@misc{1500, abstract = {In this poster, we present methods for randomly generating hybrid automata with affine differential equations, invariants, guards, and assignments. Selecting an arbitrary affine function from the set of all affine functions results in a low likelihood of generating hybrid automata with diverse and interesting behaviors, as there are an uncountable number of elements in the set of all affine functions. Instead, we partition the set of all affine functions into potentially interesting classes and randomly select elements from these classes. For example, we partition the set of all affine differential equations by using restrictions on eigenvalues such as those that yield stable, unstable, etc. equilibrium points. We partition the components describing discrete behavior (guards, assignments, and invariants) to allow either time-dependent or state-dependent switching, and in particular provide the ability to generate subclasses of piecewise-affine hybrid automata. Our preliminary experimental results with a prototype tool called HyRG (Hybrid Random Generator) illustrate the feasibility of this generation method to automatically create standard hybrid automaton examples like the bouncing ball and thermostat.}, author = {Nguyen, Luan V and Christian Schilling and Sergiy Bogomolov and Johnson, Taylor T}, booktitle = {HSCC: Hybrid Systems - Computation and Control}, pages = {289 -- 290}, publisher = {Springer}, title = {{Poster: HyRG: A random generation tool for affine hybrid automata}}, doi = {10.1145/2728606.2728650}, year = {2015}, } @article{1501, abstract = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. }, author = {Chatterjee, Krishnendu and Chmelik, Martin and Daca, Przemyslaw}, journal = {Formal Methods in System Design}, number = {2}, pages = {230 -- 264}, publisher = {Springer}, title = {{CEGAR for compositional analysis of qualitative properties in Markov decision processes}}, doi = {10.1007/s10703-015-0235-2}, volume = {47}, year = {2015}, } @inproceedings{1502, abstract = {We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system.}, author = {Beneš, Nikola and Daca, Przemyslaw and Henzinger, Thomas A and Kretinsky, Jan and Nickovic, Dejan}, isbn = {978-1-4503-3471-6}, location = {Montreal, QC, Canada}, pages = {101 -- 110}, publisher = {ACM}, title = {{Complete composition operators for IOCO-testing theory}}, doi = {10.1145/2737166.2737175}, year = {2015}, } @article{1503, abstract = {A Herman-Avila-Bochi type formula is obtained for the average sum of the top d Lyapunov exponents over a one-parameter family of double-struck G-cocycles, where double-struck G is the group that leaves a certain, non-degenerate Hermitian form of signature (c, d) invariant. The generic example of such a group is the pseudo-unitary group U(c, d) or, in the case c = d, the Hermitian-symplectic group HSp(2d) which naturally appears for cocycles related to Schrödinger operators. In the case d = 1, the formula for HSp(2d) cocycles reduces to the Herman-Avila-Bochi formula for SL(2, ℝ) cocycles.}, author = {Sadel, Christian}, journal = {Ergodic Theory and Dynamical Systems}, number = {5}, pages = {1582 -- 1591}, publisher = {Cambridge University Press}, title = {{A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles}}, doi = {10.1017/etds.2013.103}, volume = {35}, year = {2015}, } @article{1504, abstract = {Let Q = (Q1, . . . , Qn) be a random vector drawn from the uniform distribution on the set of all n! permutations of {1, 2, . . . , n}. Let Z = (Z1, . . . , Zn), where Zj is the mean zero variance one random variable obtained by centralizing and normalizing Qj , j = 1, . . . , n. Assume that Xi , i = 1, . . . ,p are i.i.d. copies of 1/√ p Z and X = Xp,n is the p × n random matrix with Xi as its ith row. Then Sn = XX is called the p × n Spearman's rank correlation matrix which can be regarded as a high dimensional extension of the classical nonparametric statistic Spearman's rank correlation coefficient between two independent random variables. In this paper, we establish a CLT for the linear spectral statistics of this nonparametric random matrix model in the scenario of high dimension, namely, p = p(n) and p/n→c ∈ (0,∞) as n→∞.We propose a novel evaluation scheme to estimate the core quantity in Anderson and Zeitouni's cumulant method in [Ann. Statist. 36 (2008) 2553-2576] to bypass the so-called joint cumulant summability. In addition, we raise a two-step comparison approach to obtain the explicit formulae for the mean and covariance functions in the CLT. Relying on this CLT, we then construct a distribution-free statistic to test complete independence for components of random vectors. Owing to the nonparametric property, we can use this test on generally distributed random variables including the heavy-tailed ones.}, author = {Bao, Zhigang and Lin, Liang and Pan, Guangming and Zhou, Wang}, journal = {Annals of Statistics}, number = {6}, pages = {2588 -- 2623}, publisher = {Institute of Mathematical Statistics}, title = {{Spectral statistics of large dimensional spearman s rank correlation matrix and its application}}, doi = {10.1214/15-AOS1353}, volume = {43}, year = {2015}, } @article{1505, abstract = {This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed.}, author = {Bao, Zhigang and Pan, Guangming and Zhou, Wang}, journal = {Annals of Statistics}, number = {1}, pages = {382 -- 421}, publisher = {Institute of Mathematical Statistics}, title = {{Universality for the largest eigenvalue of sample covariance matrices with general population}}, doi = {10.1214/14-AOS1281}, volume = {43}, year = {2015}, } @article{1506, abstract = {Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).}, author = {Bao, Zhigang and Pan, Guangming and Zhou, Wang}, journal = {Bernoulli}, number = {3}, pages = {1600 -- 1628}, publisher = {Bernoulli Society for Mathematical Statistics and Probability}, title = {{The logarithmic law of random determinant}}, doi = {10.3150/14-BEJ615}, volume = {21}, year = {2015}, } @article{1508, abstract = {We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential.}, author = {Erdös, László and Yau, Horng}, journal = {Journal of the European Mathematical Society}, number = {8}, pages = {1927 -- 2036}, publisher = {European Mathematical Society}, title = {{Gap universality of generalized Wigner and β ensembles}}, doi = {10.4171/JEMS/548}, volume = {17}, year = {2015}, } @article{1509, abstract = {The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1.}, author = {Michalko, Jaroslav and Dravecka, Marta and Bollenbach, Tobias and Friml, Jirí}, journal = {F1000 Research }, publisher = {F1000 Research}, title = {{Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene}}, doi = {10.12688/f1000research.7143.1}, volume = {4}, year = {2015}, } @inproceedings{1510, abstract = {The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r > 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. }, author = {Franek, Peter and Krcál, Marek}, location = {Eindhoven, Netherlands}, pages = {842 -- 856}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{On computability and triviality of well groups}}, doi = {10.4230/LIPIcs.SOCG.2015.842}, volume = {34}, year = {2015}, } @inproceedings{1511, abstract = {The fact that the complete graph K_5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M), where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2. Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel's conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.}, author = {Goaoc, Xavier and Mabillard, Isaac and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, location = {Eindhoven, Netherlands}, pages = {476 -- 490}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result}}, doi = {10.4230/LIPIcs.SOCG.2015.476}, volume = {34 }, year = {2015}, } @inproceedings{1512, abstract = {We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest.}, author = {Goaoc, Xavier and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, location = {Eindhoven, Netherlands}, pages = {507 -- 521}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Bounding Helly numbers via Betti numbers}}, doi = {10.4230/LIPIcs.SOCG.2015.507}, volume = {34}, year = {2015}, } @article{1513, abstract = {Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order. In this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. }, author = {Pal, Arka and Vicoso, Beatriz}, journal = {Genome Biology and Evolution}, number = {12}, pages = {3259 -- 3268}, publisher = {Oxford University Press}, title = {{The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression}}, doi = {10.1093/gbe/evv215}, volume = {7}, year = {2015}, } @article{1514, abstract = {Endocannabinoids (eCBs) play key roles in brain function, acting as modulatory signals in synaptic transmission and plasticity. They are recognized as retrograde messengers that mediate long-term synaptic depression (LTD), but their ability to induce long-term potentiation (LTP) is poorly known. We show that eCBs induce the long-term enhancement of transmitter release at single hippocampal synapses through stimulation of astrocytes when coincident with postsynaptic activity. This LTP requires the coordinated activity of the 3 elements of the tripartite synapse: 1) eCB-evoked astrocyte calcium signal that stimulates glutamate release; 2) postsynaptic nitric oxide production; and 3) activation of protein kinase C and presynaptic group I metabotropic glutamate receptors, whose location at presynaptic sites was confirmed by immunoelectron microscopy. Hence, while eCBs act as retrograde signals to depress homoneuronal synapses, they serve as lateral messengers to induce LTP in distant heteroneuronal synapses through stimulation of astrocytes. Therefore, eCBs can trigger LTP through stimulation of astrocyte-neuron signaling, revealing novel cellular mechanisms of eCB effects on synaptic plasticity.}, author = {Gómez-Gonzalo, Marta and Navarrete, Marta and Perea, Gertrudis and Covelo, Ana and Martín-Fernández, Mario and Ryuichi Shigemoto and Luján, Rafael and Araque, Alfonso}, journal = {Cerebral Cortex}, number = {10}, pages = {3699 -- 3712}, publisher = {Oxford University Press}, title = {{Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission}}, doi = {10.1093/cercor/bhu231}, volume = {25}, year = {2015}, } @article{1515, abstract = {Type 1 metabotropic glutamate (mGlu1) receptors play a pivotal role in different forms of synaptic plasticity in the cerebellar cortex, e.g. long-term depression at glutamatergic synapses and rebound potentiation at GABAergic synapses. These various forms of plasticity might depend on the subsynaptic arrangement of the receptor in Purkinje cells that can be regulated by protein-protein interactions. This study investigated, by means of the freeze-fracture replica immunogold labelling method, the subcellular localization of mGlu1 receptors in the rodent cerebellum and whether Homer proteins regulate their subsynaptic distribution. We observed a widespread extrasynaptic localization of mGlu1 receptors and confirmed their peri-synaptic enrichment at glutamatergic synapses. Conversely, we detected mGlu1 receptors within the main body of GABAergic synapses onto Purkinje cell dendrites. Although Homer proteins are known to interact with the mGlu1 receptor C-terminus, we could not detect Homer3, the most abundant Homer protein in the cerebellar cortex, at GABAergic synapses by pre-embedding and post-embedding immunoelectron microscopy. We then hypothesized a critical role for Homer proteins in the peri-junctional localization of mGlu1 receptors at glutamatergic synapses. To disrupt Homer-associated protein complexes, mice were tail-vein injected with the membrane-permeable dominant-negative TAT-Homer1a. Freeze-fracture replica immunogold labelling analysis showed no significant alteration in the mGlu1 receptor distribution pattern at parallel fibre-Purkinje cell synapses, suggesting that other scaffolding proteins are involved in the peri-synaptic confinement. The identification of interactors that regulate the subsynaptic localization of the mGlu1 receptor at neurochemically distinct synapses may offer new insight into its trafficking and intracellular signalling.}, author = {Mansouri, Mahnaz and Kasugai, Yu and Fukazawa, Yugo and Bertaso, Federica and Raynaud, Fabrice and Perroy, Julie and Fagni, Laurent and Walter Kaufmann and Watanabe, Masahiko and Ryuichi Shigemoto and Ferraguti, Francesco}, journal = {European Journal of Neuroscience}, number = {2}, pages = {157 -- 167}, publisher = {Wiley-Blackwell}, title = {{Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex}}, doi = {10.1111/ejn.12779}, volume = {41}, year = {2015}, } @article{1517, abstract = {We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions. }, author = {Erbar, Matthias and Maas, Jan and Renger, Michiel}, journal = {Electronic Communications in Probability}, publisher = {Institute of Mathematical Statistics}, title = {{From large deviations to Wasserstein gradient flows in multiple dimensions}}, doi = {10.1214/ECP.v20-4315}, volume = {20}, year = {2015}, } @article{1519, abstract = {Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so.}, author = {Barton, Nicholas H and Servedio, Maria}, journal = {Evolution}, number = {5}, pages = {1101 -- 1112}, publisher = {Wiley}, title = {{The interpretation of selection coefficients}}, doi = {10.1111/evo.12641}, volume = {69}, year = {2015}, } @inproceedings{1520, abstract = {Creating mechanical automata that can walk in stable and pleasing manners is a challenging task that requires both skill and expertise. We propose to use computational design to offset the technical difficulties of this process. A simple drag-and-drop interface allows casual users to create personalized walking toys from a library of pre-defined template mechanisms. Provided with this input, our method leverages physical simulation and evolutionary optimization to refine the mechanical designs such that the resulting toys are able to walk. The optimization process is guided by an intuitive set of objectives that measure the quality of the walking motions. We demonstrate our approach on a set of simulated mechanical toys with different numbers of legs and various distinct gaits. Two fabricated prototypes showcase the feasibility of our designs.}, author = {Bharaj, Gaurav and Coros, Stelian and Thomaszewski, Bernhard and Tompkin, James and Bickel, Bernd and Pfister, Hanspeter}, isbn = {978-1-4503-3496-9}, location = {Los Angeles, CA, United States}, pages = {93 -- 100}, publisher = {ACM}, title = {{Computational design of walking automata}}, doi = {10.1145/2786784.2786803}, year = {2015}, } @article{1525, abstract = {Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations.}, author = {Bauer, Bruno and Blechl, Guido and Bock, Christoph and Danowski, Patrick and Ferus, Andreas and Graschopf, Anton and König, Thomas and Mayer, Katja and Reckling, Falk and Rieck, Katharina and Seitz, Peter and Stöger, Herwig and Welzig, Elvira}, journal = {VÖB Mitteilungen}, number = {3}, pages = {580 -- 607}, publisher = {Verein Österreichischer Bibliothekare}, title = {{Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA}}, doi = {10.5281/zenodo.33178}, volume = {68}, year = {2015}, } @article{1530, abstract = {In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus, protein concentrations vary over the cell division cycle. We have developed a theoretical description of genetic regulatory systems in bacteria that explicitly considers the cell division cycle to investigate its impact on gene expression. We calculate the cell-to-cell variations arising from cells being at different stages in the division cycle for unregulated genes and for basic regulatory mechanisms. These variations contribute to the extrinsic noise observed in single-cell experiments, and are most significant for proteins with short lifetimes. Negative autoregulation buffers against variation of protein concentration over the division cycle, but the effect is found to be relatively weak. Stronger buffering is achieved by an increased protein lifetime. Positive autoregulation can strongly amplify such variation if the parameters are set to values that lead to resonance-like behaviour. For cooperative positive autoregulation, the concentration variation over the division cycle diminishes the parameter region of bistability and modulates the switching times between the two stable states. The same effects are seen for a two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit, the repressilator, is only weakly affected by the division cycle.}, author = {Bierbaum, Veronika and Klumpp, Stefan}, journal = {Physical Biology}, number = {6}, publisher = {IOP Publishing Ltd.}, title = {{Impact of the cell division cycle on gene circuits}}, doi = {10.1088/1478-3975/12/6/066003}, volume = {12}, year = {2015}, }