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Modeling random crawling, membrane deformation and intracellular polarity of motile amoeboid cells
(2018)
Amoeboid movement is one of the most widespread forms of cell motility that plays a key role in numerous biological contexts. While many aspects of this process are well investigated, the large cell-to-cell variability in the motile characteristics of an otherwise uniform population remains an open question that was largely ignored by previous models. In this article, we present a mathematical model of amoeboid motility that combines noisy bistable kinetics with a dynamic phase field for the cell shape. To capture cell-to-cell variability, we introduce a single parameter for tuning the balance between polarity formation and intracellular noise. We compare numerical simulations of our model to experiments with the social amoeba Dictyostelium discoideum. Despite the simple structure of our model, we found close agreement with the experimental results for the center-of-mass motion as well as for the evolution of the cell shape and the overall intracellular patterns. We thus conjecture that the building blocks of our model capture essential features of amoeboid motility and may serve as a starting point for more detailed descriptions of cell motion in chemical gradients and confined environments.
Characterization of altered inflorescence architecture in Arabidopsis thaliana BG-5 x Kro-0 hybrid
(2018)
A reciprocal cross between two A. thaliana accessions, Kro-0 (Krotzenburg, Germany) and BG-5 (Seattle, USA), displays purple rosette leaves and dwarf bushy phenotype in F1 hybrids when grown at 17 °C and a parental-like phenotype when grown at 21 °C. This F1 temperature-dependent-dwarf-bushy phenotype is characterized by reduced growth of the primary stem together with an increased number of branches. The reduced stem growth was the strongest at the first internode. In addition, we found that a temperature switch from 21 °C to 17 °C induced the phenotype only before the formation of the first internode of the stem. Similarly, the F1 dwarf-bushy phenotype could not be reversed when plants were shifted from 17 °C to 21 °C after the first internode was formed. Metabolic analysis showed that the F1 phenotype was associated with a significant upregulation of anthocyanin(s), kaempferol(s), salicylic acid, jasmonic acid and abscisic acid. As it has been previously shown that the dwarf-bushy phenotype is linked to two loci, one on chromosome 2 from Kro-0 and one on chromosome 3 from BG-5, an artificial micro-RNA approach was used to investigate the necessary genes on these intervals. From the results obtained, it was found that two genes, AT2G14120 that encodes for a DYNAMIN RELATED PROTEIN3B and AT2G14100 that encodes a member of the Cytochrome P450 family protein CYP705A13, were necessary for the appearance of the F1 phenotype on chromosome 2. It was also discovered that AT3G61035 that encodes for another cytochrome P450 family protein CYP705A13 and AT3G60840 that encodes for a MICROTUBULE-ASSOCIATED PROTEIN65-4 on chromosome 3 were both necessary for the induction of the F1 phenotype. To prove the causality of these genes, genomic constructs of the Kro-0 candidate genes on chromosome 2 were transferred to BG-5 and genomic constructs of the chromosome 3 candidate genes from BG-5 were transferred to Kro-0. The T1 lines showed that these genes are not sufficient alone to induce the phenotype. In addition to the F1 phenotype, more severe phenotypes were observed in the F2 generations that were grouped into five different phenotypic classes. Whilst seed yield was comparable between F1 hybrids and parental lines, three phenotypic classes in the F2 generation exhibited hybrid breakdown in the form of reproductive failure. This F2 hybrid breakdown was less sensitive to temperature and showed a dose-dependent effect of the loci involved in F1 phenotype. The severest class of hybrid breakdown phenotypes was observed only in the population of backcross with the parent Kro-0, which indicates a stronger contribution of the BG-5 allele when compared to the Kro-0 allele on the hybrid breakdown phenotypes. Overall, the findings of my thesis provide a further understanding of the genetic and metabolic factors underlying altered shoot architecture in hybrid dysfunction.
Al-Halbouni, Djamil ; Holohan, Eoghan P. ; Taheri, Abbas ; Schöpfer, Martin P. J. ; Emam, Sacha ; Dahm, Torsten
Mechanical and/or chemical removal of material from the subsurface may generate large subsurface cavities, the destabilisation of which can lead to ground collapse and the formation of sinkholes. Numerical simulation of the interaction of cavity growth, host material deformation and overburden collapse is desirable to better understand the sinkhole hazard but is a challenging task due to the involved high strains and material discontinuities. Here, we present 2-D distinct element method numerical simulations of cavity growth and sinkhole development. Firstly, we simulate cavity formation by quasi-static, stepwise removal of material in a single growing zone of an arbitrary geometry and depth. We benchmark this approach against analytical and boundary element method models of a deep void space in a linear elastic material. Secondly, we explore the effects of properties of different uniform materials on cavity stability and sinkhole development. We perform simulated biaxial tests to calibrate macroscopic geotechnical parameters of three model materials representative of those in which sinkholes develop at the Dead Sea shoreline: mud, alluvium and salt. We show that weak materials do not support large cavities, leading to gradual sagging or suffusion-style subsidence. Strong materials support quasi-stable to stable cavities, the overburdens of which may fail suddenly in a caprock or bedrock collapse style. Thirdly, we examine the consequences of layered arrangements of weak and strong materials. We find that these are more susceptible to sinkhole collapse than uniform materials not only due to a lower integrated strength of the overburden but also due to an inhibition of stabilising stress arching. Finally, we compare our model sinkhole geometries to observations at the Ghor Al-Haditha sinkhole site in Jordan. Sinkhole depth ∕ diameter ratios of 0.15 in mud, 0.37 in alluvium and 0.33 in salt are reproduced successfully in the calibrated model materials. The model results suggest that the observed distribution of sinkhole depth ∕ diameter values in each material type may partly reflect sinkhole growth trends.
Es gibt in Berlin eine einzigartige Vereinslandschaft im Amateur – und semiprofessionellen Fußballsport, in der einst von türkischen Migranten gegründete Vereine einen festen Platz einnehmen. Fußballsport bietet einen sozialen Raum für Jugendliche verschiedener kultureller, ethnischer und religiöser Herkunft, in dem Gruppen gebildet werden, um gegen einander zu konkurrieren. Ebenso eröffnet Fußball dem Einzelnen die Möglichkeit, die Gültigkeit und Relevanz von Vorurteilen und von gängigen Stereotypisierungen anderer Gruppen im Spielalltag einer ständigen Prüfung zu unterziehen. Fußballspieler können sich sowohl zwischen multi-kulturellen als auch mono-ethnischen Gruppenkonstellationen, in einigen Fällen auch in transnationalen Konstellationen bewegen, womit sie dabei wesentlich an der Sinngebung ihrer eigenen sozialen Zugehörigkeit mitwirken, die sich aus dem Spannungsfeld von Selbst- und Fremdwahrnehmungsmustern ergibt. In Folge dessen werden in diesem Raum Anerkennungsmechanismen konstituiert.
Die vorliegende Dissertation befasst sich mit dem alltäglichen Leben von türkisch-stämmigen, jugendlichen Amateur- und semiprofessionellen Fußballspielern (delikanli), sowie von anderen sozialen Akteuren der türkischen Fußballwelt, wie zum Beispiel „ältere“ Fußballspieler (agbi) und Fußballtrainer (hoca). Hauptanliegen der Arbeit war die Rekonstruktion kollektiver Wahrnehmungs-, Deutungs - und Handlungsmuster von Mitgliedern türkischer Fußballvereine im allgemeinen und ihrer Selbstdarstellung aber auch ihrer Wahrnehmung der „Anderen“ im besonderen. Mittels dieser Studie sollte nachvollzogen werden, ob und inwiefern sich traditionelle soziale Verhaltensmuster der gewählten Gruppe im technisch regulierten und stark Konkurrenz-orientierten Handlungsraum widerspiegeln und die reziproken Beziehungen zwischen dem „Selbst“ und den „Anderen“ regulieren. Dabei wurde die Relevanz von herkunftsbezogenen Stereotypisierungen und Vorurteilen in der kollektiven Konstitution von Selbstwahrnehmungen und Fremdverstehen im partikularen sozialen Feld (Bourdieu, 2001) des Fußballs rekonstruiert.
In dieser Arbeit wurde darüber hinaus beleuchtet, welche Rolle türkische Fußballvereine auf der einen Seite bei der Entstehung sozialer Raumzugehörigkeit zu den Stadtquartieren in Berlin einnehmen und welche Art von Mechanismen der sozialen Integration sie in diesen Vereinen herstellen. Auf der anderen Seite wurde hinterfragt, inwiefern sie zur sozialen Kohäsion zwischen diversen Kulturen beitragen. Daher wurde geprüft, ob und inwiefern die negativ konnotierte ethnozentrische Wahrnehmung von „Differenz“ (Bielefeld, 1998), die als soziales Konstrukt zwischen autochthonen und allochthonen Gruppen hergestellt wird, durch das Engagement der Vereinsakteure einen konstruktiven Wandel erfährt.
Übergeordnetes Ziel all dieser Forschungsfragen war es, ein fundiertes Verständnis über die Rolle von türkischen Fußballvereinen als soziale Mechanismen zu erlangen und deren Funktionsweise bei der Konstitution von Anpassungsstrategien in diesem sozialen Feld untersuchen. Detailliert wurde diese Rolle unter der Konzeptualisierung von sozialen Positionierungsmuster betrachtet, die als Gefüge von Deutungen des Alltäglichen verstanden werden, das individuelle und kollektive Handlungsmuster und implizit Muster des Fremdverstehens sowie des othering im Migrationskontext reguliert. Eine Rekonstruktion der sozialen Positionierungsmuster bietet eine eingehende soziologische Untersuchung dieser Teilnehmergruppe, die zudem Aufschluss über die Bedeutung und das Verständnis von ethnischer Zugehörigkeit für letztere gibt.
Neben umfangreicher Feldbeobachtung wurden in dieser qualitativen Studie mit Spielern verschiedener Vereine insgesamt zehn Gruppendiskussionen (Bohnsack, 2004) innerhalb ihrer Mannschaften zu gemeinsamen alltäglichen Erlebnissen und Erfahrungen durchgeführt, aufgezeichnet und mittels sozialwissenschaftlichem hermeneutischem Verfahren (Soeffner, 2004) interpretiert. Auch mit anderen Vereinsmitgliedern, d. h. mit Trainern bzw. hoca, Vorsitzenden, Managern und Sponsoren wurden jeweils zehn narrative und sieben biographische Einzelinterviews sowie sieben Experteninterviews durchgeführt. Deren Analyse erlaubt es, die Rolle dieser Mitglieder sowie wirkende Autoritätsmechanismen und kollektiv konstituierte Verhaltensmuster innerhalb der gesamten Vereinsgruppe zu rekonstruieren. Dabei wurde bezweckt, die Gesamtheit des sozialen Netzwerkes bzw. die Beziehungsschemata innerhalb der türkischen Fußballvereine Berlins zu verdeutlichen.
In der Arbeit werden zwei Standpunkte der theoretischen Auseinandersetzung verwendet. Auf der einen Seite wird die Lebensweltanalyse (Schütz und Luckmann, 1979, 1990) angewendet, um das soziale Erbe der in der Vergangenheit gesellschaftlich konstituierten Titulierung „Menschen mit Migrationshintergrund“ zu rekonstruieren, bzw. den Einfluss dieser sozialen Reproduktion auf die Wahrnehmungs-, Deutungs- und Handlungsmuster der Akteure zu untersuchen. Auf der anderen Seite wird die soziale Wirkung der tatsächlichen, alltäglichen Erfahrungsschemata im sozialen Feld des Fußballs auf die Selbstpositionierungen der Akteure mittels Goffmanscher Rahmenanalyse (Goffman, 1980) herausgearbeitet.
The climate is a complex dynamical system involving interactions and feedbacks among different processes at multiple temporal and spatial scales. Although numerous studies have attempted to understand the climate system, nonetheless, the studies investigating the multiscale characteristics of the climate are scarce. Further, the present set of techniques are limited in their ability to unravel the multi-scale variability of the climate system. It is completely plausible that extreme events and abrupt transitions, which are of great interest to climate community, are resultant of interactions among processes operating at multi-scale. For instance, storms, weather patterns, seasonal irregularities such as El Niño, floods and droughts, and decades-long climate variations can be better understood and even predicted by quantifying their multi-scale dynamics. This makes a strong argument to unravel the interaction and patterns of climatic processes at different scales. With this background, the thesis aims at developing measures to understand and quantify multi-scale interactions within the climate system.
In the first part of the thesis, I proposed two new methods, viz, multi-scale event synchronization (MSES) and wavelet multi-scale correlation (WMC) to capture the scale-specific features present in the climatic processes. The proposed methods were tested on various synthetic and real-world time series in order to check their applicability and replicability. The results indicate that both methods (WMC and MSES) are able to capture scale-specific associations that exist between processes at different time scales in a more detailed manner as compared to the traditional single scale counterparts.
In the second part of the thesis, the proposed multi-scale similarity measures were used in constructing climate networks to investigate the evolution of spatial connections within climatic processes at multiple timescales. The proposed methods WMC and MSES, together with complex network were applied to two different datasets.
In the first application, climate networks based on WMC were constructed for the univariate global sea surface temperature (SST) data to identify and visualize the SSTs patterns that develop very similarly over time and distinguish them from those that have long-range teleconnections to other ocean regions. Further investigations of climate networks on different timescales revealed (i) various high variability and co-variability regions, and (ii) short and long-range teleconnection regions with varying spatial distance. The outcomes of the study not only re-confirmed the existing knowledge on the link between SST patterns like El Niño Southern Oscillation and the Pacific Decadal Oscillation, but also suggested new insights into the characteristics and origins of long-range teleconnections.
In the second application, I used the developed non-linear MSES similarity measure to quantify the multivariate teleconnections between extreme Indian precipitation and climatic patterns with the highest relevance for Indian sub-continent. The results confirmed significant non-linear influences that were not well captured by the traditional methods. Further, there was a substantial variation in the strength and nature of teleconnection across India, and across time scales.
Overall, the results from investigations conducted in the thesis strongly highlight the need for considering the multi-scale aspects in climatic processes, and the proposed methods provide robust framework for quantifying the multi-scale characteristics.
Parsing of argumentative structures has become a very active line of research in recent years. Like discourse parsing or any other natural language task that requires prediction of linguistic structures, most approaches choose to learn a local model and then perform global decoding over the local probability distributions, often imposing constraints that are specific to the task at hand. Specifically for argumentation parsing, two decoding approaches have been recently proposed: Minimum Spanning Trees (MST) and Integer Linear Programming (ILP), following similar trends in discourse parsing. In contrast to discourse parsing though, where trees are not always used as underlying annotation schemes, argumentation structures so far have always been represented with trees. Using the 'argumentative microtext corpus' [in: Argumentation and Reasoned Action: Proceedings of the 1st European Conference on Argumentation, Lisbon 2015 / Vol. 2, College Publications, London, 2016, pp. 801-815] as underlying data and replicating three different decoding mechanisms, in this paper we propose a novel ILP decoder and an extension to our earlier MST work, and then thoroughly compare the approaches. The result is that our new decoder outperforms related work in important respects, and that in general, ILP and MST yield very similar performance.
Health effects, attributed to the environmental pollution resulted from using solvents such as benzene, are relatively unexplored among petroleum workers, personal use, and laboratory researchers. Solvents can cause various health problems, such as neurotoxicity, immunotoxicity, and carcinogenicity. As such it can be absorbed via epidermal or respiratory into the human body resulting in interacting with molecules that are responsible for biochemical and physiological processes of the brain.
Owing to the ever-growing demand for finding a solution, an Ionic liquid can use as an alternative solvent. Ionic liquids are salts in a liquid state at low temperature (below 100 C), or even at room temperature. Ionic liquids impart a unique architectural platform, which has been interesting because of their unusual properties that can be tuned by simple ways such as mixing two ionic liquids.
Ionic liquids not only used as reaction solvents but they became a key developing for novel applications based on their thermal stability, electric conductivity with very low vapor pressure in contrast to the conventional solvents.
In this study, ionic liquids were used as a solvent and reactant at the same time for the novel nanomaterials synthesis for different applications including solar cells, gas sensors, and water splitting.
The field of ionic liquids continues to grow, and become one of the most important branches of science. It appears to be at a point where research and industry can work together in a new way of thinking for green chemistry and sustainable production.
Natural hazards such as floods, earthquakes, landslides, and multi-hazard events heavily affect human societies and call for better management strategies. Due to the severity of such events, it is of utmost importance to understand whether and how they change in re-sponse to evolving hydro-climatological, geo-physical and socio-economic conditions. These conditions jointly determine the magnitude, frequency, and impact of disasters, and are changing in response to climate change and human behavior. Therefore methods are need-ed for hazard and risk quantification accounting for the transient nature of hazards and risks in response to changing natural and anthropogenic altered systems. The purpose of this conference is to bring together researchers from natural sciences (e.g. hydrology, meteorology, geomorphology, hydraulic engineering, environmental science, seismology, geography), risk research, nonlinear systems dynamics, and applied mathematics to discuss new insights and developments about data science, changing systems, multi-hazard events and the linkage between hazard and vulnerabilities under unstable environmental conditions. Knowledge transfer, communication and networking will be key issues of the conference. The conference is organized by means of invited talks given by outstanding experts, oral presentations, poster sessions and discussions.