--- _id: '253' author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: 'Browning TD. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 2013;60(1):101-107. doi:10.1112/S0025579313000132' apa: 'Browning, T. D. (2013). Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. Unknown. https://doi.org/10.1112/S0025579313000132' chicago: 'Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.” Mathematika. Unknown, 2013. https://doi.org/10.1112/S0025579313000132.' ieee: 'T. D. Browning, “Counting rational points on cubic hypersurfaces: Corrigendum,” Mathematika, vol. 60, no. 1. Unknown, pp. 101–107, 2013.' ista: 'Browning TD. 2013. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 60(1), 101–107.' mla: 'Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.” Mathematika, vol. 60, no. 1, Unknown, 2013, pp. 101–07, doi:10.1112/S0025579313000132.' short: T.D. Browning, Mathematika 60 (2013) 101–107. date_created: 2018-12-11T11:45:27Z date_published: 2013-09-06T00:00:00Z date_updated: 2021-01-12T06:58:03Z day: '06' doi: 10.1112/S0025579313000132 extern: 1 intvolume: ' 60' issue: '1' month: '09' page: 101 - 107 publication: Mathematika publication_status: published publisher: Unknown publist_id: '7649' quality_controlled: 0 status: public title: 'Counting rational points on cubic hypersurfaces: Corrigendum' type: journal_article volume: 60 year: '2013' ... --- _id: '2692' abstract: - lang: eng text: The group III metabotropic glutamate (mGlu) receptors mGlu7 and mGlu8 are receiving increased attention as potential novel therapeutic targets for anxiety disorders. The effects mediated by these receptors appear to result from a complex interplay of facilitatory and inhibitory actions at different brain sites in the anxiety/fear circuits. To better understand the effect of mGlu7 and mGlu8 receptors on extinction of contextual fear and their critical sites of action in the fear networks, we focused on the amygdala. Direct injection into the basolateral complex of the amygdala of the mGlu7 receptor agonist AMN082 facilitated extinction, whereas the mGlu8 receptor agonist (S)-3,4-DCPG sustained freezing during the extinction acquisition trial. We also determined at the ultrastructural level the synaptic distribution of these receptors in the basal nucleus (BA) and intercalated cell clusters (ITCs) of the amygdala. Both areas are thought to exert key roles in fear extinction. We demonstrate that mGlu7 and mGlu8 receptors are located in different presynaptic terminals forming both asymmetric and symmetric synapses, and that they preferentially target neurons expressing mGlu1α receptors mostly located around ITCs. In addition we show that mGlu7 and mGlu8 receptors were segregated to different inputs to a significant extent. In particular, mGlu7a receptors were primarily onto glutamatergic afferents arising from the BA or midline thalamic nuclei, but not the medial prefrontal cortex (mPFC), as revealed by combined anterograde tracing and pre-embedding electron microscopy. On the other hand, mGlu8a showed a more restricted distribution in the BA and appeared absent from thalamic, mPFC and intrinsic inputs. This segregation of mGlu7 and mGlu8 receptors in different neuronal pathways of the fear circuit might explain the distinct effects on fear extinction training observed with mGlu7 and mGlu8 receptor agonists. author: - first_name: Alice full_name: Dobi, Alice last_name: Dobi - first_name: Simone full_name: Sartori, Simone B last_name: Sartori - first_name: Daniela full_name: Busti, Daniela last_name: Busti - first_name: Herman full_name: Van Der Putten, Herman V last_name: Van Der Putten - first_name: Nicolas full_name: Singewald, Nicolas last_name: Singewald - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Francesco full_name: Ferraguti, Francesco last_name: Ferraguti citation: ama: Dobi A, Sartori S, Busti D, et al. Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice. Neuropharmacology. 2013;66:274-289. doi:10.1016/j.neuropharm.2012.05.025 apa: Dobi, A., Sartori, S., Busti, D., Van Der Putten, H., Singewald, N., Shigemoto, R., & Ferraguti, F. (2013). Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice. Neuropharmacology. Elsevier. https://doi.org/10.1016/j.neuropharm.2012.05.025 chicago: Dobi, Alice, Simone Sartori, Daniela Busti, Herman Van Der Putten, Nicolas Singewald, Ryuichi Shigemoto, and Francesco Ferraguti. “Neural Substrates for the Distinct Effects of Presynaptic Group III Metabotropic Glutamate Receptors on Extinction of Contextual Fear Conditioning in Mice.” Neuropharmacology. Elsevier, 2013. https://doi.org/10.1016/j.neuropharm.2012.05.025. ieee: A. Dobi et al., “Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice,” Neuropharmacology, vol. 66. Elsevier, pp. 274–289, 2013. ista: Dobi A, Sartori S, Busti D, Van Der Putten H, Singewald N, Shigemoto R, Ferraguti F. 2013. Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice. Neuropharmacology. 66, 274–289. mla: Dobi, Alice, et al. “Neural Substrates for the Distinct Effects of Presynaptic Group III Metabotropic Glutamate Receptors on Extinction of Contextual Fear Conditioning in Mice.” Neuropharmacology, vol. 66, Elsevier, 2013, pp. 274–89, doi:10.1016/j.neuropharm.2012.05.025. short: A. Dobi, S. Sartori, D. Busti, H. Van Der Putten, N. Singewald, R. Shigemoto, F. Ferraguti, Neuropharmacology 66 (2013) 274–289. date_created: 2018-12-11T11:59:06Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T06:59:05Z day: '01' doi: 10.1016/j.neuropharm.2012.05.025 extern: 1 intvolume: ' 66' month: '03' page: 274 - 289 publication: Neuropharmacology publication_status: published publisher: Elsevier publist_id: '4205' quality_controlled: 0 status: public title: Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice type: journal_article volume: 66 year: '2013' ... --- _id: '2691' abstract: - lang: eng text: P/Q-type voltage-dependent calcium channels play key roles in transmitter release, integration of dendritic signals, generation of dendritic spikes, and gene expression. High intracellular calcium concentration transient produced by these channels is restricted to tens to hundreds of nanometers from the channels. Therefore, precise localization of these channels along the plasma membrane was long sought to decipher how each neuronal cell function is controlled. Here, we analyzed the distribution of Cav2.1 subunit of the P/Q-type channel using highly sensitive SDS-digested freeze-fracture replica labeling in the rat cerebellar Purkinje cells. The labeling efficiency was such that the number of immunogold particles in each parallel fiber active zone was comparable to that of functional channels calculated from previous reports. Two distinct patterns of Cav2.1 distribution, scattered and clustered, were found in Purkinje cells. The scattered Cav2.1 had a somatodendritic gradient with the density of immunogold particles increasing 2.5-fold from soma to distal dendrites. The other population with 74-fold higher density than the scattered particles was found within clusters of intramembrane particles on the P-face of soma and primary dendrites. Both populations of Cav2.1 were found as early as P3 and increased in the second postnatal week to a mature level. Using double immunogold labeling, we found that virtually all of the Cav2.1 clusters were colocalized with two types of calcium-activated potassium channels, BK and SK2, with the nearest neighbor distance of 40∼nm. Calcium nanodomain created by the opening of Cav2.1 channels likely activates the two channels that limit the extent of depolarization. author: - first_name: Dwi full_name: Indriati, Dwi Wahyu last_name: Indriati - first_name: Naomi full_name: Kamasawa, Naomi last_name: Kamasawa - first_name: Ko full_name: Matsui, Ko last_name: Matsui - first_name: Andrea full_name: Meredith, Andrea L last_name: Meredith - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: 'Indriati D, Kamasawa N, Matsui K, Meredith A, Watanabe M, Shigemoto R. Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels. Journal of Neuroscience. 2013;33(8):3668-3678. doi:10.1523/JNEUROSCI.2921-12.2013' apa: 'Indriati, D., Kamasawa, N., Matsui, K., Meredith, A., Watanabe, M., & Shigemoto, R. (2013). Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2921-12.2013' chicago: 'Indriati, Dwi, Naomi Kamasawa, Ko Matsui, Andrea Meredith, Masahiko Watanabe, and Ryuichi Shigemoto. “Quantitative Localization of Cav2.1 (P/Q-Type) Voltage-Dependent Calcium Channels in Purkinje Cells: Somatodendritic Gradient and Distinct Somatic Coclustering with Calcium-Activated Potassium Channels.” Journal of Neuroscience. Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.2921-12.2013.' ieee: 'D. Indriati, N. Kamasawa, K. Matsui, A. Meredith, M. Watanabe, and R. Shigemoto, “Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels,” Journal of Neuroscience, vol. 33, no. 8. Society for Neuroscience, pp. 3668–3678, 2013.' ista: 'Indriati D, Kamasawa N, Matsui K, Meredith A, Watanabe M, Shigemoto R. 2013. Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels. Journal of Neuroscience. 33(8), 3668–3678.' mla: 'Indriati, Dwi, et al. “Quantitative Localization of Cav2.1 (P/Q-Type) Voltage-Dependent Calcium Channels in Purkinje Cells: Somatodendritic Gradient and Distinct Somatic Coclustering with Calcium-Activated Potassium Channels.” Journal of Neuroscience, vol. 33, no. 8, Society for Neuroscience, 2013, pp. 3668–78, doi:10.1523/JNEUROSCI.2921-12.2013.' short: D. Indriati, N. Kamasawa, K. Matsui, A. Meredith, M. Watanabe, R. Shigemoto, Journal of Neuroscience 33 (2013) 3668–3678. date_created: 2018-12-11T11:59:05Z date_published: 2013-02-20T00:00:00Z date_updated: 2021-01-12T06:59:05Z day: '20' doi: 10.1523/JNEUROSCI.2921-12.2013 extern: 1 intvolume: ' 33' issue: '8' month: '02' page: 3668 - 3678 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '4206' quality_controlled: 0 status: public title: 'Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels' type: journal_article volume: 33 year: '2013' ... --- _id: '2690' abstract: - lang: eng text: Establishing the spatiotemporal concentration profile of neurotransmitter following synaptic vesicular release is essential for our understanding of inter-neuronal communication. Such profile is a determinant of synaptic strength, short-term plasticity and inter-synaptic crosstalk. Synaptically released glutamate has been suggested to reach a few millimolar in concentration and last for <1 ms. The synaptic cleft is often conceived as a single concentration compartment, whereas a huge gradient likely exists. Modelling studies have attempted to describe this gradient, but two key parameters, the number of glutamate in a vesicle (NGlu) and its diffusion coefficient (DGlu) in the extracellular space, remained unresolved. To determine this profile, the rat calyx of Held synapse at postnatal day 12-16 was studied where diffusion of glutamate occurs two-dimensionally and where quantification of AMPA receptor distribution on individual postsynaptic specialization on medial nucleus of the trapezoid body principal cells is possible using SDS-digested freeze-fracture replica labelling. To assess the performance of these receptors as glutamate sensors, a kinetic model of the receptors was constructed from outside-out patch recordings. From here, we simulated synaptic responses and compared them with the EPSC recordings. Combinations of NGlu and DGlu with an optimum of 7000 and 0.3 μm2 ms-1 reproduced the data, suggesting slow diffusion. Further simulations showed that a single vesicle does not saturate the synaptic receptors, and that glutamate spillover does not affect the conductance amplitude at this synapse. Using the estimated profile, we also evaluated how the number of multiple vesicle releases at individual active zones affects the amplitude of postsynaptic signals. author: - first_name: Timotheus full_name: Budisantoso, Timotheus last_name: Budisantoso - first_name: Harumi full_name: Harumi Harada id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87 last_name: Harada orcid: 0000-0001-7429-7896 - first_name: Naomi full_name: Kamasawa, Naomi last_name: Kamasawa - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Ko full_name: Matsui, Ko last_name: Matsui citation: ama: Budisantoso T, Harada H, Kamasawa N, Fukazawa Y, Shigemoto R, Matsui K. Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held. Journal of Physiology. 2013;591(1):219-239. doi:10.1113/jphysiol.2012.241398 apa: Budisantoso, T., Harada, H., Kamasawa, N., Fukazawa, Y., Shigemoto, R., & Matsui, K. (2013). Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2012.241398 chicago: Budisantoso, Timotheus, Harumi Harada, Naomi Kamasawa, Yugo Fukazawa, Ryuichi Shigemoto, and Ko Matsui. “Evaluation of Glutamate Concentration Transient in the Synaptic Cleft of the Rat Calyx of Held.” Journal of Physiology. Wiley-Blackwell, 2013. https://doi.org/10.1113/jphysiol.2012.241398. ieee: T. Budisantoso, H. Harada, N. Kamasawa, Y. Fukazawa, R. Shigemoto, and K. Matsui, “Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held,” Journal of Physiology, vol. 591, no. 1. Wiley-Blackwell, pp. 219–239, 2013. ista: Budisantoso T, Harada H, Kamasawa N, Fukazawa Y, Shigemoto R, Matsui K. 2013. Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held. Journal of Physiology. 591(1), 219–239. mla: Budisantoso, Timotheus, et al. “Evaluation of Glutamate Concentration Transient in the Synaptic Cleft of the Rat Calyx of Held.” Journal of Physiology, vol. 591, no. 1, Wiley-Blackwell, 2013, pp. 219–39, doi:10.1113/jphysiol.2012.241398. short: T. Budisantoso, H. Harada, N. Kamasawa, Y. Fukazawa, R. Shigemoto, K. Matsui, Journal of Physiology 591 (2013) 219–239. date_created: 2018-12-11T11:59:05Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:59:04Z day: '01' doi: 10.1113/jphysiol.2012.241398 extern: 1 intvolume: ' 591' issue: '1' month: '01' page: 219 - 239 publication: Journal of Physiology publication_status: published publisher: Wiley-Blackwell publist_id: '4207' quality_controlled: 0 status: public title: Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held type: journal_article volume: 591 year: '2013' ... --- _id: '2693' abstract: - lang: eng text: Inhibitory parvalbumin-containing interneurons (PVIs) control neuronal discharge and support the generation of theta- and gammafrequency oscillations in cortical networks. Fast GABAergic input onto PVIs is crucial for their synchronization and oscillatory entrainment, but the role of metabotropic GABAB receptors (GABABRs) in mediating slow presynaptic and postsynaptic inhibition remains unknown. In this study, we have combined high-resolution immunoelectron microscopy, whole-cell patch-clamp recording, and computational modeling to investigate the subcellular distribution and effects of GABABRs and their postsynaptic effector Kir3 channels in rat hippocampal PVIs. Pre-embedding immunogold labeling revealed that the receptors and channels localize at high levels to the extrasynaptic membrane of parvalbumin-immunoreactive dendrites. Immunoreactivity forGABABRs was also present at lower levels on PVI axon terminals. Whole-cell recordings further showed that synaptically released GABA in response to extracellular stimulation evokes large GABABR-mediated slow IPSCs in perisomatic-targeting (PT) PVIs, but only small or no currents in dendrite-targeting (DT) PVIs. In contrast, paired recordings demonstrated that GABABR activation results in presynaptic inhibition at the output synapses of both PT and DT PVIs, but more strongly in the latter. Finally, computational analysis indicated that GABAB IPSCs can phasically modulate the discharge of PT interneurons at theta frequencies. In summary, our results show that GABABRs differentially mediate slow presynaptic and postsynaptic inhibition in PVIs and can contribute to the dynamic modulation of their activity during oscillations. Furthermore, these data provide evidence for a compartment-specific molecular divergence of hippocampal PVI subtypes, suggesting that activation of GABABRs may shift the balance between perisomatic and dendritic inhibition. author: - first_name: Sam full_name: Booker, Sam A last_name: Booker - first_name: Anna full_name: Gross, Anna last_name: Gross - first_name: Daniel full_name: Althof, Daniel last_name: Althof - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Matthew full_name: Hearing, Matthew C last_name: Hearing - first_name: Kevin full_name: Wickman, Kevin D last_name: Wickman - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Ákos full_name: Kulik, Ákos last_name: Kulik - first_name: Imre full_name: Vida, Imre last_name: Vida citation: ama: Booker S, Gross A, Althof D, et al. Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal of Neuroscience. 2013;33(18):7961-7974. doi:10.1523/JNEUROSCI.1186-12.2013 apa: Booker, S., Gross, A., Althof, D., Shigemoto, R., Bettler, B., Frotscher, M., … Vida, I. (2013). Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1186-12.2013 chicago: Booker, Sam, Anna Gross, Daniel Althof, Ryuichi Shigemoto, Bernhard Bettler, Michael Frotscher, Matthew Hearing, et al. “Differential GABAB-Receptor-Mediated Effects in Perisomatic- and Dendrite-Targeting Parvalbumin Interneurons.” Journal of Neuroscience. Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.1186-12.2013. ieee: S. Booker et al., “Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons,” Journal of Neuroscience, vol. 33, no. 18. Society for Neuroscience, pp. 7961–7974, 2013. ista: Booker S, Gross A, Althof D, Shigemoto R, Bettler B, Frotscher M, Hearing M, Wickman K, Watanabe M, Kulik Á, Vida I. 2013. Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal of Neuroscience. 33(18), 7961–7974. mla: Booker, Sam, et al. “Differential GABAB-Receptor-Mediated Effects in Perisomatic- and Dendrite-Targeting Parvalbumin Interneurons.” Journal of Neuroscience, vol. 33, no. 18, Society for Neuroscience, 2013, pp. 7961–74, doi:10.1523/JNEUROSCI.1186-12.2013. short: S. Booker, A. Gross, D. Althof, R. Shigemoto, B. Bettler, M. Frotscher, M. Hearing, K. Wickman, M. Watanabe, Á. Kulik, I. Vida, Journal of Neuroscience 33 (2013) 7961–7974. date_created: 2018-12-11T11:59:06Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T06:59:05Z day: '01' doi: 10.1523/JNEUROSCI.1186-12.2013 extern: 1 intvolume: ' 33' issue: '18' month: '05' page: 7961 - 7974 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '4204' quality_controlled: 0 status: public title: Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons type: journal_article volume: 33 year: '2013' ... --- _id: '2698' abstract: - lang: eng text: We consider non-interacting particles subject to a fixed external potential V and a self-generated magnetic field B. The total energy includes the field energy β∫B2 and we minimize over all particle states and magnetic fields. In the case of spin-1/2 particles this minimization leads to the coupled Maxwell-Pauli system. The parameter β tunes the coupling strength between the field and the particles and it effectively determines the strength of the field. We investigate the stability and the semiclassical asymptotics, h→0, of the total ground state energy E(β,h,V). The relevant parameter measuring the field strength in the semiclassical limit is κ=βh. We are not able to give the exact leading order semiclassical asymptotics uniformly in κ or even for fixed κ. We do however give upper and lower bounds on E with almost matching dependence on κ. In the simultaneous limit h→0 and κ→∞ we show that the standard non-magnetic Weyl asymptotics holds. The same result also holds for the spinless case, i.e. where the Pauli operator is replaced by the Schrödinger operator. author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Søren full_name: Fournais, Søren last_name: Fournais - first_name: Jan full_name: Solovej, Jan last_name: Solovej citation: ama: Erdös L, Fournais S, Solovej J. Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. 2013;15(6):2093-2113. doi:10.4171/JEMS/416 apa: Erdös, L., Fournais, S., & Solovej, J. (2013). Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/416 chicago: Erdös, László, Søren Fournais, and Jan Solovej. “Stability and Semiclassics in Self-Generated Fields.” Journal of the European Mathematical Society. European Mathematical Society, 2013. https://doi.org/10.4171/JEMS/416. ieee: L. Erdös, S. Fournais, and J. Solovej, “Stability and semiclassics in self-generated fields,” Journal of the European Mathematical Society, vol. 15, no. 6. European Mathematical Society, pp. 2093–2113, 2013. ista: Erdös L, Fournais S, Solovej J. 2013. Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. 15(6), 2093–2113. mla: Erdös, László, et al. “Stability and Semiclassics in Self-Generated Fields.” Journal of the European Mathematical Society, vol. 15, no. 6, European Mathematical Society, 2013, pp. 2093–113, doi:10.4171/JEMS/416. short: L. Erdös, S. Fournais, J. Solovej, Journal of the European Mathematical Society 15 (2013) 2093–2113. date_created: 2018-12-11T11:59:07Z date_published: 2013-10-16T00:00:00Z date_updated: 2021-01-12T06:59:07Z day: '16' department: - _id: LaEr doi: 10.4171/JEMS/416 external_id: arxiv: - '1105.0506' intvolume: ' 15' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1105.0506 month: '10' oa: 1 oa_version: Preprint page: 2093 - 2113 publication: Journal of the European Mathematical Society publication_status: published publisher: European Mathematical Society publist_id: '4198' quality_controlled: '1' status: public title: Stability and semiclassics in self-generated fields type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '2697' abstract: - lang: eng text: We consider Hermitian and symmetric random band matrices H = (h xy ) in d⩾1 d ⩾ 1 dimensions. The matrix entries h xy , indexed by x,y∈(Z/LZ)d x , y ∈ ( Z / L Z ) d , are independent, centred random variables with variances sxy=E|hxy|2 s x y = E | h x y | 2 . We assume that s xy is negligible if |x − y| exceeds the band width W. In one dimension we prove that the eigenvectors of H are delocalized if W≫L4/5 W ≫ L 4 / 5 . We also show that the magnitude of the matrix entries |Gxy|2 | G x y | 2 of the resolvent G=G(z)=(H−z)−1 G = G ( z ) = ( H - z ) - 1 is self-averaging and we compute E|Gxy|2 E | G x y | 2 . We show that, as L→∞ L → ∞ and W≫L4/5 W ≫ L 4 / 5 , the behaviour of E|Gxy|2 E | G x y | 2 is governed by a diffusion operator whose diffusion constant we compute. Similar results are obtained in higher dimensions. author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau - first_name: Jun full_name: Yin, Jun last_name: Yin citation: ama: Erdös L, Knowles A, Yau H, Yin J. Delocalization and diffusion profile for random band matrices. Communications in Mathematical Physics. 2013;323(1):367-416. doi:10.1007/s00220-013-1773-3 apa: Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). Delocalization and diffusion profile for random band matrices. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-013-1773-3 chicago: Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Delocalization and Diffusion Profile for Random Band Matrices.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-013-1773-3. ieee: L. Erdös, A. Knowles, H. Yau, and J. Yin, “Delocalization and diffusion profile for random band matrices,” Communications in Mathematical Physics, vol. 323, no. 1. Springer, pp. 367–416, 2013. ista: Erdös L, Knowles A, Yau H, Yin J. 2013. Delocalization and diffusion profile for random band matrices. Communications in Mathematical Physics. 323(1), 367–416. mla: Erdös, László, et al. “Delocalization and Diffusion Profile for Random Band Matrices.” Communications in Mathematical Physics, vol. 323, no. 1, Springer, 2013, pp. 367–416, doi:10.1007/s00220-013-1773-3. short: L. Erdös, A. Knowles, H. Yau, J. Yin, Communications in Mathematical Physics 323 (2013) 367–416. date_created: 2018-12-11T11:59:07Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T06:59:07Z day: '01' doi: 10.1007/s00220-013-1773-3 extern: 1 intvolume: ' 323' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1205.5669 month: '10' oa: 1 page: 367 - 416 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4199' quality_controlled: 0 status: public title: Delocalization and diffusion profile for random band matrices type: journal_article volume: 323 year: '2013' ... --- _id: '2718' abstract: - lang: eng text: Even though both population and quantitative genetics, and evolutionary computation, deal with the same questions, they have developed largely independently of each other. I review key results from each field, emphasising those that apply independently of the (usually unknown) relation between genotype and phenotype. The infinitesimal model provides a simple framework for predicting the response of complex traits to selection, which in biology has proved remarkably successful. This allows one to choose the schedule of population sizes and selection intensities that will maximise the response to selection, given that the total number of individuals realised, C = ∑t Nt, is constrained. This argument shows that for an additive trait (i.e., determined by the sum of effects of the genes), the optimum population size and the maximum possible response (i.e., the total change in trait mean) are both proportional to √C. author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: 'Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568' apa: 'Barton, N. H., & Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463568' chicago: Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM, 2013. https://doi.org/10.1145/2463372.2463568. ieee: N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 1573–1580. ista: 'Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580.' mla: Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–80, doi:10.1145/2463372.2463568. short: N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580. conference: end_date: 2013-07-10 location: Amsterdam, Netherlands name: 'GECCO: Genetic and evolutionary computation conference' start_date: 2013-07-06 date_created: 2018-12-11T11:59:14Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:59:15Z day: '01' ddc: - '570' department: - _id: NiBa - _id: CaGu doi: 10.1145/2463372.2463568 ec_funded: 1 file: - access_level: open_access checksum: 9d9be9090ce5c20766e0eb076ace5b98 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:38Z date_updated: 2020-07-14T12:45:45Z file_id: '5159' file_name: IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf file_size: 475844 relation: main_file file_date_updated: 2020-07-14T12:45:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 1573 - 1580 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Proceedings of the 15th annual conference on Genetic and evolutionary computation publication_status: published publisher: ACM publist_id: '4174' pubrep_id: '564' quality_controlled: '1' scopus_import: 1 status: public title: Can quantitative and population genetics help us understand evolutionary computation? type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2720' abstract: - lang: eng text: 'Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is <10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.' article_processing_charge: No author: - first_name: Hongan full_name: Long, Hongan last_name: Long - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Ricardo full_name: Azevedo, Ricardo last_name: Azevedo - first_name: Rebecca full_name: Zufall, Rebecca last_name: Zufall citation: ama: Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540. doi:10.1534/genetics.113.153536 apa: Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.153536 chicago: Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics. Genetics Society of America, 2013. https://doi.org/10.1534/genetics.113.153536. ieee: H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013. ista: Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540. mla: Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536. short: H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540. date_created: 2018-12-11T11:59:15Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T06:59:16Z day: '01' department: - _id: NiBa - _id: CaGu doi: 10.1534/genetics.113.153536 ec_funded: 1 external_id: pmid: - '23934880' intvolume: ' 195' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/ month: '10' oa: 1 oa_version: Submitted Version page: 527-540 pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '4172' quality_controlled: '1' scopus_import: 1 status: public title: Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 195 year: '2013' ... --- _id: '2719' abstract: - lang: eng text: Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation. author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470' apa: 'Paixao, T., & Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463470' chicago: Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470. ieee: T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852. ista: 'Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.' mla: Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470. short: T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852. conference: end_date: 2013-07-10 location: Amsterdam, Netherlands name: 'GECCO: Genetic and evolutionary computation conference' start_date: 2013-07-06 date_created: 2018-12-11T11:59:15Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:59:15Z day: '01' department: - _id: NiBa - _id: CaGu doi: 10.1145/2463372.2463470 ec_funded: 1 language: - iso: eng month: '07' oa_version: None page: 845 - 852 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Proceedings of the 15th annual conference on Genetic and evolutionary computation publication_status: published publisher: ACM publist_id: '4173' quality_controlled: '1' scopus_import: 1 status: public title: A variance decomposition approach to the analysis of genetic algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2782' abstract: - lang: eng text: We consider random n×n matrices of the form (XX*+YY*)^{-1/2}YY*(XX*+YY*)^{-1/2}, where X and Y have independent entries with zero mean and variance one. These matrices are the natural generalization of the Gaussian case, which are known as MANOVA matrices and which have joint eigenvalue density given by the third classical ensemble, the Jacobi ensemble. We show that, away from the spectral edge, the eigenvalue density converges to the limiting density of the Jacobi ensemble even on the shortest possible scales of order 1/n (up to log n factors). This result is the analogue of the local Wigner semicircle law and the local Marchenko-Pastur law for general MANOVA matrices. author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Brendan full_name: Farrell, Brendan last_name: Farrell citation: ama: Erdös L, Farrell B. Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. 2013;152(6):1003-1032. doi:10.1007/s10955-013-0807-8 apa: Erdös, L., & Farrell, B. (2013). Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-013-0807-8 chicago: Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” Journal of Statistical Physics. Springer, 2013. https://doi.org/10.1007/s10955-013-0807-8. ieee: L. Erdös and B. Farrell, “Local eigenvalue density for general MANOVA matrices,” Journal of Statistical Physics, vol. 152, no. 6. Springer, pp. 1003–1032, 2013. ista: Erdös L, Farrell B. 2013. Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. 152(6), 1003–1032. mla: Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” Journal of Statistical Physics, vol. 152, no. 6, Springer, 2013, pp. 1003–32, doi:10.1007/s10955-013-0807-8. short: L. Erdös, B. Farrell, Journal of Statistical Physics 152 (2013) 1003–1032. date_created: 2018-12-11T11:59:34Z date_published: 2013-07-18T00:00:00Z date_updated: 2021-01-12T06:59:41Z day: '18' department: - _id: LaEr doi: 10.1007/s10955-013-0807-8 external_id: arxiv: - '1207.0031' intvolume: ' 152' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1207.0031 month: '07' oa: 1 oa_version: Preprint page: 1003 - 1032 publication: Journal of Statistical Physics publication_status: published publisher: Springer publist_id: '4107' quality_controlled: '1' scopus_import: 1 status: public title: Local eigenvalue density for general MANOVA matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 152 year: '2013' ... --- _id: '2781' abstract: - lang: eng text: 'We consider the ensemble of adjacency matrices of Erdős-Rényi random graphs, that is, graphs on N vertices where every edge is chosen independently and with probability p = p(N). We rescale the matrix so that its bulk eigenvalues are of order one. We prove that, as long as pN→∞(with a speed at least logarithmic in N), the density of eigenvalues of the Erdős-Rényi ensemble is given by the Wigner semicircle law for spectral windows of length larger than N-1 (up to logarithmic corrections). As a consequence, all eigenvectors are proved to be completely delocalized in the sense that the ℓ∞-norms of the ℓ2-normalized eigenvectors are at most of order N-1/2 with a very high probability. The estimates in this paper will be used in the companion paper [Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues (2011) Preprint] to prove the universality of eigenvalue distributions both in the bulk and at the spectral edges under the further restriction that pN »N2/3.' author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau - first_name: Jun full_name: Yin, Jun last_name: Yin citation: ama: 'Erdös L, Knowles A, Yau H, Yin J. Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. 2013;41(3 B):2279-2375. doi:10.1214/11-AOP734' apa: 'Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/11-AOP734' chicago: 'Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Spectral Statistics of Erdős-Rényi Graphs I: Local Semicircle Law.” Annals of Probability. Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/11-AOP734.' ieee: 'L. Erdös, A. Knowles, H. Yau, and J. Yin, “Spectral statistics of Erdős-Rényi graphs I: Local semicircle law,” Annals of Probability, vol. 41, no. 3 B. Institute of Mathematical Statistics, pp. 2279–2375, 2013.' ista: 'Erdös L, Knowles A, Yau H, Yin J. 2013. Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. 41(3 B), 2279–2375.' mla: 'Erdös, László, et al. “Spectral Statistics of Erdős-Rényi Graphs I: Local Semicircle Law.” Annals of Probability, vol. 41, no. 3 B, Institute of Mathematical Statistics, 2013, pp. 2279–375, doi:10.1214/11-AOP734.' short: L. Erdös, A. Knowles, H. Yau, J. Yin, Annals of Probability 41 (2013) 2279–2375. date_created: 2018-12-11T11:59:34Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T06:59:41Z day: '01' doi: 10.1214/11-AOP734 extern: 1 intvolume: ' 41' issue: 3 B main_file_link: - open_access: '1' url: http://arxiv.org/abs/1103.1919 month: '05' oa: 1 page: 2279 - 2375 publication: Annals of Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '4109' quality_controlled: 0 status: public title: 'Spectral statistics of Erdős-Rényi graphs I: Local semicircle law' type: journal_article volume: 41 year: '2013' ... --- _id: '2780' abstract: - lang: eng text: We consider a general class of random matrices whose entries are centred random variables, independent up to a symmetry constraint. We establish precise high-probability bounds on the averages of arbitrary monomials in the resolvent matrix entries. Our results generalize the previous results of Erdős et al. (Ann Probab, arXiv:1103.1919, 2013; Commun Math Phys, arXiv:1103.3869, 2013; J Combin 1(2):15-85, 2011) which constituted a key step in the proof of the local semicircle law with optimal error bound in mean-field random matrix models. Our bounds apply to random band matrices and improve previous estimates from order 2 to order 4 in the cases relevant to applications. In particular, they lead to a proof of the diffusion approximation for the magnitude of the resolvent of random band matrices. This, in turn, implies new delocalization bounds on the eigenvectors. The applications are presented in a separate paper (Erdős et al., arXiv:1205.5669, 2013). author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau citation: ama: Erdös L, Knowles A, Yau H. Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. 2013;14(8):1837-1926. doi:10.1007/s00023-013-0235-y apa: Erdös, L., Knowles, A., & Yau, H. (2013). Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-013-0235-y chicago: Erdös, László, Antti Knowles, and Horng Yau. “Averaging Fluctuations in Resolvents of Random Band Matrices.” Annales Henri Poincare. Birkhäuser, 2013. https://doi.org/10.1007/s00023-013-0235-y. ieee: L. Erdös, A. Knowles, and H. Yau, “Averaging fluctuations in resolvents of random band matrices,” Annales Henri Poincare, vol. 14, no. 8. Birkhäuser, pp. 1837–1926, 2013. ista: Erdös L, Knowles A, Yau H. 2013. Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. 14(8), 1837–1926. mla: Erdös, László, et al. “Averaging Fluctuations in Resolvents of Random Band Matrices.” Annales Henri Poincare, vol. 14, no. 8, Birkhäuser, 2013, pp. 1837–926, doi:10.1007/s00023-013-0235-y. short: L. Erdös, A. Knowles, H. Yau, Annales Henri Poincare 14 (2013) 1837–1926. date_created: 2018-12-11T11:59:33Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:59:40Z day: '01' doi: 10.1007/s00023-013-0235-y extern: 1 intvolume: ' 14' issue: '8' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1205.5664 month: '12' oa: 1 page: 1837 - 1926 publication: Annales Henri Poincare publication_status: published publisher: Birkhäuser publist_id: '4110' quality_controlled: 0 status: public title: Averaging fluctuations in resolvents of random band matrices type: journal_article volume: 14 year: '2013' ... --- _id: '2807' abstract: - lang: eng text: 'We consider several basic problems of algebraic topology, with connections to combinatorial and geometric questions, from the point of view of computational complexity. The extension problem asks, given topological spaces X; Y , a subspace A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X → Y . For computational purposes, we assume that X and Y are represented as finite simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map. In this generality the problem is undecidable, as follows from Novikov''s result from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected; informally, this means that Y has \no holes up to dimension k-1" (a basic example of such a Y is the sphere Sk). We prove that, on the one hand, this problem is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2, we obtain an algorithm that solves the extension problem in polynomial time assuming Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides a classification of all extensions up to homotopy (continuous deformation). This relies on results of our SODA 2012 paper, and the main new ingredient is a machinery of objects with polynomial-time homology, which is a polynomial-time analog of objects with effective homology developed earlier by Sergeraert et al. We also consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected Y . Their computability was established by Brown in 1957; we show that πk(Y ) can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where Y is a cell complex with certain rather compact encoding. We strengthen his result to #P-hardness for Y given as a simplicial complex. ' author: - first_name: Martin full_name: Čadek, Martin last_name: Čadek - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Lukáš full_name: Vokřínek, Lukáš last_name: Vokřínek - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. Extending continuous maps: Polynomiality and undecidability. In: 45th Annual ACM Symposium on Theory of Computing. ACM; 2013:595-604. doi:10.1145/2488608.2488683' apa: 'Čadek, M., Krcál, M., Matoušek, J., Vokřínek, L., & Wagner, U. (2013). Extending continuous maps: Polynomiality and undecidability. In 45th Annual ACM Symposium on theory of computing (pp. 595–604). Palo Alto, CA, United States: ACM. https://doi.org/10.1145/2488608.2488683' chicago: 'Čadek, Martin, Marek Krcál, Jiří Matoušek, Lukáš Vokřínek, and Uli Wagner. “Extending Continuous Maps: Polynomiality and Undecidability.” In 45th Annual ACM Symposium on Theory of Computing, 595–604. ACM, 2013. https://doi.org/10.1145/2488608.2488683.' ieee: 'M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, and U. Wagner, “Extending continuous maps: Polynomiality and undecidability,” in 45th Annual ACM Symposium on theory of computing, Palo Alto, CA, United States, 2013, pp. 595–604.' ista: 'Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. 2013. Extending continuous maps: Polynomiality and undecidability. 45th Annual ACM Symposium on theory of computing. STOC: Symposium on the Theory of Computing, 595–604.' mla: 'Čadek, Martin, et al. “Extending Continuous Maps: Polynomiality and Undecidability.” 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604, doi:10.1145/2488608.2488683.' short: M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, U. Wagner, in:, 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604. conference: end_date: 2013-06-04 location: Palo Alto, CA, United States name: 'STOC: Symposium on the Theory of Computing' start_date: 2013-06-01 date_created: 2018-12-11T11:59:42Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T06:59:51Z day: '01' ddc: - '510' department: - _id: UlWa - _id: HeEd doi: 10.1145/2488608.2488683 file: - access_level: open_access checksum: 06c2ce5c1135fbc1f71ca15eeb242dcf content_type: application/pdf creator: system date_created: 2018-12-12T10:14:29Z date_updated: 2020-07-14T12:45:48Z file_id: '5081' file_name: IST-2016-533-v1+1_Extending_continuous_maps_polynomiality_and_undecidability.pdf file_size: 447945 relation: main_file file_date_updated: 2020-07-14T12:45:48Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 595 - 604 publication: 45th Annual ACM Symposium on theory of computing publication_status: published publisher: ACM publist_id: '4078' pubrep_id: '533' quality_controlled: '1' scopus_import: 1 status: public title: 'Extending continuous maps: Polynomiality and undecidability' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2808' abstract: - lang: eng text: In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs. author: - first_name: Katarina full_name: Landberg, Katarina last_name: Landberg - first_name: Eric full_name: Pederson, Eric last_name: Pederson - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Behruz full_name: Bozorg, Behruz last_name: Bozorg - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Henrik full_name: Jönsson, Henrik last_name: Jönsson - first_name: Mattias full_name: Thelander, Mattias last_name: Thelander - first_name: Eva full_name: Sundberg, Eva last_name: Sundberg citation: ama: Landberg K, Pederson E, Viaene T, et al. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. 2013;162(3):1406-1419. doi:10.1104/pp.113.214023 apa: Landberg, K., Pederson, E., Viaene, T., Bozorg, B., Friml, J., Jönsson, H., … Sundberg, E. (2013). The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.113.214023 chicago: Landberg, Katarina, Eric Pederson, Tom Viaene, Behruz Bozorg, Jiří Friml, Henrik Jönsson, Mattias Thelander, and Eva Sundberg. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” Plant Physiology. American Society of Plant Biologists, 2013. https://doi.org/10.1104/pp.113.214023. ieee: K. Landberg et al., “The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain,” Plant Physiology, vol. 162, no. 3. American Society of Plant Biologists, pp. 1406–1419, 2013. ista: Landberg K, Pederson E, Viaene T, Bozorg B, Friml J, Jönsson H, Thelander M, Sundberg E. 2013. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. 162(3), 1406–1419. mla: Landberg, Katarina, et al. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” Plant Physiology, vol. 162, no. 3, American Society of Plant Biologists, 2013, pp. 1406–19, doi:10.1104/pp.113.214023. short: K. Landberg, E. Pederson, T. Viaene, B. Bozorg, J. Friml, H. Jönsson, M. Thelander, E. Sundberg, Plant Physiology 162 (2013) 1406–1419. date_created: 2018-12-11T11:59:42Z date_published: 2013-07-03T00:00:00Z date_updated: 2021-01-12T06:59:51Z day: '03' department: - _id: JiFr doi: 10.1104/pp.113.214023 external_id: pmid: - '23669745' intvolume: ' 162' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707547/ month: '07' oa: 1 oa_version: Submitted Version page: 1406 - 1419 pmid: 1 publication: Plant Physiology publication_status: published publisher: American Society of Plant Biologists publist_id: '4079' quality_controlled: '1' scopus_import: 1 status: public title: The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 162 year: '2013' ... --- _id: '2806' abstract: - lang: eng text: A novel Taylor-Couette system has been constructed for investigations of transitional as well as high Reynolds number turbulent flows in very large aspect ratios. The flexibility of the setup enables studies of a variety of problems regarding hydrodynamic instabilities and turbulence in rotating flows. The inner and outer cylinders and the top and bottom endplates can be rotated independently with rotation rates of up to 30 Hz, thereby covering five orders of magnitude in Reynolds numbers (Re = 101-106). The radius ratio can be easily changed, the highest realized one is η = 0.98 corresponding to an aspect ratio of 260 gap width in the vertical and 300 in the azimuthal direction. For η < 0.98 the aspect ratio can be dynamically changed during measurements and complete transparency in the radial direction over the full length of the cylinders is provided by the usage of a precision glass inner cylinder. The temperatures of both cylinders are controlled independently. Overall this apparatus combines an unmatched variety in geometry, rotation rates, and temperatures, which is provided by a sophisticated high-precision bearing system. Possible applications are accurate studies of the onset of turbulence and spatio-temporal intermittent flow patterns in very large domains, transport processes of turbulence at high Re, the stability of Keplerian flows for different boundary conditions, and studies of baroclinic instabilities. article_number: '065106' author: - first_name: Kerstin full_name: Avila, Kerstin last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Avila K, Hof B. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. 2013;84(6). doi:10.1063/1.4807704 apa: Avila, K., & Hof, B. (2013). High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. American Institute of Physics. https://doi.org/10.1063/1.4807704 chicago: Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” Review of Scientific Instruments. American Institute of Physics, 2013. https://doi.org/10.1063/1.4807704. ieee: K. Avila and B. Hof, “High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects,” Review of Scientific Instruments, vol. 84, no. 6. American Institute of Physics, 2013. ista: Avila K, Hof B. 2013. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. 84(6), 065106. mla: Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” Review of Scientific Instruments, vol. 84, no. 6, 065106, American Institute of Physics, 2013, doi:10.1063/1.4807704. short: K. Avila, B. Hof, Review of Scientific Instruments 84 (2013). date_created: 2018-12-11T11:59:42Z date_published: 2013-06-06T00:00:00Z date_updated: 2021-01-12T06:59:50Z day: '06' department: - _id: BjHo doi: 10.1063/1.4807704 intvolume: ' 84' issue: '6' language: - iso: eng month: '06' oa_version: None publication: Review of Scientific Instruments publication_status: published publisher: American Institute of Physics publist_id: '4081' quality_controlled: '1' scopus_import: 1 status: public title: High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 84 year: '2013' ... --- _id: '2805' abstract: - lang: eng text: Transition in shear flows is characterized by localized turbulent regions embedded in the surrounding laminar flow. These so-called turbulent spots or puffs are observed in a variety of shear flows and in certain Reynolds-number regimes, and they are advected by the flow while keeping their characteristic length. We show here for the case of pipe flow that this seemingly passive advection of turbulent puffs involves continuous entrainment and relaminarization of laminar and turbulent fluid across strongly convoluted interfaces. Surprisingly, interface areas are almost two orders of magnitude larger than the pipe cross-section, while local entrainment velocities are much smaller than the mean speed. Even though these velocities were shown to be small and proportional to the Kolmogorov velocity scale (in agreement with a prediction by Corrsin) in a flow without mean shear before, we find that, in pipe flow, local entrainment velocities are about an order of magnitude smaller than this scale. The Lagrangian method used to study the dynamics of the laminar-turbulent interfaces allows accurate determination of the leading and trailing edge speeds. However, to resolve the highly complex interface dynamics requires much higher numerical resolutions than for ordinary turbulent flows. This method also reveals that the volume flux across the leading edge has the same radial dependence but the opposite sign as that across the trailing edge, and it is this symmetry that is responsible for the puff shape remaining constant. author: - first_name: Markus full_name: Holzner, Markus last_name: Holzner - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Holzner M, Song B, Avila M, Hof B. Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid Mechanics. 2013;723:140-162. doi:10.1017/jfm.2013.127 apa: Holzner, M., Song, B., Avila, M., & Hof, B. (2013). Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2013.127 chicago: Holzner, Markus, Baofang Song, Marc Avila, and Björn Hof. “Lagrangian Approach to Laminar-Turbulent Interfaces in Transitional Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2013. https://doi.org/10.1017/jfm.2013.127. ieee: M. Holzner, B. Song, M. Avila, and B. Hof, “Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow,” Journal of Fluid Mechanics, vol. 723. Cambridge University Press, pp. 140–162, 2013. ista: Holzner M, Song B, Avila M, Hof B. 2013. Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid Mechanics. 723, 140–162. mla: Holzner, Markus, et al. “Lagrangian Approach to Laminar-Turbulent Interfaces in Transitional Pipe Flow.” Journal of Fluid Mechanics, vol. 723, Cambridge University Press, 2013, pp. 140–62, doi:10.1017/jfm.2013.127. short: M. Holzner, B. Song, M. Avila, B. Hof, Journal of Fluid Mechanics 723 (2013) 140–162. date_created: 2018-12-11T11:59:41Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T06:59:50Z day: '01' doi: 10.1017/jfm.2013.127 extern: 1 intvolume: ' 723' month: '05' page: 140 - 162 publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press publist_id: '4084' quality_controlled: 0 status: public title: Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow type: journal_article volume: 723 year: '2013' ... --- _id: '2810' abstract: - lang: eng text: The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data. article_number: e1003580 author: - first_name: Marjon full_name: De Vos, Marjon id: 3111FFAC-F248-11E8-B48F-1D18A9856A87 last_name: De Vos - first_name: Frank full_name: Poelwijk, Frank last_name: Poelwijk - first_name: Nico full_name: Battich, Nico last_name: Battich - first_name: Joseph full_name: Ndika, Joseph last_name: Ndika - first_name: Sander full_name: Tans, Sander last_name: Tans citation: ama: de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. Environmental dependence of genetic constraint. PLoS Genetics. 2013;9(6). doi:10.1371/journal.pgen.1003580 apa: de Vos, M., Poelwijk, F., Battich, N., Ndika, J., & Tans, S. (2013). Environmental dependence of genetic constraint. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003580 chicago: Vos, Marjon de, Frank Poelwijk, Nico Battich, Joseph Ndika, and Sander Tans. “Environmental Dependence of Genetic Constraint.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003580. ieee: M. de Vos, F. Poelwijk, N. Battich, J. Ndika, and S. Tans, “Environmental dependence of genetic constraint,” PLoS Genetics, vol. 9, no. 6. Public Library of Science, 2013. ista: de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence of genetic constraint. PLoS Genetics. 9(6), e1003580. mla: de Vos, Marjon, et al. “Environmental Dependence of Genetic Constraint.” PLoS Genetics, vol. 9, no. 6, e1003580, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003580. short: M. de Vos, F. Poelwijk, N. Battich, J. Ndika, S. Tans, PLoS Genetics 9 (2013). date_created: 2018-12-11T11:59:43Z date_published: 2013-06-27T00:00:00Z date_updated: 2021-01-12T06:59:52Z day: '27' ddc: - '570' department: - _id: ToBo doi: 10.1371/journal.pgen.1003580 file: - access_level: open_access checksum: 7a4736dd80496d29ff6908b6f2329b4e content_type: application/pdf creator: system date_created: 2018-12-12T10:08:51Z date_updated: 2020-07-14T12:45:48Z file_id: '4713' file_name: IST-2016-412-v1+1_journal.pgen.1003580.pdf file_size: 474655 relation: main_file file_date_updated: 2020-07-14T12:45:48Z has_accepted_license: '1' intvolume: ' 9' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '4075' pubrep_id: '412' quality_controlled: '1' scopus_import: 1 status: public title: Environmental dependence of genetic constraint tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '2814' abstract: - lang: eng text: We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing "reset" action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies. We also discuss the memory requirement for deterministic strategies and extensions of our results to other models, such as pushdown systems and timed systems. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: Alfaro, Luca last_name: Alfaro - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: Chatterjee K, Alfaro L, Majumdar R. The complexity of coverage. International Journal of Foundations of Computer Science. 2013;24(2):165-185. doi:10.1142/S0129054113400066 apa: Chatterjee, K., Alfaro, L., & Majumdar, R. (2013). The complexity of coverage. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054113400066 chicago: Chatterjee, Krishnendu, Luca Alfaro, and Ritankar Majumdar. “The Complexity of Coverage.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2013. https://doi.org/10.1142/S0129054113400066. ieee: K. Chatterjee, L. Alfaro, and R. Majumdar, “The complexity of coverage,” International Journal of Foundations of Computer Science, vol. 24, no. 2. World Scientific Publishing, pp. 165–185, 2013. ista: Chatterjee K, Alfaro L, Majumdar R. 2013. The complexity of coverage. International Journal of Foundations of Computer Science. 24(2), 165–185. mla: Chatterjee, Krishnendu, et al. “The Complexity of Coverage.” International Journal of Foundations of Computer Science, vol. 24, no. 2, World Scientific Publishing, 2013, pp. 165–85, doi:10.1142/S0129054113400066. short: K. Chatterjee, L. Alfaro, R. Majumdar, International Journal of Foundations of Computer Science 24 (2013) 165–185. date_created: 2018-12-11T11:59:44Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T06:59:54Z day: '01' department: - _id: KrCh doi: 10.1142/S0129054113400066 ec_funded: 1 external_id: arxiv: - '0804.4525' intvolume: ' 24' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/0804.4525 month: '02' oa: 1 oa_version: Preprint page: 165 - 185 project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: International Journal of Foundations of Computer Science publication_status: published publisher: World Scientific Publishing publist_id: '4070' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of coverage type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2013' ... --- _id: '2811' abstract: - lang: eng text: 'In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers.' article_number: '063012' author: - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 2013;87(6). doi:10.1103/PhysRevE.87.063012 apa: Avila, M., & Hof, B. (2013). Nature of laminar-turbulence intermittency in shear flows. Physical Review E. American Institute of Physics. https://doi.org/10.1103/PhysRevE.87.063012 chicago: Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” Physical Review E. American Institute of Physics, 2013. https://doi.org/10.1103/PhysRevE.87.063012. ieee: M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear flows,” Physical Review E, vol. 87, no. 6. American Institute of Physics, 2013. ista: Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 87(6), 063012. mla: Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” Physical Review E, vol. 87, no. 6, 063012, American Institute of Physics, 2013, doi:10.1103/PhysRevE.87.063012. short: M. Avila, B. Hof, Physical Review E 87 (2013). date_created: 2018-12-11T11:59:43Z date_published: 2013-06-18T00:00:00Z date_updated: 2021-01-12T06:59:53Z day: '18' department: - _id: BjHo doi: 10.1103/PhysRevE.87.063012 ec_funded: 1 external_id: arxiv: - '1306.5890' intvolume: ' 87' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1306.5890 month: '06' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Physical Review E publication_status: published publisher: American Institute of Physics publist_id: '4074' quality_controlled: '1' scopus_import: 1 status: public title: Nature of laminar-turbulence intermittency in shear flows type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2013' ... --- _id: '2813' abstract: - lang: eng text: Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian fluids like water, our understanding of this phenomenon is limited. Many liquids of practical importance are more complicated (e.g., blood, polymer melts, paints), however; they exhibit elastic as well as viscous characteristics, and the relation between stress and strain is nonlinear. We demonstrate here for a model system of such complex fluids that at high shear rates, turbulence is not simply modified as previously believed but is suppressed and replaced by a different type of disordered motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties differ significantly. The friction scaling observed coincides with the so-called "maximum drag reduction" asymptote, which is exhibited by a wide range of viscoelastic fluids. author: - first_name: Devranjan full_name: Samanta, Devranjan last_name: Samanta - first_name: Yves full_name: Dubief, Yves last_name: Dubief - first_name: Markus full_name: Holzner, Markus last_name: Holzner - first_name: Christof full_name: Schäfer, Christof last_name: Schäfer - first_name: Alexander full_name: Morozov, Alexander last_name: Morozov - first_name: Christian full_name: Wagner, Christian last_name: Wagner - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Samanta D, Dubief Y, Holzner M, et al. Elasto-inertial turbulence. PNAS. 2013;110(26):10557-10562. doi:10.1073/pnas.1219666110 apa: Samanta, D., Dubief, Y., Holzner, M., Schäfer, C., Morozov, A., Wagner, C., & Hof, B. (2013). Elasto-inertial turbulence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1219666110 chicago: Samanta, Devranjan, Yves Dubief, Markus Holzner, Christof Schäfer, Alexander Morozov, Christian Wagner, and Björn Hof. “Elasto-Inertial Turbulence.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1219666110. ieee: D. Samanta et al., “Elasto-inertial turbulence,” PNAS, vol. 110, no. 26. National Academy of Sciences, pp. 10557–10562, 2013. ista: Samanta D, Dubief Y, Holzner M, Schäfer C, Morozov A, Wagner C, Hof B. 2013. Elasto-inertial turbulence. PNAS. 110(26), 10557–10562. mla: Samanta, Devranjan, et al. “Elasto-Inertial Turbulence.” PNAS, vol. 110, no. 26, National Academy of Sciences, 2013, pp. 10557–62, doi:10.1073/pnas.1219666110. short: D. Samanta, Y. Dubief, M. Holzner, C. Schäfer, A. Morozov, C. Wagner, B. Hof, PNAS 110 (2013) 10557–10562. date_created: 2018-12-11T11:59:44Z date_published: 2013-06-25T00:00:00Z date_updated: 2021-01-12T06:59:54Z day: '25' department: - _id: BjHo doi: 10.1073/pnas.1219666110 external_id: pmid: - '23757498' intvolume: ' 110' issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696777/ month: '06' oa: 1 oa_version: Submitted Version page: 10557 - 10562 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '4073' quality_controlled: '1' scopus_import: 1 status: public title: Elasto-inertial turbulence type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2812' abstract: - lang: eng text: 'We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.' acknowledgement: Some of the authors were partially supported by the GIGA ANR grant (contract ANR-09-BLAN-0331-01) and the European project CG-Learning (contract 255827). author: - first_name: Dominique full_name: Attali, Dominique last_name: Attali - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Olivier full_name: Devillers, Olivier last_name: Devillers - first_name: Marc full_name: Glisse, Marc last_name: Glisse - first_name: André full_name: Lieutier, André last_name: Lieutier citation: ama: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. In: Proceedings of the 29th Annual Symposium on Computational Geometry. ACM; 2013:117-125. doi:10.1145/2462356.2462373' apa: 'Attali, D., Bauer, U., Devillers, O., Glisse, M., & Lieutier, A. (2013). Homological reconstruction and simplification in R3. In Proceedings of the 29th annual symposium on Computational Geometry (pp. 117–125). Rio de Janeiro, Brazil: ACM. https://doi.org/10.1145/2462356.2462373' chicago: Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” In Proceedings of the 29th Annual Symposium on Computational Geometry, 117–25. ACM, 2013. https://doi.org/10.1145/2462356.2462373. ieee: D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” in Proceedings of the 29th annual symposium on Computational Geometry, Rio de Janeiro, Brazil, 2013, pp. 117–125. ista: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2013. Homological reconstruction and simplification in R3. Proceedings of the 29th annual symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 117–125.' mla: Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–25, doi:10.1145/2462356.2462373. short: D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, in:, Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–125. conference: end_date: 2013-06-20 location: Rio de Janeiro, Brazil name: 'SoCG: Symposium on Computational Geometry' start_date: 2013-06-17 date_created: 2018-12-11T11:59:44Z date_published: 2013-06-01T00:00:00Z date_updated: 2023-02-23T10:15:15Z day: '01' department: - _id: HeEd doi: 10.1145/2462356.2462373 language: - iso: eng main_file_link: - open_access: '1' url: http://hal.archives-ouvertes.fr/hal-00833791/ month: '06' oa: 1 oa_version: Submitted Version page: 117 - 125 publication: Proceedings of the 29th annual symposium on Computational Geometry publication_status: published publisher: ACM publist_id: '4072' quality_controlled: '1' related_material: record: - id: '1805' relation: later_version status: public scopus_import: 1 status: public title: Homological reconstruction and simplification in R3 type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2817' abstract: - lang: eng text: The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle. author: - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology. 2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029 apa: Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029 chicago: Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029. ieee: S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical Biology, vol. 334. Elsevier, pp. 26–34, 2013. ista: Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34. mla: Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology, vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029. short: S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34. date_created: 2018-12-11T11:59:45Z date_published: 2013-10-07T00:00:00Z date_updated: 2021-01-12T06:59:55Z day: '07' ddc: - '000' department: - _id: NiBa - _id: KrCh doi: 10.1016/j.jtbi.2013.05.029 ec_funded: 1 file: - access_level: open_access checksum: 3c29059ab03a4b8f97a07646b817ddbb content_type: application/pdf creator: system date_created: 2018-12-12T10:14:54Z date_updated: 2020-07-14T12:45:49Z file_id: '5110' file_name: IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf file_size: 834604 relation: main_file file_date_updated: 2020-07-14T12:45:49Z has_accepted_license: '1' intvolume: ' 334' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 26 - 34 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '3984' pubrep_id: '400' quality_controlled: '1' scopus_import: 1 status: public title: Density games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 334 year: '2013' ... --- _id: '2819' abstract: - lang: eng text: 'We introduce quantatitive timed refinement metrics and quantitative timed simulation functions, incorporating zenoness checks, for timed systems. These functions assign positive real numbers between zero and infinity which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximum timing mismatch that can arise, (2) the "steady-state" maximum timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation functions to within any desired degree of accuracy. In order to compute the values of the quantitative simulation functions, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives for player 1, and then use these algorithms to compute the values of the quantitative timed simulation functions. ' acknowledgement: 'This work has been financially supported in part by the European Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract # 270180 (NOP-TILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008 (Modeling and control of Networked vehicle systems in persistent autonomous operations); by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start grant (279307: Graph Games); and the Microsoft faculty fellows award' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vinayak full_name: Prabhu, Vinayak last_name: Prabhu citation: ama: 'Chatterjee K, Prabhu V. Quantitative timed simulation functions and refinement metrics for real-time systems. In: Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. Vol 1. Springer; 2013:273-282. doi:10.1145/2461328.2461370' apa: 'Chatterjee, K., & Prabhu, V. (2013). Quantitative timed simulation functions and refinement metrics for real-time systems. In Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control (Vol. 1, pp. 273–282). Philadelphia, PA USA: Springer. https://doi.org/10.1145/2461328.2461370' chicago: 'Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” In Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, 1:273–82. Springer, 2013. https://doi.org/10.1145/2461328.2461370.' ieee: 'K. Chatterjee and V. Prabhu, “Quantitative timed simulation functions and refinement metrics for real-time systems,” in Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Philadelphia, PA USA, 2013, vol. 1, pp. 273–282.' ista: 'Chatterjee K, Prabhu V. 2013. Quantitative timed simulation functions and refinement metrics for real-time systems. Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control vol. 1, 273–282.' mla: 'Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, vol. 1, Springer, 2013, pp. 273–82, doi:10.1145/2461328.2461370.' short: 'K. Chatterjee, V. Prabhu, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Springer, 2013, pp. 273–282.' conference: end_date: 2013-04-11 location: Philadelphia, PA USA name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2013-04-08 date_created: 2018-12-11T11:59:46Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T06:59:56Z day: '01' department: - _id: KrCh doi: 10.1145/2461328.2461370 ec_funded: 1 intvolume: ' 1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1212.6556 month: '04' oa: 1 oa_version: Preprint page: 273 - 282 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: 'Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control' publication_status: published publisher: Springer publist_id: '3982' quality_controlled: '1' scopus_import: 1 status: public title: Quantitative timed simulation functions and refinement metrics for real-time systems type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2013' ... --- _id: '2818' abstract: - lang: eng text: Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory–based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus. author: - first_name: Kanaka full_name: Rajan, Kanaka last_name: Rajan - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692. doi:10.1162/NECO_a_00463 apa: Rajan, K., Marre, O., & Tkačik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. MIT Press . https://doi.org/10.1162/NECO_a_00463 chicago: Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation. MIT Press , 2013. https://doi.org/10.1162/NECO_a_00463. ieee: K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” Neural Computation, vol. 25, no. 7. MIT Press , pp. 1661–1692, 2013. ista: Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692. mla: Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:10.1162/NECO_a_00463. short: K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692. date_created: 2018-12-11T11:59:45Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:59:56Z day: '01' department: - _id: GaTk doi: 10.1162/NECO_a_00463 external_id: arxiv: - '1209.0121' intvolume: ' 25' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.0121 month: '07' oa: 1 oa_version: Preprint page: 1661 - 1692 publication: Neural Computation publication_status: published publisher: 'MIT Press ' publist_id: '3983' quality_controlled: '1' scopus_import: 1 status: public title: Learning quadratic receptive fields from neural responses to natural stimuli type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '2826' abstract: - lang: eng text: Myopia, or near-sightedness, is an ocular refractive error of unfocused image quality in front of the retinal plane. Individuals with high-grade myopia (dioptric power greater than -6.00) are predisposed to ocular morbidities such as glaucoma, retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is highly heritable, and to date multiple gene loci have been reported. We performed exome sequencing in 4 individuals from an 11-member family of European descent from the United States. Affected individuals had a mean dioptric spherical equivalent of -22.00 sphere. A premature stop codon mutation c.157C>T (p.Gln53*) cosegregating with disease was discovered within SCO2 that maps to chromosome 22q13.33. Subsequent analyses identified three additional mutations in three highly myopic unrelated individuals (c.341G>A, c.418G>A, and c.776C>T). To determine differential gene expression in a developmental mouse model, we induced myopia by applying a -15.00D lens over one eye. Messenger RNA levels of SCO2 were significantly downregulated in myopic mouse retinae. Immunohistochemistry in mouse eyes confirmed SCO2 protein localization in retina, retinal pigment epithelium, and sclera. SCO2 encodes for a copper homeostasis protein influential in mitochondrial cytochrome c oxidase activity. Copper deficiencies have been linked with photoreceptor loss and myopia with increased scleral wall elasticity. Retinal thinning has been reported with an SC02 variant. Human mutation identification with support from an induced myopic animal provides biological insights of myopic development. author: - first_name: Khanh full_name: Tran Viet, Khanh last_name: Tran Viet - first_name: Caldwell full_name: Powell, Caldwell last_name: Powell - first_name: Veluchamy full_name: Barathi, Veluchamy last_name: Barathi - first_name: Thomas full_name: Klemm, Thomas last_name: Klemm - first_name: Sebastian full_name: Maurer Stroh, Sebastian last_name: Maurer Stroh - first_name: Vachiranee full_name: Limviphuvadh, Vachiranee last_name: Limviphuvadh - first_name: Vincent full_name: Soler, Vincent last_name: Soler - first_name: Candice full_name: Ho, Candice last_name: Ho - first_name: Tammy full_name: Yanovitch, Tammy last_name: Yanovitch - first_name: Georg full_name: Schneider, Georg id: 329095A0-F248-11E8-B48F-1D18A9856A87 last_name: Schneider - first_name: Yi full_name: Li, Yi last_name: Li - first_name: Erica full_name: Nading, Erica last_name: Nading - first_name: Ravikanth full_name: Metlapally, Ravikanth last_name: Metlapally - first_name: Seang full_name: Saw, Seang last_name: Saw - first_name: Liang full_name: Goh, Liang last_name: Goh - first_name: Steve full_name: Rozen, Steve last_name: Rozen - first_name: Terri full_name: Young, Terri last_name: Young citation: ama: Tran Viet K, Powell C, Barathi V, et al. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. 2013;92(5):820-826. doi:10.1016/j.ajhg.2013.04.005 apa: Tran Viet, K., Powell, C., Barathi, V., Klemm, T., Maurer Stroh, S., Limviphuvadh, V., … Young, T. (2013). Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. Cell Press. https://doi.org/10.1016/j.ajhg.2013.04.005 chicago: Tran Viet, Khanh, Caldwell Powell, Veluchamy Barathi, Thomas Klemm, Sebastian Maurer Stroh, Vachiranee Limviphuvadh, Vincent Soler, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia.” American Journal of Human Genetics. Cell Press, 2013. https://doi.org/10.1016/j.ajhg.2013.04.005. ieee: K. Tran Viet et al., “Mutations in SCO2 are associated with autosomal-dominant high-grade myopia,” American Journal of Human Genetics, vol. 92, no. 5. Cell Press, pp. 820–826, 2013. ista: Tran Viet K, Powell C, Barathi V, Klemm T, Maurer Stroh S, Limviphuvadh V, Soler V, Ho C, Yanovitch T, Schneider G, Li Y, Nading E, Metlapally R, Saw S, Goh L, Rozen S, Young T. 2013. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. 92(5), 820–826. mla: Tran Viet, Khanh, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia.” American Journal of Human Genetics, vol. 92, no. 5, Cell Press, 2013, pp. 820–26, doi:10.1016/j.ajhg.2013.04.005. short: K. Tran Viet, C. Powell, V. Barathi, T. Klemm, S. Maurer Stroh, V. Limviphuvadh, V. Soler, C. Ho, T. Yanovitch, G. Schneider, Y. Li, E. Nading, R. Metlapally, S. Saw, L. Goh, S. Rozen, T. Young, American Journal of Human Genetics 92 (2013) 820–826. date_created: 2018-12-11T11:59:48Z date_published: 2013-05-02T00:00:00Z date_updated: 2021-01-12T06:59:59Z day: '02' department: - _id: MD doi: 10.1016/j.ajhg.2013.04.005 external_id: pmid: - '23643385' intvolume: ' 92' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644634/ month: '05' oa: 1 oa_version: Submitted Version page: 820 - 826 pmid: 1 publication: American Journal of Human Genetics publication_status: published publisher: Cell Press publist_id: '3974' quality_controlled: '1' scopus_import: 1 status: public title: Mutations in SCO2 are associated with autosomal-dominant high-grade myopia type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2013' ... --- _id: '2822' abstract: - lang: eng text: Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala x Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops. author: - first_name: Christopher full_name: Topp, Christopher last_name: Topp - first_name: Anjali full_name: Iyer Pascuzzi, Anjali last_name: Iyer Pascuzzi - first_name: Jill full_name: Anderson, Jill last_name: Anderson - first_name: Cheng full_name: Lee, Cheng last_name: Lee - first_name: Paul full_name: Zurek, Paul last_name: Zurek - first_name: Olga full_name: Symonova, Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova - first_name: Ying full_name: Zheng, Ying last_name: Zheng - first_name: Alexander full_name: Bucksch, Alexander last_name: Bucksch - first_name: Yuriy full_name: Mileyko, Yuriy last_name: Mileyko - first_name: Taras full_name: Galkovskyi, Taras last_name: Galkovskyi - first_name: Brad full_name: Moore, Brad last_name: Moore - first_name: John full_name: Harer, John last_name: Harer - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Thomas full_name: Mitchell Olds, Thomas last_name: Mitchell Olds - first_name: Joshua full_name: Weitz, Joshua last_name: Weitz - first_name: Philip full_name: Benfey, Philip last_name: Benfey citation: ama: Topp C, Iyer Pascuzzi A, Anderson J, et al. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 2013;110(18):E1695-E1704. doi:10.1073/pnas.1304354110 apa: Topp, C., Iyer Pascuzzi, A., Anderson, J., Lee, C., Zurek, P., Symonova, O., … Benfey, P. (2013). 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1304354110 chicago: Topp, Christopher, Anjali Iyer Pascuzzi, Jill Anderson, Cheng Lee, Paul Zurek, Olga Symonova, Ying Zheng, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1304354110. ieee: C. Topp et al., “3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture,” PNAS, vol. 110, no. 18. National Academy of Sciences, pp. E1695–E1704, 2013. ista: Topp C, Iyer Pascuzzi A, Anderson J, Lee C, Zurek P, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore B, Harer J, Edelsbrunner H, Mitchell Olds T, Weitz J, Benfey P. 2013. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 110(18), E1695–E1704. mla: Topp, Christopher, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS, vol. 110, no. 18, National Academy of Sciences, 2013, pp. E1695–704, doi:10.1073/pnas.1304354110. short: C. Topp, A. Iyer Pascuzzi, J. Anderson, C. Lee, P. Zurek, O. Symonova, Y. Zheng, A. Bucksch, Y. Mileyko, T. Galkovskyi, B. Moore, J. Harer, H. Edelsbrunner, T. Mitchell Olds, J. Weitz, P. Benfey, PNAS 110 (2013) E1695–E1704. date_created: 2018-12-11T11:59:47Z date_published: 2013-04-30T00:00:00Z date_updated: 2021-01-12T06:59:58Z day: '30' department: - _id: MaJö - _id: HeEd doi: 10.1073/pnas.1304354110 external_id: pmid: - '25673779' intvolume: ' 110' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378147/ month: '04' oa: 1 oa_version: Submitted Version page: E1695 - E1704 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3979' quality_controlled: '1' scopus_import: 1 status: public title: 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2821' abstract: - lang: eng text: Many key aspects of plant development are regulated by the polarized transport of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this process, has been shown to rely on the coordinated action of PIN-formed (PIN) and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin transport in the Arabidopsis thaliana root also requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during shootward auxin transport at the root tip, likely by regulating plasma membrane PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1 and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular and tissue distribution of two isoforms, alternative splicing dictates a dual function for the ZIFL1 transporter. We propose that this MFS carrier regulates stomatal movements and polar auxin transport by modulating potassium and proton fluxes in Arabidopsis cells. author: - first_name: Estelle full_name: Remy, Estelle last_name: Remy - first_name: Tânia full_name: Cabrito, Tânia last_name: Cabrito - first_name: Pawel full_name: Baster, Pawel id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Rita full_name: Batista, Rita last_name: Batista - first_name: Miguel full_name: Teixeira, Miguel last_name: Teixeira - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Isabel full_name: Sá Correia, Isabel last_name: Sá Correia - first_name: Paula full_name: Duque, Paula last_name: Duque citation: ama: Remy E, Cabrito T, Baster P, et al. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. 2013;25(3):901-926. doi:10.1105/tpc.113.110353 apa: Remy, E., Cabrito, T., Baster, P., Batista, R., Teixeira, M., Friml, J., … Duque, P. (2013). A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.110353 chicago: Remy, Estelle, Tânia Cabrito, Pawel Baster, Rita Batista, Miguel Teixeira, Jiří Friml, Isabel Sá Correia, and Paula Duque. “A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.110353. ieee: E. Remy et al., “A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis,” Plant Cell, vol. 25, no. 3. American Society of Plant Biologists, pp. 901–926, 2013. ista: Remy E, Cabrito T, Baster P, Batista R, Teixeira M, Friml J, Sá Correia I, Duque P. 2013. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. 25(3), 901–926. mla: Remy, Estelle, et al. “A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.” Plant Cell, vol. 25, no. 3, American Society of Plant Biologists, 2013, pp. 901–26, doi:10.1105/tpc.113.110353. short: E. Remy, T. Cabrito, P. Baster, R. Batista, M. Teixeira, J. Friml, I. Sá Correia, P. Duque, Plant Cell 25 (2013) 901–926. date_created: 2018-12-11T11:59:46Z date_published: 2013-04-24T00:00:00Z date_updated: 2021-01-12T06:59:57Z day: '24' department: - _id: JiFr doi: 10.1105/tpc.113.110353 external_id: pmid: - '23524662' intvolume: ' 25' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634696/ month: '04' oa: 1 oa_version: Submitted Version page: 901 - 926 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3980' quality_controlled: '1' scopus_import: 1 status: public title: A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '2827' abstract: - lang: eng text: Removal of cargos from the cell surface via endocytosis is an efficient mechanism to regulate activities of plasma membrane (PM)-resident proteins, such as receptors or transporters. Salicylic acid (SA) is an important plant hormone that is traditionally associated with pathogen defense. Here, we describe an unanticipated effect of SA on subcellular endocytic cycling of proteins. Both exogenous treatments and endogenously enhanced SA levels repressed endocytosis of different PM proteins. The SA effect on endocytosis did not involve transcription or known components of the SA signaling pathway for transcriptional regulation. SA likely targets an endocytic mechanism that involves the coat protein clathrin, because SA interfered with the clathrin incidence at the PM and clathrin-deficient mutants were less sensitive to the impact of SA on the auxin distribution and root bending during the gravitropic response. By contrast, SA did not affect the ligand-induced endocytosis of the FLAGELLIN SENSING2 (FLS2) receptor during pathogen responses. Our data suggest that the established SA impact on transcription in plant immunity and the nontranscriptional effect of SA on clathrin-mediated endocytosis are independent mechanisms by which SA regulates distinct aspects of plant physiology. author: - first_name: Yunlong full_name: Du, Yunlong last_name: Du - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Martina full_name: Beck, Martina last_name: Beck - first_name: Ellie full_name: Himschoot, Ellie last_name: Himschoot - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Silke full_name: Robatzek, Silke last_name: Robatzek - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Du Y, Tejos R, Beck M, et al. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. 2013;110(19):7946-7951. doi:10.1073/pnas.1220205110 apa: Du, Y., Tejos, R., Beck, M., Himschoot, E., Li, H., Robatzek, S., … Friml, J. (2013). Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1220205110 chicago: Du, Yunlong, Ricardo Tejos, Martina Beck, Ellie Himschoot, Hongjiang Li, Silke Robatzek, Steffen Vanneste, and Jiří Friml. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic Protein Trafficking.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1220205110. ieee: Y. Du et al., “Salicylic acid interferes with clathrin-mediated endocytic protein trafficking,” PNAS, vol. 110, no. 19. National Academy of Sciences, pp. 7946–7951, 2013. ista: Du Y, Tejos R, Beck M, Himschoot E, Li H, Robatzek S, Vanneste S, Friml J. 2013. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. 110(19), 7946–7951. mla: Du, Yunlong, et al. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic Protein Trafficking.” PNAS, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7946–51, doi:10.1073/pnas.1220205110. short: Y. Du, R. Tejos, M. Beck, E. Himschoot, H. Li, S. Robatzek, S. Vanneste, J. Friml, PNAS 110 (2013) 7946–7951. date_created: 2018-12-11T11:59:48Z date_published: 2013-05-07T00:00:00Z date_updated: 2021-01-12T06:59:59Z day: '07' department: - _id: JiFr doi: 10.1073/pnas.1220205110 external_id: pmid: - '23613581' intvolume: ' 110' issue: '19' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651428/ month: '05' oa: 1 oa_version: Submitted Version page: 7946 - 7951 pmid: 1 project: - _id: 2574781E-B435-11E9-9278-68D0E5697425 name: Koerber Prize 2010 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3972' quality_controlled: '1' scopus_import: 1 status: public title: Salicylic acid interferes with clathrin-mediated endocytic protein trafficking type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2823' abstract: - lang: eng text: The primary goal of restoration is to create self-sustaining ecological communities that are resilient to periodic disturbance. Currently, little is known about how restored communities respond to disturbance events such as fire and how this response compares to remnant vegetation. Following the 2003 fires in south-eastern Australia we examined the post-fire response of revegetation plantings and compared this to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed for each of three types of vegetation (direct seeding revegetation, revegetation using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites were surveyed 6months after fire to quantify the initial survival of mid- and overstorey plant species in each type of vegetation. Three and 5years after fire all sites were resurveyed to assess vegetation structure, species diversity and vigour, as well as indicators of soil function. Overall, revegetation showed high (>60%) post-fire survival, but this varied among species depending on regeneration strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey in both types of plantings showed rapid recovery of vegetation structure and cover within 3years of fire. This recovery was similar to the burnt remnant woodlands. Non-native (exotic) ground cover initially increased after fire, but was no different in burnt and unburnt sites 5years after fire. Fire had no effect on species richness, but burnt direct seeding sites had reduced species diversity (Simpson's Diversity Index) while diversity was higher in burnt remnant woodlands. Indices of soil function in all types of vegetation had recovered to levels found in unburnt sites 5years after fire. These results indicate that even young revegetation (stands <10years old) showed substantial recovery from disturbance by fire. This suggests that revegetation can provide an important basis for restoring woodland communities in the fire-prone Australian environment. author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Susie full_name: Wilson, Susie last_name: Wilson - first_name: David full_name: Freudenberger, David last_name: Freudenberger - first_name: Nick full_name: Nicholls, Nick last_name: Nicholls - first_name: Lori full_name: Gould, Lori last_name: Gould - first_name: Sarah full_name: Hnatiuk, Sarah last_name: Hnatiuk - first_name: Jeni full_name: Delandre, Jeni last_name: Delandre citation: ama: Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312. doi:10.1111/j.1442-9993.2012.02404.x apa: Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x chicago: Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x. ieee: M. Pickup et al., “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013. ista: Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 38(3), 300–312. mla: Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x. short: M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312. date_created: 2018-12-11T11:59:47Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T06:59:58Z day: '01' department: - _id: NiBa doi: 10.1111/j.1442-9993.2012.02404.x intvolume: ' 38' issue: '3' language: - iso: eng month: '05' oa_version: None page: 300 - 312 publication: Austral Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3978' quality_controlled: '1' scopus_import: 1 status: public title: Post-fire recovery of revegetated woodland communities in south-eastern Australia type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2013' ... --- _id: '2824' abstract: - lang: eng text: We study synthesis of controllers for real-time systems, where the objective is to stay in a given safe set. The problem is solved by obtaining winning strategies in the setting of concurrent two player timed automaton games with safety objectives. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a Zeno run. We construct winning strategies for the controller which require access only to (1) the system clocks (thus, controllers which require their own internal infinitely precise clocks are not necessary), and (2) a logarithmic (in the number of clocks) number of memory bits (i.e. a linear number of memory states). Precisely, we show that for safety objectives, a memory of size (3 + lg (| C | + 1)) bits suffices for winning controller strategies, where C is the set of clocks of the timed automaton game, significantly improving the previous known exponential memory states bound. We also settle the open question of whether winning region-based strategies require memory for safety objectives by showing with an example the necessity of memory for such strategies to win for safety objectives. Finally, we show that the decision problem of determining if there exists a receptive player-1 winning strategy for safety objectives is EXPTIME-complete over timed automaton games. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vinayak full_name: Prabhu, Vinayak last_name: Prabhu citation: ama: Chatterjee K, Prabhu V. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. 2013;228-229:83-119. doi:10.1016/j.ic.2013.04.003 apa: Chatterjee, K., & Prabhu, V. (2013). Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2013.04.003 chicago: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information and Computation. Elsevier, 2013. https://doi.org/10.1016/j.ic.2013.04.003. ieee: K. Chatterjee and V. Prabhu, “Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems,” Information and Computation, vol. 228–229. Elsevier, pp. 83–119, 2013. ista: Chatterjee K, Prabhu V. 2013. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. 228–229, 83–119. mla: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information and Computation, vol. 228–229, Elsevier, 2013, pp. 83–119, doi:10.1016/j.ic.2013.04.003. short: K. Chatterjee, V. Prabhu, Information and Computation 228–229 (2013) 83–119. date_created: 2018-12-11T11:59:47Z date_published: 2013-04-24T00:00:00Z date_updated: 2021-01-12T06:59:58Z day: '24' department: - _id: KrCh doi: 10.1016/j.ic.2013.04.003 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 83-119 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '3977' quality_controlled: '1' scopus_import: 1 status: public title: Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 228-229 year: '2013' ... --- _id: '2832' abstract: - lang: eng text: PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and mediate intercellular polar transport of the plant hormone auxin that is crucial for a multitude of developmental processes in plants. PIN localization is under extensive control by environmental or developmental cues, but mechanisms regulating PIN localization are not fully understood. Here we show that early endosomal components ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively required for polar PIN localization, for their dynamic repolarization, and consequently for auxin activity gradient formation and auxin-related developmental processes including embryonic patterning, organogenesis, and vasculature venation patterning. These results show that early endosomal trafficking is crucial for cell polarity and auxin-dependent regulation of plant architecture. article_number: e1003540 author: - first_name: Hirokazu full_name: Tanaka, Hirokazu last_name: Tanaka - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Hana full_name: Rakusová, Hana last_name: Rakusová - first_name: Tomohiro full_name: Uemura, Tomohiro last_name: Uemura - first_name: Mugurel full_name: Feraru, Mugurel last_name: Feraru - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Tatsuo full_name: Kakimoto, Tatsuo last_name: Kakimoto - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Tanaka H, Kitakura S, Rakusová H, et al. Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 2013;9(5). doi:10.1371/journal.pgen.1003540 apa: Tanaka, H., Kitakura, S., Rakusová, H., Uemura, T., Feraru, M., De Rycke, R., … Friml, J. (2013). Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003540 chicago: Tanaka, Hirokazu, Saeko Kitakura, Hana Rakusová, Tomohiro Uemura, Mugurel Feraru, Riet De Rycke, Stéphanie Robert, Tatsuo Kakimoto, and Jiří Friml. “Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003540. ieee: H. Tanaka et al., “Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana,” PLoS Genetics, vol. 9, no. 5. Public Library of Science, 2013. ista: Tanaka H, Kitakura S, Rakusová H, Uemura T, Feraru M, De Rycke R, Robert S, Kakimoto T, Friml J. 2013. Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 9(5), e1003540. mla: Tanaka, Hirokazu, et al. “Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics, vol. 9, no. 5, e1003540, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003540. short: H. Tanaka, S. Kitakura, H. Rakusová, T. Uemura, M. Feraru, R. De Rycke, S. Robert, T. Kakimoto, J. Friml, PLoS Genetics 9 (2013). date_created: 2018-12-11T11:59:50Z date_published: 2013-05-05T00:00:00Z date_updated: 2021-01-12T07:00:03Z day: '05' ddc: - '570' department: - _id: JiFr doi: 10.1371/journal.pgen.1003540 ec_funded: 1 file: - access_level: open_access checksum: 050237d6c53e8d1601b26808ee1dd6d8 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:39Z date_updated: 2020-07-14T12:45:50Z file_id: '4957' file_name: IST-2016-411-v1+1_journal.pgen.1003540.pdf file_size: 3813091 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 9' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '3967' pubrep_id: '411' quality_controlled: '1' scopus_import: 1 status: public title: Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '2828' abstract: - lang: eng text: 'We study the complexity of valued constraint satisfaction problems (VCSPs) parametrized by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimize the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well understood, see Raghavendra [2008]. However, there is no characterization of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimization perspective. We consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e., relations), such languages have been called conservative and studied by Bulatov [2003, 2011] and recently by Barto [2011]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [2006] for languages over Boolean domains, by Deineko et al. [2008] for {0, 1}-valued languages (a.k.a Max-CSP), and by Takhanov [2010a] for {0, ∞}-valued languages containing all finite-valued unary cost functions (a.k.a. Min-Cost-Hom). We prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimor-phisms), then any instance can be solved in polynomial time (via a new algorithm developed in this article), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains are significantly harder than the Boolean cases. The polynomial-time algorithm we present for the tractable cases is a generalization of the submodular minimization problem and a result of Cohen et al. [2008]. Our results generalize previous results by Takhanov [2010a] and (a subset of results) by Cohen et al. [2006] and Deineko et al. [2008]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [2008], and provide a powerful tool for proving hardness of finite-valued and general-valued languages.' article_number: '10' author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Stanislav full_name: Živný, Stanislav last_name: Živný citation: ama: Kolmogorov V, Živný S. The complexity of conservative valued CSPs. Journal of the ACM. 2013;60(2). doi:10.1145/2450142.2450146 apa: Kolmogorov, V., & Živný, S. (2013). The complexity of conservative valued CSPs. Journal of the ACM. ACM. https://doi.org/10.1145/2450142.2450146 chicago: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs.” Journal of the ACM. ACM, 2013. https://doi.org/10.1145/2450142.2450146. ieee: V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,” Journal of the ACM, vol. 60, no. 2. ACM, 2013. ista: Kolmogorov V, Živný S. 2013. The complexity of conservative valued CSPs. Journal of the ACM. 60(2), 10. mla: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs.” Journal of the ACM, vol. 60, no. 2, 10, ACM, 2013, doi:10.1145/2450142.2450146. short: V. Kolmogorov, S. Živný, Journal of the ACM 60 (2013). date_created: 2018-12-11T11:59:48Z date_published: 2013-04-02T00:00:00Z date_updated: 2021-01-12T07:00:00Z day: '02' department: - _id: VlKo doi: 10.1145/2450142.2450146 external_id: arxiv: - '1110.2809' intvolume: ' 60' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1110.2809 month: '04' oa: 1 oa_version: Preprint publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '3971' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of conservative valued CSPs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2013' ... --- _id: '2829' abstract: - lang: eng text: Laminar-turbulent intermittency is intrinsic to the transitional regime of a wide range of fluid flows including pipe, channel, boundary layer, and Couette flow. In the latter turbulent spots can grow and form continuous stripes, yet in the stripe-normal direction they remain interspersed by laminar fluid. We carry out direct numerical simulations in a long narrow domain and observe that individual turbulent stripes are transient. In agreement with recent observations in pipe flow, we find that turbulence becomes sustained at a distinct critical point once the spatial proliferation outweighs the inherent decaying process. By resolving the asymptotic size distributions close to criticality we can for the first time demonstrate scale invariance at the onset of turbulence. article_number: '204502' author: - first_name: Liang full_name: Shi, Liang id: 374A3F1A-F248-11E8-B48F-1D18A9856A87 last_name: Shi - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Shi L, Avila M, Hof B. Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. 2013;110(20). doi:10.1103/PhysRevLett.110.204502 apa: Shi, L., Avila, M., & Hof, B. (2013). Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.204502 chicago: Shi, Liang, Marc Avila, and Björn Hof. “Scale Invariance at the Onset of Turbulence in Couette Flow.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.204502. ieee: L. Shi, M. Avila, and B. Hof, “Scale invariance at the onset of turbulence in couette flow,” Physical Review Letters, vol. 110, no. 20. American Physical Society, 2013. ista: Shi L, Avila M, Hof B. 2013. Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. 110(20), 204502. mla: Shi, Liang, et al. “Scale Invariance at the Onset of Turbulence in Couette Flow.” Physical Review Letters, vol. 110, no. 20, 204502, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.204502. short: L. Shi, M. Avila, B. Hof, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:59:49Z date_published: 2013-05-13T00:00:00Z date_updated: 2021-01-12T07:00:00Z day: '13' department: - _id: BjHo doi: 10.1103/PhysRevLett.110.204502 ec_funded: 1 external_id: arxiv: - '1304.5446' intvolume: ' 110' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1304.5446 month: '05' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin - _id: 2511D90C-B435-11E9-9278-68D0E5697425 grant_number: SFB 963 TP A8 name: Astrophysical instability of currents and turbulences publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '3970' quality_controlled: '1' scopus_import: 1 status: public title: Scale invariance at the onset of turbulence in couette flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2834' abstract: - lang: eng text: Although the equations governing fluid flow are well known, there are no analytical expressions that describe the complexity of turbulent motion. A recent proposition is that in analogy to low dimensional chaotic systems, turbulence is organized around unstable solutions of the governing equations which provide the building blocks of the disordered dynamics. We report the discovery of periodic solutions which just like intermittent turbulence are spatially localized and show that turbulent transients arise from one such solution branch. article_number: '224502' author: - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Fernando full_name: Mellibovsky, Fernando last_name: Mellibovsky - first_name: Nicolas full_name: Roland, Nicolas last_name: Roland - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Avila M, Mellibovsky F, Roland N, Hof B. Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. 2013;110(22). doi:10.1103/PhysRevLett.110.224502 apa: Avila, M., Mellibovsky, F., Roland, N., & Hof, B. (2013). Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.224502 chicago: Avila, Marc, Fernando Mellibovsky, Nicolas Roland, and Björn Hof. “Streamwise-Localized Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.224502. ieee: M. Avila, F. Mellibovsky, N. Roland, and B. Hof, “Streamwise-localized solutions at the onset of turbulence in pipe flow,” Physical Review Letters, vol. 110, no. 22. American Physical Society, 2013. ista: Avila M, Mellibovsky F, Roland N, Hof B. 2013. Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. 110(22), 224502. mla: Avila, Marc, et al. “Streamwise-Localized Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters, vol. 110, no. 22, 224502, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.224502. short: M. Avila, F. Mellibovsky, N. Roland, B. Hof, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:59:50Z date_published: 2013-05-29T00:00:00Z date_updated: 2021-01-12T07:00:05Z day: '29' department: - _id: BjHo doi: 10.1103/PhysRevLett.110.224502 ec_funded: 1 external_id: arxiv: - '1212.0230' intvolume: ' 110' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1212.0230 month: '05' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '3965' quality_controlled: '1' scopus_import: 1 status: public title: Streamwise-localized solutions at the onset of turbulence in pipe flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2833' abstract: - lang: eng text: During development, mechanical forces cause changes in size, shape, number, position, and gene expression of cells. They are therefore integral to any morphogenetic processes. Force generation by actin-myosin networks and force transmission through adhesive complexes are two self-organizing phenomena driving tissue morphogenesis. Coordination and integration of forces by long-range force transmission and mechanosensing of cells within tissues produce large-scale tissue shape changes. Extrinsic mechanical forces also control tissue patterning by modulating cell fate specification and differentiation. Thus, the interplay between tissue mechanics and biochemical signaling orchestrates tissue morphogenesis and patterning in development. acknowledgement: C.-P.H. is supported by the Institute of Science and Technology Austria and grants from the Deutsche Forschungsgemeinschaft (DFG) and Fonds zur Förderung der wissenschaftlichen Forschung (FWF). author: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Yohanns full_name: Bellaïche, Yohanns last_name: Bellaïche citation: ama: Heisenberg C-PJ, Bellaïche Y. Forces in tissue morphogenesis and patterning. Cell. 2013;153(5):948-962. doi:10.1016/j.cell.2013.05.008 apa: Heisenberg, C.-P. J., & Bellaïche, Y. (2013). Forces in tissue morphogenesis and patterning. Cell. Cell Press. https://doi.org/10.1016/j.cell.2013.05.008 chicago: Heisenberg, Carl-Philipp J, and Yohanns Bellaïche. “Forces in Tissue Morphogenesis and Patterning.” Cell. Cell Press, 2013. https://doi.org/10.1016/j.cell.2013.05.008. ieee: C.-P. J. Heisenberg and Y. Bellaïche, “Forces in tissue morphogenesis and patterning,” Cell, vol. 153, no. 5. Cell Press, pp. 948–962, 2013. ista: Heisenberg C-PJ, Bellaïche Y. 2013. Forces in tissue morphogenesis and patterning. Cell. 153(5), 948–962. mla: Heisenberg, Carl-Philipp J., and Yohanns Bellaïche. “Forces in Tissue Morphogenesis and Patterning.” Cell, vol. 153, no. 5, Cell Press, 2013, pp. 948–62, doi:10.1016/j.cell.2013.05.008. short: C.-P.J. Heisenberg, Y. Bellaïche, Cell 153 (2013) 948–962. date_created: 2018-12-11T11:59:50Z date_published: 2013-05-23T00:00:00Z date_updated: 2021-01-12T07:00:04Z day: '23' department: - _id: CaHe doi: 10.1016/j.cell.2013.05.008 intvolume: ' 153' issue: '5' language: - iso: eng month: '05' oa_version: None page: 948 - 962 publication: Cell publication_status: published publisher: Cell Press publist_id: '3966' quality_controlled: '1' scopus_import: 1 status: public title: Forces in tissue morphogenesis and patterning type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 153 year: '2013' ... --- _id: '2830' author: - first_name: Christine full_name: Moussion, Christine id: 3356F664-F248-11E8-B48F-1D18A9856A87 last_name: Moussion - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Moussion C, Sixt MK. A conduit to amplify innate immunity. Immunity. 2013;38(5):853-854. doi:10.1016/j.immuni.2013.05.005 apa: Moussion, C., & Sixt, M. K. (2013). A conduit to amplify innate immunity. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2013.05.005 chicago: Moussion, Christine, and Michael K Sixt. “A Conduit to Amplify Innate Immunity.” Immunity. Cell Press, 2013. https://doi.org/10.1016/j.immuni.2013.05.005. ieee: C. Moussion and M. K. Sixt, “A conduit to amplify innate immunity,” Immunity, vol. 38, no. 5. Cell Press, pp. 853–854, 2013. ista: Moussion C, Sixt MK. 2013. A conduit to amplify innate immunity. Immunity. 38(5), 853–854. mla: Moussion, Christine, and Michael K. Sixt. “A Conduit to Amplify Innate Immunity.” Immunity, vol. 38, no. 5, Cell Press, 2013, pp. 853–54, doi:10.1016/j.immuni.2013.05.005. short: C. Moussion, M.K. Sixt, Immunity 38 (2013) 853–854. date_created: 2018-12-11T11:59:49Z date_published: 2013-05-23T00:00:00Z date_updated: 2021-01-12T07:00:01Z day: '23' department: - _id: MiSi doi: 10.1016/j.immuni.2013.05.005 intvolume: ' 38' issue: '5' language: - iso: eng month: '05' oa_version: None page: 853 - 854 publication: Immunity publication_status: published publisher: Cell Press publist_id: '3969' quality_controlled: '1' scopus_import: 1 status: public title: A conduit to amplify innate immunity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2013' ... --- _id: '2842' abstract: - lang: eng text: 'We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ2, based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FS T) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a ''local scale'', κ; the rate of gene flow, σ2, cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ2. With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ2.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: 'Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001' apa: 'Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001' chicago: 'Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.' ieee: 'N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.' ista: 'Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 87(1), 105–119.' mla: 'Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology, vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.' short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 105–119. date_created: 2018-12-11T11:59:53Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T07:00:09Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1016/j.tpb.2013.03.001 ec_funded: 1 file: - access_level: open_access checksum: 9bf9d9a6fd03dd9df50906891f393bf8 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:33Z date_updated: 2020-07-14T12:45:50Z file_id: '5288' file_name: IST-2016-558-v1+1_inference_revised3101NB.pdf file_size: 1554712 relation: main_file - access_level: open_access checksum: 2bceddb76edacd0cd5fad73051e2a928 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:34Z date_updated: 2020-07-14T12:45:50Z file_id: '5289' file_name: IST-2016-558-v1+2_inference_revised3101NBApp.pdf file_size: 822964 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 87' issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 105 - 119 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Theoretical Population Biology publication_status: published publisher: Elsevier publist_id: '3953' pubrep_id: '558' quality_controlled: '1' scopus_import: 1 status: public title: 'Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2013' ... --- _id: '2838' abstract: - lang: eng text: Individuals with Down syndrome (DS) present important motor deficits that derive from altered motor development of infants and young children. DYRK1A, a candidate gene for DS abnormalities has been implicated in motor function due to its expression in motor nuclei in the adult brain, and its overexpression in DS mouse models leads to hyperactivity and altered motor learning. However, its precise role in the adult motor system, or its possible involvement in postnatal locomotor development has not yet been clarified. During the postnatal period we observed time-specific expression of Dyrk1A in discrete subsets of brainstem nuclei and spinal cord motor neurons. Interestingly, we describe for the first time the presence of Dyrk1A in the presynaptic terminal of the neuromuscular junctions and its axonal transport from the facial nucleus, suggesting a function for Dyrk1A in these structures. Relevant to DS, Dyrk1A overexpression in transgenic mice (TgDyrk1A) produces motor developmental alterations possibly contributing to DS motor phenotypes and modifies the numbers of motor cholinergic neurons, suggesting that the kinase may have a role in the development of the brainstem and spinal cord motor system. article_number: e54285 author: - first_name: Gloria full_name: Arquè Fuste, Gloria id: 3CF33908-F248-11E8-B48F-1D18A9856A87 last_name: Arquè Fuste - first_name: Anna full_name: Casanovas, Anna last_name: Casanovas - first_name: Mara full_name: Dierssen, Mara last_name: Dierssen citation: ama: 'Arquè Fuste G, Casanovas A, Dierssen M. Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. 2013;8(1). doi:10.1371/journal.pone.0054285' apa: 'Arquè Fuste, G., Casanovas, A., & Dierssen, M. (2013). Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0054285' chicago: 'Arquè Fuste, Gloria, Anna Casanovas, and Mara Dierssen. “Dyrk1A Is Dynamically Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0054285.' ieee: 'G. Arquè Fuste, A. Casanovas, and M. Dierssen, “Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome,” PLoS One, vol. 8, no. 1. Public Library of Science, 2013.' ista: 'Arquè Fuste G, Casanovas A, Dierssen M. 2013. Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. 8(1), e54285.' mla: 'Arquè Fuste, Gloria, et al. “Dyrk1A Is Dynamically Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.” PLoS One, vol. 8, no. 1, e54285, Public Library of Science, 2013, doi:10.1371/journal.pone.0054285.' short: G. Arquè Fuste, A. Casanovas, M. Dierssen, PLoS One 8 (2013). date_created: 2018-12-11T11:59:52Z date_published: 2013-01-16T00:00:00Z date_updated: 2021-01-12T07:00:07Z day: '16' ddc: - '570' department: - _id: SiHi doi: 10.1371/journal.pone.0054285 file: - access_level: open_access checksum: 512733b21419574a45f10cabef3d7f81 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:38Z date_updated: 2020-07-14T12:45:50Z file_id: '5160' file_name: IST-2016-407-v1+1_journal.pone.0054285.pdf file_size: 4795977 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '3960' pubrep_id: '407' quality_controlled: '1' scopus_import: 1 status: public title: 'Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2839' abstract: - lang: eng text: Directional guidance of cells via gradients of chemokines is considered crucial for embryonic development, cancer dissemination, and immune responses. Nevertheless, the concept still lacks direct experimental confirmation in vivo. Here, we identify endogenous gradients of the chemokine CCL21 within mouse skin and show that they guide dendritic cells toward lymphatic vessels. Quantitative imaging reveals depots of CCL21 within lymphatic endothelial cells and steeply decaying gradients within the perilymphatic interstitium. These gradients match the migratory patterns of the dendritic cells, which directionally approach vessels from a distance of up to 90-micrometers. Interstitial CCL21 is immobilized to heparan sulfates, and its experimental delocalization or swamping the endogenous gradients abolishes directed migration. These findings functionally establish the concept of haptotaxis, directed migration along immobilized gradients, in tissues. acknowledgement: We thank M. Frank for technical assistance and S. Cremer, P. Schmalhorst, and E. Kiermaier for critical reading of the manuscript. This work was supported by a Humboldt Foundation postdoctoral fellowship (to M.W.), the German Research Foundation (Si1323 1,2 to M.S.), the Human Frontier Science Program (HFSP RGP0058/2011 to M.S.), the European Research Council (ERC StG 281556 to M.S.), and the Swiss National Science Foundation (31003A 127474 to D.F.L., 130488 to S.A.L.). article_processing_charge: No article_type: original author: - first_name: Michele full_name: Weber, Michele id: 3A3FC708-F248-11E8-B48F-1D18A9856A87 last_name: Weber - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Christine full_name: Moussion, Christine id: 3356F664-F248-11E8-B48F-1D18A9856A87 last_name: Moussion - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Daniel full_name: Legler, Daniel last_name: Legler - first_name: Sanjiv full_name: Luther, Sanjiv last_name: Luther - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Weber M, Hauschild R, Schwarz J, et al. Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. 2013;339(6117):328-332. doi:10.1126/science.1228456 apa: Weber, M., Hauschild, R., Schwarz, J., Moussion, C., de Vries, I., Legler, D., … Sixt, M. K. (2013). Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1228456 chicago: Weber, Michele, Robert Hauschild, Jan Schwarz, Christine Moussion, Ingrid de Vries, Daniel Legler, Sanjiv Luther, Mark Tobias Bollenbach, and Michael K Sixt. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1228456. ieee: M. Weber et al., “Interstitial dendritic cell guidance by haptotactic chemokine gradients,” Science, vol. 339, no. 6117. American Association for the Advancement of Science, pp. 328–332, 2013. ista: Weber M, Hauschild R, Schwarz J, Moussion C, de Vries I, Legler D, Luther S, Bollenbach MT, Sixt MK. 2013. Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. 339(6117), 328–332. mla: Weber, Michele, et al. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.” Science, vol. 339, no. 6117, American Association for the Advancement of Science, 2013, pp. 328–32, doi:10.1126/science.1228456. short: M. Weber, R. Hauschild, J. Schwarz, C. Moussion, I. de Vries, D. Legler, S. Luther, M.T. Bollenbach, M.K. Sixt, Science 339 (2013) 328–332. date_created: 2018-12-11T11:59:52Z date_published: 2013-01-18T00:00:00Z date_updated: 2022-06-10T10:21:40Z day: '18' department: - _id: MiSi - _id: Bio doi: 10.1126/science.1228456 ec_funded: 1 intvolume: ' 339' issue: '6117' language: - iso: eng main_file_link: - open_access: '1' url: https://kops.uni-konstanz.de/bitstream/123456789/26341/2/Weber_263418.pdf month: '01' oa: 1 oa_version: Published Version page: 328 - 332 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) - _id: 25ABD200-B435-11E9-9278-68D0E5697425 grant_number: RGP0058/2011 name: 'Cell migration in complex environments: from in vivo experiments to theoretical models' publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '3959' quality_controlled: '1' scopus_import: '1' status: public title: Interstitial dendritic cell guidance by haptotactic chemokine gradients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 339 year: '2013' ... --- _id: '2837' abstract: - lang: eng text: We consider a general class of N × N random matrices whose entries hij are independent up to a symmetry constraint, but not necessarily identically distributed. Our main result is a local semicircle law which improves previous results [17] both in the bulk and at the edge. The error bounds are given in terms of the basic small parameter of the model, maxi,j E|hij|2. As a consequence, we prove the universality of the local n-point correlation functions in the bulk spectrum for a class of matrices whose entries do not have comparable variances, including random band matrices with band width W ≫N1-εn with some εn > 0 and with a negligible mean-field component. In addition, we provide a coherent and pedagogical proof of the local semicircle law, streamlining and strengthening previous arguments from [17, 19, 6]. author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles - first_name: Horng full_name: Yau, Horng last_name: Yau - first_name: Jun full_name: Yin, Jun last_name: Yin citation: ama: Erdös L, Knowles A, Yau H, Yin J. The local semicircle law for a general class of random matrices. Electronic Journal of Probability. 2013;18(59):1-58. doi:10.1214/EJP.v18-2473 apa: Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). The local semicircle law for a general class of random matrices. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v18-2473 chicago: Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “The Local Semicircle Law for a General Class of Random Matrices.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/EJP.v18-2473. ieee: L. Erdös, A. Knowles, H. Yau, and J. Yin, “The local semicircle law for a general class of random matrices,” Electronic Journal of Probability, vol. 18, no. 59. Institute of Mathematical Statistics, pp. 1–58, 2013. ista: Erdös L, Knowles A, Yau H, Yin J. 2013. The local semicircle law for a general class of random matrices. Electronic Journal of Probability. 18(59), 1–58. mla: Erdös, László, et al. “The Local Semicircle Law for a General Class of Random Matrices.” Electronic Journal of Probability, vol. 18, no. 59, Institute of Mathematical Statistics, 2013, pp. 1–58, doi:10.1214/EJP.v18-2473. short: L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of Probability 18 (2013) 1–58. date_created: 2018-12-11T11:59:51Z date_published: 2013-05-29T00:00:00Z date_updated: 2021-01-12T07:00:06Z day: '29' ddc: - '530' department: - _id: LaEr doi: 10.1214/EJP.v18-2473 file: - access_level: open_access checksum: aac9e52a00cb2f5149dc9e362b5ccf44 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:46Z date_updated: 2020-07-14T12:45:50Z file_id: '5169' file_name: IST-2016-406-v1+1_2473-13759-1-PB.pdf file_size: 651497 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 18' issue: '59' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1-58 publication: Electronic Journal of Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '3962' pubrep_id: '406' quality_controlled: '1' scopus_import: 1 status: public title: The local semicircle law for a general class of random matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2013' ... --- _id: '2835' abstract: - lang: eng text: The phytohormone auxin regulates virtually every aspect of plant development. To identify new genes involved in auxin activity, a genetic screen was performed for Arabidopsis (Arabidopsis thaliana) mutants with altered expression of the auxin-responsive reporter DR5rev:GFP. One of the mutants recovered in the screen, designated as weak auxin response3 (wxr3), exhibits much lower DR5rev:GFP expression when treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid and displays severe defects in root development. The wxr3 mutant decreases polar auxin transport and results in a disruption of the asymmetric auxin distribution. The levels of the auxin transporters AUXIN1 and PIN-FORMED are dramatically reduced in the wxr3 root tip. Molecular analyses demonstrate that WXR3 is ROOT ULTRAVIOLET B-SENSITIVE1 (RUS1), a member of the conserved Domain of Unknown Function647 protein family found in diverse eukaryotic organisms. Our data suggest that RUS1/WXR3 plays an essential role in the regulation of polar auxin transport by maintaining the proper level of auxin transporters on the plasma membrane. author: - first_name: Hong full_name: Yu, Hong last_name: Yu - first_name: Michael full_name: Karampelias, Michael last_name: Karampelias - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Wendy full_name: Peer, Wendy last_name: Peer - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Songqing full_name: Ye, Songqing last_name: Ye - first_name: Lei full_name: Ge, Lei last_name: Ge - first_name: Jerry full_name: Cohen, Jerry last_name: Cohen - first_name: Angus full_name: Murphy, Angus last_name: Murphy - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Mark full_name: Estelle, Mark last_name: Estelle citation: ama: Yu H, Karampelias M, Robert S, et al. Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. Plant Physiology. 2013;162(2):965-976. doi:10.1104/pp.113.217018 apa: Yu, H., Karampelias, M., Robert, S., Peer, W., Swarup, R., Ye, S., … Estelle, M. (2013). Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.113.217018 chicago: Yu, Hong, Michael Karampelias, Stéphanie Robert, Wendy Peer, Ranjan Swarup, Songqing Ye, Lei Ge, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3 Is Essential for Polar Auxin Transport in Arabidopsis.” Plant Physiology. American Society of Plant Biologists, 2013. https://doi.org/10.1104/pp.113.217018. ieee: H. Yu et al., “Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis,” Plant Physiology, vol. 162, no. 2. American Society of Plant Biologists, pp. 965–976, 2013. ista: Yu H, Karampelias M, Robert S, Peer W, Swarup R, Ye S, Ge L, Cohen J, Murphy A, Friml J, Estelle M. 2013. Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. Plant Physiology. 162(2), 965–976. mla: Yu, Hong, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3 Is Essential for Polar Auxin Transport in Arabidopsis.” Plant Physiology, vol. 162, no. 2, American Society of Plant Biologists, 2013, pp. 965–76, doi:10.1104/pp.113.217018. short: H. Yu, M. Karampelias, S. Robert, W. Peer, R. Swarup, S. Ye, L. Ge, J. Cohen, A. Murphy, J. Friml, M. Estelle, Plant Physiology 162 (2013) 965–976. date_created: 2018-12-11T11:59:51Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T07:00:05Z day: '01' department: - _id: JiFr doi: 10.1104/pp.113.217018 external_id: pmid: - '23580592' intvolume: ' 162' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668084/ month: '06' oa: 1 oa_version: Submitted Version page: 965 - 976 pmid: 1 publication: Plant Physiology publication_status: published publisher: American Society of Plant Biologists publist_id: '3964' quality_controlled: '1' scopus_import: 1 status: public title: Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 162 year: '2013' ... --- _id: '2836' abstract: - lang: eng text: 'We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents and the trusted third party as path formulas in linear temporal logic and prove that the satisfaction of these objectives imply fairness; a property required of fair exchange protocols. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of AGS as follows: (a) any solution of AGS is attack-free; no subset of participants can violate the objectives of the other participants; (b) the Asokan-Shoup-Waidner certified mail protocol that has known vulnerabilities is not a solution of AGS; (c) the Kremer-Markowitch non-repudiation protocol is a solution of AGS; and (d) AGS presents a new and symmetric fair non-repudiation protocol that is attack-free. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can both automatically discover vulnerabilities in protocols and generate correct protocols. The solution to AGS can be computed efficiently as the secure equilibrium solution of three-player graph games. ' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vishwanath full_name: Raman, Vishwanath last_name: Raman citation: ama: Chatterjee K, Raman V. Assume-guarantee synthesis for digital contract signing. Formal Aspects of Computing. 2013;26(4):825-859. doi:10.1007/s00165-013-0283-6 apa: Chatterjee, K., & Raman, V. (2013). Assume-guarantee synthesis for digital contract signing. Formal Aspects of Computing. Springer. https://doi.org/10.1007/s00165-013-0283-6 chicago: Chatterjee, Krishnendu, and Vishwanath Raman. “Assume-Guarantee Synthesis for Digital Contract Signing.” Formal Aspects of Computing. Springer, 2013. https://doi.org/10.1007/s00165-013-0283-6. ieee: K. Chatterjee and V. Raman, “Assume-guarantee synthesis for digital contract signing,” Formal Aspects of Computing, vol. 26, no. 4. Springer, pp. 825–859, 2013. ista: Chatterjee K, Raman V. 2013. Assume-guarantee synthesis for digital contract signing. Formal Aspects of Computing. 26(4), 825–859. mla: Chatterjee, Krishnendu, and Vishwanath Raman. “Assume-Guarantee Synthesis for Digital Contract Signing.” Formal Aspects of Computing, vol. 26, no. 4, Springer, 2013, pp. 825–59, doi:10.1007/s00165-013-0283-6. short: K. Chatterjee, V. Raman, Formal Aspects of Computing 26 (2013) 825–859. date_created: 2018-12-11T11:59:51Z date_published: 2013-07-04T00:00:00Z date_updated: 2021-01-12T07:00:06Z day: '04' department: - _id: KrCh doi: 10.1007/s00165-013-0283-6 ec_funded: 1 external_id: arxiv: - '1004.2697' intvolume: ' 26' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1004.2697 month: '07' oa: 1 oa_version: Preprint page: 825 - 859 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Formal Aspects of Computing publication_status: published publisher: Springer publist_id: '3963' quality_controlled: '1' scopus_import: 1 status: public title: Assume-guarantee synthesis for digital contract signing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2013' ... --- _id: '2840' abstract: - lang: eng text: It is known that the entorhinal cortex plays a crucial role in spatial cognition in rodents. Neuroanatomical and electrophysiological data suggest that there is a functional distinction between 2 subregions within the entorhinal cortex, the medial entorhinal cortex (MEC), and the lateral entorhinal cortex (LEC). Rats with MEC or LEC lesions were trained in 2 navigation tasks requiring allothetic (water maze task) or idiothetic (path integration) information processing and 2-object exploration tasks allowing testing of spatial and nonspatial processing of intramaze objects. MEC lesions mildly affected place navigation in the water maze and produced a path integration deficit. They also altered the processing of spatial information in both exploration tasks while sparing the processing of nonspatial information. LEC lesions did not affect navigation abilities in both the water maze and the path integration tasks. They altered spatial and nonspatial processing in the object exploration task but not in the one-trial recognition task. Overall, these results indicate that the MEC is important for spatial processing and path integration. The LEC has some influence on both spatial and nonspatial processes, suggesting that the 2 kinds of information interact at the level of the EC. author: - first_name: Tiffany full_name: Van Cauter, Tiffany last_name: Van Cauter - first_name: Jeremy full_name: Camon, Jeremy last_name: Camon - first_name: Alice full_name: Alvernhe, Alice id: 467FB3D4-F248-11E8-B48F-1D18A9856A87 last_name: Alvernhe - first_name: Coralie full_name: Elduayen, Coralie last_name: Elduayen - first_name: Francesca full_name: Sargolini, Francesca last_name: Sargolini - first_name: Étienne full_name: Save, Étienne last_name: Save citation: ama: Van Cauter T, Camon J, Alvernhe A, Elduayen C, Sargolini F, Save É. Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral Cortex. 2013;23(2):451-459. doi:10.1093/cercor/bhs033 apa: Van Cauter, T., Camon, J., Alvernhe, A., Elduayen, C., Sargolini, F., & Save, É. (2013). Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhs033 chicago: Van Cauter, Tiffany, Jeremy Camon, Alice Alvernhe, Coralie Elduayen, Francesca Sargolini, and Étienne Save. “Distinct Roles of Medial and Lateral Entorhinal Cortex in Spatial Cognition.” Cerebral Cortex. Oxford University Press, 2013. https://doi.org/10.1093/cercor/bhs033. ieee: T. Van Cauter, J. Camon, A. Alvernhe, C. Elduayen, F. Sargolini, and É. Save, “Distinct roles of medial and lateral entorhinal cortex in spatial cognition,” Cerebral Cortex, vol. 23, no. 2. Oxford University Press, pp. 451–459, 2013. ista: Van Cauter T, Camon J, Alvernhe A, Elduayen C, Sargolini F, Save É. 2013. Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral Cortex. 23(2), 451–459. mla: Van Cauter, Tiffany, et al. “Distinct Roles of Medial and Lateral Entorhinal Cortex in Spatial Cognition.” Cerebral Cortex, vol. 23, no. 2, Oxford University Press, 2013, pp. 451–59, doi:10.1093/cercor/bhs033. short: T. Van Cauter, J. Camon, A. Alvernhe, C. Elduayen, F. Sargolini, É. Save, Cerebral Cortex 23 (2013) 451–459. date_created: 2018-12-11T11:59:52Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T07:00:08Z day: '01' department: - _id: JoCs doi: 10.1093/cercor/bhs033 intvolume: ' 23' issue: '2' language: - iso: eng month: '02' oa_version: None page: 451 - 459 publication: Cerebral Cortex publication_status: published publisher: Oxford University Press publist_id: '3958' quality_controlled: '1' scopus_import: 1 status: public title: Distinct roles of medial and lateral entorhinal cortex in spatial cognition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '2841' abstract: - lang: eng text: In zebrafish early development, blastoderm cells undergo extensive radial intercalations, triggering the spreading of the blastoderm over the yolk cell and thereby initiating embryonic body axis formation. Now reporting in Developmental Cell, Song et al. (2013) demonstrate a critical function for EGF-dependent E-cadherin endocytosis in promoting blastoderm cell intercalations. author: - first_name: Hitoshi full_name: Morita, Hitoshi id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87 last_name: Morita - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Morita H, Heisenberg C-PJ. Holding on and letting go: Cadherin turnover in cell intercalation. Developmental Cell. 2013;24(6):567-569. doi:10.1016/j.devcel.2013.03.007' apa: 'Morita, H., & Heisenberg, C.-P. J. (2013). Holding on and letting go: Cadherin turnover in cell intercalation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2013.03.007' chicago: 'Morita, Hitoshi, and Carl-Philipp J Heisenberg. “Holding on and Letting Go: Cadherin Turnover in Cell Intercalation.” Developmental Cell. Cell Press, 2013. https://doi.org/10.1016/j.devcel.2013.03.007.' ieee: 'H. Morita and C.-P. J. Heisenberg, “Holding on and letting go: Cadherin turnover in cell intercalation,” Developmental Cell, vol. 24, no. 6. Cell Press, pp. 567–569, 2013.' ista: 'Morita H, Heisenberg C-PJ. 2013. Holding on and letting go: Cadherin turnover in cell intercalation. Developmental Cell. 24(6), 567–569.' mla: 'Morita, Hitoshi, and Carl-Philipp J. Heisenberg. “Holding on and Letting Go: Cadherin Turnover in Cell Intercalation.” Developmental Cell, vol. 24, no. 6, Cell Press, 2013, pp. 567–69, doi:10.1016/j.devcel.2013.03.007.' short: H. Morita, C.-P.J. Heisenberg, Developmental Cell 24 (2013) 567–569. date_created: 2018-12-11T11:59:52Z date_published: 2013-05-25T00:00:00Z date_updated: 2021-01-12T07:00:09Z day: '25' department: - _id: CaHe doi: 10.1016/j.devcel.2013.03.007 intvolume: ' 24' issue: '6' language: - iso: eng month: '05' oa_version: None page: 567 - 569 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '3956' quality_controlled: '1' scopus_import: 1 status: public title: 'Holding on and letting go: Cadherin turnover in cell intercalation' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2013' ... --- _id: '2846' abstract: - lang: eng text: The Red Queen hypothesis proposes that coevolving parasites select for outcrossing in the host. Outcrossing relies on males, which often show lower immune investment due to, for example, sexual selection. Here, we demonstrate that such sex differences in immunity interfere with parasite-mediated selection for outcrossing. Two independent coevolution experiments with Caenorhabditis elegans and its microparasite Bacillus thuringiensis produced decreased yet stable frequencies of outcrossing male hosts. A subsequent systematic analysis verified that male C. elegans suffered from a direct selective disadvantage under parasite pressure (i.e. lower resistance, decreased sexual activity, increased escape behaviour), which can reduce outcrossing and thus male frequencies. At the same time, males offered an indirect selective benefit, because male-mediated outcrossing increased offspring resistance, thus favouring male persistence in the evolving populations. As sex differences in immunity are widespread, such interference of opposing selective constraints is likely of central importance during host adaptation to a coevolving parasite. article_processing_charge: No author: - first_name: Leila full_name: El Masri, Leila id: 349A6E66-F248-11E8-B48F-1D18A9856A87 last_name: El Masri - first_name: Rebecca full_name: Schulte, Rebecca last_name: Schulte - first_name: Nadine full_name: Timmermeyer, Nadine last_name: Timmermeyer - first_name: Stefanie full_name: Thanisch, Stefanie last_name: Thanisch - first_name: Lena full_name: Crummenerl, Lena last_name: Crummenerl - first_name: Gunther full_name: Jansen, Gunther last_name: Jansen - first_name: Nico full_name: Michiels, Nico last_name: Michiels - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg citation: ama: El Masri L, Schulte R, Timmermeyer N, et al. Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. Ecology Letters. 2013;16(4):461-468. doi:10.1111/ele.12068 apa: El Masri, L., Schulte, R., Timmermeyer, N., Thanisch, S., Crummenerl, L., Jansen, G., … Schulenburg, H. (2013). Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. Ecology Letters. Wiley-Blackwell. https://doi.org/10.1111/ele.12068 chicago: El Masri, Leila, Rebecca Schulte, Nadine Timmermeyer, Stefanie Thanisch, Lena Crummenerl, Gunther Jansen, Nico Michiels, and Hinrich Schulenburg. “Sex Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing during Host-Parasite Coevolution.” Ecology Letters. Wiley-Blackwell, 2013. https://doi.org/10.1111/ele.12068. ieee: L. El Masri et al., “Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution,” Ecology Letters, vol. 16, no. 4. Wiley-Blackwell, pp. 461–468, 2013. ista: El Masri L, Schulte R, Timmermeyer N, Thanisch S, Crummenerl L, Jansen G, Michiels N, Schulenburg H. 2013. Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. Ecology Letters. 16(4), 461–468. mla: El Masri, Leila, et al. “Sex Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing during Host-Parasite Coevolution.” Ecology Letters, vol. 16, no. 4, Wiley-Blackwell, 2013, pp. 461–68, doi:10.1111/ele.12068. short: L. El Masri, R. Schulte, N. Timmermeyer, S. Thanisch, L. Crummenerl, G. Jansen, N. Michiels, H. Schulenburg, Ecology Letters 16 (2013) 461–468. date_created: 2018-12-11T11:59:54Z date_published: 2013-04-04T00:00:00Z date_updated: 2022-08-25T14:51:57Z day: '04' ddc: - '570' doi: 10.1111/ele.12068 extern: '1' file: - access_level: open_access checksum: aa7db788f7da7d7f102539a249ebce50 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:52Z date_updated: 2020-07-14T12:45:50Z file_id: '5176' file_name: IST-2016-404-v1+1_ele12068.pdf file_size: 763731 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 16' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 461 - 468 publication: Ecology Letters publication_status: published publisher: Wiley-Blackwell publist_id: '3948' pubrep_id: '404' quality_controlled: '1' scopus_import: '1' status: public title: Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2013' ... --- _id: '2844' abstract: - lang: eng text: As soon as a seed germinates, plant growth relates to gravity to ensure that the root penetrates the soil and the shoot expands aerially. Whereas mechanisms of positive and negative orthogravitropism of primary roots and shoots are relatively well understood [1-3], lateral organs often show more complex growth behavior [4]. Lateral roots (LRs) seemingly suppress positive gravitropic growth and show a defined gravitropic set-point angle (GSA) that allows radial expansion of the root system (plagiotropism) [3, 4]. Despite its eminent importance for root architecture, it so far remains completely unknown how lateral organs partially suppress positive orthogravitropism. Here we show that the phytohormone auxin steers GSA formation and limits positive orthogravitropism in LR. Low and high auxin levels/signaling lead to radial or axial root systems, respectively. At a cellular level, it is the auxin transport-dependent regulation of asymmetric growth in the elongation zone that determines GSA. Our data suggest that strong repression of PIN4/PIN7 and transient PIN3 expression limit auxin redistribution in young LR columella cells. We conclude that PIN activity, by temporally limiting the asymmetric auxin fluxes in the tip of LRs, induces transient, differential growth responses in the elongation zone and, consequently, controls root architecture. author: - first_name: Michel full_name: Rosquete, Michel last_name: Rosquete - first_name: Daniel full_name: Von Wangenheim, Daniel id: 49E91952-F248-11E8-B48F-1D18A9856A87 last_name: Von Wangenheim orcid: 0000-0002-6862-1247 - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Elke full_name: Barbez, Elke last_name: Barbez - first_name: Ernst full_name: Stelzer, Ernst last_name: Stelzer - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Alexis full_name: Maizel, Alexis last_name: Maizel - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn citation: ama: Rosquete M, von Wangenheim D, Marhavý P, et al. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. 2013;23(9):817-822. doi:10.1016/j.cub.2013.03.064 apa: Rosquete, M., von Wangenheim, D., Marhavý, P., Barbez, E., Stelzer, E., Benková, E., … Kleine Vehn, J. (2013). An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.03.064 chicago: Rosquete, Michel, Daniel von Wangenheim, Peter Marhavý, Elke Barbez, Ernst Stelzer, Eva Benková, Alexis Maizel, and Jürgen Kleine Vehn. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.03.064. ieee: M. Rosquete et al., “An auxin transport mechanism restricts positive orthogravitropism in lateral roots,” Current Biology, vol. 23, no. 9. Cell Press, pp. 817–822, 2013. ista: Rosquete M, von Wangenheim D, Marhavý P, Barbez E, Stelzer E, Benková E, Maizel A, Kleine Vehn J. 2013. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. 23(9), 817–822. mla: Rosquete, Michel, et al. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” Current Biology, vol. 23, no. 9, Cell Press, 2013, pp. 817–22, doi:10.1016/j.cub.2013.03.064. short: M. Rosquete, D. von Wangenheim, P. Marhavý, E. Barbez, E. Stelzer, E. Benková, A. Maizel, J. Kleine Vehn, Current Biology 23 (2013) 817–822. date_created: 2018-12-11T11:59:53Z date_published: 2013-05-06T00:00:00Z date_updated: 2021-01-12T07:00:10Z day: '06' department: - _id: JiFr - _id: EvBe doi: 10.1016/j.cub.2013.03.064 ec_funded: 1 intvolume: ' 23' issue: '9' language: - iso: eng month: '05' oa_version: None page: 817 - 822 project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3950' quality_controlled: '1' scopus_import: 1 status: public title: An auxin transport mechanism restricts positive orthogravitropism in lateral roots type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '2843' abstract: - lang: eng text: 'Mathematical objects can be measured unambiguously, but not so objects from our physical world. Even the total length of tubelike shapes has its difficulties. We introduce a combination of geometric, probabilistic, and topological methods to design a stable length estimate for tube-like shapes; that is: one that is insensitive to small shape changes.' alternative_title: - LNCS author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 citation: ama: 'Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. In: 17th IAPR International Conference on Discrete Geometry for Computer Imagery. Vol 7749. Springer; 2013:XV-XIX. doi:10.1007/978-3-642-37067-0' apa: 'Edelsbrunner, H., & Pausinger, F. (2013). Stable length estimates of tube-like shapes. In 17th IAPR International Conference on Discrete Geometry for Computer Imagery (Vol. 7749, pp. XV–XIX). Seville, Spain: Springer. https://doi.org/10.1007/978-3-642-37067-0' chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” In 17th IAPR International Conference on Discrete Geometry for Computer Imagery, 7749:XV–XIX. Springer, 2013. https://doi.org/10.1007/978-3-642-37067-0. ieee: H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” in 17th IAPR International Conference on Discrete Geometry for Computer Imagery, Seville, Spain, 2013, vol. 7749, pp. XV–XIX. ista: 'Edelsbrunner H, Pausinger F. 2013. Stable length estimates of tube-like shapes. 17th IAPR International Conference on Discrete Geometry for Computer Imagery. DGCI: Discrete Geometry for Computer Imagery, LNCS, vol. 7749, XV–XIX.' mla: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” 17th IAPR International Conference on Discrete Geometry for Computer Imagery, vol. 7749, Springer, 2013, pp. XV–XIX, doi:10.1007/978-3-642-37067-0. short: H. Edelsbrunner, F. Pausinger, in:, 17th IAPR International Conference on Discrete Geometry for Computer Imagery, Springer, 2013, pp. XV–XIX. conference: end_date: 2013-03-22 location: Seville, Spain name: 'DGCI: Discrete Geometry for Computer Imagery' start_date: 2013-03-20 date_created: 2018-12-11T11:59:53Z date_published: 2013-02-21T00:00:00Z date_updated: 2023-02-23T10:35:00Z day: '21' department: - _id: HeEd doi: 10.1007/978-3-642-37067-0 intvolume: ' 7749' language: - iso: eng month: '02' oa_version: None page: XV - XIX publication: 17th IAPR International Conference on Discrete Geometry for Computer Imagery publication_status: published publisher: Springer publist_id: '3952' quality_controlled: '1' related_material: record: - id: '2255' relation: later_version status: public scopus_import: 1 status: public title: Stable length estimates of tube-like shapes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7749 year: '2013' ... --- _id: '2845' abstract: - lang: eng text: At synapses formed between dissociated neurons, about half of all synaptic vesicles are refractory to evoked release, forming the so-called "resting pool." Here, we use optical measurements of vesicular pH to study developmental changes in pool partitioning and vesicle cycling in cultured hippocampal slices. Two-photon imaging of a genetically encoded two-color release sensor (ratio-sypHy) allowed us to perform calibrated measurements at individual Schaffer collateral boutons. Mature boutons released a large fraction of their vesicles during simulated place field activity, and vesicle retrieval rates were 7-fold higher compared to immature boutons. Saturating stimulation mobilized essentially all vesicles at mature synapses. Resting pool formation and a concomitant reduction in evoked release was induced by chronic depolarization but not by acute inhibition of the protein phosphatase calcineurin. We conclude that synapses in CA1 undergo a prominent refinement of vesicle use during early postnatal development that is not recapitulated in dissociated neuronal culture. author: - first_name: Tobias full_name: Rose, Tobias last_name: Rose - first_name: Philipp full_name: Schönenberger, Philipp id: 3B9D816C-F248-11E8-B48F-1D18A9856A87 last_name: Schönenberger - first_name: Karel full_name: Jezek, Karel last_name: Jezek - first_name: Thomas full_name: Oertner, Thomas last_name: Oertner citation: ama: Rose T, Schönenberger P, Jezek K, Oertner T. Developmental refinement of vesicle cycling at Schaffer collateral synapses. Neuron. 2013;77(6):1109-1121. doi:10.1016/j.neuron.2013.01.021 apa: Rose, T., Schönenberger, P., Jezek, K., & Oertner, T. (2013). Developmental refinement of vesicle cycling at Schaffer collateral synapses. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.01.021 chicago: Rose, Tobias, Philipp Schönenberger, Karel Jezek, and Thomas Oertner. “Developmental Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.01.021. ieee: T. Rose, P. Schönenberger, K. Jezek, and T. Oertner, “Developmental refinement of vesicle cycling at Schaffer collateral synapses,” Neuron, vol. 77, no. 6. Elsevier, pp. 1109–1121, 2013. ista: Rose T, Schönenberger P, Jezek K, Oertner T. 2013. Developmental refinement of vesicle cycling at Schaffer collateral synapses. Neuron. 77(6), 1109–1121. mla: Rose, Tobias, et al. “Developmental Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” Neuron, vol. 77, no. 6, Elsevier, 2013, pp. 1109–21, doi:10.1016/j.neuron.2013.01.021. short: T. Rose, P. Schönenberger, K. Jezek, T. Oertner, Neuron 77 (2013) 1109–1121. date_created: 2018-12-11T11:59:54Z date_published: 2013-03-20T00:00:00Z date_updated: 2021-01-12T07:00:11Z day: '20' department: - _id: JoCs doi: 10.1016/j.neuron.2013.01.021 intvolume: ' 77' issue: '6' language: - iso: eng month: '03' oa_version: None page: 1109 - 1121 publication: Neuron publication_status: published publisher: Elsevier publist_id: '3949' quality_controlled: '1' scopus_import: 1 status: public title: Developmental refinement of vesicle cycling at Schaffer collateral synapses type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2013' ... --- _id: '2854' abstract: - lang: eng text: We consider concurrent games played on graphs. At every round of a game, each player simultaneously and independently selects a move; the moves jointly determine the transition to a successor state. Two basic objectives are the safety objective to stay forever in a given set of states, and its dual, the reachability objective to reach a given set of states. First, we present a simple proof of the fact that in concurrent reachability games, for all ε>0, memoryless ε-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an ε-optimal strategy achieves the objective with probability within ε of the value of the game. In contrast to previous proofs of this fact, our proof is more elementary and more combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives. Finally, we present a strategy-improvement algorithm for turn-based stochastic games (where each player selects moves in turns) with safety objectives. Our algorithms yield sequences of player-1 strategies which ensure probabilities of winning that converge monotonically (from below) to the value of the game. © 2012 Elsevier Inc. acknowledgement: This work was partially supported in part by the NSF grants CCR-0132780, CNS-0720884, CCR-0225610, by the Swiss National Science Foundation, ERC Start Grant Graph Games (Project No. 279307), FWF NFN Grant S11407-N23 (RiSE), and a Microsoft faculty fellows article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: De Alfaro, Luca last_name: De Alfaro - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Chatterjee K, De Alfaro L, Henzinger TA. Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. 2013;79(5):640-657. doi:10.1016/j.jcss.2012.12.001 apa: Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2013). Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2012.12.001 chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.” Journal of Computer and System Sciences. Elsevier, 2013. https://doi.org/10.1016/j.jcss.2012.12.001. ieee: K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for concurrent reachability and turn based stochastic safety games,” Journal of Computer and System Sciences, vol. 79, no. 5. Elsevier, pp. 640–657, 2013. ista: Chatterjee K, De Alfaro L, Henzinger TA. 2013. Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. 79(5), 640–657. mla: Chatterjee, Krishnendu, et al. “Strategy Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.” Journal of Computer and System Sciences, vol. 79, no. 5, Elsevier, 2013, pp. 640–57, doi:10.1016/j.jcss.2012.12.001. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, Journal of Computer and System Sciences 79 (2013) 640–657. date_created: 2018-12-11T11:59:57Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T07:00:16Z day: '01' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.1016/j.jcss.2012.12.001 ec_funded: 1 file: - access_level: open_access checksum: 6d3ee12cceb946a0abe69594b6a22409 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:48Z date_updated: 2020-07-14T12:45:51Z file_id: '5370' file_name: IST-2015-388-v1+1_1-s2.0-S0022000012001778-main.pdf file_size: 425488 relation: main_file file_date_updated: 2020-07-14T12:45:51Z has_accepted_license: '1' intvolume: ' 79' issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '08' oa: 1 oa_version: Published Version page: 640 - 657 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of Computer and System Sciences publication_status: published publisher: Elsevier publist_id: '3938' pubrep_id: '388' quality_controlled: '1' scopus_import: 1 status: public title: Strategy improvement for concurrent reachability and turn based stochastic safety games tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 79 year: '2013' ...