@phdthesis{Šustr2020,
  author    = {Šustr, David},
  title     = {Molecular diffusion in polyelectrolyte multilayers},
  doi       = {10.25932/publishup-48903},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-489038},
  school      = {Universit{\"a}t Potsdam},
  pages     = {106},
  year      = {2020},
  abstract  = {Research on novel and advanced biomaterials is an indispensable step towards their applications in desirable fields such as tissue engineering, regenerative medicine, cell culture, or biotechnology. The work presented here focuses on such a promising material: polyelectrolyte multilayer (PEM) composed of hyaluronic acid (HA) and poly(L-lysine) (PLL). This gel-like polymer surface coating is able to accumulate (bio-)molecules such as proteins or drugs and release them in a controlled manner. It serves as a mimic of the extracellular matrix (ECM) in composition and intrinsic properties. These qualities make the HA/PLL multilayers a promising candidate for multiple bio-applications such as those mentioned above. The work presented aims at the development of a straightforward approach for assessment of multi-fractional diffusion in multilayers (first part) and at control of local molecular transport into or from the multilayers by laser light trigger (second part). The mechanism of the loading and release is governed by the interaction of bioactives with the multilayer constituents and by the diffusion phenomenon overall. The diffusion of a molecule in HA/PLL multilayers shows multiple fractions of different diffusion rate. Approaches, that are able to assess the mobility of molecules in such a complex system, are limited. This shortcoming motivated the design of a novel evaluation tool presented here. The tool employs a simulation-based approach for evaluation of the data acquired by fluorescence recovery after photobleaching (FRAP) method. In this approach, possible fluorescence recovery scenarios are primarily simulated and afterwards compared with the data acquired while optimizing parameters of a model until a sufficient match is achieved. Fluorescent latex particles of different sizes and fluorescein in an aqueous medium are utilized as test samples validating the analysis results. The diffusion of protein cytochrome c in HA/PLL multilayers is evaluated as well. This tool significantly broadens the possibilities of analysis of spatiotemporal FRAP data, which originate from multi-fractional diffusion, while striving to be widely applicable. This tool has the potential to elucidate the mechanisms of molecular transport and empower rational engineering of the drug release systems. The second part of the work focuses on the fabrication of such a spatiotemporarily-controlled drug release system employing the HA/PLL multilayer. This release system comprises different layers of various functionalities that together form a sandwich structure. The bottom layer, which serves as a reservoir, is formed by HA/PLL PEM deposited on a planar glass substrate. On top of the PEM, a layer of so-called hybrids is deposited. The hybrids consist of thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) -based hydrogel microparticles with surface-attached gold nanorods. The layer of hybrids is intended to serve as a gate that controls the local molecular transport through the PEM-solution-interface. The possibility of stimulating the molecular transport by near-infrared (NIR) laser irradiation is being explored. From several tested approaches for the deposition of hybrids onto the PEM surface, the drying-based approach was identified as optimal. Experiments, that examine the functionality of the fabricated sandwich at elevated temperature, document the reversible volume phase transition of the PEM-attached hybrids while sustaining the sandwich stability. Further, the gold nanorods were shown to effectively absorb light radiation in the tissue- and cell-friendly NIR spectral region while transducing the energy of light into heat. The rapid and reversible shrinkage of the PEM-attached hybrids was thereby achieved. Finally, dextran was employed as a model transport molecule. It loads into the PEM reservoir in a few seconds with the partition constant of 2.4, while it spontaneously releases in a slower, sustained manner. The local laser irradiation of the sandwich, which contains the fluorescein isothiocyanate tagged dextran, leads to a gradual reduction of fluorescence intensity in the irradiated region. The release system fabricated employs renowned photoresponsivity of the hybrids in an innovative setting. The results of the research are a step towards a spatially-controlled on-demand drug release system that paves the way to spatiotemporally controlled drug release. The approaches developed in this work have the potential to elucidate the molecular dynamics in ECM and to foster engineering of multilayers with properties tuned to mimic the ECM. The work aims at spatiotemporal control over the diffusion of bioactives and their presentation to the cells.},
  language  = {en}
}
@techreport{ŠedovaČizmaziovaCook2021,
  type      = {Working Paper},
  author    = {Šedov{\´a}, Barbora and Čizmaziov{\´a}, Lucia and Cook, Athene},
  title     = {A meta-analysis of climate migration literature},
  series = {CEPA Discussion Papers},
  journal   = {CEPA Discussion Papers},
  number    = {29},
  issn      = {2628-653X},
  doi       = {10.25932/publishup-49982},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-499827},
  pages     = {83},
  year      = {2021},
  abstract  = {The large literature that aims to find evidence of climate migration delivers mixed findings. This meta-regression analysis i) summarizes direct links between adverse climatic events and migration, ii) maps patterns of climate migration, and iii) explains the variation in outcomes. Using a set of limited dependent variable models, we meta-analyze thus-far the most comprehensive sample of 3,625 estimates from 116 original studies and produce novel insights on climate migration. We find that extremely high temperatures and drying conditions increase migration. We do not find a significant effect of sudden-onset events. Climate migration is most likely to emerge due to contemporaneous events, to originate in rural areas and to take place in middle-income countries, internally, to cities. The likelihood to become trapped in affected areas is higher for women and in low-income countries, particularly in Africa. We uniquely quantify how pitfalls typical for the broader empirical climate impact literature affect climate migration findings. We also find evidence of different publication biases.},
  language  = {en}
}
@article{ŠedovaKalkuhl2020,
  author    = {Šedov{\´a}, Barbora and Kalkuhl, Matthias},
  title     = {Who are the climate migrants and where do they go?},
  series = {World development},
  volume    = {129},
  journal   = {World development},
  publisher = {Elsevier Science},
  address   = {Amsterdam},
  issn      = {0305-750X},
  doi       = {10.1016/j.worlddev.2019.104848},
  pages     = {19},
  year      = {2020},
  abstract  = {In this paper, we move from the large strand of research that looks at evidence of climate migration to the questions: who are the climate migrants? and where do they go? These questions are crucial to design policies that mitigate welfare losses of migration choices due to climate change. We study the direct and heterogeneous associations between weather extremes and migration in rural India. We combine ERAS reanalysis data with the India Human Development Survey household panel and conduct regression analyses by applying linear probability and multinomial logit models. This enables us to establish a causal relationship between temperature and precipitation anomalies and overall migration as well as migration by destination. We show that adverse weather shocks decrease rural-rural and international migration and push people into cities in different, presumably more prosperous states. A series of positive weather shocks, however, facilitates international migration and migration to cities within the same state. Further, our results indicate that in contrast to other migrants, climate migrants are likely to be from the lower end of the skill distribution and from households strongly dependent on agricultural production. We estimate that approximately 8\% of all rural-urban moves between 2005 and 2012 can be attributed to weather. This figure might increase as a consequence of climate change. Thus, a key policy recommendation is to take steps to facilitate integration of less educated migrants into the urban labor market.},
  language  = {en}
}
@phdthesis{Šedova2022,
  author    = {Šedov{\´a}, Barbora},
  title     = {Heterogeneous effects of weather and climate change on human migration},
  doi       = {10.25932/publishup-53673},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-536733},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xix, 284},
  year      = {2022},
  abstract  = {While estimated numbers of past and future climate migrants are alarming, the growing empirical evidence suggests that the association between adverse climate-related events and migration is not universally positive. This dissertation seeks to advance our understanding of when and how climate migration emerges by analyzing heterogeneous climatic influences on migration in low- and middle-income countries. To this end, it draws on established economic theories of migration, datasets from physical and social sciences, causal inference techniques and approaches from systematic literature review. In three of its five chapters, I estimate causal effects of processes of climate change on inequality and migration in India and Sub-Saharan Africa. By employing interaction terms and by analyzing sub-samples of data, I explore how these relationships differ for various segments of the population. In the remaining two chapters, I present two systematic literature reviews. First, I undertake a comprehensive meta-regression analysis of the econometric climate migration literature to summarize general climate migration patterns and explain the conflicting findings. Second, motivated by the broad range of approaches in the field, I examine the literature from a methodological perspective to provide best practice guidelines for studying climate migration empirically. Overall, the evidence from this dissertation shows that climatic influences on human migration are highly heterogeneous. Whether adverse climate-related impacts materialize in migration depends on the socio-economic characteristics of the individual households, such as wealth, level of education, agricultural dependence or access to adaptation technologies and insurance. For instance, I show that while adverse climatic shocks are generally associated with an increase in migration in rural India, they reduce migration in the agricultural context of Sub-Saharan Africa, where the average wealth levels are much lower so that households largely cannot afford the upfront costs of moving. I find that unlike local climatic shocks which primarily enhance internal migration to cities and hence accelerate urbanization, shocks transmitted via agricultural producer prices increase migration to neighboring countries, likely due to the simultaneous decrease in real income in nearby urban areas. These findings advance our current understanding by showing when and how economic agents respond to climatic events, thus providing explicit contexts and mechanisms of climate change effects on migration in the future. The resulting collection of findings can guide policy interventions to avoid or mitigate any present and future welfare losses from climate change-related migration choices.},
  language  = {en}
}
@misc{Şener2017,
  author    = {Şener, Ula{\c{s}}},
  title     = {Rodrik, Dani (2015): Economics Rules: The Rights and Wrongs of the Dismal Science / rezensiert von Ula{\c{s}} Şener},
  series = {European journal of economics and economic policies : intervention ; EJEEP},
  volume    = {14},
  journal   = {European journal of economics and economic policies : intervention ; EJEEP},
  publisher = {Elgar},
  address   = {Cheltenham},
  issn      = {2052-7764},
  doi       = {10.4337/ejeep.2017.03.08},
  pages     = {375 -- 377},
  year      = {2017},
  language  = {en}
}
@misc{ŚlęzakMetzlerMagdziarz2019,
  author    = {Ślęzak, Jakub and Metzler, Ralf and Magdziarz, Marcin},
  title     = {Codifference can detect ergodicity breaking and non-Gaussianity},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {748},
  doi       = {10.25932/publishup-43617},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436178},
  pages     = {25},
  year      = {2019},
  abstract  = {We show that the codifference is a useful tool in studying the ergodicity breaking and non-Gaussianity properties of stochastic time series. While the codifference is a measure of dependence that was previously studied mainly in the context of stable processes, we here extend its range of applicability to random-parameter and diffusing-diffusivity models which are important in contemporary physics, biology and financial engineering. We prove that the codifference detects forms of dependence and ergodicity breaking which are not visible from analysing the covariance and correlation functions. We also discuss a related measure of dispersion, which is a nonlinear analogue of the mean squared displacement.},
  language  = {en}
}
@misc{ŚlęzakMetzlerMagdziarz2018,
  author    = {Ślęzak, Jakub and Metzler, Ralf and Magdziarz, Marcin},
  title     = {Superstatistical generalised Langevin equation},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409315},
  pages     = {25},
  year      = {2018},
  abstract  = {Recent advances in single particle tracking and supercomputing techniques demonstrate the emergence of normal or anomalous, viscoelastic diffusion in conjunction with non-Gaussian distributions in soft, biological, and active matter systems. We here formulate a stochastic model based on a generalised Langevin equation in which non-Gaussian shapes of the probability density function and normal or anomalous diffusion have a common origin, namely a random parametrisation of the stochastic force. We perform a detailed analysis demonstrating how various types of parameter distributions for the memory kernel result in exponential, power law, or power-log law tails of the memory functions. The studied system is also shown to exhibit a further unusual property: the velocity has a Gaussian one point probability density but non-Gaussian joint distributions. This behaviour is reflected in the relaxation from a Gaussian to a non-Gaussian distribution observed for the position variable. We show that our theoretical results are in excellent agreement with stochastic simulations.},
  language  = {en}
}
@article{ŚlęzakMetzlerMagdziarz2018,
  author    = {Ślęzak, Jakub and Metzler, Ralf and Magdziarz, Marcin},
  title     = {Superstatistical generalised Langevin equation},
  series = {New Journal of Physics},
  volume    = {20},
  journal   = {New Journal of Physics},
  number    = {023026},
  publisher = {Deutsche Physikalische Gesellschaft / Institute of Physics},
  address   = {Bad Honnef und London},
  issn      = {1367-2630},
  doi       = {10.1088/1367-2630/aaa3d4},
  pages     = {1 -- 25},
  year      = {2018},
  abstract  = {Recent advances in single particle tracking and supercomputing techniques demonstrate the emergence of normal or anomalous, viscoelastic diffusion in conjunction with non-Gaussian distributions in soft, biological, and active matter systems. We here formulate a stochastic model based on a generalised Langevin equation in which non-Gaussian shapes of the probability density function and normal or anomalous diffusion have a common origin, namely a random parametrisation of the stochastic force. We perform a detailed analysis demonstrating how various types of parameter distributions for the memory kernel result in exponential, power law, or power-log law tails of the memory functions. The studied system is also shown to exhibit a further unusual property: the velocity has a Gaussian one point probability density but non-Gaussian joint distributions. This behaviour is reflected in the relaxation from a Gaussian to a non-Gaussian distribution observed for the position variable. We show that our theoretical results are in excellent agreement with stochastic simulations.},
  language  = {en}
}
@article{ŚlęzakMetzlerMagdziarz2019,
  author    = {Ślęzak, Jakub and Metzler, Ralf and Magdziarz, Marcin},
  title     = {Codifference can detect ergodicity breaking and non-Gaussianity},
  series = {New Journal of Physics},
  volume    = {21},
  journal   = {New Journal of Physics},
  publisher = {Deutsche Physikalische Gesellschaft},
  address   = {Bad Honnef},
  issn      = {1367-2630},
  doi       = {10.1088/1367-2630/ab13f3},
  pages     = {25},
  year      = {2019},
  abstract  = {We show that the codifference is a useful tool in studying the ergodicity breaking and non-Gaussianity properties of stochastic time series. While the codifference is a measure of dependence that was previously studied mainly in the context of stable processes, we here extend its range of applicability to random-parameter and diffusing-diffusivity models which are important in contemporary physics, biology and financial engineering. We prove that the codifference detects forms of dependence and ergodicity breaking which are not visible from analysing the covariance and correlation functions. We also discuss a related measure of dispersion, which is a nonlinear analogue of the mean squared displacement.},
  language  = {en}
}
@misc{ŚlęzakBurneckiMetzler2019,
  author    = {Ślęzak, Jakub and Burnecki, Krzysztof and Metzler, Ralf},
  title     = {Random coefficient autoregressive processes describe Brownian yet non-Gaussian diffusion in heterogeneous systems},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {765},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43792},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437923},
  pages     = {18},
  year      = {2019},
  abstract  = {Many studies on biological and soft matter systems report the joint presence of a linear mean-squared displacement and a non-Gaussian probability density exhibiting, for instance, exponential or stretched-Gaussian tails. This phenomenon is ascribed to the heterogeneity of the medium and is captured by random parameter models such as 'superstatistics' or 'diffusing diffusivity'. Independently, scientists working in the area of time series analysis and statistics have studied a class of discrete-time processes with similar properties, namely, random coefficient autoregressive models. In this work we try to reconcile these two approaches and thus provide a bridge between physical stochastic processes and autoregressive models.Westart from the basic Langevin equation of motion with time-varying damping or diffusion coefficients and establish the link to random coefficient autoregressive processes. By exploring that link we gain access to efficient statistical methods which can help to identify data exhibiting Brownian yet non-Gaussian diffusion.},
  language  = {en}
}
@article{ŚlęzakBurneckiMetzler2019,
  author    = {Ślęzak, Jakub and Burnecki, Krzysztof and Metzler, Ralf},
  title     = {Random coefficient autoregressive processes describe Brownian yet non-Gaussian diffusion in heterogeneous systems},
  series = {New Journal of Physics},
  volume    = {21},
  journal   = {New Journal of Physics},
  publisher = {Deutsche Physikalische Gesellschaft ; IOP, Institute of Physics},
  address   = {Bad Honnef und London},
  issn      = {1367-2630},
  doi       = {10.1088/1367-2630/ab3366},
  pages     = {18},
  year      = {2019},
  abstract  = {Many studies on biological and soft matter systems report the joint presence of a linear mean-squared displacement and a non-Gaussian probability density exhibiting, for instance, exponential or stretched-Gaussian tails. This phenomenon is ascribed to the heterogeneity of the medium and is captured by random parameter models such as 'superstatistics' or 'diffusing diffusivity'. Independently, scientists working in the area of time series analysis and statistics have studied a class of discrete-time processes with similar properties, namely, random coefficient autoregressive models. In this work we try to reconcile these two approaches and thus provide a bridge between physical stochastic processes and autoregressive models.Westart from the basic Langevin equation of motion with time-varying damping or diffusion coefficients and establish the link to random coefficient autoregressive processes. By exploring that link we gain access to efficient statistical methods which can help to identify data exhibiting Brownian yet non-Gaussian diffusion.},
  language  = {en}
}
@misc{ĆwiekKupczyńskaAltmannArendetal.2016,
  author    = {Ćwiek-Kupczyńska, Hanna and Altmann, Thomas and Arend, Daniel and Arnaud, Elizabeth and Chen, Dijun and Cornut, Guillaume and Fiorani, Fabio and Frohmberg, Wojciech and Junker, Astrid and Klukas, Christian and Lange, Matthias and Mazurek, Cezary and Nafissi, Anahita and Neveu, Pascal and van Oeveren, Jan and Pommier, Cyril and Poorter, Hendrik and Rocca-Serra, Philippe and Sansone, Susanna-Assunta and Scholz, Uwe and van Schriek, Marco and Seren, {\"U}mit and Usadel, Bj{\"o}rn and Weise, Stephan and Kersey, Paul and Krajewski, Paweł},
  title     = {Measures for interoperability of phenotypic data},
  series = {Plant methods},
  journal   = {Plant methods},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407299},
  pages     = {18},
  year      = {2016},
  abstract  = {Background: Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time ‑consuming experiments, the findings can be fostered by reusing and combin‑ ing existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse. Results: In this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a docu‑ ment called "Minimum Information About a Plant Phenotyping Experiment", which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA ‑Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA ‑Tab ‑formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented. Conclusions: Acceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data.},
  language  = {en}
}
@article{UestuenSheikhGimenezIbanezetal.2016,
  author    = {{\"U}st{\"u}n, Suayib and Sheikh, Arsheed and Gimenez-Ibanez, Selena and Jones, Alexandra and Ntoukakis, Vardis and B{\"o}rnke, Frederik},
  title     = {The Proteasome Acts as a Hub for Plant Immunity and Is Targeted by Pseudomonas Type III Effectors},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {172},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.16.00808},
  pages     = {1941 -- 1958},
  year      = {2016},
  abstract  = {Recent evidence suggests that the ubiquitin-proteasome system is involved in several aspects of plant immunity and that a range of plant pathogens subvert the ubiquitin-proteasome system to enhance their virulence. Here, we show that proteasome activity is strongly induced during basal defense in Arabidopsis (Arabidopsis thaliana). Mutant lines of the proteasome subunits RPT2a and RPN12a support increased bacterial growth of virulent Pseudomonas syringae pv tomato DC3000 (Pst) and Pseudomonas syringae pv maculicola ES4326. Both proteasome subunits are required for pathogen-associated molecular pattern-triggered immunity responses. Analysis of bacterial growth after a secondary infection of systemic leaves revealed that the establishment of systemic acquired resistance (SAR) is impaired in proteasome mutants, suggesting that the proteasome also plays an important role in defense priming and SAR. In addition, we show that Pst inhibits proteasome activity in a type III secretion-dependent manner. A screen for type III effector proteins from Pst for their ability to interfere with proteasome activity revealed HopM1, HopAO1, HopA1, and HopG1 as putative proteasome inhibitors. Biochemical characterization of HopM1 by mass spectrometry indicates that HopM1 interacts with several E3 ubiquitin ligases and proteasome subunits. This supports the hypothesis that HopM1 associates with the proteasome, leading to its inhibition. Thus, the proteasome is an essential component of pathogen-associated molecular pattern-triggered immunity and SAR, which is targeted by multiple bacterial effectors.},
  language  = {en}
}
@misc{UestuenBartetzkoBoernke2015,
  author    = {{\"U}st{\"u}n, Suayib and Bartetzko, Verena and B{\"o}rnke, Frederik},
  title     = {The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid},
  series = {Frontiers in plant science},
  journal   = {Frontiers in plant science},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-406537},
  pages     = {11},
  year      = {2015},
  abstract  = {XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) - dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) -like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana.},
  language  = {en}
}
@article{UestuenBartetzkoBoernke2015,
  author    = {{\"U}st{\"u}n, Suayib and Bartetzko, Verena and B{\"o}rnke, Frederik},
  title     = {The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid},
  series = {Frontiers in plant science},
  volume    = {6},
  journal   = {Frontiers in plant science},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2015.00599},
  pages     = {11},
  year      = {2015},
  abstract  = {XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) - dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) -like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana.},
  language  = {en}
}
@article{OeztuerkMarwanvonSpechtetal.2018,
  author    = {{\"O}zt{\"u}rk, Ugur and Marwan, Norbert and von Specht, Sebastian and Korup, Oliver and Jensen, J.},
  title     = {A new centennial sea-level record for Antalya, Eastern Mediterranean},
  series = {Journal of geophysical research-oceans},
  volume    = {123},
  journal   = {Journal of geophysical research-oceans},
  number    = {7},
  publisher = {American Geophysical Union},
  address   = {Washington},
  issn      = {2169-9275},
  doi       = {10.1029/2018JC013906},
  pages     = {4503 -- 4517},
  year      = {2018},
  abstract  = {Quantitative estimates of sea-level rise in the Mediterranean Basin become increasingly accurate thanks to detailed satellite monitoring. However, such measuring campaigns cover several years to decades, while longer-term sea-level records are rare for the Mediterranean. We used a data archeological approach to reanalyze monthly mean sea-level data of the Antalya-I (1935-1977) tide gauge to fill this gap. We checked the accuracy and reliability of these data before merging them with the more recent records of the Antalya-II (1985-2009) tide gauge, accounting for an eight-year hiatus. We obtain a composite time series of monthly and annual mean sea levels spanning some 75 years, providing the longest record for the eastern Mediterranean Basin, and thus an essential tool for studying the region's recent sea-level trends. We estimate a relative mean sea-level rise of 2.2 ± 0.5 mm/year between 1935 and 2008, with an annual variability (expressed here as the standard deviation of the residuals, σresiduals = 41.4 mm) above that at the closest tide gauges (e.g., Thessaloniki, Greece, σresiduals = 29.0 mm). Relative sea-level rise accelerated to 6.0 ± 1.5 mm/year at Antalya-II; we attribute roughly half of this rate (~3.6 mm/year) to tectonic crustal motion and anthropogenic land subsidence. Our study highlights the value of data archeology for recovering and integrating historic tide gauge data for long-term sea-level and climate studies.},
  language  = {en}
}
@article{OeztuerkBozzolanHolcombeetal.2022,
  author    = {{\"O}zt{\"u}rk, Ugur and Bozzolan, Elisa and Holcombe, Elizabeth A. and Shukla, Roopam and Pianosi, Francesca and Wagener, Thorsten},
  title     = {How climate change and unplanned urban sprawl bring more landslides},
  series = {Nature : the international weekly journal of science},
  volume    = {608},
  journal   = {Nature : the international weekly journal of science},
  number    = {7922},
  publisher = {Nature portfolio},
  address   = {Berlin},
  issn      = {0028-0836},
  doi       = {10.1038/d41586-022-02141-9},
  pages     = {262 -- 265},
  year      = {2022},
  abstract  = {More settlements will suffer as heavy rains and unregulated construction destabilize slopes in the tropics, models show.},
  language  = {en}
}
@phdthesis{Oeztuerk2018,
  author    = {{\"O}zt{\"u}rk, Ugur},
  title     = {Learning more to predict landslides},
  doi       = {10.25932/publishup-42643},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-426439},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xxi, 104},
  year      = {2018},
  abstract  = {Landslides are frequent natural hazards in rugged terrain, when the resisting frictional force of the surface of rupture yields to the gravitational force. These forces are functions of geological and morphological factors, such as angle of internal friction, local slope gradient or curvature, which remain static over hundreds of years; whereas more dynamic triggering events, such as rainfall and earthquakes, compromise the force balance by temporarily reducing resisting forces or adding transient loads. This thesis investigates landslide distribution and orientation due to landslide triggers (e.g. rainfall) at different scales (6-4∙10^5 km^2) and aims to link rainfall movement with the landslide distribution. It additionally explores the local impacts of the extreme rainstorms on landsliding and the role of precursory stability conditions that could be induced by an earlier trigger, such as an earthquake. Extreme rainfall is a common landslide trigger. Although several studies assessed rainfall intensity and duration to study the distribution of thus triggered landslides, only a few case studies quantified spatial rainfall patterns (i.e. orographic effect). Quantifying the regional trajectories of extreme rainfall could aid predicting landslide prone regions in Japan. To this end, I combined a non-linear correlation metric, namely event synchronization, and radial statistics to assess the general pattern of extreme rainfall tracks over distances of hundreds of kilometers using satellite based rainfall estimates. Results showed that, although the increase in rainfall intensity and duration positively correlates with landslide occurrence, the trajectories of typhoons and frontal storms were insufficient to explain landslide distribution in Japan. Extreme rainfall trajectories inclined northwestwards and were concentrated along some certain locations, such as coastlines of southern Japan, which was unnoticed in the landslide distribution of about 5000 rainfall-triggered landslides. These landslides seemed to respond to the mean annual rainfall rates. Above mentioned findings suggest further investigation on a more local scale to better understand the mechanistic response of landscape to extreme rainfall in terms of landslides. On May 2016 intense rainfall struck southern Germany triggering high waters and landslides. The highest damage was reported at the Braunsbach, which is located on the tributary-mouth fan formed by the Orlacher Bach. Orlacher Bach is a ~3 km long creek that drains a catchment of about ~6 km^2. I visited this catchment in June 2016 and mapped 48 landslides along the creek. Such high landslide activity was not reported in the nearby catchments within ~3300 km^2, despite similar rainfall intensity and duration based on weather radar estimates. My hypothesis was that several landslides were triggered by rainfall-triggered flash floods that undercut hillslope toes along the Orlacher Bach. I found that morphometric features such as slope and curvature play an important role in landslide distribution on this micro scale study site (<10 km^2). In addition, the high number of landslides along the Orlacher Bach could also be boosted by accumulated damages on hillslopes due karst weathering over longer time scales. Precursory damages on hillslopes could also be induced by past triggering events that effect landscape evolution, but this interaction is hard to assess independently from the latest trigger. For example, an earthquake might influence the evolution of a landscape decades long, besides its direct impacts, such as landslides that follow the earthquake. Here I studied the consequences of the 2016 Kumamoto Earthquake (MW 7.1) that triggered some 1500 landslides in an area of ~4000 km^2 in central Kyushu, Japan. Topography, i.e. local slope and curvature, both amplified and attenuated seismic waves, thus controlling the failure mechanism of those landslides (e.g. progressive). I found that topography fails in explaining the distribution and the preferred orientation of the landslides after the earthquake; instead the landslides were concentrated around the northeast of the rupture area and faced mostly normal to the rupture plane. This preferred location of the landslides was dominated mainly by the directivity effect of the strike-slip earthquake, which is the propagation of wave energy along the fault in the rupture direction; whereas amplitude variations of the seismic radiation altered the preferred orientation. I suspect that the earthquake directivity and the asymmetry of seismic radiation damaged hillslopes at those preferred locations increasing landslide susceptibility. Hence a future weak triggering event, e.g. scattered rainfall, could further trigger landslides at those damaged hillslopes.},
  language  = {en}
}
@article{OezkanFikriKırkıcıetal.2020,
  author    = {{\"O}zkan, Ay{\c{s}}eg{\"u}l and Fikri, Figen Beken and K{\i}rk{\i}c{\i}, Bilal and Kliegl, Reinhold and Acart{\"u}rk, Cengiz},
  title     = {Eye movement control in Turkish sentence reading},
  series = {Quarterly journal of experimental psychology : QJEP / EPS, Experimental Psychology Society},
  volume    = {74},
  journal   = {Quarterly journal of experimental psychology : QJEP / EPS, Experimental Psychology Society},
  number    = {2},
  publisher = {Sage Publ.},
  address   = {London},
  issn      = {1747-0218},
  doi       = {10.1177/1747021820963310},
  pages     = {377 -- 397},
  year      = {2020},
  abstract  = {Reading requires the assembly of cognitive processes across a wide spectrum from low-level visual perception to high-level discourse comprehension. One approach of unravelling the dynamics associated with these processes is to determine how eye movements are influenced by the characteristics of the text, in particular which features of the words within the perceptual span maximise the information intake due to foveal, spillover, parafoveal, and predictive processing. One way to test the generalisability of current proposals of such distributed processing is to examine them across different languages. For Turkish, an agglutinative language with a shallow orthography-phonology mapping, we replicate the well-known canonical main effects of frequency and predictability of the fixated word as well as effects of incoming saccade amplitude and fixation location within the word on single-fixation durations with data from 35 adults reading 120 nine-word sentences. Evidence for previously reported effects of the characteristics of neighbouring words and interactions was mixed. There was no evidence for the expected Turkish-specific morphological effect of the number of inflectional suffixes on single-fixation durations. To control for word-selection bias associated with single-fixation durations, we also tested effects on word skipping, single-fixation, and multiple-fixation cases with a base-line category logit model, assuming an increase of difficulty for an increase in the number of fixations. With this model, significant effects of word characteristics and number of inflectional suffixes of foveal word on probabilities of the number of fixations were observed, while the effects of the characteristics of neighbouring words and interactions were mixed.},
  language  = {en}
}
@article{OezerScheffler2018,
  author    = {{\"O}zer, Aydan and Scheffler, Christiane},
  title     = {Affinity to host population stimulates physical growth in adult offspring of Turkish migrants in Germany},
  series = {Journal of biological and clinical anthropology},
  volume    = {74},
  journal   = {Journal of biological and clinical anthropology},
  number    = {5},
  publisher = {Schweizerbart},
  address   = {Stuttgart},
  issn      = {0003-5548},
  doi       = {10.1127/anthranz/2018/0825},
  pages     = {359 -- 364},
  year      = {2018},
  abstract  = {Because of political conflicts and climate change, migration will be increased worldwide and integration in host societies is a challenge also for migrants. We hypothesize that migrants, who take up the challenge in a new social environment are taller than migrants who do not pose this challenge. We analyze by a questionnaire possible social, nutritional and ethnic influencing factors to body height (BH) of adult offspring of Turkish migrants (n = 82, 39 males) aged from 18 to 34 years (mean age 24.6 years). The results of multiple regression (downward selection) show that the more a male adult offspring of Turkish migrants feels like belonging to the Turkish culture, the smaller he is (95\% CI, -3.79, -0.323). Further, the more a male adult offspring of Turkish migrants feels like belonging to the German culture, the taller he is (95\% CI, -0.152, 1.738). We discussed it comparable to primates taking up their challenge in dominance, where as a result their body size increase is associated with higher IGF-1 level. IGF-1 is associated with emotional belonging and has a fundamental role in the regulation of metabolism and growth of the human body. With all pilot characteristics of our study results show that the successful challenge of integration in a new society is strongly associated with the emotional integration and identification in the sense of a personal sense of belonging to society. We discuss taller BH as a signal of social growth adjustment. In this sense, a secular trend of BH adaptation of migrants to hosts is a sign of integration.},
  language  = {en}
}