@phdthesis{Sedaghatmehr2017, author = {Sedaghatmehr, Mastoureh}, title = {Unraveling the regulatory mechanisms of heat stress memory in Arabidopsis thaliana}, school = {Universit{\"a}t Potsdam}, pages = {176}, year = {2017}, language = {en} } @misc{HempelKoseskaNikoloskietal.2017, author = {Hempel, Sabrina and Koseska, Aneta and Nikoloski, Zoran and Kurths, J{\"u}rgen}, title = {Unraveling gene regulatory networks from time-resolved gene expression data}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-400924}, pages = {26}, year = {2017}, abstract = {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.}, language = {en} } @article{CaliendoMahlstedtMitnik2017, author = {Caliendo, Marco and Mahlstedt, Robert and Mitnik, Oscar A.}, title = {Unobservable, but unimportant? The relevance of usually unobserved variables for the evaluation of labor market policies}, series = {Labour economics : an international journal}, volume = {46}, journal = {Labour economics : an international journal}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0927-5371}, doi = {10.1016/j.labeco.2017.02.001}, pages = {14 -- 25}, year = {2017}, language = {en} } @article{GrabowYoungByrneetal.2017, author = {Grabow, Lena and Young, James D. and Byrne, Jeannette M. and Granacher, Urs and Behm, David George}, title = {Unilateral Rolling of the Foot did not Affect Non-Local Range of Motion or Balance}, series = {Journal of sports science \& medicine}, volume = {16}, journal = {Journal of sports science \& medicine}, publisher = {Department of Sports Medicine, Medical Faculty of Uludag University}, address = {Bursa}, issn = {1303-2968}, pages = {209 -- 218}, year = {2017}, abstract = {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.}, language = {en} } @article{EngelMuellerKopinskietal.2017, author = {Engel, Tilman and Mueller, Juliane and Kopinski, Stephan and Reschke, Antje and Mueller, Steffen and Mayer, Frank}, title = {Unexpected walking perturbations: Reliability and validity of a new treadmill protocol to provoke muscular reflex activities at lower extremities and the trunk}, series = {Journal of biomechanics}, volume = {55}, journal = {Journal of biomechanics}, publisher = {Elsevier}, address = {Oxford}, issn = {0021-9290}, doi = {10.1016/j.jbiomech.2017.02.026}, pages = {152 -- 155}, year = {2017}, abstract = {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.}, language = {en} } @article{MusolffSelleButtneretal.2017, author = {Musolff, Andreas and Selle, Benny and Buttner, Olaf and Opitz, Michael and Tittel, J{\"o}rg}, title = {Unexpected release of phosphate and organic carbon to streams linked to declining nitrogen depositions}, series = {Global change biology}, volume = {23}, journal = {Global change biology}, publisher = {Wiley}, address = {Hoboken}, issn = {1354-1013}, doi = {10.1111/gcb.13498}, pages = {1891 -- 1901}, year = {2017}, abstract = {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.}, language = {en} } @article{FrielerSchaubergerArnethetal.2017, author = {Frieler, Katja and Schauberger, Bernhard and Arneth, Almut and Balkovic, Juraj and Chryssanthacopoulos, James and Deryng, Delphine and Elliott, Joshua and Folberth, Christian and Khabarov, Nikolay and M{\"u}ller, Christoph and Olin, Stefan and Pugh, Thomas A. M. and Schaphoff, Sibyll and Schewe, Jacob and Schmid, Erwin and Warszawski, Lila and Levermann, Anders}, title = {Understanding the weather signal in national crop-yield variability}, series = {Earths future}, volume = {5}, journal = {Earths future}, publisher = {Wiley}, address = {Hoboken}, issn = {2328-4277}, doi = {10.1002/2016EF000525}, pages = {605 -- 616}, year = {2017}, abstract = {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.}, language = {en} } @phdthesis{Weiss2017, author = {Weiß, Lina}, title = {Understanding the emergence and maintenance of biodiversity in grasslands}, school = {Universit{\"a}t Potsdam}, pages = {153}, year = {2017}, language = {en} } @article{KoussoroplisPincebourdeWacker2017, author = {Koussoroplis, Apostolos-Manuel and Pincebourde, Sylvain and Wacker, Alexander}, title = {Understanding and predicting physiological performance of organisms in fluctuating and multifactorial environments}, series = {Ecological monographs : a publication of the Ecological Society of America.}, volume = {87}, journal = {Ecological monographs : a publication of the Ecological Society of America.}, publisher = {Wiley}, address = {Hoboken}, issn = {0012-9615}, doi = {10.1002/ecm.1247}, pages = {178 -- 197}, year = {2017}, abstract = {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.}, language = {en} } @article{HeydeClelandScobbieetal.2017, author = {Heyde, Cornelia J. and Cleland, Joanne and Scobbie, James M. and Roxburgh, Zoe}, title = {UltraPhonix: Das Erlernen von artikulatorischen Gesten mit Ultraschall-Biofeedback}, series = {Spektrum Patholinguistik (Band 10) - Schwerpunktthema: Panorama Patholinguistik: Sprachwissenschaft trifft Sprachtherapie}, journal = {Spektrum Patholinguistik (Band 10) - Schwerpunktthema: Panorama Patholinguistik: Sprachwissenschaft trifft Sprachtherapie}, number = {10}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, issn = {1866-9085}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-405283}, pages = {203 -- 214}, year = {2017}, language = {de} }