TY - THES A1 - Sedaghatmehr, Mastoureh T1 - Unraveling the regulatory mechanisms of heat stress memory in Arabidopsis thaliana Y1 - 2017 ER - TY - GEN A1 - Hempel, Sabrina A1 - Koseska, Aneta A1 - Nikoloski, Zoran A1 - Kurths, Jürgen T1 - Unraveling gene regulatory networks from time-resolved gene expression data BT - a measures comparison study 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 371 KW - unferring cellular networks KW - mutual information KW - Escherichia-coli KW - cluster-analysis KW - series KW - algorithms KW - inference KW - models KW - recognition KW - variables Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400924 ER - TY - JOUR A1 - Caliendo, Marco A1 - Mahlstedt, Robert A1 - Mitnik, Oscar A. T1 - Unobservable, but unimportant? The relevance of usually unobserved variables for the evaluation of labor market policies JF - Labour economics : an international journal KW - Matching KW - Unconfoundedness KW - Unobservables KW - Selection bias KW - Personality traits KW - Active labor market policy Y1 - 2017 U6 - https://doi.org/10.1016/j.labeco.2017.02.001 SN - 0927-5371 SN - 1879-1034 VL - 46 SP - 14 EP - 25 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Grabow, Lena A1 - Young, James D. A1 - Byrne, Jeannette M. A1 - Granacher, Urs A1 - Behm, David George T1 - Unilateral Rolling of the Foot did not Affect Non-Local Range of Motion or Balance JF - Journal of sports science & medicine N2 - Non-local or crossover (contralateral and non-stretched muscles) increases in range-of-motion (ROM) and balance have been reported following rolling of quadriceps, hamstrings and plantar flexors. Since there is limited information regarding plantar sole (foot) rolling effects, the objectives of this study were to determine if unilateral foot rolling would affect ipsilateral and contralateral measures of ROM and balance in young healthy adults. A randomized within-subject design was to examine non-local effects of unilateral foot rolling on ipsilateral and contralateral limb ankle dorsiflexion ROM and a modified sit-and-reachtest (SRT). Static balance was also tested during a 30 s single leg stance test. Twelve participants performed three bouts of 60 s unilateral plantar sole rolling using a roller on the dominant foot with 60 s rest intervals between sets. ROM and balance measures were assessed in separate sessions at pre-intervention, immediately and 10 minutes post-intervention. To evaluate repeated measures effects, two SRT pre-tests were implemented. Results demonstrated that the second pre-test SRT was 6.6% higher than the first pre-test (p = 0.009, d = 1.91). There were no statistically significant effects of foot rolling on any measures immediately or 10 min post-test. To conclude, unilateral foot rolling did not produce statistically significant increases in ipsilateral or contralateral dorsiflexion or SRT ROM nor did it affect postural sway. Our statistically non-significant findings might be attributed to a lower degree of roller-induced afferent stimulation due to the smaller volume of myofascia and muscle compared to prior studies. Furthermore, ROM results from studies utilizing a single pre-test without a sufficient warm-up should be viewed critically. KW - Crossover KW - flexibility KW - postural sway KW - myofascial KW - self massage Y1 - 2017 SN - 1303-2968 VL - 16 SP - 209 EP - 218 PB - Department of Sports Medicine, Medical Faculty of Uludag University CY - Bursa ER - TY - JOUR A1 - Engel, Tilman A1 - Mueller, Juliane A1 - Kopinski, Stephan A1 - Reschke, Antje A1 - Mueller, Steffen A1 - Mayer, Frank T1 - Unexpected walking perturbations: Reliability and validity of a new treadmill protocol to provoke muscular reflex activities at lower extremities and the trunk JF - Journal of biomechanics N2 - Instrumented treadmills offer the potential to generate standardized walking perturbations, which are particularly rapid and powerful. However, technical requirements to release adequate perturbations regarding timing, duration and amplitude are demanding. This study investigated the test-retest reliability and validity of a new treadmill perturbation protocol releasing rapid and unexpected belt perturbations to provoke muscular reflex responses at lower extremities and the trunk. Fourteen healthy participants underwent two identical treadmill walking protocols, consisting of 10 superimposed one-sided belt perturbations (100 ms duration; 2 m/s amplitude), triggered by a plantar pressure insole 200 ms after heel contact. Delay, duration and amplitude of applied perturbations were recorded by 3D-motion capture. Muscular reflex responses (within 200 ms) were measured at lower extremities and the trunk (10-lead EMG). Data was analyzed descriptively (mean +/- SD). Reliability was analyzed using test-retest variability (TRV%) and limits of agreement (LoA, bias +/- 1.96*SD). Perturbation delay was 202 14 ms, duration was 102 +/- 4 ms and amplitude was 2.1 +/- 0.01 m/s. TRV for perturbation delay, duration and amplitude ranged from 5.0% to 5.7%. LoA reached 3 +/- 36 ms for delay, 2 +/- 13 ms for duration and 0.0 +/- 0.3 m/s for amplitude. EMG amplitudes following perturbations ranged between 106 +/- 97% and 909 +/- 979% of unperturbed gait and EMG latencies between 82 +/- 14 ms and 106 +/- 16 ms. Minor differences between preset and observed perturbation characteristics and results of test-retest analysis prove a high validity with excellent reliability of the setup. Therefore, the protocol tested can be recommended to provoke muscular reflex responses at lower extremities and the trunk in perturbed walking. (C) 2017 Elsevier Ltd. All rights reserved. KW - Perturbation KW - Stumbling KW - Gait KW - Treadmill KW - Reliability KW - MiSpEx Y1 - 2017 U6 - https://doi.org/10.1016/j.jbiomech.2017.02.026 SN - 0021-9290 SN - 1873-2380 VL - 55 SP - 152 EP - 155 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Musolff, Andreas A1 - Selle, Benny A1 - Buttner, Olaf A1 - Opitz, Michael A1 - Tittel, Jörg T1 - Unexpected release of phosphate and organic carbon to streams linked to declining nitrogen depositions JF - Global change biology N2 - Reductions in emissions have successfully led to a regional decline in atmospheric nitrogen depositions over the past 20 years. By analyzing long-term data from 110 mountainous streams draining into German drinking water reservoirs, nitrate concentrations indeed declined in the majority of catchments. Furthermore, our meta-analysis indicates that the declining nitrate levels are linked to the release of dissolved iron to streams likely due to a reductive dissolution of iron(III) minerals in riparian wetland soils. This dissolution process mobilized adsorbed compounds, such as phosphate, dissolved organic carbon and arsenic, resulting in concentration increases in the streams and higher inputs to receiving drinking water reservoirs. Reductive mobilization was most significant in catchments with stream nitrate concentrations < 6 mg L-1. Here, nitrate, as a competing electron acceptor, was too low in concentration to inhibit microbial iron(III) reduction. Consequently, observed trends were strongest in forested catchments, where nitrate concentrations were unaffected by agricultural and urban sources and which were therefore sensitive to reductions of atmospheric nitrogen depositions. We conclude that there is strong evidence that the decline in nitrogen deposition toward pre-industrial conditions lowers the redox buffer in riparian soils, destabilizing formerly fixed problematic compounds, and results in serious implications for water quality. KW - atmospheric deposition KW - carbon cycle KW - nitrogen biogeochemistry KW - organic matter KW - riparian zone KW - streamwater chemistry Y1 - 2017 U6 - https://doi.org/10.1111/gcb.13498 SN - 1354-1013 SN - 1365-2486 VL - 23 SP - 1891 EP - 1901 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Frieler, Katja A1 - Schauberger, Bernhard A1 - Arneth, Almut A1 - Balkovic, Juraj A1 - Chryssanthacopoulos, James A1 - Deryng, Delphine A1 - Elliott, Joshua A1 - Folberth, Christian A1 - Khabarov, Nikolay A1 - Müller, Christoph A1 - Olin, Stefan A1 - Pugh, Thomas A. M. A1 - Schaphoff, Sibyll A1 - Schewe, Jacob A1 - Schmid, Erwin A1 - Warszawski, Lila A1 - Levermann, Anders T1 - Understanding the weather signal in national crop-yield variability JF - Earths future N2 - Year-to-year variations in crop yields can have major impacts on the livelihoods of subsistence farmers and may trigger significant global price fluctuations, with severe consequences for people in developing countries. Fluctuations can be induced by weather conditions, management decisions, weeds, diseases, and pests. Although an explicit quantification and deeper understanding of weather-induced crop-yield variability is essential for adaptation strategies, so far it has only been addressed by empirical models. Here, we provide conservative estimates of the fraction of reported national yield variabilities that can be attributed to weather by state-of-the-art, process-based crop model simulations. We find that observed weather variations can explain more than 50% of the variability in wheat yields in Australia, Canada, Spain, Hungary, and Romania. For maize, weather sensitivities exceed 50% in seven countries, including the United States. The explained variance exceeds 50% for rice in Japan and South Korea and for soy in Argentina. Avoiding water stress by simulating yields assuming full irrigation shows that water limitation is a major driver of the observed variations in most of these countries. Identifying the mechanisms leading to crop-yield fluctuations is not only fundamental for dampening fluctuations, but is also important in the context of the debate on the attribution of loss and damage to climate change. Since process-based crop models not only account for weather influences on crop yields, but also provide options to represent human-management measures, they could become essential tools for differentiating these drivers, and for exploring options to reduce future yield fluctuations. Y1 - 2017 U6 - https://doi.org/10.1002/2016EF000525 SN - 2328-4277 VL - 5 SP - 605 EP - 616 PB - Wiley CY - Hoboken ER - TY - THES A1 - Weiß, Lina T1 - Understanding the emergence and maintenance of biodiversity in grasslands BT - linking individual plant responses to community patterns Y1 - 2017 ER - TY - JOUR A1 - Koussoroplis, Apostolos-Manuel A1 - Pincebourde, Sylvain A1 - Wacker, Alexander T1 - Understanding and predicting physiological performance of organisms in fluctuating and multifactorial environments JF - Ecological monographs : a publication of the Ecological Society of America. N2 - Understanding how variance in environmental factors affects physiological performance, population growth, and persistence is central in ecology. Despite recent interest in the effects of variance in single biological drivers, such as temperature, we have lacked a comprehensive framework for predicting how the variances and covariances between multiple environmental factors will affect physiological rates. Here, we integrate current theory on variance effects with co-limitation theory into a single unified conceptual framework that has general applicability. We show how the framework can be applied (1) to generate mathematically tractable predictions of the physiological effects of multiple fluctuating co-limiting factors, (2) to understand how each co-limiting factor contributes to these effects, and (3) to detect mechanisms such as acclimation or physiological stress when they are at play. We show that the statistical covariance of co-limiting factors, which has not been considered before, can be a strong driver of physiological performance in various ecological contexts. Our framework can provide powerful insights on how the global change-induced shifts in multiple environmental factors affect the physiological performance of organisms. KW - co-limitation KW - covariance KW - eco-physiology KW - feeding rate KW - global change KW - multiple stressors KW - nonlinear averaging KW - nutrients KW - scale transition KW - temperature KW - temporal ecology KW - variance Y1 - 2017 U6 - https://doi.org/10.1002/ecm.1247 SN - 0012-9615 SN - 1557-7015 VL - 87 SP - 178 EP - 197 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Heyde, Cornelia J. A1 - Cleland, Joanne A1 - Scobbie, James M. A1 - Roxburgh, Zoe T1 - UltraPhonix: Das Erlernen von artikulatorischen Gesten mit Ultraschall-Biofeedback JF - Spektrum Patholinguistik (Band 10) - Schwerpunktthema: Panorama Patholinguistik: Sprachwissenschaft trifft Sprachtherapie Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-405283 SN - 1866-9085 IS - 10 SP - 203 EP - 214 PB - Universitätsverlag Potsdam CY - Potsdam ER -