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- ItemComplex networks for climate model evaluation with application to statistical versus dynamical modeling of South American climate(Heidelberg : Springer, 2014) Feldhoff, Jan H.; Lange, Stefan; Volkholz, Jan; Donges, Jonathan F.; Kurths, Jürgen; Gerstengarbe, Friedrich-WilhelmIn this study we introduce two new node-weighted difference measures on complex networks as a tool for climate model evaluation. The approach facilitates the quantification of a model’s ability to reproduce the spatial covariability structure of climatological time series. We apply our methodology to compare the performance of a statistical and a dynamical regional climate model simulating the South American climate, as represented by the variables 2 m temperature, precipitation, sea level pressure, and geopotential height field at 500 hPa. For each variable, networks are constructed from the model outputs and evaluated against a reference network, derived from the ERA-Interim reanalysis, which also drives the models. We compare two network characteristics, the (linear) adjacency structure and the (nonlinear) clustering structure, and relate our findings to conventional methods of model evaluation. To set a benchmark, we construct different types of random networks and compare them alongside the climate model networks. Our main findings are: (1) The linear network structure is better reproduced by the statistical model statistical analogue resampling scheme (STARS) in summer and winter for all variables except the geopotential height field, where the dynamical model CCLM prevails. (2) For the nonlinear comparison, the seasonal differences are more pronounced and CCLM performs almost as well as STARS in summer (except for sea level pressure), while STARS performs better in winter for all variables.
- ItemUnraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study(London : BioMed Central, 2011) Hempel, Sabrina; Koseska, Aneta; Nikoloski, Zoran; Kurths, Jürgen; Walther, DirkBackground 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.
- ItemDevelopment of structural correlations and synchronization from adaptive rewiring in networks of Kuramoto oscillators(Woodbury, NY : American Institute of Physics, 2017) Papadopoulos, Lia; Kim, Jason Z.; Kurths, Jürgen; Bassett, Danielle S.Synchronization of non-identical oscillators coupled through complex networks is an important example of collective behavior, and it is interesting to ask how the structural organization of network interactions influences this process. Several studies have explored and uncovered optimal topologies for synchronization by making purposeful alterations to a network. On the other hand, the connectivity patterns of many natural systems are often not static, but are rather modulated over time according to their dynamics. However, this co-evolution and the extent to which the dynamics of the individual units can shape the organization of the network itself are less well understood. Here, we study initially randomly connected but locally adaptive networks of Kuramoto oscillators. In particular, the system employs a co-evolutionary rewiring strategy that depends only on the instantaneous, pairwise phase differences of neighboring oscillators, and that conserves the total number of edges, allowing the effects of local reorganization to be isolated. We find that a simple rule-which preserves connections between more outof- phase oscillators while rewiring connections between more in-phase oscillators-can cause initially disordered networks to organize into more structured topologies that support enhanced synchronization dynamics. We examine how this process unfolds over time, finding a dependence on the intrinsic frequencies of the oscillators, the global coupling, and the network density, in terms of how the adaptive mechanism reorganizes the network and influences the dynamics. Importantly, for large enough coupling and after sufficient adaptation, the resulting networks exhibit interesting characteristics, including degree-frequency and frequency-neighbor frequency correlations. These properties have previously been associated with optimal synchronization or explosive transitions in which the networks were constructed using global information. On the contrary, by considering a time-dependent interplay between structure and dynamics, this work offers a mechanism through which emergent phenomena and organization can arise in complex systems utilizing local rules.
- ItemImproving the LPJmL4-SPITFIRE vegetation–fire model for South America using satellite data(Katlenburg-Lindau : Copernicus, 2019) Drüke, Markus; Forkel, Matthias; von Bloh, Werner; Sakschewski, Boris; Cardoso, Manoel; Bustamante, Mercedes; Kurths, Jürgen; Thonicke, KirstenVegetation fires influence global vegetation distribution, ecosystem functioning, and global carbon cycling. Specifically in South America, changes in fire occurrence together with land-use change accelerate ecosystem fragmentation and increase the vulnerability of tropical forests and savannas to climate change. Dynamic global vegetation models (DGVMs) are valuable tools to estimate the effects of fire on ecosystem functioning and carbon cycling under future climate changes. However, most fire-enabled DGVMs have problems in capturing the magnitude, spatial patterns, and temporal dynamics of burned area as observed by satellites. As fire is controlled by the interplay of weather conditions, vegetation properties, and human activities, fire modules in DGVMs can be improved in various aspects. In this study we focus on improving the controls of climate and hence fuel moisture content on fire danger in the LPJmL4-SPITFIRE DGVM in South America, especially for the Brazilian fire-prone biomes of Caatinga and Cerrado. We therefore test two alternative model formulations (standard Nesterov Index and a newly implemented water vapor pressure deficit) for climate effects on fire danger within a formal model–data integration setup where we estimate model parameters against satellite datasets of burned area (GFED4) and aboveground biomass of trees. Our results show that the optimized model improves the representation of spatial patterns and the seasonal to interannual dynamics of burned area especially in the Cerrado and Caatinga regions. In addition, the model improves the simulation of aboveground biomass and the spatial distribution of plant functional types (PFTs). We obtained the best results by using the water vapor pressure deficit (VPD) for the calculation of fire danger. The VPD includes, in comparison to the Nesterov Index, a representation of the air humidity and the vegetation density. This work shows the successful application of a systematic model–data integration setup, as well as the integration of a new fire danger formulation, in order to optimize a process-based fire-enabled DGVM. It further highlights the potential of this approach to achieve a new level of accuracy in comprehensive global fire modeling and prediction.
- ItemBlood–Brain Barrier, Lymphatic Clearance, and Recovery: Ariadne’s Thread in Labyrinths of Hypotheses(Basel : Molecular Diversity Preservation International, 2018) Semyachkina-Glushkovskaya, Oxana; Postnov, Dmitry; Kurths, JürgenThe peripheral lymphatic system plays a crucial role in the recovery mechanisms after many pathological changes, such as infection, trauma, vascular, or metabolic diseases. The lymphatic clearance of different tissues from waste products, viruses, bacteria, and toxic proteins significantly contributes to the correspondent recovery processes. However, understanding of the cerebral lymphatic functions is a challenging problem. The exploration of mechanisms of lymphatic communication with brain fluids as well as the role of the lymphatic system in brain drainage, clearance, and recovery is still in its infancy. Here we review novel concepts on the anatomy and physiology of the lymphatics in the brain, which warrant a substantial revision of our knowledge about the role of lymphatics in the rehabilitation of the brain functions after neural pathologies. We discuss a new vision on the connective bridge between the opening of a blood–brain barrier and activation of the meningeal lymphatic clearance. The ability to stimulate the lymph flow in the brain, is likely to play an important role in developing future innovative strategies in neurorehabilitation therapy.
- ItemBrain anomaly networks uncover heterogeneous functional reorganization patterns after stroke([Amsterdam u.a.] : Elsevier, 2018) Zou, Yong; Zhao, Zhiyong; Yin, Dazhi; Fan, Mingxia; Small, Michael; Liu, Zonghua; Hilgetag, Claus C.; Kurths, JürgenStroke has a large physical, psychological, and financial burden on patients, their families, and society. Based on functional networks (FNs) constructed from resting state fMRI data, network connectivity after stroke is commonly conjectured to be more randomly reconfigured. We find that this hypothesis depends on the severity of stroke. Head movement-corrected, resting-state fMRI data were acquired from 32 patients after stroke, and 37 healthy volunteers. We constructed anomaly FNs, which combine time series information of a patient with the healthy control group. We propose data-driven techniques to automatically identify regions of interest that are stroke relevant. Graph analysis based on anomaly FNs suggests consistently that strong connections in healthy controls are broken down specifically and characteristically for brain areas that are related to sensorimotor functions and frontoparietal control systems, but new links in stroke patients are rebuilt randomly from all possible areas. Entropic measures of complexity are proposed for characterizing the functional connectivity reorganization patterns, which are correlated with hand and wrist function assessments of stroke patients and show high potential for clinical use.
- ItemSee–saw relationship of the Holocene East Asian–Australian summer monsoon(London : Nature Publishing Group, 2016) Eroglu, Deniz; McRobie, Fiona H.; Ozken, Ibrahim; Stemler, Thomas; Wyrwoll, Karl-Heinz; Breitenbach, Sebastian F.M.; Marwan, Norbert; Kurths, JürgenThe East Asian–Indonesian–Australian summer monsoon (EAIASM) links the Earth’s hemispheres and provides a heat source that drives global circulation. At seasonal and inter-seasonal timescales, the summer monsoon of one hemisphere is linked via outflows from the winter monsoon of the opposing hemisphere. Long-term phase relationships between the East Asian summer monsoon (EASM) and the Indonesian–Australian summer monsoon (IASM) are poorly understood, raising questions of long-term adjustments to future greenhouse-triggered climate change and whether these changes could ‘lock in’ possible IASM and EASM phase relationships in a region dependent on monsoonal rainfall. Here we show that a newly developed nonlinear time series analysis technique allows confident identification of strong versus weak monsoon phases at millennial to sub-centennial timescales. We find a see–saw relationship over the last 9,000 years—with strong and weak monsoons opposingly phased and triggered by solar variations. Our results provide insights into centennial- to millennial-scale relationships within the wider EAIASM regime.
- ItemApplication of optical coherence tomography for in vivo monitoring of the meningeal lymphatic vessels during opening of blood–brain barrier: mechanisms of brain clearing(Bellingham, Wash. : SPIE, 2017) Semyachkina-Glushkovskaya, Oxana; Abdurashitov, Arkady; Dubrovsky, Alexander; Bragin, Denis; Bragina, Olga; Shushunova, Natalia; Maslyakova, Galina; Navolokin, Nikita; Bucharskaya, Alla; Tuchind, Valery; Kurths, Jürgen; Shirokov, AlexanderThe meningeal lymphatic vessels were discovered 2 years ago as the drainage system involved in the mechanisms underlying the clearance of waste products from the brain. The blood–brain barrier (BBB) is a gatekeeper that strongly controls the movement of different molecules from the blood into the brain. We know the scenarios during the opening of the BBB, but there is extremely limited information on how the brain clears the substances that cross the BBB. Here, using the model of sound-induced opening of the BBB, we clearly show how the brain clears dextran after it crosses the BBB via the meningeal lymphatic vessels. We first demonstrate successful application of optical coherence tomography (OCT) for imaging of the lymphatic vessels in the meninges after opening of the BBB, which might be a new useful strategy for noninvasive analysis of lymphatic drainage in daily clinical practice. Also, we give information about the depth and size of the meningeal lymphatic vessels in mice. These new fundamental data with the applied focus on the OCT shed light on the mechanisms of brain clearance and the role of lymphatic drainage in these processes that could serve as an informative platform for a development of therapy and diagnostics of diseases associated with injuries of the BBB such as stroke, brain trauma, glioma, depression, or Alzheimer disease.
- ItemStatistical mechanics and information-theoretic perspectives on complexity in the Earth system(Basel : MDPI, 2013) Balasis, Georgios; Donner, Reik V.; Potirakis, Stelios M.; Runge, Jakob; Papadimitriou, Constantinos; Daglis, Ioannis A.; Eftaxias, Konstantinos; Kurths, JürgenThis review provides a summary of methods originated in (non-equilibrium) statistical mechanics and information theory, which have recently found successful applications to quantitatively studying complexity in various components of the complex system Earth. Specifically, we discuss two classes of methods: (i) entropies of different kinds (e.g., on the one hand classical Shannon and R´enyi entropies, as well as non-extensive Tsallis entropy based on symbolic dynamics techniques and, on the other hand, approximate entropy, sample entropy and fuzzy entropy); and (ii) measures of statistical interdependence and causality (e.g., mutual information and generalizations thereof, transfer entropy, momentary information transfer). We review a number of applications and case studies utilizing the above-mentioned methodological approaches for studying contemporary problems in some exemplary fields of the Earth sciences, highlighting the potentials of different techniques.
- ItemCoupling between leg muscle activation and EEG during normal walking, intentional stops, and freezing of gait in Parkinson's disease(Lausanne : Frontiers Media, 2019) Günther, Moritz; Bartsch, Ronny P.; Miron-Shahar, Yael; Hassin-Baer, Sharon; Inzelberg, Rivka; Kurths, Jürgen; Plotnik, Meir; Kantelhardt, Jan W.In this paper, we apply novel techniques for characterizing leg muscle activation patterns via electromyograms (EMGs) and for relating them to changes in electroencephalogram (EEG) activity during gait experiments. Specifically, we investigate changes of leg-muscle EMG amplitudes and EMG frequencies during walking, intentional stops, and unintended freezing-of-gait (FOG) episodes. FOG is a frequent paroxysmal gait disturbance occurring in many patients suffering from Parkinson's disease (PD). We find that EMG amplitudes and frequencies do not change significantly during FOG episodes with respect to walking, while drastic changes occur during intentional stops. Phase synchronization between EMG signals is most pronounced during walking in controls and reduced in PD patients. By analyzing cross-correlations between changes in EMG patterns and brain-wave amplitudes (from EEGs), we find an increase in EEG-EMG coupling at the beginning of stop and FOG episodes. Our results may help to better understand the enigmatic pathophysiology of FOG, to differentiate between FOG events and other gait disturbances, and ultimately to improve diagnostic procedures for patients suffering from PD. Copyright © 2019 Günther, Bartsch, Miron-Shahar, Hassin-Baer, Inzelberg, Kurths, Plotnik and Kantelhardt.
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