@article{NeuvonenNeuvonenKochetal.2011, author = {Neuvonen, Kari and Neuvonen, Helmi and Koch, Andreas and Kleinpeter, Erich}, title = {NBO analysis of polar and steric effect using the axial-equatorial equilibrium of cyclohexyl acetates as a probe}, series = {Computational and theoretical chemistry}, volume = {964}, journal = {Computational and theoretical chemistry}, number = {1-3}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2210-271X}, doi = {10.1016/j.comptc.2010.12.033}, pages = {234 -- 242}, year = {2011}, abstract = {The proportion of the axial conformer increases in the ax reversible arrow eq equilibrium of cyclohexyl acetates (RCOOC(6)H(11), R reversible arrow Me, Et, iPr, tBu, CH(2)Cl, CHCl(2), CO(3). CH(2)Br, CHBr(2), CBr(3)) with the increasing size of the acyloxy substitution. The nature of this unexpected steric substituent effect, which is opposite to general stereochemical concepts, was studied by means of ab kiln MO method, accompanied by NBO and isodesmic calculations. NBO parameters seem to be good descriptors for quantitative prediction of the experimental Delta G degrees value of the title conformational equilibrium. The origin and propagation of the substituent effect of the polar substitutions (CH(2)Cl, CHCl(2), CCl(3), CH(2)Br, CHBr(2), CBr(3)) differ, however, from those of the pure alkyl (Me, Et, iPr, tBu) substitutions. The Delta G degrees value of the polar derivatives depends on the qC8 charges, on the occupation of the sigma(center dot)(C1-07) orbital and on the hyperconjugative pi(center dot)(c=O) -> sigma(center dot)(C10-X) and sigma(center dot)(C10-X) -> pi(center dot)(c=O) interactions. The substituent sensitivity of these NBC parameters for the two conformers differ to the effect that the ax reversible arrow eq equilibrium is shifted to the left side with increasing electron withdrawing character of the acyloxy group. The Delta G degrees values of the alkyl derivatives are interpreted in terms of the calculated dipole moments. The destabilization in the non-polar medium (the experimental Delta G degrees values used were measured in CD(2)Cl(2)) due to the enhanced dipolar character is more prominent in the case of the equatorial alkyl conformers. As the consequence, the ax reversible arrow eq equilibrium is shifted to the left despite the increasing size of the R group when going from Me to tBu substitution.}, language = {en} } @article{CarlsohnScharhagRosenbergerCasseletal.2011, author = {Carlsohn, Anja and Scharhag-Rosenberger, Friederike and Cassel, Michael and Mayer, Frank}, title = {Resting metabolic rate in elite rowers and canoeists difference between indirect calorimetry and prediction}, series = {Annals of nutrition \& metabolism : journal of nutrition, metabolic diseases and dietetics ; an official journal of International Union of Nutritional Sciences (IUNS)}, volume = {58}, journal = {Annals of nutrition \& metabolism : journal of nutrition, metabolic diseases and dietetics ; an official journal of International Union of Nutritional Sciences (IUNS)}, number = {3}, publisher = {Karger}, address = {Basel}, issn = {0250-6807}, doi = {10.1159/000330119}, pages = {239 -- 244}, year = {2011}, abstract = {Background: Athletes may differ in their resting metabolic rate (RMR) from the general population. However, to estimate the RMR in athletes, prediction equations that have not been validated in athletes are often used. The purpose of this study was therefore to verify the applicability of commonly used RMR predictions for use in athletes. Methods: The RMR was measured by indirect calorimetry in 17 highly trained rowers and canoeists of the German national teams (BMI 24 +/- 2 kg/m(2), fat-free mass 69 +/- 15 kg). In addition, the RMR was predicted using Cunningham (CUN) and Harris-Benedict (HB) equations. A two-way repeated measures ANOVA was calculated to test for differences between predicted and measured RMR (alpha = 0.05). The root mean square percentage error (RMSPE) was calculated and the Bland-Altman procedure was used to quantify the bias for each prediction. Results: Prediction equations significantly underestimated the RMR in males (p < 0.001). The RMSPE was calculated to be 18.4\% (CUN) and 20.9\% (HB) in the entire group. The bias was 133 kcal/24 h for CUN and 202 kcal/24 h for HB. Conclusions: Predictions significantly underestimate the RMR in male heavyweight endurance athletes but not in females. In athletes with a high fat-free mass, prediction equations might therefore not be applicable to estimate energy requirements. Instead, measurement of the resting energy expenditure or specific prediction equations might be needed for the individual heavyweight athlete.}, language = {en} } @article{KleinpeterKoch2011, author = {Kleinpeter, Erich and Koch, Andreas}, title = {Chelatoaromaticity-existing: yes or no? An answer given by spatial magnetic properties (through space NMR shieldings-TSNMRS)}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {13}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {46}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c1cp21942a}, pages = {20593 -- 20601}, year = {2011}, abstract = {The spatial magnetic properties (through space NMR shieldings-TSNMRS) of metal complexes (with ligands such as acetylacetone, 3-hydroxy-pyran(4) one) and "metallobenzenes" have been calculated by the GIAO perturbation method and visualized as Iso-Chemical-Shielding Surfaces (ICSS) of various sizes and directions. The TSNMRS values, thus obtained, can be successfully employed to quantify and visualize partial aromaticity of the metallocyclic ring by comparison with the spatial magnetic properties of the corresponding non-complexed ligands in comparable structural and electronic situations, and benzene, respectively. Because anisotropy/ring current effects in H-1 NMR spectra proved to be the molecular response property of TSNMRS, the results obtained concerning partial "chelatoaromaticity" are experimentally ensured.}, language = {en} } @article{KleinpeterLaemmermannKuehn2011, author = {Kleinpeter, Erich and Laemmermann, Anica and K{\"u}hn, Heiner}, title = {The anisotropic effect of functional groups in H-1 NMR spectra is the molecular response property of spatial nucleus independent chemical shifts (NICS)-Conformational equilibria of exo/endo tetrahydrodicyclopentadiene derivatives}, series = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry}, volume = {9}, journal = {Organic \& biomolecular chemistry : an international journal of synthetic, physical and biomolecular organic chemistry}, number = {4}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1477-0520}, doi = {10.1039/c0ob00356e}, pages = {1098 -- 1111}, year = {2011}, abstract = {The inversion of the flexible five-membered ring in tetrahydrodicyclopentadiene (TH-DCPD) derivatives remains fast on the NMR timescale even at 103 K. Since the intramolecular exchange process could not be sufficiently slowed for spectroscopic evaluation, the conformational equilibrium is thus inaccessible by dynamic NMR. Fortunately, the spatial magnetic properties of the aryl and carbonyl groups attached to the DCPD skeleton can be employed in order to evaluate the conformational state of the system. In this context, the anisotropic effects of the functional groups in the H-1 NMR spectra prove to be the molecular response property of spatial nucleus independent chemical shifts (NICS).}, language = {en} } @article{BaurMuellerHirschmuelleretal.2011, author = {Baur, Heiner and M{\"u}ller, Steffen and Hirschm{\"u}ller, Anja and Cassel, Michael and Weber, Josefine and Mayer, Frank}, title = {Comparison in lower leg neuromuscular activity between runners with unilateral mid-portion Achilles tendinopathy and healthy individuals}, series = {Journal of electromyography and kinesiology}, volume = {21}, journal = {Journal of electromyography and kinesiology}, number = {3}, publisher = {Elsevier}, address = {Oxford}, issn = {1050-6411}, doi = {10.1016/j.jelekin.2010.11.010}, pages = {499 -- 505}, year = {2011}, abstract = {Neuromuscular control in functional situations and possible impairments due to Achilles tendinopathy are not well understood. Thirty controls (CO) and 30 runners with Achilles tendinopathy (AT) were tested on a treadmill at 3.33 m s(-1) (12 km h(-1)). Neuromuscular activity of the lower leg (tibialis anterior, peroneal, and gastrocnemius muscle) was measured by surface electromyography. Mean amplitude values (MAV) for the gait cycle phases preactivation, weight acceptance and push-off were calculated and normalised to the mean activity of the entire gait cycle. MAVs of the tibialis anterior did not differ between CO and AT in any gait cycle phase. The activation of the peroneal muscle was lower in AT in weight acceptance (p = 0.006), whereas no difference between CO and AT was found in preactivation (p = 0.71) and push-off (p = 0.83). Also, MAVs of the gastrocnemius muscle did not differ between AT and CO in preactivity (p = 0.71) but were reduced in AT during weight acceptance (p = 0.001) and push-off (p = 0.04). Achilles tendinopathy does not seem to alter pre-programmed neural control but might induce mechanical deficits of the lower extremity during weight bearing (joint stability). This should be addressed in the therapy process of AT.}, language = {en} } @misc{KlieglWeiDambacheretal.2011, author = {Kliegl, Reinhold and Wei, Ping and Dambacher, Michael and Yan, Ming and Zhou, Xiaolin}, title = {Experimental effects and individual differences in linear mixed models: Estimating the relationship between spatial, object, and attraction effects in visual attention}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-56859}, year = {2011}, abstract = {Linear mixed models (LMMs) provide a still underused methodological perspective on combining experimental and individual-differences research. Here we illustrate this approach with two-rectangle cueing in visual attention (Egly et al., 1994). We replicated previous experimental cue-validity effects relating to a spatial shift of attention within an object (spatial effect), to attention switch between objects (object effect), and to the attraction of attention toward the display centroid (attraction effect), also taking into account the design-inherent imbalance of valid and other trials. We simultaneously estimated variance/covariance components of subject-related random effects for these spatial, object, and attraction effects in addition to their mean reaction times (RTs). The spatial effect showed a strong positive correlation with mean RT and a strong negative correlation with the attraction effect. The analysis of individual differences suggests that slow subjects engage attention more strongly at the cued location than fast subjects. We compare this joint LMM analysis of experimental effects and associated subject-related variances and correlations with two frequently used alternative statistical procedures}, language = {en} } @misc{RisseKliegl2011, author = {Risse, Sarah and Kliegl, Reinhold}, title = {Adult age differences in the perceptual span during reading}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-56935}, year = {2011}, abstract = {Following up on research suggesting an age-related reduction in the rightward extent of the perceptual span during reading (Rayner, Castelhano, \& Yang, 2009), we compared old and young adults in an N+2-boundary paradigm in which a nonword preview of word N+2 or word N+2 itself is replaced by the target word once the eyes cross an invisible boundary located after word N. The intermediate word N+1 was always three letters long. Gaze durations on word N+2 were significantly shorter for identical than nonword N+2 preview both for young and for old adults with no significant difference in this preview benefit. Young adults, however, did modulate their gaze duration on word N more strongly than old adults in response to the difficulty of the parafoveal word N+1. Taken together, the results suggest a dissociation of preview benefit and parafoveal-on-foveal effect. Results are discussed in terms of age-related decline in resilience towards distributed processing while simultaneously preserving the ability to integrate parafoveal information into foveal processing. As such, the present results relate to proposals of regulatory compensation strategies older adults use to secure an overall reading speed very similar to that of young adults.}, language = {en} } @misc{KlieglBates2011, author = {Kliegl, Reinhold and Bates, Douglas}, title = {International Collaboration in Psychology is on the Rise}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-57045}, year = {2011}, abstract = {There has been a substantial increase in the percentage for publications with co-authors located in departments from different countries in 12 major journals of psychology. The results are evidence for a remarkable internationalization of psychological research, starting in the mid 1970s and increasing in rate at the beginning of the 1990s. This growth occurs against a constant number of articles with authors from the same country; it is not due to a concomitant increase in the number of co-authors per article. Thus, international collaboration in psychology is obviously on the rise.}, language = {en} } @article{WeissHuisinga2011, author = {Weiss, Andrea Y. and Huisinga, Wilhelm}, title = {Error-controlled global sensitivity analysis of ordinary differential equations}, series = {Journal of computational physics}, volume = {230}, journal = {Journal of computational physics}, number = {17}, publisher = {Elsevier}, address = {San Diego}, issn = {0021-9991}, doi = {10.1016/j.jcp.2011.05.011}, pages = {6824 -- 6842}, year = {2011}, abstract = {We propose a novel strategy for global sensitivity analysis of ordinary differential equations. It is based on an error-controlled solution of the partial differential equation (PDE) that describes the evolution of the probability density function associated with the input uncertainty/variability. The density yields a more accurate estimate of the output uncertainty/variability, where not only some observables (such as mean and variance) but also structural properties (e.g., skewness, heavy tails, bi-modality) can be resolved up to a selected accuracy. For the adaptive solution of the PDE Cauchy problem we use the Rothe method with multiplicative error correction, which was originally developed for the solution of parabolic PDEs. We show that, unlike in parabolic problems, conservation properties necessitate a coupling of temporal and spatial accuracy to avoid accumulation of spatial approximation errors over time. We provide convergence conditions for the numerical scheme and suggest an implementation using approximate approximations for spatial discretization to efficiently resolve the coupling of temporal and spatial accuracy. The performance of the method is studied by means of low-dimensional case studies. The favorable properties of the spatial discretization technique suggest that this may be the starting point for an error-controlled sensitivity analysis in higher dimensions.}, language = {en} } @article{PilariPreusseHuisinga2011, author = {Pilari, Sabine and Preusse, Cornelia and Huisinga, Wilhelm}, title = {Gestational influences on the pharmacokinetics of gestagenic drugs a combined in silico, in vitro and in vivo analysis}, series = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences, EUFEPS}, volume = {42}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences, EUFEPS}, number = {4}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0928-0987}, doi = {10.1016/j.ejps.2010.12.003}, pages = {318 -- 331}, year = {2011}, abstract = {During preclinical development of a gestagenic drug, a significant increase of the total plasma concentration was observed after multiple dosing in pregnant rabbits, but not in (non-pregnant) rats or monkeys. We used a PBPK modeling approach in combination with in vitro and in vivo data to address the question to what extent the pharmacologically active free drug concentration is affected by pregnancy induced processes. In human, a significant increase in sex hormone binding globulin (SHBG), and an induction of hepatic CYP3A4 as well as plasma esterases is observed during pregnancy. We find that the observed increase in total plasma trough levels in rabbits can be explained as a combined result of (i) drug accumulation due to multiple dosing, (ii) increase of the binding protein SHBG, and (iii) clearance induction. For human, we predict that free drug concentrations in plasma would not increase during pregnancy above the steady state trough level for non-pregnant women.}, language = {en} } @article{vonKleistMenzStockeretal.2011, author = {von Kleist, Max and Menz, Stephan and Stocker, Hartmut and Arasteh, Keikawus and Schuette, Christof and Huisinga, Wilhelm}, title = {HIV quasispecies dynamics during pro-active treatment switching impact on multi-drug resistance and resistance archiving in latent reservoirs}, series = {PLoS one}, volume = {6}, journal = {PLoS one}, number = {3}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0018204}, pages = {12}, year = {2011}, abstract = {The human immunodeficiency virus (HIV) can be suppressed by highly active anti-retroviral therapy (HAART) in the majority of infected patients. Nevertheless, treatment interruptions inevitably result in viral rebounds from persistent, latently infected cells, necessitating lifelong treatment. Virological failure due to resistance development is a frequent event and the major threat to treatment success. Currently, it is recommended to change treatment after the confirmation of virological failure. However, at the moment virological failure is detected, drug resistant mutants already replicate in great numbers. They infect numerous cells, many of which will turn into latently infected cells. This pool of cells represents an archive of resistance, which has the potential of limiting future treatment options. The objective of this study was to design a treatment strategy for treatment-naive patients that decreases the likelihood of early treatment failure and preserves future treatment options. We propose to apply a single, pro-active treatment switch, following a period of treatment with an induction regimen. The main goal of the induction regimen is to decrease the abundance of randomly generated mutants that confer resistance to the maintenance regimen, thereby increasing subsequent treatment success. Treatment is switched before the overgrowth and archiving of mutant strains that carry resistance against the induction regimen and would limit its future re-use. In silico modelling shows that an optimal trade-off is achieved by switching treatment at \& 80 days after the initiation of antiviral therapy. Evaluation of the proposed treatment strategy demonstrated significant improvements in terms of resistance archiving and virological response, as compared to conventional HAART. While continuous pro-active treatment alternation improved the clinical outcome in a randomized trial, our results indicate that a similar improvement might also be reached after a single pro-active treatment switch. The clinical validity of this finding, however, remains to be shown by a corresponding trial.}, language = {en} } @article{HirschmuellerKonstantinidisBauretal.2011, author = {Hirschm{\"u}ller, Anja and Konstantinidis, Lukas and Baur, Heiner and M{\"u}ller, Steffen and Mehlhorn, Alexander and Kontermann, Julia and Grosse, Ulrich and S{\"u}dkamp, Norbert P. and Helwig, Peter}, title = {Do changes in dynamic plantar pressure distribution, strength capacity and postural control after intra-articular calcaneal fracture correlate with clinical and radiological outcome?}, series = {Injury : international journal of the care of the injured}, volume = {42}, journal = {Injury : international journal of the care of the injured}, number = {10}, publisher = {Elsevier}, address = {Oxford}, issn = {0020-1383}, doi = {10.1016/j.injury.2010.09.040}, pages = {1135 -- 1143}, year = {2011}, abstract = {Fractures of the calcaneus are often associated with serious permanent disability, a considerable reduction in quality of life, and high socio-economic cost. Although some studies have already reported changes in plantar pressure distribution after calcaneal fracture, no investigation has yet focused on the patient's strength and postural control. Method: 60 patients with unilateral, operatively treated, intra-articular calcaneal fractures were clinically and biomechanically evaluated >1 year postoperatively (physical examination, SF-36, AOFAS score, lower leg isokinetic strength, postural control and gait analysis including plantar pressure distribution). Results were correlated to clinical outcome and preoperative radiological findings (Bohler angle, Zwipp and Sanders Score). Results: Clinical examination revealed a statistically significant reduction in range of motion at the tibiotalar and the subtalar joint on the affected side. Additionally, there was a statistically significant reduction of plantar flexor peak torque of the injured compared to the uninjured limb (p < 0.001) as well as a reduction in postural control that was also more pronounced on the initially injured side (standing duration 4.2 +/- 2.9 s vs. 7.6 +/- 2.1 s, p < 0.05). Plantar pressure measurements revealed a statistically significant pressure reduction at the hindfoot (p = 0.0007) and a pressure increase at the midfoot (p = 0.0001) and beneath the lateral forefoot (p = 0.037) of the injured foot. There was only a weak correlation between radiological classifications and clinical outcome but a moderate correlation between strength differences and the clinical questionnaires (CC 0.27-0.4) as well as between standing duration and the clinical questionnaires. Although thigh circumference was also reduced on the injured side, there was no important relationship between changes in lower leg circumference and strength suggesting that measurement of leg circumference may not be a valid assessment of maximum strength deficits. Self-selected walking speed was the parameter that showed the best correlation with clinical outcome (AOFAS score). Conclusion: Calcaneal fractures are associated with a significant reduction in ankle joint ROM, plantar flexion strength and postural control. These impairments seem to be highly relevant to the patients. Restoration of muscular strength and proprioception should therefore be aggressively addressed in the rehabilitation process after these fractures.}, language = {en} } @article{BaurHirschmuellerMuelleretal.2011, author = {Baur, Heiner and Hirschm{\"u}ller, Anja and M{\"u}ller, Steffen and Mayer, Frank}, title = {Neuromuscular activity of the peroneal muscle after foot orthoses therapy in runners}, series = {Medicine and science in sports and exercise : official journal of the American College of Sports Medicine}, volume = {43}, journal = {Medicine and science in sports and exercise : official journal of the American College of Sports Medicine}, number = {8}, publisher = {Lippincott Williams \& Wilkins}, address = {Philadelphia}, issn = {0195-9131}, doi = {10.1249/MSS.0b013e31820c64ae}, pages = {1500 -- 1506}, year = {2011}, abstract = {BAUR, H., A. HIRSCHMULLER, S. MULLER, and F. MAYER. Neuromuscular Activity of the Peroneal Muscle after Foot Orthoses Therapy in Runners. Med. Sci. Sports Exerc., Vol. 43, No. 8, pp. 1500-1506, 2011. Purpose: Foot orthoses are a standard option to treat overuse injury. Biomechanical data providing mechanisms of foot orthoses' effectiveness are sparse. Stability of the ankle joint complex might be a key factor. The purpose was therefore to analyze neuromuscular activity of the musculus peroneus longus in runners with overuse injury symptoms treated with foot orthoses. Methods: A total of 99 male and female runners with overuse injury symptoms randomized in a control group (CO) and an orthoses group (OR) were analyzed on a treadmill at 3.3 m.s(-1) before and after an 8-wk foot orthoses intervention. Muscular activity of the musculus peroneus longus was measured and quantified in the time domain (initial onset of activation (T-ini), time of maximal activity (T-max), total time of activation (T-tot)) and amplitude domain (amplitude in preactivation (A(pre)), weight acceptance (A(wa)), push-off (A(po))). Results: Peroneal activity in the time domain did not differ initially between CO and OR, and no effect was observed after therapy (T-ini: CO = -0.88 +/- 0.09, OR = -0.88 +/- 0.08 / T-max: CO = 0.14 +/- 0.06, OR = 0.15 +/- 0.06 / T-tot: CO = 0.40 +/- 0.09, OR = 0.41 +/- 0.09; P > 0.05). In preactivation (Apre), muscle activity was higher in OR after intervention (CO = 0.97 +/- 0.32, 95\% confidence interval = 0.90-1.05; OR = 1.18 +/- 0.43, 95\% confidence interval = 1.08-1.28; P = 0.003). There was no group or intervention effect during stance (A(wa): CO = 2.33 +/- 0.66, OR = 2.33 +/- 0.74 / A(po): CO = 0.80 +/- 0.41, OR = 0.88 +/- 0.40; P > 0.05). Conclusions: Enhanced muscle activation of the musculus peroneus longus in preactivation suggests an altered preprogrammed activity, which might lead to better ankle stability providing a possible mode of action for foot orthoses therapy.}, language = {en} } @article{MuellerMayerBauretal.2011, author = {M{\"u}ller, Steffen and Mayer, Patrizia and Baur, Heiner and Mayer, Frank}, title = {Higher velocities in isokinetic dynamometry a pilot study of new test mode with active compensation of inertia}, series = {Isokinetics and exercise science : official journal of the European Isokinetic Society}, volume = {19}, journal = {Isokinetics and exercise science : official journal of the European Isokinetic Society}, number = {2}, publisher = {IOS Press}, address = {Amsterdam}, issn = {0959-3020}, doi = {10.3233/IES-2011-0398}, pages = {63 -- 70}, year = {2011}, abstract = {Isokinetic dynamometry is a standard technique for strength testing and training. Nevertheless reliability and validity is limited due to inertia effects, especially for high velocities. Therefore in a first methodological approach the purpose was to evaluate a new isokinetic measurement mode including inertia compensation compared to a classic isokinetic measurement mode for single and multijoint movements at different velocities. Isokinetic maximum strength measurements were carried out in 26 healthy active subjects. Tests were performed using classic isokinetic and new isokinetic mode in random order. Maximum torque/force, maximum movement velocity and time for acceleration were calculated. For inter-instrument agreement Bland and Altman analysis, systematic and random error was quantified. Differences between both methods were assessed (ANOVA alpha = 0.05). Bland and Altman analysis showed the highest agreement between the two modes for strength and velocity measurements (bias: < +/- 1.1\%; LOA: < 14.2\%) in knee flexion/extension at slow isokinetic velocity (60 degrees/s). Least agreement (range: bias: -67.6\% +/- 119.0\%; LOA: 53.4\% 69.3\%) was observed for shoulder/arm test at high isokinetic velocity (360 degrees/s). The Isokin(new) mode showed higher maximum movement velocities (p < 0.05). For low isokinetic velocities the new mode agrees with the classic mode. Especially at high isokinetic velocities the new isokinetic mode shows relevant benefits coupled with a possible trade-off with the force/torque measurement. In conclusion, this study offers for the first time a comparison between the 'classical' and inertia-compensated isokinetic dynamometers indicating the advantages and disadvantages associated with each individual approach, particularly as they relate to medium or high velocities in testing and training.}, language = {en} } @article{HirschmuellerBaurMuelleretal.2011, author = {Hirschm{\"u}ller, Anja and Baur, Heiner and M{\"u}ller, Steffen and Helwig, Peter and Dickhuth, Hans-Hermann and Mayer, Frank}, title = {Clinical effectiveness of customised sport shoe orthoses for overuse injuries in runners a randomised controlled study}, series = {British journal of sports medicine : the journal of sport and exercise medicine}, volume = {45}, journal = {British journal of sports medicine : the journal of sport and exercise medicine}, number = {12}, publisher = {BMJ Publ. Group}, address = {London}, issn = {0306-3674}, doi = {10.1136/bjsm.2008.055830}, pages = {959 -- 965}, year = {2011}, abstract = {Background and objectives Treatment of chronic running-related overuse injuries by orthopaedic shoe orthoses is very common but not evidence-based to date. Hypothesis Polyurethane foam orthoses adapted to a participant's barefoot plantar pressure distribution are an effective treatment option for chronic overuse injuries in runners. Design Prospective, randomised, controlled clinical trial. Intervention 51 patients with running injuries were treated with custom-made, semirigid running shoe orthoses for 8 weeks. 48 served as a randomised control group that continued regular training activity without any treatment. Main outcome measures Evaluation was made by the validated pain questionnaire Subjective Pain Experience Scale, the pain disability index and a comfort index in the orthoses group (ICI). Results There were statistically significant differences between the orthoses and control groups at 8 weeks for the pain disability index (mean difference 3.2; 95\% CI 0.9 to 5.5) and the Subjective Pain Experience Scale (6.6; 2.6 to 10.6). The patients with orthoses reported a rising wearing comfort (pre-treatment ICI 69/100; post-treatment ICI 83/100) that was most pronounced in the first 4 weeks (ICI 80.4/100). Conclusion Customised polyurethane running shoe orthoses are an effective conservative therapy strategy for chronic running injuries with high comfort and acceptance of injured runners.}, language = {en} } @phdthesis{Risse2011, author = {Risse, Sarah}, title = {Processing in the perceptual span : investigations with the n+2-boundary paradigm}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-60414}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {Cognitive psychology is traditionally interested in the interaction of perception, cognition, and behavioral control. Investigating eye movements in reading constitutes a field of research in which the processes and interactions of these subsystems can be studied in a well-defined environment. Thereby, the following questions are pursued: How much information is visually perceived during a fixation, how is processing achieved and temporally coordinated from visual letter encoding to final sentence comprehension, and how do such processes reflect on behavior such as the control of the eyes' movements during reading. Various theoretical models have been proposed to account for the specific eye-movement behavior in reading (for a review see Reichle, Rayner, \& Pollatsek, 2003). Some models are based on the idea of shifting attention serially from one word to the next within the sentence whereas others propose distributed attention allocating processing resources to more than one word at a time. As attention is assumed to drive word recognition processes one major difference between these models is that word processing must either occur in strict serial order, or that word processing is achieved in parallel. In spite of this crucial difference in the time course of word processing, both model classes perform well on explaining many of the benchmark effects in reading. In fact, there seems to be not much empirical evidence that challenges the models to a point at which their basic assumptions could be falsified. One issue often perceived as being decisive in the debate on serial and parallel word processing is how not-yet-fixated words to the right of fixation affect eye movements. Specifically, evidence is discussed as to what spatial extent such parafoveal words are previewed and how this influences current and subsequent word processing. Four experiments investigated parafoveal processing close to the spatial limits of the perceptual span. The present work aims to go beyond mere existence proofs of previewing words at such spatial distances. Introducing a manipulation that dissociates the sources of long-range preview effects, benefits and costs of parafoveal processing can be investigated in a single analysis and the differing impact is tracked across a three-word target region. In addition, the same manipulation evaluates the role of oculomotor error as the cause of non-local distributed effects. In this respect, the results contribute to a better understanding of the time course of word processing inside the perceptual span and attention allocation during reading.}, language = {en} } @misc{BostonHaleVasishthetal.2011, author = {Boston, Marisa Ferrara and Hale, John T. and Vasishth, Shravan and Kliegl, Reinhold}, title = {Parallel processing and sentence comprehension difficulty}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-57159}, year = {2011}, abstract = {Eye fixation durations during normal reading correlate with processing difficulty but the specific cognitive mechanisms reflected in these measures are not well understood. This study finds support in German readers' eyefixations for two distinct difficulty metrics: surprisal, which reflects the change in probabilities across syntactic analyses as new words are integrated, and retrieval, which quantifies comprehension difficulty in terms of working memory constraints. We examine the predictions of both metrics using a family of dependency parsers indexed by an upper limit on the number of candidate syntactic analyses they retain at successive words. Surprisal models all fixation measures and regression probability. By contrast, retrieval does not model any measure in serial processing. As more candidate analyses are considered in parallel at each word, retrieval can account for the same measures as surprisal. This pattern suggests an important role for ranked parallelism in theories of sentence comprehension.}, language = {en} } @phdthesis{Gendt2011, author = {Gendt, Anja}, title = {Eye movements under the control of working memory : the challenge of a reading-span task}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-69224}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {During reading oculomotor processes guide the eyes over the text. The visual information recorded is accessed, evaluated and processed. Only by retrieving the meaning of a word from the long-term memory, as well as through the connection and storage of the information about each individual word, is it possible to access the semantic meaning of a sentence. Therefore memory, and here in particular working memory, plays a pivotal role in the basic processes of reading. The following dissertation investigates to what extent different demands on memory and memory capacity have an effect on eye movement behavior while reading. The frequently used paradigm of the reading span task, in which test subjects read and evaluate individual sentences, was used for the experimental review of the research questions. The results speak for the fact that working memory processes have a direct effect on various eye movement measurements. Thus a high working memory load, for example, reduced the perceptual span while reading. The lower the individual working memory capacity of the reader was, the stronger was the influence of the working memory load on the processing of the sentence.}, language = {en} } @article{GrossartFrindteDziallasetal.2011, author = {Grossart, Hans-Peter and Frindte, Katharina and Dziallas, Claudia and Eckert, Werner and Tang, Kam W.}, title = {Microbial methane production in oxygenated water column of an oligotrophic lake}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {49}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1110716108}, pages = {19657 -- 19661}, year = {2011}, abstract = {The prevailing paradigm in aquatic science is that microbial methanogenesis happens primarily in anoxic environments. Here, we used multiple complementary approaches to show that microbial methane production could and did occur in the well-oxygenated water column of an oligotrophic lake (Lake Stechlin, Germany). Oversaturation of methane was repeatedly recorded in the well-oxygenated upper 10 m of the water column, and the methane maxima coincided with oxygen oversaturation at 6 m. Laboratory incubations of unamended epilimnetic lake water and inoculations of photoautotrophs with a lake-enrichment culture both led to methane production even in the presence of oxygen, and the production was not affected by the addition of inorganic phosphate or methylated compounds. Methane production was also detected by in-lake incubations of lake water, and the highest production rate was 1.8-2.4 nM.h(-1) at 6 m, which could explain 33-44\% of the observed ambient methane accumulation in the same month. Temporal and spatial uncoupling between methanogenesis and methanotrophy was supported by field and laboratory measurements, which also helped explain the oversaturation of methane in the upper water column. Potentially methanogenic Archaea were detected in situ in the oxygenated, methane-rich epilimnion, and their attachment to photoautotrophs might allow for anaerobic growth and direct transfer of substrates for methane production. Specific PCR on mRNA of the methyl coenzyme M reductase A gene revealed active methanogenesis. Microbial methane production in oxygenated water represents a hitherto overlooked source of methane and can be important for carbon cycling in the aquatic environments and water to air methane flux.}, language = {en} } @article{BelovaShchukinGorinetal.2011, author = {Belova, Valentina and Shchukin, Dmitry G. and Gorin, Dmitry A. and Kopyshev, Alexey and Moehwald, Helmuth}, title = {A new approach to nucleation of cavitation bubbles at chemically modified surfaces}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {13}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {17}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c1cp20218a}, pages = {8015 -- 8023}, year = {2011}, abstract = {Cavitation at the solid surface normally begins with nucleation, in which defects or assembled molecules located at a liquid-solid interface act as nucleation centers and are actively involved in the evolution of cavitation bubbles. Here, we propose a simple approach to evaluate the behavior of cavitation bubbles formed under high intensity ultrasound (20 kHz, 51.3 W cm (2)) at solid surfaces, based on sonication of patterned substrates with a small roughness (less than 3 nm) and controllable surface energy. A mixture of octadecylphosphonic acid (ODTA) and octadecanethiol (ODT) was stamped on the Si wafer coated with different thicknesses of an aluminium layer (20-500 nm). We investigated the growth mechanism of cavitation bubble nuclei and the evolution of individual pits (defects) formed under sonication on the modified surface. A new activation behavior as a function of Al thickness, sonication time, ultrasonic power and temperature is reported. In this process cooperativity is introduced, as initially formed pits further reduce the energy to form bubbles. Furthermore, cavitation on the patterns is a controllable process, where up to 40-50 min of sonication time only the hydrophobic areas are active nucleation sites. This study provides a convincing proof of our theoretical approach on nucleation.}, language = {en} } @article{KlieglWeiDambacheretal.2011, author = {Kliegl, Reinhold and Wei, Ping and Dambacher, Michael and Yan, Ming and Zhou, Xiaolin}, title = {Experimental effects and individual differences in linear mixed models estimating the relationship between spatial, object, and attraction effects in visual attention}, series = {Frontiers in psychology}, volume = {2}, journal = {Frontiers in psychology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-1078}, doi = {10.3389/fpsyg.2010.00238}, pages = {12}, year = {2011}, abstract = {Linear mixed models (LMMs) provide a still underused methodological perspective on combining experimental and individual-differences research. Here we illustrate this approach with two-rectangle cueing in visual attention (Egly et al., 1994). We replicated previous experimental cue-validity effects relating to a spatial shift of attention within an object (spatial effect), to attention switch between objects (object effect), and to the attraction of attention toward the display centroid (attraction effect), also taking into account the design-inherent imbalance of valid and other trials. We simultaneously estimated variance/covariance components of subject-related random effects for these spatial, object, and attraction effects in addition to their mean reaction times (RTs). The spatial effect showed a strong positive correlation with mean RT and a strong negative correlation with the attraction effect. The analysis of individual differences suggests that slow subjects engage attention more strongly at the cued location than fast subjects. We compare this joint LMM analysis of experimental effects and associated subject-related variances and correlations with two frequently used alternative statistical procedures.}, language = {en} } @article{KlieglBates2011, author = {Kliegl, Reinhold and Bates, Douglas}, title = {International collaboration in psychology is on the rise}, doi = {10.1007/s11192-010-0299-0}, year = {2011}, abstract = {There has been a substantial increase in the percentage for publications with co-authors located in departments from different countries in 12 major journals of psychology. The results are evidence for a remarkable internationalization of psychological research, starting in the mid 1970s and increasing in rate at the beginning of the 1990s. This growth occurs against a constant number of articles with authors from the same country; it is not due to a concomitant increase in the number of co-authors per article. Thus, international collaboration in psychology is obviously on the rise.}, language = {en} } @article{RisseKliegl2011, author = {Risse, Sarah and Kliegl, Reinhold}, title = {Adult age difference in the perceptual span during reading}, year = {2011}, abstract = {Following up on research suggesting an age-related reduction in the rightward extent of the perceptual span during reading (Rayner, Castelhano, \& Yang, 2009), we compared old and young adults in an N + 2-boundary paradigm in which a nonword preview of word N + 2 or word N + 2 itself is replaced by the target word once the eyes cross an invisible boundary located after word N. The intermediate word N + 1 was always three letters long. Gaze durations on word N + 2 were significantly shorter for identical than nonword N + 2 preview both for young and for old adults, with no significant difference in this preview benefit. Young adults, however, did modulate their gaze duration on word N more strongly than old adults in response to the difficulty of the parafoveal word N + 1. Taken together, the results suggest a dissociation of preview benefit and parafoveal-on-foveal effect. Results are discussed in terms of age-related decline in resilience towards distributed processing while simultaneously preserving the ability to integrate parafoveal information into foveal processing. As such, the present results relate to proposals of regulatory compensation strategies older adults use to secure an overall reading speed very similar to that of young adults. (PsycINFO Database Record (c) 2011 APA, all rights reserved)}, language = {en} } @article{BostonHalbeVasishthetal.2011, author = {Boston, Marisa Ferrara and Halbe, John T. and Vasishth, Shravan and Kliegl, Reinhold}, title = {Parallel processing and entence comprehension difficulty}, doi = {10.1080/01690965.2010.492228}, year = {2011}, abstract = {Eye fixation durations during normal reading correlate with processing difficulty, but the specific cognitive mechanisms reflected in these measures are not well understood. This study finds support in German readers' eye fixations for two distinct difficulty metrics: surprisal, which reflects the change in probabilities across syntactic analyses as new words are integrated; and retrieval, which quantifies comprehension difficulty in terms of working memory constraints. We examine the predictions of both metrics using a family of dependency parsers indexed by an upper limit on the number of candidate syntactic analyses they retain at successive words. Surprisal models all fixation measures and regression probability. By contrast, retrieval does not model any measure in serial processing. As more candidate analyses are considered in parallel at each word, retrieval can account for the same measures as surprisal. This pattern suggests an important role for ranked parallelism in theories of sentence comprehension.}, language = {en} } @article{OhlBrandtKliegl2011, author = {Ohl, Sven and Brandt, Stephan A. and Kliegl, Reinhold}, title = {Secondary (micro-)saccades the influence of primary saccade end point and target eccentricity on the process of postsaccadic fixation}, series = {Vision research : an international journal for functional aspects of vision.}, volume = {51}, journal = {Vision research : an international journal for functional aspects of vision.}, number = {23-24}, publisher = {Elsevier}, address = {Oxford}, issn = {0042-6989}, doi = {10.1016/j.visres.2011.09.005}, pages = {2340 -- 2347}, year = {2011}, abstract = {We examine how the size of saccadic under-/overshoot and target eccentricity influence the latency, amplitude and orientation of secondary (micro-)saccades. In our experiment, a target appeared at an eccentricity of either 6 degrees or 14 degrees of visual angle. Subjects were instructed to direct their gaze as quickly as possible to the target and hold fixation at the new location until the end of the trial. Typically, increasing saccadic error is associated with faster and larger secondary saccades. We show that secondary saccades at distant in contrast to close targets have in a specific error range a shorter latency, larger amplitude, and follow more often the direction of the primary saccade. Finally, we demonstrate that an undershooting primary saccade is followed almost exclusively by secondary saccades into the same direction while overshooting primary saccades are followed by secondary saccades into both directions. This supports the notion that under- and overshooting imply different consequences for postsaccadic oculomotor processing. Results are discussed using a model, introduced by Rolfs, Kliegl, and Engbert (2008), to account for the generation of microsaccades. We argue that the dynamic interplay of target eccentricity and the magnitude of the saccadic under-/overshoot can be explained by a different strength of activation in the two hemispheres of the saccadic motor map in this model.}, language = {en} } @article{KlieglBates2011, author = {Kliegl, Reinhold and Bates, Douglas}, title = {International collaboration in psychology is on the rise}, series = {Scientometrics : an international journal for all quantitative aspects of the science of science, communication in science and science policy}, volume = {87}, journal = {Scientometrics : an international journal for all quantitative aspects of the science of science, communication in science and science policy}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0138-9130}, doi = {10.1007/s11192-010-0299-0}, pages = {149 -- 158}, year = {2011}, abstract = {There has been a substantial increase in the percentage for publications with co-authors located in departments from different countries in 12 major journals of psychology. The results are evidence for a remarkable internationalization of psychological research, starting in the mid 1970s and increasing in rate at the beginning of the 1990s. This growth occurs against a constant number of articles with authors from the same country; it is not due to a concomitant increase in the number of co-authors per article. Thus, international collaboration in psychology is obviously on the rise.}, language = {en} } @misc{DimigenSommerHohlfeldetal.2011, author = {Dimigen, Olaf and Sommer, Werner and Hohlfeld, Annette and Jacobs, Arthur M. and Kliegl, Reinhold}, title = {Coregistration of eye movements and EEG in natural reading analyses and review}, series = {Journal of experimental psychology : General}, volume = {140}, journal = {Journal of experimental psychology : General}, number = {4}, publisher = {American Psychological Association}, address = {Washington}, issn = {0096-3445}, doi = {10.1037/a0023885}, pages = {552 -- 572}, year = {2011}, abstract = {Brain-electric correlates of reading have traditionally been studied with word-by-word presentation, a condition that eliminates important aspects of the normal reading process and precludes direct comparisons between neural activity and oculomotor behavior. In the present study, we investigated effects of word predictability on eye movements (EM) and fixation-related brain potentials (FRPs) during natural sentence reading. Electroencephalogram (EEG) and EM (via video-based eye tracking) were recorded simultaneously while subjects read heterogeneous German sentences, moving their eyes freely over the text. FRPs were time-locked to first-pass reading fixations and analyzed according to the cloze probability of the currently fixated word. We replicated robust effects of word predictability on EMs and the N400 component in FRPs. The data were then used to model the relation among fixation duration, gaze duration, and N400 amplitude, and to trace the time course of EEG effects relative to effects in EM behavior. In an extended Methodological Discussion section, we review 4 technical and data-analytical problems that need to be addressed when FRPs are recorded in free-viewing situations (such as reading, visual search, or scene perception) and propose solutions. Results suggest that EEG recordings during normal vision are feasible and useful to consolidate findings from EEG and eye-tracking studies.}, language = {en} } @article{ShuZhouYanetal.2011, author = {Shu, Hua and Zhou, Wei and Yan, Ming and Kliegl, Reinhold}, title = {Font size modulates saccade-target selection in Chinese reading}, series = {Attention, perception, \& psychophysics : AP\&P ; a journal of the Psychonomic Society, Inc.}, volume = {73}, journal = {Attention, perception, \& psychophysics : AP\&P ; a journal of the Psychonomic Society, Inc.}, number = {2}, publisher = {Springer}, address = {New York}, issn = {1943-3921}, doi = {10.3758/s13414-010-0029-y}, pages = {482 -- 490}, year = {2011}, abstract = {In alphabetic writing systems, saccade amplitude (a close correlate of reading speed) is independent of font size, presumably because an increase in the angular size of letters is compensated for by a decrease of visual acuity with eccentricity. We propose that this invariance may (also) be due to the presence of spaces between words, guiding the eyes across a large range of font sizes. Here, we test whether saccade amplitude is also invariant against manipulations of font size during reading Chinese, a character-based writing system without spaces as explicit word boundaries for saccade-target selection. In contrast to word-spaced alphabetic writing systems, saccade amplitude decreased significantly with increased font size, leading to an increase in the number of fixations at the beginning of words and in the number of refixations. These results are consistent with a model which assumes that word beginning (rather than word center) is the default saccade target if the length of the parafoveal word is not available.}, language = {en} } @article{BostonHaleVasishthetal.2011, author = {Boston, Marisa Ferrara and Hale, John T. and Vasishth, Shravan and Kliegl, Reinhold}, title = {Parallel processing and sentence comprehension difficulty}, series = {Language and cognitive processes}, volume = {26}, journal = {Language and cognitive processes}, number = {3}, publisher = {Wiley}, address = {Hove}, issn = {0169-0965}, doi = {10.1080/01690965.2010.492228}, pages = {301 -- 349}, year = {2011}, abstract = {Eye fixation durations during normal reading correlate with processing difficulty, but the specific cognitive mechanisms reflected in these measures are not well understood. This study finds support in German readers' eye fixations for two distinct difficulty metrics: surprisal, which reflects the change in probabilities across syntactic analyses as new words are integrated; and retrieval, which quantifies comprehension difficulty in terms of working memory constraints. We examine the predictions of both metrics using a family of dependency parsers indexed by an upper limit on the number of candidate syntactic analyses they retain at successive words. Surprisal models all fixation measures and regression probability. By contrast, retrieval does not model any measure in serial processing. As more candidate analyses are considered in parallel at each word, retrieval can account for the same measures as surprisal. This pattern suggests an important role for ranked parallelism in theories of sentence comprehension.}, language = {en} } @article{KielMoehwaldBargheer2011, author = {Kiel, Mareike and M{\"o}hwald, Helmuth and Bargheer, Matias}, title = {Broadband measurements of the transient optical complex dielectric function of a nanoparticle/polymer composite upon ultrafast excitation}, series = {Physical review : B, Condensed matter and materials physics}, volume = {84}, journal = {Physical review : B, Condensed matter and materials physics}, number = {16}, publisher = {American Physical Society}, address = {College Park}, issn = {1098-0121}, doi = {10.1103/PhysRevB.84.165121}, pages = {6}, year = {2011}, abstract = {We determined experimentally the complex transient optical dielectric function of a well-characterized polyelectrolyte/gold-nanoparticle composite system over a broad spectral range upon short pulse laser excitation by simultaneously measuring the time-dependent reflectance and transmittance of white light pulses with femtosecond pump-probe spectroscopy. We extracted directly the ultrafast changes in the real and imaginary parts of the effective dielectric function, epsilon(eff)(r) (omega,t)and epsilon(eff)(i) (omega,t), from the experiment. This complete experimental set of information on the time-dependent complex dielectric function challenges theories modeling the transient dielectric function of gold particles and the effective medium.}, language = {en} } @article{GebserSabuncuSchaub2011, author = {Gebser, Martin and Sabuncu, Orkunt and Schaub, Torsten}, title = {An incremental answer set programming based system for finite model computation}, series = {AI communications : AICOM ; the European journal on artificial intelligence}, volume = {24}, journal = {AI communications : AICOM ; the European journal on artificial intelligence}, number = {2}, publisher = {IOS Press}, address = {Amsterdam}, issn = {0921-7126}, doi = {10.3233/AIC-2011-0496}, pages = {195 -- 212}, year = {2011}, abstract = {We address the problem of Finite Model Computation (FMC) of first-order theories and show that FMC can efficiently and transparently be solved by taking advantage of a recent extension of Answer Set Programming (ASP), called incremental Answer Set Programming (iASP). The idea is to use the incremental parameter in iASP programs to account for the domain size of a model. The FMC problem is then successively addressed for increasing domain sizes until an answer set, representing a finite model of the original first-order theory, is found. We implemented a system based on the iASP solver iClingo and demonstrate its competitiveness by showing that it slightly outperforms the winner of the FNT division of CADE's 2009 Automated Theorem Proving (ATP) competition on the respective benchmark collection.}, language = {en} } @article{FettkeNunesNesiFernieetal.2011, author = {Fettke, J{\"o}rg and Nunes-Nesi, Adriano and Fernie, Alisdair and Steup, Martin}, title = {Identification of a novel heteroglycan-interacting protein, HIP 1.3, from Arabidopsis thaliana}, series = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, volume = {168}, journal = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, number = {12}, publisher = {Elsevier}, address = {Jena}, issn = {0176-1617}, doi = {10.1016/j.jplph.2010.09.008}, pages = {1415 -- 1425}, year = {2011}, abstract = {Plastidial degradation of transitory starch yields mainly maltose and glucose. Following the export into the cytosol, maltose acts as donor for a glucosyl transfer to cytosolic heteroglycans as mediated by a cytosolic transglucosidase (DPE2; EC 2.4.1.25) and the second glucosyl residue is liberated as glucose. The cytosolic phosphorylase (Pho2/PHS2; EC 2.4.1.1) also interacts with heteroglycans using the same intramolecular sites as DPE2. Thus, the two glucosyl transferases interconnect the cytosolic pools of glucose and glucose 1-phosphate. Due to the complex monosaccharide pattern, other heteroglycan-interacting proteins (Hips) are expected to exist. Identification of those proteins was approached by using two types of affinity chromatography. Heteroglycans from leaves of Arabidopsis thaliana (Col-0) covalently bound to Sepharose served as ligands that were reacted with a complex mixture of buffer-soluble proteins from Arabidopsis leaves. Binding proteins were eluted by sodium chloride. For identification, SDS-PAGE, tryptic digestion and MALDI-TOF analyses were applied. A strongly interacting polypeptide (approximately 40 kDa; designated as HIP1.3) was observed as product of locus At1g09340. Arabidopsis mutants deficient in HIP1.3 were reduced in growth and contained heteroglycans displaying an altered monosaccharide pattern. Wild type plants express HIP1.3 most strongly in leaves. As revealed by immuno fluorescence, HIP1.3 is located in the cytosol of mesophyll cells but mostly associated with the cytosolic surface of the chloroplast envelope membranes. In an HIP1.3-deficient mutant the immunosignal was undetectable. Metabolic profiles from leaves of this mutant and wild type plants as well were determined by GC-MS. As compared to the wild type control, more than ten metabolites, such as ascorbic acid, fructose, fructose bisphosphate, glucose, glycine, were elevated in darkness but decreased in the light. Although the biochemical function of HIP1.3 has not yet been elucidated, it is likely to possess an important function in the central carbon metabolism of higher plants.}, language = {en} } @article{RohrmannTohgeAlbaetal.2011, author = {Rohrmann, Johannes and Tohge, Takayuki and Alba, Rob and Osorio, Sonia and Caldana, Camila and McQuinn, Ryan and Arvidsson, Samuel Janne and van der Merwe, Margaretha J. and Riano-Pachon, Diego Mauricio and M{\"u}ller-R{\"o}ber, Bernd and Fei, Zhangjun and Nesi, Adriano Nunes and Giovannoni, James J. and Fernie, Alisdair}, title = {Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development}, series = {The plant journal}, volume = {68}, journal = {The plant journal}, number = {6}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0960-7412}, doi = {10.1111/j.1365-313X.2011.04750.x}, pages = {999 -- 1013}, year = {2011}, abstract = {Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes.}, language = {en} } @article{HuberKlamroth2011, author = {Huber, Christian and Klamroth, Tillmann}, title = {Explicitly time-dependent coupled cluster singles doubles calculations of laser-driven many-electron dynamics}, series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistry}, volume = {134}, journal = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistry}, number = {5}, publisher = {American Institute of Physics}, address = {Melville}, issn = {0021-9606}, doi = {10.1063/1.3530807}, pages = {8}, year = {2011}, abstract = {We report explicitly time-dependent coupled cluster singles doubles (TD-CCSD) calculations, which simulate the laser-driven correlated many-electron dynamics in molecular systems. Small molecules, i.e., HF, H(2)O, NH(3), and CH(4), are treated mostly with polarized valence double zeta basis sets. We determine the coupled cluster ground states by imaginary time propagation for these molecules. Excited state energies are obtained from the Fourier transform of the time-dependent dipole moment after an ultrashort, broadband laser excitation. The time-dependent expectation values are calculated from the complex cluster amplitudes using the corresponding configuration interaction singles doubles wave functions. Also resonant laser excitations of these excited states are simulated, in order to explore the limits for the numerical stability of our current TD-CCSD implementation, which uses time-independent molecular orbitals to form excited configurations.}, language = {en} } @article{DeFrenneGraaeKolbetal.2011, author = {De Frenne, Pieter and Graae, Bente J. and Kolb, Annette and Shevtsova, Anna and Baeten, Lander and Brunet, J{\"o}rg and Chabrerie, Olivier and Cousins, Sara A. O. and Decocq, Guillaume and Dhondt, Rob and Diekmann, Martin and Gruwez, Robert and Heinken, Thilo and Hermy, Martin and Oster, Mathias and Saguez, Robert and Stanton, Sharon and Tack, Wesley and Vanhellemont, Margot and Verheyen, Kris}, title = {An intraspecific application of the leaf-height-seed ecology strategy scheme to forest herbs along a latitudinal gradient}, series = {Ecography : pattern and diversity in ecology ; research papers forum}, volume = {34}, journal = {Ecography : pattern and diversity in ecology ; research papers forum}, number = {1}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0906-7590}, doi = {10.1111/j.1600-0587.2010.06399.x}, pages = {132 -- 140}, year = {2011}, abstract = {We measured LHS traits in 41 Anemone nemorosa and 44 Milium effusum populations along a 1900-2300 km latitudinal gradient from N France to N Sweden. We then applied multilevel models to identify the effects of regional (temperature, latitude) and local (soil fertility and acidity, overstorey canopy cover) environmental factors on LHS traits. Both species displayed a significant 4\% increase in plant height with every degree northward shift (almost a two-fold plant height difference between the southernmost and northernmost populations). Neither seed mass nor SLA showed a significant latitudinal cline. Temperature had a large effect on the three LHS traits of Anemone. Latitude, canopy cover and soil nutrients were related to the SLA and plant height of Milium. None of the investigated variables appeared to be related to the seed mass of Milium. The variation in LHS traits indicates that the ecological strategy determined by the position of each population in this three-factor triangle is not constant along the latitudinal gradient. The significant increase in plant height suggests greater competitive abilities for both species in the northernmost populations. We also found that the studied environmental factors affected the LHS traits of the two species on various scales: spring-flowering Anemone was affected more by temperature, whereas early-summer flowering Milium was affected more by local and other latitude-related factors. Finally, previously reported cross-species correlations between LHS traits and latitude were generally unsupported by our within-species approach.}, language = {en} } @article{SteinhoefelBreuervonBlanckenburgetal.2011, author = {Steinhoefel, Grit and Breuer, J{\"o}rn and von Blanckenburg, Friedhelm and Horn, Ingo and Kaczorek, Danuta and Sommer, Michael}, title = {Micrometer silicon isotope diagnostics of soils by UV femtosecond laser ablation}, series = {Chemical geology : official journal of the European Association for Geochemistry}, volume = {286}, journal = {Chemical geology : official journal of the European Association for Geochemistry}, number = {3-4}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0009-2541}, doi = {10.1016/j.chemgeo.2011.05.013}, pages = {280 -- 289}, year = {2011}, abstract = {This study presents the first Si isotope data of the principle Si pools in soils determined by a UV femtosecond laser ablation system coupled to a multicollector inductively coupled plasma mass spectrometer (MC-ICP-MS). This method reveals accurate and precise Si isotope data on bulk materials, and at high spatial resolution, on the mineral scale. The following Si pools have been investigated: a) the Si source to soils on all major silicate minerals on thin sections from bedrock fragments in the soil profiles; b) bulk soils (particle size <2 mm) after fusion to glass beads with an iridium-strip heater or pressed into powder pellets: c) separated clay fractions as pressed powder pellets and e) separated phytoliths as pressed powder pellets. Multiple analyses of three rock standards, BHVO-2, AGV-1 and RGM-1 as fused glass beads and as pressed powder pellets, reveal delta(30)Si values within the expected range of igneous rocks. The MPI-DING reference glass KL2-G exhibits the same Si isotope composition after remelting by an iridium-strip heater showing that this technique does not alter the isotope composition of the glass. We used this approach to investigated two immature Cambisols developed on sandstone and paragneiss in the Black Forest (Germany), respectively. Bulk soils show a largely uniform Si isotope signature for different horizons and locations, which is close to those of primary quartz and feldspar with delta(30)Si values around -0.4 parts per thousand. Soil clay formation is associated with limited Si mobility, which preserves initial Si isotope signatures of parental minerals. An exception is the organic horizon of the paragneiss catchment where intense weathering leads to a high mobility of Si and significant negative isotope signatures as low as to -1.00 parts per thousand in bulk soils. Biogenic opal in the form of phytoliths, exhibits negative Si isotope signatures of about -0.4 parts per thousand. These results demonstrate that UV femtosecond laser ablation MC-ICP-MS provides a tool to characterize the Si isotope signature of the principle Si pools left behind after weathering and Si transport have altered soils. These results can now serve as a fingerprint of the residual solids that can be used to explain the isotope composition of dissolved Si in soil solutions and river water, which is mostly enriched in the heavy isotopes.}, language = {en} } @article{ZhangWielandReicheetal.2011, author = {Zhang, Zhuodong and Wieland, Ralf and Reiche, Matthias and Funk, Roger and Hoffmann, Carsten and Li, Yong and Sommer, Michael}, title = {Wind modelling for wind erosion research by open source computational fluid dynamics}, series = {Ecological informatics : an international journal on ecoinformatics and computational ecolog}, volume = {6}, journal = {Ecological informatics : an international journal on ecoinformatics and computational ecolog}, number = {5}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1574-9541}, doi = {10.1016/j.ecoinf.2011.02.001}, pages = {316 -- 324}, year = {2011}, abstract = {The open source computational fluid dynamics (CFD) wind model (CFD-WEM) for wind erosion research in the Xilingele grassland in Inner Mongolia (autonomous region, China) is compared with two open source CFD models Gerris and OpenFOAM. The evaluation of these models was made according to software technology, implemented methods, handling, accuracy and calculation speed. All models were applied to the same wind tunnel data set. Results show that the simplest CFD-WEM has the highest calculation speed with acceptable accuracy, and the most powerful OpenFOAM produces the simulation with highest accuracy and the lowest calculation speed. Gerris is between CFD-WEM and OpenFOAM. It calculates faster than OpenFOAM, and it is capable to solve different CFD problems. CFD-WEM is the optimal model to be further developed for wind erosion research in Inner Mongolia grassland considering its efficiency and the uncertainties of other input data. However, for other applications using CFD technology, Gerris and OpenFOAM can be good choices. This paper shows the powerful capability of open source CFD software in wind erosion study, and advocates more involvement of open source technology in wind erosion and related ecological researches.}, language = {en} } @article{KaylerKaiserGessleretal.2011, author = {Kayler, Zachary and Kaiser, Michael and Gessler, Arthur and Ellerbrock, Ruth H. and Sommer, Michael}, title = {Application of delta C-13 and delta N-15 isotopic signatures of organic matter fractions sequentially separated from adjacent arable and forest soils to identify carbon stabilization mechanisms}, series = {Biogeosciences}, volume = {8}, journal = {Biogeosciences}, number = {10}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1726-4170}, doi = {10.5194/bg-8-2895-2011}, pages = {2895 -- 2906}, year = {2011}, abstract = {Identifying the chemical mechanisms behind soil carbon bound in organo-mineral complexes is necessary to determine the degree to which soil organic carbon is stabilized belowground. Analysis of delta C-13 and delta N-15 isotopic signatures of stabilized OM fractions along with soil mineral characteristics may yield important information about OM-mineral associations and their processing history. We anlayzed the delta C-13 and delta N-15 isotopic signatures from two organic matter (OM) fractions along with soil mineral proxies to identify the likely binding mechanisms involved. We analyzed OM fractions hypothesized to contain carbon stabilized through organo-mineral complexes: (1) OM separated chemically with sodium pyrophosphate (OM(PY)) and (2) OM occluded in micro-structures found in the chemical extraction residue (OM(ER)). Because the OM fractions were separated from five different soils with paired forest and arable land use histories, we could address the impact of land use change on carbon binding and processing mechanisms. We used partial least squares regression to analyze patterns in the isotopic signature of OM with established mineral and chemical proxies indicative for certain binding mechanisms. We found different mechanisms predominate in each land use type. For arable soils, the formation of OM(PY)-Ca-mineral associations was identified as an important OM binding mechanism. Therefore, we hypothesize an increased stabilization of microbial processed OM(PY) through Ca2+ interactions. In general, we found the forest soils to contain on average 10\% more stabilized carbon relative to total carbon stocks, than the agricultural counter part. In forest soils, we found a positive relationship between isotopic signatures of OM(PY) and the ratio of soil organic carbon content to soil surface area (SOC/SSA). This indicates that the OM(PY) fractions of forest soils represent layers of slower exchange not directly attached to mineral surfaces. From the isotopic composition of the OM(ER) fraction, we conclude that the OM in this fraction from both land use types have undergone a different pathway to stabilization that does not involve microbial processing, which may include OM which is highly protected within soil micro-structures.}, language = {en} } @article{KaiserWalterEllerbrocketal.2011, author = {Kaiser, Michael and Walter, K. and Ellerbrock, Ruth H. and Sommer, Michael}, title = {Effects of land use and mineral characteristics on the organic carbon content, and the amount and composition of Na-pyrophosphate-soluble organic matter, in subsurface soils}, series = {European journal of soil science}, volume = {62}, journal = {European journal of soil science}, number = {2}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1351-0754}, doi = {10.1111/j.1365-2389.2010.01340.x}, pages = {226 -- 236}, year = {2011}, abstract = {Land use and mineral characteristics affect the ability of surface as well as subsurface soils to sequester organic carbon and their contribution to mitigation of the greenhouse effect. There is less information about the effects of land use and soil properties on the amount and composition of organic matter (OM) for subsurface soils as compared with surface soils. Here we aimed to analyse the long-term (>= 100 years) impact of arable and forest land use and soil mineral characteristics on subsurface soil organic carbon (SOC) contents, as well as on amount and composition of OM sequentially separated by Na pyrophosphate solution (OM(PY)) from subsurface soil samples. Seven soils with different mineral characteristics (Albic and Haplic Luvisol, Colluvic and Haplic Regosol, Haplic and Vertic Cambisol, Haplic Stagnosol) were selected from within Germany. Soil samples were taken from subsurface horizons of forest and adjacent arable sites continuously used for > 100 years. The OM(PY) fractions were analysed for their OC content (OC(PY)) and characterized by Fourier transform infrared spectroscopy. Multiple regression analyses for the arable subsurface soils indicated significant positive relationships between the SOC contents and combined effects of the (i) exchangeable Ca (Ca(ex)) and oxalate-soluble Fe (Fe(ox)) and (ii) the Ca(ex) and Al(ox) contents. For these soils the increase in OC (OC(PY) multiplied by the relative C=O content of OM(PY)) and increasing contents of Ca(ex) indicated that OM(PY) mainly interacts with Ca2+. For the forest subsurface soils (pH < 5), the OC(PY) contents were related to the contents of Na-pyrophosphate-soluble Fe and Al. The long-term arable and forest land use seems to result in different OM(PY)-mineral interactions in subsurface soils. On the basis of this, we hypothesize that a long-term land-use change from arable to forest may lead to a shift from mainly OM(PY)-Ca2+ to mainly OM(PY)-Fe3+ and -Al3+ interactions if the pH of subsurface soils significantly decreases to < 5.}, language = {en} } @article{MuellerKoszinskiBrenningetal.2011, author = {Mueller, Marina Elsa Herta and Koszinski, Sylvia and Brenning, Alexander and Verch, Gernot and Korn, Ulrike and Sommer, Michael}, title = {Within-field variation of mycotoxin contamination of winter wheat is related to indicators of soil moisture}, series = {Plant and soil}, volume = {342}, journal = {Plant and soil}, number = {1-2}, publisher = {Springer}, address = {Dordrecht}, issn = {0032-079X}, doi = {10.1007/s11104-010-0695-5}, pages = {289 -- 300}, year = {2011}, abstract = {Humidity is an important determinant of the mycotoxin production (DON, ZEA) by Fusarium species in the grain ears. From a landscape perspective humidity is not evenly distributed across fields. The topographically-controlled redistribution of water within a single field rather leads to spatially heterogeneous soil water content and air humidity. Therefore we hypothesized that the spatial distribution of mycotoxins is related to these topographically-controlled factors. To test this hypothesis we studied the mycotoxin concentrations at contrasting topographic relief positions, i.e. hilltops and depressions characterized by soils of different soil moisture regimes, on ten winter wheat fields in 2006 and 2007. Maize was the preceding crop and minimum tillage was practiced in the fields. The different topographic positions were associated with moderate differences in DON and ZEA concentrations in 2006, but with significant differences in 2007, with six times higher median ZEA and two times higher median DON detected at depression sites compared to the hilltops. The depression sites correspond to a higher topographic wetness index as well as redoximorphic properties in soil profiles, which empirically supports our hypothesis at least for years showing wetter conditions in sensitive time windows for Fusarium infections.}, language = {en} } @article{WielandDalchowSommeretal.2011, author = {Wieland, Ralf and Dalchow, Claus and Sommer, Michael and Fukuda, Kyoko}, title = {Multi-Scale Landscape Analysis (MSLA) a method to identify correlation of relief with ecological point data}, series = {Ecological informatics : an international journal on ecoinformatics and computational ecolog}, volume = {6}, journal = {Ecological informatics : an international journal on ecoinformatics and computational ecolog}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1574-9541}, doi = {10.1016/j.ecoinf.2010.09.002}, pages = {164 -- 169}, year = {2011}, abstract = {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.}, language = {en} } @phdthesis{Bergner2011, author = {Bergner, Andr{\´e}}, title = {Synchronization in complex systems with multiple time scales}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-53407}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {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.}, language = {en} } @article{ParisiPaternosterKohfahletal.2011, author = {Parisi, Serena and Paternoster, Michele and Kohfahl, Claus and Pekdeger, Asaf and Meyer, Hanno and Hubberten, Hans-Wolfgang and Spilotro, Giuseppe and Mongelli, Giovanni}, title = {Groundwater recharge areas of a volcanic aquifer system inferred from hydraulic, hydrogeochemical and stable isotope data mount Vulture, southern Italy}, series = {Hydrogeology journal : official journal of the International Association of Hydrogeologists}, volume = {19}, journal = {Hydrogeology journal : official journal of the International Association of Hydrogeologists}, number = {1}, publisher = {Springer}, address = {New York}, issn = {1431-2174}, doi = {10.1007/s10040-010-0619-8}, pages = {133 -- 153}, year = {2011}, abstract = {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.}, language = {en} } @article{GrimbsArnoldKoseskaetal.2011, author = {Grimbs, Sergio and Arnold, Anne and Koseska, Aneta and Kurths, J{\"u}rgen and Selbig, Joachim and Nikoloski, Zoran}, title = {Spatiotemporal dynamics of the Calvin cycle multistationarity and symmetry breaking instabilities}, series = {Biosystems : journal of biological and information processing sciences}, volume = {103}, journal = {Biosystems : journal of biological and information processing sciences}, number = {2}, publisher = {Elsevier}, address = {Oxford}, issn = {0303-2647}, doi = {10.1016/j.biosystems.2010.10.015}, pages = {212 -- 223}, year = {2011}, abstract = {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.}, language = {en} } @article{DongesDonnerRehfeldetal.2011, author = {Donges, Jonathan and Donner, Reik Volker and Rehfeld, Kira and Marwan, Norbert and Trauth, Martin H. and Kurths, J{\"u}rgen}, title = {Identification of dynamical transitions in marine palaeoclimate records by recurrence network analysis}, series = {Nonlinear processes in geophysics}, volume = {18}, journal = {Nonlinear processes in geophysics}, number = {5}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1023-5809}, doi = {10.5194/npg-18-545-2011}, pages = {545 -- 562}, year = {2011}, abstract = {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.}, language = {en} } @article{SrinivasanSenthilkumarMuralietal.2011, author = {Srinivasan, K. and Senthilkumar, Dharmapuri Vijayan and Murali, K. and Lakshmanan, Muthusamy and Kurths, J{\"u}rgen}, title = {Synchronization transitions in coupled time-delay electronic circuits with a threshold nonlinearity}, series = {Chaos : an interdisciplinary journal of nonlinear science}, volume = {21}, journal = {Chaos : an interdisciplinary journal of nonlinear science}, number = {2}, publisher = {American Institute of Physics}, address = {Melville}, issn = {1054-1500}, doi = {10.1063/1.3591791}, pages = {11}, year = {2011}, abstract = {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.}, language = {en} } @article{ZakharovaKurthsVadivasovaetal.2011, author = {Zakharova, Anna and Kurths, J{\"u}rgen and Vadivasova, Tatyana and Koseska, Aneta}, title = {Analysing dynamical behavior of cellular networks via stochastic bifurcations}, series = {PLoS one}, volume = {6}, journal = {PLoS one}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0019696}, pages = {12}, year = {2011}, abstract = {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.}, language = {en} } @article{HempelKoseskaNikoloskietal.2011, 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 - a measures comparison study}, series = {BMC bioinformatics}, volume = {12}, journal = {BMC bioinformatics}, number = {1}, publisher = {BioMed Central}, address = {London}, issn = {1471-2105}, doi = {10.1186/1471-2105-12-292}, pages = {26}, year = {2011}, 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{SanhuezaPinoKorupHetzeletal.2011, author = {Sanhueza-Pino, Katia and Korup, Oliver and Hetzel, Ralf and Munack, Henry and Weidinger, Johannes T. and Dunning, Stuart A. and Ormukov, Cholponbek and Kubik, Peter W.}, title = {Glacial advances constrained by Be-10 exposure dating of bedrock landslides, Kyrgyz Tien Shan}, series = {Quaternary research : an interdisciplinary journal}, volume = {76}, journal = {Quaternary research : an interdisciplinary journal}, number = {3}, publisher = {Elsevier}, address = {San Diego}, issn = {0033-5894}, doi = {10.1016/j.yqres.2011.06.013}, pages = {295 -- 304}, year = {2011}, abstract = {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.}, language = {en} } @article{DongesDonnerTrauthetal.2011, author = {Donges, Jonathan and Donner, Reik Volker and Trauth, Martin H. and Marwan, Norbert and Schellnhuber, Hans Joachim and Kurths, J{\"u}rgen}, title = {Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {51}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1117052108}, pages = {20422 -- 20427}, year = {2011}, abstract = {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.}, language = {en} } @article{HuangChenKurths2011, author = {Huang, Tingwen and Chen, Guanrong and Kurths, J{\"u}rgen}, title = {Synchronization of chaotic of chaotic systems with time-varying coup{\"o}ing delays}, series = {Discrete and continuous dynamical systems : a journal bridging mathematics and sciences ; Series B, Mathematical modelling, analysis and computations}, volume = {16}, journal = {Discrete and continuous dynamical systems : a journal bridging mathematics and sciences ; Series B, Mathematical modelling, analysis and computations}, number = {4}, publisher = {American Institute of Mathematical Sciences}, address = {Springfield}, issn = {1531-3492}, doi = {10.3934/dcdsb.2011.16.1071}, pages = {1071 -- 1082}, year = {2011}, abstract = {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.}, language = {en} } @article{KoseskaVolkovKurths2011, author = {Koseska, Aneta and Volkov, Evgenii and Kurths, J{\"u}rgen}, title = {Synthetic multicellular oscillatory systems controlling protein dynamics with genetic circuits}, series = {Physica scripta : an international journal for experimental and theoretical physics}, volume = {84}, journal = {Physica scripta : an international journal for experimental and theoretical physics}, number = {4}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0031-8949}, doi = {10.1088/0031-8949/84/04/045007}, pages = {10}, year = {2011}, abstract = {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.}, language = {en} } @article{HempelKoseskaKurthsetal.2011, author = {Hempel, Stefan and Koseska, Aneta and Kurths, J{\"u}rgen and Nikoloski, Zoran}, title = {Inner composition alignment for inferring directed networks from short time series}, series = {Physical review letters}, volume = {107}, journal = {Physical review letters}, number = {5}, publisher = {American Physical Society}, address = {College Park}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.107.054101}, pages = {4}, year = {2011}, abstract = {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.}, language = {en} }