@inproceedings{2212,
  abstract     = {The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2 1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2 1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic). We present an algorithm running in time O(d·n2d·MeanGame) to compute the set of almost-sure winning states from which the objective can be ensured with probability 1, where n is the number of states of the game, d the number of priorities of the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states in 2 1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective). },
  author       = {Chatterjee, Krishnendu and Doyen, Laurent and Gimbert, Hugo and Oualhadj, Youssouf},
  location     = {Grenoble, France},
  pages        = {210 -- 225},
  publisher    = {Springer},
  title        = {{Perfect-information stochastic mean-payoff parity games}},
  doi          = {10.1007/978-3-642-54830-7_14},
  volume       = {8412},
  year         = {2014},
}

@inproceedings{2213,
  abstract     = {We consider two-player partial-observation stochastic games on finitestate graphs where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are ε-regular conditions specified as parity objectives. The qualitative-analysis problem given a partial-observation stochastic game and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). These qualitative-analysis problems are known to be undecidable. However in many applications the relevant question is the existence of finite-memory strategies, and the qualitative-analysis problems under finite-memory strategies was recently shown to be decidable in 2EXPTIME.We improve the complexity and show that the qualitative-analysis problems for partial-observation stochastic parity games under finite-memory strategies are EXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis.},
  author       = {Chatterjee, Krishnendu and Doyen, Laurent and Nain, Sumit and Vardi, Moshe},
  location     = {Grenoble, France},
  pages        = {242 -- 257},
  publisher    = {Springer},
  title        = {{The complexity of partial-observation stochastic parity games with finite-memory strategies}},
  doi          = {10.1007/978-3-642-54830-7_16},
  volume       = {8412},
  year         = {2014},
}

@article{2214,
  abstract     = {A hallmark of immune cell trafficking is directional guidance via gradients of soluble or surface bound chemokines. Vascular endothelial cells produce, transport and deposit either their own chemokines or chemokines produced by the underlying stroma. Endothelial heparan sulfate (HS) was suggested to be a critical scaffold for these chemokine pools, but it is unclear how steep chemokine gradients are sustained between the lumenal and ablumenal aspects of blood vessels. Addressing this question by semi-quantitative immunostaining of HS moieties around blood vessels with a pan anti-HS IgM mAb, we found a striking HS enrichment in the basal lamina of resting and inflamed post capillary skin venules, as well as in high endothelial venules (HEVs) of lymph nodes. Staining of skin vessels with a glycocalyx probe further suggested that their lumenal glycocalyx contains much lower HS density than their basolateral extracellular matrix (ECM). This polarized HS pattern was observed also in isolated resting and inflamed microvascular dermal cells. Notably, progressive skin inflammation resulted in massive ECM deposition and in further HS enrichment around skin post capillary venules and their associated pericytes. Inflammation-dependent HS enrichment was not compromised in mice deficient in the main HS degrading enzyme, heparanase. Our results suggest that the blood vasculature patterns steep gradients of HS scaffolds between their lumenal and basolateral endothelial aspects, and that inflammatory processes can further enrich the HS content nearby inflamed vessels. We propose that chemokine gradients between the lumenal and ablumenal sides of vessels could be favored by these sharp HS scaffold gradients.},
  author       = {Stoler Barak, Liat and Moussion, Christine and Shezen, Elias and Hatzav, Miki and Sixt, Michael K and Alon, Ronen},
  journal      = {PLoS One},
  number       = {1},
  publisher    = {Public Library of Science},
  title        = {{Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects}},
  doi          = {10.1371/journal.pone.0085699},
  volume       = {9},
  year         = {2014},
}

@article{2215,
  abstract     = {Homologous recombination is crucial for genome stability and for genetic exchange. Although our knowledge of the principle steps in recombination and its machinery is well advanced, homology search, the critical step of exploring the genome for homologous sequences to enable recombination, has remained mostly enigmatic. However, recent methodological advances have provided considerable new insights into this fundamental step in recombination that can be integrated into a mechanistic model. These advances emphasize the importance of genomic proximity and nuclear organization for homology search and the critical role of homology search mediators in this process. They also aid our understanding of how homology search might lead to unwanted and potentially disease-promoting recombination events.},
  author       = {Renkawitz, Jörg and Lademann, Claudio and Jentsch, Stefan},
  journal      = {Nature Reviews Molecular Cell Biology},
  number       = {6},
  pages        = {369 -- 383},
  publisher    = {Nature Publishing Group},
  title        = {{Mechanisms and principles of homology search during recombination}},
  doi          = {10.1038/nrm3805},
  volume       = {15},
  year         = {2014},
}

@inproceedings{2216,
  abstract     = {The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition. In this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in time stamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than δ away from the parameter, for δ > 0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and analogous decidability results hold for rectangular automata.},
  author       = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Majumdar, Ritankar},
  location     = {Berlin, Germany},
  pages        = {303 -- 312},
  publisher    = {Springer},
  title        = {{Edit distance for timed automata}},
  doi          = {10.1145/2562059.2562141},
  year         = {2014},
}

@inproceedings{2217,
  abstract     = {As hybrid systems involve continuous behaviors, they should be evaluated by quantitative methods, rather than qualitative methods. In this paper we adapt a quantitative framework, called model measuring, to the hybrid systems domain. The model-measuring problem asks, given a model M and a specification, what is the maximal distance such that all models within that distance from M satisfy (or violate) the specification. A distance function on models is given as part of the input of the problem. Distances, especially related to continuous behaviors are more natural in the hybrid case than the discrete case. We are interested in distances represented by monotonic hybrid automata, a hybrid counterpart of (discrete) weighted automata, whose recognized timed languages are monotone (w.r.t. inclusion) in the values of parameters.

The contributions of this paper are twofold. First, we give sufficient conditions under which the model-measuring problem can be solved. Second, we discuss the modeling of distances and applications of the model-measuring problem.},
  author       = {Henzinger, Thomas A and Otop, Jan},
  booktitle    = {Proceedings of the 17th international conference on Hybrid systems: computation and control},
  location     = {Berlin, Germany},
  pages        = {213 -- 222},
  publisher    = {Springer},
  title        = {{Model measuring for hybrid systems}},
  doi          = {10.1145/2562059.2562130},
  year         = {2014},
}

@inproceedings{2218,
  abstract     = {While fixing concurrency bugs, program repair algorithms may introduce new concurrency bugs. We present an algorithm that avoids such regressions. The solution space is given by a set of program transformations we consider in the repair process. These include reordering of instructions within a thread and inserting atomic sections. The new algorithm learns a constraint on the space of candidate solutions, from both positive examples (error-free traces) and counterexamples (error traces). From each counterexample, the algorithm learns a constraint necessary to remove the errors. From each positive examples, it learns a constraint that is necessary in order to prevent the repair from turning the trace into an error trace. We implemented the algorithm and evaluated it on simplified Linux device drivers with known bugs.},
  author       = {Cerny, Pavol and Henzinger, Thomas A and Radhakrishna, Arjun and Ryzhyk, Leonid and Tarrach, Thorsten},
  isbn         = {978-331908866-2},
  location     = {Vienna, Austria},
  pages        = {568 -- 584},
  publisher    = {Springer},
  title        = {{Regression-free synthesis for concurrency}},
  doi          = {10.1007/978-3-319-08867-9_38},
  volume       = {8559},
  year         = {2014},
}

@inproceedings{2219,
  abstract     = {Recently, Döttling et al. (ASIACRYPT 2012) proposed the first chosen-ciphertext (IND-CCA) secure public-key encryption scheme from the learning parity with noise (LPN) assumption. In this work we give an alternative scheme which is conceptually simpler and more efficient. At the core of our construction is a trapdoor technique originally proposed for lattices by Micciancio and Peikert (EUROCRYPT 2012), which we adapt to the LPN setting. The main technical tool is a new double-trapdoor mechanism, together with a trapdoor switching lemma based on a computational variant of the leftover hash lemma.},
  author       = {Kiltz, Eike and Masny, Daniel and Pietrzak, Krzysztof Z},
  isbn         = {978-364254630-3},
  pages        = {1 -- 18},
  publisher    = {Springer},
  title        = {{Simple chosen-ciphertext security from low noise LPN}},
  doi          = {10.1007/978-3-642-54631-0_1},
  volume       = {8383},
  year         = {2014},
}

@article{2220,
  abstract     = {In this issue of Chemistry & Biology, Cokol and colleagues report a systematic study of drug interactions between antifungal compounds. Suppressive drug interactions occur more frequently than previously realized and come in different flavors with interesting implications.},
  author       = {De Vos, Marjon and Bollenbach, Mark Tobias},
  issn         = {10745521},
  journal      = {Chemistry and Biology},
  number       = {4},
  pages        = {439 -- 440},
  publisher    = {Cell Press},
  title        = {{Suppressive drug interactions between antifungals}},
  doi          = {10.1016/j.chembiol.2014.04.004},
  volume       = {21},
  year         = {2014},
}

@article{2222,
  abstract     = {Leaf venation develops complex patterns in angiosperms, but the mechanism underlying this process is largely unknown. To elucidate the molecular mechanisms governing vein pattern formation, we previously isolated vascular network defective (van) mutants that displayed venation discontinuities. Here, we report the phenotypic analysis of van4 mutants, and we identify and characterize the VAN4 gene. Detailed phenotypic analysis shows that van4 mutants are defective in procambium cell differentiation and subsequent vascular cell differentiation. Reduced shoot and root cell growth is observed in van4 mutants, suggesting that VAN4 function is important for cell growth and the establishment of venation continuity. Consistent with these phenotypes, the VAN4 gene is strongly expressed in vascular and meristematic cells. VAN4 encodes a putative TRS120, which is a known guanine nucleotide exchange factor (GEF) for Rab GTPase involved in regulating vesicle transport, and a known tethering factor that determines the specificity of membrane fusion. VAN4 protein localizes at the trans-Golgi network/early endosome (TGN/EE). Aberrant recycling of the auxin efflux carrier PIN proteins is observed in van4 mutants. These results suggest that VAN4-mediated exocytosis at the TGN plays important roles in plant vascular development and cell growth in shoot and root. Our identification of VAN4 as a putative TRS120 shows that Rab GTPases are crucial (in addition to ARF GTPases) for continuous vascular development, and provides further evidence for the importance of vesicle transport in leaf vascular formation.},
  author       = {Naramoto, Satoshi and Nodzyński, Tomasz and Dainobu, Tomoko and Takatsuka, Hirotomo and Okada, Teruyo and Friml, Jirí and Fukuda, Hiroo},
  issn         = {00320781},
  journal      = {Plant and Cell Physiology},
  number       = {4},
  pages        = {750 -- 763},
  publisher    = {Oxford University Press},
  title        = {{VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis}},
  doi          = {10.1093/pcp/pcu012},
  volume       = {55},
  year         = {2014},
}

@article{2223,
  abstract     = {Correct positioning of membrane proteins is an essential process in eukaryotic organisms. The plant hormone auxin is distributed through intercellular transport and triggers various cellular responses. Auxin transporters of the PIN-FORMED (PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA), inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes 19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization have been genetically poorly defined. Using a fluorescence imaging-based forward genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent protein (GFP) as well as development is hypersensitive to BFA. We found that in bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent with the developmental importance of PIN proteins, functional interference with ARF1 resulted in an impaired auxin response gradient and various developmental defects including embryonic patterning defects and growth arrest. Our results show that ARF1A1C is essential for recycling of PIN auxin transporters and for various auxin-dependent developmental processes.},
  author       = {Tanaka, Hirokazu and Nodzyński, Tomasz and Kitakura, Saeko and Feraru, Mugurel and Sasabe, Michiko and Ishikawa, Tomomi and Kleine Vehn, Jürgen and Kakimoto, Tatsuo and Friml, Jirí},
  issn         = {00320781},
  journal      = {Plant and Cell Physiology},
  number       = {4},
  pages        = {737 -- 749},
  publisher    = {Oxford University Press},
  title        = {{BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis}},
  doi          = {10.1093/pcp/pct196},
  volume       = {55},
  year         = {2014},
}

@article{2224,
  abstract     = {This work investigates the transition between different traveling helical waves (spirals, SPIs) in the setup of differentially independent rotating cylinders. We use direct numerical simulations to consider an infinite long and periodic Taylor-Couette apparatus with fixed axial periodicity length. We find so-called mixed-cross-spirals (MCSs), that can be seen as nonlinear superpositions of SPIs, to establish stable footbridges connecting SPI states. While bridging the bifurcation branches of SPIs, the corresponding contributions within the MCS vary continuously with the control parameters. Here discussed MCSs presenting footbridge solutions start and end in different SPI branches. Therefore they differ significantly from the already known MCSs that present bypass solutions (Altmeyer and Hoffmann 2010 New J. Phys. 12 113035). The latter start and end in the same SPI branch, while they always bifurcate out of those SPI branches with the larger mode amplitude. Meanwhile, these only appear within the coexisting region of both SPIs. In contrast, the footbridge solutions can also bifurcate out of the minor SPI contribution. We also find they exist in regions where only one of the SPIs contributions exists. In addition, MCS as footbridge solution can appear either stable or unstable. The latter detected transient solutions offer similar spatio-temporal characteristics to the flow establishing stable footbridges. Such transition processes are interesting for pattern-forming systems in general because they accomplish transitions between traveling waves of different azimuthal wave numbers and have not been described in the literature yet.},
  author       = {Altmeyer, Sebastian},
  issn         = {01695983},
  journal      = {Fluid Dynamics Research},
  number       = {2},
  publisher    = {IOP Publishing Ltd.},
  title        = {{On secondary instabilities generating footbridges between spiral vortex flow}},
  doi          = {10.1088/0169-5983/46/2/025503},
  volume       = {46},
  year         = {2014},
}

@article{2225,
  abstract     = {We consider sample covariance matrices of the form X∗X, where X is an M×N matrix with independent random entries.  We prove the isotropic local Marchenko-Pastur law, i.e. we prove that the resolvent (X∗X−z)−1 converges to a multiple of the identity in the sense of quadratic forms. More precisely, we establish sharp high-probability bounds on the quantity ⟨v,(X∗X−z)−1w⟩−⟨v,w⟩m(z), where m is the Stieltjes transform of the Marchenko-Pastur law and v,w∈CN. We require the logarithms of the dimensions M and N to be comparable. Our result holds down to scales Iz≥N−1+ε and throughout the entire spectrum away from 0. We also prove analogous results for generalized Wigner matrices.
},
  author       = {Bloemendal, Alex and Erdös, László and Knowles, Antti and Yau, Horng and Yin, Jun},
  issn         = {10836489},
  journal      = {Electronic Journal of Probability},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Isotropic local laws for sample covariance and generalized Wigner matrices}},
  doi          = {10.1214/EJP.v19-3054},
  volume       = {19},
  year         = {2014},
}

@article{2226,
  abstract     = {Coriolis force effects on shear flows are important in geophysical and astrophysical contexts. We report a study on the linear stability and the transient energy growth of the plane Couette flow with system rotation perpendicular to the shear direction. External rotation causes linear instability. At small rotation rates, the onset of linear instability scales inversely with the rotation rate and the optimal transient growth in the linearly stable region is slightly enhanced ∼Re2. The corresponding optimal initial perturbations are characterized by roll structures inclined in the streamwise direction and are twisted under external rotation. At large rotation rates, the transient growth is significantly inhibited and hence linear stability analysis is a reliable indicator for instability.},
  author       = {Shi, Liang and Hof, Björn and Tilgner, Andreas},
  issn         = {15393755},
  journal      = {Physical Review E Statistical Nonlinear and Soft Matter Physics},
  number       = {1},
  publisher    = {American Institute of Physics},
  title        = {{Transient growth of Ekman-Couette flow}},
  doi          = {10.1103/PhysRevE.89.013001},
  volume       = {89},
  year         = {2014},
}

@article{2227,
  abstract     = {The Balkan Peninsula, characterized by high rates of endemism, is recognised as one of the most diverse and species-rich areas of Europe. However, little is known about the origin of Balkan endemics. The present study addresses the phylogenetic position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic status and relationship with the widespread R. parnassiifolius, based on nuclear DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ, trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with the latter as the maternal parent.},
  author       = {Cires Rodriguez, Eduardo and Baltisberger, Matthias and Cuesta, Candela and Vargas, Pablo and Prieto, José},
  issn         = {14396092},
  journal      = {Organisms Diversity and Evolution},
  number       = {1},
  pages        = {1 -- 10},
  publisher    = {Springer},
  title        = {{Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences}},
  doi          = {10.1007/s13127-013-0150-6},
  volume       = {14},
  year         = {2014},
}

@article{2228,
  abstract     = {Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion of which are basket cells (BCs), have a key role in feedforward and feedback inhibition, gamma oscillations and complex information processing. For these functions, fast propagation of action potentials (APs) from the soma to the presynaptic terminals is important. However, the functional properties of interneuron axons remain elusive. We examined interneuron axons by confocally targeted subcellular patch-clamp recording in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from the soma and propagated to the distal axon with high reliability and speed. Subcellular mapping revealed a stepwise increase of Na^+ conductance density from the soma to the proximal axon, followed by a further gradual increase in the distal axon. Active cable modeling and experiments with partial channel block revealed that low axonal Na^+ conductance density was sufficient for reliability, but high Na^+ density was necessary for both speed of propagation and fast-spiking AP phenotype. Our results suggest that a supercritical density of Na^+ channels compensates for the morphological properties of interneuron axons (small segmental diameter, extensive branching and high bouton density), ensuring fast AP propagation and high-frequency repetitive firing.},
  author       = {Hu, Hua and Jonas, Peter M},
  issn         = {10976256},
  journal      = {Nature Neuroscience},
  number       = {5},
  pages        = {686--693},
  publisher    = {Nature Publishing Group},
  title        = {{A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons}},
  doi          = {10.1038/nn.3678},
  volume       = {17},
  year         = {2014},
}

@article{2229,
  abstract     = {The distance between Ca^2+ channels and release sensors determines the speed and efficacy of synaptic transmission. Tight "nanodomain" channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose "microdomain" coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca^2+ buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity.},
  author       = {Vyleta, Nicholas and Jonas, Peter M},
  issn         = {00368075},
  journal      = {Science},
  number       = {6171},
  pages        = {665 -- 670},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse}},
  doi          = {10.1126/science.1244811},
  volume       = {343},
  year         = {2014},
}

@article{2230,
  abstract     = {Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals.},
  author       = {Guzmán, José and Schlögl, Alois and Schmidt Hieber, Christoph},
  issn         = {16625196},
  journal      = {Frontiers in Neuroinformatics},
  number       = {FEB},
  publisher    = {Frontiers Research Foundation},
  title        = {{Stimfit: Quantifying electrophysiological data with Python}},
  doi          = {10.3389/fninf.2014.00016},
  volume       = {8},
  year         = {2014},
}

@article{2231,
  abstract     = {Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail.},
  author       = {Rieckh, Georg and Tkacik, Gasper},
  issn         = {00063495},
  journal      = {Biophysical Journal},
  number       = {5},
  pages        = {1194 -- 1204},
  publisher    = {Biophysical Society},
  title        = {{Noise and information transmission in promoters with multiple internal states}},
  doi          = {10.1016/j.bpj.2014.01.014},
  volume       = {106},
  year         = {2014},
}

@article{2232,
  abstract     = {The purpose of this contribution is to summarize and discuss recent advances regarding the onset of turbulence in shear flows. The absence of a clear-cut instability mechanism, the spatio-temporal intermittent character and extremely long lived transients are some of the major difficulties encountered in these flows and have hindered progress towards understanding the transition process. We will show for the case of pipe flow that concepts from nonlinear dynamics and statistical physics can help to explain the onset of turbulence. In particular, the turbulent structures (puffs) observed close to onset are spatially localized chaotic transients and their lifetimes increase super-exponentially with Reynolds number. At the same time fluctuations of individual turbulent puffs can (although very rarely) lead to the nucleation of new puffs. The competition between these two stochastic processes gives rise to a non-equilibrium phase transition where turbulence changes from a super-transient to a sustained state.},
  author       = {Song, Baofang and Hof, Björn},
  issn         = {17425468},
  journal      = {Journal of Statistical Mechanics Theory and Experiment},
  number       = {2},
  publisher    = {IOP Publishing},
  title        = {{Deterministic and stochastic aspects of the transition to turbulence}},
  doi          = {10.1088/1742-5468/2014/02/P02001},
  volume       = {2014},
  year         = {2014},
}