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To understand the complex relationship governing transcript abundance and the level of the encoded protein, we integrate genome-wide experimental data of ribosomal density on mRNAs with a novel stochastic model describing ribosome traffic dynamics during translation elongation. This analysis reveals that codon arrangement, rather than simply codon bias, has a key role in determining translational efficiency. It also reveals that translation output is governed both by initiation efficiency and elongation dynamics. By integrating genome-wide experimental data sets with simulation of ribosome traffic on all Saccharomyces cerevisiae ORFs, mRNA-specific translation initiation rates are for the first time estimated across the entire transcriptome. Our analysis identifies different classes of mRNAs characterised by their initiation rates, their ribosome traffic dynamics, and by their response to ribosome availability. Strikingly, this classification based on translational dynamics maps onto key gene ontological classifications, revealing evolutionary optimisation of translation responses to be strongly influenced by gene function.

We present a new method to detect phase as well as generalized synchronization in a wide class of complex systems. It is based on the recurrences of the system's trajectory to the neighborhood of a former state in phase space. We illustrate the applicability of the algorithm for the paradigmatic chaotic Rössler system in the funnel regime and for noisy data, where other methods to detect phase synchronization fail. Furthermore, we demonstrate for electrochemical experiments that the method can easily detect phase and generalized synchronization in nonphase-coherent and even non-stationary time series.

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In this paper we show that two dynamical invariants, the second order Renyi entropy and the correlation dimension, can be estimated from recurrence plots (RPs) with arbitrary embedding dimension and delay. This fact is interesting as these quantities are even invariant if no embedding is used. This is an important advantage of RPs compared to other techniques of nonlinear data analysis. These estimates for the correlation dimension and entropy are robust and, moreover, can be obtained at a low numerical cost. We exemplify our results for the Rossler system, the funnel attractor and the Mackey-Glass system. In the last part of the paper we estimate dynamical invariants for data from some fluid dynamical experiments and confirm previous evidence for low dimensional chaos in this experimental system.

We introduce a mean-field theoretical framework to describe multiple totally asymmetric simple exclusion processes (TASEPs) with different lattice lengths and entry and exit rates, competing for a finite reservoir of particles. We present relations for the partitioning of particles between the reservoir and the lattices: These relations allow us to show that competition for particles can have nontrivial effects on the phase behavior of individual lattices. For a system with nonidentical lattices, we find that when a subset of lattices undergoes a phase transition from low to high density, the entire set of lattice currents becomes independent of total particle number. We generalize our approach to systems with a continuous distribution of lattice parameters, for which we demonstrate that measurements of the current carried by a single lattice type can be used to extract the entire distribution of lattice parameters. Our approach applies to populations of TASEPs with any distribution of lattice parameters and could easily be extended beyond the mean-field case.

Abstract. -We present an approach to generate (multivariate) twin surrogates (TS) based on recurrence properties. This technique generates surrogates which correspond to an independent copy of the underlying system, i.e. they induce a trajectory of the underlying system starting at different initial conditions. We show that these surrogates are well suited to test for complex synchronisation and exemplify this for the paradigmatic system of Rössler oscillators. The proposed test enables to assess the statistical relevance of a synchronisation analysis from passive experiments which are typical in natural systems.

Pregnant mothers often report a special awareness of and bonding with their unborn child. Little is known about this relationship although it may offer potential for the assessment of the fetal condition. Recently we found evidence of short epochs of fetalmaternal heart rate synchronization under uncontrolled conditions with spontaneous maternal breathing. Here, we examine whether the occurrence of such epochs can be influenced by maternal respiratory arrhythmia induced by paced breathing at several different rates (10, 12, 15, and 20 cycles per minute). To test for such weak and nonstationary synchronizations among the fetal-maternal subsystems, we apply a multivariate synchronization analysis technique and test statistics based on twin surrogates. We find a clear increase in synchronization epochs mostly at high maternal respiratory rates in the original but not in the surrogate data. On the other hand, fewer epochs are found at low respiratory rates both in original and surrogate data. The results suggest that the fetal cardiac system seems to possess the capability to adjust its rate of activation in response to external-i.e., maternal-stimulation. Hence, the pregnant mothers' special awareness to the unborn child may also be reflected by fetal-maternal interaction of cardiac activity. Our approach opens up the chance to examine this interaction between independent but closely linked physiological systems.fetal heart rate ͉ maternal heart rate ͉ respiration ͉ synchronization ͉ surrogate data P renatal development involves increased neural integration as pregnancy progresses. Among other things, this neural integration is indicated by the increasing coincidence of fetal heart rate and fetal motor activity in the second and third trimester (1). Apart from such intrafetal coordination of function, the fetus also interacts with its environment. This interaction can often be documented in the fetal heart rate, which remains one of the primary descriptors of fetal physiological activity accessible to systematic study.The mother is central to the fetal environment. Her condition sets the framework for the state and development of the fetus. So far, however, only anecdotal evidence exists for maternal perception of the condition of the fetus. Physiologically, prenatal interaction between mother and fetus has been postulated and various studies confirm a relationship between maternal and fetal conditions on the basis of fetal heart rate. These studies show changes in fetal heart rate and heart rate variability (HRV) associated with altered maternal arterial oxygen content (2, 3), maternal hypothermia (4) and maternal exercise (5). Furthermore, links between maternal and fetal heart rate have been examined. A positive correlation between these rates has been found over periods of 1 and 24 h (6) and the entrainment of the fetal heart rate rhythm to the maternal diurnal rhythm has been observed (7). However, short-term interaction between fetal and maternal heart rate is elusive.In previous work we have examined a large...