--- _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 license: https://creativecommons.org/licenses/by/4.0/ 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' ...