees of applicability and feasibility for practical use. Presumably the most data-driven of these theories is the paradigm that comes with the Penn Discourse TreeBank, a corpus annotated for discourse relations containing over 1 million words. Any language other than English however, can be considered a low-resource language when it comes to discourse processing. This dissertation is about shallow discourse parsing (discourse parsing following the paradigm of the Penn Discourse TreeBank) for German. The limited availability of annotated data for German means the potential of modern, deep-learning based methods relying on such data is also limited. This dissertation explores to what extent machine-learning and more recent deep-learning based methods can be combined with traditional, linguistic feature engineering to improve performance for the discourse parsing task. A pivotal role is played by connective lexicons that exhaustively list the discourse connectives of a particular language along with some of their core properties. To facilitate training and evaluation of the methods proposed in this dissertation, an existing corpus (the Potsdam Commentary Corpus) has been extended and additional data has been annotated from scratch. The approach to end-to-end shallow discourse parsing for German adopts a pipeline architecture and either presents the first results or improves over state-of-the-art for German for the individual sub-tasks of the discourse parsing task, which are, in processing order, connective identification, argument extraction and sense classification. The end-to-end shallow discourse parser for German that has been developed for the purpose of this dissertation is open-source and available online. In the course of writing this dissertation, work has been carried out on several connective lexicons in different languages. Due to their central role and demonstrated usefulness for the methods proposed in this dissertation, strategies are discussed for creating or further developing such lexicons for a particular language, as well as suggestions on how to further increase their usefulness for shallow discourse parsing.},
  language  = {en}
}
@phdthesis{Bouma2021,
  author    = {Bouma, Sietske},
  title     = {The circum- and intergalactic medium and its connection to the large scale structure in the nearby universe},
  doi       = {10.25932/publishup-52085},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-520852},
  school      = {Universit{\"a}t Potsdam},
  pages     = {iii, 102},
  year      = {2021},
  abstract  = {The majority of baryons in the Universe is believed to reside in the intergalactic medium (IGM). This makes the IGM an important component in understanding cosmological structure formation. It is expected to trace the same dark matter distribution as galaxies, forming structures like filaments and clusters. However, whereas galaxies can be observed to be arranged along these large-scale structures, the spatial distribution of the diffuse IGM is not as easily unveiled. Absorption line studies of quasar (QSO) spectra can help with mapping the IGM, as well as the boundary layer between IGM and galaxies: the circumgalactic medium (CGM). By studying gas in the Local Group, as well as in the IGM, this study aims to get a better understanding of how the gas is linked to the large-scale structure of the local Universe and the galaxies residing in that structure. Chapter 1 gives an introduction to the CGM and IGM, while the methods used in this study are explained in Chapter 2. Chapter 3 starts on a relatively small cosmological scale, namely that of our Local Group, which includes i.a. the Milky Way (MW) and the M31. Within the CGM of the MW, there exist denser clouds, some of which are infalling while others are moving away from the Galactic disc. To study these clouds, 29 QSO spectra obtained with the Cosmic Origins Spectrograph (COS) aboard the Hubble Space Telescope (HST) were analysed. Abundances of Si II, Si III, Si IV, C II, and C IV were measured for 69 HVCs belonging to two samples: one in the direction of the LG's barycentre and the other in the anti-barycentre direction. Their velocities range from -100 ≥ vLSR ≥ -400 km/s for the barycentre sample and between +100 ≤ vLSR ≤ +300 km/s for the anti-barycentre sample. By using Cloudy models, these data could then be used to derive gas volume densities for the HVCs. Because of the relationship between density and pressure of the ambient medium, which is in turn determined by the Galactic radiation field, the distances of the HVCs could be estimated. From this, a subsample of absorbers located in the direction of M31 was found to exist outside of the MW's virial radius, their low densities (log nH ≤ -3.54) making it likely for them to be part of the gas in between the MW and M31. No such low-density absorbers were found in the anti-barycentre sample. Our results thus hint at gas following the dark matter potential, which would be deeper between the MW and M31 as they are by far the most massive members of the LG. From this bridge of gas in the LG, this study zooms out to the large-scale structure of the local Universe (z ~ 0) in Chapter 4. Galaxy data from the V8k catalogue and QSO spectra from COS were used to study the relation between the galaxies tracing large-scale filaments and the gas existing outside of those galaxies. This study used the filaments defined in Courtois et al. (2013). A total of 587 Lyman α (Lyα) absorbers were found in the 302 QSO spectra in the velocity range 1070 - 6700 km/s. After selecting sightlines passing through or close to these filaments, model spectra were made for 91 sightlines and 215 (227) Lyα absorbers (components) were measured in this sample. The velocity gradient along each filament was calculated and 74 absorbers were found within 1000 km/s of the nearest filament segment. In order to find whether the absorbers are more tied to galaxies or to the large-scale structure, equivalent widths of the Lyα absorbers were plotted against both galaxy and filament impact parameters. While stronger absorbers do tend to be closer to either galaxies or filaments, there is a large scatter in this relation. Despite this large scatter, this study found that the absorbers do not follow a random distribution either. They cluster less strongly around filaments than galaxies, but stronger than random distributions, as confirmed by a Kolmogorov-Smirnov test. Furthermore, the column density distribution function found in this study has a slope of -β = 1.63±0.12 for the total sample and -β =1.47±0.24 for the absorbers within 1000 km/s of a filament. The shallower slope for the latter subsample could indicate an excess of denser absorbers within the filament, but they are consistent within errors. These values are in agreement with values found in e.g. Lehner et al. (2007); Danforth et al. (2016). The picture that emerges from this study regarding the relation between the IGM and the large-scale structure in the local Universe fits with what is found in other studies: while at least part of the gas traces the same filamentary structure as galaxies, the relation is complex. This study has shown that by taking a large sample of sightlines and comparing the data gathered from those with galaxy data, it is possible to study the gaseous large-scale structure. This approach can be used in the future together with simulations to get a better understanding of structure formation and evolution in the Universe.},
  language  = {en}
}
@phdthesis{Bostroem2004,
  author    = {Bostr{\"o}m, Kim},
  title     = {Lossless quantum data compression and secure direct communication},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001383},
  school      = {Universit{\"a}t Potsdam},
  year      = {2004},
  abstract  = {Diese Dissertation behandelt die Kodierung und Verschickung von Information durch einen Quantenkanal. Ein Quantenkanal besteht aus einem quantenmechanischen System, welches vom Sender manipuliert und vom Empf{\"a}nger ausgelesen werden kann. Dabei repr{\"a}sentiert der individuelle Zustand des Kanals die Nachricht. Die zwei Themen der Dissertation umfassen 1) die M{\"o}glichkeit, eine Nachricht in einem Quantenkanal verlustfrei zu komprimieren und 2) die M{\"o}glichkeit eine Nachricht von einer Partei zu einer einer anderen direkt und auf sichere Weise zu {\"u}bermitteln, d.h. ohne dass es einer dritte Partei m{\"o}glich ist, die Nachricht abzuh{\"o}ren und dabei unerkannt zu bleiben. Die wesentlichen Ergebnisse der Dissertation sind die folgenden. Ein allgemeiner Formalismus f{\"u}r Quantencodes mit variabler L{\"a}nge wird ausgearbeitet. Diese Codes sind notwendig um verlustfreie Kompression zu erm{\"o}glichen. Wegen der Quantennatur des Kanals sind die codierten Nachrichten allgemein in einer Superposition von verschiedenen L{\"a}ngen. Es zeigt sich, daß es unm{\"o}glich ist eine Quantennachricht verlustfrei zu komprimieren, wenn diese dem Sender nicht apriori bekannt ist. Im anderen Falle wird die M{\"o}glichkeit verlustfreier Quantenkompression gezeigt und eine untere Schranke f{\"u}r die Kompressionsrate abgeleitet. Des weiteren wird ein expliziter Kompressionsalgorithmus konstruiert, der f{\"u}r beliebig vorgegebene Ensembles aus Quantennachrichten funktioniert. Ein quantenkryptografisches Prokoll - das \“Ping-Pong Protokoll\” - wird vorgestellt, welches die sichere direkte {\"u}bertragung von klassischen Nachrichten durch einen Quantenkanal erm{\"o}glicht. Die Sicherheit des Protokolls gegen beliebige Abh{\"o}rangriffe wird bewiesen f{\"u}r den Fall eines idealen Quantenkanals. Im Gegensatz zu anderen quantenkryptografischen Verfahren ist das Ping-Pong Protokoll deterministisch und kann somit sowohl f{\"u}r die {\"U}bermittlung eines zuf{\"a}lligen Schl{\"u}ssels als auch einer komponierten Nachricht verwendet werden. Das Protokoll is perfekt sicher f{\"u}r die {\"U}bertragung eines Schl{\"u}ssels und quasi-sicher f{\"u}r die direkte {\"U}bermittlung einer Nachricht. Letzteres bedeutet, dass die Wahrscheinlichkeit eines erfolgreichen Abh{\"o}rangriffs exponenziell mit der L{\"a}nge der Nachricht abnimmt.},
  language  = {en}
}
@phdthesis{Bortfeld2013,
  author    = {Bortfeld, Silvia},
  title     = {Analysis of Medicago truncatula transcription factors involved in the arbuscular mycorrhizal symbiosis},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70664},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {For the first time the transcriptional reprogramming of distinct root cortex cells during the arbuscular mycorrhizal (AM) symbiosis was investigated by combining Laser Capture Mirodissection and Affymetrix GeneChip® Medicago genome array hybridization. The establishment of cryosections facilitated the isolation of high quality RNA in sufficient amounts from three different cortical cell types. The transcript profiles of arbuscule-containing cells (arb cells), non-arbuscule-containing cells (nac cells) of Rhizophagus irregularis inoculated Medicago truncatula roots and cortex cells of non-inoculated roots (cor) were successfully explored. The data gave new insights in the symbiosis-related cellular reorganization processes and indicated that already nac cells seem to be prepared for the upcoming fungal colonization. The mycorrhizal- and phosphate-dependent transcription of a GRAS TF family member (MtGras8) was detected in arb cells and mycorrhizal roots. MtGRAS shares a high sequence similarity to a GRAS TF suggested to be involved in the fungal colonization processes (MtRAM1). The function of MtGras8 was unraveled upon RNA interference- (RNAi-) mediated gene silencing. An AM symbiosis-dependent expression of a RNAi construct (MtPt4pro::gras8-RNAi) revealed a successful gene silencing of MtGras8 leading to a reduced arbuscule abundance and a higher proportion of deformed arbuscules in root with reduced transcript levels. Accordingly, MtGras8 might control the arbuscule development and life-time. The targeting of MtGras8 by the phosphate-dependent regulated miRNA5204* was discovered previously (Devers et al., 2011). Since miRNA5204* is known to be affected by phosphate, the posttranscriptional regulation might represent a link between phosphate signaling and arbuscule development. In this work, the posttranscriptional regulation was confirmed by mis-expression of miRNA5204* in M. truncatula roots. The miRNA-mediated gene silencing affects the MtGras8 transcript abundance only in the first two weeks of the AM symbiosis and the mis-expression lines seem to mimic the phenotype of MtGras8-RNAi lines. Additionally, MtGRAS8 seems to form heterodimers with NSP2 and RAM1, which are known to be key regulators of the fungal colonization process (Hirsch et al., 2009; Gobbato et al., 2012). These data indicate that MtGras8 and miRNA5204* are linked to the sym pathway and regulate the arbuscule development in phosphate-dependent manner.},
  language  = {en}
}
@phdthesis{Boroudjerdi2005,
  author    = {Boroudjerdi, Hoda},
  title     = {Charged polymer-macroion complexes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6282},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {This work explores the equilibrium structure and thermodynamic phase behavior of complexes formed by charged polymer chains (polyelectrolytes) and oppositely charged spheres (macroions). Polyelectrolyte-macroion complexes form a common pattern in soft-matter physics, chemistry and biology, and enter in numerous technological applications as well. From a fundamental point of view, such complexes are interesting in that they combine the subtle interplay between electrostatic interactions and elastic as well as entropic effects due to conformational changes of the polymer chain, giving rise to a wide range of structural properties. This forms the central theme of theoretical studies presented in this thesis, which concentrate on a number of different problems involving strongly coupled complexes, i.e. complexes that are characterized by a large adsorption energy and small chain fluctuations. In the first part, a global analysis of the structural phase behavior of a single polyelectrolyte-macroion complex is presented based on a dimensionless representation, yielding results that cover a wide range of realistic system parameters. Emphasize is made on the interplay between the effects due to the polyelectrolytes chain length, salt concentration and the macroion charge as well as the mechanical chain persistence length. The results are summarized into generic phase diagrams characterizing the wrapping-dewrapping behavior of a polyelectrolyte chain on a macroion. A fully wrapped chain state is typically obtained at intermediate salt concentrations and chain lengths, where the amount of polyelectrolyte charge adsorbed on the macroion typically exceeds the bare macroion charge leading thus to a highly overcharged complex. Perhaps the most striking features occur when a single long polyelectrolyte chain is complexed with many oppositely charged spheres. In biology, such complexes form between DNA (which carries the cell's genetic information) and small oppositely charged histone proteins serving as an efficient mechanism for packing a huge amount of DNA into the micron-size cell nucleus in eucaryotic cells. The resultant complex fiber, known as the chromatin fiber, appears with a diameter of 30~nm under physiological conditions. Recent experiments indicate a zig-zag spatial arrangement for individual DNA-histone complexes (nucleosome core particles) along the chromatin fiber. A numerical method is introduced in this thesis based on a simple generic chain-sphere cell model that enables one to investigate the mechanism of fiber formation on a systematic level by incorporating electrostatic and elastic contributions. As will be shown, stable complex fibers exhibit an impressive variety of structures including zig-zag, solenoidal and beads-on-a-string patterns, depending on system parameters such as salt concentration, sphere charge as well as the chain contour length (per sphere). The present results predict fibers of compact zig-zag structure within the physiologically relevant regime with a diameter of about 30~nm, when DNA-histone parameters are adopted. In the next part, a numerical method is developed in order to investigate the role of thermal fluctuations on the structure and thermodynamic phase behavior of polyelectrolyte-macroion complexes. This is based on a saddle-point approximation, which allows to describe the experimentally observed reaction (or complexation) equilibrium in a dilute solution of polyelectrolytes and macroions on a systematic level. This equilibrium is determined by the entropy loss a single polyelectrolyte chain suffers as it binds to an oppositely charged macroion. This latter quantity can be calculated from the spectrum of polyelectrolyte fluctuations around a macroion, which is determined by means of a normal-mode analysis. Thereby, a stability phase diagram is obtained, which exhibits qualitative agreement with experimental findings. At elevated complex concentrations, one needs to account for the inter-complex interactions as well. It will be shown that at small separations, complexes undergo structural changes in such a way that positive patches from one complex match up with negative patches on the other. Furthermore, one of the polyelectrolyte chains may bridge between the two complexes. These mechanisms lead to a strong inter-complex attraction. As a result, the second virial coefficient associated with the inter-complex interaction becomes negative at intermediate salt concentrations in qualitative agreement with recent experiments on solutions of nucleosome core particles.},
  subject      = {Biopolymere},
  language  = {en}
}
@phdthesis{Borisova2012,
  author    = {Borisova, Dimitriya},
  title     = {Feedback active coatings based on mesoporous silica containers},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-63505},
  school      = {Universit{\"a}t Potsdam},
  year      = {2012},
  abstract  = {Metalle werden oft w{\"a}hrend ihrer Anwendung korrosiven Bedingungen ausgesetzt, was ihre Alterungsbest{\"a}ndigkeit reduziert. Deswegen werden korrosionsanf{\"a}llige Metalle, wie Aluminiumlegierungen mit Schutzbeschichtungen versehen, um den Korrosionsprozess aktiv oder passiv zu verhindern. Die klassischen Schutzbeschichtungen funktionieren als physikalische Barriere zwischen Metall und korrosiver Umgebung und bieten einen passiven Korrosionsschutz nur, wenn sie unbesch{\"a}digt sind. Im Gegensatz dazu kann die Korrosion auch im Fall einer Besch{\"a}digung mittels aktiver Schutzbeschichtungen gehemmt werden. Chromathaltige Beschichtungen bieten heutzutage den besten aktiven Korrosionsschutz f{\"u}r Aluminiumlegierungen. Aufgrund ihrer Giftigkeit wurden diese weltweit verboten und m{\"u}ssen durch neue umweltfreundliche Schutzbeschichtungen ersetzt werden. Ein potentieller Ersatz sind Schutzbeschichtungen mit integrierten Nano- und Mikrobeh{\"a}ltern, die mit ungiftigem Inhibitor gef{\"u}llt sind. In dieser Arbeit werden die Entwicklung und Optimierung solcher aktiver Schutzbeschichtungen f{\"u}r die industriell wichtige Aluminiumlegierung AA2024-T3 dargestellt Mesopor{\"o}se Silika-Beh{\"a}lter wurden mit dem ungiftigen Inhibitor (2-Mercaptobenzothiazol) beladen und dann in die Matrix anorganischer (SiOx/ZrOx) oder organischer (wasserbasiert) Schichten dispergiert. Zwei Sorten von Silika-Beh{\"a}ltern mit unterschiedlichen Gr{\"o}ßen (d ≈ 80 and 700 nm) wurden verwendet. Diese haben eine große spezifische Oberfl{\"a}che (≈ 1000 m² g-1), eine enge Porengr{\"o}ßenverteilung mit mittlerer Porenweite ≈ 3 nm und ein großes Porenvolumen (≈ 1 mL g-1). Dank dieser Eigenschaften k{\"o}nnen große Inhibitormengen im Beh{\"a}lterinneren adsorbiert und gehalten werden. Die Inhibitormolek{\"u}le werden bei korrosionsbedingter Erh{\"o}hung des pH-Wertes gel{\"o}st und freigegeben. Die Konzentration, Position und Gr{\"o}ße der integrierten Beh{\"a}lter wurden variiert um die besten Bedingungen f{\"u}r einen optimalen Korrosionsschutz zu bestimmen. Es wurde festgestellt, dass eine gute Korrosionsschutzleistung durch einen Kompromiss zwischen ausreichender Inhibitormenge und guten Barriereeigenschaften hervorgerufen wird. Diese Studie erweitert das Wissen {\"u}ber die wichtigsten Faktoren, die den Korrosionsschutz beeinflussen. Somit wurde die Entwicklung effizienter, aktiver Schutzbeschichtungen erm{\"o}glicht, die auf mit Inhibitor beladenen Beh{\"a}ltern basieren.},
  language  = {en}
}
@phdthesis{Borghini2020,
  author    = {Borghini, Alessia},
  title     = {Melt inclusions in mafic rocks as witnesses of metasomatism in the Bohemian Massif},
  doi       = {10.25932/publishup-47363},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-473639},
  school      = {Universit{\"a}t Potsdam},
  pages     = {205},
  year      = {2020},
  abstract  = {Orogenic peridotites represent portions of upper subcontinental mantle now incorporated in mountain belts. They often contain layers, lenses and irregular bodies of pyroxenite and eclogite. The origin of this heterogeneity and the nature of these layers is still debated but it is likely to involve processes such as transient melts coming from the crust or the mantle and segregating in magma conduits, crust-mantle interaction, upwelling of the asthenosphere and metasomatism. All these processes occur in the lithospheric mantle and are often related with the subduction of crustal rocks to mantle depths. In fact, during subduction, fluids and melts are released from the slab and can interact with the overlying mantle, making the study of deep melts in this environment crucial to understand mantle heterogeneity and crust-mantle interaction. The aim of this thesis is precisely to better constrain how such processes take place studying directly the melt trapped as primary inclusions in pyroxenites and eclogites. The Bohemian Massif, crystalline core of the Variscan belt, is targeted for these purposes because it contains orogenic peridotites with layers of pyroxenite and eclogite and other mafic rocks enclosed in felsic high pressure and ultra-high pressure crustal rocks. Within this Massif mafic rocks from two areas have been selected: the garnet clinopyroxenite in orogenic peridotite of the Granulitgebirge and the ultra-high pressure eclogite in the diamond-bearing gneisses of the Erzgebirge. In both areas primary melt inclusions were recognized in the garnet, ranging in size between 2-25 µm and with different degrees of crystallization, from glassy to polycrystalline. They have been investigated with Micro Raman spectroscopy and EDS mapping and the mineral assemblage is kumdykolite, phlogopite, quartz, kokchetavite, phase with a main Raman peak at 430 cm-1, phase with a main Raman peak at 412 cm-1, white mica and calcite with some variability in relative abundance depending on the case study. In the Granulitgebirge osumilite and pyroxene are also present, whereas calcite is one of the main phases in the Erzgebirge. The presence of glass and the mineral assemblage in the nanogranitoids suggest that they were former droplets of melt trapped in the garnet while it was growing. Glassy inclusions and re-homogenized nanogranitoids show a silicate melt that is granitic, hydrous, high in alkalis and weakly peraluminous. The melt is also enriched in both case studies in Cs, Pb, Rb, U, Th, Li and B suggesting the involvement of crustal component, i.e. white mica (main carrier of Cs, Pb, Rb, Li and B), and a fluid (Cs, Th and U) in the melt producing reaction. The whole rock in both cases mainly consists of garnet and clinopyroxene with, in Erzgebirge samples, the additional presence of quartz both in the matrix and as a polycrystalline inclusion in the garnet. The latter is interpreted as a quartz pseudomorph after coesite and occurs in the same microstructural position as the melt inclusions. Both rock types show a crustal and subduction zone signature with garnet and clinopyroxene in equilibrium. Melt was likely present during the metamorphic peak of the rock, as it occurs in garnet. Our data suggest that the processes most likely responsible for the formation of the investigated rocks in both areas is a metasomatic reaction between a melt produced in the crust and mafic layers formerly located in the mantle wedge for the Granulitgebirge and in the subducted continental crust itself in the Erzgebirge. Thus metasomatism in the first case took place in the mantle overlying the slab, whereas in the second case metasomatism took place in the continental crust that already contained, before subduction, mafic layers. Moreover, the presence of former coesite in the same microstructural position of the melt inclusions in the Erzgebirge garnets suggest that metasomatism took place at ultra-high pressure conditions. Summarizing, in this thesis we provide new insights into the geodynamic evolution of the Bohemian Massif based on the study of melt inclusions in garnet in two different mafic rock types, combining the direct microstructural and geochemical investigation of the inclusions with the whole-rock and mineral geochemistry. We report for the first time data, directly extracted from natural rocks, on the metasomatic melt responsible for the metasomatism of several areas of the Bohemian Massif. Besides the two locations here investigated, belonging to the Saxothuringian Zone, a signature similar to the investigated melt is clearly visible in pyroxenite and peridotite of the T-7 borehole (again Saxothuringian Zone) and the durbachite suite located in the Moldanubian Zone.},
  language  = {en}
}
@phdthesis{Borghi2021,
  author    = {Borghi, Gian Luca},
  title     = {Evolution and diversity of photosynthetic metabolism in C3, C3-C4 intermediate and C4 plants},
  doi       = {10.25932/publishup-52220},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-522200},
  school      = {Universit{\"a}t Potsdam},
  pages     = {163},
  year      = {2021},
  abstract  = {In C3 plants, CO2 diffuses into the leaf and is assimilated by the Calvin-Benson cycle in the mesophyll cells. It leaves Rubisco open to its side reaction with O2, resulting in a wasteful cycle known as photorespiration. A sharp fall in atmospheric CO2 levels about 30 million years ago have further increased the side reaction with O2. The pressure to reduce photorespiration led, in over 60 plant genera, to the evolution of a CO2-concentrating mechanism called C4 photosynthesis; in this mode, CO2 is initially incorporated into 4-carbon organic acids, which diffuse to the bundle sheath and are decarboxylated to provide CO2 to Rubisco. Some genera, like Flaveria, contain several species that represent different steps in this complex evolutionary process. However, the majority of terrestrial plant species did not evolve a CO2-concentrating mechanism and perform C3 photosynthesis. This thesis compares photosynthetic metabolism in several species with C3, C4 and intermediate modes of photosynthesis. Metabolite profiling and stable isotope labelling were performed to detect inter-specific differences changes in metabolite profile and, hence, how a pathway operates. The results obtained were subjected to integrative data analyses like hierarchical clustering and principal component analysis, and were deepened by correlation analyses to uncover specific metabolic features and reaction steps that were conserved or differed between species. The main findings are that Calvin-Benson cycle metabolite profiles differ between C3 and C4 species and between different C3 species, including a very different response to rising irradiance in Arabidopsis and rice. These findings confirm Calvin-Benson cycle operation diverged between C3 and C4 species and, most unexpectedly, even between different C3 species. Moreover, primary metabolic profiles supported the current C4 evolutionary model in the genus Flaveria and also provided new insights and opened up new questions. Metabolite profiles also point toward a progressive adjustment of the Calvin-Benson cycle during the evolution of C4 photosynthesis. Overall, this thesis point out the importance of a metabolite-centric approach to uncover underlying differences in species apparently sharing the same photosynthetic routes and as a valid method to investigate evolutionary transition between C3 and C4 photosynthesis.},
  language  = {en}
}
@phdthesis{Borchert2010,
  author    = {Borchert, Manuela},
  title     = {Interactions between aqueous fluids and silicate melts : equilibration, partitioning and complexation of trace elements},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42088},
  school      = {Universit{\"a}t Potsdam},
  year      = {2010},
  abstract  = {The origin and evolution of granites has been widely studied because granitoid rocks constitute a major portion of the Earth's crust. The formation of granitic magma is, besides temperature mainly triggered by the water content of these rocks. The presence of water in magmas plays an important role due to the ability of aqueous fluids to change the chemical composition of the magma. The exsolution of aqueous fluids from melts is closely linked to a fractionation of elements between the two phases. Then, aqueous fluids migrate to shallower parts of the Earth's crust because of it's lower density compared to that of melts and adjacent rocks. This process separates fluids and melts, and furthermore, during the ascent, aqueous fluids can react with the adjacent rocks and alter their chemical signature. This is particularly impor- tant during the formation of magmatic-hydrothermal ore deposits or in the late stages of the evolution of magmatic complexes. For a deeper insight to these processes, it is essential to improve our knowledge on element behavior in such systems. In particular, trace elements are used for these studies and petrogenetic interpretations because, unlike major elements, they are not essential for the stability of the phases involved and often reflect magmatic processes with less ambiguity. However, for the majority of important trace elements, the dependence of the geochemical behavior on temperature, pressure, and in particular on the composition of the system are only incompletely or not at all experimentally studied. Former studies often fo- cus on the determination of fluid-melt partition coefficients (Df/m=cfluid/cmelt) of economically interesting elements, e.g., Mo, Sn, Cu, and there are some partitioning data available for ele- ments that are also commonly used for petrological interpretations. At present, no systematic experimental data on trace element behavior in fluid-melt systems as function of pressure, temperature, and chemical composition are available. Additionally, almost all existing data are based on the analysis of quenched phases. This results in substantial uncertainties, particularly for the quenched aqueous fluid because trace element concentrations may change upon cooling. The objective of this PhD thesis consisted in the study of fluid-melt partition coefficients between aqueous solutions and granitic melts for different trace elements (Rb, Sr, Ba, La, Y, and Yb) as a function of temperature, pressure, salinity of the fluid, composition of the melt, and experimental and analytical approach. The latter included the refinement of an existing method to measure trace element concentrations in fluids equilibrated with silicate melts di- rectly at elevated pressures and temperatures using a hydrothermal diamond-anvil cell and synchrotron radiation X-ray fluorescence microanalysis. The application of this in-situ method enables to avoid the main source of error in data from quench experiments, i.e., trace element concentration in the fluid. A comparison of the in-situ results to data of conventional quench experiments allows a critical evaluation of quench data from this study and literature data. In detail, starting materials consisted of a suite of trace element doped haplogranitic glasses with ASI varying between 0.8 and 1.4 and H2O or a chloridic solution with m NaCl/KCl=1 and different salinities (1.16 to 3.56 m (NaCl+KCl)). Experiments were performed at 750 to 950◦C and 0.2 or 0.5 GPa using conventional quench devices (externally and internally heated pressure vessels) with different quench rates, and at 750◦C and 0.2 to 1.4 GPa with in-situ analysis of the trace element concentration in the fluids. The fluid-melt partitioning data of all studied trace elements show 1. a preference for the melt (Df/m < 1) at all studied conditions, 2. one to two orders of magnitude higher Df/m using chloridic solutions compared to experiments with H2O, 3. a clear dependence on the melt composition for fluid-melt partitioning of Sr, Ba, La, Y, and Yb in experiments using chloridic solutions, 4. quench rate-related differences of fluid-melt partition coefficients of Rb and Sr, and 5. distinctly higher fluid-melt partitioning data obtained from in-situ experiments than from comparable quench runs, particularly in the case of H2O as starting solution. The data point to a preference of all studied trace elements for the melt even at fairly high salinities, which contrasts with other experimental studies, but is supported by data from studies of natural co-genetically trapped fluid and melt inclusions. The in-situ measurements of trace element concentrations in the fluid verify that aqueous fluids will change their composition upon cooling, which is in particular important for Cl free systems. The distinct differences of the in-situ results to quench data of this study as well as to data from the literature signify the im- portance of a careful fluid sampling and analysis. Therefore, the direct measurement of trace element contents in fluids equilibrated with silicate melts at elevated PT conditions represents an important development to obtain more reliable fluid-melt partition coefficients. For further improvement, both the aqueous fluid and the silicate melt need to be analyzed in-situ because partitioning data that are based on the direct measurement of the trace element content in the fluid and analysis of a quenched melt are still not completely free of quench effects. At present, all available data on element complexation in aqueous fluids in equilibrium with silicate melts at high PT are indirectly derived from partitioning data, which involves in these experiments assumptions on the species present in the fluid. However, the activities of chemical components in these partitioning experiments are not well constrained, which is required for the definition of exchange equilibria between melt and fluid species. For example, the melt-dependent variation of partition coefficient observed for Sr imply that this element can not only be complexed by Cl- as suggested previously. The data indicate a more complicated complexation of Sr in the aqueous fluid. To verify this hypothesis, the in-situ setup was also used to determine strontium complexation in fluids equilibrated with silicate melts at desired PT conditions by the application of X-ray absorption near edge structure (XANES) spectroscopy. First results show a strong effect of both fluid and melt composition on the resulting XANES spectra, which indicates different complexation environments for Sr.},
  language  = {en}
}
@phdthesis{Borchers2010,
  author    = {Borchers, Andreas},
  title     = {Glaciomarine sedimentation at the continental margin of Prydz Bay, East Antarctica : implications on palaeoenvironmental changes during the Quaternary},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-52620},
  school      = {Universit{\"a}t Potsdam},
  year      = {2010},
  abstract  = {The Antarctic plays an important role in the global climate system. On the one hand, the Antarctic Ice Sheet is the largest freshwater reservoir on Earth. On the other hand, a major proportion of the global bottom-water formation takes place in Antarctic shelf regions, forcing the global thermohaline circulation. The main goal of this dissertation is to provide new insights into the dynamics and stability of the EAIS during the Quaternary. Additionally, variations in the activity of bottom-water formation and their causes are investigated. The dissertation is a German contribution to the International Polar Year 2007/ 2008 and was funded by the 'Deutsche Forschungsgesellschaft' (DFG) within the scope of priority program 1158 'Antarctic research with comparative studies in Arctic ice regions'. During RV Polarstern expedition ANT-XXIII/9, glaciomarine sediments were recovered from the Prydz Bay-Kerguelen region. Prydz Bay is a key region for the study of East EAIS dynamics, as 16\% of the EAIS are drained through the Lambert Glacier into the bay. Thereby, the glacier transports sediment into Prydz Bay which is then further distributed by calving icebergs or by current transport. The scientific approach of this dissertation is the reconstruction of past glaciomarine environments to infer on the response of the Lambert Glacier-Amery Ice Shelf system to climate shifts during the Quaternary. To characterize the depositional setting, sedimentological methods are used and statistical analyses are applied. Mineralogical and (bio)geochemical methods provide a means to reconstruct sediment provenances and to provide evidence on changes in the primary production in the surface water column. Age-depth models were constructed based on palaeomagnetic and palaeointensity measurements, diatom stratigraphy and radiocarbon dating. Sea-bed surface sediments in the investigation area show distinct variations in terms of their clay minerals and heavy-mineral assemblages. Considerable differences in the mineralogical composition of surface sediments are determined on the continental shelf. Clay minerals as well as heavy minerals provide useful parameters to differentiate between sediments which originated from erosion of crystalline rocks and sediments originating from Permo-Triassic deposits. Consequently, mineralogical parameters can be used to reconstruct the provenance of current-transported and ice-rafted material. The investigated sediment cores cover the time intervals of the last 1.4 Ma (continental slope) and the last 12.8 cal. ka BP (MacRobertson shelf). The sediment deposits were mainly influenced by glacial and oceanographic processes and further by biological activity (continental shelf), meltwater input and possibly gravitational transport. Sediments from the continental slope document two major deglacial events: the first deglaciation is associated with the mid-Pleistocene warming recognized around the Antarctic. In Prydz Bay, the Lambert Glacier-Amery Ice Shelf retreated far to the south and high biogenic productivity commenced or biogenic remains were better preserved due to increased sedimentation rates. Thereafter, stable glacial conditions continued until 400 - 500 ka BP. Calving of icebergs was restricted to the western part of the Lambert Glacier. The deeper bathymetry in this area allows for floating ice shelf even during times of decreased sea-level. Between 400 - 500 ka BP and the last interglacial (marine isotope stage 5) the glacier was more dynamic. During or shortly after the last interglacial the LAIS retreated again due to sea-level rise of 6 - 9 m. Both deglacial events correlate with a reduction in the thickness of ice masses in the Prince Charles Mountains. It indicates that a disintegration of the Amery Ice Shelf possibly led to increased drainage of ice masses from the Prydz Bay hinterland. A new end-member modelling algorithm was successfully applied on sediments from the MacRobertson shelf used to unmix the sand grain size fractions sorted by current activity and ice transport, respectively. Ice retreat on MacRobertson Shelf commenced 12.8 cal. ka BP and ended around 5.5 cal. ka BP. During the Holocene, strong fluctuations of the bottomwater activity were observed, probably related to variations of sea-ice formation in the Cape Darnley polynya. Increased activity of bottom-water flow was reconstructed at transitions from warm to cool conditions, whereas bottom-water activity receded during the mid- Holocene climate optimum. It can be concluded that the Lambert Glacier-Amery Ice Shelf system was relatively stable in terms of climate variations during the Quaternary. In contrast, bottom-water formation due to polynya activity was very sensitive to changes in atmospheric forcing and should gain more attention in future research.},
  language  = {en}
}
@phdthesis{Bora2015,
  author    = {Bora, Sanjay Singh},
  title     = {Regionally adaptable ground-motion Prediction Equations (GMPEs) for seismic hazard analysis},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-88806},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xiv, 138},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Bookhagen2004,
  author    = {Bookhagen, Bodo},
  title     = {Late quaternary climate changes and landscape evolution in the Northwest Himalaya : geomorphologic processes in the Indian Summer Monsoon Domain},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001956},
  school      = {Universit{\"a}t Potsdam},
  year      = {2004},
  abstract  = {The India-Eurasia continental collision zone provides a spectacular example of active mountain building and climatic forcing. In order to quantify the critically important process of mass removal, I analyzed spatial and temporal precipitation patterns of the oscillating monsoon system and their geomorphic imprints. I processed passive microwave satellite data to derive high-resolution rainfall estimates for the last decade and identified an abnormal monsoon year in 2002. During this year, precipitation migrated far into the Sutlej Valley in the northwestern part of the Himalaya and reached regions behind orographic barriers that are normally arid. There, sediment flux, mean basin denudation rates, and channel-forming processes such as erosion by debris-flows increased significantly. Similarly, during the late Pleistocene and early Holocene, solar forcing increased the strength of the Indian summer monsoon for several millennia and presumably lead to analogous precipitation distribution as were observed during 2002. However, the persistent humid conditions in the steep, high-elevation parts of the Sutlej River resulted in deep-seated landsliding. Landslides were exceptionally large, mainly due to two processes that I infer for this time: At the onset of the intensified monsoon at 9.7 ka BP heavy rainfall and high river discharge removed material stored along the river, and lowered the baselevel. Second, enhanced discharge, sediment flux, and increased pore-water pressures along the hillslopes eventually lead to exceptionally large landslides that have not been observed in other periods. The excess sediments that were removed from the upstream parts of the Sutlej Valley were rapidly deposited in the low-gradient sectors of the lower Sutlej River. Timing of downcutting correlates with centennial-long weaker monsoon periods that were characterized by lower rainfall. I explain this relationship by taking sediment flux and rainfall dynamics into account: High sediment flux derived from the upstream parts of the Sutlej River during strong monsoon phases prevents fluvial incision due to oversaturation the fluvial sediment-transport capacity. In contrast, weaker monsoons result in a lower sediment flux that allows incision in the low-elevation parts of the Sutlej River.},
  language  = {en}
}
@phdthesis{Bombart2020,
  author    = {Bombart, Diane},
  title     = {The geometry of a complex institution},
  doi       = {10.25932/publishup-48872},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-488724},
  school      = {Universit{\"a}t Potsdam},
  pages     = {181},
  year      = {2020},
  abstract  = {Organizations incorporate the institutional demands from their environment in order to be deemed legitimate and survive. Yet, complexifying societies promulgate multiple and sometimes inconsistent institutional prescriptions. When these prescriptions collide, organizations are said to face "institutional complexity". How does an organization then incorporate incompatible demands? What are the consequences of institutional complexity for an organization? The literature provides contradictory conceptual and empirical insights on the matter. A central assumption, however, remains that internal incompatibilities generate tensions that, under certain conditions, can escalate into intractable conflicts, resulting in dysfunctionality and loss of legitimacy. The present research is an inquiry into what happens inside an organization when it incorporates complex institutional demands. To answer this question, I focus on how individuals inside an organization interpret a complex institutional prescription. I examine how members of the French Development Agency interpret 'results-based management', a central but complex concept of organizing in the field of development aid. I use an inductive mixed methods design to systematically explore how different interpretations of results-based management relate to one another and to the organizational context in which they are embedded. The results reveal that results-based management is a contested concept in the French Development Agency. I find multiple interpretations of the concept, which are attached to partly incompatible rationales about "who we are" and "what we do as an organization". These rationales nevertheless coexist as balanced forces, without escalating into open conflict. The analysis points to four reasons for this peaceful coexistence of diverging rationales inside one and the same organization: 1) individuals' capacity to manipulate different interpretations of a complex institutional demand, 2) the nature of interpretations, which makes them more or less prone to conflict, 3) the balanced distribution of rationales across the organizational sub-contexts and 4) the shared rules of interpretation provided by the larger socio-cultural context. This research shows that an organization that incorporates institutional complexity comes to represent different, partly incompatible things to its members without being at war with itself. In doing so, it contributes to our knowledge of institutional complexity and organizational hybridity. It also advances our understanding of internal organizational legitimacy and of the translation of managerial concepts in organizations.},
  language  = {en}
}
@phdthesis{Bojdys2009,
  author    = {Bojdys, Michael Janus},
  title     = {On new allotropes and nanostructures of carbon nitrides},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41236},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {In the first section of the thesis graphitic carbon nitride was for the first time synthesised using the high-temperature condensation of dicyandiamide (DCDA) - a simple molecular precursor - in a eutectic salt melt of lithium chloride and potassium chloride. The extent of condensation, namely next to complete conversion of all reactive end groups, was verified by elemental microanalysis and vibrational spectroscopy. TEM- and SEM-measurements gave detailed insight into the well-defined morphology of these organic crystals, which are not based on 0D or 1D constituents like known molecular or short-chain polymeric crystals but on the packing motif of extended 2D frameworks. The proposed crystal structure of this g-C3N4 species was derived in analogy to graphite by means of extensive powder XRD studies, indexing and refinement. It is based on sheets of hexagonally arranged s-heptazine (C6N7) units that are held together by covalent bonds between C and N atoms. These sheets stack in a graphitic, staggered fashion adopting an AB-motif, as corroborated by powder X-ray diffractometry and high-resolution transmission electron microscopy. This study was contrasted with one of many popular - yet unsuccessful - approaches in the last 30 years of scientific literature to perform the condensation of an extended carbon nitride species through synthesis in the bulk. The second section expands the repertoire of available salt melts introducing the lithium bromide and potassium bromide eutectic as an excellent medium to obtain a new phase of graphitic carbon nitride. The combination of SEM, TEM, PXRD and electron diffraction reveals that the new graphitic carbon nitride phase stacks in an ABA' motif forming unprecedentedly large crystals. This section seizes the notion of the preceding chapter, that condensation in a eutectic salt melt is the key to obtain a high degree of conversion mainly through a solvatory effect. At the close of this chapter ionothermal synthesis is seen established as a powerful tool to overcome the inherent kinetic problems of solid state reactions such as incomplete polymerisation and condensation in the bulk especially when the temperature requirement of the reaction in question falls into the proverbial "no man's land" of classical solvents, i.e. above 250 to 300 °C. The following section puts the claim to the test, that the crystalline carbon nitrides obtained from a salt melt are indeed graphitic. A typical property of graphite - namely the accessibility of its interplanar space for guest molecules - is transferred to the graphitic carbon nitride system. Metallic potassium and graphitic carbon nitride are converted to give the potassium intercalation compound, K(C6N8)3 designated according to its stoichiometry and proposed crystal structure. Reaction of the intercalate with aqueous solvents triggers the exfoliation of the graphitic carbon nitride material and - for the first time - enables the access of singular (or multiple) carbon nitride sheets analogous to graphene as seen in the formation of sheets, bundles and scrolls of carbon nitride in TEM imaging. The thus exfoliated sheets form a stable, strongly fluorescent solution in aqueous media, which shows no sign in UV/Vis spectroscopy that the aromaticity of individual sheets was subject to degradation. The final section expands on the mechanism underlying the formation of graphitic carbon nitride by literally expanding the distance between the covalently linked heptazine units which constitute these materials. A close examination of all proposed reaction mechanisms to-date in the light of exhaustive DSC/MS experiments highlights the possibility that the heptazine unit can be formed from smaller molecules, even if some of the designated leaving groups (such as ammonia) are substituted by an element, R, which later on remains linked to the nascent heptazine. Furthermore, it is suggested that the key functional groups in the process are the triazine- (Tz) and the carbonitrile- (CN) group. On the basis of these assumptions, molecular precursors are tailored which encompass all necessary functional groups to form a central heptazine unit of threefold, planar symmetry and then still retain outward functionalities for self-propagated condensation in all three directions. Two model systems based on a para-aryl (ArCNTz) and para-biphenyl (BiPhCNTz) precursors are devised via a facile synthetic procedure and then condensed in an ionothermal process to yield the heptazine based frameworks, HBF-1 and HBF-2. Due to the structural motifs of their molecular precursors, individual sheets of HBF-1 and HBF-2 span cavities of 14.2 {\AA} and 23.0 {\AA} respectively which makes both materials attractive as potential organic zeolites. Crystallographic analysis confirms the formation of ABA' layered, graphitic systems, and the extent of condensation is confirmed as next-to-perfect by elemental analysis and vibrational spectroscopy.},
  language  = {en}
}
@phdthesis{Bojahr2016,
  author    = {Bojahr, Andre},
  title     = {Hypersound interaction studied by time-resolved inelastic light and x-ray scattering},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93860},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xxiii, 201},
  year      = {2016},
  abstract  = {This publications-based thesis summarizes my contribution to the scientific field of ultrafast structural dynamics. It consists of 16 publications, about the generation, detection and coupling of coherent gigahertz longitudinal acoustic phonons, also called hypersonic waves. To generate such high frequency phonons, femtosecond near infrared laser pulses were used to heat nanostructures composed of perovskite oxides on an ultrashort timescale. As a consequence the heated regions of such a nanostructure expand and a high frequency acoustic phonon pulse is generated. To detect such coherent acoustic sound pulses I use ultrafast variants of optical Brillouin and x-ray scattering. Here an incident optical or x-ray photon is scattered by the excited sound wave in the sample. The scattered light intensity measures the occupation of the phonon modes. The central part of this work is the investigation of coherent high amplitude phonon wave packets which can behave nonlinearly, quite similar to shallow water waves which show a steepening of wave fronts or solitons well known as tsunamis. Due to the high amplitude of the acoustic wave packets in the solid, the acoustic properties can change significantly in the vicinity of the sound pulse. This may lead to a shape change of the pulse. I have observed by time-resolved Brillouin scattering, that a single cycle hypersound pulse shows a wavefront steepening. I excited hypersound pulses with strain amplitudes until 1\% which I have calibrated by ultrafast x-ray diffraction (UXRD). On the basis of this first experiment we developed the idea of the nonlinear mixing of narrowband phonon wave packets which we call "nonlinear phononics" in analogy with the nonlinear optics, which summarizes a kaleidoscope of surprising optical phenomena showing up at very high electric fields. Such phenomena are for instance Second Harmonic Generation, four-wave-mixing or solitons. But in case of excited coherent phonons the wave packets have usually very broad spectra which make it nearly impossible to look at elementary scattering processes between phonons with certain momentum and energy. For that purpose I tested different techniques to excite narrowband phonon wave packets which mainly consist of phonons with a certain momentum and frequency. To this end epitaxially grown metal films on a dielectric substrate were excited with a train of laser pulses. These excitation pulses drive the metal film to oscillate with the frequency given by their inverse temporal displacement and send a hypersonic wave of this frequency into the substrate. The monochromaticity of these wave packets was proven by ultrafast optical Brillouin and x-ray scattering. Using the excitation of such narrowband phonon wave packets I was able to observe the Second Harmonic Generation (SHG) of coherent phonons as a first example of nonlinear wave mixing of nanometric phonon wave packets.},
  language  = {en}
}
@phdthesis{Boila2024,
  author    = {Boila, Chiara},
  title     = {The processing of OVS and passive sentences in German monolingual and German-Italian simultaneous bilingual children},
  doi       = {10.25932/publishup-62972},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-629723},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xv, 223},
  year      = {2024},
  abstract  = {It is a common finding that preschoolers have difficulties in identifying who is doing what to whom in non-canonical sentences, such as (object-verb-subject) OVS and passive sentences in German. This dissertation investigates how German monolingual and German-Italian simultaneous bilingual children process German OVS sentences in Study 1 and German passives in Study 2. Offline data (i.e., accuracy data) and online data (i.e., eye-gaze and pupillometry data) were analyzed to explore whether children can assign thematic roles during sentence comprehension and processing. Executive functions, language-internal and -external factors were investigated as potential predictors for children's sentence comprehension and processing. Throughout the literature, there are contradicting findings on the relation between language and executive functions. While some results show a bilingual cognitive advantage over monolingual speakers, others suggest there is no relationship between bilingualism and executive functions. If bilingual children possess more advanced executive function abilities than monolingual children, then this might also be reflected in a better performance on linguistic tasks. In the current studies monolingual and bilingual children were tested by means of two executive function tasks: the Flanker task and the task-switching paradigm. However, these findings showed no bilingual cognitive advantages and no better performance by bilingual children in the linguistic tasks. The performance was rather comparable between bilingual and monolingual children, or even better for the monolingual group. This may be due to cross-linguistic influences and language experience (i.e., language input and output). Italian was used because it does not syntactically overlap with the structure of German OVS sentences, and it only overlapped with one of the two types of sentence condition used for the passive study - considering the subject-(finite)verb alignment. The findings showed a better performance of bilingual children in the passive sentence structure that syntactically overlapped in the two languages, providing evidence for cross-linguistic influences. Further factors for children's sentence comprehension were considered. The parents' education, the number of older siblings and language experience variables were derived from a language background questionnaire completed by parents. Scores of receptive vocabulary and grammar, visual and short-term memory and reasoning ability were measured by means of standardized tests. It was shown that higher German language experience by bilinguals correlates with better accuracy in German OVS sentences but not in passive sentences. Memory capacity had a positive effect on the comprehension of OVS and passive sentences in the bilingual group. Additionally, a role was played by executive function abilities in the comprehension of OVS sentences and not of passive sentences. It is suggested that executive function abilities might help children in the sentence comprehension task when the linguistic structures are not yet fully mastered. Altogether, these findings show that bilinguals' poorer performance in the comprehension and processing of German OVS is mainly due to reduced language experience in German, and that the different performance of bilingual children with the two types of passives is mainly due to cross-linguistic influences.},
  language  = {en}
}
@phdthesis{Boeuf2002,
  author    = {Boeuf, St{\´e}phane},
  title     = {Comparative study of gene expression during the differentiation of white and brown preadipocytes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0000542},
  school      = {Universit{\"a}t Potsdam},
  year      = {2002},
  abstract  = {Einleitung S{\"a}ugetiere haben zwei verschiedene Arten von Fettgewebe: das weiße Fettgewebe, welches vorwiegend zur Lipidspeicherung dient, und das braune Fettgewebe, welches sich durch seine F{\"a}higkeit zur zitterfreien Thermogenese auszeichnet. Weiße und braune Adipozyten sind beide mesodermalen Ursprungs. Die Mechanismen, die zur Entwicklung von Vorl{\"a}uferzellen in den weißen oder braunen Fettzellphenotyp f{\"u}hren, sind jedoch unbekannt. Durch verschiedene experimentelle Ans{\"a}tze konnte gezeigt werden, daß diese Adipocyten vermutlich durch die Differenzierung zweier Typen unterschiedlicher Vorl{\"a}uferzellen entstehen: weiße und braune Preadipozyten. Von dieser Hypothese ausgehend, war das Ziel dieser Studie, die Genexpression weißer und brauner Preadipozyten auf Unterschiede systematisch zu analysieren. Methoden Die zu vergleichenden Zellen wurden aus prim{\"a}ren Zellkulturen weißer und brauner Preadipozyten des dsungarischen Zwerghamsters gewonnen. „Representational Difference Analysis" wurde angewandt, um potentiell unterschiedlich exprimierte Gene zu isolieren. Die daraus resultierenden cDNA Fragmente von Kandidatengenen wurden mit Hilfe der Microarraytechnik untersucht. Die Expression dieser Gene wurde in braunen und weißen Fettzellen in verschiedenen Differenzierungsstadien und in braunem und weißem Fettgewebe verglichen. Ergebnisse 12 Gene, die in braunen und weißen Preadipozyten unterschiedlich exprimiert werden, konnten identifiziert werden. Drei Komplement Faktoren und eine Fetts{\"a}uren Desaturase werden in weißen Preadipozyten h{\"o}her exprimiert; drei Struktur Gene (Fibronectin, Metargidin und a Actinin 4), drei Gene verbunden mit transkriptioneller Regulation (Necdin, Vigilin und das „small nuclear ribonucleoprotein polypeptide A") sowie zwei Gene unbekannter Funktion werden in braunen Preadipozyten h{\"o}her exprimiert. Mittels Clusteranalyse (oder Gruppenanalyse) wurden die gesamten Genexpressionsdaten charakterisiert. Dabei konnten die Gene in 4 typischen Expressionsmuster aufgeteilt werden: in weißen Preadipozyten h{\"o}her exprimierte Gene, in braunen Preadipozyten h{\"o}her exprimierte Gene, w{\"a}hrend der Differenzierung herunter regulierte Gene und w{\"a}hrend der Differenzierung hoch regulierte Gene. Schlußfolgerungen In dieser Studie konnte gezeigt werden, daß weiße und braune Preadipozyten aufgrund der Expression verschiedener Gene unterschieden werden k{\"o}nnen. Es wurden mehrere Kandidatengene zur Bestimmung weißer und brauner Preadipozyten identifiziert. Außerdem geht aus den Genexpressionsdaten hervor, daß funktionell unterschiedliche Gruppen von Genen eine wichtige Rolle bei der Differenzierung von weißen und braunen Preadipozyten spielen k{\"o}nnten, wie z.B. Gene des Komplementsystems und der extrazellul{\"a}ren Matrix.},
  subject      = {S{\"a}ugetiere ; Fettgewebe ; Zelldifferenzierung ; Genexpression},
  language  = {en}
}
@phdthesis{Boedecker2013,
  author    = {Boedecker, Geesche},
  title     = {Resonance Fluorescence in a Photonic Crystal},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-69591},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Boeche2011,
  author    = {Boeche, Corrado},
  title     = {Chemical gradients in the Milky Way from unsupervised chemical abundances measurements of the RAVE spectroscopic data set},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-52478},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {The present thesis was born and evolved within the RAdial Velocity Experiment (RAVE) with the goal of measuring chemical abundances from the RAVE spectra and exploit them to investigate the chemical gradients along the plane of the Galaxy to provide constraints on possible Galactic formation scenarios. RAVE is a large spectroscopic survey which aims to observe spectroscopically ~10^6 stars by the end of 2012 and measures their radial velocities, atmospheric parameters and chemical abundances. The project makes use of the UK Schmidt telescope at Australian Astronomical Observatory (AAO) in Siding Spring, Australia, equipped with the multiobject spectrograph 6dF. To date, RAVE collected and measured more than 450,000 spectra. The precision of the chemical abundance estimations depends on the reliability of the atomic and atmosphere parameters adopted (in particular the oscillator strengths of the absorption lines and the effective temperature, gravity, and metallicity of the stars measured). Therefore we first identified 604 absorption lines in the RAVE wavelength range and refined their oscillator strengths with an inverse spectral analysis. Then, we improved the RAVE stellar parameters by modifying the RAVE pipeline and the spectral library the pipeline rely on. The modifications removed some systematic errors in stellar parameters discovered during this work. To obtain chemical abundances, we developed two different processing pipelines. Both of them perform chemical abundances measurements by assuming stellar atmospheres in Local Thermodynamic Equilibrium (LTE). The first one determines elements abundances from equivalent widths of absorption lines. Since this pipeline showed poor sensibility on abundances relative to iron, it has been superseded. The second one exploits the chi^2 minimization technique between observed and model spectra. Thanks to its precision, it has been adopted for the creation of the RAVE chemical catalogue. This pipeline provides abundances with uncertains of about ~0.2dex for spectra with signal-to-noise ratio S/N>40 and ~0.3dex for spectra with 20>S/N>40. For this work, the pipeline measured chemical abundances up to 7 elements for 217,358 RAVE stars. With these data we investigated the chemical gradients along the Galactic radius of the Milky Way. We found that stars with low vertical velocities |W| (which stay close to the Galactic plane) show an iron abundance gradient in agreement with previous works (~-0.07\$ dex kpc^-1) whereas stars with larger |W| which are able to reach larger heights above the Galactic plane, show progressively flatter gradients. The gradients of the other elements follow the same trend. This suggests that an efficient radial mixing acts in the Galaxy or that the thick disk formed from homogeneous interstellar matter. In particular, we found hundreds of stars which can be kinetically classified as thick disk stars exhibiting a chemical composition typical of the thin disk. A few stars of this kind have already been detected by other authors, and their origin is still not clear. One possibility is that they are thin disk stars kinematically heated, and then underwent an efficient radial mixing process which blurred (and so flattened) the gradient. Alternatively they may be a transition population" which represents an evolutionary bridge between thin and thick disk. Our analysis shows that the two explanations are not mutually exclusive. Future follow-up high resolution spectroscopic observations will clarify their role in the Galactic disk evolution.},
  language  = {en}
}
@phdthesis{Blume2008,
  author    = {Blume, Theresa},
  title     = {Hydrological processes in volcanic ash soils : measuring, modelling and understanding runoff generation in an undisturbed catchment},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-16552},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {Streamflow dynamics in mountainous environments are controlled by runoff generation processes in the basin upstream. Runoff generation processes are thus a major control of the terrestrial part of the water cycle, influencing both, water quality and water quantity as well as their dynamics. The understanding of these processes becomes especially important for the prediction of floods, erosion, and dangerous mass movements, in particular as hydrological systems often show threshold behavior. In case of extensive environmental changes, be it in climate or in landuse, the understanding of runoff generation processes will allow us to better anticipate the consequences and can thus lead to a more responsible management of resources as well as risks. In this study the runoff generation processes in a small undisturbed catchment in the Chilean Andes were investigated. The research area is characterized by steep hillslopes, volcanic ash soils, undisturbed old growth forest and high rainfall amounts. The investigation of runoff generation processes in this data scarce area is of special interest as a) little is known on the hydrological functioning of the young volcanic ash soils, which are characterized by extremely high porosities and hydraulic conductivities, b) no process studies have been carried out in this area at either slope or catchment scale, and c) understanding the hydrological processes in undisturbed catchments will provide a basis to improve our understanding of disturbed systems, the shift in processes that followed the disturbance and maybe also future process evolution necessary for the achievement of a new steady state. The here studied catchment has thus the potential to serve as a reference catchment for future investigations. As no long term data of rainfall and runoff exists, it was necessary to replace long time series of data with a multitude of experimental methods, using the so called "multi-method approach". These methods cover as many aspects of runoff generation as possible and include not only the measurement of time series such as discharge, rainfall, soil water dynamics and groundwater dynamics, but also various short term measurements and experiments such as determination of throughfall amounts and variability, water chemistry, soil physical parameters, soil mineralogy, geo-electrical soundings and tracer techniques. Assembling the results like pieces of a puzzle produces a maybe not complete but nevertheless useful picture of the dynamic ensemble of runoff generation processes in this catchment. The employed methods were then evaluated for their usefulness vs. expenditures (labour and financial costs). Finally, the hypotheses - the perceptual model of runoff generation generated from the experimental findings - were tested with the physically based model Catflow. Additionally the process-based model Wasim-ETH was used to investigate the influence of landuse on runoff generation at the catchment scale. An initial assessment of hydrologic response of the catchment was achieved with a linear statistical model for the prediction of event runoff coefficients. The parameters identified as best predictors give a first indication of important processes. Various results acquired with the "multi-method approach" show that response to rainfall is generally fast. Preferential vertical flow is of major importance and is reinforced by hydrophobicity during the summer months. Rapid lateral water transport is necessary to produce the fast response signal, however, while lateral subsurface flow was observed at several soil moisture profiles, the location and type of structures causing fast lateral flow on the hillslope scale is still not clear and needs to be investigated in more detail. Surface runoff has not been observed and is unlikely due to the high hydraulic conductivities of the volcanic ash soils. Additionally, a large subsurface storage retains most of the incident rainfall amount during events (>90\%, often even >95\%) and produces streamflow even after several weeks of drought. Several findings suggest a shift in processes from summer to winter causing changes in flow patterns, changes in response of stream chemistry to rainfall events and also in groundwater-surface water interactions. The results of the modelling study confirm the importance of rapid and preferential flow processes. However, due to the limited knowledge on subsurface structures the model still does not fully capture runoff response. Investigating the importance of landuse on runoff generation showed that while peak runoff generally increased with deforested area, the location of these areas also had an effect. Overall, the "multi-method approach" of replacing long time series with a multitude of experimental methods was successful in the identification of dominant hydrological processes and thus proved its applicability for data scarce catchments under the constraint of limited resources.},
  language  = {en}
}
@phdthesis{Blum2010,
  author    = {Blum, Niklas},
  title     = {Formalization of a converged internet and telecommunications service environment},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-51146},
  school      = {Universit{\"a}t Potsdam},
  year      = {2010},
  abstract  = {The programmable network envisioned in the 1990s within standardization and research for the Intelligent Network is currently coming into reality using IPbased Next Generation Networks (NGN) and applying Service-Oriented Architecture (SOA) principles for service creation, execution, and hosting. SOA is the foundation for both next-generation telecommunications and middleware architectures, which are rapidly converging on top of commodity transport services. Services such as triple/quadruple play, multimedia messaging, and presence are enabled by the emerging service-oriented IPMultimedia Subsystem (IMS), and allow telecommunications service providers to maintain, if not improve, their position in the marketplace. SOA becomes the de facto standard in next-generation middleware systems as the system model of choice to interconnect service consumers and providers within and between enterprises. We leverage previous research activities in overlay networking technologies along with recent advances in network abstraction, service exposure, and service creation to develop a paradigm for a service environment providing converged Internet and Telecommunications services that we call Service Broker. Such a Service Broker provides mechanisms to combine and mediate between different service paradigms from the two domains Internet/WWW and telecommunications. Furthermore, it enables the composition of services across these domains and is capable of defining and applying temporal constraints during creation and execution time. By adding network-awareness into the service fabric, such a Service Broker may also act as a next generation network-to-service element allowing the composition of crossdomain and cross-layer network and service resources. The contribution of this research is threefold: first, we analyze and classify principles and technologies from Information Technologies (IT) and telecommunications to identify and discuss issues allowing cross-domain composition in a converging service layer. Second, we discuss service composition methods allowing the creation of converged services on an abstract level; in particular, we present a formalized method for model-checking of such compositions. Finally, we propose a Service Broker architecture converging Internet and Telecom services. This environment enables cross-domain feature interaction in services through formalized obligation policies acting as constraints during service discovery, creation, and execution time.},
  language  = {en}
}
@phdthesis{Blaser2024,
  author    = {Blaser, Berenike Lisa},
  title     = {Premenstrual symptoms as a function of altered central autonomous nervous activity},
  doi       = {10.25932/publishup-64597},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-645970},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XII, 265},
  year      = {2024},
  abstract  = {The experience of premenstrual syndrome (PMS) affects up to 90\% of individuals with an active menstrual cycle and involves a spectrum of aversive physiological and psychological symptoms in the days leading up to menstruation (Tschudin et al., 2010). Despite its high prevalence, the precise origins of PMS remain elusive, with influences ranging from hormonal fluctuations to cognitive, social, and cultural factors (Hunter, 2007; Matsumoto et al., 2013). Biologically, hormonal fluctuations, particularly in gonadal steroids, are commonly believed to be implicated in PMS, with the central factor being varying susceptibilities to the fluctuations between individuals and cycles (Rapkin \& Akopians, 2012). Allopregnanolone (ALLO), a neuroactive steroid and progesterone metabolite, has emerged as a potential link to PMS symptoms (Hantsoo \& Epperson, 2020). ALLO is a positive allosteric modulator of the GABAA receptor, influencing inhibitory communication (Rupprecht, 2003; Andr{\´e}en et al., 2006). Different susceptibility to ALLO fluctuations throughout the cycle may lead to reduced GABAergic signal transmission during the luteal phase of the menstrual cycle. The GABAergic system's broad influence leads to a number of affected physiological systems, including a consistent reduction in vagally mediated heart rate variability (vmHRV) during the luteal phase (Schmalenberger et al., 2019). This reduction in vmHRV is more pronounced in individuals with high PMS symptoms (Baker et al., 2008; Matsumoto et al., 2007). Fear conditioning studies have shown inconsistent associations with cycle phases, suggesting a complex interplay between physiological parameters and PMS-related symptoms (Carpenter et al., 2022; Epperson et al., 2007; Milad et al., 2006). The neurovisceral integration model posits that vmHRV reflects the capacity of the central autonomous network (CAN), which is responsible for regulatory processes on behavioral, cognitive, and autonomous levels (Thayer \& Lane, 2000, 2009). Fear learning, mediated within the CAN, is suggested to be indicative of vmHRV's capacity for successful VI regulation (Battaglia \& Thayer, 2022). Given the GABAergic mediation of central inhibitory functional connectivity in the CAN, which may be affected by ALLO fluctuations, this thesis proposes that fluctuating CAN activity in the luteal phase contributes to diverse aversive symptoms in PMS. A research program was designed to empirically test these propositions. Study 1 investigated fear discrimination during different menstrual cycle phases and its interaction with vmHRV, revealing nuanced effects on acoustic startle response and skin conductance response. While there was heightened fear discrimination in acoustic startle responses in participants in the luteal phase, there was an interaction between menstrual cycle phase and vmHRV in skin conductance responses. In this measure, heightened fear discrimination during the luteal phase was only visible in individuals with high resting vmHRV; those with low vmHRV showed reduced fear discrimination and higher overall responses. Despite affecting the vast majority of menstruating people, there are very limited tools available to reliably assess these symptoms in the German speaking area. Study 2 aimed at closing this gap, by translating and validating a German version of the short version of the Premenstrual Assessment Form (Allen et al., 1991), providing a reliable tool for future investigations, which closes the gap in PMS questionnaires in the German-speaking research area. Study 3 employed a diary study paradigm to explore daily associations between vmHRV and PMS symptoms. The results showed clear simultaneous fluctuations between the two constructs with a peak in PMS and a low point in vmHRV a few days before menstruation onset. The association between vmHRV and PMS was driven by psychological PMS symptoms. Based on the theoretical considerations regarding the neurovisceral perspective on PMS, another interesting construct to consider is attentional control, as it is closely related to functions of the CAN. Study 4 delved into attentional control and vmHRV differences between menstrual cycle phases, demonstrating an interaction between cycle phase and PMS symptoms. In a pilot, we found reduced vmHRV and attentional control during the luteal phase only in participants who reported strong PMS. While Studies 1-4 provided evidence for the mechanisms underlying PMS, Studies 5 and 6 investigated short- and long-term intervention protocols to ameliorate PMS symptomatology. Study 5 explored the potential of heart rate variability biofeedback (HRVB) in alleviating PMS symptoms and a number of other outcome measures. In a waitlist-control design, participants underwent a 4-week smartphone-based HRVB intervention. The results revealed positive effects on PMS, with larger effect sizes on psychological symptoms, as well as on depressive symptoms, anxiety/stress and attentional control. Finally, Study 6 examined the acute effects of HRVB on attentional control. The study found positive impact but only in highly stressed individuals. The thesis, based on this comprehensive research program, expands our understanding of PMS as an outcome of CAN fluctuations mediated by GABAA receptor reactivity. The results largely support the model. These findings not only deepen our understanding of PMS but also offer potential avenues for therapeutic interventions. The promising results of smartphone-based HRVB training suggest a non-pharmacological approach to managing PMS symptoms, although further research is needed to confirm its efficacy. In conclusion, this thesis illuminates the complex web of factors contributing to PMS, providing valuable insights into its etiological underpinnings and potential interventions. By elucidating the relationships between hormonal fluctuations, CAN activity, and psychological responses, this research contributes to more effective treatments for individuals grappling with the challenges of PMS. The findings hold promise for improving the quality of life for those affected by this prevalent and often debilitating condition.},
  language  = {en}
}
@phdthesis{Blacha2009,
  author    = {Blacha, Anna Maria},
  title     = {Investigating the role of regulatory genes in heterosis for superior growth and biomass production in Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-46146},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {'Heterosis' is a term used in genetics and breeding referring to hybrid vigour or the superiority of hybrids over their parents in terms of traits such as size, growth rate, biomass, fertility, yield, nutrient content, disease resistance or tolerance to abiotic and abiotic stress. Parental plants which are two different inbred (pure) lines that have desired traits are crossed to obtain hybrids. Maximum heterosis is observed in the first generation (F1) of crosses. Heterosis has been utilised in plant and animal breeding programs for at least 90 years: by the end of the 21st century, 65\% of worldwide maize production was hybrid-based. Generally, it is believed that an understanding of the molecular basis of heterosis will allow the creation of new superior genotypes which could either be used directly as F1 hybrids or form the basis for the future breeding selection programmes. Two selected accessions of a research model plant Arabidopsis thaliana (thale cress) were crossed to obtain hybrids. These typically exhibited a 60-80\% increase of biomass when compared to the average weight of both parents. This PhD project focused on investigating the role of selected regulatory genes given their potentially key involvement in heterosis. In the first part of the project, the most appropriate developmental stage for this heterosis study was determined by metabolite level measurements and growth observations in parents and hybrids. At the selected stage, around 60 candidate regulatory genes (i.e. differentially expressed in hybrids when compared to parents) were identified. Of these, the majority were transcription factors, genes that coordinate the expression of other genes. Subsequent expression analyses of the candidate genes in biomass-heterotic hybrids of other Arabidopsis accessions revealed a differential expression in a gene subset, highlighting their relevance for heterosis. Moreover, a fraction of the candidate regulatory genes were found within DNA regions closely linked to the genes that underlie the biomass or growth heterosis. Additional analyses to validate the role of selected candidate regulatory genes in heterosis appeared insufficient to establish their role in heterosis. This uncovered a need for using novel approaches as discussed in the thesis. Taken together, the work provided an insight into studies on the molecular mechanisms underlying heterosis. Although studies on heterosis date back to more than one hundred years, this project as many others revealed that more investigations will be needed to uncover this phenomenon.},
  language  = {en}
}
@phdthesis{BivigouKoumba2009,
  author    = {Bivigou Koumba, Achille Mayelle},
  title     = {Design, Synthesis and Characterisation of Amphiphilic Symmetrical triblock copolymers by the RAFT process : their self-organisation in dilute and concentrated aqueous solutions},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-39549},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {This work presents the synthesis and the self-assembly of symmetrical amphiphilic ABA and BAB triblock copolymers in dilute, semi-concentrated and highly concentrated aqueous solution. A series of new bifunctional bistrithiocarbonates as RAFT agents was used to synthesise these triblock copolymers, which are characterised by a long hydrophilic middle block and relatively small, but strongly hydrophobic end blocks. As hydrophilic A blocks, poly(N-isopropylacrylamide) (PNIPAM) and poly(methoxy diethylene glycol acrylate) (PMDEGA) were employed, while as hydrophobic B blocks, poly(4-tert-butyl styrene), polystyrene, poly(3,5-dibromo benzyl acrylate), poly(2-ethylhexyl acrylate), and poly(octadecyl acrylate) were explored as building blocks with different hydrophobicities and glass transition temperatures. The five bifunctional trithiocarbonates synthesised belong to two classes: the first are RAFT agents, which position the active group of the growing polymer chain at the outer ends of the polymer (Z-C(=S)-S-R-S-C(=S)-Z, type I). The second class places the active groups in the middle of the growing polymer chain (R-S-C(=S)-Z-C(=S)-S-R, type II). These RAFT agents enable the straightforward synthesis of amphiphilic triblock copolymers in only two steps, allowing to vary the nature of the hydrophobic blocks as well as the length of the hydrophobic and hydrophilic blocks broadly with good molar mass control and narrow polydispersities. Specific side reactions were observed among some RAFT agents including the elimination of ethylenetrithiocarbonate in the early stage of the polymerisation of styrene mediated by certain agents of the type II, while the use of the RAFT agents of type I resulted in retardation of the chain extension of PNIPAM with styrene. These results underline the need of a careful choice of RAFT agents for a given task. The various copolymers self-assemble in dilute and semi-concentrated aqueous solution into small flower-like micelles. No indication for the formation of micellar clusters was found, while only at high concentration, physical hydrogels are formed. The reversible thermoresponsive behaviour of the ABA and BAB type copolymer solutions in water with A made of PNIPAM was examined by turbidimetry and dynamic light scattering (DLS). The cloud point of the copolymers was nearly identical to the cloud point of the homopolymer and varied between 28-32 °C with concentrations from 0.01 to 50 wt\%. This is attributed to the formation of micelles where the hydrophobic blocks are shielded from a direct contact with water, so that the hydrophobic interactions of the copolymers are nearly the same as for pure PNIPAM. Dynamic light scattering measurements showed the presence of small micelles at ambient temperature. The aggregate size dramatically increased above the cloud point, indicating a change of aggregate morphology into clusters due to the thermosensitivity of the PNIPAM block. The rheological behaviour of the amphiphilic BAB triblock copolymers demonstrated the formation of hydrogels at high concentrations, typically above 30-35 wt\%. The minimum concentration to induce hydrogels decreased with the increasing glass transition temperatures and increasing length of the end blocks. The weak tendency to form hydrogels was attributed to a small share of bridged micelles only, due to the strong segregation regime occurring. In order to learn about the role of the nature of the thermoresponsive block for the aggregation, a new BAB triblock copolymer consisting of short polystyrene end blocks and PMDEGA as stimuli-responsive middle block was prepared and investigated. Contrary to PNIPAM, dilute aqueous solutions of PMDEGA and of its block copolymers showed reversible phase transition temperatures characterised by a strong dependence on the polymer composition. Moreover, the PMDEGA block copolymer allowed the formation of physical hydrogels at lower concentration, i.e. from 20 wt\%. This result suggests that PMDEGA has a higher degree of water-swellability than PNIPAM.},
  language  = {en}
}
@phdthesis{Bittermann2015,
  author    = {Bittermann, Klaus},
  title     = {Semi-empirical sea-level modelling},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93881},
  school      = {Universit{\"a}t Potsdam},
  pages     = {v, 88},
  year      = {2015},
  abstract  = {Semi-empirical sea-level models (SEMs) exploit physically motivated empirical relationships between global sea level and certain drivers, in the following global mean temperature. This model class evolved as a supplement to process-based models (Rahmstorf (2007)) which were unable to fully represent all relevant processes. They thus failed to capture past sea-level change (Rahmstorf et al. (2012)) and were thought likely to underestimate future sea-level rise. Semi-empirical models were found to be a fast and useful tool for exploring the uncertainties in future sea-level rise, consistently giving significantly higher projections than process-based models. In the following different aspects of semi-empirical sea-level modelling have been studied. Models were first validated using various data sets of global sea level and temperature. SEMs were then used on the glacier contribution to sea level, and to infer past global temperature from sea-level data via inverse modelling. Periods studied encompass the instrumental period, covered by tide gauges (starting 1700 CE (Common Era) in Amsterdam) and satellites (first launched in 1992 CE), the era from 1000 BCE (before CE) to present, and the full length of the Holocene (using proxy data). Accordingly different data, model formulations and implementations have been used. It could be shown in Bittermann et al. (2013) that SEMs correctly predict 20th century sea-level when calibrated with data until 1900 CE. SEMs also turned out to give better predictions than the Intergovernmental Panel on Climate Change (IPCC) 4th assessment report (AR4, IPCC (2007)) models, for the period from 1961-2003 CE. With the first multi-proxy reconstruction of global sea-level as input, estimate of the human-induced component of modern sea-level change and projections of future sea-level rise were calculated (Kopp et al. (2016)). It turned out with 90\% confidence that more than 40 \% of the observed 20th century sea-level rise is indeed anthropogenic. With the new semi-empirical and IPCC (2013) 5th assessment report (AR5) projections the gap between SEM and process-based model projections closes, giving higher credibility to both. Combining all scenarios, from strong mitigation to business as usual, a global sea-level rise of 28-131 cm relative to 2000 CE, is projected with 90\% confidence. The decision for a low carbon pathway could halve the expected global sea-level rise by 2100 CE. Present day temperature and thus sea level are driven by the globally acting greenhouse-gas forcing. Unlike that, the Milankovich forcing, acting on Holocene timescales, results mainly in a northern-hemisphere temperature change. Therefore a semi-empirical model can be driven with northernhemisphere temperatures, which makes it possible to model the main subcomponent of sea-level change over this period. It showed that an additional positive constant rate of the order of the estimated Antarctic sea-level contribution is then required to explain the sea-level evolution over the Holocene. Thus the global sea level, following the climatic optimum, can be interpreted as the sum of a temperature induced sea-level drop and a positive long-term contribution, likely an ongoing response to deglaciation coming from Antarctica.},
  language  = {en}
}
@phdthesis{Bissinger2003,
  author    = {Bissinger, Vera},
  title     = {Factors determining growth and vertical distribution of planktonic algae in extremely acidic mining lakes (pH 2.7)},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0000695},
  school      = {Universit{\"a}t Potsdam},
  year      = {2003},
  abstract  = {Die vorliegende Dissertation besch{\"a}ftigt sich mit den Faktoren, die das Wachstum und die Vertikalverteilung von Planktonalgen in extrem sauren Tagebaurestseen (TBS; pH 2-3) beeinflussen. Im exemplarisch untersuchten TBS 111 (pH 2.7; Lausitzer Revier) dominiert die Goldalge Ochromonas sp. in oberen und die Gr{\"u}nalge Chlamydomonas sp. in tieferen Wasserschichten, wobei letztere ein ausgepr{\"a}gtes Tiefenchlorophyll-Maximum (DCM) ausbildet. Es wurde ein deutlicher Einfluss von Limitation durch anorganischen Kohlenstoff (IC) auf das phototrophe Wachstum von Chlamydomonas sp. in oberen Wasserschichten nachgewiesen, die mit zunehmender Tiefe von Lichtlimitation abgel{\"o}st wird. Im Vergleich mit Arbeiten aus neutralen Seen zeigte Chlamydomonas sp. erniedrigte maximale Wachstumsraten, einen gesteigerten Kompensationspunkt und erh{\"o}hte Dunkelrespirationsraten, was auf gesteigerte metabolische Kosten unter den extremen physikalisch-chemischen Bedingungen hinweist. Die Photosyntheseleistungen von Chlamydomonas sp. waren in Starklicht-adaptierten Zellen durch IC-Limitation deutlich verringert. Außerdem ergaben die ermittelten minimalen Zellquoten f{\"u}r Phosphor (P) einen erh{\"o}hten P-Bedarf unter IC-Limitation. Anschließend konnte gezeigt werden, dass Chlamydomonas sp. ein mixotropher Organismus ist, der seine Wachstumsraten {\"u}ber die osmotrophe Aufnahme gel{\"o}sten organischen Kohlenstoffs (DOC) erh{\"o}hen kann. Dadurch ist dieser Organismus f{\"a}hig, in tieferen, Licht-limitierten Wasserschichten zu {\"u}berleben, die einen h{\"o}heren DOC-Gehalt aufweisen. Da die Vertikalverteilung der Algen im TBS 111 jedoch weder durch IC-Limitation, P-Verf{\"u}gbarkeit noch die in situ DOC-Konzentrationen abschließend erkl{\"a}rt werden konnte (bottom-up Kontrolle), wurde eine neue Theorie zur Entstehung der Vertikalverteilung gepr{\"u}ft. Grazing der phagotrophen und phototrophen Alge Ochromonas sp. auf der phototrophen Alge Chlamydomonas sp. erwies sich als herausragender Faktor, der {\"u}ber top-down Kontrolle die Abundanz der Beute in h{\"o}heren Wasserschichten beeinflussen kann. Gemeinsam mit der Tatsache, dass Chlamydomonas sp. DOC zur Wachstumssteigerung verwendet, f{\"u}hrt dies zu einer Akkumulation von Chlamydomonas sp. in der Tiefe, ausgepr{\"a}gt als DCM. Daher erscheint grazing als der Hauptfaktor, der die beobachtete Vertikalschichtung der Algen im TBS 111 hervorruft. Die erzielten Ergebnisse liefern grundlegende Informationen, um die Auswirkungen von Strategien zur Neutralisierung der TBS auf das Nahrungsnetz absch{\"a}tzen zu k{\"o}nnen.},
  language  = {en}
}
@phdthesis{Bishop2022,
  author    = {Bishop, Christopher Allen},
  title     = {Influence of dairy intake on odd-chain fatty acids and energy metabolism},
  doi       = {10.25932/publishup-56154},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-561541},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xii, 104, xv},
  year      = {2022},
  abstract  = {As of late, epidemiological studies have highlighted a strong association of dairy intake with lower disease risk, and similarly with an increased amount of odd-chain fatty acids (OCFA). While the OCFA also demonstrate inverse associations with disease incidence, the direct dietary sources and mode of action of the OCFA remain poorly understood. The overall aim of this thesis was to determine the impact of two main fractions of dairy, milk fat and milk protein, on OCFA levels and their influence on health outcomes under high-fat (HF) diet conditions. Both fractions represent viable sources of OCFA, as milk fats contain a significant amount of OCFA and milk proteins are high in branched chain amino acids (BCAA), namely valine (Val) and isoleucine (Ile), which can produce propionyl-CoA (Pr-CoA), a precursor for endogenous OCFA synthesis, while leucine (Leu) does not. Additionally, this project sought to clarify the specific metabolic effects of the OCFA heptadecanoic acid (C17:0). Both short-term and long-term feeding studies were performed using male C57BL/6JRj mice fed HF diets supplemented with milk fat or C17:0, as well as milk protein or individual BCAA (Val; Leu) to determine their influences on OCFA and metabolic health. Short-term feeding revealed that both milk fractions induce OCFA in vivo, and the increases elicited by milk protein could be, in part, explained by Val intake. In vitro studies using primary hepatocytes further showed an induction of OCFA after Val treatment via de novo lipogenesis and increased α-oxidation. In the long-term studies, both milk fat and milk protein increased hepatic and circulating OCFA levels; however, only milk protein elicited protective effects on adiposity and hepatic fat accumulation—likely mediated by the anti-obesogenic effects of an increased Leu intake. In contrast, Val feeding did not increase OCFA levels nor improve obesity, but rather resulted in glucotoxicity-induced insulin resistance in skeletal muscle mediated by its metabolite 3-hydroxyisobutyrate (3-HIB). Finally, while OCFA levels correlated with improved health outcomes, C17:0 produced negligible effects in preventing HF-diet induced health impairments. The results presented herein demonstrate that the beneficial health outcomes associated with dairy intake are likely mediated through the effects of milk protein, while OCFA levels are likely a mere association and do not play a significant causal role in metabolic health under HF conditions. Furthermore, the highly divergent metabolic effects of the two BCAA, Leu and Val, unraveled herein highlight the importance of protein quality.},
  language  = {en}
}
@phdthesis{Bischofs2004,
  author    = {Bischofs, Ilka Bettina},
  title     = {Elastic interactions of cellular force patterns},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001767},
  school      = {Universit{\"a}t Potsdam},
  year      = {2004},
  abstract  = {Gewebezellen sammeln st{\"a}ndig Informationen {\"u}ber die mechanischen Eigenschaften ihrer Umgebung, indem sie aktiv an dieser ziehen. Diese Kr{\"a}fte werden an Zell-Matrix-Kontakten {\"u}bertragen, die als Mechanosensoren fungieren. J{\"u}ngste Experimente mit Zellen auf elastischen Substraten zeigen, dass Zellen sehr empfindlich auf Ver{\"a}nderungen der effektiven Steifigkeit ihrer Umgebung reagieren, die zu einer Reorganisation des Zytoskeletts f{\"u}hren k{\"o}nnen. In dieser Arbeit wird ein theoretisches Model entwickelt, um die Selbstorganisation von Zellen in weichen Materialien vorherzusagen. Obwohl das Zellverhalten durch komplexe regulatorische Vorg{\"a}nge in der Zelle gesteuert wird, scheint die typische Antwort von Zellen auf mechanische Reize eine einfache Pr{\"a}ferenz f{\"u}r große effektive Steifigkeit der Umgebung zu sein, m{\"o}glicherweise weil in einer steiferen Umgebung Kr{\"a}fte an den Kontakten effektiver aufgebaut werden k{\"o}nnen. Der Begriff Steifigkeit umfasst dabei sowohl Effekte, die durch gr{\"o}ßere H{\"a}rte als auch durch elastische Verzerrungsfelder in der Umgebung verursacht werden. Diese Beobachtung kann man als ein Extremalprinzip in der Elastizit{\"a}tstheorie formulieren. Indem man das zellul{\"a}re Kraftmuster spezifiziert, mit dem Zellen mit ihrer Umgebung wechselwirken, und die Umgebung selbst als linear elastisches Material modelliert, kann damit die optimale Orientierung und Position von Zellen vorhergesagt werden. Es werden mehrere praktisch relevante Beispiele f{\"u}r Zellorganisation theoretisch betrachtet: Zellen in externen Spannungsfeldern und Zellen in der N{\"a}he von Grenzfl{\"a}chen f{\"u}r verschiedene Geometrien und Randbedingungen des elastischen Mediums. Daf{\"u}r werden die entsprechenden elastischen Randwertprobleme in Vollraum, Halbraum und Kugel exakt gel{\"o}st. Die Vorhersagen des Models stimmen hervorragend mit experimentellen Befunden f{\"u}r Fibroblastzellen {\"u}berein, sowohl auf elastischen Substraten als auch in physiologischen Hydrogelen. Mechanisch aktive Zellen wie Fibroblasten k{\"o}nnen auch elastisch miteinander wechselwirken. Es werden daher optimale Strukturen als Funktion von Materialeigenschaften und Zelldichte bzw. der Geometrie der Zellpositionen berechnet. Schließlich wird mit Hilfe von Monte Carlo Simulationen der Einfluss stochastischer St{\"o}rungen auf die Strukturbildung untersucht. Das vorliegende Model tr{\"a}gt nicht nur zu einem besseren Verst{\"a}ndnis von vielen physiologischen Situationen bei, sondern k{\"o}nnte in Zukunft auch f{\"u}r biomedizinische Anwendungen benutzt werden, um zum Beispiel Protokolle f{\"u}r k{\"u}nstliche Gewebe im Bezug auf Substratgeometrie, Randbedingungen, Materialeigenschaften oder Zelldichte zu optimieren.},
  language  = {en}
}
@phdthesis{Bischoff2013,
  author    = {Bischoff, Juliane},
  title     = {Microbial communities and their response to Pleistocene and Holocene climate variabilities in the Russian Arctic},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-68895},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {The Arctic is considered as a focal region in the ongoing climate change debate. The currently observed and predicted climate warming is particularly pronounced in the high northern latitudes. Rising temperatures in the Arctic cause progressive deepening and duration of permafrost thawing during the arctic summer, creating an 'active layer' with high bioavailability of nutrients and labile carbon for microbial consumption. The microbial mineralization of permafrost carbon creates large amounts of greenhouse gases, including carbon dioxide and methane, which can be released to the atmosphere, creating a positive feedback to global warming. However, to date, the microbial communities that drive the overall carbon cycle and specifically methane production in the Arctic are poorly constrained. To assess how these microbial communities will respond to the predicted climate changes, such as an increase in atmospheric and soil temperatures causing increased bioavailability of organic carbon, it is necessary to investigate the current status of this environment, but also how these microbial communities reacted to climate changes in the past. This PhD thesis investigated three records from two different study sites in the Russian Arctic, including permafrost, lake shore and lake deposits from Siberia and Chukotka. A combined stratigraphic approach of microbial and molecular organic geochemical techniques were used to identify and quantify characteristic microbial gene and lipid biomarkers. Based on this data it was possible to characterize and identify the climate response of microbial communities involved in past carbon cycling during the Middle Pleistocene and the Late Pleistocene to Holocene. It is shown that previous warmer periods were associated with an expansion of bacterial and archaeal communities throughout the Russian Arctic, similar to present day conditions. Different from this situation, past glacial and stadial periods experienced a substantial decrease in the abundance of Bacteria and Archaea. This trend can also be confirmed for the community of methanogenic archaea that were highly abundant and diverse during warm and particularly wet conditions. For the terrestrial permafrost, a direct effect of the temperature on the microbial communities is likely. In contrast, it is suggested that the temperature rise in scope of the glacial-interglacial climate variations led to an increase of the primary production in the Arctic lake setting, as can be seen in the corresponding biogenic silica distribution. The availability of this algae-derived carbon is suggested to be a driver for the observed pattern in the microbial abundance. This work demonstrates the effect of climate changes on the community composition of methanogenic archae. Methanosarcina-related species were abundant throughout the Russian Arctic and were able to adapt to changing environmental conditions. In contrast, members of Methanocellales and Methanomicrobiales were not able to adapt to past climate changes. This PhD thesis provides first evidence that past climatic warming led to an increased abundance of microbial communities in the Arctic, closely linked to the cycling of carbon and methane production. With the predicted climate warming, it may, therefore, be anticipated that extensive amounts of microbial communities will develop. Increasing temperatures in the Arctic will affect the temperature sensitive parts of the current microbiological communities, possibly leading to a suppression of cold adapted species and the prevalence of methanogenic archaea that tolerate or adapt to increasing temperatures. These changes in the composition of methanogenic archaea will likely increase the methane production potential of high latitude terrestrial regions, changing the Arctic from a carbon sink to a source.},
  language  = {en}
}
@phdthesis{Birkemeyer2005,
  author    = {Birkemeyer, Claudia Sabine},
  title     = {Signal-metabolome interactions in plants},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7144},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {From its first use in the field of biochemistry, instrumental analysis offered a variety of invaluable tools for the comprehensive description of biological systems. Multi-selective methods that aim to cover as many endogenous compounds as possible in biological samples use different analytical platforms and include methods like gene expression profile and metabolite profile analysis. The enormous amount of data generated in application of profiling methods needs to be evaluated in a manner appropriate to the question under investigation. The new field of system biology rises to the challenge to develop strategies for collecting, processing, interpreting, and archiving this vast amount of data; to make those data available in form of databases, tools, models, and networks to the scientific community. On the background of this development a multi-selective method for the determination of phytohormones was developed and optimised, complementing the profile analyses which are already in use (Chapter I). The general feasibility of a simultaneous analysis of plant metabolites and phytohormones in one sample set-up was tested by studies on the analytical robustness of the metabolite profiling protocol. The recovery of plant metabolites proved to be satisfactory robust against variations in the extraction protocol by using common extraction procedures for phytohormones; a joint extraction of metabolites and hormones from plant tissue seems practicable (Chapter II). Quantification of compounds within the context of profiling methods requires particular scrutiny (Chapter II). In Chapter III, the potential of stable-isotope in vivo labelling as normalisation strategy for profiling data acquired with mass spectrometry is discussed. First promising results were obtained for a reproducible quantification by stable-isotope in vivo labelling, which was applied in metabolomic studies. In-parallel application of metabolite and phytohormone analysis to seedlings of the model plant Arabidopsis thaliana exposed to sulfate limitation was used to investigate the relationship between the endogenous concentration of signal elements and the 'metabolic phenotype' of a plant. An automated evaluation strategy was developed to process data of compounds with diverse physiological nature, such as signal elements, genes and metabolites - all which act in vivo in a conditional, time-resolved manner (Chapter IV). Final data analysis focussed on conditionality of signal-metabolome interactions.},
  subject      = {Pflanzenhormon},
  language  = {en}
}
@phdthesis{BinTareaf2022,
  author    = {Bin Tareaf, Raad},
  title     = {Social media based personality prediction models},
  doi       = {10.25932/publishup-54914},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-549142},
  school      = {Universit{\"a}t Potsdam},
  pages     = {x, 137},
  year      = {2022},
  abstract  = {Individuals have an intrinsic need to express themselves to other humans within a given community by sharing their experiences, thoughts, actions, and opinions. As a means, they mostly prefer to use modern online social media platforms such as Twitter, Facebook, personal blogs, and Reddit. Users of these social networks interact by drafting their own statuses updates, publishing photos, and giving likes leaving a considerable amount of data behind them to be analyzed. Researchers recently started exploring the shared social media data to understand online users better and predict their Big five personality traits: agreeableness, conscientiousness, extraversion, neuroticism, and openness to experience. This thesis intends to investigate the possible relationship between users' Big five personality traits and the published information on their social media profiles. Facebook public data such as linguistic status updates, meta-data of likes objects, profile pictures, emotions, or reactions records were adopted to address the proposed research questions. Several machine learning predictions models were constructed with various experiments to utilize the engineered features correlated with the Big 5 Personality traits. The final predictive performances improved the prediction accuracy compared to state-of-the-art approaches, and the models were evaluated based on established benchmarks in the domain. The research experiments were implemented while ethical and privacy points were concerned. Furthermore, the research aims to raise awareness about privacy between social media users and show what third parties can reveal about users' private traits from what they share and act on different social networking platforms. In the second part of the thesis, the variation in personality development is studied within a cross-platform environment such as Facebook and Twitter platforms. The constructed personality profiles in these social platforms are compared to evaluate the effect of the used platforms on one user's personality development. Likewise, personality continuity and stability analysis are performed using two social media platforms samples. The implemented experiments are based on ten-year longitudinal samples aiming to understand users' long-term personality development and further unlock the potential of cooperation between psychologists and data scientists.},
  language  = {en}
}
@phdthesis{Biewald2008,
  author    = {Biewald, Anne},
  title     = {A dynamic life cycle model for Germany with unemployment uncertainty},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33111},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {This work analyzes the saving and consumption behavior of agents faced with the possibility of unemployment in a dynamic and stochastic life cycle model. The intertemporal optimization is based on Dynamic Programming with a backward recursion algorithm. The implemented uncertainty is not based on income shocks as it is done in traditional life cycle models but uses Markov probabilities where the probability for the next employment status of the agent depends on the current status. The utility function used is a CRRA function (constant relative risk aversion), combined with a CES function (constant elasticity of substitution) and has several consumption goods, a subsistence level, money and a bequest function.},
  language  = {en}
}
@phdthesis{Bierbaum2011,
  author    = {Bierbaum, Veronika},
  title     = {Chemomechanical coupling and motor cycles of the molecular motor myosin V},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-53614},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {In the living cell, the organization of the complex internal structure relies to a large extent on molecular motors. Molecular motors are proteins that are able to convert chemical energy from the hydrolysis of adenosine triphosphate (ATP) into mechanical work. Being about 10 to 100 nanometers in size, the molecules act on a length scale, for which thermal collisions have a considerable impact onto their motion. In this way, they constitute paradigmatic examples of thermodynamic machines out of equilibrium. This study develops a theoretical description for the energy conversion by the molecular motor myosin V, using many different aspects of theoretical physics. Myosin V has been studied extensively in both bulk and single molecule experiments. Its stepping velocity has been characterized as a function of external control parameters such as nucleotide concentration and applied forces. In addition, numerous kinetic rates involved in the enzymatic reaction of the molecule have been determined. For forces that exceed the stall force of the motor, myosin V exhibits a 'ratcheting' behaviour: For loads in the direction of forward stepping, the velocity depends on the concentration of ATP, while for backward loads there is no such influence. Based on the chemical states of the motor, we construct a general network theory that incorporates experimental observations about the stepping behaviour of myosin V. The motor's motion is captured through the network description supplemented by a Markov process to describe the motor dynamics. This approach has the advantage of directly addressing the chemical kinetics of the molecule, and treating the mechanical and chemical processes on equal grounds. We utilize constraints arising from nonequilibrium thermodynamics to determine motor parameters and demonstrate that the motor behaviour is governed by several chemomechanical motor cycles. In addition, we investigate the functional dependence of stepping rates on force by deducing the motor's response to external loads via an appropriate Fokker-Planck equation. For substall forces, the dominant pathway of the motor network is profoundly different from the one for superstall forces, which leads to a stepping behaviour that is in agreement with the experimental observations. The extension of our analysis to Markov processes with absorbing boundaries allows for the calculation of the motor's dwell time distributions. These reveal aspects of the coordination of the motor's heads and contain direct information about the backsteps of the motor. Our theory provides a unified description for the myosin V motor as studied in single motor experiments.},
  language  = {en}
}
@phdthesis{Bieniawska2006,
  author    = {Bieniawska, Zuzanna},
  title     = {Functional analysis of the sucrose synthase gene family in Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-13132},
  school      = {Universit{\"a}t Potsdam},
  year      = {2006},
  abstract  = {Sucrose synthase (Susy) is a key enzyme of sucrose metabolism, catalysing the reversible conversion of sucrose and UDP to UDP-glucose and fructose. Therefore, its activity, localization and function have been studied in various plant species. It has been shown that Susy can play a role in supplying energy in companion cells for phloem loading (Fu and Park, 1995), provides substrates for starch synthesis (Zrenner et al., 1995), and supplies UDP-glucose for cell wall synthesis (Haigler et al., 2001). Analysis of the Arabidopsis genome identifies six Susy isoforms. The expression of these isoforms was investigated using promoter-reporter gene constructs (GUS) and real time RT-PCR. Although these isoforms are closely related at the protein level they have radically different spatial and temporal patterns of expression in the plant with no two isoforms showing the same distribution. More than one isoform is expressed in all organs examined. Some of them have high but specific expression in particular organs or developmental stages whilst others are constantly expressed throughout the whole plant and across various stages of development. The in planta function of the six Susy isoforms were explored through analysis of T-DNA insertion mutants and RNAi lines. Plants without the expression of individual isoforms show no differences in growth and development, and are not significantly different from wild type plants in soluble sugars, starch and cellulose contents under all growth conditions investigated. Analysis of T-DNA insertion mutant lacking Sus3 isoform that was exclusively expressed in stomata cells only had a minor influence on guard cell osmoregulation and/or bioenergetics. Although none of the sucrose synthases appear to be essential for normal growth under our standard growth conditions, they may be necessary for growth under stress conditions. Different isoforms of sucrose synthase respond differently to various abiotic stresses. It has been shown that oxygen deprivation up regulates Sus1 and Sus4 and increases total Susy activity. However, the analysis of the plants with reduced expression of both Sus1 and Sus4 revealed no obvious effects on plant performance under oxygen deprivation. Low temperature up regulates Sus1 expression but the loss of this isoform has no effect on the freezing tolerance of non acclimated and cold acclimated plants. These data provide a comprehensive overview of the expression of this gene family which supports some of the previously reported roles for Susy and indicates the involvement of specific isoforms in metabolism and/or signalling.},
  language  = {en}
}
@phdthesis{Bielecka2007,
  author    = {Bielecka, Monika},
  title     = {Analysis of transcription factors under sulphur deficiency stress},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-14812},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Sulphur, a macronutrient essential for plant growth, is among the most versatile elements in living organisms. Unfortunately, little is known about regulation of sulphate uptake and assimilation by plants. Identification of sulphate signalling processes will allow to control sulphate acquisition and assimilation and may prove useful in the future to improve sulphur-use efficiency in agriculture. Many of genes involved in sulphate metabolism are regulated on transcriptional level by products of other genes called transcription factors (TF). Several published experiments revealed TF genes that respond to sulphate deprivation, but none of these have been so far been characterized functionally. Thus, we aimed at identifying and characterising transcription factors that control sulphate metabolism in the model plant Arabidopsis thaliana. To achieve that goal we postulated that factors regulating Arabidopsis responses to inorganic sulphate deficiency change their transcriptional levels under sulphur-limited conditions. By comparing TF transcript profiles from plants grown on different sulphate regimes, we identified TF genes that may specifically induce or repress changes in expression of genes that allow plants to adapt to changes in sulphate availability. Candidate genes obtained from this screening were tested by reverse genetics approaches. Transgenic plants constitutively overproducing selected TF genes and mutant plants, lacking functional selected TF genes (knock out), were used. By comparing metabolite and transcript profiles from transgenic and wild type plants we aimed at confirming the role of selected AP2 TF candidate genes in plant adaptation to sulphur unavailability. After preliminary characterisation of WRKY24 and MYB93 TF genes, we postulate that these factors are involved in a complex multifactorial regulatory network, in which WRKY24 and MYB93 would act as superior factors regulating other transcription factors directly involved in the regulation of S-metabolism genes. Results obtained for plants overproducing TOE1 and TOE2 TF genes suggests that these factors may be involved in a mechanism, which is promoting synthesis of an essential amino acid, methionine, over synthesis of another amino acid, cysteine. Thus, TOE1 and TOE2 genes might be a part of transcriptional regulation of methionine synthesis. Approaches creating genetically manipulated plants may produce plant phenotypes of immediate biotechnological interest, such as plants with increased sulphate or sulphate-containing amino acid content, or better adapted to the sulphate unavailability.},
  language  = {en}
}
@phdthesis{Biedermann2020,
  author    = {Biedermann, Nicole},
  title     = {Carbonate-silicate reactions at conditions of the Earth's mantle and the role of carbonates as possible trace-element carriers},
  doi       = {10.25932/publishup-48277},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-482772},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xvii, 127},
  year      = {2020},
  abstract  = {Carbonates play a key role in the chemistry and dynamics of our planet. They are directly connected to the CO2 budget of our atmosphere and have a great impact on the deep carbon cycle. Moreover, recent studies have shown that carbonates are stable along the geothermal gradient down to Earth's lower mantle conditions, changing their crystal structure and related properties. Subducted carbonates may also react with silicates to form new phases. These reactions will redistribute elements, such as calcium (Ca), magnesium (Mg), iron (Fe) and carbon in the form of carbon dioxide (CO2), but also trace elements, that are carried by the carbonates. The trace elements of most interest are strontium (Sr) and rare earth elements (REE) which have been found to be important constituents in the composition of the primitive lower mantle and in mineral inclusions found in super-deep diamonds. However, the stability of carbonates in presence of mantle silicates at relevant temperatures is far from being well understood. Related to this, very little is known about distribution processes of trace elements between carbonates and mantle silicates. To shed light on these processes, we studied reactions between Sr- and REE-containing CaCO3 and Mg/Fe-bearing silicates of the system (Mg,Fe)2SiO4 - (Mg,Fe)SiO3 at high pressure and high temperature using synchrotron radiation based μ-X-ray diffraction (μ-XRD) and μ-X-ray fluorescence (μ-XRF) with μm-resolution in a laser-heated diamond anvil cell. X-ray diffraction is used to derive the structural changes of the phase reactions whereas X-ray fluorescence gives information on the chemical changes in the sample. In-situ experiments at high pressure and high temperature were performed at beamline P02.2 at PETRA III (Hamburg, Germany) and at beamline ID27 at ESRF (Grenoble, France). In addition to μ-XRD and μ-XRF, ex-situ measurements were made on the recovered sample material using transmission electron microscopy (TEM) and provided further insights into the reaction kinetics of carbonate-silicate reactions. Our investigations show that CaCO3 is unstable in presence of mantle silicates above 1700 K and a reaction takes place in which magnesite plus CaSiO3-perovskite are formed. In addition, we observed that a high content of iron in the carbonate-silicate system favours dolomite formation during the reaction. The subduction of natural carbonates with significant amounts of Sr leads to a comprehensive investigation of the stability not only of CaCO3 phases in contact with mantle silicates but also of SrCO3 (and of Sr-bearing CaCO3). We found that SrCO3 reacts with (Mg,Fe)SiO3-perovskite to form magnesite and gained evidence for the formation of SrSiO3-perovskite. To complement our study on the stability of SrCO3 at conditions of the Earth's lower mantle, we performed powder X-ray diffraction and single crystal X-ray diffraction experiments at ambient temperature and up to 49 GPa. We observed a transformation from SrCO3-I into a new high-pressure phase SrCO3-II at around 26 GPa with Pmmn crystal structure and a bulk modulus of 103(10) GPa. This information is essential to fully understand the phase behaviour and stability of carbonates in the Earth's lower mantle and to elucidate the possibility of introducing Sr into mantle silicates by carbonate-silicate reactions. Simultaneous recording of μ-XRD and μ-XRF in the μm-range over the heated areas provides spatial information not only about phase reactions but also on the elemental redistribution during the reactions. A comparison of the spatial intensity distribution of the XRF signal before and after heating indicates a change in the elemental distribution of Sr and an increase in Sr-concentration was found around the newly formed SrSiO3-perovskite. With the help of additional TEM analyses on the quenched sample material the elemental redistribution was studied at a sub-micrometer scale. Contrary to expectations from combined μ-XRD and μ-XRF measurements, we found that La and Eu were not incorporated into the silicate phases, instead they tend to form either isolated oxide phases (e.g. Eu2O3, La2O3) or hydroxyl-bastn{\"a}site (La(CO3)(OH)). In addition, we observed the transformation from (Mg,Fe)SiO3-perovskite to low-pressure clinoenstatite during pressure release. The monoclinic structure (P21/c) of this phase allows the incorporation of Ca as shown by additional EDX analyses and, to a minor extent, Sr too. Based on our experiments, we can conclude that a detection of the trace elements in-situ at high pressure and high temperature remains challenging. However, our first findings imply that silicates may incorporate the trace elements provided by the carbonates and indicate that carbonates may have a major effect on the trace element contents of mantle phases.},
  language  = {en}
}
@phdthesis{Bickel2008,
  author    = {Bickel, Steffen},
  title     = {Learning under differing training and test distributions},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33331},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {One of the main problems in machine learning is to train a predictive model from training data and to make predictions on test data. Most predictive models are constructed under the assumption that the training data is governed by the exact same distribution which the model will later be exposed to. In practice, control over the data collection process is often imperfect. A typical scenario is when labels are collected by questionnaires and one does not have access to the test population. For example, parts of the test population are underrepresented in the survey, out of reach, or do not return the questionnaire. In many applications training data from the test distribution are scarce because they are difficult to obtain or very expensive. Data from auxiliary sources drawn from similar distributions are often cheaply available. This thesis centers around learning under differing training and test distributions and covers several problem settings with different assumptions on the relationship between training and test distributions-including multi-task learning and learning under covariate shift and sample selection bias. Several new models are derived that directly characterize the divergence between training and test distributions, without the intermediate step of estimating training and test distributions separately. The integral part of these models are rescaling weights that match the rescaled or resampled training distribution to the test distribution. Integrated models are studied where only one optimization problem needs to be solved for learning under differing distributions. With a two-step approximation to the integrated models almost any supervised learning algorithm can be adopted to biased training data. In case studies on spam filtering, HIV therapy screening, targeted advertising, and other applications the performance of the new models is compared to state-of-the-art reference methods.},
  language  = {en}
}
@phdthesis{Bhattacharryya2006,
  author    = {Bhattacharryya, Saroj Kumar},
  title     = {Development of detector for analytical ultracentrifuge. - [korr. Fassung]},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-8215},
  school      = {Universit{\"a}t Potsdam},
  year      = {2006},
  abstract  = {In this work approaches for new detection system development for an Analytical Ultracentrifuge (AUC) were explored. Unlike its counterpart in chromatography fractionation techniques, the use of a Multidetection system for AUC has not yet been implemented to full extent despite its potential benefit. In this study we tried to couple existing fundamental spectroscopic and scattering techniques that are used in day to day science as tool for extracting analyte information. Trials were performed for adapting Raman, Light scattering and UV/Vis (with possibility to work with the whole range of wavelengths) to AUC. Conclusions were drawn for Raman and Light scattering to be a possible detection system for AUC, while the development for a fast fiber optics based multiwavelength detector was completed. The multiwavelength detector demonstrated the capability of data generation matching the literature and reference measurement data and faster data collection than that of the commercial instrument. It became obvious that with the generation of data in 3-D space in the UV/Vis detection system, the user can select the wavelength for the evaluation of experimental results as the data set contains the whole range of information from UV/Vis wavelength. The detector showed the data generation with much faster speed unlike the commercial instruments. The advantage of fast data generation was exemplified with the evaluation of data for a mixture of three colloids. These data were in conformity with measurement results from normal radial experiments and without significant diffusion broadening. Thus conclusions were drawn that with our designed Multiwavelength detector, meaningful data in 3-D space can be collected with much faster speed of data generation.},
  subject      = {Ultrazentrifuge},
  language  = {en}
}
@phdthesis{Beyvers2008,
  author    = {Beyvers, Stephanie},
  title     = {Selective excitation of adsorbate vibrations on dissipative surfaces},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-25516},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {The selective infrared (IR) excitation of molecular vibrations is a powerful tool to control the photoreactivity prior to electronic excitation in the ultraviolet / visible (UV/Vis) light regime ("vibrationally mediated chemistry"). For adsorbates on surfaces it has been theoretically predicted that IR preexcitation will lead to higher UV/Vis photodesorption yields and larger cross sections for other photoreactions. In a recent experiment, IR-mediated desorption of molecular hydrogen from a Si(111) surface on which atomic hydrogen and deuterium were co-adsorbed was achieved, following a vibrational mechanism as indicated by the isotope-selectivity. In the present work, selective vibrational IR excitation of adsorbate molecules, treated as multi-dimensional oscillators on dissipative surfaces, has been simulated within the framework of open-system density matrix theory. Not only potential-mediated, inter-mode coupling poses an obstacle to selective excitation but also the coupling of the adsorbate ("system") modes to the electronic and phononic degrees of freedom of the surface ("bath") does. Vibrational relaxation thereby takes place, depending on the availabilty of energetically fitting electron-hole (e/h) pairs and/or phonons (lattice vibrations) in the surface, on time-scales ranging from milliseconds to several hundreds of femtoseconds. On metal surfaces, where the relaxation process of the adsorbate via the e/h pair mechanism dominates, vibrational lifetimes are usually shorter than on insulator or semiconductor surfaces, in the range of picoseconds, being also the timescale of the IR pulses used here. Further inhibiting factors for selectivity can be the harmonicity of a mode and weak dipole activities ("dark modes") rendering vibrational excitation with moderate field intensities difficult. In addition to simple analytical pulses, optimal control theory (OCT) has been employed here to generate a suitable electric field to populate the target state/mode maximally. The complex OCT fields were analyzed by Husimi transformation, resolving the control field in time and energy. The adsorbate/surface systems investigated were CO/Cu(100), H/Si(100) and 2H/Ru(0001). These systems proved to be suitable models to study the above mentioned effects. Further, effects of temperature, pure dephasing (elastic scattering processes), pulse duration and dimensionality (up to four degrees of freedom) were studied. It was possible to selectively excite single vibrational modes, often even state-selective. Special processes like hot-band excitation, vibrationally mediated desorption and the excitation of "dark modes" were simulated. Finally, a novel OCT algorithm in density matrix representation has been developed which allows for time-dependent target operators and thus enables to control the excitation mechanism instead of only the final state. The algorithm is based on a combination of global (iterative) and local (non-iterative) OCT schemes, such that short, globally controlled time-intervals are coupled locally in time. Its numerical performance and accuracy were tested and verified and it was successfully applied to stabilize a two-state linear-combination and to enforce a successive "ladder climbing" in a rather harmonic system, where monochromatic, analytical pulses simultaneously excited several states, leading to a population loss in the target state.},
  language  = {en}
}
@phdthesis{Beyhl2017,
  author    = {Beyhl, Thomas},
  title     = {A framework for incremental view graph maintenance},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-405929},
  school      = {Universit{\"a}t Potsdam},
  pages     = {VII, 293},
  year      = {2017},
  abstract  = {Nowadays, graph data models are employed, when relationships between entities have to be stored and are in the scope of queries. For each entity, this graph data model locally stores relationships to adjacent entities. Users employ graph queries to query and modify these entities and relationships. These graph queries employ graph patterns to lookup all subgraphs in the graph data that satisfy certain graph structures. These subgraphs are called graph pattern matches. However, this graph pattern matching is NP-complete for subgraph isomorphism. Thus, graph queries can suffer a long response time, when the number of entities and relationships in the graph data or the graph patterns increases. One possibility to improve the graph query performance is to employ graph views that keep ready graph pattern matches for complex graph queries for later retrieval. However, these graph views must be maintained by means of an incremental graph pattern matching to keep them consistent with the graph data from which they are derived, when the graph data changes. This maintenance adds subgraphs that satisfy a graph pattern to the graph views and removes subgraphs that do not satisfy a graph pattern anymore from the graph views. Current approaches for incremental graph pattern matching employ Rete networks. Rete networks are discrimination networks that enumerate and maintain all graph pattern matches of certain graph queries by employing a network of condition tests, which implement partial graph patterns that together constitute the overall graph query. Each condition test stores all subgraphs that satisfy the partial graph pattern. Thus, Rete networks suffer high memory consumptions, because they store a large number of partial graph pattern matches. But, especially these partial graph pattern matches enable Rete networks to update the stored graph pattern matches efficiently, because the network maintenance exploits the already stored partial graph pattern matches to find new graph pattern matches. However, other kinds of discrimination networks exist that can perform better in time and space than Rete networks. Currently, these other kinds of networks are not used for incremental graph pattern matching. This thesis employs generalized discrimination networks for incremental graph pattern matching. These discrimination networks permit a generalized network structure of condition tests to enable users to steer the trade-off between memory consumption and execution time for the incremental graph pattern matching. For that purpose, this thesis contributes a modeling language for the effective definition of generalized discrimination networks. Furthermore, this thesis contributes an efficient and scalable incremental maintenance algorithm, which updates the (partial) graph pattern matches that are stored by each condition test. Moreover, this thesis provides a modeling evaluation, which shows that the proposed modeling language enables the effective modeling of generalized discrimination networks. Furthermore, this thesis provides a performance evaluation, which shows that a) the incremental maintenance algorithm scales, when the graph data becomes large, and b) the generalized discrimination network structures can outperform Rete network structures in time and space at the same time for incremental graph pattern matching.},
  language  = {en}
}
@phdthesis{Bettenbuehl2015,
  author    = {Bettenb{\"u}hl, Mario},
  title     = {Microsaccades},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-122-6},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72622},
  school      = {Universit{\"a}t Potsdam},
  pages     = {iv, 126},
  year      = {2015},
  abstract  = {The first thing we do upon waking is open our eyes. Rotating them in our eye sockets, we scan our surroundings and collect the information into a picture in our head. Eye movements can be split into saccades and fixational eye movements, which occur when we attempt to fixate our gaze. The latter consists of microsaccades, drift and tremor. Before we even lift our eye lids, eye movements - such as saccades and microsaccades that let the eyes jump from one to another position - have partially been prepared in the brain stem. Saccades and microsaccades are often assumed to be generated by the same mechanisms. But how saccades and microsaccades can be classified according to shape has not yet been reported in a statistical manner. Research has put more effort into the investigations of microsaccades' properties and generation only since the last decade. Consequently, we are only beginning to understand the dynamic processes governing microsaccadic eye movements. Within this thesis, the dynamics governing the generation of microsaccades is assessed and the development of a model for the underlying processes. Eye movement trajectories from different experiments are used, recorded with a video-based eye tracking technique, and a novel method is proposed for the scale-invariant detection of saccades (events of large amplitude) and microsaccades (events of small amplitude). Using a time-frequency approach, the method is examined with different experiments and validated against simulated data. A shape model is suggested that allows for a simple estimation of saccade- and microsaccade related properties. For sequences of microsaccades, in this thesis a time-dynamic Markov model is proposed, with a memory horizon that changes over time and which can best describe sequences of microsaccades.},
  language  = {en}
}
@phdthesis{Berner2016,
  author    = {Berner, Nadine},
  title     = {Deciphering multiple changes in complex climate time series using Bayesian inference},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-100065},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xvi, 135},
  year      = {2016},
  abstract  = {Change points in time series are perceived as heterogeneities in the statistical or dynamical characteristics of the observations. Unraveling such transitions yields essential information for the understanding of the observed system's intrinsic evolution and potential external influences. A precise detection of multiple changes is therefore of great importance for various research disciplines, such as environmental sciences, bioinformatics and economics. The primary purpose of the detection approach introduced in this thesis is the investigation of transitions underlying direct or indirect climate observations. In order to develop a diagnostic approach capable to capture such a variety of natural processes, the generic statistical features in terms of central tendency and dispersion are employed in the light of Bayesian inversion. In contrast to established Bayesian approaches to multiple changes, the generic approach proposed in this thesis is not formulated in the framework of specialized partition models of high dimensionality requiring prior specification, but as a robust kernel-based approach of low dimensionality employing least informative prior distributions. First of all, a local Bayesian inversion approach is developed to robustly infer on the location and the generic patterns of a single transition. The analysis of synthetic time series comprising changes of different observational evidence, data loss and outliers validates the performance, consistency and sensitivity of the inference algorithm. To systematically investigate time series for multiple changes, the Bayesian inversion is extended to a kernel-based inference approach. By introducing basic kernel measures, the weighted kernel inference results are composed into a proxy probability to a posterior distribution of multiple transitions. The detection approach is applied to environmental time series from the Nile river in Aswan and the weather station Tuscaloosa, Alabama comprising documented changes. The method's performance confirms the approach as a powerful diagnostic tool to decipher multiple changes underlying direct climate observations. Finally, the kernel-based Bayesian inference approach is used to investigate a set of complex terrigenous dust records interpreted as climate indicators of the African region of the Plio-Pleistocene period. A detailed inference unravels multiple transitions underlying the indirect climate observations, that are interpreted as conjoint changes. The identified conjoint changes coincide with established global climate events. In particular, the two-step transition associated to the establishment of the modern Walker-Circulation contributes to the current discussion about the influence of paleoclimate changes on the environmental conditions in tropical and subtropical Africa at around two million years ago.},
  language  = {en}
}
@phdthesis{Bergner2011,
  author    = {Bergner, Andr{\´e}},
  title     = {Synchronization in complex systems with multiple time scales},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-53407},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {In the present work synchronization phenomena in complex dynamical systems exhibiting multiple time scales have been analyzed. Multiple time scales can be active in different manners. Three different systems have been analyzed with different methods from data analysis. The first system studied is a large heterogenous network of bursting neurons, that is a system with two predominant time scales, the fast firing of action potentials (spikes) and the burst of repetitive spikes followed by a quiescent phase. This system has been integrated numerically and analyzed with methods based on recurrence in phase space. An interesting result are the different transitions to synchrony found in the two distinct time scales. Moreover, an anomalous synchronization effect can be observed in the fast time scale, i.e. there is range of the coupling strength where desynchronization occurs. The second system analyzed, numerically as well as experimentally, is a pair of coupled CO₂ lasers in a chaotic bursting regime. This system is interesting due to its similarity with epidemic models. We explain the bursts by different time scales generated from unstable periodic orbits embedded in the chaotic attractor and perform a synchronization analysis of these different orbits utilizing the continuous wavelet transform. We find a diverse route to synchrony of these different observed time scales. The last system studied is a small network motif of limit cycle oscillators. Precisely, we have studied a hub motif, which serves as elementary building block for scale-free networks, a type of network found in many real world applications. These hubs are of special importance for communication and information transfer in complex networks. Here, a detailed study on the mechanism of synchronization in oscillatory networks with a broad frequency distribution has been carried out. In particular, we find a remote synchronization of nodes in the network which are not directly coupled. We also explain the responsible mechanism and its limitations and constraints. Further we derive an analytic expression for it and show that information transmission in pure phase oscillators, such as the Kuramoto type, is limited. In addition to the numerical and analytic analysis an experiment consisting of electrical circuits has been designed. The obtained results confirm the former findings.},
  language  = {en}
}
@phdthesis{Bergner2003,
  author    = {Bergner, Andreas G. N.},
  title     = {Lake-level fluctuations and Late Quaternary climate change in the Central Kenya Rift},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001428},
  school      = {Universit{\"a}t Potsdam},
  year      = {2003},
  abstract  = {Diese Arbeit besch{\"a}ftigt sich mit der Rekonstruktion von Klima in historischen Zeiten im tropischen Ostafrika. Nach einer {\"U}bersicht {\"u}ber die heutigen klimatischen Bedingungen der Tropen und den Besonderheiten des ostafrikanischen Klimas, werden die M{\"o}glichkeiten der Klimarekonstruktion anhand von Seesedimenten diskutiert. Es zeigt sich, dass die hoch gelegenen Seen des Zentralen Keniarifts, als Teil des Ostafrikanischen Grabensystems, besonders geeignete Klimaarchive darstellen, da sie sensibel auf klimatische Ver{\"a}nderungen reagieren. Ver{\"a}nderungen der Seechemie, wie sie in den Sedimenten aufgezeichnet werden, eignen sich um die nat{\"u}rlichen Schwankungen in der Quart{\"a}ren Klimageschichte Ostafrikas nachzuzeichnen. Basierend auf der guten 40Ar/39Ar- und 14C-Datierbarkeit der Seesedimente wird eine Chronologie der pal{\"a}o{\"o}kologischen Bedingungen anhand von Diatomeenvergesellschaftungen restauriert. Dabei zeigen sich f{\"u}r die Seen Nakuru, Elmenteita und Naivasha kurzfristige Transgression/ Regressions-Zyklen im Intervall von ca. 11.000 Jahren w{\"a}hrend des letzten (ca. 12.000 bis 6.000 J.v.H.) und vorletzten Interglazials (ca. 140.000 bis 60.000 J.v.H.). Zus{\"a}tzlich kann ein allgemeiner, langfristiger Trend der Seeentwicklung von großen Frischwasserseen hin zu st{\"a}rker salinen Gew{\"a}ssern innerhalb der letzen 1 Mio. Jahre festgestellt werden. Mittels Transferfunktionen und einem hydro-klimatischen Modellansatz k{\"o}nnen die restaurierten limnologischen Bedingungen als klimatische Schwankungen des Einzugsgebietes interpretiert werden. Wenngleich auch der zus{\"a}tzliche Einfluss von tektonischen Ver{\"a}nderungen auf das Seeeinzugsgebiet und das Gewicht ver{\"a}nderter Grundwasserstr{\"o}me abgewogen werden, zeigt sich, dass allein geringf{\"u}gig erh{\"o}hte Niederschlagswerte von ca. 30±10 \% zu dramatischen Seespiegelanstiegen im Zentralen Keniarift f{\"u}hren. Aufgrund der etablierten hydrrologisch-klimatischen Wechselwirkungen werden R{\"u}ckschl{\"u}sse auf die nat{\"u}rliche Variabilit{\"a}t des ostafrikanischen Klimas gezogen. Zudem wird die Sensitivit{\"a}t der Keniarift-Seen in Bezug auf die St{\"a}rke der {\"a}quatorialen Insolation und hinsichtilch variabler Oberfl{\"a}chenwassertemperaturen des Indischen Ozeans bewertet.},
  language  = {en}
}
@phdthesis{Bergholz2018,
  author    = {Bergholz, Kolja},
  title     = {Trait-based understanding of plant species distributions along environmental gradients},
  doi       = {10.25932/publishup-42634},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-426341},
  school      = {Universit{\"a}t Potsdam},
  pages     = {128},
  year      = {2018},
  abstract  = {For more than two centuries, plant ecologists have aimed to understand how environmental gradients and biotic interactions shape the distribution and co-occurrence of plant species. In recent years, functional trait-based approaches have been increasingly used to predict patterns of species co-occurrence and species distributions along environmental gradients (trait-environment relationships). Functional traits are measurable properties at the individual level that correlate well with important processes. Thus, they allow us to identify general patterns by synthesizing studies across specific taxonomic compositions, thereby fostering our understanding of the underlying processes of species assembly. However, the importance of specific processes have been shown to be highly dependent on the spatial scale under consideration. In particular, it remains uncertain which mechanisms drive species assembly and allow for plant species coexistence at smaller, more local spatial scales. Furthermore, there is still no consensus on how particular environmental gradients affect the trait composition of plant communities. For example, increasing drought because of climate change is predicted to be a main threat to plant diversity, although it remains unclear which traits of species respond to increasing aridity. Similarly, there is conflicting evidence of how soil fertilization affects the traits related to establishment ability (e.g., seed mass). In this cumulative dissertation, I present three empirical trait-based studies that investigate specific research questions in order to improve our understanding of species distributions along environmental gradients. In the first case study, I analyze how annual species assemble at the local scale and how environmental heterogeneity affects different facets of biodiversity—i.e. taxonomic, functional, and phylogenetic diversity—at different spatial scales. The study was conducted in a semi-arid environment at the transition zone between desert and Mediterranean ecosystems that features a sharp precipitation gradient (Israel). Different null model analyses revealed strong support for environmentally driven species assembly at the local scale, since species with similar traits tended to co-occur and shared high abundances within microsites (trait convergence). A phylogenetic approach, which assumes that closely related species are functionally more similar to each other than distantly related ones, partly supported these results. However, I observed that species abundances within microsites were, surprisingly, more evenly distributed across the phylogenetic tree than expected (phylogenetic overdispersion). Furthermore, I showed that environmental heterogeneity has a positive effect on diversity, which was higher on functional than on taxonomic diversity and increased with spatial scale. The results of this case study indicate that environmental heterogeneity may act as a stabilizing factor to maintain species diversity at local scales, since it influenced species distribution according to their traits and positively influenced diversity. All results were constant along the precipitation gradient. In the second case study (same study system as case study one), I explore the trait responses of two Mediterranean annuals (Geropogon hybridus and Crupina crupinastrum) along a precipitation gradient that is comparable to the maximum changes in precipitation predicted to occur by the end of this century (i.e., -30\%). The heterocarpic G. hybridus showed strong trends in seed traits, suggesting that dispersal ability increased with aridity. By contrast, the homocarpic C. crupinastrum showed only a decrease in plant height as aridity increased, while leaf traits of both species showed no consistent pattern along the precipitation gradient. Furthermore, variance decomposition of traits revealed that most of the trait variation observed in the study system was actually found within populations. I conclude that trait responses towards aridity are highly species-specific and that the amount of precipitation is not the most striking environmental factor at this particular scale. In the third case study, I assess how soil fertilization mediates—directly by increased nutrient addition and indirectly by increased competition—the effect of seed mass on establishment ability. For this experiment, I used 22 species differing in seed mass from dry grasslands in northeastern Germany and analyzed the interacting effects of seed mass with nutrient availability and competition on four key components of seedling establishment: seedling emergence, time of seedling emergence, seedling survival, and seedling growth. (Time of) seedling emergence was not affected by seed mass. However, I observed that the positive effect of seed mass on seedling survival is lowered under conditions of high nutrient availability, whereas the positive effect of seed mass on seedling growth was only reduced by competition. Based on these findings, I developed a conceptual model of how seed mass should change along a soil fertility gradient in order to reconcile conflicting findings from the literature. In this model, seed mass shows a U-shaped pattern along the soil fertility gradient as a result of changing nutrient availability and competition. Overall, the three case studies highlight the role of environmental factors on species distribution and co-occurrence. Moreover, the findings of this thesis indicate that spatial heterogeneity at local scales may act as a stabilizing factor that allows species with different traits to coexist. In the concluding discussion, I critically debate intraspecific trait variability in plant community ecology, the use of phylogenetic relationships and easily measured key functional traits as a proxy for species' niches. Finally, I offer my outlook for the future of functional plant community research.},
  language  = {en}
}
@phdthesis{Berger2012,
  author    = {Berger, Florian},
  title     = {Different modes of cooperative transport by molecular motors},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-60319},
  school      = {Universit{\"a}t Potsdam},
  year      = {2012},
  abstract  = {Cargo transport by molecular motors is ubiquitous in all eukaryotic cells and is typically driven cooperatively by several molecular motors, which may belong to one or several motor species like kinesin, dynein or myosin. These motor proteins transport cargos such as RNAs, protein complexes or organelles along filaments, from which they unbind after a finite run length. Understanding how these motors interact and how their movements are coordinated and regulated is a central and challenging problem in studies of intracellular transport. In this thesis, we describe a general theoretical framework for the analysis of such transport processes, which enables us to explain the behavior of intracellular cargos based on the transport properties of individual motors and their interactions. Motivated by recent in vitro experiments, we address two different modes of transport: unidirectional transport by two identical motors and cooperative transport by actively walking and passively diffusing motors. The case of cargo transport by two identical motors involves an elastic coupling between the motors that can reduce the motors' velocity and/or the binding time to the filament. We show that this elastic coupling leads, in general, to four distinct transport regimes. In addition to a weak coupling regime, kinesin and dynein motors are found to exhibit a strong coupling and an enhanced unbinding regime, whereas myosin motors are predicted to attain a reduced velocity regime. All of these regimes, which we derive both by analytical calculations and by general time scale arguments, can be explored experimentally by varying the elastic coupling strength. In addition, using the time scale arguments, we explain why previous studies came to different conclusions about the effect and relevance of motor-motor interference. In this way, our theory provides a general and unifying framework for understanding the dynamical behavior of two elastically coupled molecular motors. The second mode of transport studied in this thesis is cargo transport by actively pulling and passively diffusing motors. Although these passive motors do not participate in active transport, they strongly enhance the overall cargo run length. When an active motor unbinds, the cargo is still tethered to the filament by the passive motors, giving the unbound motor the chance to rebind and continue its active walk. We develop a stochastic description for such cooperative behavior and explicitly derive the enhanced run length for a cargo transported by one actively pulling and one passively diffusing motor. We generalize our description to the case of several pulling and diffusing motors and find an exponential increase of the run length with the number of involved motors.},
  language  = {en}
}
@phdthesis{Berg2013,
  author    = {Berg, Gregor},
  title     = {Virtual prototypes for the model-based elicitation and validation of collaborative scenarios},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-69729},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Requirements engineers have to elicit, document, and validate how stakeholders act and interact to achieve their common goals in collaborative scenarios. Only after gathering all information concerning who interacts with whom to do what and why, can a software system be designed and realized which supports the stakeholders to do their work. To capture and structure requirements of different (groups of) stakeholders, scenario-based approaches have been widely used and investigated. Still, the elicitation and validation of requirements covering collaborative scenarios remains complicated, since the required information is highly intertwined, fragmented, and distributed over several stakeholders. Hence, it can only be elicited and validated collaboratively. In times of globally distributed companies, scheduling and conducting workshops with groups of stakeholders is usually not feasible due to budget and time constraints. Talking to individual stakeholders, on the other hand, is feasible but leads to fragmented and incomplete stakeholder scenarios. Going back and forth between different individual stakeholders to resolve this fragmentation and explore uncovered alternatives is an error-prone, time-consuming, and expensive task for the requirements engineers. While formal modeling methods can be employed to automatically check and ensure consistency of stakeholder scenarios, such methods introduce additional overhead since their formal notations have to be explained in each interaction between stakeholders and requirements engineers. Tangible prototypes as they are used in other disciplines such as design, on the other hand, allow designers to feasibly validate and iterate concepts and requirements with stakeholders. This thesis proposes a model-based approach for prototyping formal behavioral specifications of stakeholders who are involved in collaborative scenarios. By simulating and animating such specifications in a remote domain-specific visualization, stakeholders can experience and validate the scenarios captured so far, i.e., how other stakeholders act and react. This interactive scenario simulation is referred to as a model-based virtual prototype. Moreover, through observing how stakeholders interact with a virtual prototype of their collaborative scenarios, formal behavioral specifications can be automatically derived which complete the otherwise fragmented scenarios. This, in turn, enables requirements engineers to elicit and validate collaborative scenarios in individual stakeholder sessions - decoupled, since stakeholders can participate remotely and are not forced to be available for a joint session at the same time. This thesis discusses and evaluates the feasibility, understandability, and modifiability of model-based virtual prototypes. Similarly to how physical prototypes are perceived, the presented approach brings behavioral models closer to being tangible for stakeholders and, moreover, combines the advantages of joint stakeholder sessions and decoupled sessions.},
  language  = {en}
}
@phdthesis{Benson2024,
  author    = {Benson, Lawrence},
  title     = {Efficient state management with persistent memory},
  doi       = {10.25932/publishup-62563},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-625637},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xiii, 124},
  year      = {2024},
  abstract  = {Efficiently managing large state is a key challenge for data management systems. Traditionally, state is split into fast but volatile state in memory for processing and persistent but slow state on secondary storage for durability. Persistent memory (PMem), as a new technology in the storage hierarchy, blurs the lines between these states by offering both byte-addressability and low latency like DRAM as well persistence like secondary storage. These characteristics have the potential to cause a major performance shift in database systems. Driven by the potential impact that PMem has on data management systems, in this thesis we explore their use of PMem. We first evaluate the performance of real PMem hardware in the form of Intel Optane in a wide range of setups. To this end, we propose PerMA-Bench, a configurable benchmark framework that allows users to evaluate the performance of customizable database-related PMem access. Based on experimental results obtained with PerMA-Bench, we discuss findings and identify general and implementation-specific aspects that influence PMem performance and should be considered in future work to improve PMem-aware designs. We then propose Viper, a hybrid PMem-DRAM key-value store. Based on PMem-aware access patterns, we show how to leverage PMem and DRAM efficiently to design a key database component. Our evaluation shows that Viper outperforms existing key-value stores by 4-18x for inserts while offering full data persistence and achieving similar or better lookup performance. Next, we show which changes must be made to integrate PMem components into larger systems. By the example of stream processing engines, we highlight limitations of current designs and propose a prototype engine that overcomes these limitations. This allows our prototype to fully leverage PMem's performance for its internal state management. Finally, in light of Optane's discontinuation, we discuss how insights from PMem research can be transferred to future multi-tier memory setups by the example of Compute Express Link (CXL). Overall, we show that PMem offers high performance for state management, bridging the gap between fast but volatile DRAM and persistent but slow secondary storage. Although Optane was discontinued, new memory technologies are continuously emerging in various forms and we outline how novel designs for them can build on insights from existing PMem research.},
  language  = {en}
}
@phdthesis{Bendre2016,
  author    = {Bendre, Abhijit B.},
  title     = {Growth and saturation of dynamo in spiral galaxies via direct simulations},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407517},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xviii, 133},
  year      = {2016},
  abstract  = {We do magnetohydrodynamic (MHD) simulations of local box models of turbulent Interstellar Medium (ISM) and analyse the process of amplification and saturation of mean magnetic fields with methods of mean field dynamo theory. It is shown that the process of saturation of mean fields can be partially described by the prolonged diffusion time scales in presence of the dynamically significant magnetic fields. However, the outward wind also plays an essential role in the saturation in higher SN rate case. Algebraic expressions for the back reaction of the magnetic field onto the turbulent transport coefficients are derived, which allow a complete description of the nonlinear dynamo. We also present the effects of dynamically significant mean fields on the ISM configuration and pressure distribution. We further add the cosmic ray component in the simulations and investigate the kinematic growth of mean fields with a dynamo perspective.},
  language  = {en}
}
@phdthesis{Bekeraitė2017,
  author    = {Bekeraitė, Simona},
  title     = {Distribution functions of rotating galaxies},
  doi       = {10.25932/publishup-42095},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-420950},
  school      = {Universit{\"a}t Potsdam},
  pages     = {V, 91},
  year      = {2017},
  abstract  = {The work done during the PhD studies has been focused on measurements of distribution functions of rotating galaxies using integral field spectroscopy observations. Throughout the main body of research presented here we have been using CALIFA (Calar Alto Legacy Integral Field Area) survey stellar velocity fields to obtain robust measurements of circular velocities for rotating galaxies of all morphological types. A crucial part of the work was enabled by well-defined CALIFA sample selection criteria: it enabled reconstructing sample-independent distributions of galaxy properties. In Chapter 2, we measure the distribution in absolute magnitude - circular velocity space for a well-defined sample of 199 rotating CALIFA galaxies using their stellar kinematics. Our aim in this analysis is to avoid subjective selection criteria and to take volume and large-scale structure factors into account. Using stellar velocity fields instead of gas emission line kinematics allows including rapidly rotating early type galaxies. Our initial sample contains 277 galaxies with available stellar velocity fields and growth curve r-band photometry. After rejecting 51 velocity fields that could not be modelled due to the low number of bins, foreground contamination or significant interaction we perform Markov Chain Monte Carlo (MCMC) modelling of the velocity fields, obtaining the rotation curve and kinematic parameters and their realistic uncertainties. We perform an extinction correction and calculate the circular velocity v_circ accounting for pressure support a given galaxy has. The resulting galaxy distribution on the M_r - v_circ plane is then modelled as a mixture of two distinct populations, allowing robust and reproducible rejection of outliers, a significant fraction of which are slow rotators. The selection effects are understood well enough that the incompleteness of the sample can be corrected and the 199 galaxies can be weighted by volume and large-scale structure factors enabling us to fit a volume-corrected Tully-Fisher relation (TFR). More importantly, we also provide the volume-corrected distribution of galaxies in the M_r - v_circ plane, which can be compared with cosmological simulations. The joint distribution of the luminosity and circular velocity space densities, representative over the range of -20 > M_r > -22 mag, can place more stringent constraints on the galaxy formation and evolution scenarios than linear TFR fit parameters or the luminosity function alone. In Chapter 3, we measure one of the marginal distributions of the M_r - v_circ distribution: the circular velocity function of rotating galaxies. The velocity function is a fundamental observable statistic of the galaxy population, being of a similar importance as the luminosity function, but much more difficult to measure. We present the first directly measured circular velocity function that is representative between 60 < v_circ < 320 km s^-1 for galaxies of all morphological types at a given rotation velocity. For the low mass galaxy population 60 < v_circ < 170 km s^-1, we use the HIPASS velocity function. For the massive galaxy population 170 < v_circ < 320 km s^-1, we use stellar circular velocities from CALIFA. The CALIFA velocity function includes homogeneous velocity measurements of both late and early-type rotation-supported galaxies. It has the crucial advantage of not missing gas-poor massive ellipticals that HI surveys are blind to. We show that both velocity functions can be combined in a seamless manner, as their ranges of validity overlap. The resulting observed velocity function is compared to velocity functions derived from cosmological simulations of the z = 0 galaxy population. We find that dark matter-only simulations show a strong mismatch with the observed VF. Hydrodynamic Illustris simulations fare better, but still do not fully reproduce observations. In Chapter 4, we present some other work done during the PhD studies, namely, a method that improves the precision of specific angular measurements by combining simultaneous Markov Chain Monte Carlo modelling of ionised gas 2D velocity fields and HI linewidths. To test the method we use a sample of 25 galaxies from the Sydney-AAO Multi-object Integral field (SAMI) survey that had matching ALFALFA HI linewidths. Such a method allows constraining the rotation curve both in the inner regions of a galaxy and in its outskirts, leading to increased precision of specific angular momentum measurements. It could be used to further constrain the observed relation between galaxy mass, specific angular momentum and morphology (Obreschkow \& Glazebrook 2014). Mathematical and computational methods are presented in the appendices.},
  language  = {en}
}
@phdthesis{Behrens2018,
  author    = {Behrens, Ricarda},
  title     = {Causes for slow weathering and erosion in the steep, warm, monsoon-subjected Highlands of Sri Lanka},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-408503},
  school      = {Universit{\"a}t Potsdam},
  pages     = {ix, 107, XXIV},
  year      = {2018},
  abstract  = {In the Highlands of Sri Lanka, erosion and chemical weathering rates are among the lowest for global mountain denudation. In this tropical humid setting, highly weathered deep saprolite profiles have developed from high-grade metamorphic charnockite during spheroidal weathering of the bedrock. The spheroidal weathering produces rounded corestones and spalled rindlets at the rock-saprolite interface. I used detailed textural, mineralogical, chemical, and electron-microscopic (SEM, FIB, TEM) analyses to identify the factors limiting the rate of weathering front advance in the profile, the sequence of weathering reactions, and the underlying mechanisms. The first mineral attacked by weathering was found to be pyroxene initiated by in situ Fe oxidation, followed by in situ biotite oxidation. Bulk dissolution of the primary minerals is best described with a dissolution - re-precipitation process, as no chemical gradients towards the mineral surface and sharp structural boundaries are observed at the nm scale. Only the local oxidation in pyroxene and biotite is better described with an ion by ion process. The first secondary phases are oxides and amorphous precipitates from which secondary minerals (mainly smectite and kaolinite) form. Only for biotite direct solid state transformation to kaolinite is likely. The initial oxidation of pyroxene and biotite takes place in locally restricted areas and is relatively fast: log J = -11 molmin/(m2 s). However, calculated corestone-scale mineral oxidation rates are comparable to corestone-scale mineral dissolution rates: log R = -13 molpx/(m2 s) and log R = -15 molbt/(m2 s). The oxidation reaction results in a volume increase. Volumetric calculations suggest that this observed oxidation leads to the generation of porosity due to the formation of micro-fractures in the minerals and the bedrock allowing for fluid transport and subsequent dissolution of plagioclase. At the scale of the corestone, this fracture reaction is responsible for the larger fractures that lead to spheroidal weathering and to the formation of rindlets. Since these fractures have their origin from the initial oxidational induced volume increase, oxidation is the rate limiting parameter for weathering to take place. The ensuing plagioclase weathering leads to formation of high secondary porosity in the corestone over a distance of only a few cm and eventually to the final disaggregation of bedrock to saprolite. As oxidation is the first weathering reaction, the supply of O2 is a rate-limiting factor for chemical weathering. Hence, the supply of O2 and its consumption at depth connects processes at the weathering front with erosion at the surface in a feedback mechanism. The strength of the feedback depends on the relative weight of advective versus diffusive transport of O2 through the weathering profile. The feedback will be stronger with dominating diffusive transport. The low weathering rate ultimately depends on the transport of O2 through the whole regolith, and on lithological factors such as low bedrock porosity and the amount of Fe-bearing primary minerals. In this regard the low-porosity charnockite with its low content of Fe(II) bearing minerals impedes fast weathering reactions. Fresh weatherable surfaces are a pre-requisite for chemical weathering. However, in the case of the charnockite found in the Sri Lankan Highlands, the only process that generates these surfaces is the fracturing induced by oxidation. Tectonic quiescence in this region and low pre-anthropogenic erosion rate (attributed to a dense vegetation cover) minimize the rejuvenation of the thick and cohesive regolith column, and lowers weathering through the feedback with erosion.},
  language  = {en}
}
@phdthesis{Behrendt2018,
  author    = {Behrendt, Felix Nicolas},
  title     = {New bio-based polymers},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-418316},
  school      = {Universit{\"a}t Potsdam},
  pages     = {vii, 153},
  year      = {2018},
  abstract  = {Redox-responsive polymers, such as poly(disulfide)s, are a versatile class of polymers with potential applications including gene- and drug-carrier systems. Their degradability under reductive conditions allows for a controlled response to the different redox states that are present throughout the body. Poly(disulfide)s are typically synthesized by step growth polymerizations. Step growth polymerizations, however, may suffer from low conversions and therefore low molar masses, limiting potential applications. The purpose of this thesis was therefore to find and investigate new synthetic routes towards the synthesis of amino acid-based poly(disulfide)s. The different routes in this thesis include entropy-driven ring opening polymerizations of novel macrocyclic monomers, derived from cystine derivatives. These monomers were obtained with overall yields of up to 77\% and were analyzed by mass spectrometry as well as by 1D and 2D NMR spectroscopy. The kinetics of the entropy-driven ring-opening metathesis polymerization (ED-ROMP) were thoroughly investigated in dependence of temperature, monomer concentration, and catalyst concentration. The polymerization was optimized to yield poly(disulfide)s with weight average molar masses of up to 80 kDa and conversions of ~80\%, at the thermodynamic equilibrium. Additionally, an alternative metal free polymerization, namely the entropy-driven ring-opening disulfide metathesis polymerization (ED-RODiMP) was established for the polymerization of the macrocyclic monomers. The effect of different solvents, concentrations and catalyst loadings on the polymerization process and its kinetics were studied. Polymers with very high weight average molar masses of up to 177 kDa were obtained. Moreover, various post-polymerization reactions were successfully performed. This work provides the first example of the homopolymerization of endo-cyclic disulfides by ED-ROMP and the first substantial study into the kinetics of the ED-RODiMP process.},
  language  = {en}
}
@phdthesis{Begu2007,
  author    = {Begu, Enkela},
  title     = {Elections in a spatial context : a case study of Albanian parliamentary elections, 1991-2005},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15923},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Exploring elections features from a geographical perspective is the focus of this study. Its primary objective is to develop a scientific approach based on geoinformation technology (GIT) that promotes deeper understanding how geographical settings affect the spatial and temporal variations of voting behaviour and election outcomes. For this purpose, the five parliamentary elections (1991-2005) following the political turnaround in 1990 in the South East European reform country Albania have been selected as a case study. Elections, like other social phenomena that do not develop uniformly over a territory, inherit a spatial dimension. Despite of fact that elections have been researched by various scientific disciplines ranging from political science to geography, studies that incorporate their spatial dimension are still limited in number and approaches. Consequently, the methodologies needed to generate an integrated knowledge on many facets that constitute election features are lacking. This study addresses characteristics and interactions of the essential elements involved in an election process. Thus, the baseline of the approach presented here is the exploration of relations between three entities: electorate (political and sociodemographic features), election process (electoral system and code) and place (environment where voters reside). To express this interaction the concept of electoral pattern is introduced. Electoral patterns are defined by the study as the final view of election results, chiefly in tabular and/or map form, generated by the complex interaction of social, economic, juridical, and spatial features of the electorate, which has occurred at a specific time and in a particular geographical location. GIT methods of geoanalysis and geovisualization are used to investigate the characteristics of electoral patterns in their spatial and temporal distribution. Aggregate-level data modelled in map form were used to analyse and visualize the spatial distribution of election patterns components and relations. The spatial dimension of the study is addressed in the following three main relations: One, the relation between place and electorate and its expression through the social, demographic and economic features of the electorate resulting in the profile of the electorate's context; second, the electorate-election interaction which forms the baseline to explore the perspective of local contextual effects in voting behaviour and election results; third, the relation between geographical location and election outcomes reflecting the implication of determining constituency boundaries on election results. To address the above relations, three types of variables: geo, independent and dependent, have been elaborated and two models have been created. The Data Model, developed in a GIS environment, facilitates structuring of election data in order to perform spatial analysis. The peculiarity of electoral patterns - a multidimensional array that contains information on three variables, stored in data layers of dissimilar spatial units of reference and scales of value measurement - prohibit spatial analysis based on the original source data. To perform a joint spatial analysis it is therefore mandatory to restructure the spatial units of reference while preserving their semantic content. In this operation, all relevant electoral as well as socio-demographic data referenced to different administrative spatial entities are re-referenced to uniform grid cells as virtual spatial units of reference. Depending on the scale of data acquisition and map presentation, a cell width of 0.5 km has been determined. The resulting fine grid forms the basis of subsequent data analyses and correlations. Conversion of the original vector data layers into target raster layers allows for unification of spatial units, at the same time retaining the existing level of detail of the data (variables, uniform distribution over space). This in turn facilitates the integration of the variables studied and the performance of GIS-based spatial analysis. In addition, conversion to raster format makes it possible to assign new values to the original data, which are based on a common scale eliminating existing differences in scale of measurement. Raster format operations of the type described are well-established data analysis techniques in GIT, yet they have rarely been employed to process and analyse electoral data. The Geovisualization Model, developed in a cartographic environment, complements the Data Model. As an analog graphic model it facilitates efficient communication and exploration of geographical information through cartographic visualization. Based on this model, 52 choropleth maps have been generated. They represent the outcome of the GIS-based electoral data analysis. The analog map form allows for in-depth visual analysis and interpretation of the distribution and correlation of the electoral data studied. For researchers, decision makers and a wider public the maps provide easy-to-access information on and promote easy-to-understand insight into the spatial dimension, regional variation and resulting structures of the electoral patterns defined.},
  language  = {en}
}
@phdthesis{Beeg2007,
  author    = {Beeg, Janina},
  title     = {Cooperative behavior of motor proteins},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15712},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {The cytoskeletal motor protein kinesin-1 (conventional kinesin) is the fast carrier for intracellular cargo transport along microtubules. So far most studies aimed at investigating the transport properties of individual motor molecules. However, the transport in cells usually involves the collective work of more than one motor. In the present work, we have studied the movement of beads as artificial loads/organelles pulled by several kinesin-1 motors in vitro. For a wide range of motor coverage of the beads and different bead (cargo) sizes the transport parameters walking distance or run length, velocity and force generation are measured. The results indicate that the transport parameters are influenced by the number of motors carrying the bead. While the transport velocity slightly decreases, an increase in the run length was measured and higher forces are determined, when more motors are involved. The effective number of motors pulling a bead is estimated by measuring the change in the hydrodynamic diameter of kinesin-coated beads using dynamic light scattering. The geometrical constraints imposed by the transport system have been taken into account. Thus, results for beads of different size and motor-surface coverage could be compared. In addition, run length-distributions obtained for the smallest bead size were matched to theoretically calculated distributions. The latter yielded an average number of pulling motors, which is in agreement with the effective motor numbers determined experimentally.},
  language  = {en}
}
@phdthesis{Becker2005,
  author    = {Becker, Christian},
  title     = {On the Riemannian geometry of Seiberg-Witten moduli spaces},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-5425},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {In this thesis, we give two constructions for Riemannian metrics on Seiberg-Witten moduli spaces. Both these constructions are naturally induced from the L2-metric on the configuration space. The construction of the so called quotient L2-metric is very similar to the one construction of an L2-metric on Yang-Mills moduli spaces as given by Groisser and Parker. To construct a Riemannian metric on the total space of the Seiberg-Witten bundle in a similar way, we define the reduced gauge group as a subgroup of the gauge group. We show, that the quotient of the premoduli space by the reduced gauge group is isomorphic as a U(1)-bundle to the quotient of the premoduli space by the based gauge group. The total space of this new representation of the Seiberg-Witten bundle carries a natural quotient L2-metric, and the bundle projection is a Riemannian submersion with respect to these metrics. We compute explicit formulae for the sectional curvature of the moduli space in terms of Green operators of the elliptic complex associated with a monopole. Further, we construct a Riemannian metric on the cobordism between moduli spaces for different perturbations. The second construction of a Riemannian metric on the moduli space uses a canonical global gauge fixing, which represents the total space of the Seiberg-Witten bundle as a finite dimensional submanifold of the configuration space. We consider the Seiberg-Witten moduli space on a simply connected K\&auml;uhler surface. We show that the moduli space (when nonempty) is a complex projective space, if the perturbation does not admit reducible monpoles, and that the moduli space consists of a single point otherwise. The Seiberg-Witten bundle can then be identified with the Hopf fibration. On the complex projective plane with a special Spin-C structure, our Riemannian metrics on the moduli space are Fubini-Study metrics. Correspondingly, the metrics on the total space of the Seiberg-Witten bundle are Berger metrics. We show that the diameter of the moduli space shrinks to 0 when the perturbation approaches the wall of reducible perturbations. Finally we show, that the quotient L2-metric on the Seiberg-Witten moduli space on a K\&auml;hler surface is a K\&auml;hler metric.},
  subject      = {Eichtheorie},
  language  = {en}
}
@phdthesis{Becker2013,
  author    = {Becker, Basil},
  title     = {Architectural modelling and verification of open service-oriented systems of systems},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70158},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Systems of Systems (SoS) have received a lot of attention recently. In this thesis we will focus on SoS that are built atop the techniques of Service-Oriented Architectures and thus combine the benefits and challenges of both paradigms. For this thesis we will understand SoS as ensembles of single autonomous systems that are integrated to a larger system, the SoS. The interesting fact about these systems is that the previously isolated systems are still maintained, improved and developed on their own. Structural dynamics is an issue in SoS, as at every point in time systems can join and leave the ensemble. This and the fact that the cooperation among the constituent systems is not necessarily observable means that we will consider these systems as open systems. Of course, the system has a clear boundary at each point in time, but this can only be identified by halting the complete SoS. However, halting a system of that size is practically impossible. Often SoS are combinations of software systems and physical systems. Hence a failure in the software system can have a serious physical impact what makes an SoS of this kind easily a safety-critical system. The contribution of this thesis is a modelling approach that extends OMG's SoaML and basically relies on collaborations and roles as an abstraction layer above the components. This will allow us to describe SoS at an architectural level. We will also give a formal semantics for our modelling approach which employs hybrid graph-transformation systems. The modelling approach is accompanied by a modular verification scheme that will be able to cope with the complexity constraints implied by the SoS' structural dynamics and size. Building such autonomous systems as SoS without evolution at the architectural level --- i. e. adding and removing of components and services --- is inadequate. Therefore our approach directly supports the modelling and verification of evolution.},
  language  = {en}
}
@phdthesis{Beamish2019,
  author    = {Beamish, Alison Leslie},
  title     = {Hyperspectral remote sensing of the spatial and temporal heterogeneity of low Arctic vegetation},
  doi       = {10.25932/publishup-42592},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-425922},
  school      = {Universit{\"a}t Potsdam},
  pages     = {v, 102},
  year      = {2019},
  abstract  = {Arctic tundra ecosystems are experiencing warming twice the global average and Arctic vegetation is responding in complex and heterogeneous ways. Shifting productivity, growth, species composition, and phenology at local and regional scales have implications for ecosystem functioning as well as the global carbon and energy balance. Optical remote sensing is an effective tool for monitoring ecosystem functioning in this remote biome. However, limited field-based spectral characterization of the spatial and temporal heterogeneity limits the accuracy of quantitative optical remote sensing at landscape scales. To address this research gap and support current and future satellite missions, three central research questions were posed: • Does canopy-level spectral variability differ between dominant low Arctic vegetation communities and does this variability change between major phenological phases? • How does canopy-level vegetation colour images recorded with high and low spectral resolution devices relate to phenological changes in leaf-level photosynthetic pigment concentrations? • How does spatial aggregation of high spectral resolution data from the ground to satellite scale influence low Arctic tundra vegetation signatures and thereby what is the potential of upcoming hyperspectral spaceborne systems for low Arctic vegetation characterization? To answer these questions a unique and detailed database was assembled. Field-based canopy-level spectral reflectance measurements, nadir digital photographs, and photosynthetic pigment concentrations of dominant low Arctic vegetation communities were acquired at three major phenological phases representing early, peak and late season. Data were collected in 2015 and 2016 in the Toolik Lake Research Natural Area located in north central Alaska on the North Slope of the Brooks Range. In addition to field data an aerial AISA hyperspectral image was acquired in the late season of 2016. Simulations of broadband Sentinel-2 and hyperspectral Environmental and Mapping Analysis Program (EnMAP) satellite reflectance spectra from ground-based reflectance spectra as well as simulations of EnMAP imagery from aerial hyperspectral imagery were also obtained. Results showed that canopy-level spectral variability within and between vegetation communities differed by phenological phase. The late season was identified as the most discriminative for identifying many dominant vegetation communities using both ground-based and simulated hyperspectral reflectance spectra. This was due to an overall reduction in spectral variability and comparable or greater differences in spectral reflectance between vegetation communities in the visible near infrared spectrum. Red, green, and blue (RGB) indices extracted from nadir digital photographs and pigment-driven vegetation indices extracted from ground-based spectral measurements showed strong significant relationships. RGB indices also showed moderate relationships with chlorophyll and carotenoid pigment concentrations. The observed relationships with the broadband RGB channels of the digital camera indicate that vegetation colour strongly influences the response of pigment-driven spectral indices and digital cameras can track the seasonal development and degradation of photosynthetic pigments. Spatial aggregation of hyperspectral data from the ground to airborne, to simulated satel-lite scale was influenced by non-photosynthetic components as demonstrated by the distinct shift of the red edge to shorter wavelengths. Correspondence between spectral reflectance at the three scales was highest in the red spectrum and lowest in the near infra-red. By artificially mixing litter spectra at different proportions to ground-based spectra, correspondence with aerial and satellite spectra increased. Greater proportions of litter were required to achieve correspondence at the satellite scale. Overall this thesis found that integrating multiple temporal, spectral, and spatial data is necessary to monitor the complexity and heterogeneity of Arctic tundra ecosystems. The identification of spectrally similar vegetation communities can be optimized using non-peak season hyperspectral data leading to more detailed identification of vegetation communities. The results also highlight the power of vegetation colour to link ground-based and satellite data. Finally, a detailed characterization non-photosynthetic ecosystem components is crucial for accurate interpretation of vegetation signals at landscape scales.},
  language  = {en}
}
@phdthesis{Bazhenova2018,
  author    = {Bazhenova, Ekaterina},
  title     = {Discovery of Decision Models Complementary to Process Models},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-410020},
  school      = {Universit{\"a}t Potsdam},
  year      = {2018},
  abstract  = {Business process management is an acknowledged asset for running an organization in a productive and sustainable way. One of the most important aspects of business process management, occurring on a daily basis at all levels, is decision making. In recent years, a number of decision management frameworks have appeared in addition to existing business process management systems. More recently, Decision Model and Notation (DMN) was developed by the OMG consortium with the aim of complementing the widely used Business Process Model and Notation (BPMN). One of the reasons for the emergence of DMN is the increasing interest in the evolving paradigm known as the separation of concerns. This paradigm states that modeling decisions complementary to processes reduces process complexity by externalizing decision logic from process models and importing it into a dedicated decision model. Such an approach increases the agility of model design and execution. This provides organizations with the flexibility to adapt to the ever increasing rapid and dynamic changes in the business ecosystem. The research gap, identified by us, is that the separation of concerns, recommended by DMN, prescribes the externalization of the decision logic of process models in one or more separate decision models, but it does not specify this can be achieved. The goal of this thesis is to overcome the presented gap by developing a framework for discovering decision models in a semi-automated way from information about existing process decision making. Thus, in this thesis we develop methodologies to extract decision models from: (1) control flow and data of process models that exist in enterprises; and (2) from event logs recorded by enterprise information systems, encapsulating day-to-day operations. Furthermore, we provide an extension of the methodologies to discover decision models from event logs enriched with fuzziness, a tool dealing with partial knowledge of the process execution information. All the proposed techniques are implemented and evaluated in case studies using real-life and synthetic process models and event logs. The evaluation of these case studies shows that the proposed methodologies provide valid and accurate output decision models that can serve as blueprints for executing decisions complementary to process models. Thus, these methodologies have applicability in the real world and they can be used, for example, for compliance checks, among other uses, which could improve the organization's decision making and hence it's overall performance.},
  language  = {en}
}
@phdthesis{BayonaViveros2021,
  author    = {Bayona Viveros, Jose},
  title     = {Constructing global stationary seismicity models from the long-term balance of interseismic strain measurements and earthquake-catalog data},
  doi       = {10.25932/publishup-50927},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-509270},
  school      = {Universit{\"a}t Potsdam},
  pages     = {ix, 83},
  year      = {2021},
  abstract  = {One third of the world's population lives in areas where earthquakes causing at least slight damage are frequently expected. Thus, the development and testing of global seismicity models is essential to improving seismic hazard estimates and earthquake-preparedness protocols for effective disaster-risk mitigation. Currently, the availability and quality of geodetic data along plate-boundary regions provides the opportunity to construct global models of plate motion and strain rate, which can be translated into global maps of forecasted seismicity. Moreover, the broad coverage of existing earthquake catalogs facilitates in present-day the calibration and testing of global seismicity models. As a result, modern global seismicity models can integrate two independent factors necessary for physics-based, long-term earthquake forecasting, namely interseismic crustal strain accumulation and sudden lithospheric stress release. In this dissertation, I present the construction of and testing results for two global ensemble seismicity models, aimed at providing mean rates of shallow (0-70 km) earthquake activity for seismic hazard assessment. These models depend on the Subduction Megathrust Earthquake Rate Forecast (SMERF2), a stationary seismicity approach for subduction zones, based on the conservation of moment principle and the use of regional "geodesy-to-seismicity" parameters, such as corner magnitudes, seismogenic thicknesses and subduction dip angles. Specifically, this interface-earthquake model combines geodetic strain rates with instrumentally-recorded seismicity to compute long-term rates of seismic and geodetic moment. Based on this, I derive analytical solutions for seismic coupling and earthquake activity, which provide this earthquake model with the initial abilities to properly forecast interface seismicity. Then, I integrate SMERF2 interface-seismicity estimates with earthquake computations in non-subduction zones provided by the Seismic Hazard Inferred From Tectonics based on the second iteration of the Global Strain Rate Map seismicity approach to construct the global Tectonic Earthquake Activity Model (TEAM). Thus, TEAM is designed to reduce number, and potentially spatial, earthquake inconsistencies of its predecessor tectonic earthquake model during the 2015-2017 period. Also, I combine this new geodetic-based earthquake approach with a global smoothed-seismicity model to create the World Hybrid Earthquake Estimates based on Likelihood scores (WHEEL) model. This updated hybrid model serves as an alternative earthquake-rate approach to the Global Earthquake Activity Rate model for forecasting long-term rates of shallow seismicity everywhere on Earth. Global seismicity models provide scientific hypotheses about when and where earthquakes may occur, and how big they might be. Nonetheless, the veracity of these hypotheses can only be either confirmed or rejected after prospective forecast evaluation. Therefore, I finally test the consistency and relative performance of these global seismicity models with independent observations recorded during the 2014-2019 pseudo-prospective evaluation period. As a result, hybrid earthquake models based on both geodesy and seismicity are the most informative seismicity models during the testing time frame, as they obtain higher information scores than their constituent model components. These results support the combination of interseismic strain measurements with earthquake-catalog data for improved seismicity modeling. However, further prospective evaluations are required to more accurately describe the capacities of these global ensemble seismicity models to forecast longer-term earthquake activity.},
  language  = {en}
}
@phdthesis{Bayer2013,
  author    = {Bayer, Anita},
  title     = {Methodological developments for mapping soil constituents using imaging spectroscopy},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-64399},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Climatic variations and human activity now and increasingly in the future cause land cover changes and introduce perturbations in the terrestrial carbon reservoirs in vegetation, soil and detritus. Optical remote sensing and in particular Imaging Spectroscopy has shown the potential to quantify land surface parameters over large areas, which is accomplished by taking advantage of the characteristic interactions of incident radiation and the physico-chemical properties of a material. The objective of this thesis is to quantify key soil parameters, including soil organic carbon, using field and Imaging Spectroscopy. Organic carbon, iron oxides and clay content are selected to be analyzed to provide indicators for ecosystem function in relation to land degradation, and additionally to facilitate a quantification of carbon inventories in semiarid soils. The semiarid Albany Thicket Biome in the Eastern Cape Province of South Africa is chosen as study site. It provides a regional example for a semiarid ecosystem that currently undergoes land changes due to unadapted management practices and furthermore has to face climate change induced land changes in the future. The thesis is divided in three methodical steps. Based on reflectance spectra measured in the field and chemically determined constituents of the upper topsoil, physically based models are developed to quantify soil organic carbon, iron oxides and clay content. Taking account of the benefits limitations of existing methods, the approach is based on the direct application of known diagnostic spectral features and their combination with multivariate statistical approaches. It benefits from the collinearity of several diagnostic features and a number of their properties to reduce signal disturbances by influences of other spectral features. In a following step, the acquired hyperspectral image data are prepared for an analysis of soil constituents. The data show a large spatial heterogeneity that is caused by the patchiness of the natural vegetation in the study area that is inherent to most semiarid landscapes. Spectral mixture analysis is performed and used to deconvolve non-homogenous pixels into their constituent components. For soil dominated pixels, the subpixel information is used to remove the spectral influence of vegetation and to approximate the pure spectral signature coming from the soil. This step is an integral part when working in natural non-agricultural areas where pure bare soil pixels are rare. It is identified as the largest benefit within the multi-stage methodology, providing the basis for a successful and unbiased prediction of soil constituents from hyperspectral imagery. With the proposed approach it is possible (1) to significantly increase the spatial extent of derived information of soil constituents to areas with about 40 \% vegetation coverage and (2) to reduce the influence of materials such as vegetation on the quantification of soil constituents to a minimum. Subsequently, soil parameter quantities are predicted by the application of the feature-based soil prediction models to the maps of locally approximated soil signatures. Thematic maps showing the spatial distribution of the three considered soil parameters in October 2009 are produced for the Albany Thicket Biome of South Africa. The maps are evaluated for their potential to detect erosion affected areas as effects of land changes and to identify degradation hot spots in regard to support local restoration efforts. A regional validation, carried out using available ground truth sites, suggests remaining factors disturbing the correlation of spectral characteristics and chemical soil constituents. The approach is developed for semiarid areas in general and not adapted to specific conditions in the study area. All processing steps of the developed methodology are implemented in software modules, where crucial steps of the workflow are fully automated. The transferability of the methodology is shown for simulated data of the future EnMAP hyperspectral satellite. Soil parameters are successfully predicted from these data despite intense spectral mixing within the lower spatial resolution EnMAP pixels. This study shows an innovative approach to use Imaging Spectroscopy for mapping of key soil constituents, including soil organic carbon, for large areas in a non-agricultural ecosystem and under consideration of a partially vegetation coverage. It can contribute to a better assessment of soil constituents that describe ecosystem processes relevant to detect and monitor land changes. The maps further provide an assessment of the current carbon inventory in soils, valuable for carbon balances and carbon mitigation products.},
  language  = {en}
}
@phdthesis{BaumannWilke2013,
  author    = {Baumann-Wilke, Maria},
  title     = {Combining body wave tomography, surface wave inversion, seismic interferometry and laboratory measurements to characterize the black shales on Bornholm at different scales},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-69007},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Black shales are sedimentary rocks with a high content of organic carbon, which leads to a dark grayish to black color. Due to their potential to contain oil or gas, black shales are of great interest for the support of the worldwide energy supply. An integrated seismic investigation of the Lower Palaeozoic black shales was carried out at the Danish island Bornholm to locate the shallow-lying Alum Shale layer and its surrounding formations and to characterize its potential as a source rock. Therefore, two seismic experiments at a total of three crossing profiles were carried out in October 2010 and in June 2012 in the southern part of the island. Two different active measurements were conducted with either a weight drop source or a minivibrator. Additionally, the ambient noise field was recorded at the study location over a time interval of about one day, and also a laboratory analysis of borehole samples was carried out. The seismic profiles were positioned as close as possible to two scientific boreholes which were used for comparative purposes. The seismic field data was analyzed with traveltime tomography, surface wave inversion and seismic interferometry to obtain the P-wave and S-wave velocity models of the subsurface. The P-wave velocity models which were determined for all three profiles clearly locate the Alum Shale layer between the Komstad Limestone layer on top and the L{\ae}s{\aa} Sandstone Formation at the base of the models. The black shale layer has P-wave velocities around 3 km/s which are lower compared to the adjacent formations. Due to a very good agreement of the sonic log and the vertical velocity profiles of the two seismic lines, which are directly crossing the borehole where the sonic log was conducted, the reliability of the traveltime tomography is proven. A correlation of the seismic velocities with the content of organic carbon is an important task for the characterization of the reservoir properties of a black shale formation. It is not possible without calibration but in combination with a full 2D tomographic image of the subsurface it gives the subsurface distribution of the organic material. The S-wave model obtained with surface wave inversion of the vibroseis data of one of the profiles images the Alum Shale layer also very well with S-wave velocities around 2 km/s. Although individual 1D velocity models for each of the source positions were determined, the subsurface S-wave velocity distribution is very uniform with a good match between the single models. A really new approach described here is the application of seismic interferometry to a really small study area and a quite short time interval. Also new is the selective procedure of only using time windows with the best crosscorrelation signals to achieve the final interferograms. Due to the small scale of the interferometry even P-wave signals can be observed in the final crosscorrelations. In the laboratory measurements the seismic body waves were recorded for different pressure and temperature stages. Therefore, samples of different depths of the Alum Shale were available from one of the scientific boreholes at the study location. The measured velocities have a high variance with changing pressure or temperature. Recordings with wave propagation both parallel and perpendicular to the bedding of the samples reveal a great amount of anisotropy for the P-wave velocity, whereas the S-wave velocity is almost independent of the wave direction. The calculated velocity ratio is also highly anisotropic with very low values for the perpendicular samples and very high values for the parallel ones. Interestingly, the laboratory velocities of the perpendicular samples are comparable to the velocities of the field experiments indicating that the field measurements are sensitive to wave propagation in vertical direction. The velocity ratio is also calculated with the P-wave and S-wave velocity models of the field experiments. Again, the Alum Shale can be clearly separated from the adjacent formations because it shows overall very low vP/vS ratios around 1.4. The very low velocity ratio indicates the content of gas in the black shale formation. With the combination of all the different methods described here, a comprehensive interpretation of the seismic response of the black shale layer can be made and the hydrocarbon source rock potential can be estimated.},
  language  = {en}
}
@phdthesis{Bauer2005,
  author    = {Bauer, Niclas Alexandre},
  title     = {Carbon capture and sequestration : an option to buy time?},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6544},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {The thesis assesses the contribution of technology option of Carbon Capture and Sequestration (CCS) to climate change mitigation. CCS means that CO2 is captured at large industrial facilities and sequestered in goelogical structures. The technology uses the endogenous growth model MIND. Herein the various climate change mitigation options of reducing economic growth, increasing energy efficiency, changing the energy mix and CCS are assessed simultaneously. An important question is whether CCS is a temporary or long-term solution. The results show that in the middle of the 21st century CCS has its peak contribution, which allows prolonged use of relatively cheap fossil energy carriers. However, this leads to delayed introduction of renewable energy carriers. The technology path ways are accombined with different costs of climate change mitigation. The use of CCS delays and reduces the costs of climate change mitigation. However, the delayed introduction of renewable energy carriers leads to reduced technological learning, which induces higher costs in the longer term. All in all the temporary use of CCS reduces the costs of climate change mitigation costs. The result is robust, which is tested with various uncertainty analysis.},
  subject      = {Endogenes Wirtschaftswachstum},
  language  = {en}
}
@phdthesis{Bauckmann2013,
  author    = {Bauckmann, Jana},
  title     = {Dependency discovery for data integration},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66645},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Data integration aims to combine data of different sources and to provide users with a unified view on these data. This task is as challenging as valuable. In this thesis we propose algorithms for dependency discovery to provide necessary information for data integration. We focus on inclusion dependencies (INDs) in general and a special form named conditional inclusion dependencies (CINDs): (i) INDs enable the discovery of structure in a given schema. (ii) INDs and CINDs support the discovery of cross-references or links between schemas. An IND "A in B" simply states that all values of attribute A are included in the set of values of attribute B. We propose an algorithm that discovers all inclusion dependencies in a relational data source. The challenge of this task is the complexity of testing all attribute pairs and further of comparing all of each attribute pair's values. The complexity of existing approaches depends on the number of attribute pairs, while ours depends only on the number of attributes. Thus, our algorithm enables to profile entirely unknown data sources with large schemas by discovering all INDs. Further, we provide an approach to extract foreign keys from the identified INDs. We extend our IND discovery algorithm to also find three special types of INDs: (i) Composite INDs, such as "AB in CD", (ii) approximate INDs that allow a certain amount of values of A to be not included in B, and (iii) prefix and suffix INDs that represent special cross-references between schemas. Conditional inclusion dependencies are inclusion dependencies with a limited scope defined by conditions over several attributes. Only the matching part of the instance must adhere the dependency. We generalize the definition of CINDs distinguishing covering and completeness conditions and define quality measures for conditions. We propose efficient algorithms that identify covering and completeness conditions conforming to given quality thresholds. The challenge for this task is twofold: (i) Which (and how many) attributes should be used for the conditions? (ii) Which attribute values should be chosen for the conditions? Previous approaches rely on pre-selected condition attributes or can only discover conditions applying to quality thresholds of 100\%. Our approaches were motivated by two application domains: data integration in the life sciences and link discovery for linked open data. We show the efficiency and the benefits of our approaches for use cases in these domains.},
  language  = {en}
}
@phdthesis{Batoulis2019,
  author    = {Batoulis, Kimon},
  title     = {Sound integration of process and decision models},
  doi       = {10.25932/publishup-43738},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437386},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xviii, 155},
  year      = {2019},
  abstract  = {Business process management is an established technique for business organizations to manage and support their processes. Those processes are typically represented by graphical models designed with modeling languages, such as the Business Process Model and Notation (BPMN). Since process models do not only serve the purpose of documentation but are also a basis for implementation and automation of the processes, they have to satisfy certain correctness requirements. In this regard, the notion of soundness of workflow nets was developed, that can be applied to BPMN process models in order to verify their correctness. Because the original soundness criteria are very restrictive regarding the behavior of the model, different variants of the soundness notion have been developed for situations in which certain violations are not even harmful. All of those notions do only consider the control-flow structure of a process model, however. This poses a problem, taking into account the fact that with the recent release and the ongoing development of the Decision Model and Notation (DMN) standard, an increasing number of process models are complemented by respective decision models. DMN is a dedicated modeling language for decision logic and separates the concerns of process and decision logic into two different models, process and decision models respectively. Hence, this thesis is concerned with the development of decisionaware soundness notions, i.e., notions of soundness that build upon the original soundness ideas for process models, but additionally take into account complementary decision models. Similar to the various notions of workflow net soundness, this thesis investigates different notions of decision soundness that can be applied depending on the desired degree of restrictiveness. Since decision tables are a standardized means of DMN to represent decision logic, this thesis also puts special focus on decision tables, discussing how they can be translated into an unambiguous format and how their possible output values can be efficiently determined. Moreover, a prototypical implementation is described that supports checking a basic version of decision soundness. The decision soundness notions were also empirically evaluated on models from participants of an online course on process and decision modeling as well as from a process management project of a large insurance company. The evaluation demonstrates that violations of decision soundness indeed occur and can be detected with our approach.},
  language  = {en}
}
@phdthesis{Bathke2014,
  author    = {Bathke, Hannes},
  title     = {An investigation of complex deformation patterns detected by using InSAR at Llaima and Tend{\"u}rek volcanoes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70522},
  school      = {Universit{\"a}t Potsdam},
  year      = {2014},
  abstract  = {Surface displacement at volcanic edifices is related to subsurface processes associated with magma movements, fluid transfers within the volcano edifice and gravity-driven deformation processes. Understanding of associated ground displacements is of importance for assessment of volcanic hazards. For example, volcanic unrest is often preceded by surface uplift, caused by magma intrusion and followed by subsidence, after the withdrawal of magma. Continuous monitoring of the surface displacement at volcanoes therefore might allow the forecasting of upcoming eruptions to some extent. In geophysics, the measured surface displacements allow the parameters of possible deformation sources to be estimated through analytical or numerical modeling. This is one way to improve the understanding of subsurface processes acting at volcanoes. Although the monitoring of volcanoes has significantly improved in the last decades (in terms of technical advancements and number of monitored volcanoes), the forecasting of volcanic eruptions remains puzzling. In this work I contribute towards the understanding of the subsurface processes at volcanoes and thus to the improvement of volcano eruption forecasting. I have investigated the displacement field of Llaima volcano in Chile and of Tend{\"u}rek volcano in East Turkey by using synthetic aperture radar interferometry (InSAR). Through modeling of the deformation sources with the extracted displacement data, it was possible to gain insights into potential subsurface processes occurring at these two volcanoes that had been barely studied before. The two volcanoes, although of very different origin, composition and geometry, both show a complexity of interacting deformation sources. At Llaima volcano, the InSAR technique was difficult to apply, due to the large decorrelation of the radar signal between the acquisition of images. I developed a model-based unwrapping scheme, which allows the production of reliable displacement maps at the volcano that I used for deformation source modeling. The modeling results show significant differences in pre- and post-eruptive magmatic deformation source parameters. Therefore, I conjecture that two magma chambers exist below Llaima volcano: a post-eruptive deep one and a shallow one possibly due to the pre-eruptive ascent of magma. Similar reservoir depths at Llaima have been confirmed by independent petrologic studies. These reservoirs are interpreted to be temporally coupled. At Tend{\"u}rek volcano I have found long-term subsidence of the volcanic edifice, which can be described by a large, magmatic, sill-like source that is subject to cooling contraction. The displacement data in conjunction with high-resolution optical images, however, reveal arcuate fractures at the eastern and western flank of the volcano. These are most likely the surface expressions of concentric ring-faults around the volcanic edifice that show low magnitudes of slip over a long time. This might be an alternative mechanism for the development of large caldera structures, which are so far assumed to be generated during large catastrophic collapse events. To investigate the potential subsurface geometry and relation of the two proposed interacting sources at Tend{\"u}rek, a sill-like magmatic source and ring-faults, I have performed a more sophisticated numerical modeling approach. The optimum source geometries show, that the size of the sill-like source was overestimated in the simple models and that it is difficult to determine the dip angle of the ring-faults with surface displacement data only. However, considering physical and geological criteria a combination of outward-dipping reverse faults in the west and inward-dipping normal faults in the east seem to be the most likely. Consequently, the underground structure at the Tend{\"u}rek volcano consists of a small, sill-like, contracting, magmatic source below the western summit crater that causes a trapdoor-like faulting along the ring-faults around the volcanic edifice. Therefore, the magmatic source and the ring-faults are also interpreted to be temporally coupled. In addition, a method for data reduction has been improved. The modeling of subsurface deformation sources requires only a relatively small number of well distributed InSAR observations at the earth's surface. Satellite radar images, however, consist of several millions of these observations. Therefore, the large amount of data needs to be reduced by several orders of magnitude for source modeling, to save computation time and increase model flexibility. I have introduced a model-based subsampling approach in particular for heterogeneously-distributed observations. It allows a fast calculation of the data error variance-covariance matrix, also supports the modeling of time dependent displacement data and is, therefore, an alternative to existing methods.},
  language  = {en}
}
@phdthesis{Bastian2022,
  author    = {Bastian, Philipp U.},
  title     = {Core-shell upconversion nanoparticles - investigation of dopant intermixing and surface modification},
  doi       = {10.25932/publishup-55160},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-551607},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XII, 108, xxiii},
  year      = {2022},
  abstract  = {Frequency upconversion nanoparticles (UCNPs) are inorganic nanocrystals capable to up-convert incident photons of the near-infrared electromagnetic spectrum (NIR) into higher energy photons. These photons are re-emitted in the range of the visible (Vis) and even ultraviolet (UV) light. The frequency upconversion process (UC) is realized with nanocrystals doped with trivalent lanthanoid ions (Ln(III)). The Ln(III) ions provide the electronic (excited) states forming a ladder-like electronic structure for the Ln(III) electrons in the nanocrystals. The absorption of at least two low energy photons by the nanoparticle and the subsequent energy transfer to one Ln(III) ion leads to the promotion of one Ln(III) electron into higher excited electronic states. One high energy photon will be emitted during the radiative relaxation of the electron in the excited state back into the electronic ground state of the Ln(III) ion. The excited state electron is the result of the previous absorption of at least two low energy photons. The UC process is very interesting in the biological/medical context. Biological samples (like organic tissue, blood, urine, and stool) absorb high-energy photons (UV and blue light) more strongly than low-energy photons (red and NIR light). Thanks to a naturally occurring optical window, NIR light can penetrate deeper than UV light into biological samples. Hence, UCNPs in bio-samples can be excited by NIR light. This possibility opens a pathway for in vitro as well as in vivo applications, like optical imaging by cell labeling or staining of specific organic tissue. Furthermore, early detection and diagnosis of diseases by predictive and diagnostic biomarkers can be realized with bio-recognition elements being labeled to the UCNPs. Additionally, "theranostic" becomes possible, in which the identification and the treatment of a disease are tackled simultaneously. For this to succeed, certain parameters for the UCNPs must be met: high upconversion efficiency, high photoluminescence quantum yield, dispersibility, and dispersion stability in aqueous media, as well as availability of functional groups to introduce fast and easy bio-recognition elements. The UCNPs used in this work were prepared with a solvothermal decomposition synthesis yielding in particles with NaYF4 or NaGdF4 as host lattice. They have been doped with the Ln(III) ions Yb3+ and Er3+, which is only one possible upconversion pair. Their upconversion efficiency and photoluminescence quantum yield were improved by adding a passivating shell to reduce surface quenching. However, the brightness of core-shell UCNPs stays behind the expectations compared to their bulk material (being at least μm-sized particles). The core-shell structures are not clearly separated from each other, which is a topic in literature. Instead, there is a transition layer between the core and the shell structure, which relates to the migration of the dopants within the host lattice during the synthesis. The ion migration has been examined by time-resolved laser spectroscopy and the interlanthanoid resonance energy transfer (LRET) in the two different host lattices from above. The results are presented in two publications, which dealt with core-shell-shell structured nanoparticles. The core is doped with the LRET-acceptor (either Nd3+ or Pr3+). The intermediate shell serves as an insulation shell of pure host lattice material, whose shell thickness has been varied within one set of samples having the same composition, so that the spatial separation of LRET-acceptor and -donor changes. The outer shell with the same host lattice is doped with the LRET-donor (Eu3+). The effect of the increasing insulation shell thickness is significant, although the LRET cannot be suppressed completely. Next to the Ln(III) migration within a host lattice, various phase transfer reactions were investigated in order to subsequently perform surface modifications for bioapplications. One result out of this research has been published using a promising ligand, that equips the UCNP with bio-modifiable groups and has good potential for bio-medical applications. This particular ligand mimics natural occurring mechanisms of mussel protein adhesion and of blood coagulation, which is why the UCNPs are encapsulated very effectively. At the same time, bio-functional groups are introduced. In a proof-of-concept, the encapsulated UCNP has been coupled successfully with a dye (which is representative for a biomarker) and the system's photoluminescence properties have been investigated.},
  language  = {en}
}
@phdthesis{Basler2012,
  author    = {Basler, Georg},
  title     = {Mass-balanced randomization : a significance measure for metabolic networks},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-62037},
  school      = {Universit{\"a}t Potsdam},
  year      = {2012},
  abstract  = {Complex networks have been successfully employed to represent different levels of biological systems, ranging from gene regulation to protein-protein interactions and metabolism. Network-based research has mainly focused on identifying unifying structural properties, including small average path length, large clustering coefficient, heavy-tail degree distribution, and hierarchical organization, viewed as requirements for efficient and robust system architectures. Existing studies estimate the significance of network properties using a generic randomization scheme - a Markov-chain switching algorithm - which generates unrealistic reactions in metabolic networks, as it does not account for the physical principles underlying metabolism. Therefore, it is unclear whether the properties identified with this generic approach are related to the functions of metabolic networks. Within this doctoral thesis, I have developed an algorithm for mass-balanced randomization of metabolic networks, which runs in polynomial time and samples networks almost uniformly at random. The properties of biological systems result from two fundamental origins: ubiquitous physical principles and a complex history of evolutionary pressure. The latter determines the cellular functions and abilities required for an organism's survival. Consequently, the functionally important properties of biological systems result from evolutionary pressure. By employing randomization under physical constraints, the salient structural properties, i.e., the smallworld property, degree distributions, and biosynthetic capabilities of six metabolic networks from all kingdoms of life are shown to be independent of physical constraints, and thus likely to be related to evolution and functional organization of metabolism. This stands in stark contrast to the results obtained from the commonly applied switching algorithm. In addition, a novel network property is devised to quantify the importance of reactions by simulating the impact of their knockout. The relevance of the identified reactions is verified by the findings of existing experimental studies demonstrating the severity of the respective knockouts. The results suggest that the novel property may be used to determine the reactions important for viability of organisms. Next, the algorithm is employed to analyze the dependence between mass balance and thermodynamic properties of Escherichia coli metabolism. The thermodynamic landscape in the vicinity of the metabolic network reveals two regimes of randomized networks: those with thermodynamically favorable reactions, similar to the original network, and those with less favorable reactions. The results suggest that there is an intrinsic dependency between thermodynamic favorability and evolutionary optimization. The method is further extended to optimizing metabolic pathways by introducing novel chemically feasibly reactions. The results suggest that, in three organisms of biotechnological importance, introduction of the identified reactions may allow for optimizing their growth. The approach is general and allows identifying chemical reactions which modulate the performance with respect to any given objective function, such as the production of valuable compounds or the targeted suppression of pathway activity. These theoretical developments can find applications in metabolic engineering or disease treatment. The developed randomization method proposes a novel approach to measuring the significance of biological network properties, and establishes a connection between large-scale approaches and biological function. The results may provide important insights into the functional principles of metabolic networks, and open up new possibilities for their engineering.},
  language  = {en}
}
@phdthesis{Bartz2022,
  author    = {Bartz, Christian},
  title     = {Reducing the annotation burden: deep learning for optical character recognition using less manual annotations},
  doi       = {10.25932/publishup-55540},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-555407},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xxiv, 183},
  year      = {2022},
  abstract  = {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!},
  language  = {en}
}
@phdthesis{Bartholomaeus2021,
  author    = {Bartholom{\"a}us, Lisa},
  title     = {Impact of growth-related genes on petal size in Arabidopsis thaliana and the formation of two distinct floral morphs in Amsinckia spectabilis},
  doi       = {10.25932/publishup-51986},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-519861},
  school      = {Universit{\"a}t Potsdam},
  pages     = {158},
  year      = {2021},
  abstract  = {Der Lebenszyklus von Pflanzen ist gepr{\"a}gt von sich wiederholenden Wachstums- und Entwicklungsphasen, die auf wiederkehrenden Abl{\"a}ufen, bestehend aus Zellteilung, Zellvergr{\"o}ßerung und Zelldifferenzierung, basieren. Diese Dissertation ist aus zwei Projekten aufgebaut, die sich beide mit unterschiedlichen Blickwinkeln des Zellwachstums besch{\"a}ftigen. Im ersten steht die Charakterisierung einer Arabidopsis thaliana Mutante, die eine generelle Zellvergr{\"o}ßerung aufweist, im Vordergrund. Das zweite fokussiert sich auf zwei nat{\"u}rlich vorkommende Bl{\"u}tenmorphologien in Amsinckia spectabilis (Boraginaceae), die sich, aufgrund von Zelll{\"a}ngenunterschieden, in Griffell{\"a}nge und H{\"o}he der Staubblattposition unterscheiden. Es wurde gezeigt, dass die EMS-Mutante eop1 durch gr{\"o}ßere Zellen 26\% gr{\"o}ßere Bl{\"u}tenbl{\"a}tter aufweist. Außerdem wurden weitere Ph{\"a}notypen beschrieben, wie zum Beispiel, vergr{\"o}ßerte Kotyledonen, (ebenfalls aufgrund von Zellvergr{\"o}ßerung), Fruchtbl{\"a}tter, Kelchbl{\"a}tter, Rosettenbl{\"a}tter und Pollen. Die Gesamtwuchsh{\"o}he der Mutante zeigte sich ebenfalls erh{\"o}ht und zus{\"a}tzliche Trichom{\"a}ste erkl{\"a}rten den haarigen Ph{\"a}notyp. Feinkartierung enth{\"u}llte eine C zu T Transition des letzten Nukleotids des Introns 7 des INCURVATA 11 (ICU11) Gens, einer 2-oxoglutarat/Fe(II)-abh{\"a}ngigen Dioxygenase, als urs{\"a}chlichen SNP, welcher missgespleißte mRNA verursacht. Zwei T-DNA Insertionslinien (icu11-2 \& icu11-4), ebenfalls mit vergr{\"o}ßerten Bl{\"u}tenbl{\"a}ttern, best{\"a}tigten ICU11 als kausales Gen, und erlaubten somit die Analyse von drei verschiedenen icu11 Allelen. Ein Vergleich der verursachten molekularen Ver{\"a}nderung durch die jeweiligen Mutationen ermittelte Unterschiede in den drei Mutanten, wie zum Beispiel {\"U}berexpression von ICU11, als auch die Modifikation von ICU11 mRNA. Zusammen bildete das die Grundlage f{\"u}r die Untersuchung des molekularen Mechanismus, der f{\"u}r den beobachteten Ph{\"a}notyp verantwortlich ist. Verschiedene Ans{\"a}tze ermittelten widerspr{\"u}chliche Ergebnisse hinsichtlich der Proteinfunktion von ICU11 in den drei Mutanten. So zeigte eine Komplementierungsanalyse, dass alle drei Mutationen austauschbar sind, was, zusammen mit der Beobachtung, dass eine ICU11 {\"U}berexpression im Wildtyp zu einem icu11-{\"a}hnlichen Ph{\"a}notyp zeigte, dazu f{\"u}hrte, dass die icu11 Mutanten als gain-of-function Mutationen eingeordnet wurden. Im Widerspruch dazu stand die Entdeckung, dass sich icu11-4 durch ein genomisches ICU11 Transgen retten ließ. So wurde ein Model, basierend auf der Annahme, dass eine ICU11 {\"U}berexpression die Proteinfunktion ebenso hemmt wie ein nichtfunktionales Protein, vorgeschlagen. Außerdem wurde eine erh{\"o}hte Resistenz der icu11-3 (eop1) gegen{\"u}ber Paclobutrazol, einem Gibberellin (GA)-Inhibitor, und die Aktivierung der Expression von AtGA20ox2, einem Haupt-GA-Biosynthese-Gen, festgestellt. Zus{\"a}tzlich wurde eine zytoplasmatische Lokalisation von ICU11 detektiert, sodass ein Einfluss von ICU11 auf die GA- Biosynthese und somit auf das Gesamt-GA-Level angenommen wird, der den beobachteten (GA-{\"u}berdosierten) Ph{\"a}notyp erkl{\"a}ren k{\"o}nnte. Das zweite Projekt strebte die Identifizierung der genetischen Grundlage des S-Locus in Amsinckia spectabilis an, da die Gattung Amsinckia einige untypische Charakteristiken f{\"u}r eine heterostyle Art, wie zum Beispiel das Fehlen einer offensichtlichen Selbstinkompatibilit{\"a}t (SI), sowie die mehrmalige Entwicklung zu Homostyly und 100\% autonomem Selbsten, aufweist. Die Analyse basierte auf drei Amsinckia spectabilis Varianten: einer heterostylen Form, bestehend aus zwei Bl{\"u}tenmorphologien mit gegens{\"a}tzlich positionierten Sexualorganen (S-Morph: hohe Staubblattposition und kurzer Griffel und L-Morph: niedrige Staubblattans{\"a}tze und langer Griffel), und zwei homostylen Formen, einer großbl{\"u}tigen teilweise selbstenden und einer kleinbl{\"u}tigen voll selbstenden. Nat{\"u}rliche Populationen weisen ungef{\"a}hr ein 1:1 S:L Morph-Verh{\"a}ltnis auf, welches sich durch vorherrschend disassortative Paarung beider Morphs erkl{\"a}ren lasst. Dadurch kann das dominante S-Allel ausschließlich heterozygot auftreten (heterozygot (Ss) im S-morph und homozygot rezessiv (ss) im L-morph). Die Suche nach Morph-spezifischen Ph{\"a}notypen offenbarte 56\% l{\"a}ngere L-Morph Griffel und 58\% h{\"o}here S-Morph Staubblattans{\"a}tze. Zus{\"a}tzlich wurden 21\% gr{\"o}ßere S-Morph Pollen, sowie das Fehlen einer offensichtlichen SI gefunden. Dies war die Grundlage f{\"u}r die Annahme, dass der Amsinckia spec. S-Locus mindestens aus G- (Griffel), A- (Staubblatt) und P- (Pollen) Locus besteht. Vergleichende Transkriptom-Analyse beider Morphs offenbarte 22 unterschiedlich exprimierte Marker, die in 2 Contigs der PacBio Genom-Assemblierung eines SS-Individuums lokalisiert werden konnten. Dies erlaubte die genetische Einengung des S-Locus auf einen Bereich von circa 23 Mb. Gegens{\"a}tzlich zu bisher aufgekl{\"a}rten S-Loci in anderen Pflanzenarten konnte kein Hinweis auf eine hemizygote Region gefunden werden, die die supprimierte Rekombination am S-Locus erkl{\"a}ren k{\"o}nnte, sodass eine Inversion als Ursache dieser vermutet wurde.},
  language  = {en}
}
@phdthesis{Barrionuevo2020,
  author    = {Barrionuevo, Mat{\´i}as},
  title     = {The role of the upper plate in the Andean tectonic evolution (33-36°S): insights from structural geology and numerical modeling},
  doi       = {10.25932/publishup-51590},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-515909},
  school      = {Universit{\"a}t Potsdam},
  pages     = {148, S2},
  year      = {2020},
  abstract  = {Los Andes Centrales del Sur (33-36°S) son un gran laboratorio para el estudio de los procesos de deformaci{\´o}n orog{\´e}nica, donde las condiciones de borde, como la geometr{\´i}a de la placa subductada, imponen un importante control sobre la deformaci{\´o}n andina. Por otro lado, la Placa Sudamericana presenta una serie de heterogeneidades que tambi{\´e}n imparten un control sobre el modo de deformaci{\´o}n. El objetivo de esta tesis es probar el control de este {\´u}ltimo factor sobre la construcci{\´o}n del sistema orog{\´e}nico andino. A partir de la integraci{\´o}n de la informaci{\´o}n superficial y de subsuelo en el {\´a}rea sur (34°-36°S), se estudi{\´o} la evoluci{\´o}n de la deformaci{\´o}n andina sobre el segmento de subducci{\´o}n normal. Se desarroll{\´o} un modelo estructural que eval{\´u}a el estado de esfuerzos desde el Mioceno hasta la actualidad, el rol de estructuras previas y su influencia en la migraci{\´o}n de fluidos. Con estos datos y publicaciones previas de la zona norte del {\´a}rea de estudio (33°-34ºS), se realiz{\´o} un modelado num{\´e}rico geodin{\´a}mico para probar la hip{\´o}tesis del papel de las heterogeneidades de la placa superior en la evoluci{\´o}n andina. Se utilizaron dos c{\´o}digos (LAPEX-2D y ASPECT) basados en elementos finitos/diferencias finitas, que simulan el comportamiento de materiales con reolog{\´i}as elastoviscopl{\´a}sticas bajo deformaci{\´o}n. Los resultados del modelado sugieren que la deformaci{\´o}n contraccional de la placa superior est{\´a} significativamente controlada por la resistencia de la lit{\´o}sfera, que est{\´a} definida por la composici{\´o}n de la corteza superior e inferior y por la proporci{\´o}n del manto litosf{\´e}rico, que a su vez est{\´a} definida por eventos tect{\´o}nicos previos. Estos eventos previos tambi{\´e}n definieron la composici{\´o}n de la corteza y su geometr{\´i}a, que es otro factor que controla la localizaci{\´o}n de la deformaci{\´o}n. Con una composici{\´o}n de corteza inferior m{\´a}s f{\´e}lsica, la deformaci{\´o}n sigue un modo de cizalla pura mientras que las composiciones m{\´a}s m{\´a}ficas provocan un modo de deformaci{\´o}n tipo cizalla simple. Por otro lado, observamos que el espesor inicial de la lit{\´o}sfera controla la localizaci{\´o}n de la deformaci{\´o}n, donde zonas con lit{\´o}sfera m{\´a}s fina es propensa a concentrar la deformaci{\´o}n. Un l{\´i}mite lit{\´o}sfera-asten{\´o}sfera asim{\´e}trico, como resultado del flujo de la cu{\~n}a mant{\´e}lica tiende a generar despegues vergentes al E.},
  language  = {en}
}
@phdthesis{Barchewitz2021,
  author    = {Barchewitz, Tino},
  title     = {Impact of microcystin on the non-canonical localization of RubisCO in the toxic bloom-forming cyanobacterium Microcystis aeruginosa PCC7806},
  doi       = {10.25932/publishup-50829},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-508299},
  school      = {Universit{\"a}t Potsdam},
  pages     = {vii, 106},
  year      = {2021},
  abstract  = {Cyanobacteria are an abundant bacterial group and are found in a variety of ecological niches all around the globe. They can serve as a real threat for fish or mammals and can restrict the use of lakes or rivers for recreational purposes or as a source of drinking water, when they form blooms. One of the most abundant bloom-forming cyanobacteria is Microcystis aeruginosa. In the first part of the study, the role and possible dynamics of RubisCO in M. aeruginosa during high-light irradiation were examined. Its response was analyzed on the protein and peptide level via immunoblotting, immunofluorescence microscopy and with high performance liquid chromatography (HPLC). It was revealed that large amounts of RubisCO were located outside of carboxysomes under the applied high light stress. RubisCO aggregated mainly underneath the cytoplasmic membrane. There it forms a putative Calvin-Benson-Bassham (CBB) super complex together with other enzymes of photosynthesis. This complex could be part of an alternative carbon-concentrating mechanism (CCM) in M. aeruginosa, which enables a faster, and energy saving adaptation to high light stress of the whole bloom. Furthermore, the re-localization of RubisCO was delayed in the microcystin-deficient mutant ΔmcyB and RubisCO was more evenly distributed over the cell in comparison to the wild type. Since ΔmcyB is not harmed in its growth, possibly other produced cyanopeptides as aeruginosin or cyanopeptolin also play a role in the stabilization of RubisCO and the putative CBB complex, especially in the microcystin-free mutant. In the second part of this work, the possible role of microcystin as an extracellular signaling peptide during the diurnal cycle was studied. HPLC analysis showed a strong increase of extracellular microcystin in the wild type when the population entered nighttime and it resumed into the next day as well. Together with the increase of extracellular microcystin, a strong decrease of protein-bound intracellular microcystin was observed via immunoblot analysis. Interestingly, the signal of the large subunit of RubisCO (RbcL) also diminished when high amounts of microcystin were present in the surrounding medium. Microcystin addition experiments to M. aeruginosa WT and ΔmcyB cultures support this observation, since the immunoblot signal of both subunits of RubisCO and CcmK, a shell protein of carboxysomes, diminished after the addition of microcystin. In addition, the fluctuation of cyanopeptolin during the diurnal cycle indicates a more prominent role of other cyanopeptides besides microcystin as a signaling peptide, intracellularly as well as extracellularly.},
  language  = {en}
}
@phdthesis{BarbosaPfannes2011,
  author    = {Barbosa Pfannes, Eva Katharina},
  title     = {Probing the regulatory mechanisms of the actomyosin system in motile cells},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-57812},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Actin-based directional motility is important for embryonic development, wound healing, immune responses, and development of tissues. Actin and myosin are essential players in this process that can be subdivided into protrusion, adhesion, and traction. Protrusion is the forward movement of the membrane at the leading edge of the cell. Adhesion is required to enable movement along a substrate, and traction finally leads to the forward movement of the entire cell body, including its organelles. While actin polymerization is the main driving force in cell protrusions, myosin motors lead to the contraction of the cell body. The goal of this work was to study the regulatory mechanisms of the motile machinery by selecting a representative key player for each stage of the signaling process: the regulation of Arp2/3 activity by WASP (actin system), the role of cGMP in myosin II assembly (myosin system), and the influence of phosphoinositide signaling (upstream receptor pathway). The model organism chosen for this work was the social ameba Dictyostelium discoideum, due to the well-established knowledge of its cytoskeletal machinery, the easy handling, and the high motility of its vegetative and starvation developed cells. First, I focused on the dynamics of the actin cytoskeleton by modulating the activity of one of its key players, the Arp2/3 complex. This was achieved using the carbazole derivative Wiskostatin, an inhibitor of the Arp2/3 activator WASP. Cells treated with Wiskostatin adopted a round shape, with no of few pseudopodia. With the help of a microfluidic cell squeezer device, I could show that Wiskostatin treated cells display a reduced mechanical stability, comparable to cells treated with the actin disrupting agent Latrunculin A. Furthermore, the WASP inhibited cells adhere stronger to a surface and show a reduced motility and chemotactic performance. However, the overall F-actin content in the cells was not changed. Confocal microscopy and TIRF microscopy imaging showed that the cells maintained an intact actin cortex. Localized dynamic patches of increased actin polymerization were observed that, however, did not lead to membrane deformation. This indicated that the mechanisms of actin-driven force generation were impaired in Wiskostatin treated cells. It is concluded that in these cells, an altered architecture of the cortical network leads to a reduced overall stiffness of the cell, which is insufficient to support the force generation required for membrane deformation and pseudopod formation. Second, the role of cGMP in myosin II dynamics was investigated. Cyclic GMP is known to regulate the association of myosin II with the cytoskeleton. In Dictyostelium, intracellular cGMP levels increase when cells are exposed to chemoattractants, but also in response to osmotic stress. To study the influence of cyclic GMP on actin and myosin II dynamics, I used the laser-induced photoactivation of a DMACM-caged-Br-cGMP to locally release cGMP inside the cell. My results show that cGMP directly activates the myosin II machinery, but is also able to induce an actin response independently of cAMP receptor activation and signaling. The actin response was observed in both vegetative and developed cells. Possible explanations include cGMP-induced actin polymerization through VASP (vasodilator-stimulated phosphoprotein) or through binding of cGMP to cyclic nucleotide-dependent kinases. Finally, I investigated the role of phosphoinositide signaling using the Polyphosphoinositide-Binding Peptide (PBP10) that binds preferentially to PIP2. Phosphoinositides can recruit actin-binding proteins to defined subcellular sites and alter their activity. Neutrophils, as well as developed Dictyostelium cells produce PIP3 in the plasma membrane at their leading edge in response to an external chemotactic gradient. Although not essential for chemotaxis, phosphoinositides are proposed to act as an internal compass in the cell. When treated with the peptide PBP10, cells became round, with fewer or no pseudopods. PH-CRAC translocation to the membrane still occurs, even at low cAMP stimuli, but cell motility (random and directional) was reduced. My data revealed that the decrease in the pool of available PIP2 in the cell is sufficient to impair cell motility, but enough PIP2 remains so that PIP3 is formed in response to chemoattractant stimuli. My data thus highlights how sensitive cell motility and morphology are to changes in the phosphoinositide signaling. In summary, I have analyzed representative regulatory mechanisms that govern key parts of the motile machinery and characterized their impact on cellular properties including mechanical stability, adhesion and chemotaxis.},
  language  = {en}
}
@phdthesis{Barbosa2020,
  author    = {Barbosa, Lu{\´i}s Romero},
  title     = {Groundwater recharge in tropical wet regions via GIS-based and cosmic-ray neutron sensing},
  doi       = {10.25932/publishup-46064},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-460641},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XXVI, 175},
  year      = {2020},
  abstract  = {Studies on the unsustainable use of groundwater resources are still considered incipient since it is frequently a poorly understood and managed, devalued and inadequately protected natural resource. Groundwater Recharge (GWR) is one of the most challenging elements to estimate since it can rarely be measured directly and cannot easily be derived from existing data. To overcome these limitations, many hydro(geo)logists have combined different approaches to estimate large-scale GWR, namely: remote sensing products, such as IMERG product; Water Budget Equation, also in combination with hydrological models, and; Geographic Information System (GIS), using estimation formulas. For intermediary-scale GWR estimation, there exist: Non-invasive Cosmic-Ray Neutron Sensing (CRNS); wireless networks from local soil probes; and soil hydrological models, such as HYDRUS. Accordingly, this PhD thesis aims, on the one hand, to demonstrate a GIS-based model coupling for estimating the GWR distribution on a large scale in tropical wet basins. On the other hand, it aims to use the time series from CRNS and invasive soil moisture probes to inversely calibrate the soil hydraulic properties, and based on this, estimating the intermediary-scale GWR using a soil hydrological model. For such purpose, two tropical wet basins located in a complex sedimentary aquifer in the coastal Northeast region of Brazil were selected. These are the Jo{\~a}o Pessoa Case Study Area and the Guara{\´i}ra Experimental Basin. Several satellite products in the first area were used as input to the GIS-based water budget equation model for estimating the water balance components and GWR in 2016 and 2017. In addition, the point-scale measurement and CRNS data were used in the second area to determine the soil hydraulic properties, and to estimate the GWR in the 2017-2018 and 2018-2019 hydrological years. The resulting values of GWR on large- and intermediary-scale were then compared and validated by the estimates obtained by groundwater table fluctuations. The GWR rates for IMERG- and rain-gauge-based scenarios showed similar coefficients between 68\% and 89\%, similar mean errors between 30\% and 34\%, and slightly-different bias between -13\% and 11\%. The results of GWR rates for soil probes and CRNS soil moisture scenarios ranged from -5.87 to -61.81 cm yr-1, which corresponds to 5\% and 38\% of the precipitation. The calculations of the mean GWR rates on large-scale, based on remote sensing data, and on intermediary-scale, based on CRNS data, held similar results for the Podzol soil type, namely 17.87\% and 17\% of the precipitation. It is then concluded that the proposed methodologies allowed for estimating realistically the GWR over the study areas, which can be a ground-breaking step towards improving the water management and decision-making in the Northeast of Brazil.},
  language  = {en}
}
@phdthesis{Bano2023,
  author    = {Bano, Dorina},
  title     = {Discovering data models from event logs},
  doi       = {10.25932/publishup-58542},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-585427},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xvii, 137},
  year      = {2023},
  abstract  = {In the last two decades, process mining has developed from a niche discipline to a significant research area with considerable impact on academia and industry. Process mining enables organisations to identify the running business processes from historical execution data. The first requirement of any process mining technique is an event log, an artifact that represents concrete business process executions in the form of sequence of events. These logs can be extracted from the organization's information systems and are used by process experts to retrieve deep insights from the organization's running processes. Considering the events pertaining to such logs, the process models can be automatically discovered and enhanced or annotated with performance-related information. Besides behavioral information, event logs contain domain specific data, albeit implicitly. However, such data are usually overlooked and, thus, not utilized to their full potential. Within the process mining area, we address in this thesis the research gap of discovering, from event logs, the contextual information that cannot be captured by applying existing process mining techniques. Within this research gap, we identify four key problems and tackle them by looking at an event log from different angles. First, we address the problem of deriving an event log in the absence of a proper database access and domain knowledge. The second problem is related to the under-utilization of the implicit domain knowledge present in an event log that can increase the understandability of the discovered process model. Next, there is a lack of a holistic representation of the historical data manipulation at the process model level of abstraction. Last but not least, each process model presumes to be independent of other process models when discovered from an event log, thus, ignoring possible data dependencies between processes within an organization. For each of the problems mentioned above, this thesis proposes a dedicated method. The first method provides a solution to extract an event log only from the transactions performed on the database that are stored in the form of redo logs. The second method deals with discovering the underlying data model that is implicitly embedded in the event log, thus, complementing the discovered process model with important domain knowledge information. The third method captures, on the process model level, how the data affects the running process instances. Lastly, the fourth method is about the discovery of the relations between business processes (i.e., how they exchange data) from a set of event logs and explicitly representing such complex interdependencies in a business process architecture. All the methods introduced in this thesis are implemented as a prototype and their feasibility is proven by being applied on real-life event logs.},
  language  = {en}
}
@phdthesis{Bange2009,
  author    = {Bange, Sebastian},
  title     = {Transient optical and electrical effects in polymeric semiconductors},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-36314},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {Classical semiconductor physics has been continuously improving electronic components such as diodes, light-emitting diodes, solar cells and transistors based on highly purified inorganic crystals over the past decades. Organic semiconductors, notably polymeric, are a comparatively young field of research, the first light-emitting diode based on conjugated polymers having been demonstrated in 1990. Polymeric semiconductors are of tremendous interest for high-volume, low-cost manufacturing ("printed electronics"). Due to their rather simple device structure mostly comprising only one or two functional layers, polymeric diodes are much more difficult to optimize compared to small-molecular organic devices. Usually, functions such as charge injection and transport are handled by the same material which thus needs to be highly optimized. The present work contributes to expanding the knowledge on the physical mechanisms determining device performance by analyzing the role of charge injection and transport on device efficiency for blue and white-emitting devices, based on commercially relevant spiro-linked polyfluorene derivatives. It is shown that such polymers can act as very efficient electron conductors and that interface effects such as charge trapping play the key role in determining the overall device efficiency. This work contributes to the knowledge of how charges drift through the polymer layer to finally find neutral emissive trap states and thus allows a quantitative prediction of the emission color of multichromophoric systems, compatible with the observed color shifts upon driving voltage and temperature variation as well as with electrical conditioning effects. In a more methodically oriented part, it is demonstrated that the transient device emission observed upon terminating the driving voltage can be used to monitor the decay of geminately-bound species as well as to determine trapped charge densities. This enables direct comparisons with numerical simulations based on the known properties of charge injection, transport and recombination. The method of charge extraction under linear increasing voltages (CELIV) is investigated in some detail, correcting for errors in the published approach and highlighting the role of non-idealized conditions typically present in experiments. An improved method is suggested to determine the field dependence of charge mobility in a more accurate way. Finally, it is shown that the neglect of charge recombination has led to a misunderstanding of experimental results in terms of a time-dependent mobility relaxation.},
  language  = {en}
}
@phdthesis{Banerjee2020,
  author    = {Banerjee, Pallavi},
  title     = {Glycosylphosphatidylinositols (GPIs) and GPI-anchored proteins tethered to lipid bilayers},
  doi       = {10.25932/publishup-48956},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-489561},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xv, 141},
  year      = {2020},
  abstract  = {Glycosylphosphatidylinositols (GPIs) are highly complex glycolipids that serve as membrane anchors to a large variety of eukaryotic proteins. These are covalently attached to a group of peripheral proteins called GPI-anchored proteins (GPI-APs) through a post-translational modification in the endoplasmic reticulum. The GPI anchor is a unique structure composed of a glycan, with phospholipid tail at one end and a phosphoethanolamine linker at the other where the protein attaches. The glycan part of the GPI comprises a conserved pseudopentasaccharide core that could branch out to carry additional glycosyl or phosphoethanolamine units. GPI-APs are involved in a diverse range of cellular processes, few of which are signal transduction, protein trafficking, pathogenesis by protozoan parasites like the malaria- causing parasite Plasmodium falciparum. GPIs can also exist freely on the membrane surface without an attached protein such as those found in parasites like Toxoplasma gondii, the causative agent of Toxoplasmosis. These molecules are both structurally and functionally diverse, however, their structure-function relationship is still poorly understood. This is mainly because no clear picture exists regarding how the protein and the glycan arrange with respect to the lipid layer. Direct experimental evidence is rather scarce, due to which inconclusive pictures have emerged, especially regarding the orientation of GPIs and GPI-APs on membrane surfaces and the role of GPIs in membrane organization. It appears that computational modelling through molecular dynamics simulations would be a useful method to make progress. In this thesis, we attempt to explore characteristics of GPI anchors and GPI-APs embedded in lipid bilayers by constructing molecular models at two different resolutions - all-atom and coarse-grained. First, we show how to construct a modular molecular model of GPIs and GPI-anchored proteins that can be readily extended to a broad variety of systems, addressing the micro-heterogeneity of GPIs. We do so by creating a hybrid link to which GPIs of diverse branching and lipid tails of varying saturation with their optimized force fields, GLYCAM06 and Lipid14 respectively, can be attached. Using microsecond simulations, we demonstrate that GPI prefers to "flop-down" on the membrane, thereby, strongly interacting with the lipid heads, over standing upright like a "lollipop". Secondly, we extend the model of the GPI core to carry out a systematic study of the structural aspects of GPIs carrying different side chains (parasitic and human GPI variants) inserted in lipid bilayers. Our results demonstrate the importance of the side branch residues as these are the most accessible, and thereby, recognizable epitopes. This finding qualitatively agrees with experimental observations that highlight the role of the side branches in immunogenicity of GPIs and the specificity thereof. The overall flop-down orientation of the GPIs with respect to the bilayer surface presents the side chain residues to face the solvent. Upon attaching the green fluorescent protein (GFP) to the GPI, it is seen to lie in close proximity to the bilayer, interacting both with the lipid heads and glycan part of the GPI. However the orientation of GFP is sensitive to the type of GPI it is attached to. Finally, we construct a coarse-grained model of the GPI and GPI-anchored GFP using a modified version of the MARTINI force-field, using which the timescale is enhanced by at least an order of magnitude compared to the atomistic system. This study provides a theoretical perspective on the conformational behavior of the GPI core and some of its branched variations in presence of lipid bilayers, as well as draws comparisons with experimental observations. Our modular atomistic model of GPI can be further employed to study GPIs of variable branching, and thereby, aid in designing future experiments especially in the area of vaccines and drug therapies. Our coarse-grained model can be used to study dynamic aspects of GPIs and GPI-APs w.r.t plasma membrane organization. Furthermore, the backmapping technique of converting coarse-grained trajectory back to the atomistic model would enable in-depth structural analysis with ample conformational sampling.},
  language  = {en}
}
@phdthesis{Banerjee2022,
  author    = {Banerjee, Abhirup},
  title     = {Characterizing the spatio-temporal patterns of extreme events},
  doi       = {10.25932/publishup-55983},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-559839},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xiv, 91},
  year      = {2022},
  abstract  = {Over the past decades, there has been a growing interest in 'extreme events' owing to the increasing threats that climate-related extremes such as floods, heatwaves, droughts, etc., pose to society. While extreme events have diverse definitions across various disciplines, ranging from earth science to neuroscience, they are characterized mainly as dynamic occurrences within a limited time frame that impedes the normal functioning of a system. Although extreme events are rare in occurrence, it has been found in various hydro-meteorological and physiological time series (e.g., river flows, temperatures, heartbeat intervals) that they may exhibit recurrent behavior, i.e., do not end the lifetime of the system. The aim of this thesis to develop some sophisticated methods to study various properties of extreme events. One of the main challenges in analyzing such extreme event-like time series is that they have large temporal gaps due to the paucity of the number of observations of extreme events. As a result, existing time series analysis tools are usually not helpful to decode the underlying information. I use the edit distance (ED) method to analyze extreme event-like time series in their unaltered form. ED is a specific distance metric, mainly designed to measure the similarity/dissimilarity between point process-like data. I combine ED with recurrence plot techniques to identify the recurrence property of flood events in the Mississippi River in the United States. I also use recurrence quantification analysis to show the deterministic properties and serial dependency in flood events. After that, I use this non-linear similarity measure (ED) to compute the pairwise dependency in extreme precipitation event series. I incorporate the similarity measure within the framework of complex network theory to study the collective behavior of climate extremes. Under this architecture, the nodes are defined by the spatial grid points of the given spatio-temporal climate dataset. Each node is associated with a time series corresponding to the temporal evolution of the climate observation at that grid point. Finally, the network links are functions of the pairwise statistical interdependence between the nodes. Various network measures, such as degree, betweenness centrality, clustering coefficient, etc., can be used to quantify the network's topology. We apply the methodology mentioned above to study the spatio-temporal coherence pattern of extreme rainfall events in the United States and the Ganga River basin, which reveals its relation to various climate processes and the orography of the region. The identification of precursors associated with the occurrence of extreme events in the near future is extremely important to prepare the masses for an upcoming disaster and mitigate the potential risks associated with such events. Under this motivation, I propose an in-data prediction recipe for predicting the data structures that typically occur prior to extreme events using the Echo state network, a type of Recurrent Neural Network which is a part of the reservoir computing framework. However, unlike previous works that identify precursory structures in the same variable in which extreme events are manifested (active variable), I try to predict these structures by using data from another dynamic variable (passive variable) which does not show large excursions from the nominal condition but carries imprints of these extreme events. Furthermore, my results demonstrate that the quality of prediction depends on the magnitude of events, i.e., the higher the magnitude of the extreme, the better is its predictability skill. I show quantitatively that this is because the input signals collectively form a more coherent pattern for an extreme event of higher magnitude, which enhances the efficiency of the machine to predict the forthcoming extreme events.},
  language  = {en}
}
@phdthesis{Bande2016,
  author    = {Bande, Alejandro},
  title     = {The tectonic evolution of the western Tien Shan},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-398933},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xiv, 119},
  year      = {2016},
  abstract  = {Intracontinental deformation usually is a result of tectonic forces associated with distant plate collisions. In general, the evolution of mountain ranges and basins in this environment is strongly controlled by the distribution and geometries of preexisting structures. Thus, predictive models usually fail in forecasting the deformation evolution in these kinds of settings. Detailed information on each range and basin-fill is vital to comprehend the evolution of intracontinental mountain belts and basins. In this dissertation, I have investigated the complex Cenozoic tectonic evolution of the western Tien Shan in Central Asia, which is one of the most active intracontinental ranges in the world. The work presented here combines a broad array of datasets, including thermo- and geochronology, paleoenvironmental interpretations, sediment provenance and subsurface interpretations in order to track changes in tectonic deformation. Most of the identified changes are connected and can be related to regional-scale processes that governed the evolution of the western Tien Shan. The NW-SE trending Talas-Fergana fault (TFF) separates the western from the central Tien Shan and constitutes a world-class example of the influence of preexisting anisotropies on the subsequent structural development of a contractile orogen. While to the east most of ranges and basins have a sub-parallel E-W trend, the triangular-shaped Fergana basin forms a substantial feature in the western Tien Shan morphology with ranges on all three sides. In this thesis, I present 55 new thermochronologic ages (apatite fission track and zircon (U-Th)/He)) used to constrain exhumation histories of several mountain ranges in the western Tien Shan. At the same time, I analyzed the Fergana basin-fill looking for progressive changes in sedimentary paleoenvironments, source areas and stratal geometrical configurations in the subsurface and outcrops. The data presented in this thesis suggests that low cooling rates (<1°C Myr-1), calm depositional environments, and low depositional rates (<10 m Myr-1) were widely distributed across the western Tien Shan, describing a quiescent tectonic period throughout the Paleogene. Increased cooling rates in the late Cenozoic occurred diachronously and with variable magnitudes in different ranges. This rapid cooling stage is interpreted to represent increased erosion caused by active deformation and constrains the onset of Cenozoic deformation in the western Tien Shan. Time-temperature histories derived from the northwestern Tien Shan samples show an increase in cooling rates by ~25 Ma. This event is correlated with a synchronous pulse iv in the South Tien Shan. I suggest that strike-slip motion along the TFF commenced at the Oligo-Miocene boundary, facilitating CCW rotation of the Fergana basin and enabling exhumation of the linked horsetail splays. Higher depositional rates (~150 m Myr-1) in the Oligo-Miocene section (Massaget Fm.) of the Fergana basin suggest synchronous deformation in the surrounding ranges. The central Alai Range also experienced rapid cooling around this time, suggesting that the onset of intramontane basin fragmentation and isolation is coeval. These results point to deformation starting simultaneously in the late Oligocene - early Miocene in geographically distant mountain ranges. I suggest that these early uplifts are controlled by reactivated structures (like the TFF), which are probably the frictionally weakest and most-suitably oriented for accommodating and transferring N-S horizontal shortening along the western Tien Shan. Afterwards, in the late Miocene (~10 Ma), a period of renewed rapid cooling affected the Tien Shan and most mountain ranges and inherited structures started to actively deform. This episode is widely distributed and an increase in exhumation is interpreted in most of the sampled ranges. Moreover, the Pliocene section in the basin subsurface shows the higher depositional rates (>180 m Myr-1) and higher energy facies. The deformation and exhumation increase further contributed to intramontane basin partitioning. Overall, the interpretation is that the Tien Shan and much of Central Asia suffered a global increase in the rate of horizontal crustal shortening. Previously, stress transfer along the rigid Tarim block or Pamir indentation has been proposed to account for Himalayan hinterland deformation. However, the extent of the episode requires a different and broader geodynamic driver.},
  language  = {en}
}
@phdthesis{Bamberg2014,
  author    = {Bamberg, Marlene},
  title     = {Planetary mapping tools applied to floor-fractured craters on Mars},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72104},
  school      = {Universit{\"a}t Potsdam},
  year      = {2014},
  abstract  = {Planetary research is often user-based and requires considerable skill, time, and effort. Unfortunately, self-defined boundary conditions, definitions, and rules are often not documented or not easy to comprehend due to the complexity of research. This makes a comparison to other studies, or an extension of the already existing research, complicated. Comparisons are often distorted, because results rely on different, not well defined, or even unknown boundary conditions. The purpose of this research is to develop a standardized analysis method for planetary surfaces, which is adaptable to several research topics. The method provides a consistent quality of results. This also includes achieving reliable and comparable results and reducing the time and effort of conducting such studies. A standardized analysis method is provided by automated analysis tools that focus on statistical parameters. Specific key parameters and boundary conditions are defined for the tool application. The analysis relies on a database in which all key parameters are stored. These databases can be easily updated and adapted to various research questions. This increases the flexibility, reproducibility, and comparability of the research. However, the quality of the database and reliability of definitions directly influence the results. To ensure a high quality of results, the rules and definitions need to be well defined and based on previously conducted case studies. The tools then produce parameters, which are obtained by defined geostatistical techniques (measurements, calculations, classifications). The idea of an automated statistical analysis is tested to proof benefits but also potential problems of this method. In this study, I adapt automated tools for floor-fractured craters (FFCs) on Mars. These impact craters show a variety of surface features, occurring in different Martian environments, and having different fracturing origins. They provide a complex morphological and geological field of application. 433 FFCs are classified by the analysis tools due to their fracturing process. Spatial data, environmental context, and crater interior data are analyzed to distinguish between the processes involved in floor fracturing. Related geologic processes, such as glacial and fluvial activity, are too similar to be separately classified by the automated tools. Glacial and fluvial fracturing processes are merged together for the classification. The automated tools provide probability values for each origin model. To guarantee the quality and reliability of the results, classification tools need to achieve an origin probability above 50 \%. This analysis method shows that 15 \% of the FFCs are fractured by intrusive volcanism, 20 \% by tectonic activity, and 43 \% by water \& ice related processes. In total, 75 \% of the FFCs are classified to an origin type. This can be explained by a combination of origin models, superposition or erosion of key parameters, or an unknown fracturing model. Those features have to be manually analyzed in detail. Another possibility would be the improvement of key parameters and rules for the classification. This research shows that it is possible to conduct an automated statistical analysis of morphologic and geologic features based on analysis tools. Analysis tools provide additional information to the user and are therefore considered assistance systems.},
  language  = {en}
}
@phdthesis{Balzer2014,
  author    = {Balzer, Arnim},
  title     = {Crab flare observations with H.E.S.S. phase II},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72545},
  school      = {Universit{\"a}t Potsdam},
  year      = {2014},
  abstract  = {The H.E.S.S. array is a third generation Imaging Atmospheric Cherenkov Telescope (IACT) array. It is located in the Khomas Highland in Namibia, and measures very high energy (VHE) gamma-rays. In Phase I, the array started data taking in 2004 with its four identical 13 m telescopes. Since then, H.E.S.S. has emerged as the most successful IACT experiment to date. Among the almost 150 sources of VHE gamma-ray radiation found so far, even the oldest detection, the Crab Nebula, keeps surprising the scientific community with unexplained phenomena such as the recently discovered very energetic flares of high energy gamma-ray radiation. During its most recent flare, which was detected by the Fermi satellite in March 2013, the Crab Nebula was simultaneously observed with the H.E.S.S. array for six nights. The results of the observations will be discussed in detail during the course of this work. During the nights of the flare, the new 24 m × 32 m H.E.S.S. II telescope was still being commissioned, but participated in the data taking for one night. To be able to reconstruct and analyze the data of the H.E.S.S. Phase II array, the algorithms and software used by the H.E.S.S. Phase I array had to be adapted. The most prominent advanced shower reconstruction technique developed by de Naurois and Rolland, the template-based model analysis, compares real shower images taken by the Cherenkov telescope cameras with shower templates obtained using a semi-analytical model. To find the best fitting image, and, therefore, the relevant parameters that describe the air shower best, a pixel-wise log-likelihood fit is done. The adaptation of this advanced shower reconstruction technique to the heterogeneous H.E.S.S. Phase II array for stereo events (i.e. air showers seen by at least two telescopes of any kind), its performance using MonteCarlo simulations as well as its application to real data will be described.},
  language  = {en}
}
@phdthesis{Ballato2009,
  author    = {Ballato, Paolo},
  title     = {Tectonic and climatic forcing in orogenic processes : the foreland basin point of view, Alborz mountains, N Iran},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41068},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {Systeme von Vorlandbecken repr{\"a}sentieren bedeutende geologische Archive und dienen dem Verst{\"a}ndnis von R{\"u}ckkopplungen zwischen oberfl{\"a}chennahen und tektonischen Prozessen. Außerdem dokumentieren sie die Entwicklung unmittelbar angrenzender Bergketten. Die sediment{\"a}ren Abfolgen in Vorlandbecken reflektieren das Gleichgewicht zwischen tektonischer Subsidenz, der Bildung langzeitlichen Akkommodationsraumes und des Sedimenteintrages, welcher wiederum die Wirksamkeit von Erosions- und Massenneuverteilungsprozessen wiederspiegelt. Um die Effekte von Klima und Tektonik in einem solchen System zu erforschen, untersuchte ich die Oligo-Mioz{\"a}nen Sedimente in den Vorlandbecken der s{\"u}dlichen Elburs Bergkette, einem intrakontinentalen Gebirge in Nord-Iran, das im Zuge der Arabisch-Eurasischen Kontinent-Kollision herausgehoben wurde. In dieser Studie der Vorlandbeckensedimente wurden Datierungstechniken angewandt (40Ar/39Ar, (U-Th)/He Thermochronologie und Magnetostratigraphie), die Sedimente und deren Herkunft analysiert und die Tonmineralogie, sowie Sauerstoff- und Kohlenstoffisotope untersucht. Die Ergebnisse zeigen, dass auf einer Zeitskala von 105 bis 106 Jahren eine systematische Korrelation zwischen „coarsening upward" Zyklen und den sediment{\"a}ren Akkumulationsraten besteht. W{\"a}hrend sukzessiver {\"U}berschiebungsphasen werden die durch Hebung der Bergkette bereitgestellten groben Kornfraktionen in proximale Bereiche des Beckens geliefert und feink{\"o}rnige Fazies in distalen Beckenregionen abgelagert. Variationen in der Sedimentherkunft in Phasen gr{\"o}ßerer tektonischer Aktivit{\"a}t zeugen von erosionaler Abdeckung und/oder der Umorganisation nat{\"u}rlicher Entw{\"a}sserungsstrukturen. Außerdem zeigen die Untersuchungen an stabilen Isotopen, dass die verst{\"a}rkte tektonische Aktivit{\"a}t das Anwachsen der Topographie f{\"o}rderte und damit die Wirksamkeit einer topographischen Barriere erh{\"o}hte. Wenn aufgrund nachlassender Beckenabsenkung die grobe Kornfraktion nicht vollst{\"a}ndig im Nahbereich des Beckens aufgenommen werden kann breitet sie sich in ferne Beckenregionen aus. Im Elburs wird die verringerte Subsidenz durch eine interne Hebung des Vorlandes hervorgerufen und ist mit einer lateralen Stapelung von Flussbetten assoziiert. Dokumentiert wird dies anhand konsequenten Schichtwachstums, tektonischer Schr{\"a}gstellung und sediment{\"a}rer Umlagerung. Gleichzeitig nehmen die Sedimentationsraten zu. Die Sauerstoff-Isotope der Pal{\"a}ob{\"o}den zeigen, dass dieser Anstieg mit einer Phase feuchteren Klimas einhergeht, wodurch Oberfl{\"a}chenprozesse effizienter werden und Heraushebungssraten steigen, was eine positive R{\"u}ckkopplung erzeugt. Des Weiteren zeigen die isotopischen und sediment{\"a}ren Daten, dass seit 10-9 Millionen Jahren (Ma) das Klima durch saisonalen Anstieg der Niederschl{\"a}ge zunehmend feuchter wurde. Da bedeutende klimatische Ver{\"a}nderungen zu dieser Zeit auch im Mittelmeerraum und Asien beobachtet wurden, ist anzunehmen, dass die klimatische Ver{\"a}nderung, die im Elburs Gebirge beobachtet wird, h{\"o}chstwahrscheinlich {\"A}nderungen der atmosph{\"a}rischen Zirkulationen der n{\"o}rdlichen Hemisph{\"a}re reflektiert. Aus den Ergebnissen dieser Studie lassen sich zus{\"a}tzliche Implikationen f{\"u}r die Entwicklung des Elburs Gebirges und die Arabisch-Eurasische kontinentale Kollisionszone ableiten. Die orogen-weite Hauptdeformation propagierte nicht gleichm{\"a}ßig nach S{\"u}den, sondern seit dem Oligoz{\"a}n schrittweise vorw{\"a}rts und r{\"u}ckw{\"a}rts. Insbesondere von ~17,5 bis 6,2 Ma wurde das Gebirge durch eine Kombination aus frontaler Akkretion und interner Keildeformation in Schritten von 0,7 bis 2 Millionen Jahren herausgehoben. Dar{\"u}ber hinaus deuten die Sedimentherkunftsdaten darauf hin, dass sich noch vor 10-9 Ma die Haupteinengungsrichtung von NW-SE nach NNE-SSW ver{\"a}nderte. Regional erlaubt die Geschichte der untersuchten Becken und angrenzenden Gebirgsz{\"u}ge R{\"u}ckschl{\"u}sse auf ein neues geodynamisches Model zur Entwicklung der Arabisch-Eurasischen kontinentalen Kollisionszone. Zahlreiche Sedimentbecken des Elburs Gebirges und anderer Lokalit{\"a}ten der Arabisch-Eurasischen Deformationszone belegen einen Wechsel von einem tensionalen zu einem kompressionalen tektonischen Regime vor ~36 Ma . Dieser Wechsel k{\"o}nnte den Beginn der Subduktion von gedehnter arabischer kontinentaler Lithosph{\"a}re unter Zentral-Iran bedeuten, was zu einer moderaten Plattenkopplung und Deformation von Unter- sowie Oberplatte gef{\"u}hrt hat. Der Anstieg der Deformationsraten im s{\"u}dlichen Elburs Gebirge seit ~17,5 Ma l{\"a}sst vermuten, dass die Oberplatte, wahrscheinlich aufgrund steigender Plattenkopplung, seit dem fr{\"u}hen Mioz{\"a}n signifikant deformiert wurde. Diese Ver{\"a}nderung k{\"o}nnte der Subduktion m{\"a}chtigerer arabischer kontinentaler Lithosph{\"a}re zugeschrieben werden und den Anfang echter kontinentaler Kollision bedeuten. Dieses Model erkl{\"a}rt daher die Zeitverz{\"o}gerung zwischen der Initiation der Arabisch-Eurasischen kontinentalen Kollision (Eoz{\"a}n-Oligoz{\"a}n) and dem Beginn ausgedehnter Deformation in der Kollisionszone (Mioz{\"a}n).},
  language  = {en}
}
@phdthesis{Bajerski2013,
  author    = {Bajerski, Felizitas},
  title     = {Bacterial communities in glacier forefields of the Larsemann Hills, East Antarctica : structure, development \& adaptation},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-67424},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Antarctic glacier forfields are extreme environments and pioneer sites for ecological succession. The Antarctic continent shows microbial community development as a natural laboratory because of its special environment, geographic isolation and little anthropogenic influence. Increasing temperatures due to global warming lead to enhanced deglaciation processes in cold-affected habitats and new terrain is becoming exposed to soil formation and accessible for microbial colonisation. This study aims to understand the structure and development of glacier forefield bacterial communities, especially how soil parameters impact the microorganisms and how those are adapted to the extreme conditions of the habitat. To this effect, a combination of cultivation experiments, molecular, geophysical and geochemical analysis was applied to examine two glacier forfields of the Larsemann Hills, East Antarctica. Culture-independent molecular tools such as terminal restriction length polymorphism (T-RFLP), clone libraries and quantitative real-time PCR (qPCR) were used to determine bacterial diversity and distribution. Cultivation of yet unknown species was carried out to get insights in the physiology and adaptation of the microorganisms. Adaptation strategies of the microorganisms were studied by determining changes of the cell membrane phospholipid fatty acid (PLFA) inventory of an isolated bacterium in response to temperature and pH fluctuations and by measuring enzyme activity at low temperature in environmental soil samples. The two studied glacier forefields are extreme habitats characterised by low temperatures, low water availability and small oligotrophic nutrient pools and represent sites of different bacterial succession in relation to soil parameters. The investigated sites showed microbial succession at an early step of soil formation near the ice tongue in comparison to closely located but rather older and more developed soil from the forefield. At the early step the succession is influenced by a deglaciation-dependent areal shift of soil parameters followed by a variable and prevalently depth-related distribution of the soil parameters that is driven by the extreme Antarctic conditions. The dominant taxa in the glacier forefields are Actinobacteria, Acidobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria and Chloroflexi. The connection of soil characteristics with bacterial community structure showed that soil parameter and soil formation along the glacier forefield influence the distribution of certain phyla. In the early step of succession the relative undifferentiated bacterial diversity reflects the undifferentiated soil development and has a high potential to shift according to past and present environmental conditions. With progressing development environmental constraints such as water or carbon limitation have a greater influence. Adapting the culturing conditions to the cold and oligotrophic environment, the number of culturable heterotrophic bacteria reached up to 108 colony forming units per gram soil and 148 isolates were obtained. Two new psychrotolerant bacteria, Herbaspirillum psychrotolerans PB1T and Chryseobacterium frigidisoli PB4T, were characterised in detail and described as novel species in the family of Oxalobacteraceae and Flavobacteriaceae, respectively. The isolates are able to grow at low temperatures tolerating temperature fluctuations and they are not specialised to a certain substrate, therefore they are well-adapted to the cold and oligotrophic environment. The adaptation strategies of the microorganisms were analysed in environmental samples and cultures focussing on extracellular enzyme activity at low temperature and PLFA analyses. Extracellular phosphatases (pH 11 and pH 6.5), β-glucosidase, invertase and urease activity were detected in the glacier forefield soils at low temperature (14°C) catalysing the conversion of various compounds providing necessary substrates and may further play a role in the soil formation and total carbon turnover of the habitat. The PLFA analysis of the newly isolated species C. frigidisoli showed that the cold-adapted strain develops different strategies to maintain the cell membrane function under changing environmental conditions by altering the PLFA inventory at different temperatures and pH values. A newly discovered fatty acid, which was not found in any other microorganism so far, significantly increased at decreasing temperature and low pH and thus plays an important role in the adaption of C. frigidisoli. This work gives insights into the diversity, distribution and adaptation mechanisms of microbial communities in oligotrophic cold-affected soils and shows that Antarctic glacier forefields are suitable model systems to study bacterial colonisation in connection to soil formation.},
  language  = {en}
}
@phdthesis{Baier2015,
  author    = {Baier, Thomas},
  title     = {Matching events and activities},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-84548},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xxii, 213},
  year      = {2015},
  abstract  = {Nowadays, business processes are increasingly supported by IT services that produce massive amounts of event data during process execution. Aiming at a better process understanding and improvement, this event data can be used to analyze processes using process mining techniques. Process models can be automatically discovered and the execution can be checked for conformance to specified behavior. Moreover, existing process models can be enhanced and annotated with valuable information, for example for performance analysis. While the maturity of process mining algorithms is increasing and more tools are entering the market, process mining projects still face the problem of different levels of abstraction when comparing events with modeled business activities. Mapping the recorded events to activities of a given process model is essential for conformance checking, annotation and understanding of process discovery results. Current approaches try to abstract from events in an automated way that does not capture the required domain knowledge to fit business activities. Such techniques can be a good way to quickly reduce complexity in process discovery. Yet, they fail to enable techniques like conformance checking or model annotation, and potentially create misleading process discovery results by not using the known business terminology. In this thesis, we develop approaches that abstract an event log to the same level that is needed by the business. Typically, this abstraction level is defined by a given process model. Thus, the goal of this thesis is to match events from an event log to activities in a given process model. To accomplish this goal, behavioral and linguistic aspects of process models and event logs as well as domain knowledge captured in existing process documentation are taken into account to build semiautomatic matching approaches. The approaches establish a pre--processing for every available process mining technique that produces or annotates a process model, thereby reducing the manual effort for process analysts. While each of the presented approaches can be used in isolation, we also introduce a general framework for the integration of different matching approaches. The approaches have been evaluated in case studies with industry and using a large industry process model collection and simulated event logs. The evaluation demonstrates the effectiveness and efficiency of the approaches and their robustness towards nonconforming execution logs.},
  language  = {en}
}
@phdthesis{Bahrke2008,
  author    = {Bahrke, Sven},
  title     = {Mass spectrometric analysis of chitooligosaccharides and their interaction with proteins},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-20179},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {Chitooligosaccharides are composed of glycosamin and N-acetylglycisamin residues. Gel permeations chromatography is employed for the separation of oligomers, cation exchange chromatography is used for the separation of homologes and isomers. Trideuterioacetylation of the chitooligosaccharides followed by MALDI-TOF mass spectrometry allowes for the quantitation of mixtures of homologes. vMALDI LTQ multiple-stage MS is employed for quantitative sequencing of complex mixtures of heterochitooligosaccharides. Pure homologes and isomers are applied to biological assays. Chitooligosaccahrides form high-affinity non-covalent complexes with HC gp-39 (human cartilage glycoprotein of 39 kDa). The affinity of the chitooligosaccharides depends on DP, FA and the sequence of glycosamin and N-acetylglycosamin moieties. (+)nanoESI Q TOF MS/MS is used for identification of a high-affinity binding chitooligosaccharide of a non-covalent chitinase B - chitooligosaccharide complex. DADAA is identified as the heterochitoisomer binding with highest affinity and biostability to HC gp-39. Fluorescence based enzyme assays confirm the results.},
  language  = {en}
}
@phdthesis{Baczyński2009,
  author    = {Baczyński, Krzysztof Konrad},
  title     = {Buckling instabilities of semiflexible filaments in biological systems},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-37927},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {In dieser Arbeit werden Knickinstabilit{\"a}ten von Filamenten in biologischen Systemen untersucht. Das Zytoskelett von Zellen ist aus solchen Filamenten aufgebaut. Sie sind f{\"u}r die mechanische Stabilit{\"a}t der Zelle verantwortlich und spielen eine große Rolle bei intrazellul{\"a}ren Transportprozessen durch molekulare Motoren, die verschiedene Lasten wie beispielsweise Organellen entlang der Filamente des Zytoskeletts transportieren. Filamente sind semiflexible Polymere, deren Biegeenergie {\"a}hnlich groß ist wie die thermische Energie, so dass sie auch als elastische Balken auf der Nanoskala gesehen werden k{\"o}nnen, die signifikante thermische Fluktuationen zeigen. Wie ein makroskopischer elastischer Balken k{\"o}nnen auch Filamente eine mechanische Knickinstabilit{\"a}t unter Kompression zeigen. Im ersten Teil dieser Arbeit wird untersucht, wie diese Instabilit{\"a}t durch thermische Fluktuationen der Filamente beeinflusst wird. In Zellen k{\"o}nnen Kompressionskr{\"a}fte durch molekulare Motoren erzeugt werden. Das geschieht zum Beispiel w{\"a}hrend der Zellteilung in der mitotischen Spindel. Im zweiten Teil der Arbeit untersuchen wir, wie die stochastische Natur einer von Motoren generierten Kraft die Knickinstabilit{\"a}t von Filamenten beeinflusst. Zun{\"a}chst stellen wir kurz das Problem von Knickinstabilit{\"a}ten auf der makroskopischen Skala dar und f{\"u}hren ein Modell f{\"u}r das Knicken von Filamenten oder elastischen St{\"a}ben in zwei Raumdimensionen und in Anwesenheit thermischer Fluktuationen ein. Wir pr{\"a}sentieren eine analytische L{\"o}sung f{\"u}r Knickinstabilit{\"a}ten in Anwesenheit thermischer Fluktuationen, die auf einer Renormierungsgruppenrechnung im Rahmen des nichtlinearen Sigma-Models basiert. Wir integrieren die kurzwelligen Fluktuationen aus, um eine effektive Theorie f{\"u}r die langwelligen Moden zu erhalten, die die Knickinstabilit{\"a}t bestimmen. Wir berechnen die {\"A}nderung der kritischen Kraft f{\"u}r die Knickinstabilit{\"a}t und zeigen, dass die thermischen Fluktuationen in zwei Raumdimensionen zu einer Zunahme der kritischen Kraft f{\"u}hren. Außerdem zeigen wir, dass thermische Fluktuationen im geknickten Zustand zu einer Zunahme der mittleren projizierten L{\"a}nge des Filaments in Richtung der wirkenden Kraft f{\"u}hren. Als Funktion der Konturl{\"a}nge des Filaments besitzt die mittlere projizierte L{\"a}nge eine Spitze an der Knickinstabilit{\"a}t, die durch thermische Fluktuationen abgerundet wird. Unser Hauptresultat ist die Beobachtung, dass ein geknicktes Filament unter dem Einfluss thermischer Fluktuationen gestreckt wird, d.h. dass seine mittlere projizierte L{\"a}nge in Richtung der Kompressionskraft auf Grund der thermischen Fluktuationen zunimmt. Unsere analytischen Resultate werden durch Monte-Carlo Simulationen der Knickinstabilit{\"a}t semiflexibler Filamente in zwei Raumdimensionen best{\"a}tigt. Wir f{\"u}hren auch Monte-Carlo Simulationen in h{\"o}heren Raumdimensionen durch und zeigen, dass die Zunahme der projizierten L{\"a}nge unter dem Einfluss thermischer Fluktuationen weniger ausgepr{\"a}gt ist und stark von der Wahl der Randbedingungen abh{\"a}ngt. Im zweiten Teil der Arbeit formulieren wir ein Modell f{\"u}r die Knickinstabilit{\"a}t semiflexibler Filamente unter dem Einfluss molekularer Motoren. Wir untersuchen ein System, in dem sich eine Gruppe von Motoren entlang eines fixierten Filaments bewegt, und dabei ein zweites Filament als Last tr{\"a}gt. Das Last-Filament wird gegen eine Wand gedr{\"u}ckt und knickt. W{\"a}hrend des Knickvorgangs k{\"o}nnen die Motoren, die die Kraft auf das Filament generieren, stochastisch von dem Filament ab- und an das Filament anbinden. Wir formulieren ein stochastisches Model f{\"u}r dieses System und berechnen die "mean first passage time", d.h. die mittlere Zeit f{\"u}r den {\"U}bergang von einem Zustand, in dem alle Motoren gebundenen sind zu einem Zustand, in dem alle Motoren abgebunden sind. Dieser {\"U}bergang entspricht auch einem {\"U}bergang aus dem gebogenen zur{\"u}ck in einen ungebogenen Zustand des Last-Filaments. Unser Resultat zeigt, dass f{\"u}r gen{\"u}gend kurze Mikrotubuli die Bewegung der Motoren von der durch das Last-Filament generierten Kraft beeinflusst wird. Diese Ergebnisse k{\"o}nnen in zuk{\"u}nftigen Experimenten {\"u}berpr{\"u}ft werden.},
  language  = {en}
}
@phdthesis{BacskaiAtkari2014,
  author    = {Bacskai-Atkari, Julia},
  title     = {The syntax of comparative constructions : operators, ellipsis phenomena and functional left peripheries},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-301-5},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-71255},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xiii, 310},
  year      = {2014},
  abstract  = {Adopting a minimalist framework, the dissertation provides an analysis for the syntactic structure of comparatives, with special attention paid to the derivation of the subclause. The proposed account explains how the comparative subclause is connected to the matrix clause, how the subclause is formed in the syntax and what additional processes contribute to its final structure. In addition, it casts light upon these problems in cross-linguistic terms and provides a model that allows for synchronic and diachronic differences. This also enables one to give a more adequate explanation for the phenomena found in English comparatives since the properties of English structures can then be linked to general settings of the language and hence need no longer be considered as idiosyncratic features of the grammar of English. First, the dissertation provides a unified analysis of degree expressions, relating the structure of comparatives to that of other degrees. It is shown that gradable adjectives are located within a degree phrase (DegP), which in turn projects a quantifier phrase (QP) and that these two functional layers are always present, irrespectively of whether there is a phonologically visible element in these layers. Second, the dissertation presents a novel analysis of Comparative Deletion by reducing it to an overtness constraint holding on operators: in this way, it is reduced to morphological differences and cross-linguistic variation is not conditioned by way of postulating an arbitrary parameter. Cross-linguistic differences are ultimately dependent on whether a language has overt operators equipped with the relevant - [+compr] and [+rel] - features. Third, the dissertation provides an adequate explanation for the phenomenon of Attributive Comparative Deletion, as attested in English, by way of relating it to the regular mechanism of Comparative Deletion. I assume that Attributive Comparative Deletion is not a universal phenomenon, and its presence in English can be conditioned by independent, more general rules, while the absence of such restrictions leads to its absence in other languages. Fourth, the dissertation accounts for certain phenomena related to diachronic changes, examining how the changes in the status of comparative operators led to changes in whether Comparative Deletion is attested in a given language: I argue that only operators without a lexical XP can be grammaticalised. The underlying mechanisms underlying are essentially general economy principles and hence the processes are not language-specific or exceptional. Fifth, the dissertation accounts for optional ellipsis processes that play a crucial role in the derivation of typical comparative subclauses. These processes are not directly related to the structure of degree expressions and hence the elimination of the quantified expression from the subclause; nevertheless, they are shown to be in interaction with the mechanisms underlying Comparative Deletion or the absence thereof.},
  language  = {en}
}
@phdthesis{Backers2004,
  author    = {Backers, Tobias},
  title     = {Fracture toughness determination and micromechanics of rock under Mode I and Mode II loading},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-2294},
  school      = {Universit{\"a}t Potsdam},
  year      = {2004},
  abstract  = {This thesis work describes a new experimental method for the determination of Mode II (shear) fracture toughness, KIIC of rock and compares the outcome to results from Mode I (tensile) fracture toughness, KIC, testing using the International Society of Rock Mechanics Chevron-Bend method.Critical Mode I fracture growth at ambient conditions was studied by carrying out a series of experiments on a sandstone at different loading rates. The mechanical and microstructural data show that time- and loading rate dependent crack growth occurs in the test material at constant energy requirement.The newly developed set-up for determination of the Mode II fracture toughness is called the Punch-Through Shear test. Notches were drilled to the end surfaces of core samples. An axial load punches down the central cylinder introducing a shear load in the remaining rock bridge. To the mantle of the cores a confining pressure may be applied. The application of confining pressure favours the growth of Mode II fractures as large pressures suppress the growth of tensile cracks.Variation of geometrical parameters leads to an optimisation of the PTS- geometry. Increase of normal load on the shear zone increases KIIC bi-linear. High slope is observed at low confining pressures; at pressures above 30 MPa low slope increase is evident. The maximum confining pressure applied is 70 MPa. The evolution of fracturing and its change with confining pressure is described.The existence of Mode II fracture in rock is a matter of debate in the literature. Comparison of the results from Mode I and Mode II testing, mainly regarding the resulting fracture pattern, and correlation analysis of KIC and KIIC to physico-mechanical parameters emphasised the differences between the response of rock to Mode I and Mode II loading. On the microscale, neither the fractures resulting from Mode I the Mode II loading are pure mode fractures. On macroscopic scale, Mode I and Mode II do exist.},
  language  = {en}
}
@phdthesis{Bach2013,
  author    = {Bach, Christoph},
  title     = {Improving statistical seismicity models},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70591},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Several mechanisms are proposed to be part of the earthquake triggering process, including static stress interactions and dynamic stress transfer. Significant differences of these mechanisms are particularly expected in the spatial distribution of aftershocks. However, testing the different hypotheses is challenging because it requires the consideration of the large uncertainties involved in stress calculations as well as the appropriate consideration of secondary aftershock triggering which is related to stress changes induced by smaller pre- and aftershocks. In order to evaluate the forecast capability of different mechanisms, I take the effect of smaller--magnitude earthquakes into account by using the epidemic type aftershock sequence (ETAS) model where the spatial probability distribution of direct aftershocks, if available, is correlated to alternative source information and mechanisms. Surface shaking, rupture geometry, and slip distributions are tested. As an approximation of the shaking level, ShakeMaps are used which are available in near real-time after a mainshock and thus could be used for first-order forecasts of the spatial aftershock distribution. Alternatively, the use of empirical decay laws related to minimum fault distance is tested and Coulomb stress change calculations based on published and random slip models. For comparison, the likelihood values of the different model combinations are analyzed in the case of several well-known aftershock sequences (1992 Landers, 1999 Hector Mine, 2004 Parkfield). The tests show that the fault geometry is the most valuable information for improving aftershock forecasts. Furthermore, they reveal that static stress maps can additionally improve the forecasts of off--fault aftershock locations, while the integration of ground shaking data could not upgrade the results significantly. In the second part of this work, I focused on a procedure to test the information content of inverted slip models. This allows to quantify the information gain if this kind of data is included in aftershock forecasts. For this purpose, the ETAS model based on static stress changes, which is introduced in part one, is applied. The forecast ability of the models is systematically tested for several earthquake sequences and compared to models using random slip distributions. The influence of subfault resolution and segment strike and dip is tested. Some of the tested slip models perform very good, in that cases almost no random slip models are found to perform better. Contrastingly, for some of the published slip models, almost all random slip models perform better than the published slip model. Choosing a different subfault resolution hardly influences the result, as long the general slip pattern is still reproducible. Whereas different strike and dip values strongly influence the results depending on the standard deviation chosen, which is applied in the process of randomly selecting the strike and dip values.},
  language  = {en}
}
@phdthesis{Ba2006,
  author    = {Ba, Jianhua},
  title     = {Nonaqueous synthesis of metal oxide nanoparticles and their assembly into mesoporous materials},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-10173},
  school      = {Universit{\"a}t Potsdam},
  year      = {2006},
  abstract  = {This thesis mainly consist of two parts, the synthesis of several kinds of technologically interesting crystalline metal oxide nanoparticles via nonaqueous sol-gel process and the formation of mesoporous metal oxides using some of these nanoparticles as building blocks via evaporation induced self-assembly (EISA) technique. In the first part, the experimental procedures and characterization results of successful syntheses of crystalline tin oxide and tin doped indium oxide (ITO) nanoparticles are reported. SnO2 nanoparticles exhibit monodisperse particle size (3.5 nm in average), high crystallinity and particularly high dispersibility in THF, which enable them to become the ideal particulate precursor for the formation of mesoporous SnO2. ITO nanoparticles possess uniform particle morphology, narrow particle size distribution (5-10 nm), high crystallinity as well as high electrical conductivity. The synthesis approaches and characterization of various mesoporous metal oxides, including TiO2, SnO2, mixture of CeO2 and TiO2, mixture of BaTiO3 and SnO2, are reported in the second part of this thesis. Mesoporous TiO2 and SnO2 are presented as highlights of this part. Mesoporous TiO2 was produced in the forms of both films and bulk material. In the case of mesoporous SnO2, the study was focused on the high order of the porous structure. All these mesoporous metal oxides show high crystallinity, high surface area and rather monodisperse pore sizes, which demonstrate the validity of EISA process and the usage of preformed crystalline nanoparticles as nanobuilding blocks (NBBs) to produce mesoporous metal oxides.},
  subject      = {Nanopartikel},
  language  = {en}
}
@phdthesis{Ayzel2021,
  author    = {Ayzel, Georgy},
  title     = {Advancing radar-based precipitation nowcasting},
  doi       = {10.25932/publishup-50426},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-504267},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xx, 68},
  year      = {2021},
  abstract  = {Precipitation forecasting has an important place in everyday life - during the day we may have tens of small talks discussing the likelihood that it will rain this evening or weekend. Should you take an umbrella for a walk? Or should you invite your friends for a barbecue? It will certainly depend on what your weather application shows. While for years people were guided by the precipitation forecasts issued for a particular region or city several times a day, the widespread availability of weather radars allowed us to obtain forecasts at much higher spatiotemporal resolution of minutes in time and hundreds of meters in space. Hence, radar-based precipitation nowcasting, that is, very-short-range forecasting (typically up to 1-3 h), has become an essential technique, also in various professional application contexts, e.g., early warning, sewage control, or agriculture. There are two major components comprising a system for precipitation nowcasting: radar-based precipitation estimates, and models to extrapolate that precipitation to the imminent future. While acknowledging the fundamental importance of radar-based precipitation retrieval for precipitation nowcasts, this thesis focuses only on the model development: the establishment of open and competitive benchmark models, the investigation of the potential of deep learning, and the development of procedures for nowcast errors diagnosis and isolation that can guide model development. The present landscape of computational models for precipitation nowcasting still struggles with the availability of open software implementations that could serve as benchmarks for measuring progress. Focusing on this gap, we have developed and extensively benchmarked a stack of models based on different optical flow algorithms for the tracking step and a set of parsimonious extrapolation procedures based on image warping and advection. We demonstrate that these models provide skillful predictions comparable with or even superior to state-of-the-art operational software. We distribute the corresponding set of models as a software library, rainymotion, which is written in the Python programming language and openly available at GitHub (https://github.com/hydrogo/rainymotion). That way, the library acts as a tool for providing fast, open, and transparent solutions that could serve as a benchmark for further model development and hypothesis testing. One of the promising directions for model development is to challenge the potential of deep learning - a subfield of machine learning that refers to artificial neural networks with deep architectures, which may consist of many computational layers. Deep learning showed promising results in many fields of computer science, such as image and speech recognition, or natural language processing, where it started to dramatically outperform reference methods. The high benefit of using "big data" for training is among the main reasons for that. Hence, the emerging interest in deep learning in atmospheric sciences is also caused and concerted with the increasing availability of data - both observational and model-based. The large archives of weather radar data provide a solid basis for investigation of deep learning potential in precipitation nowcasting: one year of national 5-min composites for Germany comprises around 85 billion data points. To this aim, we present RainNet, a deep convolutional neural network for radar-based precipitation nowcasting. RainNet was trained to predict continuous precipitation intensities at a lead time of 5 min, using several years of quality-controlled weather radar composites provided by the German Weather Service (DWD). That data set covers Germany with a spatial domain of 900 km x 900 km and has a resolution of 1 km in space and 5 min in time. Independent verification experiments were carried out on 11 summer precipitation events from 2016 to 2017. In these experiments, RainNet was applied recursively in order to achieve lead times of up to 1 h. In the verification experiments, trivial Eulerian persistence and a conventional model based on optical flow served as benchmarks. The latter is available in the previously developed rainymotion library. RainNet significantly outperformed the benchmark models at all lead times up to 60 min for the routine verification metrics mean absolute error (MAE) and critical success index (CSI) at intensity thresholds of 0.125, 1, and 5 mm/h. However, rainymotion turned out to be superior in predicting the exceedance of higher intensity thresholds (here 10 and 15 mm/h). The limited ability of RainNet to predict high rainfall intensities is an undesirable property which we attribute to a high level of spatial smoothing introduced by the model. At a lead time of 5 min, an analysis of power spectral density confirmed a significant loss of spectral power at length scales of 16 km and below. Obviously, RainNet had learned an optimal level of smoothing to produce a nowcast at 5 min lead time. In that sense, the loss of spectral power at small scales is informative, too, as it reflects the limits of predictability as a function of spatial scale. Beyond the lead time of 5 min, however, the increasing level of smoothing is a mere artifact - an analogue to numerical diffusion - that is not a property of RainNet itself but of its recursive application. In the context of early warning, the smoothing is particularly unfavorable since pronounced features of intense precipitation tend to get lost over longer lead times. Hence, we propose several options to address this issue in prospective research on model development for precipitation nowcasting, including an adjustment of the loss function for model training, model training for longer lead times, and the prediction of threshold exceedance. The model development together with the verification experiments for both conventional and deep learning model predictions also revealed the need to better understand the source of forecast errors. Understanding the dominant sources of error in specific situations should help in guiding further model improvement. The total error of a precipitation nowcast consists of an error in the predicted location of a precipitation feature and an error in the change of precipitation intensity over lead time. So far, verification measures did not allow to isolate the location error, making it difficult to specifically improve nowcast models with regard to location prediction. To fill this gap, we introduced a framework to directly quantify the location error. To that end, we detect and track scale-invariant precipitation features (corners) in radar images. We then consider these observed tracks as the true reference in order to evaluate the performance (or, inversely, the error) of any model that aims to predict the future location of a precipitation feature. Hence, the location error of a forecast at any lead time ahead of the forecast time corresponds to the Euclidean distance between the observed and the predicted feature location at the corresponding lead time. Based on this framework, we carried out a benchmarking case study using one year worth of weather radar composites of the DWD. We evaluated the performance of four extrapolation models, two of which are based on the linear extrapolation of corner motion; and the remaining two are based on the Dense Inverse Search (DIS) method: motion vectors obtained from DIS are used to predict feature locations by linear and Semi-Lagrangian extrapolation. For all competing models, the mean location error exceeds a distance of 5 km after 60 min, and 10 km after 110 min. At least 25\% of all forecasts exceed an error of 5 km after 50 min, and of 10 km after 90 min. Even for the best models in our experiment, at least 5 percent of the forecasts will have a location error of more than 10 km after 45 min. When we relate such errors to application scenarios that are typically suggested for precipitation nowcasting, e.g., early warning, it becomes obvious that location errors matter: the order of magnitude of these errors is about the same as the typical extent of a convective cell. Hence, the uncertainty of precipitation nowcasts at such length scales - just as a result of locational errors - can be substantial already at lead times of less than 1 h. Being able to quantify the location error should hence guide any model development that is targeted towards its minimization. To that aim, we also consider the high potential of using deep learning architectures specific to the assimilation of sequential (track) data. Last but not least, the thesis demonstrates the benefits of a general movement towards open science for model development in the field of precipitation nowcasting. All the presented models and frameworks are distributed as open repositories, thus enhancing transparency and reproducibility of the methodological approach. Furthermore, they are readily available to be used for further research studies, as well as for practical applications.},
  language  = {en}
}
@phdthesis{Ayguel2015,
  author    = {Ayg{\"u}l, Mesut},
  title     = {Pre-collisional accretion and exhumation along the southern Laurasian active margin, Central Pontides, Turkey},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-416769},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xxxiv, 206},
  year      = {2015},
  abstract  = {The Central Pontides is an accretionary-type orogenic area within the Alpine-Himalayan orogenic belt characterized by pre-collisional tectonic continental growth. The region comprises Mesozoic subduction-accretionary complexes and an accreted intra-oceanic arc that are sandwiched between the Laurasian active continental margin and Gondwana-derived the K{\i}r{\c{s}}ehir Block. The subduction-accretion complexes mainly consist of an Albian-Turonian accretionary wedge representing the Laurasian active continental margin. To the north, the wedge consists of slate/phyllite and metasandstone intercalation with recrystallized limestone, Na-amphibole-bearing metabasite (PT= 7-12 kbar and 400 ± 70 ºC) and tectonic slices of serpentinite representing accreted distal part of a large Lower Cretaceous submarine turbidite fan deposited on the Laurasian active continental margin that was subsequently accreted and metamorphosed. Raman spectra of carbonaceous material (RSCM) of the metapelitic rocks revealed that the metaflysch sequence consists of metamorphic packets with distinct peak metamorphic temperatures. The majority of the metapelites are low-temperature (ca. 330 °C) slates characterized by lack of differentiation of the graphite (G) and D2 defect bands. They possibly represent offscraped distal turbidites along the toe of the Albian accretionary wedge. The rest are phyllites that are characterized by slightly pronounced G band with D2 defect band occurring on its shoulder. Peak metamorphic temperatures of these phyllites are constrained to 370-385 °C. The phyllites are associated with a strip of incipient blueschist facies metabasites which are found as slivers within the offscraped distal turbidites. They possibly represent underplated continental metasediments together with oceanic crustal basalt along the basal d{\´e}collement. Tectonic emplacement of the underplated rocks into the offscraped distal turbidites was possibly achieved by out-of-sequence thrusting causing tectonic thickening and uplift of the wedge. 40Ar/39Ar phengite ages from the phyllites are ca. 100 Ma, indicating Albian subduction and regional HP metamorphism. The accreted continental metasediments are underlain by HP/LT metamorphic rocks of oceanic origin along an extensional shear zone. The oceanic metamorphic sequence mainly comprises tectonically thickened deep-seated eclogite to blueschist facies metabasites and micaschists. In the studied area, metabasites are epidote-blueschists locally with garnet (PT= 17 ± 1 kbar and 500 ± 40 °C). Lawsonite-blueschists are exposed as blocks along the extensional shear zone (PT= 14 ± 2 kbar and 370-440 °C). They are possibly associated with low shear stress regime of the initial stage of convergence. Close to the shear zone, the footwall micaschists consist of quartz, phengite, paragonite, chlorite, rutile with syn-kinematic albite porphyroblast formed by pervasive shearing during exhumation. These types of micaschists are tourmaline-bearing and their retrograde nature suggests high-fluid flux along shear zones. Peak metamorphic mineral assemblages are partly preserved in the chloritoid-micaschist farther away from the shear zone representing the zero strain domains during exhumation. Three peak metamorphic assemblages are identified and their PT conditions are constrained by pseudosections produced by Theriak-Domino and by Raman spectra of carbonaceous material: 1) garnet-chloritoid-glaucophane with lawsonite pseudomorphs (P= 17.5 ± 1 kbar, T: 390-450 °C) 2) chloritoid with glaucophane pseudomorphs (P= 16-18 kbar, T: 475 ± 40 °C) and 3) relatively high-Mg chloritoid (17\%) with jadeite pseudomorphs (P= 22-25 kbar; T: 440 ± 30 °C) in addition to phengite, paragonite, quartz, chlorite, rutile and apatite. The last mineral assemblage is interpreted as transformation of the chloritoid + glaucophane assemblage to chloritoid + jadeite paragenesis with increasing pressure. Absence of tourmaline suggests that the chloritoid-micaschist did not interact with B-rich fluids during zero strain exhumation. 40Ar/39Ar phengite age of a pervasively sheared footwall micaschist is constrained to 100.6 ± 1.3 Ma and that of a chloritoid-micaschist is constrained to 91.8 ± 1.8 Ma suggesting exhumation during on-going subduction with a southward younging of the basal accretion and the regional metamorphism. To the south, accretionary wedge consists of blueschist and greenschist facies metabasite, marble and volcanogenic metasediment intercalation. 40Ar/39Ar phengite dating reveals that this part of the wedge is of Middle Jurassic age partly overprinted during the Albian. Emplacement of the Middle Jurassic subduction-accretion complexes is possibly associated with obliquity of the Albian convergence. Peak metamorphic assemblages and PT estimates of the deep-seated oceanic metamorphic sequence suggest tectonic stacking within wedge with different depths of burial. Coupling and exhumation of the distinct metamorphic slices are controlled by decompression of the wedge possibly along a retreating slab. Structurally, decompression of the wedge is evident by an extensional shear zone and the footwall micaschists with syn-kinematic albite porphyroblasts. Post-kinematic garnets with increasing grossular content and pseudomorphing minerals within the chloritoid-micaschists also support decompression model without an extra heating. Thickening of subduction-accretionary complexes is attributed to i) significant amount of clastic sediment supply from the overriding continental domain and ii) deep level basal underplating by propagation of the d{\´e}collement along a retreating slab. Underplating by basal d{\´e}collement propagation and subsequent exhumation of the deep-seated subduction-accretion complexes are connected and controlled by slab rollback creating a necessary space for progressive basal accretion along the plate interface and extension of the wedge above for exhumation of the tectonically thickened metamorphic sequences. This might be the most common mechanism of the tectonic thickening and subsequent exhumation of deep-seated HP/LT subduction-accretion complexes. To the south, the Albian-Turonian accretionary wedge structurally overlies a low-grade volcanic arc sequence consisting of low-grade metavolcanic rocks and overlying metasedimentary succession is exposed north of the İzmir-Ankara-Erzincan suture (İAES), separating Laurasia from Gondwana-derived terranes. The metavolcanic rocks mainly consist of basaltic andesite/andesite and mafic cognate xenolith-bearing rhyolite with their pyroclastic equivalents, which are interbedded with recrystallized pelagic limestone and chert. The metavolcanic rocks are stratigraphically overlain by recrystallized micritic limestone with rare volcanogenic metaclastic rocks. Two groups can be identified based on trace and rare earth element characteristics. The first group consists of basaltic andesite/andesite (BA1) and rhyolite with abundant cognate gabbroic xenoliths. It is characterized by relative enrichment of LREE with respect to HREE. The rocks are enriched in fluid mobile LILE, and strongly depleted in Ti and P reflecting fractionation of Fe-Ti oxides and apatite, which are found in the mafic cognate xenoliths. Abundant cognate gabbroic xenoliths and identical trace and rare earth elements compositions suggest that rhyolites and basaltic andesites/andesites (BA1) are cogenetic and felsic rocks were derived from a common mafic parental magma by fractional crystallization and accumulation processes. The second group consists only of basaltic andesites (BA2) with flat REE pattern resembling island arc tholeiites. Although enriched in LILE, this group is not depleted in Ti or P. Geochemistry of the metavolcanic rocks indicates supra-subduction volcanism evidenced by depletion of HFSE and enrichment of LILE. The arc sequence is sandwiched between an Albian-Turonian subduction-accretionary complex representing the Laurasian active margin and an ophiolitic m{\´e}lange. Absence of continent derived detritus in the arc sequence and its tectonic setting in a wide Cretaceous accretionary complex suggest that the K{\"o}sdağ Arc was intra-oceanic. This is in accordance with basaltic andesites (BA2) with island arc tholeiite REE pattern. Zircons from two metarhyolite samples give Late Cretaceous (93.8 ± 1.9 and 94.4 ± 1.9 Ma) U/Pb ages. Low-grade regional metamorphism of the intra-oceanic arc sequence is constrained 69.9 ± 0.4 Ma by 40Ar/39Ar dating on metamorphic muscovite from a metarhyolite indicating that the arc sequence became part of a wide Tethyan Cretaceous accretionary complex by the latest Cretaceous. The youngest 40Ar/39Ar phengite age from the overlying subduction-accretion complexes is 92 Ma confirming southward younging of an accretionary-type orogenic belt. Hence, the arc sequence represents an intra-oceanic paleo-arc that formed above the sinking Tethyan slab and finally accreted to Laurasian active continental margin. Abrupt non-collisional termination of arc volcanism was possibly associated with southward migration of the arc volcanism similar to the Izu-Bonin-Mariana arc system. The intra-oceanic K{\"o}sdağ Arc is coeval with the obducted supra-subduction ophiolites in NW Turkey suggesting that it represents part of the presumed but missing incipient intra-oceanic arc associated with the generation of the regional supra-subduction ophiolites. Remnants of a Late Cretaceous intra-oceanic paleo-arc and supra-subduction ophiolites can be traced eastward within the Alp-Himalayan orogenic belt. This reveals that Late Cretaceous intra-oceanic subduction occurred as connected event above the sinking Tethyan slab. It resulted as arc accretion to Laurasian active margin and supra-subduction ophiolite obduction on Gondwana-derived terranes.},
  language  = {en}
}
@phdthesis{AyBryson2021,
  author    = {Ay-Bryson, Destina Sevde},
  title     = {The authenticity of simulated patients in psychotherapy training and research},
  doi       = {10.25932/publishup-53373},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-533735},
  school      = {Universit{\"a}t Potsdam},
  year      = {2021},
  abstract  = {Mental health problems are highly prevalent worldwide. Fortunately, psychotherapy has proven highly effective in the treatment of a number of mental health issues, such as depression and anxiety disorders. In contrast, psychotherapy training as is practised currently cannot be considered evidence-based. Thus, there is much room for improvement. The integration of simulated patients (SPs) into psychotherapy training and research is on the rise. SPs originate from the medical education and have, in a number of studies, been demonstrated to contribute to effective learning environments. Nevertheless, there has been voiced criticism regarding the authenticity of SP portrayals, but few studies have examined this to date. Based on these considerations, this dissertation explores SPs' authenticity while portraying a mental disorder, depression. Altogether, the present cumulative dissertation consists of three empirical papers. At the time of printing, Paper I and Paper III have been accepted for publication, and Paper II is under review after a minor revision. First, Paper I develops and validates an observer-based rating-scale to assess SP authenticity in psychotherapeutic contexts. Based on the preliminary findings, it can be concluded that the Authenticity of Patient Demonstrations scale is a reliable and valid tool that can be used for recruiting, training, and evaluating the authenticity of SPs. Second, Paper II tests whether student SPs are perceived as more authentic after they receive an in-depth role-script compared to those SPs who only receive basic information on the patient case. To test this assumption, a randomised controlled study design was implemented and the hypothesis could be confirmed. As a consequence, when engaging SPs, an in-depth role-script with details, e.g. on nonverbal behaviour and feelings of the patient, should be provided. Third, Paper III demonstrates that psychotherapy trainees cannot distinguish between trained SPs and real patients and therefore suggests that, with proper training, SPs are a promising training method for psychotherapy. Altogether, the dissertation shows that SPs can be trained to portray a depressive patient authentically and thus delivers promising evidence for the further dissemination of SPs.},
  language  = {en}
}
@phdthesis{Axtner2012,
  author    = {Axtner, Jan},
  title     = {Immune gene expression and diversity in relation to gastrointestinal parasite burden in small mammals},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-65639},
  school      = {Universit{\"a}t Potsdam},
  year      = {2012},
  abstract  = {MHC genes encode proteins that are responsible for the recognition of foreign antigens and the triggering of a subsequent, adequate immune response of the organism. Thus they hold a key position in the immune system of vertebrates. It is believed that the extraordinary genetic diversity of MHC genes is shaped by adaptive selectional processes in response to the reoccurring adaptations of parasites and pathogens. A large number of MHC studies were performed in a wide range of wildlife species aiming to understand the role of immune gene diversity in parasite resistance under natural selection conditions. Methodically, most of this work with very few exceptions has focussed only upon the structural, i.e. sequence diversity of regions responsible for antigen binding and presentation. Most of these studies found evidence that MHC gene variation did indeed underlie adaptive processes and that an individual's allelic diversity explains parasite and pathogen resistance to a large extent. Nevertheless, our understanding of the effective mechanisms is incomplete. A neglected, but potentially highly relevant component concerns the transcriptional differences of MHC alleles. Indeed, differences in the expression levels MHC alleles and their potential functional importance have remained unstudied. The idea that also transcriptional differences might play an important role relies on the fact that lower MHC gene expression is tantamount with reduced induction of CD4+ T helper cells and thus with a reduced immune response. Hence, I studied the expression of MHC genes and of immune regulative cytokines as additional factors to reveal the functional importance of MHC diversity in two free-ranging rodent species (Delomys sublineatus, Apodemus flavicollis) in association with their gastrointestinal helminths under natural selection conditions. I established the method of relative quantification of mRNA on liver and spleen samples of both species in our laboratory. As there was no available information on nucleic sequences of potential reference genes in both species, PCR primer systems that were established in laboratory mice have to be tested and adapted for both non-model organisms. In the due course, sets of stable reference genes for both species were found and thus the preconditions for reliable measurements of mRNA levels established. For D. sublineatus it could be demonstrated that helminth infection elicits aspects of a typical Th2 immune response. Whereas mRNA levels of the cytokine interleukin Il4 increased with infection intensity by strongyle nematodes neither MHC nor cytokine expression played a significant role in D. sublineatus. For A. flavicollis I found a negative association between the parasitic nematode Heligmosomoides polygyrus and hepatic MHC mRNA levels. As a lower MHC expression entails a lower immune response, this could be evidence for an immune evasive strategy of the nematode, as it has been suggested for many micro-parasites. This implies that H. polygyrus is capable to interfere actively with the MHC transcription. Indeed, this parasite species has long been suspected to be immunosuppressive, e.g. by induction of regulatory T-helper cells that respond with a higher interleukin Il10 and tumor necrosis factor Tgfb production. Both cytokines in turn cause an abated MHC expression. By disabling recognition by the MHC molecule H. polygyrus might be able to prevent an activation of the immune system. Indeed, I found a strong tendency in animals carrying the allele Apfl-DRB*23 to have an increased infection intensity with H. polygyrus. Furthermore, I found positive and negative associations between specific MHC alleles and other helminth species, as well as typical signs of positive selection acting on the nucleic sequences of the MHC. The latter was evident by an elevated rate of non-synonymous to synonymous substitutions in the MHC sequences of exon 2 encoding the functionally important antigen binding sites whereas the first and third exons of the MHC DRB gene were highly conserved. In conclusion, the studies in this thesis demonstrate that valid procedures to quantify expression of immune relevant genes are also feasible in non-model wildlife organisms. In addition to structural MHC diversity, also MHC gene expression should be considered to obtain a more complete picture on host-pathogen coevolutionary selection processes. This is especially true if parasites are able to interfere with systemic MHC expression. In this case advantageous or disadvantageous effects of allelic binding motifs are abated. The studies could not define the role of MHC gene expression in antagonistic coevolution as such but the results suggest that it depends strongly on the specific parasite species that is involved.},
  language  = {en}
}
@phdthesis{Awad2010,
  author    = {Awad, Ahmed Mahmoud Hany Aly},
  title     = {A compliance management framework for business process models},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-49222},
  school      = {Universit{\"a}t Potsdam},
  year      = {2010},
  abstract  = {Companies develop process models to explicitly describe their business operations. In the same time, business operations, business processes, must adhere to various types of compliance requirements. Regulations, e.g., Sarbanes Oxley Act of 2002, internal policies, best practices are just a few sources of compliance requirements. In some cases, non-adherence to compliance requirements makes the organization subject to legal punishment. In other cases, non-adherence to compliance leads to loss of competitive advantage and thus loss of market share. Unlike the classical domain-independent behavioral correctness of business processes, compliance requirements are domain-specific. Moreover, compliance requirements change over time. New requirements might appear due to change in laws and adoption of new policies. Compliance requirements are offered or enforced by different entities that have different objectives behind these requirements. Finally, compliance requirements might affect different aspects of business processes, e.g., control flow and data flow. As a result, it is infeasible to hard-code compliance checks in tools. Rather, a repeatable process of modeling compliance rules and checking them against business processes automatically is needed. This thesis provides a formal approach to support process design-time compliance checking. Using visual patterns, it is possible to model compliance requirements concerning control flow, data flow and conditional flow rules. Each pattern is mapped into a temporal logic formula. The thesis addresses the problem of consistency checking among various compliance requirements, as they might stem from divergent sources. Also, the thesis contributes to automatically check compliance requirements against process models using model checking. We show that extra domain knowledge, other than expressed in compliance rules, is needed to reach correct decisions. In case of violations, we are able to provide a useful feedback to the user. The feedback is in the form of parts of the process model whose execution causes the violation. In some cases, our approach is capable of providing automated remedy of the violation.},
  language  = {en}
}
@phdthesis{Avila2011,
  author    = {Avila, Gast{\´o}n},
  title     = {Asymptotic staticity and tensor decompositions with fast decay conditions},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-54046},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Corvino, Corvino and Schoen, Chruściel and Delay have shown the existence of a large class of asymptotically flat vacuum initial data for Einstein's field equations which are static or stationary in a neighborhood of space-like infinity, yet quite general in the interior. The proof relies on some abstract, non-constructive arguments which makes it difficult to calculate such data numerically by using similar arguments. A quasilinear elliptic system of equations is presented of which we expect that it can be used to construct vacuum initial data which are asymptotically flat, time-reflection symmetric, and asymptotic to static data up to a prescribed order at space-like infinity. A perturbation argument is used to show the existence of solutions. It is valid when the order at which the solutions approach staticity is restricted to a certain range. Difficulties appear when trying to improve this result to show the existence of solutions that are asymptotically static at higher order. The problems arise from the lack of surjectivity of a certain operator. Some tensor decompositions in asymptotically flat manifolds exhibit some of the difficulties encountered above. The Helmholtz decomposition, which plays a role in the preparation of initial data for the Maxwell equations, is discussed as a model problem. A method to circumvent the difficulties that arise when fast decay rates are required is discussed. This is done in a way that opens the possibility to perform numerical computations. The insights from the analysis of the Helmholtz decomposition are applied to the York decomposition, which is related to that part of the quasilinear system which gives rise to the difficulties. For this decomposition analogous results are obtained. It turns out, however, that in this case the presence of symmetries of the underlying metric leads to certain complications. The question, whether the results obtained so far can be used again to show by a perturbation argument the existence of vacuum initial data which approach static solutions at infinity at any given order, thus remains open. The answer requires further analysis and perhaps new methods.},
  language  = {en}
}
@phdthesis{Aue2024,
  author    = {Aue, Lars},
  title     = {Cyclone impacts on sea ice in the Atlantic Arctic Ocean},
  doi       = {10.25932/publishup-63445},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-634458},
  school      = {Universit{\"a}t Potsdam},
  pages     = {VIII, 131},
  year      = {2024},
  abstract  = {The Arctic is the hot spot of the ongoing, global climate change. Over the last decades, near-surface temperatures in the Arctic have been rising almost four times faster than on global average. This amplified warming of the Arctic and the associated rapid changes of its environment are largely influenced by interactions between individual components of the Arctic climate system. On daily to weekly time scales, storms can have major impacts on the Arctic sea-ice cover and are thus an important part of these interactions within the Arctic climate. The sea-ice impacts of storms are related to high wind speeds, which enhance the drift and deformation of sea ice, as well as to changes in the surface energy budget in association with air mass advection, which impact the seasonal sea-ice growth and melt. The occurrence of storms in the Arctic is typically associated with the passage of transient cyclones. Even though the above described mechanisms how storms/cyclones impact the Arctic sea ice are in principal known, there is a lack of statistical quantification of these effects. In accordance with that, the overarching objective of this thesis is to statistically quantify cyclone impacts on sea-ice concentration (SIC) in the Atlantic Arctic Ocean over the last four decades. In order to further advance the understanding of the related mechanisms, an additional objective is to separate dynamic and thermodynamic cyclone impacts on sea ice and assess their relative importance. Finally, this thesis aims to quantify recent changes in cyclone impacts on SIC. These research objectives are tackled utilizing various data sets, including atmospheric and oceanic reanalysis data as well as a coupled model simulation and a cyclone tracking algorithm. Results from this thesis demonstrate that cyclones are significantly impacting SIC in the Atlantic Arctic Ocean from autumn to spring, while there are mostly no significant impacts in summer. The strength and the sign (SIC decreasing or SIC increasing) of the cyclone impacts strongly depends on the considered daily time scale and the region of the Atlantic Arctic Ocean. Specifically, an initial decrease in SIC (day -3 to day 0 relative to the cyclone) is found in the Greenland, Barents and Kara Seas, while SIC increases following cyclones (day 0 to day 5 relative to the cyclone) are mostly limited to the Barents and Kara Seas. For the cold season, this results in a pronounced regional difference between overall (day -3 to day 5 relative to the cyclone) SIC-decreasing cyclone impacts in the Greenland Sea and overall SIC-increasing cyclone impacts in the Barents and Kara Seas. A cyclone case study based on a coupled model simulation indicates that both dynamic and thermodynamic mechanisms contribute to cyclone impacts on sea ice in winter. A typical pattern consisting of an initial dominance of dynamic sea-ice changes followed by enhanced thermodynamic ice growth after the cyclone passage was found. This enhanced ice growth after the cyclone passage most likely also explains the (statistical) overall SIC-increasing effects of cyclones in the Barents and Kara Seas in the cold season. Significant changes in cyclone impacts on SIC over the last four decades have emerged throughout the year. These recent changes are strongly varying from region to region and month to month. The strongest trends in cyclone impacts on SIC are found in autumn in the Barents and Kara Seas. Here, the magnitude of destructive cyclone impacts on SIC has approximately doubled over the last four decades. The SIC-increasing effects following the cyclone passage have particularly weakened in the Barents Sea in autumn. As a consequence, previously existing overall SIC-increasing cyclone impacts in this region in autumn have recently disappeared. Generally, results from this thesis show that changes in the state of the sea-ice cover (decrease in mean sea-ice concentration and thickness) and near-surface air temperature are most important for changed cyclone impacts on SIC, while changes in cyclone properties (i.e. intensity) do not play a significant role.},
  language  = {en}
}
@phdthesis{Atasoy2022,
  author    = {Atasoy, Atilla},
  title     = {Production, perception, and processing of focus in Turkish},
  doi       = {10.25932/publishup-54815},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-548156},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xxiii, 267},
  year      = {2022},
  abstract  = {The main goal of this dissertation is to experimentally investigate how focus is realised, perceived, and processed by native Turkish speakers, independent of preconceived notions of positional restrictions. Crucially, there are various issues and scientific debates surrounding focus in the Turkish language in the existing literature (chapter 1). It is argued in this dissertation that two factors led to the stagnant literature on focus in Turkish: the lack of clearly defined, modern understandings of information structure and its fundamental notion of focus, and the ongoing and ill-defined debate surrounding the question of whether there is an immediately preverbal focus position in Turkish. These issues gave rise to specific research questions addressed across this dissertation. Specifically, we were interested in how the focus dimensions such as focus size (comparing narrow constituent and broad sentence focus), focus target (comparing narrow subject and narrow object focus), and focus type (comparing new-information and contrastive focus) affect Turkish focus realisation and, in turn, focus comprehension when speakers are provided syntactic freedom to position focus as they see fit. To provide data on these core goals, we presented three behavioural experiments based on a systematic framework of information structure and its notions (chapter 2): (i) a production task with trigger wh-questions and contextual animations manipulated to elicit the focus dimensions of interest (chapter 3), (ii) a timed acceptability judgment task in listening to the recorded answers in our production task (chapter 4), and (iii) a self-paced reading task to gather on-line processing data (chapter 5). Based on the results of the conducted experiments, multiple conclusions are made in this dissertation (chapter 6). Firstly, this dissertation demonstrated empirically that there is no focus position in Turkish, neither in the sense of a strict focus position language nor as a focally loaded position facilitating focus perception and/or processing. While focus is, in fact, syntactically variable in the Turkish preverbal area, this is a consequence of movement triggered by other IS aspects like topicalisation and backgrounding, and the observational markedness of narrow subject focus compared to narrow object focus. As for focus type in Turkish, this dimension is not associated with word order in production, perception, or processing. Significant acoustic correlates of focus size (broad sentence focus vs narrow constituent focus) and focus target (narrow subject focus vs narrow object focus) were observed in fundamental frequency and intensity, representing focal boost, (postfocal) deaccentuation, and the presence or absence of a phrase-final rise in the prenucleus, while the perceivability of these effects remains to be investigated. In contrast, no acoustic correlates of focus type in simple, three-word transitive structures were observed, with focus types being interchangeable in mismatched question-answer pairs. Overall, the findings of this dissertation highlight the need for experimental investigations regarding focus in Turkish, as theoretical predictions do not necessarily align with experimental data. As such, the fallacy of implying causation from correlation should be strictly kept in mind, especially when constructions coincide with canonical structures, such as the immediately preverbal position in narrow object foci. Finally, numerous open questions remain to be explored, especially as focus and word order in Turkish are multifaceted. As shown, givenness is a confounding factor when investigating focus types, while thematic role assignment potentially confounds word order preferences. Further research based on established, modern information structure frameworks is needed, with chapter 5 concluding with specific recommendations for such future research.},
  language  = {en}
}
@phdthesis{Ata2016,
  author    = {Ata, Metin},
  title     = {Phase-space reconstructions of cosmic velocities and the cosmic web},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-403565},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xi, 155},
  year      = {2016},
  abstract  = {In the current paradigm of cosmology, the formation of large-scale structures is mainly driven by non-radiating dark matter, making up the dominant part of the matter budget of the Universe. Cosmological observations however, rely on the detection of luminous galaxies, which are biased tracers of the underlying dark matter. In this thesis I present cosmological reconstructions of both, the dark matter density field that forms the cosmic web, and cosmic velocities, for which both aspects of my work are delved into, the theoretical formalism and the results of its applications to cosmological simulations and also to a galaxy redshift survey.The foundation of our method is relying on a statistical approach, in which a given galaxy catalogue is interpreted as a biased realization of the underlying dark matter density field. The inference is computationally performed on a mesh grid by sampling from a probability density function, which describes the joint posterior distribution of matter density and the three dimensional velocity field. The statistical background of our method is described in Chapter "Implementation of argo", where the introduction in sampling methods is given, paying special attention to Markov Chain Monte-Carlo techniques. In Chapter "Phase-Space Reconstructions with N-body Simulations", I introduce and implement a novel biasing scheme to relate the galaxy number density to the underlying dark matter, which I decompose into a deterministic part, described by a non-linear and scale-dependent analytic expression, and a stochastic part, by presenting a negative binomial (NB) likelihood function that models deviations from Poissonity. Both bias components had already been studied theoretically, but were so far never tested in a reconstruction algorithm. I test these new contributions againstN-body simulations to quantify improvements and show that, compared to state-of-the-art methods, the stochastic bias is inevitable at wave numbers of k≥0.15h Mpc^-1 in the power spectrum in order to obtain unbiased results from the reconstructions. In the second part of Chapter "Phase-Space Reconstructions with N-body Simulations" I describe and validate our approach to infer the three dimensional cosmic velocity field jointly with the dark matter density. I use linear perturbation theory for the large-scale bulk flows and a dispersion term to model virialized galaxy motions, showing that our method is accurately recovering the real-space positions of the redshift-space distorted galaxies. I analyze the results with the isotropic and also the two-dimensional power spectrum.Finally, in Chapter "Phase-space Reconstructions with Galaxy Redshift Surveys", I show how I combine all findings and results and apply the method to the CMASS (for Constant (stellar) Mass) galaxy catalogue of the Baryon Oscillation Spectroscopic Survey (BOSS). I describe how our method is accounting for the observational selection effects inside our reconstruction algorithm. Also, I demonstrate that the renormalization of the prior distribution function is mandatory to account for higher order contributions in the structure formation model, and finally a redshift-dependent bias factor is theoretically motivated and implemented into our method. The various refinements yield unbiased results of the dark matter until scales of k≤0.2 h Mpc^-1in the power spectrum and isotropize the galaxy catalogue down to distances of r∼20h^-1 Mpc in the correlation function. We further test the results of our cosmic velocity field reconstruction by comparing them to a synthetic mock galaxy catalogue, finding a strong correlation between the mock and the reconstructed velocities. The applications of both, the density field without redshift-space distortions, and the velocity reconstructions, are very broad and can be used for improved analyses of the baryonic acoustic oscillations, environmental studies of the cosmic web, the kinematic Sunyaev-Zel'dovic or integrated Sachs-Wolfe effect.},
  language  = {en}
}
@phdthesis{Aseev2020,
  author    = {Aseev, Nikita},
  title     = {Modeling and understanding dynamics of charged particles in the Earth's inner magnetosphere},
  doi       = {10.25932/publishup-47921},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-479211},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xxii, 154},
  year      = {2020},
  abstract  = {The Earth's inner magnetosphere is a very dynamic system, mostly driven by the external solar wind forcing exerted upon the magnetic field of our planet. Disturbances in the solar wind, such as coronal mass ejections and co-rotating interaction regions, cause geomagnetic storms, which lead to prominent changes in charged particle populations of the inner magnetosphere - the plasmasphere, ring current, and radiation belts. Satellites operating in the regions of elevated energetic and relativistic electron fluxes can be damaged by deep dielectric or surface charging during severe space weather events. Predicting the dynamics of the charged particles and mitigating their effects on the infrastructure is of particular importance, due to our increasing reliance on space technologies. The dynamics of particles in the plasmasphere, ring current, and radiation belts are strongly coupled by means of collisions and collisionless interactions with electromagnetic fields induced by the motion of charged particles. Multidimensional numerical models simplify the treatment of transport, acceleration, and loss processes of these particles, and allow us to predict how the near-Earth space environment responds to solar storms. The models inevitably rely on a number of simplifications and assumptions that affect model accuracy and complicate the interpretation of the results. In this dissertation, we quantify the processes that control electron dynamics in the inner magnetosphere, paying particular attention to the uncertainties of the employed numerical codes and tools. We use a set of convenient analytical solutions for advection and diffusion equations to test the accuracy and stability of the four-dimensional Versatile Electron Radiation Belt (VERB-4D) code. We show that numerical schemes implemented in the code converge to the analytical solutions and that the VERB-4D code demonstrates stable behavior independent of the assumed time step. The order of the numerical scheme for the convection equation is demonstrated to affect results of ring current and radiation belt simulations, and it is crucially important to use high-order numerical schemes to decrease numerical errors in the model. Using the thoroughly tested VERB-4D code, we model the dynamics of the ring current electrons during the 17 March 2013 storm. The discrepancies between the model and observations above 4.5 Earth's radii can be explained by uncertainties in the outer boundary conditions. Simulation results indicate that the electrons were transported from the geostationary orbit towards the Earth by the global-scale electric and magnetic fields. We investigate how simulation results depend on the input models and parameters. The model is shown to be particularly sensitive to the global electric field and electron lifetimes below 4.5 Earth's radii. The effects of radial diffusion and subauroral polarization streams are also quantified. We developed a data-assimilative code that blends together a convection model of energetic electron transport and loss and Van Allen Probes satellite data by means of the Kalman filter. We show that the Kalman filter can correct model uncertainties in the convection electric field, electron lifetimes, and boundary conditions. It is also demonstrated how the innovation vector - the difference between observations and model prediction - can be used to identify physical processes missing in the model of energetic electron dynamics. We computed radial profiles of phase space density of ultrarelativistic electrons, using Van Allen Probes measurements. We analyze the shape of the profiles during geomagnetically quiet and disturbed times and show that the formation of new local minimums in the radial profiles coincides with the ground observations of electromagnetic ion-cyclotron (EMIC) waves. This correlation indicates that EMIC waves are responsible for the loss of ultrarelativistic electrons from the heart of the outer radiation belt into the Earth's atmosphere.},
  language  = {en}
}