TY - JOUR A1 - Wieland, Ralf A1 - Dalchow, Claus A1 - Sommer, Michael A1 - Fukuda, Kyoko T1 - Multi-Scale Landscape Analysis (MSLA) a method to identify correlation of relief with ecological point data JF - Ecological informatics : an international journal on ecoinformatics and computational ecolog N2 - A common problem in ecology is identifying the relationship between relief and site properties obtainable only by point measurements. The method of Multi-Scale Landscape Analysis (MSLA) identifies such correlations. MSLA combines frequency filtering of the digital elevation model (DEM) with an estimation of the optimum filter coefficients using an optimization procedure. Tested using point data of soil decarbonation from a German young moraine landscape, MSLA provided significant results. Implemented within open source software SAMT. MSLA is comfortable and flexible to use, offering applications for numerous other spatial analysis problems. KW - Landscape structure KW - DEM KW - Fourier transformation KW - Wavelet transformation KW - Singular value decomposition KW - SAMT Y1 - 2011 U6 - https://doi.org/10.1016/j.ecoinf.2010.09.002 SN - 1574-9541 VL - 6 IS - 2 SP - 164 EP - 169 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Hempel, Sabrina A1 - Koseska, Aneta A1 - Nikoloski, Zoran A1 - Kurths, Jürgen T1 - Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study JF - BMC bioinformatics N2 - Background: Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications. Results: Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study. Conclusions: Our study is intended to serve as a guide for choosing a particular combination of similarity measures and scoring schemes suitable for reconstruction of gene regulatory networks from short time series data. We show that further improvement of algorithms for reverse engineering can be obtained if one considers measures that are rooted in the study of symbolic dynamics or ranks, in contrast to the application of common similarity measures which do not consider the temporal character of the employed data. Moreover, we establish that the asymmetric weighting scoring scheme together with symbol based measures (for low noise level) and rank based measures (for high noise level) are the most suitable choices. Y1 - 2011 U6 - https://doi.org/10.1186/1471-2105-12-292 SN - 1471-2105 VL - 12 IS - 1 PB - BioMed Central CY - London ER - TY - JOUR A1 - Sanhueza-Pino, Katia A1 - Korup, Oliver A1 - Hetzel, Ralf A1 - Munack, Henry A1 - Weidinger, Johannes T. A1 - Dunning, Stuart A. A1 - Ormukov, Cholponbek A1 - Kubik, Peter W. T1 - Glacial advances constrained by Be-10 exposure dating of bedrock landslides, Kyrgyz Tien Shan JF - Quaternary research : an interdisciplinary journal N2 - Numerous large landslide deposits occur in the Tien Shan, a tectonically active intraplate orogen in Central Asia. Yet their significance in Quaternary landscape evolution and natural hazard assessment remains unresolved due to the lack of "absolute" age constraints. Here we present the first Be-10 exposure ages for three prominent (>10(7) m(3)) bedrock landslides that blocked major rivers and formed lakes, two of which subsequently breached, in the northern Kyrgyz Tien Shan. Three Be-10 ages reveal that one landslide in the Alamyedin River occurred at 11-15 ka, which is consistent with two C-14 ages of gastropod shells from reworked loess capping the landslide. One large landslide in Aksu River is among the oldest documented in semi-arid continental interiors, with a Be-10 age of 63-67 ka. The Ukok River landslide deposit(s) yielded variable Be-10 ages, which may result from multiple landslides, and inheritance of Be-10. Two Be-10 ages of 8.2 and 5.9 ka suggest that one major landslide occurred in the early to mid-Holocene, followed by at least one other event between 1.5 and 0.4 ka. Judging from the regional glacial chronology, all three landslides have occurred between major regional glacial advances. Whereas Alamyedin and Ukok can be considered as postglacial in this context, Aksu is of interglacial age. None of the landslide deposits show traces of glacial erosion, hence their locations and I Be ages mark maximum extents and minimum ages of glacial advances, respectively. Using toe-to-headwall altitude ratios of 0.4-0.5, we reconstruct minimum equilibrium-line altitudes that exceed previous estimates by as much as 400 m along the moister northern fringe of the Tien Shan. Our data show that deposits from large landslides can provide valuable spatio-temporal constraints for glacial advances in landscapes where moraines and glacial deposits have low preservation potential. (C) 2011 University of Washington. Published by Elsevier Inc. All rights reserved. KW - Landslide KW - Rock avalanche KW - Be-10 exposure dating KW - Quaternary glaciations KW - Tien Shan Y1 - 2011 U6 - https://doi.org/10.1016/j.yqres.2011.06.013 SN - 0033-5894 VL - 76 IS - 3 SP - 295 EP - 304 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Donges, Jonathan A1 - Donner, Reik Volker A1 - Trauth, Martin H. A1 - Marwan, Norbert A1 - Schellnhuber, Hans Joachim A1 - Kurths, Jürgen T1 - Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Potential paleoclimatic driving mechanisms acting on human evolution present an open problem of cross-disciplinary scientific interest. The analysis of paleoclimate archives encoding the environmental variability in East Africa during the past 5 Ma has triggered an ongoing debate about possible candidate processes and evolutionary mechanisms. In this work, we apply a nonlinear statistical technique, recurrence network analysis, to three distinct marine records of terrigenous dust flux. Our method enables us to identify three epochs with transitions between qualitatively different types of environmental variability in North and East Africa during the (i) Middle Pliocene (3.35-3.15 Ma B. P.), (ii) Early Pleistocene (2.25-1.6 Ma B. P.), and (iii) Middle Pleistocene (1.1-0.7 Ma B. P.). A deeper examination of these transition periods reveals potential climatic drivers, including (i) large-scale changes in ocean currents due to a spatial shift of the Indonesian throughflow in combination with an intensification of Northern Hemisphere glaciation, (ii) a global reorganization of the atmospheric Walker circulation induced in the tropical Pacific and Indian Ocean, and (iii) shifts in the dominating temporal variability pattern of glacial activity during the Middle Pleistocene, respectively. A reexamination of the available fossil record demonstrates statistically significant coincidences between the detected transition periods and major steps in hominin evolution. This result suggests that the observed shifts between more regular and more erratic environmental variability may have acted as a trigger for rapid change in the development of humankind in Africa. KW - African climate KW - Plio-Pleistocene KW - climate-driven evolution KW - dynamical transitions KW - nonlinear time series analysis Y1 - 2011 U6 - https://doi.org/10.1073/pnas.1117052108 SN - 0027-8424 VL - 108 IS - 51 SP - 20422 EP - 20427 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Huang, Tingwen A1 - Chen, Guanrong A1 - Kurths, Jürgen T1 - Synchronization of chaotic of chaotic systems with time-varying coupöing delays JF - Discrete and continuous dynamical systems : a journal bridging mathematics and sciences ; Series B, Mathematical modelling, analysis and computations N2 - In this paper, we study the complete synchronization of a class of time-varying delayed coupled chaotic systems using feedback control. In terms of Linear Matrix Inequalities, a sufficient condition is obtained through using a Lyapunov-Krasovskii functional and differential equation in equalities. The conditions can be easily verified and implemented. We present two simulation examples to illustrate the effectiveness of the proposed method. KW - Synchronization KW - Chaotic System KW - Time-varying Delay Y1 - 2011 U6 - https://doi.org/10.3934/dcdsb.2011.16.1071 SN - 1531-3492 VL - 16 IS - 4 SP - 1071 EP - 1082 PB - American Institute of Mathematical Sciences CY - Springfield ER - TY - JOUR A1 - Koseska, Aneta A1 - Volkov, Evgenii A1 - Kurths, Jürgen T1 - Synthetic multicellular oscillatory systems controlling protein dynamics with genetic circuits JF - Physica scripta : an international journal for experimental and theoretical physics N2 - Synthetic biology is a relatively new research discipline that combines standard biology approaches with the constructive nature of engineering. Thus, recent efforts in the field of synthetic biology have given a perspective to consider cells as 'programmable matter'. Here, we address the possibility of using synthetic circuits to control protein dynamics. In particular, we show how intercellular communication and stochasticity can be used to manipulate the dynamical behavior of a population of coupled synthetic units and, in this manner, finely tune the expression of specific proteins of interest, e.g. in large bioreactors. Y1 - 2011 U6 - https://doi.org/10.1088/0031-8949/84/04/045007 SN - 0031-8949 VL - 84 IS - 4 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Hempel, Stefan A1 - Koseska, Aneta A1 - Kurths, Jürgen A1 - Nikoloski, Zoran T1 - Inner composition alignment for inferring directed networks from short time series JF - Physical review letters N2 - Identifying causal links (couplings) is a fundamental problem that facilitates the understanding of emerging structures in complex networks. We propose and analyze inner composition alignment-a novel, permutation-based asymmetric association measure to detect regulatory links from very short time series, currently applied to gene expression. The measure can be used to infer the direction of couplings, detect indirect (superfluous) links, and account for autoregulation. Applications to the gene regulatory network of E. coli are presented. Y1 - 2011 U6 - https://doi.org/10.1103/PhysRevLett.107.054101 SN - 0031-9007 VL - 107 IS - 5 PB - American Physical Society CY - College Park ER - TY - THES A1 - Bergner, André T1 - Synchronization in complex systems with multiple time scales T1 - Synchronisation in komplexen Systemen mit mehreren Zeitskalen N2 - In the present work synchronization phenomena in complex dynamical systems exhibiting multiple time scales have been analyzed. Multiple time scales can be active in different manners. Three different systems have been analyzed with different methods from data analysis. The first system studied is a large heterogenous network of bursting neurons, that is a system with two predominant time scales, the fast firing of action potentials (spikes) and the burst of repetitive spikes followed by a quiescent phase. This system has been integrated numerically and analyzed with methods based on recurrence in phase space. An interesting result are the different transitions to synchrony found in the two distinct time scales. Moreover, an anomalous synchronization effect can be observed in the fast time scale, i.e. there is range of the coupling strength where desynchronization occurs. The second system analyzed, numerically as well as experimentally, is a pair of coupled CO₂ lasers in a chaotic bursting regime. This system is interesting due to its similarity with epidemic models. We explain the bursts by different time scales generated from unstable periodic orbits embedded in the chaotic attractor and perform a synchronization analysis of these different orbits utilizing the continuous wavelet transform. We find a diverse route to synchrony of these different observed time scales. The last system studied is a small network motif of limit cycle oscillators. Precisely, we have studied a hub motif, which serves as elementary building block for scale-free networks, a type of network found in many real world applications. These hubs are of special importance for communication and information transfer in complex networks. Here, a detailed study on the mechanism of synchronization in oscillatory networks with a broad frequency distribution has been carried out. In particular, we find a remote synchronization of nodes in the network which are not directly coupled. We also explain the responsible mechanism and its limitations and constraints. Further we derive an analytic expression for it and show that information transmission in pure phase oscillators, such as the Kuramoto type, is limited. In addition to the numerical and analytic analysis an experiment consisting of electrical circuits has been designed. The obtained results confirm the former findings. N2 - In der vorliegenden Arbeit wurden Synchronisationsphänomene in komplexen Systemen mit mehreren Zeitskalen untersucht. Es gibt mehrere Möglichkeiten wie diese verschiedenen Zeitskalen vorkommen können. Drei verschiedene Systeme, jedes mit einer anderen Art von zeitlicher Multiskalität, wurden mit unterschiedlichen Methoden der Datenanalyse untersucht. Das erste untersuchte System ist ein ausgedehntes heterogenes Netzwerk von Neuronen mit zwei dominanten Zeitskalen, zum einen die schnelle Folge von Aktionspotenzialen und zum anderen einer abwechselnden Folge von einer Phase von Aktionspotenzialen und einer Ruhephase. Dieses System wurde numerisch integriert und mit Methoden der Phasenraumrekurrenz untersucht. Ein interessantes Ergebnis ist der unterschiedliche Übergang zur Synchronisation der Neuronen auf den beiden verschiedenen Zeitskalen. Des weiteren kann auf der schnellen Zeitskala eine anomale Synchronisation beobachtet werden, d.h. es gibt einen Bereich der Kopplungsstärke in dem es zu einer Desynchronisation kommt. Als zweites wurde, sowohl numerisch als auch experimentell, ein System von gekoppelten CO₂ Lasern untersucht, welche in einem chaotischen bursting Modus arbeiten. Dieses System ist auch durch seine Äquivalenz zu Epidemiemodellen interessant. Wir erklären die Bursts durch unterschiedliche Zeitskalen, welche durch in den chaotischen Attraktor eingebettete instabile periodische Orbits generiert werden. Wir führen eine Synchronisationsanalyse mit Hilfe der kontinuierlichen Wavelettransformation durch und finden einen unterschiedlichen Übergang zur Synchronisation auf den unterschiedlichen Zeitskalen. Das dritte analysierte System ist ein Netzwerkmotiv von Grenzzyklusoszillatoren. Genauer handelt es sich um ein Nabenmotiv, welches einen elementaren Grundbaustein von skalenfreien Netzwerken darstellt, das sind Netzwerke die eine bedeutende Rolle in vielen realen Anwendungen spielen. Diese Naben sind von besonderer Bedeutung für die Kommunikation und den Informationstransport in komplexen Netzwerken. Hierbei wurde eine detaillierte Untersuchung des Synchronisationsmechanismus in oszillatorischen Netzwerken mit einer breiten Frequenzverteilung durchgeführt. Insbesondere beobachten wir eine Fernsynchronisation von Netzwerkknoten, die nur indirekt über andere Oszillatoren miteinander gekoppelt sind. Wir erklären den zu Grunde liegenden Mechanismus und zeigen dessen Grenzen und Bedingungen auf. Des weiteren leiten wir einen analytischen Ausdruck für den Mechanismus her und zeigen, dass eine Informationsübertragung in reinen Phasenoszillatoren, wie beispielsweise vom Kuramototyp, eingeschränkt ist. Diese Ergebnisse konnten wir durch Experimente mit elektrischen Schaltkreisen bestätigen. KW - Komplexe Systeme KW - Synchronisation KW - Nichtlineare Dynamik KW - Datenanalyse KW - complex systems KW - synchronization KW - nonlinear dynamics KW - data analysis Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-53407 ER - TY - JOUR A1 - Grimbs, Sergio A1 - Arnold, Anne A1 - Koseska, Aneta A1 - Kurths, Jürgen A1 - Selbig, Joachim A1 - Nikoloski, Zoran T1 - Spatiotemporal dynamics of the Calvin cycle multistationarity and symmetry breaking instabilities JF - Biosystems : journal of biological and information processing sciences N2 - The possibility of controlling the Calvin cycle has paramount implications for increasing the production of biomass. Multistationarity, as a dynamical feature of systems, is the first obvious candidate whose control could find biotechnological applications. Here we set out to resolve the debate on the multistationarity of the Calvin cycle. Unlike the existing simulation-based studies, our approach is based on a sound mathematical framework, chemical reaction network theory and algebraic geometry, which results in provable results for the investigated model of the Calvin cycle in which we embed a hierarchy of realistic kinetic laws. Our theoretical findings demonstrate that there is a possibility for multistationarity resulting from two sources, homogeneous and inhomogeneous instabilities, which partially settle the debate on multistability of the Calvin cycle. In addition, our tractable analytical treatment of the bifurcation parameters can be employed in the design of validation experiments. KW - Multistationarity KW - Calvin cycle KW - Algebraic geometry KW - Bifurcation parameters KW - Biomass Y1 - 2011 U6 - https://doi.org/10.1016/j.biosystems.2010.10.015 SN - 0303-2647 VL - 103 IS - 2 SP - 212 EP - 223 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Donges, Jonathan A1 - Donner, Reik Volker A1 - Rehfeld, Kira A1 - Marwan, Norbert A1 - Trauth, Martin H. A1 - Kurths, Jürgen T1 - Identification of dynamical transitions in marine palaeoclimate records by recurrence network analysis JF - Nonlinear processes in geophysics N2 - The analysis of palaeoclimate time series is usually affected by severe methodological problems, resulting primarily from non-equidistant sampling and uncertain age models. As an alternative to existing methods of time series analysis, in this paper we argue that the statistical properties of recurrence networks - a recently developed approach - are promising candidates for characterising the system's nonlinear dynamics and quantifying structural changes in its reconstructed phase space as time evolves. In a first order approximation, the results of recurrence network analysis are invariant to changes in the age model and are not directly affected by non-equidistant sampling of the data. Specifically, we investigate the behaviour of recurrence network measures for both paradigmatic model systems with non-stationary parameters and four marine records of long-term palaeoclimate variations. We show that the obtained results are qualitatively robust under changes of the relevant parameters of our method, including detrending, size of the running window used for analysis, and embedding delay. We demonstrate that recurrence network analysis is able to detect relevant regime shifts in synthetic data as well as in problematic geoscientific time series. This suggests its application as a general exploratory tool of time series analysis complementing existing methods. Y1 - 2011 U6 - https://doi.org/10.5194/npg-18-545-2011 SN - 1023-5809 VL - 18 IS - 5 SP - 545 EP - 562 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Srinivasan, K. A1 - Senthilkumar, Dharmapuri Vijayan A1 - Murali, K. A1 - Lakshmanan, Muthusamy A1 - Kurths, Jürgen T1 - Synchronization transitions in coupled time-delay electronic circuits with a threshold nonlinearity JF - Chaos : an interdisciplinary journal of nonlinear science N2 - Experimental observations of typical kinds of synchronization transitions are reported in unidirectionally coupled time-delay electronic circuits with a threshold nonlinearity and two time delays, namely feedback delay tau(1) and coupling delay tau(2). We have observed transitions from anticipatory to lag via complete synchronization and their inverse counterparts with excitatory and inhibitory couplings, respectively, as a function of the coupling delay tau(2). The anticipating and lag times depend on the difference between the feedback and the coupling delays. A single stability condition for all the different types of synchronization is found to be valid as the stability condition is independent of both the delays. Further, the existence of different kinds of synchronizations observed experimentally is corroborated by numerical simulations and from the changes in the Lyapunov exponents of the coupled time-delay systems. Y1 - 2011 U6 - https://doi.org/10.1063/1.3591791 SN - 1054-1500 VL - 21 IS - 2 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Zakharova, Anna A1 - Kurths, Jürgen A1 - Vadivasova, Tatyana A1 - Koseska, Aneta T1 - Analysing dynamical behavior of cellular networks via stochastic bifurcations JF - PLoS one N2 - The dynamical structure of genetic networks determines the occurrence of various biological mechanisms, such as cellular differentiation. However, the question of how cellular diversity evolves in relation to the inherent stochasticity and intercellular communication remains still to be understood. Here, we define a concept of stochastic bifurcations suitable to investigate the dynamical structure of genetic networks, and show that under stochastic influence, the expression of given proteins of interest is defined via the probability distribution of the phase variable, representing one of the genes constituting the system. Moreover, we show that under changing stochastic conditions, the probabilities of expressing certain concentration values are different, leading to different functionality of the cells, and thus to differentiation of the cells in the various types. Y1 - 2011 U6 - https://doi.org/10.1371/journal.pone.0019696 SN - 1932-6203 VL - 6 IS - 5 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Parisi, Serena A1 - Paternoster, Michele A1 - Kohfahl, Claus A1 - Pekdeger, Asaf A1 - Meyer, Hanno A1 - Hubberten, Hans-Wolfgang A1 - Spilotro, Giuseppe A1 - Mongelli, Giovanni T1 - Groundwater recharge areas of a volcanic aquifer system inferred from hydraulic, hydrogeochemical and stable isotope data mount Vulture, southern Italy JF - Hydrogeology journal : official journal of the International Association of Hydrogeologists N2 - Environmental isotope techniques, hydrogeochemical analysis and hydraulic data are employed to identify the main recharge areas of the Mt. Vulture hydrogeological basin, one of the most important aquifers of southern Italy. The groundwaters are derived from seepage of rainwater, flowing from the highest to the lowest elevations through the shallow volcanic weathered host-rock fracture zones. Samples of shallow and deep groundwater were collected at 48 locations with elevations ranging from 352 to 1,100 m above sea level (a.s.l.), for stable isotope (delta(18)O, delta D) and major ion analyses. A complete dataset of available hydraulic information has been integrated with measurements carried out in the present study. Inferred recharge elevations, estimated on the basis of the local vertical isotopic gradient of delta(18)O, range between 550 and 1,200 m a.s.l. The isotope pattern of the Quaternary aquifer reflects the spatial separation of different recharge sources. Knowledge of the local hydrogeological setting was the starting point for a detailed hydrogeochemical and isotopic study to define the recharge and discharge patterns identifying the groundwater flow pathways of the Mt. Vulture basin. The integration of all the data allowed for the tracing of the groundwater flows of the Mt. Vulture basin. KW - Volcanic aquifer KW - Groundwater recharge/water budget KW - Recharge elevation KW - Stable isotopes KW - Italy Y1 - 2011 U6 - https://doi.org/10.1007/s10040-010-0619-8 SN - 1431-2174 VL - 19 IS - 1 SP - 133 EP - 153 PB - Springer CY - New York ER -