@phdthesis{Pregla2024, author = {Pregla, Andreas}, title = {Word order variability in OV languages}, doi = {10.25932/publishup-64363}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-643636}, school = {Universit{\"a}t Potsdam}, pages = {xv, 265}, year = {2024}, abstract = {This thesis explores word order variability in verb-final languages. Verb-final languages have a reputation for a high amount of word order variability. However, that reputation amounts to an urban myth due to a lack of systematic investigation. This thesis provides such a systematic investigation by presenting original data from several verb-final languages with a focus on four Uralic ones: Estonian, Udmurt, Meadow Mari, and South S{\´a}mi. As with every urban myth, there is a kernel of truth in that many unrelated verb-final languages share a particular kind of word order variability, A-scrambling, in which the fronted elements do not receive a special information-structural role, such as topic or contrastive focus. That word order variability goes hand in hand with placing focussed phrases further to the right in the position directly in front of the verb. Variations on this pattern are exemplified by Uyghur, Standard Dargwa, Eastern Armenian, and three of the Uralic languages, Estonian, Udmurt, and Meadow Mari. So far for the kernel of truth, but the fourth Uralic language, South S{\´a}mi, is comparably rigid and does not feature this particular kind of word order variability. Further such comparably rigid, non-scrambling verb-final languages are Dutch, Afrikaans, Amharic, and Korean. In contrast to scrambling languages, non-scrambling languages feature obligatory subject movement, causing word order rigidity next to other typical EPP effects. The EPP is a defining feature of South S{\´a}mi clause structure in general. South S{\´a}mi exhibits a one-of-a-kind alternation between SOV and SAuxOV order that is captured by the assumption of the EPP and obligatory movement of auxiliaries but not lexical verbs. Other languages that allow for SAuxOV order either lack an alternation because the auxiliary is obligatorily present (Macro-Sudan SAuxOVX languages), or feature an alternation between SVO and SAuxOV (Kru languages; V2 with underlying OV as a fringe case). In the SVO-SAuxOV languages, both auxiliaries and lexical verbs move. Hence, South S{\´a}mi shows that the textbook difference between the VO languages English and French, whether verb movement is restricted to auxiliaries, also extends to OV languages. SAuxOV languages are an outlier among OV languages in general but are united by the presence of the EPP. Word order variability is not restricted to the preverbal field in verb-final languages, as most of them feature postverbal elements (PVE). PVE challenge the notion of verb-finality in a language. Strictly verb-final languages without any clause-internal PVE are rare. This thesis charts the first structural and descriptive typology of PVE. Verb-final languages vary in the categories they allow as PVE. Allowing for non-oblique PVE is a pivotal threshold: when non-oblique PVE are allowed, PVE can be used for information-structural effects. Many areally and genetically unrelated languages only allow for given PVE but differ in whether the PVE are contrastive. In those languages, verb-finality is not at stake since verb-medial orders are marked. In contrast, the Uralic languages Estonian and Udmurt allow for any PVE, including information focus. Verb-medial orders can be used in the same contexts as verb-final orders without semantic and pragmatic differences. As such, verb placement is subject to actual free variation. The underlying verb-finality of Estonian and Udmurt can only be inferred from a range of diagnostics indicating optional verb movement in both languages. In general, it is not possible to account for PVE with a uniform analysis: rightwards merge, leftward verb movement, and rightwards phrasal movement are required to capture the cross- and intralinguistic variation. Knowing that a language is verb-final does not allow one to draw conclusions about word order variability in that language. There are patterns of homogeneity, such as the word order variability driven by directly preverbal focus and the givenness of postverbal elements, but those are not brought about by verb-finality alone. Preverbal word order variability is restricted by the more abstract property of obligatory subject movement, whereas the determinant of postverbal word order variability has to be determined in the future.}, language = {en} } @phdthesis{Haskamp2024, author = {Haskamp, Thomas}, title = {Products design organizations}, doi = {10.25932/publishup-64695}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-646954}, school = {Universit{\"a}t Potsdam}, pages = {IX, 148}, year = {2024}, abstract = {The automotive industry is a prime example of digital technologies reshaping mobility. Connected, autonomous, shared, and electric (CASE) trends lead to new emerging players that threaten existing industrial-aged companies. To respond, incumbents need to bridge the gap between contrasting product architecture and organizational principles in the physical and digital realms. Over-the-air (OTA) technology, that enables seamless software updates and on-demand feature additions for customers, is an example of CASE-driven digital product innovation. Through an extensive longitudinal case study of an OTA initiative by an industrial- aged automaker, this dissertation explores how incumbents accomplish digital product innovation. Building on modularity, liminality, and the mirroring hypothesis, it presents a process model that explains the triggers, mechanisms, and outcomes of this process. In contrast to the literature, the findings emphasize the primacy of addressing product architecture challenges over organizational ones and highlight the managerial implications for success.}, language = {en} } @phdthesis{Wojcik2024, author = {Wojcik, Laurie Anne Myriam}, title = {Beyond a single diversity facet: implications for the links between biodiversity, environmental changes and ecosystem functioning}, doi = {10.25932/publishup-64692}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-646925}, school = {Universit{\"a}t Potsdam}, pages = {vi, 189}, year = {2024}, abstract = {Human activities modify nature worldwide via changes in the environment, biodiversity and the functioning of ecosystems, which in turn disrupt ecosystem services and feed back negatively on humans. A pressing challenge is thus to limit our impact on nature, and this requires detailed understanding of the interconnections between the environment, biodiversity and ecosystem functioning. These three components of ecosystems each include multiple dimensions, which interact with each other in different ways, but we lack a comprehensive picture of their interconnections and underlying mechanisms. Notably, diversity is often viewed as a single facet, namely species diversity, while many more facets exist at different levels of biological organisation (e.g. genetic, phenotypic, functional, multitrophic diversity), and multiple diversity facets together constitute the raw material for adaptation to environmental changes and shape ecosystem functioning. Consequently, investigating the multidimensionality of ecosystems, and in particular the links between multifaceted diversity, environmental changes and ecosystem functions, is crucial for ecological research, management and conservation. This thesis aims to explore several aspects of this question theoretically. I investigate three broad topics in this thesis. First, I focus on how food webs with varying levels of functional diversity across three trophic levels buffer environmental changes, such as a sudden addition of nutrients or long-term changes (e.g. warming or eutrophication). I observed that functional diversity generally enhanced ecological stability (i.e. the buffering capacity of the food web) by increasing trophic coupling. More precisely, two aspects of ecological stability (resistance and resilience) increased even though a third aspect (the inverse of the time required for the system to reach its post-perturbation state) decreased with increasing functional diversity. Second, I explore how several diversity facets served as a raw material for different sources of adaptation and how these sources affected multiple ecosystem functions across two trophic levels. Considering several sources of adaptation enabled the interplay between ecological and evolutionary processes, which affected trophic coupling and thereby ecosystem functioning. Third, I reflect further on the multifaceted nature of diversity by developing an index K able to quantify the facet of functional diversity, which is itself multifaceted. K can provide a comprehensive picture of functional diversity and is a rather good predictor of ecosystem functioning. Finally I synthesise the interdependent mechanisms (complementarity and selection effects, trophic coupling and adaptation) underlying the relationships between multifaceted diversity, ecosystem functioning and the environment, and discuss the generalisation of my findings across ecosystems and further perspectives towards elaborating an operational biodiversity-ecosystem functioning framework for research and conservation.}, language = {en} } @phdthesis{Lagodzinski2024, author = {Lagodzinski, Julius Albert Gregor}, title = {Counting homomorphisms over fields of prime order}, doi = {10.25932/publishup-64603}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-646037}, school = {Universit{\"a}t Potsdam}, pages = {xii, 240}, year = {2024}, abstract = {Homomorphisms are a fundamental concept in mathematics expressing the similarity of structures. They provide a framework that captures many of the central problems of computer science with close ties to various other fields of science. Thus, many studies over the last four decades have been devoted to the algorithmic complexity of homomorphism problems. Despite their generality, it has been found that non-uniform homomorphism problems, where the target structure is fixed, frequently feature complexity dichotomies. Exploring the limits of these dichotomies represents the common goal of this line of research. We investigate the problem of counting homomorphisms to a fixed structure over a finite field of prime order and its algorithmic complexity. Our emphasis is on graph homomorphisms and the resulting problem \#_{p}Hom[H] for a graph H and a prime p. The main research question is how counting over a finite field of prime order affects the complexity. In the first part of this thesis, we tackle the research question in its generality and develop a framework for studying the complexity of counting problems based on category theory. In the absence of problem-specific details, results in the language of category theory provide a clear picture of the properties needed and highlight common ground between different branches of science. The proposed problem \#Mor^{C}[B] of counting the number of morphisms to a fixed object B of C is abstract in nature and encompasses important problems like constraint satisfaction problems, which serve as a leading example for all our results. We find explanations and generalizations for a plethora of results in counting complexity. Our main technical result is that specific matrices of morphism counts are non-singular. The strength of this result lies in its algebraic nature. First, our proofs rely on carefully constructed systems of linear equations, which we know to be uniquely solvable. Second, by exchanging the field that the matrix is defined by to a finite field of order p, we obtain analogous results for modular counting. For the latter, cancellations are implied by automorphisms of order p, but intriguingly we find that these present the only obstacle to translating our results from exact counting to modular counting. If we restrict our attention to reduced objects without automorphisms of order p, we obtain results analogue to those for exact counting. This is underscored by a confluent reduction that allows this restriction by constructing a reduced object for any given object. We emphasize the strength of the categorial perspective by applying the duality principle, which yields immediate consequences for the dual problem of counting the number of morphisms from a fixed object. In the second part of this thesis, we focus on graphs and the problem \#_{p}Hom[H]. We conjecture that automorphisms of order p capture all possible cancellations and that, for a reduced graph H, the problem \#_{p}Hom[H] features the complexity dichotomy analogue to the one given for exact counting by Dyer and Greenhill. This serves as a generalization of the conjecture by Faben and Jerrum for the modulus 2. The criterion for tractability is that H is a collection of complete bipartite and reflexive complete graphs. From the findings of part one, we show that the conjectured dichotomy implies dichotomies for all quantum homomorphism problems, in particular counting vertex surjective homomorphisms and compactions modulo p. Since the tractable cases in the dichotomy are solved by trivial computations, the study of the intractable cases remains. As an initial problem in a series of reductions capable of implying hardness, we employ the problem of counting weighted independent sets in a bipartite graph modulo prime p. A dichotomy for this problem is shown, stating that the trivial cases occurring when a weight is congruent modulo p to 0 are the only tractable cases. We reduce the possible structure of H to the bipartite case by a reduction to the restricted homomorphism problem \#_{p}Hom^{bip}[H] of counting modulo p the number of homomorphisms between bipartite graphs that maintain a given order of bipartition. This reduction does not have an impact on the accessibility of the technical results, thanks to the generality of the findings of part one. In order to prove the conjecture, it suffices to show that for a connected bipartite graph that is not complete, \#_{p}Hom^{bip}[H] is \#_{p}P-hard. Through a rigorous structural study of bipartite graphs, we establish this result for the rich class of bipartite graphs that are (K_{3,3}\{e}, domino)-free. This overcomes in particular the substantial hurdle imposed by squares, which leads us to explore the global structure of H and prove the existence of explicit structures that imply hardness.}, language = {en} } @phdthesis{Felisatti2024, author = {Felisatti, Arianna}, title = {Spatial-numerical associations: From biological foundations to embodied learning to contextual flexibility}, doi = {10.25932/publishup-64179}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-641791}, school = {Universit{\"a}t Potsdam}, pages = {x, 195}, year = {2024}, abstract = {Among the different meanings carried by numerical information, cardinality is fundamental for survival and for the development of basic as well as of higher numerical skills. Importantly, the human brain inherits from evolution a predisposition to map cardinality onto space, as revealed by the presence of spatial-numerical associations (SNAs) in humans and animals. Here, the mapping of cardinal information onto physical space is addressed as a hallmark signature characterizing numerical cognition. According to traditional approaches, cognition is defined as complex forms of internal information processing, taking place in the brain (cognitive processor). On the contrary, embodied cognition approaches define cognition as functionally linked to perception and action, in the continuous interaction between a biological body and its physical and sociocultural environment. Embracing the principles of the embodied cognition perspective, I conducted four novel studies designed to unveil how SNAs originate, develop, and adapt, depending on characteristics of the organism, the context, and their interaction. I structured my doctoral thesis in three levels. At the grounded level (Study 1), I unfold the biological foundations underlying the tendency to map cardinal information across space; at the embodied level (Study 2), I reveal the impact of atypical motor development on the construction of SNAs; at the situated level (Study 3), I document the joint influence of visuospatial attention and task properties on SNAs. Furthermore, I experimentally investigate the presence of associations between physical and numerical distance, another numerical property fundamental for the development of efficient mathematical minds (Study 4). In Study 1, I present the Brain's Asymmetric Frequency Tuning hypothesis that relies on hemispheric asymmetries for processing spatial frequencies, a low-level visual feature that the (in)vertebrate brain extracts from any visual scene to create a coherent percept of the world. Computational analyses of the power spectra of the original stimuli used to document the presence of SNAs in human newborns and animals, support the brain's asymmetric frequency tuning as a theoretical account and as an evolutionarily inherited mechanism scaffolding the universal and innate tendency to represent cardinality across horizontal space. In Study 2, I explore SNAs in children with rare genetic neuromuscular diseases: spinal muscular atrophy (SMA) and Duchenne muscular dystrophy (DMD). SMA children never accomplish independent motoric exploration of their environment; in contrast, DMD children do explore but later lose this ability. The different SNAs reported by the two groups support the critical role of early sensorimotor experiences in the spatial representation of cardinality. In Study 3, I directly compare the effects of overt attentional orientation during explicit and implicit processing of numerical magnitude. First, the different effects of attentional orienting based on the type of assessment support different mechanisms underlying SNAs during explicit and implicit assessment of numerical magnitude. Secondly, the impact of vertical shifts of attention on the processing of numerical distance sheds light on the correspondence between numerical distance and peri-personal distance. In Study 4, I document the presence of different SNAs, driven by numerical magnitude and numerical distance, by employing different response mappings (left vs. right and near vs. distant). In the field of numerical cognition, the four studies included in the present thesis contribute to unveiling how the characteristics of the organism and the environment influence the emergence, the development, and the flexibility of our attitude to represent cardinal information across space, thus supporting the predictions of the embodied cognition approach. Furthermore, they inform a taxonomy of body-centred factors (biological properties of the brain and sensorimotor system) modulating the spatial representation of cardinality throughout the course of life, at the grounded, embodied, and situated levels. If the awareness for different variables influencing SNAs over the course of life is important, it is equally important to consider the organism as a whole in its sensorimotor interaction with the world. Inspired by my doctoral research, here I propose a holistic perspective that considers the role of evolution, embodiment, and environment in the association of cardinal information with directional space. The new perspective advances the current approaches to SNAs, both at the conceptual and at the methodological levels. Unveiling how the mental representation of cardinality emerges, develops, and adapts is necessary to shape efficient mathematical minds and achieve economic productivity, technological progress, and a higher quality of life.}, language = {en} } @phdthesis{Rasche2024, author = {Rasche, Daniel}, title = {Cosmic-ray neutron sensing for the estimation of soil moisture}, doi = {10.25932/publishup-63646}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-636465}, school = {Universit{\"a}t Potsdam}, pages = {xvi, 194}, year = {2024}, abstract = {Water stored in the unsaturated soil as soil moisture is a key component of the hydrological cycle influencing numerous hydrological processes including hydrometeorological extremes. Soil moisture influences flood generation processes and during droughts when precipitation is absent, it provides plant with transpirable water, thereby sustaining plant growth and survival in agriculture and natural ecosystems. Soil moisture stored in deeper soil layers e.g. below 100 cm is of particular importance for providing plant transpirable water during dry periods. Not being directly connected to the atmosphere and located outside soil layers with the highest root densities, water in these layers is less susceptible to be rapidly evaporated and transpired. Instead, it provides longer-term soil water storage increasing the drought tolerance of plants and ecosystems. Given the importance of soil moisture in the context of hydro-meteorological extremes in a warming climate, its monitoring is part of official national adaption strategies to a changing climate. Yet, soil moisture is highly variable in time and space which challenges its monitoring on spatio-temporal scales relevant for flood and drought risk modelling and forecasting. Introduced over a decade ago, Cosmic-Ray Neutron Sensing (CRNS) is a noninvasive geophysical method that allows for the estimation of soil moisture at relevant spatio-temporal scales of several hectares at a high, subdaily temporal resolution. CRNS relies on the detection of secondary neutrons above the soil surface which are produced from high-energy cosmic-ray particles in the atmosphere and the ground. Neutrons in a specific epithermal energy range are sensitive to the amount of hydrogen present in the surroundings of the CRNS neutron detector. Due to same mass as the hydrogen nucleus, neutrons lose kinetic energy upon collision and are subsequently absorbed when reaching low, thermal energies. A higher amount of hydrogen therefore leads to fewer neutrons being detected per unit time. Assuming that the largest amount of hydrogen is stored in most terrestrial ecosystems as soil moisture, changes of soil moisture can be estimated through an inverse relationship with observed neutron intensities. Although important scientific advancements have been made to improve the methodological framework of CRNS, several open challenges remain, of which some are addressed in the scope of this thesis. These include the influence of atmospheric variables such as air pressure and absolute air humidity, as well as, the impact of variations in incoming primary cosmic-ray intensity on observed epithermal and thermal neutron signals and their correction. Recently introduced advanced neutron-to-soil moisture transfer functions are expected to improve CRNS-derived soil moisture estimates, but potential improvements need to be investigated at study sites with differing environmental conditions. Sites with strongly heterogeneous, patchy soil moisture distributions challenge existing transfer functions and further research is required to assess the impact of, and correction of derived soil moisture estimates under heterogeneous site conditions. Despite its capability of measuring representative averages of soil moisture at the field scale, CRNS lacks an integration depth below the first few decimetres of the soil. Given the importance of soil moisture also in deeper soil layers, increasing the observational window of CRNS through modelling approaches or in situ measurements is of high importance for hydrological monitoring applications. By addressing these challenges, this thesis aids to closing knowledge gaps and finding answers to some of the open questions in CRNS research. Influences of different environmental variables are quantified, correction approaches are being tested and developed. Neutron-to-soil moisture transfer functions are evaluated and approaches to reduce effects of heterogeneous soil moisture distributions are presented. Lastly, soil moisture estimates from larger soil depths are derived from CRNS through modified, simple modelling approaches and in situ estimates by using CRNS as a downhole technique. Thereby, this thesis does not only illustrate the potential of new, yet undiscovered applications of CRNS in future but also opens a new field of CRNS research. Consequently, this thesis advances the methodological framework of CRNS for above-ground and downhole applications. Although the necessity of further research in order to fully exploit the potential of CRNS needs to be emphasised, this thesis contributes to current hydrological research and not least to advancing hydrological monitoring approaches being of utmost importance in context of intensifying hydro-meteorological extremes in a changing climate.}, language = {en} } @phdthesis{Dronsella2024, author = {Dronsella, Beau B.}, title = {Overcoming natural biomass limitations in gram-negative bacteria through synthetic carbon fixation}, doi = {10.25932/publishup-64627}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-646273}, school = {Universit{\"a}t Potsdam}, pages = {174}, year = {2024}, abstract = {The carbon demands of an ever-increasing human population and the concomitant rise in net carbon emissions requires CO2 sequestering approaches for production of carbon-containing molecules. Microbial production of carbon-containing products from plant-based sugars could replace current fossil-based production. However, this form of sugar-based microbial production directly competes with human food supply and natural ecosystems. Instead, one-carbon feedstocks derived from CO2 and renewable energy were proposed as an alternative. The one carbon molecule formate is a stable, readily soluble and safe-to-store energetic mediator that can be electrochemically generated from CO2 and (excess off-peak) renewable electricity. Formate-based microbial production could represent a promising approach for a circular carbon economy. However, easy-to-engineer and efficient formate-utilizing microbes are lacking. Multiple synthetic metabolic pathways were designed for better-than-nature carbon fixation. Among them, the reductive glycine pathway was proposed as the most efficient pathway for aerobic formate assimilation. While some of these pathways have been successfully engineered in microbial hosts, these synthetic strains did so far not exceed the performance of natural strains. In this work, I engineered and optimized two different synthetic formate assimilation pathways in gram-negative bacteria to exceed the limits of a natural carbon fixation pathway, the Calvin cycle. The first chapter solidified Cupriavidus necator as a promising formatotrophic host to produce value-added chemicals. The formate tolerance of C. necator was assessed and a production pathway for crotonate established in a modularized fashion. Last, bioprocess optimization was leveraged to produce crotonate from formate at a titer of 148 mg/L. In the second chapter, I chromosomally integrated and optimized the synthetic reductive glycine pathway in C. necator using a transposon-mediated selection approach. The insertion methodology allowed selection for condition-specific tailored pathway expression as improved pathway performance led to better growth. I then showed my engineered strains to exceed the biomass yields of the Calvin cycle utilizing wildtype C. necator on formate. This demonstrated for the first time the superiority of a synthetic formate assimilation pathway and by extension of synthetic carbon fixation efforts as a whole. In chapter 3, I engineered a segment of a synthetic carbon fixation cycle in Escherichia coli. The GED cycle was proposed as a Calvin cycle alternative that does not perform a wasteful oxygenation reaction and is more energy efficient. The pathways simple architecture and reasonable driving force made it a promising candidate for enhanced carbon fixation. I created a deletion strain that coupled growth to carboxylation via the GED pathway segment. The CO2 dependence of the engineered strain and 13C-tracer analysis confirmed operation of the pathway in vivo. In the final chapter, I present my efforts of implementing the GED cycle also in C. necator, which might be a better-suited host, as it is accustomed to formatotrophic and hydrogenotrophic growth. To provide the carboxylation substrate in vivo, I engineered C. necator to utilize xylose as carbon source and created a selection strain for carboxylase activity. I verify activity of the key enzyme, the carboxylase, in the decarboxylative direction. Although CO2-dependent growth of the strain was not obtained, I showed that all enzymes required for operation of the GED cycle are active in vivo in C. necator. I then evaluate my success with engineering a linear and cyclical one-carbon fixation pathway in two different microbial hosts. The linear reductive glycine pathway presents itself as a much simpler metabolic solution for formate dependent growth over the sophisticated establishment of hard-to-balance carbon fixation cycles. Last, I highlight advantages and disadvantages of C. necator as an upcoming microbial benchmark organism for synthetic metabolism efforts and give and outlook on its potential for the future of C1-based manufacturing.}, language = {en} } @phdthesis{Ranaee2022, author = {Ranaee, Mahdi}, title = {Skepticism}, doi = {10.25932/publishup-64565}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-645652}, school = {Universit{\"a}t Potsdam}, pages = {164}, year = {2022}, abstract = {This dissertation offers new and original readings of three major texts in the history of Western philosophy: Descartes's "First Meditation," Kant's "Transcendental Deduction," and his "Refutation of Idealism." The book argues that each text addresses the problem of skepticism and posits that they have a hitherto underappreciated, organic relationship to one another. The dissertation begins with an analysis of Descartes' "First Meditation," which I argue offers two distinct and independent skeptical arguments that differ in both aim and scope. I call these arguments the "veil of ideas" argument and the "author of my origin" argument. My reading counters the standard interpretation of the text, which sees it as offering three stages of doubt, namely the occasional fallibility of the senses, the dream hypothesis, and the evil demon hypothesis. Building on this, the central argument of the dissertation is that Kant's "Transcendental Deduction" actually transforms and radicalizes Descartes's Author of My Origin argument, reconceiving its meaning within the framework of Kant's own transcendental idealist philosophy. Finally, I argue that the Refutation of Idealism offers a similarly radicalized version of Descartes's Veil of Ideas argument, albeit translated into the framework of transcendental idealism.}, 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{Taleb2024, author = {Taleb, Aiham}, title = {Self-supervised deep learning methods for medical image analysis}, doi = {10.25932/publishup-64408}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-644089}, school = {Universit{\"a}t Potsdam}, pages = {xii, 171}, year = {2024}, abstract = {Deep learning has seen widespread application in many domains, mainly for its ability to learn data representations from raw input data. Nevertheless, its success has so far been coupled with the availability of large annotated (labelled) datasets. This is a requirement that is difficult to fulfil in several domains, such as in medical imaging. Annotation costs form a barrier in extending deep learning to clinically-relevant use cases. The labels associated with medical images are scarce, since the generation of expert annotations of multimodal patient data at scale is non-trivial, expensive, and time-consuming. This substantiates the need for algorithms that learn from the increasing amounts of unlabeled data. Self-supervised representation learning algorithms offer a pertinent solution, as they allow solving real-world (downstream) deep learning tasks with fewer annotations. Self-supervised approaches leverage unlabeled samples to acquire generic features about different concepts, enabling annotation-efficient downstream task solving subsequently. Nevertheless, medical images present multiple unique and inherent challenges for existing self-supervised learning approaches, which we seek to address in this thesis: (i) medical images are multimodal, and their multiple modalities are heterogeneous in nature and imbalanced in quantities, e.g. MRI and CT; (ii) medical scans are multi-dimensional, often in 3D instead of 2D; (iii) disease patterns in medical scans are numerous and their incidence exhibits a long-tail distribution, so it is oftentimes essential to fuse knowledge from different data modalities, e.g. genomics or clinical data, to capture disease traits more comprehensively; (iv) Medical scans usually exhibit more uniform color density distributions, e.g. in dental X-Rays, than natural images. Our proposed self-supervised methods meet these challenges, besides significantly reducing the amounts of required annotations. We evaluate our self-supervised methods on a wide array of medical imaging applications and tasks. Our experimental results demonstrate the obtained gains in both annotation-efficiency and performance; our proposed methods outperform many approaches from related literature. Additionally, in case of fusion with genetic modalities, our methods also allow for cross-modal interpretability. In this thesis, not only we show that self-supervised learning is capable of mitigating manual annotation costs, but also our proposed solutions demonstrate how to better utilize it in the medical imaging domain. Progress in self-supervised learning has the potential to extend deep learning algorithms application to clinical scenarios.}, language = {en} } @phdthesis{Khosravi2023, author = {Khosravi, Sara}, title = {The effect of new turbulence parameterizations for the stable surface layer on simulations of the Arctic climate}, doi = {10.25932/publishup-64352}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-643520}, school = {Universit{\"a}t Potsdam}, pages = {XIV, 119}, year = {2023}, abstract = {Arctic climate change is marked by intensified warming compared to global trends and a significant reduction in Arctic sea ice which can intricately influence mid-latitude atmospheric circulation through tropo- and stratospheric pathways. Achieving accurate simulations of current and future climate demands a realistic representation of Arctic climate processes in numerical climate models, which remains challenging. Model deficiencies in replicating observed Arctic climate processes often arise due to inadequacies in representing turbulent boundary layer interactions that determine the interactions between the atmosphere, sea ice, and ocean. Many current climate models rely on parameterizations developed for mid-latitude conditions to handle Arctic turbulent boundary layer processes. This thesis focuses on modified representation of the Arctic atmospheric processes and understanding their resulting impact on large-scale mid-latitude atmospheric circulation within climate models. The improved turbulence parameterizations, recently developed based on Arctic measurements, were implemented in the global atmospheric circulation model ECHAM6. This involved modifying the stability functions over sea ice and ocean for stable stratification and changing the roughness length over sea ice for all stratification conditions. Comprehensive analyses are conducted to assess the impacts of these modifications on ECHAM6's simulations of the Arctic boundary layer, overall atmospheric circulation, and the dynamical pathways between the Arctic and mid-latitudes. Through a step-wise implementation of the mentioned parameterizations into ECHAM6, a series of sensitivity experiments revealed that the combined impacts of the reduced roughness length and the modified stability functions are non-linear. Nevertheless, it is evident that both modifications consistently lead to a general decrease in the heat transfer coefficient, being in close agreement with the observations. Additionally, compared to the reference observations, the ECHAM6 model falls short in accurately representing unstable and strongly stable conditions. The less frequent occurrence of strong stability restricts the influence of the modified stability functions by reducing the affected sample size. However, when focusing solely on the specific instances of a strongly stable atmosphere, the sensible heat flux approaches near-zero values, which is in line with the observations. Models employing commonly used surface turbulence parameterizations were shown to have difficulties replicating the near-zero sensible heat flux in strongly stable stratification. I also found that these limited changes in surface layer turbulence parameterizations have a statistically significant impact on the temperature and wind patterns across multiple pressure levels, including the stratosphere, in both the Arctic and mid-latitudes. These significant signals vary in strength, extent, and direction depending on the specific month or year, indicating a strong reliance on the background state. Furthermore, this research investigates how the modified surface turbulence parameterizations may influence the response of both stratospheric and tropospheric circulation to Arctic sea ice loss. The most suitable parameterizations for accurately representing Arctic boundary layer turbulence were identified from the sensitivity experiments. Subsequently, the model's response to sea ice loss is evaluated through extended ECHAM6 simulations with different prescribed sea ice conditions. The simulation with adjusted surface turbulence parameterizations better reproduced the observed Arctic tropospheric warming in vertical extent, demonstrating improved alignment with the reanalysis data. Additionally, unlike the control experiments, this simulation successfully reproduced specific circulation patterns linked to the stratospheric pathway for Arctic-mid-latitude linkages. Specifically, an increased occurrence of the Scandinavian-Ural blocking regime (negative phase of the North Atlantic Oscillation) in early (late) winter is observed. Overall, it can be inferred that improving turbulence parameterizations at the surface layer can improve the ECHAM6's response to sea ice loss.}, language = {en} } @phdthesis{Richly2024, author = {Richly, Keven}, title = {Memory-efficient data management for spatio-temporal applications}, doi = {10.25932/publishup-63547}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-635473}, school = {Universit{\"a}t Potsdam}, pages = {xii, 181}, year = {2024}, abstract = {The wide distribution of location-acquisition technologies means that large volumes of spatio-temporal data are continuously being accumulated. Positioning systems such as GPS enable the tracking of various moving objects' trajectories, which are usually represented by a chronologically ordered sequence of observed locations. The analysis of movement patterns based on detailed positional information creates opportunities for applications that can improve business decisions and processes in a broad spectrum of industries (e.g., transportation, traffic control, or medicine). Due to the large data volumes generated in these applications, the cost-efficient storage of spatio-temporal data is desirable, especially when in-memory database systems are used to achieve interactive performance requirements. To efficiently utilize the available DRAM capacities, modern database systems support various tuning possibilities to reduce the memory footprint (e.g., data compression) or increase performance (e.g., additional indexes structures). By considering horizontal data partitioning, we can independently apply different tuning options on a fine-grained level. However, the selection of cost and performance-balancing configurations is challenging, due to the vast number of possible setups consisting of mutually dependent individual decisions. In this thesis, we introduce multiple approaches to improve spatio-temporal data management by automatically optimizing diverse tuning options for the application-specific access patterns and data characteristics. Our contributions are as follows: (1) We introduce a novel approach to determine fine-grained table configurations for spatio-temporal workloads. Our linear programming (LP) approach jointly optimizes the (i) data compression, (ii) ordering, (iii) indexing, and (iv) tiering. We propose different models which address cost dependencies at different levels of accuracy to compute optimized tuning configurations for a given workload, memory budgets, and data characteristics. To yield maintainable and robust configurations, we further extend our LP-based approach to incorporate reconfiguration costs as well as optimizations for multiple potential workload scenarios. (2) To optimize the storage layout of timestamps in columnar databases, we present a heuristic approach for the workload-driven combined selection of a data layout and compression scheme. By considering attribute decomposition strategies, we are able to apply application-specific optimizations that reduce the memory footprint and improve performance. (3) We introduce an approach that leverages past trajectory data to improve the dispatch processes of transportation network companies. Based on location probabilities, we developed risk-averse dispatch strategies that reduce critical delays. (4) Finally, we used the use case of a transportation network company to evaluate our database optimizations on a real-world dataset. We demonstrate that workload-driven fine-grained optimizations allow us to reduce the memory footprint (up to 71\% by equal performance) or increase the performance (up to 90\% by equal memory size) compared to established rule-based heuristics. Individually, our contributions provide novel approaches to the current challenges in spatio-temporal data mining and database research. Combining them allows in-memory databases to store and process spatio-temporal data more cost-efficiently.}, language = {en} } @phdthesis{Frank2024, author = {Frank, Mario}, title = {On synthesising Linux kernel module components from Coq formalisations}, doi = {10.25932/publishup-64255}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-642558}, school = {Universit{\"a}t Potsdam}, pages = {IX, 78}, year = {2024}, abstract = {This thesis presents an attempt to use source code synthesised from Coq formalisations of device drivers for existing (micro)kernel operating systems, with a particular focus on the Linux Kernel. In the first part, the technical background and related work are described. The focus is here on the possible approaches to synthesising certified software with Coq, namely the extraction to functional languages using the Coq extraction plugin and the extraction to Clight code using the CertiCoq plugin. It is noted that the implementation of CertiCoq is verified, whereas this is not the case for the Coq extraction plugin. Consequently, there is a correctness guarantee for the generated Clight code which does not hold for the code being generated by the Coq extraction plugin. Furthermore, the differences between user space and kernel space software are discussed in relation to Linux device drivers. It is elaborated that it is not possible to generate working Linux kernel module components using the Coq extraction plugin without significant modifications. In contrast, it is possible to produce working user space drivers both with the Coq extraction plugin and CertiCoq. The subsequent parts describe the main contributions of the thesis. In the second part, it is demonstrated how to extend the Coq extraction plugin to synthesise foreign function calls between the functional language OCaml and the imperative language C. This approach has the potential to improve the type-safety of user space drivers. Furthermore, it is shown that the code being synthesised by CertiCoq cannot be used in kernel space without modifications to the necessary runtime. Consequently, the necessary modifications to the runtimes of CertiCoq and VeriFFI are introduced, resulting in the runtimes becoming compatible components of a Linux kernel module. Furthermore, justifications for the transformations are provided and possible further extensions to both plugins and solutions to failing garbage collection calls in kernel space are discussed. The third part presents a proof of concept device driver for the Linux Kernel. To achieve this, the event handler of the original PC Speaker driver is partially formalised in Coq. Furthermore, some relevant formal properties of the formalised functionality are discussed. Subsequently, a kernel module is defined, utilising the modified variants of CertiCoq and VeriFFI to compile a working device driver. It is furthermore shown that it is possible to compile the synthesised code with CompCert, thereby extending the guarantee of correctness to the assembly layer. This is followed by a performance evaluation that compares a naive formalisation of the PC speaker functionality with the original PC Speaker driver pointing out the weaknesses in the formalisation and possible improvements. The part closes with a summary of the results, their implications and open questions being raised. The last part lists all used sources, separated into scientific literature, documentations or reference manuals and artifacts, i.e. source code.}, language = {en} } @phdthesis{Hagemann2024, author = {Hagemann, Justus}, title = {On the molecular evolution of sengis (Macroscelidea)}, doi = {10.25932/publishup-64197}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-641975}, school = {Universit{\"a}t Potsdam}, pages = {xiii, 144}, year = {2024}, abstract = {This thesis focuses on the molecular evolution of Macroscelidea, commonly referred to as sengis. Sengis are a mammalian order belonging to the Afrotherians, one of the four major clades of placental mammals. Sengis currently consist of twenty extant species, all of which are endemic to the African continent. They can be separated in two families, the soft-furred sengis (Macroscelididae) and the giant sengis (Rhynchocyonidae). While giant sengis can be exclusively found in forest habitats, the different soft-furred sengi species dwell in a broad range of habitats, from tropical rain-forests to rocky deserts. Our knowledge on the evolutionary history of sengis is largely incomplete. The high level of superficial morphological resemblance among different sengi species (especially the soft-furred sengis) has for example led to misinterpretations of phylogenetic relationships, based on morphological characters. With the rise of DNA based taxonomic inferences, multiple new genera were defined and new species described. Yet, no full taxon molecular phylogeny exists, hampering the answering of basic taxonomic questions. This lack of knowledge can be to some extent attributed to the limited availability of fresh-tissue samples for DNA extraction. The broad African distribution, partly in political unstable regions and low population densities complicate contemporary sampling approaches. Furthermore, the DNA information available usually covers only short stretches of the mitochondrial genome and thus a single genetic locus with limited informational content. Developments in DNA extraction and library protocols nowadays offer the opportunity to access DNA from museum specimens, collected over the past centuries and stored in natural history museums throughout the world. Thus, the difficulties in fresh-sample acquisition for molecular biological studies can be overcome by the application of museomics, the research field which emerged from those laboratory developments. This thesis uses fresh-tissue samples as well as a vast collection museum specimens to investigate multiple aspects about the macroscelidean evolutionary history. Chapter 4 of this thesis focuses on the phylogenetic relationships of all currently known sengi species. By accessing DNA information from museum specimens in combination of fresh tissue samples and publicly available genetic resources it produces the first full taxon molecular phylogeny of sengis. It confirms the monophyly of the genus Elephantulus and discovers multiple deeply divergent lineages within different species, highlighting the need for species specific approaches. The study furthermore focuses on the evolutionary time frame of sengis by evaluating the impact of commonly varied parameters on tree dating. The results of the study show, that the mitochondrial information used in previous studies to temporal calibrate the Macroscelidean phylogeny led to an overestimation of node ages within sengis. Especially soft-furred sengis are thus much younger than previously assumed. The refined knowledge of nodes ages within sengis offer the opportunity to link e.g. speciation events to environmental changes. Chapter 5 focuses on the genus Petrodromus with its single representative Petrodromus tetradactylus. It again exploits the opportunities of museomics and gathers a comprehensive, multi-locus genetic dataset of P. tetradactylus individuals, distributed across most the known range of this species. It reveals multiple deeply divergent lineages within Petrodromus, whereby some could possibly be associated to previously described sub-species, at least one was formerly unknown. It underscores the necessity for a revision of the genus Petrodromus through the integration of both molecular and morphological evidence. The study, furthermore identifies changing forest distributions through climatic oscillations as main factor shaping the genetic structure of Petrodromus. Chapter 6 uses fresh tissue samples to extent the genomic resources of sengis by thirteen new nuclear genomes, of which two were de-novo assembled. An extensive dataset of more than 8000 protein coding one-to-one orthologs allows to further refine and confirm the temporal time frame of sengi evolution found in Chapter 4. This study moreover investigates the role of gene-flow and incomplete lineage sorting (ILS) in sengi evolution. In addition it identifies clade specific genes of possible outstanding evolutionary importance and links them to potential phenotypic traits affected. A closer investigation of olfactory receptor proteins reveals clade specific differences. A comparison of the demographic past of sengis to other small African mammals does not reveal a sengi specific pattern.}, language = {en} } @phdthesis{Pfalz2024, author = {Pfalz, Gregor}, title = {Advancing knowledge of Arctic lake system dynamics: A data-driven perspective on spatiotemporal patterns}, doi = {10.25932/publishup-63655}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-636554}, school = {Universit{\"a}t Potsdam}, pages = {xiii, 136}, year = {2024}, abstract = {Ecosystems play a pivotal role in addressing climate change but are also highly susceptible to drastic environmental changes. Investigating their historical dynamics can enhance our understanding of how they might respond to unprecedented future environmental shifts. With Arctic lakes currently under substantial pressure from climate change, lessons from the past can guide our understanding of potential disruptions to these lakes. However, individual lake systems are multifaceted and complex. Traditional isolated lake studies often fail to provide a global perspective because localized nuances—like individual lake parameters, catchment areas, and lake histories—can overshadow broader conclusions. In light of these complexities, a more nuanced approach is essential to analyze lake systems in a global context. A key to addressing this challenge lies in the data-driven analysis of sedimentological records from various northern lake systems. This dissertation emphasizes lake systems in the northern Eurasian region, particularly in Russia (n=59). For this doctoral thesis, we collected sedimentological data from various sources, which required a standardized framework for further analysis. Therefore, we designed a conceptual model for integrating and standardizing heterogeneous multi-proxy data into a relational database management system (PostgreSQL). Creating a database from the collected data enabled comparative numerical analyses between spatially separated lakes as well as between different proxies. When analyzing numerous lakes, establishing a common frame of reference was crucial. We achieved this by converting proxy values from depth dependency to age dependency. This required consistent age calculations across all lakes and proxies using one age-depth modeling software. Recognizing the broader implications and potential pitfalls of this, we developed the LANDO approach ("Linked Age and Depth Modelling"). LANDO is an innovative integration of multiple age-depth modeling software into a singular, cohesive platform (Jupyter Notebook). Beyond its ability to aggregate data from five renowned age-depth modeling software, LANDO uniquely empowers users to filter out implausible model outcomes using robust geoscientific data. Our method is not only novel but also significantly enhances the accuracy and reliability of lake analyses. Considering the preceding steps, this doctoral thesis further examines the relationship between carbon in sediments and temperature over the last 21,000 years. Initially, we hypothesized a positive correlation between carbon accumulation in lakes and modelled paleotemperature. Our homogenized dataset from heterogeneous lakes confirmed this association, even if the highest temperatures throughout our observation period do not correlate with the highest carbon values. We assume that rapid warming events contribute more to high accumulation, while sustained warming leads to carbon outgassing. Considering the current high concentration of carbon in the atmosphere and rising temperatures, ongoing climate change could cause northern lake systems to contribute to a further increase in atmospheric carbon (positive feedback loop). While our findings underscore the reliability of both our standardized data and the LANDO method, expanding our dataset might offer even greater assurance in our conclusions.}, language = {en} } @phdthesis{Damseaux2024, author = {Damseaux, Adrien}, title = {Improving permafrost dynamics in land surface models: insights from dual sensitivity experiments}, doi = {10.25932/publishup-63945}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-639450}, school = {Universit{\"a}t Potsdam}, pages = {xiii, 143}, year = {2024}, abstract = {The thawing of permafrost and the subsequent release of greenhouse gases constitute one of the most significant and uncertain positive feedback loops in the context of climate change, making predictions regarding changes in permafrost coverage of paramount importance. To address these critical questions, climate scientists have developed Land Surface Models (LSMs) that encompass a multitude of physical soil processes. This thesis is committed to advancing our understanding and refining precise representations of permafrost dynamics within LSMs, with a specific focus on the accurate modeling of heat fluxes, an essential component for simulating permafrost physics. The first research question overviews fundamental model prerequisites for the representation of permafrost soils within land surface modeling. It includes a first-of-its-kind comparison between LSMs in CMIP6 to reveal their differences and shortcomings in key permafrost physics parameters. Overall, each of these LSMs represents a unique approach to simulating soil processes and their interactions with the climate system. Choosing the most appropriate model for a particular application depends on factors such as the spatial and temporal scale of the simulation, the specific research question, and available computational resources. The second research question evaluates the performance of the state-of-the-art Community Land Model (CLM5) in simulating Arctic permafrost regions. Our approach overcomes traditional evaluation limitations by individually addressing depth, seasonality, and regional variations, providing a comprehensive assessment of permafrost and soil temperature dynamics. I compare CLM5's results with three extensive datasets: (1) soil temperatures from 295 borehole stations, (2) active layer thickness (ALT) data from the Circumpolar Active Layer Monitoring Network (CALM), and (3) soil temperatures, ALT, and permafrost extent from the ESA Climate Change Initiative (ESA-CCI). The results show that CLM5 aligns well with ESA-CCI and CALM for permafrost extent and ALT but reveals a significant global cold temperature bias, notably over Siberia. These results echo a persistent challenge identified in numerous studies: the existence of a systematic 'cold bias' in soil temperature over permafrost regions. To address this challenge, the following research questions propose dual sensitivity experiments. The third research question represents the first study to apply a Plant Functional Type (PFT)-based approach to derive soil texture and soil organic matter (SOM), departing from the conventional use of coarse-resolution global data in LSMs. This novel method results in a more uniform distribution of soil organic matter density (OMD) across the domain, characterized by reduced OMD values in most regions. However, changes in soil texture exhibit a more intricate spatial pattern. Comparing the results to observations reveals a significant reduction in the cold bias observed in the control run. This method shows noticeable improvements in permafrost extent, but at the cost of an overestimation in ALT. These findings emphasize the model's high sensitivity to variations in soil texture and SOM content, highlighting the crucial role of soil composition in governing heat transfer processes and shaping the seasonal variation of soil temperatures in permafrost regions. Expanding upon a site experiment conducted in Trail Valley Creek by \citet{dutch_impact_2022}, the fourth research question extends the application of the snow scheme proposed by \citet{sturm_thermal_1997} to cover the entire Arctic domain. By employing a snow scheme better suited to the snow density profile observed over permafrost regions, this thesis seeks to assess its influence on simulated soil temperatures. Comparing this method to observational datasets reveals a significant reduction in the cold bias that was present in the control run. In most regions, the Sturm run exhibits a substantial decrease in the cold bias. However, there is a distinctive overshoot with a warm bias observed in mountainous areas. The Sturm experiment effectively addressed the overestimation of permafrost extent in the control run, albeit resulting in a substantial reduction in permafrost extent over mountainous areas. ALT results remain relatively consistent compared to the control run. These outcomes align with our initial hypothesis, which anticipated that the reduced snow insulation in the Sturm run would lead to higher winter soil temperatures and a more accurate representation of permafrost physics. In summary, this thesis demonstrates significant advancements in understanding permafrost dynamics and its integration into LSMs. It has meticulously unraveled the intricacies involved in the interplay between heat transfer, soil properties, and snow dynamics in permafrost regions. These insights offer novel perspectives on model representation and performance.}, language = {en} } @phdthesis{Koyan2024, author = {Koyan, Philipp}, title = {3D attribute analysis and classification to interpret ground-penetrating radar (GPR) data collected across sedimentary environments: Synthetic studies and field examples}, doi = {10.25932/publishup-63948}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-639488}, school = {Universit{\"a}t Potsdam}, pages = {xi, 115, A51}, year = {2024}, abstract = {Die Untersuchung des oberfl{\"a}chennahen Untergrundes erfolgt heutzutage bei Frage- stellungen aus den Bereichen des Bauwesens, der Arch{\"a}ologie oder der Geologie und Hydrologie oft mittels zerst{\"o}rungsfreier beziehungsweise zerst{\"o}rungsarmer Methoden der angewandten Geophysik. Ein Bereich, der eine immer zentralere Rolle in Forschung und Ingenieurwesen einnimmt, ist die Untersuchung von sediment{\"a}ren Umgebungen, zum Beispiel zur Charakterisierung oberfl{\"a}chennaher Grundwassersysteme. Ein in diesem Kontext h{\"a}ufig eingesetztes Verfahren ist das des Georadars (oftmals GPR - aus dem Englischen ground-penetrating radar). Dabei werden kurze elektromagnetische Impulse von einer Antenne in den Untergrund ausgesendet, welche dort wiederum an Kontrasten der elektromagnetischen Eigenschaften (wie zum Beispiel an der Grundwasseroberfl{\"a}che) reflektiert, gebrochen oder gestreut werden. Eine Empfangsantenne zeichnet diese Signale in Form derer Amplituden und Laufzeiten auf. Eine Analyse dieser aufgezeichneten Signale erm{\"o}glicht Aussagen {\"u}ber den Untergrund, beispielsweise {\"u}ber die Tiefenlage der Grundwasseroberfl{\"a}che oder die Lagerung und Charakteristika oberfl{\"a}chennaher Sedimentschichten. Dank des hohen Aufl{\"o}sungsverm{\"o}gens der GPR-Methode sowie stetiger technologischer Entwicklungen erfolgt heutzutage die Aufzeichnung von GPR- Daten immer h{\"a}ufiger in 3D. Trotz des hohen zeitlichen und technischen Aufwandes f{\"u}r die Datenakquisition und -bearbeitung werden die resultierenden 3D-Datens{\"a}tze, welche den Untergrund hochaufl{\"o}send abbilden, typischerweise von Hand interpretiert. Dies ist in der Regel ein {\"a}ußerst zeitaufwendiger Analyseschritt. Daher werden oft repr{\"a}sentative 2D-Schnitte aus dem 3D-Datensatz gew{\"a}hlt, in denen markante Reflektionsstrukuren markiert werden. Aus diesen Strukturen werden dann sich {\"a}hnelnde Bereiche im Untergrund als so genannte Radar-Fazies zusammengefasst. Die anhand von 2D-Schnitten erlangten Resultate werden dann als repr{\"a}sentativ f{\"u}r die gesamte untersuchte Fl{\"a}che angesehen. In dieser Form durchgef{\"u}hrte Interpretationen sind folglich oft unvollst{\"a}ndig sowie zudem in hohem Maße von der Expertise der Interpretierenden abh{\"a}ngig und daher in der Regel nicht reproduzierbar. Eine vielversprechende Alternative beziehungsweise Erg{\"a}nzung zur manuellen In- terpretation ist die Verwendung von so genannten GPR-Attributen. Dabei werden nicht die aufgezeichneten Daten selbst, sondern daraus abgeleitete Gr{\"o}ßen, welche die markanten Reflexionsstrukturen in 3D charakterisieren, zur Interpretation herangezogen. In dieser Arbeit wird anhand verschiedener Feld- und Modelldatens{\"a}tze untersucht, welche Attribute sich daf{\"u}r insbesondere eignen. Zudem zeigt diese Arbeit, wie ausgew{\"a}hlte Attribute mittels spezieller Bearbeitungs- und Klassifizierungsmethoden zur Erstellung von 3D-Faziesmodellen genutzt werden k{\"o}nnen. Dank der M{\"o}glichkeit der Erstellung so genannter attributbasierter 3D-GPR-Faziesmodelle k{\"o}nnen zuk{\"u}nftige Interpretationen zu gewissen Teilen automatisiert und somit effizienter durchgef{\"u}hrt werden. Weiterhin beschreiben die so erhaltenen Resultate den untersuchten Untergrund in reproduzierbarer Art und Weise sowie umf{\"a}nglicher als es bisher mittels manueller Interpretationsmethoden typischerweise m{\"o}glich war.}, language = {en} } @phdthesis{Lorson2024, author = {Lorson, Annalena}, title = {Understanding early stage evolution of digital innovation units in manufacturing companies}, doi = {10.25932/publishup-63914}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-639141}, school = {Universit{\"a}t Potsdam}, pages = {XI, 149}, year = {2024}, abstract = {The dynamic landscape of digital transformation entails an impact on industrial-age manufacturing companies that goes beyond product offerings, changing operational paradigms, and requiring an organization-wide metamorphosis. An initiative to address the given challenges is the creation of Digital Innovation Units (DIUs) - departments or distinct legal entities that use new structures and practices to develop digital products, services, and business models and support or drive incumbents' digital transformation. With more than 300 units in German-speaking countries alone and an increasing number of scientific publications, DIUs have become a widespread phenomenon in both research and practice. This dissertation examines the evolution process of DIUs in the manufacturing industry during their first three years of operation, through an extensive longitudinal single-case study and several cross-case syntheses of seven DIUs. Building on the lenses of organizational change and development, time, and socio-technical systems, this research provides insights into the fundamentals, temporal dynamics, socio-technical interactions, and relational dynamics of a DIU's evolution process. Thus, the dissertation promotes a dynamic understanding of DIUs and adds a two-dimensional perspective to the often one-dimensional view of these units and their interactions with the main organization throughout the startup and growth phases of a DIU. Furthermore, the dissertation constructs a phase model that depicts the early stages of DIU evolution based on these findings and by incorporating literature from information systems research. As a result, it illustrates the progressive intensification of collaboration between the DIU and the main organization. After being implemented, the DIU sparks initial collaboration and instigates change within (parts of) the main organization. Over time, it adapts to the corporate environment to some extent, responding to changing circumstances in order to contribute to long-term transformation. Temporally, the DIU drives the early phases of cooperation and adaptation in particular, while the main organization triggers the first major evolutionary step and realignment of the DIU. Overall, the thesis identifies DIUs as malleable organizational structures that are crucial for digital transformation. Moreover, it provides guidance for practitioners on the process of building a new DIU from scratch or optimizing an existing one.}, language = {en} } @phdthesis{Sharma2024, author = {Sharma, Shubham}, title = {Integrated approaches to earthquake forecasting}, doi = {10.25932/publishup-63612}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-636125}, school = {Universit{\"a}t Potsdam}, pages = {xvi, 76}, year = {2024}, abstract = {A comprehensive study on seismic hazard and earthquake triggering is crucial for effective mitigation of earthquake risks. The destructive nature of earthquakes motivates researchers to work on forecasting despite the apparent randomness of the earthquake occurrences. Understanding their underlying mechanisms and patterns is vital, given their potential for widespread devastation and loss of life. This thesis combines methodologies, including Coulomb stress calculations and aftershock analysis, to shed light on earthquake complexities, ultimately enhancing seismic hazard assessment. The Coulomb failure stress (CFS) criterion is widely used to predict the spatial distributions of aftershocks following large earthquakes. However, uncertainties associated with CFS calculations arise from non-unique slip inversions and unknown fault networks, particularly due to the choice of the assumed aftershocks (receiver) mechanisms. Recent studies have proposed alternative stress quantities and deep neural network approaches as superior to CFS with predefined receiver mechanisms. To challenge these propositions, I utilized 289 slip inversions from the SRCMOD database to calculate more realistic CFS values for a layered-half space and variable receiver mechanisms. The analysis also investigates the impact of magnitude cutoff, grid size variation, and aftershock duration on the ranking of stress metrics using receiver operating characteristic (ROC) analysis. Results reveal the performance of stress metrics significantly improves after accounting for receiver variability and for larger aftershocks and shorter time periods, without altering the relative ranking of the different stress metrics. To corroborate Coulomb stress calculations with the findings of earthquake source studies in more detail, I studied the source properties of the 2005 Kashmir earthquake and its aftershocks, aiming to unravel the seismotectonics of the NW Himalayan syntaxis. I simultaneously relocated the mainshock and its largest aftershocks using phase data, followed by a comprehensive analysis of Coulomb stress changes on the aftershock planes. By computing the Coulomb failure stress changes on the aftershock faults, I found that all large aftershocks lie in regions of positive stress change, indicating triggering by either co-seismic or post-seismic slip on the mainshock fault. Finally, I investigated the relationship between mainshock-induced stress changes and associated seismicity parameters, in particular those of the frequency-magnitude (Gutenberg-Richter) distribution and the temporal aftershock decay (Omori-Utsu law). For that purpose, I used my global data set of 127 mainshock-aftershock sequences with the calculated Coulomb Stress (ΔCFS) and the alternative receiver-independent stress metrics in the vicinity of the mainshocks and analyzed the aftershocks properties depend on the stress values. Surprisingly, the results show a clear positive correlation between the Gutenberg-Richter b-value and induced stress, contrary to expectations from laboratory experiments. This observation highlights the significance of structural heterogeneity and strength variations in seismicity patterns. Furthermore, the study demonstrates that aftershock productivity increases nonlinearly with stress, while the Omori-Utsu parameters c and p systematically decrease with increasing stress changes. These partly unexpected findings have significant implications for future estimations of aftershock hazard. The findings in this thesis provides valuable insights into earthquake triggering mechanisms by examining the relationship between stress changes and aftershock occurrence. The results contribute to improved understanding of earthquake behavior and can aid in the development of more accurate probabilistic-seismic hazard forecasts and risk reduction strategies.}, language = {en} } @phdthesis{Mostafa2024, author = {Mostafa, Amr}, title = {DNA origami nanoforks: A platform for cytochrome c single molecule surface enhanced Raman spectroscopy}, doi = {10.25932/publishup-63548}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-635482}, school = {Universit{\"a}t Potsdam}, pages = {xi, 90, x}, year = {2024}, abstract = {This thesis presents a comprehensive exploration of the application of DNA origami nanofork antennas (DONAs) in the field of spectroscopy, with a particular focus on the structural analysis of Cytochrome C (CytC) at the single-molecule level. The research encapsulates the design, optimization, and application of DONAs in enhancing the sensitivity and specificity of Raman spectroscopy, thereby offering new insights into protein structures and interactions. The initial phase of the study involved the meticulous optimization of DNA origami structures. This process was pivotal in developing nanoscale tools that could significantly enhance the capabilities of Raman spectroscopy. The optimized DNA origami nanoforks, in both dimer and aggregate forms, demonstrated an enhanced ability to detect and analyze molecular vibrations, contributing to a more nuanced understanding of protein dynamics. A key aspect of this research was the comparative analysis between the dimer and aggregate forms of DONAs. This comparison revealed that while both configurations effectively identified oxidation and spin states of CytC, the aggregate form offered a broader range of detectable molecular states due to its prolonged signal emission and increased number of molecules. This extended duration of signal emission in the aggregates was attributed to the collective hotspot area, enhancing overall signal stability and sensitivity. Furthermore, the study delved into the analysis of the Amide III band using the DONA system. Observations included a transient shift in the Amide III band's frequency, suggesting dynamic alterations in the secondary structure of CytC. These shifts, indicative of transitions between different protein structures, were crucial in understanding the protein's functional mechanisms and interactions. The research presented in this thesis not only contributes significantly to the field of spectroscopy but also illustrates the potential of interdisciplinary approaches in biosensing. The use of DNA origami-based systems in spectroscopy has opened new avenues for research, offering a detailed and comprehensive understanding of protein structures and interactions. The insights gained from this research are expected to have lasting implications in scientific fields ranging from drug development to the study of complex biochemical pathways. This thesis thus stands as a testament to the power of integrating nanotechnology, biochemistry, and spectroscopic techniques in addressing complex scientific questions.}, language = {en} }