[{"month":"09","day":"06","doi":"10.1112/S0025579313000132","date_published":"2013-09-06T00:00:00Z","citation":{"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.","chicago":"Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.” Mathematika. Unknown, 2013. https://doi.org/10.1112/S0025579313000132.","ama":"Browning TD. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 2013;60(1):101-107. doi:10.1112/S0025579313000132","ista":"Browning TD. 2013. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 60(1), 101–107.","apa":"Browning, T. D. (2013). Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. Unknown. 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."},"publication":"Mathematika","page":"101 - 107","quality_controlled":0,"issue":"1","publist_id":"7649","extern":1,"type":"journal_article","author":[{"last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Timothy Browning"}],"volume":60,"date_created":"2018-12-11T11:45:27Z","date_updated":"2021-01-12T06:58:03Z","year":"2013","_id":"253","publisher":"Unknown","intvolume":" 60","publication_status":"published","title":"Counting rational points on cubic hypersurfaces: Corrigendum","status":"public"},{"date_published":"2013-03-01T00:00:00Z","doi":"10.1016/j.neuropharm.2012.05.025","publication":"Neuropharmacology","citation":{"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.","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","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.","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","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.","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."},"quality_controlled":0,"page":"274 - 289","day":"01","month":"03","author":[{"full_name":"Dobi, Alice","last_name":"Dobi","first_name":"Alice"},{"last_name":"Sartori","first_name":"Simone","full_name":"Sartori, Simone B"},{"full_name":"Busti, Daniela","last_name":"Busti","first_name":"Daniela"},{"last_name":"Van Der Putten","first_name":"Herman","full_name":"Van Der Putten, Herman V"},{"last_name":"Singewald","first_name":"Nicolas","full_name":"Singewald, Nicolas"},{"full_name":"Ryuichi Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"first_name":"Francesco","last_name":"Ferraguti","full_name":"Ferraguti, Francesco"}],"date_updated":"2021-01-12T06:59:05Z","date_created":"2018-12-11T11:59:06Z","volume":66,"_id":"2692","year":"2013","publication_status":"published","title":"Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice","status":"public","publisher":"Elsevier","intvolume":" 66","abstract":[{"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.","lang":"eng"}],"publist_id":"4205","extern":1,"type":"journal_article"},{"type":"journal_article","extern":1,"issue":"8","publist_id":"4206","abstract":[{"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.","lang":"eng"}],"intvolume":" 33","publisher":"Society for Neuroscience","publication_status":"published","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","status":"public","_id":"2691","year":"2013","volume":33,"date_created":"2018-12-11T11:59:05Z","date_updated":"2021-01-12T06:59:05Z","author":[{"full_name":"Indriati, Dwi Wahyu","first_name":"Dwi","last_name":"Indriati"},{"full_name":"Kamasawa, Naomi","first_name":"Naomi","last_name":"Kamasawa"},{"first_name":"Ko","last_name":"Matsui","full_name":"Matsui, Ko"},{"full_name":"Meredith, Andrea L","last_name":"Meredith","first_name":"Andrea"},{"first_name":"Masahiko","last_name":"Watanabe","full_name":"Watanabe, Masahiko"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Ryuichi Shigemoto"}],"month":"02","day":"20","page":"3668 - 3678","quality_controlled":0,"citation":{"short":"D. Indriati, N. Kamasawa, K. Matsui, A. Meredith, M. Watanabe, R. Shigemoto, Journal of Neuroscience 33 (2013) 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.","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.","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","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.","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","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."},"publication":"Journal of Neuroscience","date_published":"2013-02-20T00:00:00Z","doi":"10.1523/JNEUROSCI.2921-12.2013"},{"extern":1,"abstract":[{"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.","lang":"eng"}],"issue":"1","publist_id":"4207","type":"journal_article","date_updated":"2021-01-12T06:59:04Z","date_created":"2018-12-11T11:59:05Z","volume":591,"author":[{"first_name":"Timotheus","last_name":"Budisantoso","full_name":"Budisantoso, Timotheus"},{"full_name":"Harumi Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896","first_name":"Harumi","last_name":"Harada"},{"full_name":"Kamasawa, Naomi","first_name":"Naomi","last_name":"Kamasawa"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"full_name":"Ryuichi Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"full_name":"Matsui, Ko","last_name":"Matsui","first_name":"Ko"}],"publication_status":"published","title":"Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held","status":"public","publisher":"Wiley-Blackwell","intvolume":" 591","_id":"2690","year":"2013","month":"01","day":"01","date_published":"2013-01-01T00:00:00Z","doi":"10.1113/jphysiol.2012.241398","quality_controlled":0,"page":"219 - 239","publication":"Journal of Physiology","citation":{"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.","short":"T. Budisantoso, H. Harada, N. Kamasawa, Y. Fukazawa, R. Shigemoto, K. Matsui, Journal of Physiology 591 (2013) 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.","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","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.","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"}},{"publication_status":"published","title":"Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons","status":"public","publisher":"Society for Neuroscience","intvolume":" 33","year":"2013","_id":"2693","date_updated":"2021-01-12T06:59:05Z","date_created":"2018-12-11T11:59:06Z","volume":33,"author":[{"first_name":"Sam","last_name":"Booker","full_name":"Booker, Sam A"},{"full_name":"Gross, Anna","first_name":"Anna","last_name":"Gross"},{"last_name":"Althof","first_name":"Daniel","full_name":"Althof, Daniel"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"last_name":"Frotscher","first_name":"Michael","full_name":"Frotscher, Michael"},{"full_name":"Hearing, Matthew C","first_name":"Matthew","last_name":"Hearing"},{"last_name":"Wickman","first_name":"Kevin","full_name":"Wickman, Kevin D"},{"first_name":"Masahiko","last_name":"Watanabe","full_name":"Watanabe, Masahiko"},{"full_name":"Kulik, Ákos","first_name":"Ákos","last_name":"Kulik"},{"full_name":"Vida, Imre","last_name":"Vida","first_name":"Imre"}],"type":"journal_article","extern":1,"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."}],"publist_id":"4204","issue":"18","quality_controlled":0,"page":"7961 - 7974","publication":"Journal of Neuroscience","citation":{"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.","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.","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.","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","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."},"date_published":"2013-05-01T00:00:00Z","doi":"10.1523/JNEUROSCI.1186-12.2013","month":"05","day":"01"},{"type":"journal_article","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."}],"publist_id":"4198","issue":"6","_id":"2698","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","status":"public","title":"Stability and semiclassics in self-generated fields","publication_status":"published","intvolume":" 15","department":[{"_id":"LaEr"}],"publisher":"European Mathematical Society","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"},{"full_name":"Fournais, Søren","first_name":"Søren","last_name":"Fournais"},{"full_name":"Solovej, Jan","last_name":"Solovej","first_name":"Jan"}],"date_created":"2018-12-11T11:59:07Z","date_updated":"2021-01-12T06:59:07Z","volume":15,"oa_version":"Preprint","day":"16","month":"10","publication":"Journal of the European Mathematical Society","oa":1,"citation":{"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.","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.","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.","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","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.","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"},"external_id":{"arxiv":["1105.0506"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1105.0506"}],"quality_controlled":"1","page":"2093 - 2113","date_published":"2013-10-16T00:00:00Z","doi":"10.4171/JEMS/416","language":[{"iso":"eng"}]},{"day":"01","month":"10","page":"367 - 416","quality_controlled":0,"citation":{"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.","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","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.","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","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.","short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Communications in Mathematical Physics 323 (2013) 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."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.5669"}],"oa":1,"publication":"Communications in Mathematical Physics","doi":"10.1007/s00220-013-1773-3","date_published":"2013-10-01T00:00:00Z","type":"journal_article","extern":1,"publist_id":"4199","issue":"1","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."}],"publisher":"Springer","intvolume":" 323","title":"Delocalization and diffusion profile for random band matrices","status":"public","publication_status":"published","year":"2013","_id":"2697","volume":323,"date_updated":"2021-01-12T06:59:07Z","date_created":"2018-12-11T11:59:07Z","author":[{"full_name":"László Erdös","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Antti","last_name":"Knowles","full_name":"Knowles, Antti"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng-Tzer"},{"last_name":"Yin","first_name":"Jun","full_name":"Yin, Jun"}]},{"month":"07","language":[{"iso":"eng"}],"doi":"10.1145/2463372.2463568","conference":{"end_date":"2013-07-10","start_date":"2013-07-06","location":"Amsterdam, Netherlands","name":"GECCO: Genetic and evolutionary computation conference"},"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"publist_id":"4174","ec_funded":1,"file_date_updated":"2020-07-14T12:45:45Z","date_updated":"2021-01-12T06:59:15Z","date_created":"2018-12-11T11:59:14Z","author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago"}],"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","publication_status":"published","year":"2013","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2013-07-01T00:00:00Z","page":"1573 - 1580","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","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.","short":"N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 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.","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."},"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","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."}],"type":"conference","file":[{"file_name":"IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf","access_level":"open_access","file_size":475844,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5159","date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-12T10:15:38Z","checksum":"9d9be9090ce5c20766e0eb076ace5b98"}],"oa_version":"Submitted Version","pubrep_id":"564","status":"public","title":"Can quantitative and population genetics help us understand evolutionary computation?","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2718"},{"ec_funded":1,"publist_id":"4172","author":[{"first_name":"Hongan","last_name":"Long","full_name":"Long, Hongan"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"},{"full_name":"Azevedo, Ricardo","last_name":"Azevedo","first_name":"Ricardo"},{"last_name":"Zufall","first_name":"Rebecca","full_name":"Zufall, Rebecca"}],"volume":195,"date_created":"2018-12-11T11:59:15Z","date_updated":"2021-01-12T06:59:16Z","pmid":1,"year":"2013","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","month":"10","doi":"10.1534/genetics.113.153536","language":[{"iso":"eng"}],"external_id":{"pmid":["23934880"]},"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/","open_access":"1"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"quality_controlled":"1","issue":"2","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."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2720","intvolume":" 195","title":"Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila","status":"public","article_processing_charge":"No","day":"01","scopus_import":1,"date_published":"2013-10-01T00:00:00Z","citation":{"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.","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.","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","ista":"Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.","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","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."},"publication":"Genetics","page":"527-540"},{"language":[{"iso":"eng"}],"doi":"10.1145/2463372.2463470","date_published":"2013-07-01T00:00:00Z","conference":{"location":"Amsterdam, Netherlands","start_date":"2013-07-06","end_date":"2013-07-10","name":"GECCO: Genetic and evolutionary computation conference"},"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"page":"845 - 852","quality_controlled":"1","citation":{"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.","short":"T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 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.","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.","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","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.","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"},"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","month":"07","day":"01","scopus_import":1,"oa_version":"None","date_updated":"2021-01-12T06:59:15Z","date_created":"2018-12-11T11:59:15Z","author":[{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publisher":"ACM","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"title":"A variance decomposition approach to the analysis of genetic algorithms","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2719","year":"2013","publist_id":"4173","ec_funded":1,"abstract":[{"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.","lang":"eng"}],"type":"conference"},{"publist_id":"4107","publisher":"Springer","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2013","volume":152,"date_created":"2018-12-11T11:59:34Z","date_updated":"2021-01-12T06:59:41Z","author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"last_name":"Farrell","first_name":"Brendan","full_name":"Farrell, Brendan"}],"month":"07","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1207.0031","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1207.0031"]},"language":[{"iso":"eng"}],"doi":"10.1007/s10955-013-0807-8","type":"journal_article","issue":"6","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."}],"intvolume":" 152","status":"public","title":"Local eigenvalue density for general MANOVA matrices","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2782","oa_version":"Preprint","scopus_import":1,"day":"18","page":"1003 - 1032","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","ista":"Erdös L, Farrell B. 2013. Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. 152(6), 1003–1032.","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","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.","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.","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."},"publication":"Journal of Statistical Physics","date_published":"2013-07-18T00:00:00Z"},{"page":"2279 - 2375","quality_controlled":0,"citation":{"short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Annals of Probability 41 (2013) 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.","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.","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","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.","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","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."},"main_file_link":[{"url":"http://arxiv.org/abs/1103.1919","open_access":"1"}],"oa":1,"publication":"Annals of Probability","date_published":"2013-05-01T00:00:00Z","doi":"10.1214/11-AOP734","day":"01","month":"05","publisher":"Institute of Mathematical Statistics","intvolume":" 41","title":"Spectral statistics of Erdős-Rényi graphs I: Local semicircle law","publication_status":"published","status":"public","year":"2013","_id":"2781","volume":41,"date_created":"2018-12-11T11:59:34Z","date_updated":"2021-01-12T06:59:41Z","author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"László Erdös"},{"last_name":"Knowles","first_name":"Antti","full_name":"Knowles, Antti"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng-Tzer"},{"full_name":"Yin, Jun","last_name":"Yin","first_name":"Jun"}],"type":"journal_article","extern":1,"issue":"3 B","publist_id":"4109","abstract":[{"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.","lang":"eng"}]},{"month":"12","day":"01","citation":{"ista":"Erdös L, Knowles A, Yau H. 2013. Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. 14(8), 1837–1926.","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.","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","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","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.","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."},"main_file_link":[{"url":"http://arxiv.org/abs/1205.5664","open_access":"1"}],"oa":1,"publication":"Annales Henri Poincare","page":"1837 - 1926","quality_controlled":0,"date_published":"2013-12-01T00:00:00Z","doi":"10.1007/s00023-013-0235-y","type":"journal_article","issue":"8","publist_id":"4110","abstract":[{"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).","lang":"eng"}],"extern":1,"year":"2013","_id":"2780","publisher":"Birkhäuser","intvolume":" 14","title":"Averaging fluctuations in resolvents of random band matrices","status":"public","publication_status":"published","author":[{"full_name":"László Erdös","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"last_name":"Knowles","first_name":"Antti","full_name":"Knowles, Antti"},{"full_name":"Yau, Horng-Tzer","last_name":"Yau","first_name":"Horng"}],"volume":14,"date_updated":"2021-01-12T06:59:40Z","date_created":"2018-12-11T11:59:33Z"},{"scopus_import":1,"has_accepted_license":"1","day":"01","page":"595 - 604","citation":{"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.","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.","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.","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","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.","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","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."},"publication":"45th Annual ACM Symposium on theory of computing","date_published":"2013-06-01T00:00:00Z","type":"conference","abstract":[{"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. ","lang":"eng"}],"status":"public","ddc":["510"],"title":"Extending continuous maps: Polynomiality and undecidability","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2807","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2016-533-v1+1_Extending_continuous_maps_polynomiality_and_undecidability.pdf","file_size":447945,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5081","checksum":"06c2ce5c1135fbc1f71ca15eeb242dcf","date_updated":"2020-07-14T12:45:48Z","date_created":"2018-12-12T10:14:29Z"}],"pubrep_id":"533","month":"06","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/2488608.2488683","conference":{"name":"STOC: Symposium on the Theory of Computing","location":"Palo Alto, CA, United States","start_date":"2013-06-01","end_date":"2013-06-04"},"publist_id":"4078","file_date_updated":"2020-07-14T12:45:48Z","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publisher":"ACM","publication_status":"published","year":"2013","date_updated":"2021-01-12T06:59:51Z","date_created":"2018-12-11T11:59:42Z","author":[{"full_name":"Čadek, Martin","first_name":"Martin","last_name":"Čadek"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál","first_name":"Marek","full_name":"Krcál, Marek"},{"full_name":"Matoušek, Jiří","last_name":"Matoušek","first_name":"Jiří"},{"last_name":"Vokřínek","first_name":"Lukáš","full_name":"Vokřínek, Lukáš"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}]},{"page":"1406 - 1419","citation":{"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.","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.","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","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.","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","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."},"publication":"Plant Physiology","date_published":"2013-07-03T00:00:00Z","scopus_import":1,"day":"03","intvolume":" 162","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","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2808","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","external_id":{"pmid":["23669745"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707547/"}],"language":[{"iso":"eng"}],"doi":"10.1104/pp.113.214023","month":"07","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2013","volume":162,"date_updated":"2021-01-12T06:59:51Z","date_created":"2018-12-11T11:59:42Z","author":[{"full_name":"Landberg, Katarina","first_name":"Katarina","last_name":"Landberg"},{"first_name":"Eric","last_name":"Pederson","full_name":"Pederson, Eric"},{"last_name":"Viaene","first_name":"Tom","full_name":"Viaene, Tom"},{"first_name":"Behruz","last_name":"Bozorg","full_name":"Bozorg, Behruz"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jönsson, Henrik","last_name":"Jönsson","first_name":"Henrik"},{"full_name":"Thelander, Mattias","first_name":"Mattias","last_name":"Thelander"},{"full_name":"Sundberg, Eva","last_name":"Sundberg","first_name":"Eva"}],"publist_id":"4079"},{"scopus_import":1,"month":"06","day":"06","quality_controlled":"1","citation":{"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.","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","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.","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","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.","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)."},"publication":"Review of Scientific Instruments","language":[{"iso":"eng"}],"date_published":"2013-06-06T00:00:00Z","doi":"10.1063/1.4807704","type":"journal_article","article_number":"065106","issue":"6","publist_id":"4081","abstract":[{"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.","lang":"eng"}],"publisher":"American Institute of Physics","department":[{"_id":"BjHo"}],"intvolume":" 84","publication_status":"published","title":"High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects","status":"public","_id":"2806","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":84,"date_updated":"2021-01-12T06:59:50Z","date_created":"2018-12-11T11:59:42Z","author":[{"full_name":"Avila, Kerstin","first_name":"Kerstin","last_name":"Avila"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}]},{"type":"journal_article","extern":1,"publist_id":"4084","abstract":[{"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.","lang":"eng"}],"intvolume":" 723","publisher":"Cambridge University Press","title":"Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow","status":"public","publication_status":"published","year":"2013","_id":"2805","volume":723,"date_created":"2018-12-11T11:59:41Z","date_updated":"2021-01-12T06:59:50Z","author":[{"first_name":"Markus","last_name":"Holzner","full_name":"Holzner, Markus"},{"full_name":"Song, Baofang","first_name":"Baofang","last_name":"Song"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"},{"full_name":"Björn Hof","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"month":"05","day":"01","page":"140 - 162","quality_controlled":0,"citation":{"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.","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.","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","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.","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.","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"},"publication":"Journal of Fluid Mechanics","date_published":"2013-05-01T00:00:00Z","doi":"10.1017/jfm.2013.127"},{"scopus_import":1,"has_accepted_license":"1","day":"27","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","ista":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence of genetic constraint. PLoS Genetics. 9(6), e1003580.","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.","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","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).","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."},"publication":"PLoS Genetics","date_published":"2013-06-27T00:00:00Z","type":"journal_article","issue":"6","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."}],"intvolume":" 9","title":"Environmental dependence of genetic constraint","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2810","oa_version":"Published Version","file":[{"file_size":474655,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-412-v1+1_journal.pgen.1003580.pdf","checksum":"7a4736dd80496d29ff6908b6f2329b4e","date_created":"2018-12-12T10:08:51Z","date_updated":"2020-07-14T12:45:48Z","relation":"main_file","file_id":"4713"}],"pubrep_id":"412","month":"06","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1003580","article_number":"e1003580","publist_id":"4075","file_date_updated":"2020-07-14T12:45:48Z","publisher":"Public Library of Science","department":[{"_id":"ToBo"}],"publication_status":"published","year":"2013","volume":9,"date_updated":"2021-01-12T06:59:52Z","date_created":"2018-12-11T11:59:43Z","author":[{"full_name":"De Vos, Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos","first_name":"Marjon"},{"last_name":"Poelwijk","first_name":"Frank","full_name":"Poelwijk, Frank"},{"last_name":"Battich","first_name":"Nico","full_name":"Battich, Nico"},{"full_name":"Ndika, Joseph","last_name":"Ndika","first_name":"Joseph"},{"full_name":"Tans, Sander","last_name":"Tans","first_name":"Sander"}]},{"status":"public","title":"The complexity of coverage","intvolume":" 24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2814","oa_version":"Preprint","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"2","page":"165 - 185","publication":"International Journal of Foundations of Computer Science","citation":{"ista":"Chatterjee K, Alfaro L, Majumdar R. 2013. The complexity of coverage. International Journal of Foundations of Computer Science. 24(2), 165–185.","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.","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","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","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.","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_published":"2013-02-01T00:00:00Z","scopus_import":1,"day":"01","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"World Scientific Publishing","year":"2013","date_updated":"2021-01-12T06:59:54Z","date_created":"2018-12-11T11:59:44Z","volume":24,"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Alfaro, Luca","first_name":"Luca","last_name":"Alfaro"},{"full_name":"Majumdar, Ritankar","last_name":"Majumdar","first_name":"Ritankar"}],"publist_id":"4070","ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"external_id":{"arxiv":["0804.4525"]},"main_file_link":[{"url":"https://arxiv.org/abs/0804.4525","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1142/S0129054113400066","month":"02"},{"year":"2013","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"American Institute of Physics","author":[{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"date_created":"2018-12-11T11:59:43Z","date_updated":"2021-01-12T06:59:53Z","volume":87,"article_number":"063012","ec_funded":1,"publist_id":"4074","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1306.5890","open_access":"1"}],"external_id":{"arxiv":["1306.5890"]},"quality_controlled":"1","project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7"}],"doi":"10.1103/PhysRevE.87.063012","language":[{"iso":"eng"}],"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2811","status":"public","title":"Nature of laminar-turbulence intermittency in shear flows","intvolume":" 87","oa_version":"Preprint","type":"journal_article","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."}],"issue":"6","publication":"Physical Review E","citation":{"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.","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).","ista":"Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 87(6), 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.","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","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"},"date_published":"2013-06-18T00:00:00Z","scopus_import":1,"day":"18"}]