--- _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 license: https://creativecommons.org/licenses/by/4.0/ month: '10' oa: 1 oa_version: Published Version page: 26 - 34 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '3984' pubrep_id: '400' quality_controlled: '1' scopus_import: 1 status: public title: Density games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 334 year: '2013' ... --- _id: '2819' abstract: - lang: eng text: 'We introduce quantatitive timed refinement metrics and quantitative timed simulation functions, incorporating zenoness checks, for timed systems. These functions assign positive real numbers between zero and infinity which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximum timing mismatch that can arise, (2) the "steady-state" maximum timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation functions to within any desired degree of accuracy. In order to compute the values of the quantitative simulation functions, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives for player 1, and then use these algorithms to compute the values of the quantitative timed simulation functions. ' acknowledgement: 'This work has been financially supported in part by the European Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract # 270180 (NOP-TILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008 (Modeling and control of Networked vehicle systems in persistent autonomous operations); by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start grant (279307: Graph Games); and the Microsoft faculty fellows award' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vinayak full_name: Prabhu, Vinayak last_name: Prabhu citation: ama: 'Chatterjee K, Prabhu V. Quantitative timed simulation functions and refinement metrics for real-time systems. In: Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. Vol 1. Springer; 2013:273-282. doi:10.1145/2461328.2461370' apa: 'Chatterjee, K., & Prabhu, V. (2013). Quantitative timed simulation functions and refinement metrics for real-time systems. In Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control (Vol. 1, pp. 273–282). Philadelphia, PA USA: Springer. https://doi.org/10.1145/2461328.2461370' chicago: 'Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” In Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, 1:273–82. Springer, 2013. https://doi.org/10.1145/2461328.2461370.' ieee: 'K. Chatterjee and V. Prabhu, “Quantitative timed simulation functions and refinement metrics for real-time systems,” in Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Philadelphia, PA USA, 2013, vol. 1, pp. 273–282.' ista: 'Chatterjee K, Prabhu V. 2013. Quantitative timed simulation functions and refinement metrics for real-time systems. Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control vol. 1, 273–282.' mla: 'Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, vol. 1, Springer, 2013, pp. 273–82, doi:10.1145/2461328.2461370.' short: 'K. Chatterjee, V. Prabhu, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Springer, 2013, pp. 273–282.' conference: end_date: 2013-04-11 location: Philadelphia, PA USA name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2013-04-08 date_created: 2018-12-11T11:59:46Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T06:59:56Z day: '01' department: - _id: KrCh doi: 10.1145/2461328.2461370 ec_funded: 1 intvolume: ' 1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1212.6556 month: '04' oa: 1 oa_version: Preprint page: 273 - 282 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: 'Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control' publication_status: published publisher: Springer publist_id: '3982' quality_controlled: '1' scopus_import: 1 status: public title: Quantitative timed simulation functions and refinement metrics for real-time systems type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2013' ... --- _id: '2818' abstract: - lang: eng text: Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory–based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus. author: - first_name: Kanaka full_name: Rajan, Kanaka last_name: Rajan - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692. doi:10.1162/NECO_a_00463 apa: Rajan, K., Marre, O., & Tkačik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. MIT Press . https://doi.org/10.1162/NECO_a_00463 chicago: Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation. MIT Press , 2013. https://doi.org/10.1162/NECO_a_00463. ieee: K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” Neural Computation, vol. 25, no. 7. MIT Press , pp. 1661–1692, 2013. ista: Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692. mla: Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:10.1162/NECO_a_00463. short: K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692. date_created: 2018-12-11T11:59:45Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:59:56Z day: '01' department: - _id: GaTk doi: 10.1162/NECO_a_00463 external_id: arxiv: - '1209.0121' intvolume: ' 25' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.0121 month: '07' oa: 1 oa_version: Preprint page: 1661 - 1692 publication: Neural Computation publication_status: published publisher: 'MIT Press ' publist_id: '3983' quality_controlled: '1' scopus_import: 1 status: public title: Learning quadratic receptive fields from neural responses to natural stimuli type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '2826' abstract: - lang: eng text: Myopia, or near-sightedness, is an ocular refractive error of unfocused image quality in front of the retinal plane. Individuals with high-grade myopia (dioptric power greater than -6.00) are predisposed to ocular morbidities such as glaucoma, retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is highly heritable, and to date multiple gene loci have been reported. We performed exome sequencing in 4 individuals from an 11-member family of European descent from the United States. Affected individuals had a mean dioptric spherical equivalent of -22.00 sphere. A premature stop codon mutation c.157C>T (p.Gln53*) cosegregating with disease was discovered within SCO2 that maps to chromosome 22q13.33. Subsequent analyses identified three additional mutations in three highly myopic unrelated individuals (c.341G>A, c.418G>A, and c.776C>T). To determine differential gene expression in a developmental mouse model, we induced myopia by applying a -15.00D lens over one eye. Messenger RNA levels of SCO2 were significantly downregulated in myopic mouse retinae. Immunohistochemistry in mouse eyes confirmed SCO2 protein localization in retina, retinal pigment epithelium, and sclera. SCO2 encodes for a copper homeostasis protein influential in mitochondrial cytochrome c oxidase activity. Copper deficiencies have been linked with photoreceptor loss and myopia with increased scleral wall elasticity. Retinal thinning has been reported with an SC02 variant. Human mutation identification with support from an induced myopic animal provides biological insights of myopic development. author: - first_name: Khanh full_name: Tran Viet, Khanh last_name: Tran Viet - first_name: Caldwell full_name: Powell, Caldwell last_name: Powell - first_name: Veluchamy full_name: Barathi, Veluchamy last_name: Barathi - first_name: Thomas full_name: Klemm, Thomas last_name: Klemm - first_name: Sebastian full_name: Maurer Stroh, Sebastian last_name: Maurer Stroh - first_name: Vachiranee full_name: Limviphuvadh, Vachiranee last_name: Limviphuvadh - first_name: Vincent full_name: Soler, Vincent last_name: Soler - first_name: Candice full_name: Ho, Candice last_name: Ho - first_name: Tammy full_name: Yanovitch, Tammy last_name: Yanovitch - first_name: Georg full_name: Schneider, Georg id: 329095A0-F248-11E8-B48F-1D18A9856A87 last_name: Schneider - first_name: Yi full_name: Li, Yi last_name: Li - first_name: Erica full_name: Nading, Erica last_name: Nading - first_name: Ravikanth full_name: Metlapally, Ravikanth last_name: Metlapally - first_name: Seang full_name: Saw, Seang last_name: Saw - first_name: Liang full_name: Goh, Liang last_name: Goh - first_name: Steve full_name: Rozen, Steve last_name: Rozen - first_name: Terri full_name: Young, Terri last_name: Young citation: ama: Tran Viet K, Powell C, Barathi V, et al. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. 2013;92(5):820-826. doi:10.1016/j.ajhg.2013.04.005 apa: Tran Viet, K., Powell, C., Barathi, V., Klemm, T., Maurer Stroh, S., Limviphuvadh, V., … Young, T. (2013). Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. Cell Press. https://doi.org/10.1016/j.ajhg.2013.04.005 chicago: Tran Viet, Khanh, Caldwell Powell, Veluchamy Barathi, Thomas Klemm, Sebastian Maurer Stroh, Vachiranee Limviphuvadh, Vincent Soler, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia.” American Journal of Human Genetics. Cell Press, 2013. https://doi.org/10.1016/j.ajhg.2013.04.005. ieee: K. Tran Viet et al., “Mutations in SCO2 are associated with autosomal-dominant high-grade myopia,” American Journal of Human Genetics, vol. 92, no. 5. Cell Press, pp. 820–826, 2013. ista: Tran Viet K, Powell C, Barathi V, Klemm T, Maurer Stroh S, Limviphuvadh V, Soler V, Ho C, Yanovitch T, Schneider G, Li Y, Nading E, Metlapally R, Saw S, Goh L, Rozen S, Young T. 2013. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. 92(5), 820–826. mla: Tran Viet, Khanh, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia.” American Journal of Human Genetics, vol. 92, no. 5, Cell Press, 2013, pp. 820–26, doi:10.1016/j.ajhg.2013.04.005. short: K. Tran Viet, C. Powell, V. Barathi, T. Klemm, S. Maurer Stroh, V. Limviphuvadh, V. Soler, C. Ho, T. Yanovitch, G. Schneider, Y. Li, E. Nading, R. Metlapally, S. Saw, L. Goh, S. Rozen, T. Young, American Journal of Human Genetics 92 (2013) 820–826. date_created: 2018-12-11T11:59:48Z date_published: 2013-05-02T00:00:00Z date_updated: 2021-01-12T06:59:59Z day: '02' department: - _id: MD doi: 10.1016/j.ajhg.2013.04.005 external_id: pmid: - '23643385' intvolume: ' 92' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644634/ month: '05' oa: 1 oa_version: Submitted Version page: 820 - 826 pmid: 1 publication: American Journal of Human Genetics publication_status: published publisher: Cell Press publist_id: '3974' quality_controlled: '1' scopus_import: 1 status: public title: Mutations in SCO2 are associated with autosomal-dominant high-grade myopia type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2013' ... --- _id: '2822' abstract: - lang: eng text: Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala x Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops. author: - first_name: Christopher full_name: Topp, Christopher last_name: Topp - first_name: Anjali full_name: Iyer Pascuzzi, Anjali last_name: Iyer Pascuzzi - first_name: Jill full_name: Anderson, Jill last_name: Anderson - first_name: Cheng full_name: Lee, Cheng last_name: Lee - first_name: Paul full_name: Zurek, Paul last_name: Zurek - first_name: Olga full_name: Symonova, Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova - first_name: Ying full_name: Zheng, Ying last_name: Zheng - first_name: Alexander full_name: Bucksch, Alexander last_name: Bucksch - first_name: Yuriy full_name: Mileyko, Yuriy last_name: Mileyko - first_name: Taras full_name: Galkovskyi, Taras last_name: Galkovskyi - first_name: Brad full_name: Moore, Brad last_name: Moore - first_name: John full_name: Harer, John last_name: Harer - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Thomas full_name: Mitchell Olds, Thomas last_name: Mitchell Olds - first_name: Joshua full_name: Weitz, Joshua last_name: Weitz - first_name: Philip full_name: Benfey, Philip last_name: Benfey citation: ama: Topp C, Iyer Pascuzzi A, Anderson J, et al. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 2013;110(18):E1695-E1704. doi:10.1073/pnas.1304354110 apa: Topp, C., Iyer Pascuzzi, A., Anderson, J., Lee, C., Zurek, P., Symonova, O., … Benfey, P. (2013). 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1304354110 chicago: Topp, Christopher, Anjali Iyer Pascuzzi, Jill Anderson, Cheng Lee, Paul Zurek, Olga Symonova, Ying Zheng, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1304354110. ieee: C. Topp et al., “3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture,” PNAS, vol. 110, no. 18. National Academy of Sciences, pp. E1695–E1704, 2013. ista: Topp C, Iyer Pascuzzi A, Anderson J, Lee C, Zurek P, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore B, Harer J, Edelsbrunner H, Mitchell Olds T, Weitz J, Benfey P. 2013. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 110(18), E1695–E1704. mla: Topp, Christopher, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS, vol. 110, no. 18, National Academy of Sciences, 2013, pp. E1695–704, doi:10.1073/pnas.1304354110. short: C. Topp, A. Iyer Pascuzzi, J. Anderson, C. Lee, P. Zurek, O. Symonova, Y. Zheng, A. Bucksch, Y. Mileyko, T. Galkovskyi, B. Moore, J. Harer, H. Edelsbrunner, T. Mitchell Olds, J. Weitz, P. Benfey, PNAS 110 (2013) E1695–E1704. date_created: 2018-12-11T11:59:47Z date_published: 2013-04-30T00:00:00Z date_updated: 2021-01-12T06:59:58Z day: '30' department: - _id: MaJö - _id: HeEd doi: 10.1073/pnas.1304354110 external_id: pmid: - '25673779' intvolume: ' 110' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378147/ month: '04' oa: 1 oa_version: Submitted Version page: E1695 - E1704 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3979' quality_controlled: '1' scopus_import: 1 status: public title: 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2821' abstract: - lang: eng text: Many key aspects of plant development are regulated by the polarized transport of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this process, has been shown to rely on the coordinated action of PIN-formed (PIN) and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin transport in the Arabidopsis thaliana root also requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during shootward auxin transport at the root tip, likely by regulating plasma membrane PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1 and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular and tissue distribution of two isoforms, alternative splicing dictates a dual function for the ZIFL1 transporter. We propose that this MFS carrier regulates stomatal movements and polar auxin transport by modulating potassium and proton fluxes in Arabidopsis cells. author: - first_name: Estelle full_name: Remy, Estelle last_name: Remy - first_name: Tânia full_name: Cabrito, Tânia last_name: Cabrito - first_name: Pawel full_name: Baster, Pawel id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Rita full_name: Batista, Rita last_name: Batista - first_name: Miguel full_name: Teixeira, Miguel last_name: Teixeira - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Isabel full_name: Sá Correia, Isabel last_name: Sá Correia - first_name: Paula full_name: Duque, Paula last_name: Duque citation: ama: Remy E, Cabrito T, Baster P, et al. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. 2013;25(3):901-926. doi:10.1105/tpc.113.110353 apa: Remy, E., Cabrito, T., Baster, P., Batista, R., Teixeira, M., Friml, J., … Duque, P. (2013). A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.110353 chicago: Remy, Estelle, Tânia Cabrito, Pawel Baster, Rita Batista, Miguel Teixeira, Jiří Friml, Isabel Sá Correia, and Paula Duque. “A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.110353. ieee: E. Remy et al., “A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis,” Plant Cell, vol. 25, no. 3. American Society of Plant Biologists, pp. 901–926, 2013. ista: Remy E, Cabrito T, Baster P, Batista R, Teixeira M, Friml J, Sá Correia I, Duque P. 2013. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. 25(3), 901–926. mla: Remy, Estelle, et al. “A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.” Plant Cell, vol. 25, no. 3, American Society of Plant Biologists, 2013, pp. 901–26, doi:10.1105/tpc.113.110353. short: E. Remy, T. Cabrito, P. Baster, R. Batista, M. Teixeira, J. Friml, I. Sá Correia, P. Duque, Plant Cell 25 (2013) 901–926. date_created: 2018-12-11T11:59:46Z date_published: 2013-04-24T00:00:00Z date_updated: 2021-01-12T06:59:57Z day: '24' department: - _id: JiFr doi: 10.1105/tpc.113.110353 external_id: pmid: - '23524662' intvolume: ' 25' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634696/ month: '04' oa: 1 oa_version: Submitted Version page: 901 - 926 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3980' quality_controlled: '1' scopus_import: 1 status: public title: A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '2827' abstract: - lang: eng text: Removal of cargos from the cell surface via endocytosis is an efficient mechanism to regulate activities of plasma membrane (PM)-resident proteins, such as receptors or transporters. Salicylic acid (SA) is an important plant hormone that is traditionally associated with pathogen defense. Here, we describe an unanticipated effect of SA on subcellular endocytic cycling of proteins. Both exogenous treatments and endogenously enhanced SA levels repressed endocytosis of different PM proteins. The SA effect on endocytosis did not involve transcription or known components of the SA signaling pathway for transcriptional regulation. SA likely targets an endocytic mechanism that involves the coat protein clathrin, because SA interfered with the clathrin incidence at the PM and clathrin-deficient mutants were less sensitive to the impact of SA on the auxin distribution and root bending during the gravitropic response. By contrast, SA did not affect the ligand-induced endocytosis of the FLAGELLIN SENSING2 (FLS2) receptor during pathogen responses. Our data suggest that the established SA impact on transcription in plant immunity and the nontranscriptional effect of SA on clathrin-mediated endocytosis are independent mechanisms by which SA regulates distinct aspects of plant physiology. author: - first_name: Yunlong full_name: Du, Yunlong last_name: Du - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Martina full_name: Beck, Martina last_name: Beck - first_name: Ellie full_name: Himschoot, Ellie last_name: Himschoot - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Silke full_name: Robatzek, Silke last_name: Robatzek - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Du Y, Tejos R, Beck M, et al. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. 2013;110(19):7946-7951. doi:10.1073/pnas.1220205110 apa: Du, Y., Tejos, R., Beck, M., Himschoot, E., Li, H., Robatzek, S., … Friml, J. (2013). Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1220205110 chicago: Du, Yunlong, Ricardo Tejos, Martina Beck, Ellie Himschoot, Hongjiang Li, Silke Robatzek, Steffen Vanneste, and Jiří Friml. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic Protein Trafficking.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1220205110. ieee: Y. Du et al., “Salicylic acid interferes with clathrin-mediated endocytic protein trafficking,” PNAS, vol. 110, no. 19. National Academy of Sciences, pp. 7946–7951, 2013. ista: Du Y, Tejos R, Beck M, Himschoot E, Li H, Robatzek S, Vanneste S, Friml J. 2013. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. 110(19), 7946–7951. mla: Du, Yunlong, et al. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic Protein Trafficking.” PNAS, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7946–51, doi:10.1073/pnas.1220205110. short: Y. Du, R. Tejos, M. Beck, E. Himschoot, H. Li, S. Robatzek, S. Vanneste, J. Friml, PNAS 110 (2013) 7946–7951. date_created: 2018-12-11T11:59:48Z date_published: 2013-05-07T00:00:00Z date_updated: 2021-01-12T06:59:59Z day: '07' department: - _id: JiFr doi: 10.1073/pnas.1220205110 external_id: pmid: - '23613581' intvolume: ' 110' issue: '19' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651428/ month: '05' oa: 1 oa_version: Submitted Version page: 7946 - 7951 pmid: 1 project: - _id: 2574781E-B435-11E9-9278-68D0E5697425 name: Koerber Prize 2010 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3972' quality_controlled: '1' scopus_import: 1 status: public title: Salicylic acid interferes with clathrin-mediated endocytic protein trafficking type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2823' abstract: - lang: eng text: The primary goal of restoration is to create self-sustaining ecological communities that are resilient to periodic disturbance. Currently, little is known about how restored communities respond to disturbance events such as fire and how this response compares to remnant vegetation. Following the 2003 fires in south-eastern Australia we examined the post-fire response of revegetation plantings and compared this to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed for each of three types of vegetation (direct seeding revegetation, revegetation using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites were surveyed 6months after fire to quantify the initial survival of mid- and overstorey plant species in each type of vegetation. Three and 5years after fire all sites were resurveyed to assess vegetation structure, species diversity and vigour, as well as indicators of soil function. Overall, revegetation showed high (>60%) post-fire survival, but this varied among species depending on regeneration strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey in both types of plantings showed rapid recovery of vegetation structure and cover within 3years of fire. This recovery was similar to the burnt remnant woodlands. Non-native (exotic) ground cover initially increased after fire, but was no different in burnt and unburnt sites 5years after fire. Fire had no effect on species richness, but burnt direct seeding sites had reduced species diversity (Simpson's Diversity Index) while diversity was higher in burnt remnant woodlands. Indices of soil function in all types of vegetation had recovered to levels found in unburnt sites 5years after fire. These results indicate that even young revegetation (stands <10years old) showed substantial recovery from disturbance by fire. This suggests that revegetation can provide an important basis for restoring woodland communities in the fire-prone Australian environment. author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Susie full_name: Wilson, Susie last_name: Wilson - first_name: David full_name: Freudenberger, David last_name: Freudenberger - first_name: Nick full_name: Nicholls, Nick last_name: Nicholls - first_name: Lori full_name: Gould, Lori last_name: Gould - first_name: Sarah full_name: Hnatiuk, Sarah last_name: Hnatiuk - first_name: Jeni full_name: Delandre, Jeni last_name: Delandre citation: ama: Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312. doi:10.1111/j.1442-9993.2012.02404.x apa: Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x chicago: Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x. ieee: M. Pickup et al., “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013. ista: Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 38(3), 300–312. mla: Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x. short: M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312. date_created: 2018-12-11T11:59:47Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T06:59:58Z day: '01' department: - _id: NiBa doi: 10.1111/j.1442-9993.2012.02404.x intvolume: ' 38' issue: '3' language: - iso: eng month: '05' oa_version: None page: 300 - 312 publication: Austral Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3978' quality_controlled: '1' scopus_import: 1 status: public title: Post-fire recovery of revegetated woodland communities in south-eastern Australia type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2013' ... --- _id: '2824' abstract: - lang: eng text: We study synthesis of controllers for real-time systems, where the objective is to stay in a given safe set. The problem is solved by obtaining winning strategies in the setting of concurrent two player timed automaton games with safety objectives. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a Zeno run. We construct winning strategies for the controller which require access only to (1) the system clocks (thus, controllers which require their own internal infinitely precise clocks are not necessary), and (2) a logarithmic (in the number of clocks) number of memory bits (i.e. a linear number of memory states). Precisely, we show that for safety objectives, a memory of size (3 + lg (| C | + 1)) bits suffices for winning controller strategies, where C is the set of clocks of the timed automaton game, significantly improving the previous known exponential memory states bound. We also settle the open question of whether winning region-based strategies require memory for safety objectives by showing with an example the necessity of memory for such strategies to win for safety objectives. Finally, we show that the decision problem of determining if there exists a receptive player-1 winning strategy for safety objectives is EXPTIME-complete over timed automaton games. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vinayak full_name: Prabhu, Vinayak last_name: Prabhu citation: ama: Chatterjee K, Prabhu V. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. 2013;228-229:83-119. doi:10.1016/j.ic.2013.04.003 apa: Chatterjee, K., & Prabhu, V. (2013). Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2013.04.003 chicago: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information and Computation. Elsevier, 2013. https://doi.org/10.1016/j.ic.2013.04.003. ieee: K. Chatterjee and V. Prabhu, “Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems,” Information and Computation, vol. 228–229. Elsevier, pp. 83–119, 2013. ista: Chatterjee K, Prabhu V. 2013. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. 228–229, 83–119. mla: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information and Computation, vol. 228–229, Elsevier, 2013, pp. 83–119, doi:10.1016/j.ic.2013.04.003. short: K. Chatterjee, V. Prabhu, Information and Computation 228–229 (2013) 83–119. date_created: 2018-12-11T11:59:47Z date_published: 2013-04-24T00:00:00Z date_updated: 2021-01-12T06:59:58Z day: '24' department: - _id: KrCh doi: 10.1016/j.ic.2013.04.003 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 83-119 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '3977' quality_controlled: '1' scopus_import: 1 status: public title: Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 228-229 year: '2013' ... --- _id: '2832' abstract: - lang: eng text: PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and mediate intercellular polar transport of the plant hormone auxin that is crucial for a multitude of developmental processes in plants. PIN localization is under extensive control by environmental or developmental cues, but mechanisms regulating PIN localization are not fully understood. Here we show that early endosomal components ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively required for polar PIN localization, for their dynamic repolarization, and consequently for auxin activity gradient formation and auxin-related developmental processes including embryonic patterning, organogenesis, and vasculature venation patterning. These results show that early endosomal trafficking is crucial for cell polarity and auxin-dependent regulation of plant architecture. article_number: e1003540 author: - first_name: Hirokazu full_name: Tanaka, Hirokazu last_name: Tanaka - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Hana full_name: Rakusová, Hana last_name: Rakusová - first_name: Tomohiro full_name: Uemura, Tomohiro last_name: Uemura - first_name: Mugurel full_name: Feraru, Mugurel last_name: Feraru - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Tatsuo full_name: Kakimoto, Tatsuo last_name: Kakimoto - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Tanaka H, Kitakura S, Rakusová H, et al. Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 2013;9(5). doi:10.1371/journal.pgen.1003540 apa: Tanaka, H., Kitakura, S., Rakusová, H., Uemura, T., Feraru, M., De Rycke, R., … Friml, J. (2013). Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003540 chicago: Tanaka, Hirokazu, Saeko Kitakura, Hana Rakusová, Tomohiro Uemura, Mugurel Feraru, Riet De Rycke, Stéphanie Robert, Tatsuo Kakimoto, and Jiří Friml. “Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003540. ieee: H. Tanaka et al., “Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana,” PLoS Genetics, vol. 9, no. 5. Public Library of Science, 2013. ista: Tanaka H, Kitakura S, Rakusová H, Uemura T, Feraru M, De Rycke R, Robert S, Kakimoto T, Friml J. 2013. Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 9(5), e1003540. mla: Tanaka, Hirokazu, et al. “Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics, vol. 9, no. 5, e1003540, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003540. short: H. Tanaka, S. Kitakura, H. Rakusová, T. Uemura, M. Feraru, R. De Rycke, S. Robert, T. Kakimoto, J. Friml, PLoS Genetics 9 (2013). date_created: 2018-12-11T11:59:50Z date_published: 2013-05-05T00:00:00Z date_updated: 2021-01-12T07:00:03Z day: '05' ddc: - '570' department: - _id: JiFr doi: 10.1371/journal.pgen.1003540 ec_funded: 1 file: - access_level: open_access checksum: 050237d6c53e8d1601b26808ee1dd6d8 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:39Z date_updated: 2020-07-14T12:45:50Z file_id: '4957' file_name: IST-2016-411-v1+1_journal.pgen.1003540.pdf file_size: 3813091 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 9' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '3967' pubrep_id: '411' quality_controlled: '1' scopus_import: 1 status: public title: Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '2828' abstract: - lang: eng text: 'We study the complexity of valued constraint satisfaction problems (VCSPs) parametrized by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimize the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well understood, see Raghavendra [2008]. However, there is no characterization of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimization perspective. We consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e., relations), such languages have been called conservative and studied by Bulatov [2003, 2011] and recently by Barto [2011]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [2006] for languages over Boolean domains, by Deineko et al. [2008] for {0, 1}-valued languages (a.k.a Max-CSP), and by Takhanov [2010a] for {0, ∞}-valued languages containing all finite-valued unary cost functions (a.k.a. Min-Cost-Hom). We prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimor-phisms), then any instance can be solved in polynomial time (via a new algorithm developed in this article), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains are significantly harder than the Boolean cases. The polynomial-time algorithm we present for the tractable cases is a generalization of the submodular minimization problem and a result of Cohen et al. [2008]. Our results generalize previous results by Takhanov [2010a] and (a subset of results) by Cohen et al. [2006] and Deineko et al. [2008]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [2008], and provide a powerful tool for proving hardness of finite-valued and general-valued languages.' article_number: '10' author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Stanislav full_name: Živný, Stanislav last_name: Živný citation: ama: Kolmogorov V, Živný S. The complexity of conservative valued CSPs. Journal of the ACM. 2013;60(2). doi:10.1145/2450142.2450146 apa: Kolmogorov, V., & Živný, S. (2013). The complexity of conservative valued CSPs. Journal of the ACM. ACM. https://doi.org/10.1145/2450142.2450146 chicago: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs.” Journal of the ACM. ACM, 2013. https://doi.org/10.1145/2450142.2450146. ieee: V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,” Journal of the ACM, vol. 60, no. 2. ACM, 2013. ista: Kolmogorov V, Živný S. 2013. The complexity of conservative valued CSPs. Journal of the ACM. 60(2), 10. mla: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs.” Journal of the ACM, vol. 60, no. 2, 10, ACM, 2013, doi:10.1145/2450142.2450146. short: V. Kolmogorov, S. Živný, Journal of the ACM 60 (2013). date_created: 2018-12-11T11:59:48Z date_published: 2013-04-02T00:00:00Z date_updated: 2021-01-12T07:00:00Z day: '02' department: - _id: VlKo doi: 10.1145/2450142.2450146 external_id: arxiv: - '1110.2809' intvolume: ' 60' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1110.2809 month: '04' oa: 1 oa_version: Preprint publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '3971' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of conservative valued CSPs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2013' ... --- _id: '2829' abstract: - lang: eng text: Laminar-turbulent intermittency is intrinsic to the transitional regime of a wide range of fluid flows including pipe, channel, boundary layer, and Couette flow. In the latter turbulent spots can grow and form continuous stripes, yet in the stripe-normal direction they remain interspersed by laminar fluid. We carry out direct numerical simulations in a long narrow domain and observe that individual turbulent stripes are transient. In agreement with recent observations in pipe flow, we find that turbulence becomes sustained at a distinct critical point once the spatial proliferation outweighs the inherent decaying process. By resolving the asymptotic size distributions close to criticality we can for the first time demonstrate scale invariance at the onset of turbulence. article_number: '204502' author: - first_name: Liang full_name: Shi, Liang id: 374A3F1A-F248-11E8-B48F-1D18A9856A87 last_name: Shi - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Shi L, Avila M, Hof B. Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. 2013;110(20). doi:10.1103/PhysRevLett.110.204502 apa: Shi, L., Avila, M., & Hof, B. (2013). Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.204502 chicago: Shi, Liang, Marc Avila, and Björn Hof. “Scale Invariance at the Onset of Turbulence in Couette Flow.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.204502. ieee: L. Shi, M. Avila, and B. Hof, “Scale invariance at the onset of turbulence in couette flow,” Physical Review Letters, vol. 110, no. 20. American Physical Society, 2013. ista: Shi L, Avila M, Hof B. 2013. Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. 110(20), 204502. mla: Shi, Liang, et al. “Scale Invariance at the Onset of Turbulence in Couette Flow.” Physical Review Letters, vol. 110, no. 20, 204502, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.204502. short: L. Shi, M. Avila, B. Hof, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:59:49Z date_published: 2013-05-13T00:00:00Z date_updated: 2021-01-12T07:00:00Z day: '13' department: - _id: BjHo doi: 10.1103/PhysRevLett.110.204502 ec_funded: 1 external_id: arxiv: - '1304.5446' intvolume: ' 110' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1304.5446 month: '05' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin - _id: 2511D90C-B435-11E9-9278-68D0E5697425 grant_number: SFB 963 TP A8 name: Astrophysical instability of currents and turbulences publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '3970' quality_controlled: '1' scopus_import: 1 status: public title: Scale invariance at the onset of turbulence in couette flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2834' abstract: - lang: eng text: Although the equations governing fluid flow are well known, there are no analytical expressions that describe the complexity of turbulent motion. A recent proposition is that in analogy to low dimensional chaotic systems, turbulence is organized around unstable solutions of the governing equations which provide the building blocks of the disordered dynamics. We report the discovery of periodic solutions which just like intermittent turbulence are spatially localized and show that turbulent transients arise from one such solution branch. article_number: '224502' author: - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Fernando full_name: Mellibovsky, Fernando last_name: Mellibovsky - first_name: Nicolas full_name: Roland, Nicolas last_name: Roland - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Avila M, Mellibovsky F, Roland N, Hof B. Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. 2013;110(22). doi:10.1103/PhysRevLett.110.224502 apa: Avila, M., Mellibovsky, F., Roland, N., & Hof, B. (2013). Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.224502 chicago: Avila, Marc, Fernando Mellibovsky, Nicolas Roland, and Björn Hof. “Streamwise-Localized Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.224502. ieee: M. Avila, F. Mellibovsky, N. Roland, and B. Hof, “Streamwise-localized solutions at the onset of turbulence in pipe flow,” Physical Review Letters, vol. 110, no. 22. American Physical Society, 2013. ista: Avila M, Mellibovsky F, Roland N, Hof B. 2013. Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. 110(22), 224502. mla: Avila, Marc, et al. “Streamwise-Localized Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters, vol. 110, no. 22, 224502, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.224502. short: M. Avila, F. Mellibovsky, N. Roland, B. Hof, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:59:50Z date_published: 2013-05-29T00:00:00Z date_updated: 2021-01-12T07:00:05Z day: '29' department: - _id: BjHo doi: 10.1103/PhysRevLett.110.224502 ec_funded: 1 external_id: arxiv: - '1212.0230' intvolume: ' 110' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1212.0230 month: '05' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '3965' quality_controlled: '1' scopus_import: 1 status: public title: Streamwise-localized solutions at the onset of turbulence in pipe flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2833' abstract: - lang: eng text: During development, mechanical forces cause changes in size, shape, number, position, and gene expression of cells. They are therefore integral to any morphogenetic processes. Force generation by actin-myosin networks and force transmission through adhesive complexes are two self-organizing phenomena driving tissue morphogenesis. Coordination and integration of forces by long-range force transmission and mechanosensing of cells within tissues produce large-scale tissue shape changes. Extrinsic mechanical forces also control tissue patterning by modulating cell fate specification and differentiation. Thus, the interplay between tissue mechanics and biochemical signaling orchestrates tissue morphogenesis and patterning in development. acknowledgement: C.-P.H. is supported by the Institute of Science and Technology Austria and grants from the Deutsche Forschungsgemeinschaft (DFG) and Fonds zur Förderung der wissenschaftlichen Forschung (FWF). author: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Yohanns full_name: Bellaïche, Yohanns last_name: Bellaïche citation: ama: Heisenberg C-PJ, Bellaïche Y. Forces in tissue morphogenesis and patterning. Cell. 2013;153(5):948-962. doi:10.1016/j.cell.2013.05.008 apa: Heisenberg, C.-P. J., & Bellaïche, Y. (2013). Forces in tissue morphogenesis and patterning. Cell. Cell Press. https://doi.org/10.1016/j.cell.2013.05.008 chicago: Heisenberg, Carl-Philipp J, and Yohanns Bellaïche. “Forces in Tissue Morphogenesis and Patterning.” Cell. Cell Press, 2013. https://doi.org/10.1016/j.cell.2013.05.008. ieee: C.-P. J. Heisenberg and Y. Bellaïche, “Forces in tissue morphogenesis and patterning,” Cell, vol. 153, no. 5. Cell Press, pp. 948–962, 2013. ista: Heisenberg C-PJ, Bellaïche Y. 2013. Forces in tissue morphogenesis and patterning. Cell. 153(5), 948–962. mla: Heisenberg, Carl-Philipp J., and Yohanns Bellaïche. “Forces in Tissue Morphogenesis and Patterning.” Cell, vol. 153, no. 5, Cell Press, 2013, pp. 948–62, doi:10.1016/j.cell.2013.05.008. short: C.-P.J. Heisenberg, Y. Bellaïche, Cell 153 (2013) 948–962. date_created: 2018-12-11T11:59:50Z date_published: 2013-05-23T00:00:00Z date_updated: 2021-01-12T07:00:04Z day: '23' department: - _id: CaHe doi: 10.1016/j.cell.2013.05.008 intvolume: ' 153' issue: '5' language: - iso: eng month: '05' oa_version: None page: 948 - 962 publication: Cell publication_status: published publisher: Cell Press publist_id: '3966' quality_controlled: '1' scopus_import: 1 status: public title: Forces in tissue morphogenesis and patterning type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 153 year: '2013' ... --- _id: '2830' author: - first_name: Christine full_name: Moussion, Christine id: 3356F664-F248-11E8-B48F-1D18A9856A87 last_name: Moussion - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Moussion C, Sixt MK. A conduit to amplify innate immunity. Immunity. 2013;38(5):853-854. doi:10.1016/j.immuni.2013.05.005 apa: Moussion, C., & Sixt, M. K. (2013). A conduit to amplify innate immunity. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2013.05.005 chicago: Moussion, Christine, and Michael K Sixt. “A Conduit to Amplify Innate Immunity.” Immunity. Cell Press, 2013. https://doi.org/10.1016/j.immuni.2013.05.005. ieee: C. Moussion and M. K. Sixt, “A conduit to amplify innate immunity,” Immunity, vol. 38, no. 5. Cell Press, pp. 853–854, 2013. ista: Moussion C, Sixt MK. 2013. A conduit to amplify innate immunity. Immunity. 38(5), 853–854. mla: Moussion, Christine, and Michael K. Sixt. “A Conduit to Amplify Innate Immunity.” Immunity, vol. 38, no. 5, Cell Press, 2013, pp. 853–54, doi:10.1016/j.immuni.2013.05.005. short: C. Moussion, M.K. Sixt, Immunity 38 (2013) 853–854. date_created: 2018-12-11T11:59:49Z date_published: 2013-05-23T00:00:00Z date_updated: 2021-01-12T07:00:01Z day: '23' department: - _id: MiSi doi: 10.1016/j.immuni.2013.05.005 intvolume: ' 38' issue: '5' language: - iso: eng month: '05' oa_version: None page: 853 - 854 publication: Immunity publication_status: published publisher: Cell Press publist_id: '3969' quality_controlled: '1' scopus_import: 1 status: public title: A conduit to amplify innate immunity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2013' ... --- _id: '2842' abstract: - lang: eng text: 'We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ2, based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FS T) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a ''local scale'', κ; the rate of gene flow, σ2, cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ2. With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ2.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: 'Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001' apa: 'Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001' chicago: 'Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.' ieee: 'N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.' ista: 'Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 87(1), 105–119.' mla: 'Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology, vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.' short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 105–119. date_created: 2018-12-11T11:59:53Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T07:00:09Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1016/j.tpb.2013.03.001 ec_funded: 1 file: - access_level: open_access checksum: 9bf9d9a6fd03dd9df50906891f393bf8 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:33Z date_updated: 2020-07-14T12:45:50Z file_id: '5288' file_name: IST-2016-558-v1+1_inference_revised3101NB.pdf file_size: 1554712 relation: main_file - access_level: open_access checksum: 2bceddb76edacd0cd5fad73051e2a928 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:34Z date_updated: 2020-07-14T12:45:50Z file_id: '5289' file_name: IST-2016-558-v1+2_inference_revised3101NBApp.pdf file_size: 822964 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 87' issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 105 - 119 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Theoretical Population Biology publication_status: published publisher: Elsevier publist_id: '3953' pubrep_id: '558' quality_controlled: '1' scopus_import: 1 status: public title: 'Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2013' ... --- _id: '2838' abstract: - lang: eng text: Individuals with Down syndrome (DS) present important motor deficits that derive from altered motor development of infants and young children. DYRK1A, a candidate gene for DS abnormalities has been implicated in motor function due to its expression in motor nuclei in the adult brain, and its overexpression in DS mouse models leads to hyperactivity and altered motor learning. However, its precise role in the adult motor system, or its possible involvement in postnatal locomotor development has not yet been clarified. During the postnatal period we observed time-specific expression of Dyrk1A in discrete subsets of brainstem nuclei and spinal cord motor neurons. Interestingly, we describe for the first time the presence of Dyrk1A in the presynaptic terminal of the neuromuscular junctions and its axonal transport from the facial nucleus, suggesting a function for Dyrk1A in these structures. Relevant to DS, Dyrk1A overexpression in transgenic mice (TgDyrk1A) produces motor developmental alterations possibly contributing to DS motor phenotypes and modifies the numbers of motor cholinergic neurons, suggesting that the kinase may have a role in the development of the brainstem and spinal cord motor system. article_number: e54285 author: - first_name: Gloria full_name: Arquè Fuste, Gloria id: 3CF33908-F248-11E8-B48F-1D18A9856A87 last_name: Arquè Fuste - first_name: Anna full_name: Casanovas, Anna last_name: Casanovas - first_name: Mara full_name: Dierssen, Mara last_name: Dierssen citation: ama: 'Arquè Fuste G, Casanovas A, Dierssen M. Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. 2013;8(1). doi:10.1371/journal.pone.0054285' apa: 'Arquè Fuste, G., Casanovas, A., & Dierssen, M. (2013). Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0054285' chicago: 'Arquè Fuste, Gloria, Anna Casanovas, and Mara Dierssen. “Dyrk1A Is Dynamically Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0054285.' ieee: 'G. Arquè Fuste, A. Casanovas, and M. Dierssen, “Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome,” PLoS One, vol. 8, no. 1. Public Library of Science, 2013.' ista: 'Arquè Fuste G, Casanovas A, Dierssen M. 2013. Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. 8(1), e54285.' mla: 'Arquè Fuste, Gloria, et al. “Dyrk1A Is Dynamically Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.” PLoS One, vol. 8, no. 1, e54285, Public Library of Science, 2013, doi:10.1371/journal.pone.0054285.' short: G. Arquè Fuste, A. Casanovas, M. Dierssen, PLoS One 8 (2013). date_created: 2018-12-11T11:59:52Z date_published: 2013-01-16T00:00:00Z date_updated: 2021-01-12T07:00:07Z day: '16' ddc: - '570' department: - _id: SiHi doi: 10.1371/journal.pone.0054285 file: - access_level: open_access checksum: 512733b21419574a45f10cabef3d7f81 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:38Z date_updated: 2020-07-14T12:45:50Z file_id: '5160' file_name: IST-2016-407-v1+1_journal.pone.0054285.pdf file_size: 4795977 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '3960' pubrep_id: '407' quality_controlled: '1' scopus_import: 1 status: public title: 'Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2839' abstract: - lang: eng text: Directional guidance of cells via gradients of chemokines is considered crucial for embryonic development, cancer dissemination, and immune responses. Nevertheless, the concept still lacks direct experimental confirmation in vivo. Here, we identify endogenous gradients of the chemokine CCL21 within mouse skin and show that they guide dendritic cells toward lymphatic vessels. Quantitative imaging reveals depots of CCL21 within lymphatic endothelial cells and steeply decaying gradients within the perilymphatic interstitium. These gradients match the migratory patterns of the dendritic cells, which directionally approach vessels from a distance of up to 90-micrometers. Interstitial CCL21 is immobilized to heparan sulfates, and its experimental delocalization or swamping the endogenous gradients abolishes directed migration. These findings functionally establish the concept of haptotaxis, directed migration along immobilized gradients, in tissues. acknowledgement: We thank M. Frank for technical assistance and S. Cremer, P. Schmalhorst, and E. Kiermaier for critical reading of the manuscript. This work was supported by a Humboldt Foundation postdoctoral fellowship (to M.W.), the German Research Foundation (Si1323 1,2 to M.S.), the Human Frontier Science Program (HFSP RGP0058/2011 to M.S.), the European Research Council (ERC StG 281556 to M.S.), and the Swiss National Science Foundation (31003A 127474 to D.F.L., 130488 to S.A.L.). article_processing_charge: No article_type: original author: - first_name: Michele full_name: Weber, Michele id: 3A3FC708-F248-11E8-B48F-1D18A9856A87 last_name: Weber - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Christine full_name: Moussion, Christine id: 3356F664-F248-11E8-B48F-1D18A9856A87 last_name: Moussion - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Daniel full_name: Legler, Daniel last_name: Legler - first_name: Sanjiv full_name: Luther, Sanjiv last_name: Luther - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Weber M, Hauschild R, Schwarz J, et al. Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. 2013;339(6117):328-332. doi:10.1126/science.1228456 apa: Weber, M., Hauschild, R., Schwarz, J., Moussion, C., de Vries, I., Legler, D., … Sixt, M. K. (2013). Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1228456 chicago: Weber, Michele, Robert Hauschild, Jan Schwarz, Christine Moussion, Ingrid de Vries, Daniel Legler, Sanjiv Luther, Mark Tobias Bollenbach, and Michael K Sixt. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1228456. ieee: M. Weber et al., “Interstitial dendritic cell guidance by haptotactic chemokine gradients,” Science, vol. 339, no. 6117. American Association for the Advancement of Science, pp. 328–332, 2013. ista: Weber M, Hauschild R, Schwarz J, Moussion C, de Vries I, Legler D, Luther S, Bollenbach MT, Sixt MK. 2013. Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. 339(6117), 328–332. mla: Weber, Michele, et al. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.” Science, vol. 339, no. 6117, American Association for the Advancement of Science, 2013, pp. 328–32, doi:10.1126/science.1228456. short: M. Weber, R. Hauschild, J. Schwarz, C. Moussion, I. de Vries, D. Legler, S. Luther, M.T. Bollenbach, M.K. Sixt, Science 339 (2013) 328–332. date_created: 2018-12-11T11:59:52Z date_published: 2013-01-18T00:00:00Z date_updated: 2022-06-10T10:21:40Z day: '18' department: - _id: MiSi - _id: Bio doi: 10.1126/science.1228456 ec_funded: 1 intvolume: ' 339' issue: '6117' language: - iso: eng main_file_link: - open_access: '1' url: https://kops.uni-konstanz.de/bitstream/123456789/26341/2/Weber_263418.pdf month: '01' oa: 1 oa_version: Published Version page: 328 - 332 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) - _id: 25ABD200-B435-11E9-9278-68D0E5697425 grant_number: RGP0058/2011 name: 'Cell migration in complex environments: from in vivo experiments to theoretical models' publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '3959' quality_controlled: '1' scopus_import: '1' status: public title: Interstitial dendritic cell guidance by haptotactic chemokine gradients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 339 year: '2013' ... --- _id: '2837' abstract: - lang: eng text: We consider a general class of N × N random matrices whose entries hij are independent up to a symmetry constraint, but not necessarily identically distributed. Our main result is a local semicircle law which improves previous results [17] both in the bulk and at the edge. The error bounds are given in terms of the basic small parameter of the model, maxi,j E|hij|2. As a consequence, we prove the universality of the local n-point correlation functions in the bulk spectrum for a class of matrices whose entries do not have comparable variances, including random band matrices with band width W ≫N1-εn with some εn > 0 and with a negligible mean-field component. In addition, we provide a coherent and pedagogical proof of the local semicircle law, streamlining and strengthening previous arguments from [17, 19, 6]. author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles - first_name: Horng full_name: Yau, Horng last_name: Yau - first_name: Jun full_name: Yin, Jun last_name: Yin citation: ama: Erdös L, Knowles A, Yau H, Yin J. The local semicircle law for a general class of random matrices. Electronic Journal of Probability. 2013;18(59):1-58. doi:10.1214/EJP.v18-2473 apa: Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). The local semicircle law for a general class of random matrices. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v18-2473 chicago: Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “The Local Semicircle Law for a General Class of Random Matrices.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/EJP.v18-2473. ieee: L. Erdös, A. Knowles, H. Yau, and J. Yin, “The local semicircle law for a general class of random matrices,” Electronic Journal of Probability, vol. 18, no. 59. Institute of Mathematical Statistics, pp. 1–58, 2013. ista: Erdös L, Knowles A, Yau H, Yin J. 2013. The local semicircle law for a general class of random matrices. Electronic Journal of Probability. 18(59), 1–58. mla: Erdös, László, et al. “The Local Semicircle Law for a General Class of Random Matrices.” Electronic Journal of Probability, vol. 18, no. 59, Institute of Mathematical Statistics, 2013, pp. 1–58, doi:10.1214/EJP.v18-2473. short: L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of Probability 18 (2013) 1–58. date_created: 2018-12-11T11:59:51Z date_published: 2013-05-29T00:00:00Z date_updated: 2021-01-12T07:00:06Z day: '29' ddc: - '530' department: - _id: LaEr doi: 10.1214/EJP.v18-2473 file: - access_level: open_access checksum: aac9e52a00cb2f5149dc9e362b5ccf44 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:46Z date_updated: 2020-07-14T12:45:50Z file_id: '5169' file_name: IST-2016-406-v1+1_2473-13759-1-PB.pdf file_size: 651497 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 18' issue: '59' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1-58 publication: Electronic Journal of Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '3962' pubrep_id: '406' quality_controlled: '1' scopus_import: 1 status: public title: The local semicircle law for a general class of random matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2013' ... --- _id: '2835' abstract: - lang: eng text: The phytohormone auxin regulates virtually every aspect of plant development. To identify new genes involved in auxin activity, a genetic screen was performed for Arabidopsis (Arabidopsis thaliana) mutants with altered expression of the auxin-responsive reporter DR5rev:GFP. One of the mutants recovered in the screen, designated as weak auxin response3 (wxr3), exhibits much lower DR5rev:GFP expression when treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid and displays severe defects in root development. The wxr3 mutant decreases polar auxin transport and results in a disruption of the asymmetric auxin distribution. The levels of the auxin transporters AUXIN1 and PIN-FORMED are dramatically reduced in the wxr3 root tip. Molecular analyses demonstrate that WXR3 is ROOT ULTRAVIOLET B-SENSITIVE1 (RUS1), a member of the conserved Domain of Unknown Function647 protein family found in diverse eukaryotic organisms. Our data suggest that RUS1/WXR3 plays an essential role in the regulation of polar auxin transport by maintaining the proper level of auxin transporters on the plasma membrane. author: - first_name: Hong full_name: Yu, Hong last_name: Yu - first_name: Michael full_name: Karampelias, Michael last_name: Karampelias - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Wendy full_name: Peer, Wendy last_name: Peer - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Songqing full_name: Ye, Songqing last_name: Ye - first_name: Lei full_name: Ge, Lei last_name: Ge - first_name: Jerry full_name: Cohen, Jerry last_name: Cohen - first_name: Angus full_name: Murphy, Angus last_name: Murphy - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Mark full_name: Estelle, Mark last_name: Estelle citation: ama: Yu H, Karampelias M, Robert S, et al. Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. Plant Physiology. 2013;162(2):965-976. doi:10.1104/pp.113.217018 apa: Yu, H., Karampelias, M., Robert, S., Peer, W., Swarup, R., Ye, S., … Estelle, M. (2013). Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.113.217018 chicago: Yu, Hong, Michael Karampelias, Stéphanie Robert, Wendy Peer, Ranjan Swarup, Songqing Ye, Lei Ge, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3 Is Essential for Polar Auxin Transport in Arabidopsis.” Plant Physiology. American Society of Plant Biologists, 2013. https://doi.org/10.1104/pp.113.217018. ieee: H. Yu et al., “Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis,” Plant Physiology, vol. 162, no. 2. American Society of Plant Biologists, pp. 965–976, 2013. ista: Yu H, Karampelias M, Robert S, Peer W, Swarup R, Ye S, Ge L, Cohen J, Murphy A, Friml J, Estelle M. 2013. Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. Plant Physiology. 162(2), 965–976. mla: Yu, Hong, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3 Is Essential for Polar Auxin Transport in Arabidopsis.” Plant Physiology, vol. 162, no. 2, American Society of Plant Biologists, 2013, pp. 965–76, doi:10.1104/pp.113.217018. short: H. Yu, M. Karampelias, S. Robert, W. Peer, R. Swarup, S. Ye, L. Ge, J. Cohen, A. Murphy, J. Friml, M. Estelle, Plant Physiology 162 (2013) 965–976. date_created: 2018-12-11T11:59:51Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T07:00:05Z day: '01' department: - _id: JiFr doi: 10.1104/pp.113.217018 external_id: pmid: - '23580592' intvolume: ' 162' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668084/ month: '06' oa: 1 oa_version: Submitted Version page: 965 - 976 pmid: 1 publication: Plant Physiology publication_status: published publisher: American Society of Plant Biologists publist_id: '3964' quality_controlled: '1' scopus_import: 1 status: public title: Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 162 year: '2013' ... --- _id: '2836' abstract: - lang: eng text: 'We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents and the trusted third party as path formulas in linear temporal logic and prove that the satisfaction of these objectives imply fairness; a property required of fair exchange protocols. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of AGS as follows: (a) any solution of AGS is attack-free; no subset of participants can violate the objectives of the other participants; (b) the Asokan-Shoup-Waidner certified mail protocol that has known vulnerabilities is not a solution of AGS; (c) the Kremer-Markowitch non-repudiation protocol is a solution of AGS; and (d) AGS presents a new and symmetric fair non-repudiation protocol that is attack-free. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can both automatically discover vulnerabilities in protocols and generate correct protocols. The solution to AGS can be computed efficiently as the secure equilibrium solution of three-player graph games. ' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vishwanath full_name: Raman, Vishwanath last_name: Raman citation: ama: Chatterjee K, Raman V. Assume-guarantee synthesis for digital contract signing. Formal Aspects of Computing. 2013;26(4):825-859. doi:10.1007/s00165-013-0283-6 apa: Chatterjee, K., & Raman, V. (2013). Assume-guarantee synthesis for digital contract signing. Formal Aspects of Computing. Springer. https://doi.org/10.1007/s00165-013-0283-6 chicago: Chatterjee, Krishnendu, and Vishwanath Raman. “Assume-Guarantee Synthesis for Digital Contract Signing.” Formal Aspects of Computing. Springer, 2013. https://doi.org/10.1007/s00165-013-0283-6. ieee: K. Chatterjee and V. Raman, “Assume-guarantee synthesis for digital contract signing,” Formal Aspects of Computing, vol. 26, no. 4. Springer, pp. 825–859, 2013. ista: Chatterjee K, Raman V. 2013. Assume-guarantee synthesis for digital contract signing. Formal Aspects of Computing. 26(4), 825–859. mla: Chatterjee, Krishnendu, and Vishwanath Raman. “Assume-Guarantee Synthesis for Digital Contract Signing.” Formal Aspects of Computing, vol. 26, no. 4, Springer, 2013, pp. 825–59, doi:10.1007/s00165-013-0283-6. short: K. Chatterjee, V. Raman, Formal Aspects of Computing 26 (2013) 825–859. date_created: 2018-12-11T11:59:51Z date_published: 2013-07-04T00:00:00Z date_updated: 2021-01-12T07:00:06Z day: '04' department: - _id: KrCh doi: 10.1007/s00165-013-0283-6 ec_funded: 1 external_id: arxiv: - '1004.2697' intvolume: ' 26' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1004.2697 month: '07' oa: 1 oa_version: Preprint page: 825 - 859 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Formal Aspects of Computing publication_status: published publisher: Springer publist_id: '3963' quality_controlled: '1' scopus_import: 1 status: public title: Assume-guarantee synthesis for digital contract signing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2013' ... --- _id: '2840' abstract: - lang: eng text: It is known that the entorhinal cortex plays a crucial role in spatial cognition in rodents. Neuroanatomical and electrophysiological data suggest that there is a functional distinction between 2 subregions within the entorhinal cortex, the medial entorhinal cortex (MEC), and the lateral entorhinal cortex (LEC). Rats with MEC or LEC lesions were trained in 2 navigation tasks requiring allothetic (water maze task) or idiothetic (path integration) information processing and 2-object exploration tasks allowing testing of spatial and nonspatial processing of intramaze objects. MEC lesions mildly affected place navigation in the water maze and produced a path integration deficit. They also altered the processing of spatial information in both exploration tasks while sparing the processing of nonspatial information. LEC lesions did not affect navigation abilities in both the water maze and the path integration tasks. They altered spatial and nonspatial processing in the object exploration task but not in the one-trial recognition task. Overall, these results indicate that the MEC is important for spatial processing and path integration. The LEC has some influence on both spatial and nonspatial processes, suggesting that the 2 kinds of information interact at the level of the EC. author: - first_name: Tiffany full_name: Van Cauter, Tiffany last_name: Van Cauter - first_name: Jeremy full_name: Camon, Jeremy last_name: Camon - first_name: Alice full_name: Alvernhe, Alice id: 467FB3D4-F248-11E8-B48F-1D18A9856A87 last_name: Alvernhe - first_name: Coralie full_name: Elduayen, Coralie last_name: Elduayen - first_name: Francesca full_name: Sargolini, Francesca last_name: Sargolini - first_name: Étienne full_name: Save, Étienne last_name: Save citation: ama: Van Cauter T, Camon J, Alvernhe A, Elduayen C, Sargolini F, Save É. Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral Cortex. 2013;23(2):451-459. doi:10.1093/cercor/bhs033 apa: Van Cauter, T., Camon, J., Alvernhe, A., Elduayen, C., Sargolini, F., & Save, É. (2013). Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhs033 chicago: Van Cauter, Tiffany, Jeremy Camon, Alice Alvernhe, Coralie Elduayen, Francesca Sargolini, and Étienne Save. “Distinct Roles of Medial and Lateral Entorhinal Cortex in Spatial Cognition.” Cerebral Cortex. Oxford University Press, 2013. https://doi.org/10.1093/cercor/bhs033. ieee: T. Van Cauter, J. Camon, A. Alvernhe, C. Elduayen, F. Sargolini, and É. Save, “Distinct roles of medial and lateral entorhinal cortex in spatial cognition,” Cerebral Cortex, vol. 23, no. 2. Oxford University Press, pp. 451–459, 2013. ista: Van Cauter T, Camon J, Alvernhe A, Elduayen C, Sargolini F, Save É. 2013. Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral Cortex. 23(2), 451–459. mla: Van Cauter, Tiffany, et al. “Distinct Roles of Medial and Lateral Entorhinal Cortex in Spatial Cognition.” Cerebral Cortex, vol. 23, no. 2, Oxford University Press, 2013, pp. 451–59, doi:10.1093/cercor/bhs033. short: T. Van Cauter, J. Camon, A. Alvernhe, C. Elduayen, F. Sargolini, É. Save, Cerebral Cortex 23 (2013) 451–459. date_created: 2018-12-11T11:59:52Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T07:00:08Z day: '01' department: - _id: JoCs doi: 10.1093/cercor/bhs033 intvolume: ' 23' issue: '2' language: - iso: eng month: '02' oa_version: None page: 451 - 459 publication: Cerebral Cortex publication_status: published publisher: Oxford University Press publist_id: '3958' quality_controlled: '1' scopus_import: 1 status: public title: Distinct roles of medial and lateral entorhinal cortex in spatial cognition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '2841' abstract: - lang: eng text: In zebrafish early development, blastoderm cells undergo extensive radial intercalations, triggering the spreading of the blastoderm over the yolk cell and thereby initiating embryonic body axis formation. Now reporting in Developmental Cell, Song et al. (2013) demonstrate a critical function for EGF-dependent E-cadherin endocytosis in promoting blastoderm cell intercalations. author: - first_name: Hitoshi full_name: Morita, Hitoshi id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87 last_name: Morita - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Morita H, Heisenberg C-PJ. Holding on and letting go: Cadherin turnover in cell intercalation. Developmental Cell. 2013;24(6):567-569. doi:10.1016/j.devcel.2013.03.007' apa: 'Morita, H., & Heisenberg, C.-P. J. (2013). Holding on and letting go: Cadherin turnover in cell intercalation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2013.03.007' chicago: 'Morita, Hitoshi, and Carl-Philipp J Heisenberg. “Holding on and Letting Go: Cadherin Turnover in Cell Intercalation.” Developmental Cell. Cell Press, 2013. https://doi.org/10.1016/j.devcel.2013.03.007.' ieee: 'H. Morita and C.-P. J. Heisenberg, “Holding on and letting go: Cadherin turnover in cell intercalation,” Developmental Cell, vol. 24, no. 6. Cell Press, pp. 567–569, 2013.' ista: 'Morita H, Heisenberg C-PJ. 2013. Holding on and letting go: Cadherin turnover in cell intercalation. Developmental Cell. 24(6), 567–569.' mla: 'Morita, Hitoshi, and Carl-Philipp J. Heisenberg. “Holding on and Letting Go: Cadherin Turnover in Cell Intercalation.” Developmental Cell, vol. 24, no. 6, Cell Press, 2013, pp. 567–69, doi:10.1016/j.devcel.2013.03.007.' short: H. Morita, C.-P.J. Heisenberg, Developmental Cell 24 (2013) 567–569. date_created: 2018-12-11T11:59:52Z date_published: 2013-05-25T00:00:00Z date_updated: 2021-01-12T07:00:09Z day: '25' department: - _id: CaHe doi: 10.1016/j.devcel.2013.03.007 intvolume: ' 24' issue: '6' language: - iso: eng month: '05' oa_version: None page: 567 - 569 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '3956' quality_controlled: '1' scopus_import: 1 status: public title: 'Holding on and letting go: Cadherin turnover in cell intercalation' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2013' ... --- _id: '2846' abstract: - lang: eng text: The Red Queen hypothesis proposes that coevolving parasites select for outcrossing in the host. Outcrossing relies on males, which often show lower immune investment due to, for example, sexual selection. Here, we demonstrate that such sex differences in immunity interfere with parasite-mediated selection for outcrossing. Two independent coevolution experiments with Caenorhabditis elegans and its microparasite Bacillus thuringiensis produced decreased yet stable frequencies of outcrossing male hosts. A subsequent systematic analysis verified that male C. elegans suffered from a direct selective disadvantage under parasite pressure (i.e. lower resistance, decreased sexual activity, increased escape behaviour), which can reduce outcrossing and thus male frequencies. At the same time, males offered an indirect selective benefit, because male-mediated outcrossing increased offspring resistance, thus favouring male persistence in the evolving populations. As sex differences in immunity are widespread, such interference of opposing selective constraints is likely of central importance during host adaptation to a coevolving parasite. article_processing_charge: No author: - first_name: Leila full_name: El Masri, Leila id: 349A6E66-F248-11E8-B48F-1D18A9856A87 last_name: El Masri - first_name: Rebecca full_name: Schulte, Rebecca last_name: Schulte - first_name: Nadine full_name: Timmermeyer, Nadine last_name: Timmermeyer - first_name: Stefanie full_name: Thanisch, Stefanie last_name: Thanisch - first_name: Lena full_name: Crummenerl, Lena last_name: Crummenerl - first_name: Gunther full_name: Jansen, Gunther last_name: Jansen - first_name: Nico full_name: Michiels, Nico last_name: Michiels - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg citation: ama: El Masri L, Schulte R, Timmermeyer N, et al. Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. Ecology Letters. 2013;16(4):461-468. doi:10.1111/ele.12068 apa: El Masri, L., Schulte, R., Timmermeyer, N., Thanisch, S., Crummenerl, L., Jansen, G., … Schulenburg, H. (2013). Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. Ecology Letters. Wiley-Blackwell. https://doi.org/10.1111/ele.12068 chicago: El Masri, Leila, Rebecca Schulte, Nadine Timmermeyer, Stefanie Thanisch, Lena Crummenerl, Gunther Jansen, Nico Michiels, and Hinrich Schulenburg. “Sex Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing during Host-Parasite Coevolution.” Ecology Letters. Wiley-Blackwell, 2013. https://doi.org/10.1111/ele.12068. ieee: L. El Masri et al., “Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution,” Ecology Letters, vol. 16, no. 4. Wiley-Blackwell, pp. 461–468, 2013. ista: El Masri L, Schulte R, Timmermeyer N, Thanisch S, Crummenerl L, Jansen G, Michiels N, Schulenburg H. 2013. Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. Ecology Letters. 16(4), 461–468. mla: El Masri, Leila, et al. “Sex Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing during Host-Parasite Coevolution.” Ecology Letters, vol. 16, no. 4, Wiley-Blackwell, 2013, pp. 461–68, doi:10.1111/ele.12068. short: L. El Masri, R. Schulte, N. Timmermeyer, S. Thanisch, L. Crummenerl, G. Jansen, N. Michiels, H. Schulenburg, Ecology Letters 16 (2013) 461–468. date_created: 2018-12-11T11:59:54Z date_published: 2013-04-04T00:00:00Z date_updated: 2022-08-25T14:51:57Z day: '04' ddc: - '570' doi: 10.1111/ele.12068 extern: '1' file: - access_level: open_access checksum: aa7db788f7da7d7f102539a249ebce50 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:52Z date_updated: 2020-07-14T12:45:50Z file_id: '5176' file_name: IST-2016-404-v1+1_ele12068.pdf file_size: 763731 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 16' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 461 - 468 publication: Ecology Letters publication_status: published publisher: Wiley-Blackwell publist_id: '3948' pubrep_id: '404' quality_controlled: '1' scopus_import: '1' status: public title: Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2013' ... --- _id: '2844' abstract: - lang: eng text: As soon as a seed germinates, plant growth relates to gravity to ensure that the root penetrates the soil and the shoot expands aerially. Whereas mechanisms of positive and negative orthogravitropism of primary roots and shoots are relatively well understood [1-3], lateral organs often show more complex growth behavior [4]. Lateral roots (LRs) seemingly suppress positive gravitropic growth and show a defined gravitropic set-point angle (GSA) that allows radial expansion of the root system (plagiotropism) [3, 4]. Despite its eminent importance for root architecture, it so far remains completely unknown how lateral organs partially suppress positive orthogravitropism. Here we show that the phytohormone auxin steers GSA formation and limits positive orthogravitropism in LR. Low and high auxin levels/signaling lead to radial or axial root systems, respectively. At a cellular level, it is the auxin transport-dependent regulation of asymmetric growth in the elongation zone that determines GSA. Our data suggest that strong repression of PIN4/PIN7 and transient PIN3 expression limit auxin redistribution in young LR columella cells. We conclude that PIN activity, by temporally limiting the asymmetric auxin fluxes in the tip of LRs, induces transient, differential growth responses in the elongation zone and, consequently, controls root architecture. author: - first_name: Michel full_name: Rosquete, Michel last_name: Rosquete - first_name: Daniel full_name: Von Wangenheim, Daniel id: 49E91952-F248-11E8-B48F-1D18A9856A87 last_name: Von Wangenheim orcid: 0000-0002-6862-1247 - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Elke full_name: Barbez, Elke last_name: Barbez - first_name: Ernst full_name: Stelzer, Ernst last_name: Stelzer - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Alexis full_name: Maizel, Alexis last_name: Maizel - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn citation: ama: Rosquete M, von Wangenheim D, Marhavý P, et al. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. 2013;23(9):817-822. doi:10.1016/j.cub.2013.03.064 apa: Rosquete, M., von Wangenheim, D., Marhavý, P., Barbez, E., Stelzer, E., Benková, E., … Kleine Vehn, J. (2013). An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.03.064 chicago: Rosquete, Michel, Daniel von Wangenheim, Peter Marhavý, Elke Barbez, Ernst Stelzer, Eva Benková, Alexis Maizel, and Jürgen Kleine Vehn. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.03.064. ieee: M. Rosquete et al., “An auxin transport mechanism restricts positive orthogravitropism in lateral roots,” Current Biology, vol. 23, no. 9. Cell Press, pp. 817–822, 2013. ista: Rosquete M, von Wangenheim D, Marhavý P, Barbez E, Stelzer E, Benková E, Maizel A, Kleine Vehn J. 2013. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. 23(9), 817–822. mla: Rosquete, Michel, et al. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” Current Biology, vol. 23, no. 9, Cell Press, 2013, pp. 817–22, doi:10.1016/j.cub.2013.03.064. short: M. Rosquete, D. von Wangenheim, P. Marhavý, E. Barbez, E. Stelzer, E. Benková, A. Maizel, J. Kleine Vehn, Current Biology 23 (2013) 817–822. date_created: 2018-12-11T11:59:53Z date_published: 2013-05-06T00:00:00Z date_updated: 2021-01-12T07:00:10Z day: '06' department: - _id: JiFr - _id: EvBe doi: 10.1016/j.cub.2013.03.064 ec_funded: 1 intvolume: ' 23' issue: '9' language: - iso: eng month: '05' oa_version: None page: 817 - 822 project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3950' quality_controlled: '1' scopus_import: 1 status: public title: An auxin transport mechanism restricts positive orthogravitropism in lateral roots type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '2843' abstract: - lang: eng text: 'Mathematical objects can be measured unambiguously, but not so objects from our physical world. Even the total length of tubelike shapes has its difficulties. We introduce a combination of geometric, probabilistic, and topological methods to design a stable length estimate for tube-like shapes; that is: one that is insensitive to small shape changes.' alternative_title: - LNCS author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 citation: ama: 'Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. In: 17th IAPR International Conference on Discrete Geometry for Computer Imagery. Vol 7749. Springer; 2013:XV-XIX. doi:10.1007/978-3-642-37067-0' apa: 'Edelsbrunner, H., & Pausinger, F. (2013). Stable length estimates of tube-like shapes. In 17th IAPR International Conference on Discrete Geometry for Computer Imagery (Vol. 7749, pp. XV–XIX). Seville, Spain: Springer. https://doi.org/10.1007/978-3-642-37067-0' chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” In 17th IAPR International Conference on Discrete Geometry for Computer Imagery, 7749:XV–XIX. Springer, 2013. https://doi.org/10.1007/978-3-642-37067-0. ieee: H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” in 17th IAPR International Conference on Discrete Geometry for Computer Imagery, Seville, Spain, 2013, vol. 7749, pp. XV–XIX. ista: 'Edelsbrunner H, Pausinger F. 2013. Stable length estimates of tube-like shapes. 17th IAPR International Conference on Discrete Geometry for Computer Imagery. DGCI: Discrete Geometry for Computer Imagery, LNCS, vol. 7749, XV–XIX.' mla: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” 17th IAPR International Conference on Discrete Geometry for Computer Imagery, vol. 7749, Springer, 2013, pp. XV–XIX, doi:10.1007/978-3-642-37067-0. short: H. Edelsbrunner, F. Pausinger, in:, 17th IAPR International Conference on Discrete Geometry for Computer Imagery, Springer, 2013, pp. XV–XIX. conference: end_date: 2013-03-22 location: Seville, Spain name: 'DGCI: Discrete Geometry for Computer Imagery' start_date: 2013-03-20 date_created: 2018-12-11T11:59:53Z date_published: 2013-02-21T00:00:00Z date_updated: 2023-02-23T10:35:00Z day: '21' department: - _id: HeEd doi: 10.1007/978-3-642-37067-0 intvolume: ' 7749' language: - iso: eng month: '02' oa_version: None page: XV - XIX publication: 17th IAPR International Conference on Discrete Geometry for Computer Imagery publication_status: published publisher: Springer publist_id: '3952' quality_controlled: '1' related_material: record: - id: '2255' relation: later_version status: public scopus_import: 1 status: public title: Stable length estimates of tube-like shapes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7749 year: '2013' ... --- _id: '2845' abstract: - lang: eng text: At synapses formed between dissociated neurons, about half of all synaptic vesicles are refractory to evoked release, forming the so-called "resting pool." Here, we use optical measurements of vesicular pH to study developmental changes in pool partitioning and vesicle cycling in cultured hippocampal slices. Two-photon imaging of a genetically encoded two-color release sensor (ratio-sypHy) allowed us to perform calibrated measurements at individual Schaffer collateral boutons. Mature boutons released a large fraction of their vesicles during simulated place field activity, and vesicle retrieval rates were 7-fold higher compared to immature boutons. Saturating stimulation mobilized essentially all vesicles at mature synapses. Resting pool formation and a concomitant reduction in evoked release was induced by chronic depolarization but not by acute inhibition of the protein phosphatase calcineurin. We conclude that synapses in CA1 undergo a prominent refinement of vesicle use during early postnatal development that is not recapitulated in dissociated neuronal culture. author: - first_name: Tobias full_name: Rose, Tobias last_name: Rose - first_name: Philipp full_name: Schönenberger, Philipp id: 3B9D816C-F248-11E8-B48F-1D18A9856A87 last_name: Schönenberger - first_name: Karel full_name: Jezek, Karel last_name: Jezek - first_name: Thomas full_name: Oertner, Thomas last_name: Oertner citation: ama: Rose T, Schönenberger P, Jezek K, Oertner T. Developmental refinement of vesicle cycling at Schaffer collateral synapses. Neuron. 2013;77(6):1109-1121. doi:10.1016/j.neuron.2013.01.021 apa: Rose, T., Schönenberger, P., Jezek, K., & Oertner, T. (2013). Developmental refinement of vesicle cycling at Schaffer collateral synapses. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.01.021 chicago: Rose, Tobias, Philipp Schönenberger, Karel Jezek, and Thomas Oertner. “Developmental Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.01.021. ieee: T. Rose, P. Schönenberger, K. Jezek, and T. Oertner, “Developmental refinement of vesicle cycling at Schaffer collateral synapses,” Neuron, vol. 77, no. 6. Elsevier, pp. 1109–1121, 2013. ista: Rose T, Schönenberger P, Jezek K, Oertner T. 2013. Developmental refinement of vesicle cycling at Schaffer collateral synapses. Neuron. 77(6), 1109–1121. mla: Rose, Tobias, et al. “Developmental Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” Neuron, vol. 77, no. 6, Elsevier, 2013, pp. 1109–21, doi:10.1016/j.neuron.2013.01.021. short: T. Rose, P. Schönenberger, K. Jezek, T. Oertner, Neuron 77 (2013) 1109–1121. date_created: 2018-12-11T11:59:54Z date_published: 2013-03-20T00:00:00Z date_updated: 2021-01-12T07:00:11Z day: '20' department: - _id: JoCs doi: 10.1016/j.neuron.2013.01.021 intvolume: ' 77' issue: '6' language: - iso: eng month: '03' oa_version: None page: 1109 - 1121 publication: Neuron publication_status: published publisher: Elsevier publist_id: '3949' quality_controlled: '1' scopus_import: 1 status: public title: Developmental refinement of vesicle cycling at Schaffer collateral synapses type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2013' ... --- _id: '2854' abstract: - lang: eng text: We consider concurrent games played on graphs. At every round of a game, each player simultaneously and independently selects a move; the moves jointly determine the transition to a successor state. Two basic objectives are the safety objective to stay forever in a given set of states, and its dual, the reachability objective to reach a given set of states. First, we present a simple proof of the fact that in concurrent reachability games, for all ε>0, memoryless ε-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an ε-optimal strategy achieves the objective with probability within ε of the value of the game. In contrast to previous proofs of this fact, our proof is more elementary and more combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives. Finally, we present a strategy-improvement algorithm for turn-based stochastic games (where each player selects moves in turns) with safety objectives. Our algorithms yield sequences of player-1 strategies which ensure probabilities of winning that converge monotonically (from below) to the value of the game. © 2012 Elsevier Inc. acknowledgement: This work was partially supported in part by the NSF grants CCR-0132780, CNS-0720884, CCR-0225610, by the Swiss National Science Foundation, ERC Start Grant Graph Games (Project No. 279307), FWF NFN Grant S11407-N23 (RiSE), and a Microsoft faculty fellows article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: De Alfaro, Luca last_name: De Alfaro - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Chatterjee K, De Alfaro L, Henzinger TA. Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. 2013;79(5):640-657. doi:10.1016/j.jcss.2012.12.001 apa: Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2013). Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2012.12.001 chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.” Journal of Computer and System Sciences. Elsevier, 2013. https://doi.org/10.1016/j.jcss.2012.12.001. ieee: K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for concurrent reachability and turn based stochastic safety games,” Journal of Computer and System Sciences, vol. 79, no. 5. Elsevier, pp. 640–657, 2013. ista: Chatterjee K, De Alfaro L, Henzinger TA. 2013. Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. 79(5), 640–657. mla: Chatterjee, Krishnendu, et al. “Strategy Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.” Journal of Computer and System Sciences, vol. 79, no. 5, Elsevier, 2013, pp. 640–57, doi:10.1016/j.jcss.2012.12.001. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, Journal of Computer and System Sciences 79 (2013) 640–657. date_created: 2018-12-11T11:59:57Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T07:00:16Z day: '01' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.1016/j.jcss.2012.12.001 ec_funded: 1 file: - access_level: open_access checksum: 6d3ee12cceb946a0abe69594b6a22409 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:48Z date_updated: 2020-07-14T12:45:51Z file_id: '5370' file_name: IST-2015-388-v1+1_1-s2.0-S0022000012001778-main.pdf file_size: 425488 relation: main_file file_date_updated: 2020-07-14T12:45:51Z has_accepted_license: '1' intvolume: ' 79' issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '08' oa: 1 oa_version: Published Version page: 640 - 657 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of Computer and System Sciences publication_status: published publisher: Elsevier publist_id: '3938' pubrep_id: '388' quality_controlled: '1' scopus_import: 1 status: public title: Strategy improvement for concurrent reachability and turn based stochastic safety games tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 79 year: '2013' ... --- _id: '2850' abstract: - lang: eng text: "Recent work emphasizes that the maximum entropy principle provides a bridge between statistical mechanics models for collective behavior in neural networks and experiments on networks of real neurons. Most of this work has focused on capturing the measured correlations among pairs of neurons. Here we suggest an alternative, constructing models that are consistent with the distribution of global network activity, i.e. the probability that K out of N cells in the network generate action potentials in the same small time bin. The inverse problem that we need to solve in constructing the model is analytically tractable, and provides a natural 'thermodynamics' for the network in the limit of large N. We analyze the responses of neurons in a small patch of the retina to naturalistic stimuli, and find that the implied thermodynamics is very close to an unusual critical point, in which the entropy (in proper units) is exactly equal to the energy. © 2013 IOP Publishing Ltd and SISSA Medialab srl.\r\n" acknowledgement: "his work was supported in part by NSF Grants IIS-0613435 and PHY-0957573, by NIH Grants R01 EY14196 and P50 GM071508, by the Fannie and John Hertz Foundation, by the Human Frontiers Science Program, by the Swartz Foundation, and by the WM Keck Foundation.\r\n" article_number: P03011 article_processing_charge: No article_type: original author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Thierry full_name: Mora, Thierry last_name: Mora - first_name: Dario full_name: Amodei, Dario last_name: Amodei - first_name: Michael full_name: Berry, Michael last_name: Berry - first_name: William full_name: Bialek, William last_name: Bialek citation: ama: Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03011 apa: Tkačik, G., Marre, O., Mora, T., Amodei, D., Berry, M., & Bialek, W. (2013). The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/03/P03011 chicago: Tkačik, Gašper, Olivier Marre, Thierry Mora, Dario Amodei, Michael Berry, and William Bialek. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/03/P03011. ieee: G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, and W. Bialek, “The simplest maximum entropy model for collective behavior in a neural network,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3. IOP Publishing Ltd., 2013. ista: Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. 2013. The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment. 2013(3), P03011. mla: Tkačik, Gašper, et al. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, P03011, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03011. short: G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013). date_created: 2018-12-11T11:59:55Z date_published: 2013-03-12T00:00:00Z date_updated: 2021-01-12T07:00:14Z day: '12' department: - _id: GaTk doi: 10.1088/1742-5468/2013/03/P03011 external_id: arxiv: - '1207.6319' intvolume: ' 2013' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1207.6319 month: '03' oa: 1 oa_version: Preprint publication: Journal of Statistical Mechanics Theory and Experiment publication_status: published publisher: IOP Publishing Ltd. publist_id: '3942' quality_controlled: '1' scopus_import: 1 status: public title: The simplest maximum entropy model for collective behavior in a neural network type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2013 year: '2013' ... --- _id: '2851' abstract: - lang: eng text: The number of possible activity patterns in a population of neurons grows exponentially with the size of the population. Typical experiments explore only a tiny fraction of the large space of possible activity patterns in the case of populations with more than 10 or 20 neurons. It is thus impossible, in this undersampled regime, to estimate the probabilities with which most of the activity patterns occur. As a result, the corresponding entropy - which is a measure of the computational power of the neural population - cannot be estimated directly. We propose a simple scheme for estimating the entropy in the undersampled regime, which bounds its value from both below and above. The lower bound is the usual 'naive' entropy of the experimental frequencies. The upper bound results from a hybrid approximation of the entropy which makes use of the naive estimate, a maximum entropy fit, and a coverage adjustment. We apply our simple scheme to artificial data, in order to check their accuracy; we also compare its performance to those of several previously defined entropy estimators. We then apply it to actual measurements of neural activity in populations with up to 100 cells. Finally, we discuss the similarities and differences between the proposed simple estimation scheme and various earlier methods. © 2013 IOP Publishing Ltd and SISSA Medialab srl. article_number: P03015 author: - first_name: Michael full_name: Berry, Michael last_name: Berry - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Julien full_name: Dubuis, Julien last_name: Dubuis - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Ravá full_name: Da Silveira, Ravá last_name: Da Silveira citation: ama: Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03015 apa: Berry, M., Tkačik, G., Dubuis, J., Marre, O., & Da Silveira, R. (2013). A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/03/P03015 chicago: Berry, Michael, Gašper Tkačik, Julien Dubuis, Olivier Marre, and Ravá Da Silveira. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/03/P03015. ieee: M. Berry, G. Tkačik, J. Dubuis, O. Marre, and R. Da Silveira, “A simple method for estimating the entropy of neural activity,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3. IOP Publishing Ltd., 2013. ista: Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. 2013. A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment. 2013(3), P03015. mla: Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, P03015, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03015. short: M. Berry, G. Tkačik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013). date_created: 2018-12-11T11:59:56Z date_published: 2013-03-12T00:00:00Z date_updated: 2021-01-12T07:00:14Z day: '12' department: - _id: GaTk doi: 10.1088/1742-5468/2013/03/P03015 intvolume: ' 2013' issue: '3' language: - iso: eng month: '03' oa_version: None publication: Journal of Statistical Mechanics Theory and Experiment publication_status: published publisher: IOP Publishing Ltd. publist_id: '3941' quality_controlled: '1' scopus_import: 1 status: public title: A simple method for estimating the entropy of neural activity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2013 year: '2013' ... --- _id: '2857' abstract: - lang: eng text: In the vibrant field of optogenetics, optics and genetic targeting are combined to commandeer cellular functions, such as the neuronal action potential, by optically stimulating light-sensitive ion channels expressed in the cell membrane. One broadly applicable manifestation of this approach are covalently attached photochromic tethered ligands (PTLs) that allow activating ligand-gated ion channels with outstanding spatial and temporal resolution. Here, we describe all steps towards the successful development and application of PTL-gated ion channels in cell lines and primary cells. The basis for these experiments forms a combination of molecular modeling, genetic engineering, cell culture, and electrophysiology. The light-gated glutamate receptor (LiGluR), which consists of the PTL-functionalized GluK2 receptor, serves as a model. alternative_title: - MIMB author: - first_name: Stephanie full_name: Szobota, Stephanie last_name: Szobota - first_name: Catherine full_name: Mckenzie, Catherine id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87 last_name: Mckenzie - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: Szobota S, Mckenzie C, Janovjak HL. Optical control of ligand-gated ion channels. Methods in Molecular Biology. 2013;998:417-435. doi:10.1007/978-1-62703-351-0_32 apa: Szobota, S., Mckenzie, C., & Janovjak, H. L. (2013). Optical control of ligand-gated ion channels. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-62703-351-0_32 chicago: Szobota, Stephanie, Catherine Mckenzie, and Harald L Janovjak. “Optical Control of Ligand-Gated Ion Channels.” Methods in Molecular Biology. Springer, 2013. https://doi.org/10.1007/978-1-62703-351-0_32. ieee: S. Szobota, C. Mckenzie, and H. L. Janovjak, “Optical control of ligand-gated ion channels,” Methods in Molecular Biology, vol. 998. Springer, pp. 417–435, 2013. ista: Szobota S, Mckenzie C, Janovjak HL. 2013. Optical control of ligand-gated ion channels. Methods in Molecular Biology. 998, 417–435. mla: Szobota, Stephanie, et al. “Optical Control of Ligand-Gated Ion Channels.” Methods in Molecular Biology, vol. 998, Springer, 2013, pp. 417–35, doi:10.1007/978-1-62703-351-0_32. short: S. Szobota, C. Mckenzie, H.L. Janovjak, Methods in Molecular Biology 998 (2013) 417–435. date_created: 2018-12-11T11:59:57Z date_published: 2013-02-22T00:00:00Z date_updated: 2021-01-12T07:00:17Z day: '22' ddc: - '570' department: - _id: HaJa doi: 10.1007/978-1-62703-351-0_32 ec_funded: 1 file: - access_level: open_access checksum: 1701f0d989f27ddac471b19a894ec0d1 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:34Z date_updated: 2020-07-14T12:45:51Z file_id: '4952' file_name: IST-2017-834-v1+1_szobota.pdf file_size: 336734 relation: main_file file_date_updated: 2020-07-14T12:45:51Z has_accepted_license: '1' intvolume: ' 998' language: - iso: eng month: '02' oa: 1 oa_version: Submitted Version page: 417 - 435 project: - _id: 255BFFFA-B435-11E9-9278-68D0E5697425 grant_number: RGY0084/2012 name: In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator) - _id: 25548C20-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303564' name: Microbial Ion Channels for Synthetic Neurobiology publication: Methods in Molecular Biology publication_status: published publisher: Springer publist_id: '3932' pubrep_id: '834' quality_controlled: '1' scopus_import: 1 status: public title: Optical control of ligand-gated ion channels type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 998 year: '2013' ... --- _id: '2860' abstract: - lang: eng text: 'In the hippocampus, cell assemblies forming mnemonic representations of space are thought to arise as a result of changes in functional connections of pyramidal cells. We have found that CA1 interneuron circuits are also reconfigured during goal-oriented spatial learning through modification of inputs from pyramidal cells. As learning progressed, new pyramidal assemblies expressed in theta cycles alternated with previously established ones, and eventually overtook them. The firing patterns of interneurons developed a relationship to new, learning-related assemblies: some interneurons associated their activity with new pyramidal assemblies while some others dissociated from them. These firing associations were explained by changes in the weight of monosynaptic inputs received by interneurons from new pyramidal assemblies, as these predicted the associational changes. Spatial learning thus engages circuit modifications in the hippocampus that incorporate a redistribution of inhibitory activity that might assist in the segregation of competing pyramidal cell assembly patterns in space and time.' acknowledgement: D.D. and J.C. were supported by a MRC Intramural Programme Grant U138197111 author: - first_name: David full_name: Dupret, David last_name: Dupret - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Dupret D, O’Neill J, Csicsvari JL. Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. Neuron. 2013;78(1):166-180. doi:10.1016/j.neuron.2013.01.033 apa: Dupret, D., O’Neill, J., & Csicsvari, J. L. (2013). Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.01.033 chicago: Dupret, David, Joseph O’Neill, and Jozsef L Csicsvari. “Dynamic Reconfiguration of Hippocampal Interneuron Circuits during Spatial Learning.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.01.033. ieee: D. Dupret, J. O’Neill, and J. L. Csicsvari, “Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning,” Neuron, vol. 78, no. 1. Elsevier, pp. 166–180, 2013. ista: Dupret D, O’Neill J, Csicsvari JL. 2013. Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning. Neuron. 78(1), 166–180. mla: Dupret, David, et al. “Dynamic Reconfiguration of Hippocampal Interneuron Circuits during Spatial Learning.” Neuron, vol. 78, no. 1, Elsevier, 2013, pp. 166–80, doi:10.1016/j.neuron.2013.01.033. short: D. Dupret, J. O’Neill, J.L. Csicsvari, Neuron 78 (2013) 166–180. date_created: 2018-12-11T11:59:59Z date_published: 2013-03-21T00:00:00Z date_updated: 2021-01-12T07:00:19Z day: '21' ddc: - '570' department: - _id: JoCs doi: 10.1016/j.neuron.2013.01.033 ec_funded: 1 file: - access_level: open_access checksum: 0e18cb8561153ddb50bb5af16e7c9e97 content_type: application/pdf creator: dernst date_created: 2019-01-23T08:08:07Z date_updated: 2020-07-14T12:45:52Z file_id: '5877' file_name: 2013_Neuron_Dupret.pdf file_size: 2637837 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 78' issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 166 - 180 project: - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex publication: Neuron publication_status: published publisher: Elsevier publist_id: '3929' quality_controlled: '1' scopus_import: 1 status: public title: Dynamic reconfiguration of hippocampal interneuron circuits during spatial learning 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: 78 year: '2013' ... --- _id: '2855' abstract: - lang: eng text: Genomic imprinting leads to preferred expression of either the maternal or paternal alleles of a subset of genes. Imprinting is essential for mammalian development, and its deregulation causes many diseases. However, the functional relevance of imprinting at the cellular level is poorly understood for most imprinted genes. We used mosaic analysis with double markers (MADM) in mice to create uniparental disomies (UPDs) and to visualize imprinting effects with single-cell resolution. Although chromosome 12 UPD did not produce detectable phenotypes, chromosome 7 UPD caused highly significant paternal growth dominance in the liver and lung, but not in the brain or heart. A single gene on chromosome 7, encoding the secreted insulin-like growth factor 2 (IGF2), accounts for most of the paternal dominance effect. Mosaic analyses implied additional imprinted loci on chromosome 7 acting cell autonomously to transmit the IGF2 signal. Our study reveals chromosome- and cell-type specificity of genomic imprinting effects. author: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Randy full_name: Johnson, Randy last_name: Johnson - first_name: Liqun full_name: Luo, Liqun last_name: Luo citation: ama: Hippenmeyer S, Johnson R, Luo L. Mosaic analysis with double markers reveals cell type specific paternal growth dominance. Cell Reports. 2013;3(3):960-967. doi:10.1016/j.celrep.2013.02.002 apa: Hippenmeyer, S., Johnson, R., & Luo, L. (2013). Mosaic analysis with double markers reveals cell type specific paternal growth dominance. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2013.02.002 chicago: Hippenmeyer, Simon, Randy Johnson, and Liqun Luo. “Mosaic Analysis with Double Markers Reveals Cell Type Specific Paternal Growth Dominance.” Cell Reports. Cell Press, 2013. https://doi.org/10.1016/j.celrep.2013.02.002. ieee: S. Hippenmeyer, R. Johnson, and L. Luo, “Mosaic analysis with double markers reveals cell type specific paternal growth dominance,” Cell Reports, vol. 3, no. 3. Cell Press, pp. 960–967, 2013. ista: Hippenmeyer S, Johnson R, Luo L. 2013. Mosaic analysis with double markers reveals cell type specific paternal growth dominance. Cell Reports. 3(3), 960–967. mla: Hippenmeyer, Simon, et al. “Mosaic Analysis with Double Markers Reveals Cell Type Specific Paternal Growth Dominance.” Cell Reports, vol. 3, no. 3, Cell Press, 2013, pp. 960–67, doi:10.1016/j.celrep.2013.02.002. short: S. Hippenmeyer, R. Johnson, L. Luo, Cell Reports 3 (2013) 960–967. date_created: 2018-12-11T11:59:57Z date_published: 2013-03-28T00:00:00Z date_updated: 2021-01-12T07:00:16Z day: '28' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.celrep.2013.02.002 file: - access_level: open_access checksum: 6e977b918e81384cd571ec5a9d812289 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:20Z date_updated: 2020-07-14T12:45:51Z file_id: '5274' file_name: IST-2016-405-v1+1_1-s2.0-S2211124713000612-main.pdf file_size: 1907211 relation: main_file file_date_updated: 2020-07-14T12:45:51Z has_accepted_license: '1' intvolume: ' 3' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 960 - 967 publication: Cell Reports publication_status: published publisher: Cell Press publist_id: '3937' pubrep_id: '405' quality_controlled: '1' scopus_import: 1 status: public title: Mosaic analysis with double markers reveals cell type specific paternal growth dominance tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2013' ... --- _id: '2856' abstract: - lang: eng text: 'G protein–coupled receptors (GPCRs), the largest family of membrane signaling proteins, respond to neurotransmitters, hormones and small environmental molecules. The neuronal function of many GPCRs has been difficult to resolve because of an inability to gate them with subtype specificity, spatial precision, speed and reversibility. To address this, we developed an approach for opto-chemical engineering of native GPCRs. We applied this to the metabotropic glutamate receptors (mGluRs) to generate light-agonized and light-antagonized mGluRs (LimGluRs). The light-agonized LimGluR2, on which we focused, was fast, bistable and supported multiple rounds of on/off switching. Light gated two of the primary neuronal functions of mGluR2: suppression of excitability and inhibition of neurotransmitter release. We found that the light-antagonized tool LimGluR2-block was able to manipulate negative feedback of synaptically released glutamate on transmitter release. We generalized the optical control to two additional family members: mGluR3 and mGluR6. This system worked in rodent brain slices and in zebrafish in vivo, where we found that mGluR2 modulated the threshold for escape behavior. These light-gated mGluRs pave the way for determining the roles of mGluRs in synaptic plasticity, memory and disease.' acknowledgement: National Science Foundation grants CHE-0233882 and CHE-0840505 (to the College of Chemistry at the University of California, Berkeley), a postdoctoral fellowship of the European Molecular Biology Organization (H.J.) author: - first_name: Joshua full_name: Levitz, Joshua last_name: Levitz - first_name: Carlos full_name: Pantoja, Carlos last_name: Pantoja - first_name: Benjamin full_name: Gaub, Benjamin last_name: Gaub - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Andreas full_name: Reiner, Andreas last_name: Reiner - first_name: Adam full_name: Hoagland, Adam last_name: Hoagland - first_name: David full_name: Schoppik, David last_name: Schoppik - first_name: Brian full_name: Kane, Brian last_name: Kane - first_name: Philipp full_name: Stawski, Philipp last_name: Stawski - first_name: Alexander full_name: Schier, Alexander last_name: Schier - first_name: Dirk full_name: Trauner, Dirk last_name: Trauner - first_name: Ehud full_name: Isacoff, Ehud last_name: Isacoff citation: ama: Levitz J, Pantoja C, Gaub B, et al. Optical control of metabotropic glutamate receptors. Nature Neuroscience. 2013;16:507-516. doi:10.1038/nn.3346 apa: Levitz, J., Pantoja, C., Gaub, B., Janovjak, H. L., Reiner, A., Hoagland, A., … Isacoff, E. (2013). Optical control of metabotropic glutamate receptors. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3346 chicago: Levitz, Joshua, Carlos Pantoja, Benjamin Gaub, Harald L Janovjak, Andreas Reiner, Adam Hoagland, David Schoppik, et al. “Optical Control of Metabotropic Glutamate Receptors.” Nature Neuroscience. Nature Publishing Group, 2013. https://doi.org/10.1038/nn.3346. ieee: J. Levitz et al., “Optical control of metabotropic glutamate receptors,” Nature Neuroscience, vol. 16. Nature Publishing Group, pp. 507–516, 2013. ista: Levitz J, Pantoja C, Gaub B, Janovjak HL, Reiner A, Hoagland A, Schoppik D, Kane B, Stawski P, Schier A, Trauner D, Isacoff E. 2013. Optical control of metabotropic glutamate receptors. Nature Neuroscience. 16, 507–516. mla: Levitz, Joshua, et al. “Optical Control of Metabotropic Glutamate Receptors.” Nature Neuroscience, vol. 16, Nature Publishing Group, 2013, pp. 507–16, doi:10.1038/nn.3346. short: J. Levitz, C. Pantoja, B. Gaub, H.L. Janovjak, A. Reiner, A. Hoagland, D. Schoppik, B. Kane, P. Stawski, A. Schier, D. Trauner, E. Isacoff, Nature Neuroscience 16 (2013) 507–516. date_created: 2018-12-11T11:59:57Z date_published: 2013-03-03T00:00:00Z date_updated: 2021-01-12T07:00:16Z day: '03' department: - _id: HaJa doi: 10.1038/nn.3346 external_id: pmid: - '23455609' intvolume: ' 16' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681425/ month: '03' oa: 1 oa_version: Submitted Version page: 507 - 516 pmid: 1 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '3936' quality_controlled: '1' scopus_import: 1 status: public title: Optical control of metabotropic glutamate receptors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2013' ... --- _id: '2859' abstract: - lang: eng text: Given a continuous function f:X-R on a topological space, we consider the preimages of intervals and their homology groups and show how to read the ranks of these groups from the extended persistence diagram of f. In addition, we quantify the robustness of the homology classes under perturbations of f using well groups, and we show how to read the ranks of these groups from the same extended persistence diagram. The special case X=R3 has ramifications in the fields of medical imaging and scientific visualization. author: - first_name: Paul full_name: Bendich, Paul id: 43F6EC54-F248-11E8-B48F-1D18A9856A87 last_name: Bendich - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov - first_name: Amit full_name: Patel, Amit id: 34A254A0-F248-11E8-B48F-1D18A9856A87 last_name: Patel citation: ama: Bendich P, Edelsbrunner H, Morozov D, Patel A. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 2013;15(1):51-72. doi:10.4310/HHA.2013.v15.n1.a3 apa: Bendich, P., Edelsbrunner, H., Morozov, D., & Patel, A. (2013). Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2013.v15.n1.a3 chicago: Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “Homology and Robustness of Level and Interlevel Sets.” Homology, Homotopy and Applications. International Press, 2013. https://doi.org/10.4310/HHA.2013.v15.n1.a3. ieee: P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness of level and interlevel sets,” Homology, Homotopy and Applications, vol. 15, no. 1. International Press, pp. 51–72, 2013. ista: Bendich P, Edelsbrunner H, Morozov D, Patel A. 2013. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 15(1), 51–72. mla: Bendich, Paul, et al. “Homology and Robustness of Level and Interlevel Sets.” Homology, Homotopy and Applications, vol. 15, no. 1, International Press, 2013, pp. 51–72, doi:10.4310/HHA.2013.v15.n1.a3. short: P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, Homology, Homotopy and Applications 15 (2013) 51–72. date_created: 2018-12-11T11:59:58Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T07:00:18Z day: '01' department: - _id: HeEd doi: 10.4310/HHA.2013.v15.n1.a3 external_id: arxiv: - '1102.3389' intvolume: ' 15' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1102.3389v1 month: '05' oa: 1 oa_version: Preprint page: 51 - 72 publication: Homology, Homotopy and Applications publication_status: published publisher: International Press publist_id: '3930' quality_controlled: '1' scopus_import: 1 status: public title: Homology and robustness of level and interlevel sets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '2863' abstract: - lang: eng text: Neural populations encode information about their stimulus in a collective fashion, by joint activity patterns of spiking and silence. A full account of this mapping from stimulus to neural activity is given by the conditional probability distribution over neural codewords given the sensory input. For large populations, direct sampling of these distributions is impossible, and so we must rely on constructing appropriate models. We show here that in a population of 100 retinal ganglion cells in the salamander retina responding to temporal white-noise stimuli, dependencies between cells play an important encoding role. We introduce the stimulus-dependent maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear model of a single neuron, to a pairwise-coupled neural population. We find that the SDME model gives a more accurate account of single cell responses and in particular significantly outperforms uncoupled models in reproducing the distributions of population codewords emitted in response to a stimulus. We show how the SDME model, in conjunction with static maximum entropy models of population vocabulary, can be used to estimate information-theoretic quantities like average surprise and information transmission in a neural population. article_number: e1002922 author: - first_name: Einat full_name: Granot Atedgi, Einat last_name: Granot Atedgi - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Ronen full_name: Segev, Ronen last_name: Segev - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman citation: ama: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 2013;9(3). doi:10.1371/journal.pcbi.1002922 apa: Granot Atedgi, E., Tkačik, G., Segev, R., & Schneidman, E. (2013). Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1002922 chicago: Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1002922. ieee: E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” PLoS Computational Biology, vol. 9, no. 3. Public Library of Science, 2013. ista: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. 2013. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 9(3), e1002922. mla: Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922. short: E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013). date_created: 2018-12-11T12:00:00Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T07:00:20Z day: '01' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1002922 file: - access_level: open_access checksum: 5a30876c193209fa05b26db71845dd16 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:45Z date_updated: 2020-07-14T12:45:52Z file_id: '5099' file_name: IST-2013-120-v1+1_journal.pcbi.1002922.pdf file_size: 1548120 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 9' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '3926' pubrep_id: '120' quality_controlled: '1' scopus_import: 1 status: public title: Stimulus-dependent maximum entropy models of neural population codes 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: '2862' abstract: - lang: eng text: Motile cilia perform crucial functions during embryonic development and throughout adult life. Development of organs containing motile cilia involves regulation of cilia formation (ciliogenesis) and formation of a luminal space (lumenogenesis) in which cilia generate fluid flows. Control of ciliogenesis and lumenogenesis is not yet fully understood, and it remains unclear whether these processes are coupled. In the zebrafish embryo, lethal giant larvae 2 (lgl2) is expressed prominently in ciliated organs. Lgl proteins are involved in establishing cell polarity and have been implicated in vesicle trafficking. Here, we identified a role for Lgl2 in development of ciliated epithelia in Kupffer's vesicle, which directs left-right asymmetry of the embryo; the otic vesicles, which give rise to the inner ear; and the pronephric ducts of the kidney. Using Kupffer's vesicle as a model ciliated organ, we found that depletion of Lgl2 disrupted lumen formation and reduced cilia number and length. Immunofluorescence and time-lapse imaging of Kupffer's vesicle morphogenesis in Lgl2-deficient embryos suggested cell adhesion defects and revealed loss of the adherens junction component E-cadherin at lateral membranes. Genetic interaction experiments indicate that Lgl2 interacts with Rab11a to regulate E-cadherin and mediate lumen formation that is uncoupled from cilia formation. These results uncover new roles and interactions for Lgl2 that are crucial for both lumenogenesis and ciliogenesis and indicate that these processes are genetically separable in zebrafish. acknowledgement: Deposited in PMC for release after 12 months. We thank members of the Amack lab for helpful discussions and Mahendra Sonawane for donating reagents. author: - first_name: Hwee full_name: Tay, Hwee last_name: Tay - first_name: Sabrina full_name: Schulze, Sabrina last_name: Schulze - first_name: Julien full_name: Compagnon, Julien id: 2E3E0988-F248-11E8-B48F-1D18A9856A87 last_name: Compagnon - first_name: Fiona full_name: Foley, Fiona last_name: Foley - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: H Joseph full_name: Yost, H Joseph last_name: Yost - first_name: Salim full_name: Abdelilah Seyfried, Salim last_name: Abdelilah Seyfried - first_name: Jeffrey full_name: Amack, Jeffrey last_name: Amack citation: ama: Tay H, Schulze S, Compagnon J, et al. Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. Development. 2013;140(7):1550-1559. doi:10.1242/dev.087130 apa: Tay, H., Schulze, S., Compagnon, J., Foley, F., Heisenberg, C.-P. J., Yost, H. J., … Amack, J. (2013). Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. Development. Company of Biologists. https://doi.org/10.1242/dev.087130 chicago: Tay, Hwee, Sabrina Schulze, Julien Compagnon, Fiona Foley, Carl-Philipp J Heisenberg, H Joseph Yost, Salim Abdelilah Seyfried, and Jeffrey Amack. “Lethal Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.” Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.087130. ieee: H. Tay et al., “Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle,” Development, vol. 140, no. 7. Company of Biologists, pp. 1550–1559, 2013. ista: Tay H, Schulze S, Compagnon J, Foley F, Heisenberg C-PJ, Yost HJ, Abdelilah Seyfried S, Amack J. 2013. Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle. Development. 140(7), 1550–1559. mla: Tay, Hwee, et al. “Lethal Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.” Development, vol. 140, no. 7, Company of Biologists, 2013, pp. 1550–59, doi:10.1242/dev.087130. short: H. Tay, S. Schulze, J. Compagnon, F. Foley, C.-P.J. Heisenberg, H.J. Yost, S. Abdelilah Seyfried, J. Amack, Development 140 (2013) 1550–1559. date_created: 2018-12-11T11:59:59Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T07:00:20Z day: '01' department: - _id: CaHe doi: 10.1242/dev.087130 external_id: pmid: - '23482490' intvolume: ' 140' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/ month: '04' oa: 1 oa_version: Submitted Version page: 1550 - 1559 pmid: 1 publication: Development publication_status: published publisher: Company of Biologists publist_id: '3927' quality_controlled: '1' scopus_import: 1 status: public title: Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s vesicle type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 140 year: '2013' ... --- _id: '2861' abstract: - lang: eng text: We consider a two-parameter family of piecewise linear maps in which the moduli of the two slopes take different values. We provide numerical evidence of the existence of some parameter regions in which the Lyapunov exponent and the topological entropy remain constant. Analytical proof of this phenomenon is also given for certain cases. Surprisingly however, the systems with that property are not conjugate as we prove by using kneading theory. article_number: '125101' author: - first_name: Vicente full_name: Botella Soler, Vicente id: 421234E8-F248-11E8-B48F-1D18A9856A87 last_name: Botella Soler orcid: 0000-0002-8790-1914 - first_name: José full_name: Oteo, José last_name: Oteo - first_name: Javier full_name: Ros, Javier last_name: Ros - first_name: Paul full_name: Glendinning, Paul last_name: Glendinning citation: ama: 'Botella Soler V, Oteo J, Ros J, Glendinning P. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 2013;46(12). doi:10.1088/1751-8113/46/12/125101' apa: 'Botella Soler, V., Oteo, J., Ros, J., & Glendinning, P. (2013). Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. IOP Publishing Ltd. https://doi.org/10.1088/1751-8113/46/12/125101' chicago: 'Botella Soler, Vicente, José Oteo, Javier Ros, and Paul Glendinning. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1751-8113/46/12/125101.' ieee: 'V. Botella Soler, J. Oteo, J. Ros, and P. Glendinning, “Lyapunov exponent and topological entropy plateaus in piecewise linear maps,” Journal of Physics A: Mathematical and Theoretical, vol. 46, no. 12. IOP Publishing Ltd., 2013.' ista: 'Botella Soler V, Oteo J, Ros J, Glendinning P. 2013. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 46(12), 125101.' mla: 'Botella Soler, Vicente, et al. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” Journal of Physics A: Mathematical and Theoretical, vol. 46, no. 12, 125101, IOP Publishing Ltd., 2013, doi:10.1088/1751-8113/46/12/125101.' short: 'V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A: Mathematical and Theoretical 46 (2013).' date_created: 2018-12-11T11:59:59Z date_published: 2013-03-29T00:00:00Z date_updated: 2021-01-12T07:00:19Z day: '29' department: - _id: GaTk doi: 10.1088/1751-8113/46/12/125101 intvolume: ' 46' issue: '12' language: - iso: eng month: '03' oa_version: None publication: 'Journal of Physics A: Mathematical and Theoretical' publication_status: published publisher: IOP Publishing Ltd. publist_id: '3928' quality_controlled: '1' scopus_import: 1 status: public title: Lyapunov exponent and topological entropy plateaus in piecewise linear maps type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 46 year: '2013' ... --- _id: '2877' abstract: - lang: eng text: 'Premise of the study: To reach favorable conditions for photosynthesis, seedlings grow upward when deprived of light upon underground germination. To direct their growth, they use their negative gravitropic capacity. Negative gravitropism is under tight control of multiple hormones. • Methods: By counting the number of standing plants in a population or by real time monitoring of the reorientation of gravistimulated seedlings of Arabidopsis thaliana, we evaluated the negative gravitropism of ethylene or brassinosteroid (BR) treated plants. Meta-analysis of transcriptomic data on AUX / IAA genes was gathered, and subsequent mutant analysis was performed. • Key results: Ethylene and BR have opposite effects in regulating shoot gravitropism. Lack of BR enhances gravitropic reorientation in 2-d-old seedlings, whereas ethylene does not. Lack of ethylene signaling results in enhanced BR sensitivity. Ethylene and BRs regulate overlapping sets of AUX / IAA genes. BRs regulate a wider range of auxin signaling components than ethylene. • Conclusions: Upward growth in seedlings depends strongly on the internal hormonal balance. Endogenous ethylene stimulates, whereas BRs reduce negative gravitropism in a manner that depends on the function of different, yet overlapping sets of auxin signaling components.' author: - first_name: Filip full_name: Vandenbussche, Filip last_name: Vandenbussche - first_name: Pieter full_name: Callebert, Pieter last_name: Callebert - first_name: Petra full_name: Žádníková, Petra last_name: Žádníková - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Dominique full_name: Van Der Straeten, Dominique last_name: Van Der Straeten citation: ama: Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. American Journal of Botany. 2013;100(1):215-225. doi:10.3732/ajb.1200264 apa: Vandenbussche, F., Callebert, P., Žádníková, P., Benková, E., & Van Der Straeten, D. (2013). Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. American Journal of Botany. Botanical Society of America. https://doi.org/10.3732/ajb.1200264 chicago: Vandenbussche, Filip, Pieter Callebert, Petra Žádníková, Eva Benková, and Dominique Van Der Straeten. “Brassinosteroid Control of Shoot Gravitropism Interacts with Ethylene and Depends on Auxin Signaling Components.” American Journal of Botany. Botanical Society of America, 2013. https://doi.org/10.3732/ajb.1200264. ieee: F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, and D. Van Der Straeten, “Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components,” American Journal of Botany, vol. 100, no. 1. Botanical Society of America, pp. 215–225, 2013. ista: Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. 2013. Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components. American Journal of Botany. 100(1), 215–225. mla: Vandenbussche, Filip, et al. “Brassinosteroid Control of Shoot Gravitropism Interacts with Ethylene and Depends on Auxin Signaling Components.” American Journal of Botany, vol. 100, no. 1, Botanical Society of America, 2013, pp. 215–25, doi:10.3732/ajb.1200264. short: F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, D. Van Der Straeten, American Journal of Botany 100 (2013) 215–225. date_created: 2018-12-11T12:00:06Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:00:25Z day: '01' doi: 10.3732/ajb.1200264 extern: 1 intvolume: ' 100' issue: '1' month: '01' page: 215 - 225 publication: American Journal of Botany publication_status: published publisher: Botanical Society of America publist_id: '3883' quality_controlled: 0 status: public title: Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components type: journal_article volume: 100 year: '2013' ... --- _id: '2883' abstract: - lang: eng text: Plant architecture is influenced by the polar, cell-to-cell transport of auxin that is primarily provided and regulated by plasma membrane efflux catalysts of the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were shown to require the functionality of the FK506 binding protein42 TWISTED DWARF1 (TWD1), although underlying mechanisms are unclear. By genetic manipulation of TWD1 expression, we show here that TWD1 affects shootward root auxin reflux and, thus, downstream developmental traits, such as epidermal twisting and gravitropism of the root. Using immunological assays, we demonstrate a predominant lateral, mainly outward-facing, plasma membrane location for TWD1 in the root epidermis characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3. At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1. In planta bioluminescence resonance energy transfer analysis was used to verify specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein interaction at the plasma membrane, minimizing reflux from the root apoplast into the cytoplasm. acknowledgement: We would thank Vincent Vincenzetti and Laurence Charrier for excellent technical assistance, A. von Arnim for the donation of BRET vectors, E. Spalding for TWD1-CFP, TWD1-CFP/29-1-GFP/ER-YFP, and ABCB4-GFP lines, M. Palmgren for discussion and support, and E. Martinoia for TT12 cDNA, support, and mentorship. Imaging data were partially collected at the Center for Advanced Bioimaging, University of Copenhagen, Denmark. This work was supported by grants from the Novartis Foundation (to M.G.), from the Danish Research School for Biotechnology (to M.G. and A.S.), from the Forschungskredit of the University of Zurich (to A.B.), from the Pool de Recherche of the University of Fribourg (to M.G.), and from the Swiss National Funds (to M.G.). M.G. dedicates this work to his father, who passed away during the resubmission process. author: - first_name: Bangjun full_name: Wang, Bangjun last_name: Wang - first_name: Aurélien full_name: Bailly, Aurélien last_name: Bailly - first_name: Marta full_name: Zwiewk, Marta last_name: Zwiewk - first_name: Sina full_name: Henrichs, Sina last_name: Henrichs - first_name: Elisa full_name: Azzarello, Elisa last_name: Azzarello - first_name: Stefano full_name: Mancuso, Stefano last_name: Mancuso - first_name: Masayoshi full_name: Maeshima, Masayoshi last_name: Maeshima - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Alexander full_name: Schulz, Alexander last_name: Schulz - first_name: Markus full_name: Geisler, Markus last_name: Geisler citation: ama: Wang B, Bailly A, Zwiewk M, et al. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 2013;25(1):202-214. doi:10.1105/tpc.112.105999 apa: Wang, B., Bailly, A., Zwiewk, M., Henrichs, S., Azzarello, E., Mancuso, S., … Geisler, M. (2013). Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.105999 chicago: Wang, Bangjun, Aurélien Bailly, Marta Zwiewk, Sina Henrichs, Elisa Azzarello, Stefano Mancuso, Masayoshi Maeshima, Jiří Friml, Alexander Schulz, and Markus Geisler. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.112.105999. ieee: B. Wang et al., “Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane,” Plant Cell, vol. 25, no. 1. American Society of Plant Biologists, pp. 202–214, 2013. ista: Wang B, Bailly A, Zwiewk M, Henrichs S, Azzarello E, Mancuso S, Maeshima M, Friml J, Schulz A, Geisler M. 2013. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 25(1), 202–214. mla: Wang, Bangjun, et al. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” Plant Cell, vol. 25, no. 1, American Society of Plant Biologists, 2013, pp. 202–14, doi:10.1105/tpc.112.105999. short: B. Wang, A. Bailly, M. Zwiewk, S. Henrichs, E. Azzarello, S. Mancuso, M. Maeshima, J. Friml, A. Schulz, M. Geisler, Plant Cell 25 (2013) 202–214. date_created: 2018-12-11T12:00:08Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:00:28Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.112.105999 external_id: pmid: - '23321285' intvolume: ' 25' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/ month: '01' oa: 1 oa_version: Submitted Version page: 202 - 214 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3878' quality_controlled: '1' scopus_import: 1 status: public title: Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '2880' abstract: - lang: eng text: Lateral root (LR) formation is initiated when pericycle cells accumulate auxin, thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions, giving rise to a new primordium. How this auxin maximum in pericycle cells builds up and remains focused is not understood. We report that the endodermis plays an active role in the regulation of auxin accumulation and is instructive for FCs to progress during the LR initiation (LRI) phase. We describe the functional importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux pathway causes dramatic defects in the progress of FCs towards the next initiation phase. Our data identify an unexpected regulatory function for the endodermis in LRI as part of the fine-tuning mechanism that appears to act as a check point in LR organogenesis after FCs are specified. author: - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Marleen full_name: Vanstraelen, Marleen last_name: Vanstraelen - first_name: Bert full_name: De Rybel, Bert last_name: De Rybel - first_name: Ding full_name: Zhaojun, Ding last_name: Zhaojun - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Marhavý P, Vanstraelen M, De Rybel B, et al. Auxin reflux between the endodermis and pericycle promotes lateral root initiation. EMBO Journal. 2013;32(1):149-158. doi:10.1038/emboj.2012.303 apa: Marhavý, P., Vanstraelen, M., De Rybel, B., Zhaojun, D., Bennett, M., Beeckman, T., & Benková, E. (2013). Auxin reflux between the endodermis and pericycle promotes lateral root initiation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.303 chicago: Marhavý, Peter, Marleen Vanstraelen, Bert De Rybel, Ding Zhaojun, Malcolm Bennett, Tom Beeckman, and Eva Benková. “Auxin Reflux between the Endodermis and Pericycle Promotes Lateral Root Initiation.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2012.303. ieee: P. Marhavý et al., “Auxin reflux between the endodermis and pericycle promotes lateral root initiation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell, pp. 149–158, 2013. ista: Marhavý P, Vanstraelen M, De Rybel B, Zhaojun D, Bennett M, Beeckman T, Benková E. 2013. Auxin reflux between the endodermis and pericycle promotes lateral root initiation. EMBO Journal. 32(1), 149–158. mla: Marhavý, Peter, et al. “Auxin Reflux between the Endodermis and Pericycle Promotes Lateral Root Initiation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 149–58, doi:10.1038/emboj.2012.303. short: P. Marhavý, M. Vanstraelen, B. De Rybel, D. Zhaojun, M. Bennett, T. Beeckman, E. Benková, EMBO Journal 32 (2013) 149–158. date_created: 2018-12-11T12:00:07Z date_published: 2013-01-09T00:00:00Z date_updated: 2021-01-12T07:00:27Z day: '09' department: - _id: EvBe doi: 10.1038/emboj.2012.303 ec_funded: 1 external_id: pmid: - '23178590' intvolume: ' 32' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/ month: '01' oa: 1 oa_version: Submitted Version page: 149 - 158 pmid: 1 project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3882' quality_controlled: '1' scopus_import: 1 status: public title: Auxin reflux between the endodermis and pericycle promotes lateral root initiation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '2882' abstract: - lang: eng text: Gravitropic bending of plant organs is mediated by an asymmetric signaling of the plant hormone auxin between the upper and lower side of the respective organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows asymmetric action during gravitropic responses. Immunodetection using an antibody against GA and monitoring GA signaling output by downstream degradation of DELLA proteins revealed an asymmetric GA distribution and response with the maximum at the lower side of gravistimulated roots. Genetic or pharmacological manipulation of GA levels or response affects gravity-mediated auxin redistribution and root bending response. The higher GA levels at the lower side of the root correlate with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane. The observed increase in PIN2 stability is caused by a specific GA effect on trafficking of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin A-sensitive endosomes. Our results suggest that asymmetric auxin distribution instructive for gravity-induced differential growth is consolidated by the asymmetric action of GA that stabilizes the PIN-dependent auxin stream along the lower side of gravistimulated roots. author: - first_name: Christian full_name: Löfke, Christian last_name: Löfke - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Ingo full_name: Heilmann, Ingo last_name: Heilmann - first_name: Marc full_name: Van Montagu, Marc last_name: Van Montagu - first_name: Thomas full_name: Teichmann, Thomas last_name: Teichmann - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. PNAS. 2013;110(9):3627-3632. doi:10.1073/pnas.1300107110 apa: Löfke, C., Zwiewka, M., Heilmann, I., Van Montagu, M., Teichmann, T., & Friml, J. (2013). Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1300107110 chicago: Löfke, Christian, Marta Zwiewka, Ingo Heilmann, Marc Van Montagu, Thomas Teichmann, and Jiří Friml. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1300107110. ieee: C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, and J. Friml, “Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism,” PNAS, vol. 110, no. 9. National Academy of Sciences, pp. 3627–3632, 2013. ista: Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. 2013. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. PNAS. 110(9), 3627–3632. mla: Löfke, Christian, et al. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS, vol. 110, no. 9, National Academy of Sciences, 2013, pp. 3627–32, doi:10.1073/pnas.1300107110. short: C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml, PNAS 110 (2013) 3627–3632. date_created: 2018-12-11T12:00:07Z date_published: 2013-02-26T00:00:00Z date_updated: 2021-01-12T07:00:27Z day: '26' department: - _id: JiFr doi: 10.1073/pnas.1300107110 external_id: pmid: - '23391733' intvolume: ' 110' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/ month: '02' oa: 1 oa_version: Submitted Version page: 3627 - 3632 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3879' quality_controlled: '1' scopus_import: 1 status: public title: Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2885' abstract: - lang: eng text: 'This volume contains the post-proceedings of the 8th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, MEMICS 2012, held in Znojmo, Czech Republic, in October, 2012. The 13 thoroughly revised papers were carefully selected out of 31 submissions and are presented together with 6 invited papers. The topics covered by the papers include: computer-aided analysis and verification, applications of game theory in computer science, networks and security, modern trends of graph theory in computer science, electronic systems design and testing, and quantum information processing.' acknowledgement: Red Hat Czech Republic, Y Soft alternative_title: - LNCS citation: ama: Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D, eds. Mathematical and Engineering Methods in Computer Science. Vol 7721. Springer; 2013:1-228. doi:10.1007/978-3-642-36046-6 apa: 'Kucera, A., Henzinger, T. A., Nesetril, J., Vojnar, T., & Antos, D. (Eds.). (2013). Mathematical and Engineering Methods in Computer Science (Vol. 7721, pp. 1–228). Presented at the MEMICS: Mathematical and Engineering methods in computer science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6' chicago: Kucera, Antonin, Thomas A Henzinger, Jaroslav Nesetril, Tomas Vojnar, and David Antos, eds. Mathematical and Engineering Methods in Computer Science. Vol. 7721. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6. ieee: A. Kucera, T. A. Henzinger, J. Nesetril, T. Vojnar, and D. Antos, Eds., Mathematical and Engineering Methods in Computer Science, vol. 7721. Springer, 2013, pp. 1–228. ista: Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D eds. 2013. Mathematical and Engineering Methods in Computer Science, Springer,p. mla: Kucera, Antonin, et al., editors. Mathematical and Engineering Methods in Computer Science. Vol. 7721, Springer, 2013, pp. 1–228, doi:10.1007/978-3-642-36046-6. short: A. Kucera, T.A. Henzinger, J. Nesetril, T. Vojnar, D. Antos, eds., Mathematical and Engineering Methods in Computer Science, Springer, 2013. conference: end_date: 2012-10-28 location: Znojmo, Czech Republic name: 'MEMICS: Mathematical and Engineering methods in computer science' start_date: 2012-10-25 date_created: 2018-12-11T12:00:08Z date_published: 2013-01-09T00:00:00Z date_updated: 2019-08-02T12:37:55Z day: '09' department: - _id: ToHe doi: 10.1007/978-3-642-36046-6 editor: - first_name: Antonin full_name: Kucera, Antonin last_name: Kucera - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jaroslav full_name: Nesetril, Jaroslav last_name: Nesetril - first_name: Tomas full_name: Vojnar, Tomas last_name: Vojnar - first_name: David full_name: Antos, David last_name: Antos intvolume: ' 7721' language: - iso: eng month: '01' oa_version: None page: 1 - 228 publication_status: published publisher: Springer publist_id: '3874' quality_controlled: '1' series_title: Lecture Notes in Computer Science status: public title: Mathematical and Engineering Methods in Computer Science type: conference_editor user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7721 year: '2013' ... --- _id: '2881' abstract: - lang: eng text: The puzzle piece-shaped Arabidopsis leaf pavement cells (PCs) with interdigitated lobes and indents is a good model system to investigate the mechanisms that coordinate cell polarity and shape formation within a tissue. Auxin has been shown to coordinate the interdigitation by activating ROP GTPase-dependent signaling pathways. To identify additional components or mechanisms, we screened for mutants with abnormal PC morphogenesis and found that cytokinin signaling regulates the PC interdigitation pattern. Reduction in cytokinin accumulation and defects in cytokinin signaling (such as in ARR7-over-expressing lines, the ahk3cre1 cytokinin receptor mutant, and the ahp12345 cytokinin signaling mutant) enhanced PC interdigitation, whereas over-production of cytokinin and over-activation of cytokinin signaling in an ARR20 over-expression line delayed or abolished PC interdigitation throughout the cotyledon. Genetic and biochemical analyses suggest that cytokinin signaling acts upstream of ROPs to suppress the formation of interdigitated pattern. Our results provide novel mechanistic understanding of the pathways controlling PC shape and uncover a new role for cytokinin signaling in cell morphogenesis. acknowledgement: is work was supported by grants from the US National Institute of General Medical Sciences (GM081451 and GM081451-03S2) to ZY. We thank National Science Foundation grant (IOS-1147250) to GVR and MX. HL and DL were partially supported by the Chinese Scholarship Council. author: - first_name: Hongjiang full_name: Hongjiang Li id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Tongda full_name: Xu, Tongda last_name: Xu - first_name: Deshu full_name: Lin, Deshu last_name: Lin - first_name: Mingzhang full_name: Wen, Mingzhang last_name: Wen - first_name: Mingtang full_name: Xie, Mingtang last_name: Xie - first_name: Jérôme full_name: Duclercq, Jérôme last_name: Duclercq - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Jungmook full_name: Kim, Jungmook last_name: Kim - first_name: G Venugopala full_name: Reddy, G Venugopala last_name: Reddy - first_name: Jianru full_name: Zuo, Jianru last_name: Zuo - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Hongwei full_name: Guo, Hongwei last_name: Guo - first_name: Zhenbiao full_name: Yang, Zhenbiao last_name: Yang citation: ama: Li H, Xu T, Lin D, et al. Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell Research. 2013;23(2):290-299. doi:10.1038/cr.2012.146 apa: Li, H., Xu, T., Lin, D., Wen, M., Xie, M., Duclercq, J., … Yang, Z. (2013). Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell Research. Nature Publishing Group. https://doi.org/10.1038/cr.2012.146 chicago: Li, Hongjiang, Tongda Xu, Deshu Lin, Mingzhang Wen, Mingtang Xie, Jérôme Duclercq, Agnieszka Bielach, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis in Arabidopsis.” Cell Research. Nature Publishing Group, 2013. https://doi.org/10.1038/cr.2012.146. ieee: H. Li et al., “Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis,” Cell Research, vol. 23, no. 2. Nature Publishing Group, pp. 290–299, 2013. ista: Li H, Xu T, Lin D, Wen M, Xie M, Duclercq J, Bielach A, Kim J, Reddy GV, Zuo J, Benková E, Friml J, Guo H, Yang Z. 2013. Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell Research. 23(2), 290–299. mla: Li, Hongjiang, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis in Arabidopsis.” Cell Research, vol. 23, no. 2, Nature Publishing Group, 2013, pp. 290–99, doi:10.1038/cr.2012.146. short: H. Li, T. Xu, D. Lin, M. Wen, M. Xie, J. Duclercq, A. Bielach, J. Kim, G.V. Reddy, J. Zuo, E. Benková, J. Friml, H. Guo, Z. Yang, Cell Research 23 (2013) 290–299. date_created: 2018-12-11T12:00:07Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T07:00:27Z day: '01' doi: 10.1038/cr.2012.146 extern: 1 intvolume: ' 23' issue: '2' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567823/ month: '02' oa: 1 page: 290 - 299 publication: Cell Research publication_status: published publisher: Nature Publishing Group publist_id: '3881' quality_controlled: 0 status: public title: Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis type: journal_article volume: 23 year: '2013' ... --- _id: '2884' author: - first_name: Jean-Léon full_name: Maître, Jean-Léon id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87 last_name: Maître orcid: 0000-0002-3688-1474 - first_name: Hélène full_name: Berthoumieux, Hélène last_name: Berthoumieux - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Guillaume full_name: Salbreux, Guillaume last_name: Salbreux - first_name: Frank full_name: Julicher, Frank last_name: Julicher - first_name: Ewa full_name: Paluch, Ewa last_name: Paluch - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Maître J-L, Berthoumieux H, Krens G, et al. Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. 2013;29(2):147-150. doi:10.1051/medsci/2013292011 apa: Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch, E., & Heisenberg, C.-P. J. (2013). Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. Éditions Médicales et Scientifiques. https://doi.org/10.1051/medsci/2013292011 chicago: Maître, Jean-Léon, Hélène Berthoumieux, Gabriel Krens, Guillaume Salbreux, Frank Julicher, Ewa Paluch, and Carl-Philipp J Heisenberg. “Cell Adhesion Mechanics of Zebrafish Gastrulation.” Medecine Sciences. Éditions Médicales et Scientifiques, 2013. https://doi.org/10.1051/medsci/2013292011. ieee: J.-L. Maître et al., “Cell adhesion mechanics of zebrafish gastrulation,” Medecine Sciences, vol. 29, no. 2. Éditions Médicales et Scientifiques, pp. 147–150, 2013. ista: Maître J-L, Berthoumieux H, Krens G, Salbreux G, Julicher F, Paluch E, Heisenberg C-PJ. 2013. Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. 29(2), 147–150. mla: Maître, Jean-Léon, et al. “Cell Adhesion Mechanics of Zebrafish Gastrulation.” Medecine Sciences, vol. 29, no. 2, Éditions Médicales et Scientifiques, 2013, pp. 147–50, doi:10.1051/medsci/2013292011. short: J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Medecine Sciences 29 (2013) 147–150. date_created: 2018-12-11T12:00:08Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T07:00:28Z day: '01' department: - _id: CaHe doi: 10.1051/medsci/2013292011 intvolume: ' 29' issue: '2' language: - iso: eng month: '02' oa_version: None page: 147 - 150 project: - _id: 252064B8-B435-11E9-9278-68D0E5697425 grant_number: HE_3231/6-1 name: Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo - _id: 2527D5CC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 812-B12 name: Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation publication: Medecine Sciences publication_status: published publisher: Éditions Médicales et Scientifiques publist_id: '3877' quality_controlled: '1' scopus_import: 1 status: public title: Cell adhesion mechanics of zebrafish gastrulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2013' ... --- _id: '2886' abstract: - lang: eng text: We focus on the realizability problem of Message Sequence Graphs (MSG), i.e. the problem whether a given MSG specification is correctly distributable among parallel components communicating via messages. This fundamental problem of MSG is known to be undecidable. We introduce a well motivated restricted class of MSG, so called controllable-choice MSG, and show that all its models are realizable and moreover it is decidable whether a given MSG model is a member of this class. In more detail, this class of MSG specifications admits a deadlock-free realization by overloading existing messages with additional bounded control data. We also show that the presented class is the largest known subclass of MSG that allows for deadlock-free realization. alternative_title: - LNCS author: - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Vojtěch full_name: Řehák, Vojtěch last_name: Řehák citation: ama: Chmelik M, Řehák V. Controllable-choice message sequence graphs. 2013;7721:118-130. doi:10.1007/978-3-642-36046-6_12 apa: 'Chmelik, M., & Řehák, V. (2013). Controllable-choice message sequence graphs. Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6_12' chicago: Chmelik, Martin, and Vojtěch Řehák. “Controllable-Choice Message Sequence Graphs.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6_12. ieee: M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol. 7721. Springer, pp. 118–130, 2013. ista: Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721, 118–130. mla: Chmelik, Martin, and Vojtěch Řehák. Controllable-Choice Message Sequence Graphs. Vol. 7721, Springer, 2013, pp. 118–30, doi:10.1007/978-3-642-36046-6_12. short: M. Chmelik, V. Řehák, 7721 (2013) 118–130. conference: end_date: 2012-10-28 location: Znojmo, Czech Republic name: 'MEMICS: Mathematical and Engineering Methods in Computer Science' start_date: 2012-10-25 date_created: 2018-12-11T12:00:09Z date_published: 2013-01-09T00:00:00Z date_updated: 2020-08-11T10:09:52Z day: '09' department: - _id: KrCh doi: 10.1007/978-3-642-36046-6_12 ec_funded: 1 intvolume: ' 7721' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.4499 month: '01' oa: 1 oa_version: Submitted Version page: 118 - 130 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '3873' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Controllable-choice message sequence graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7721 year: '2013' ... --- _id: '2887' abstract: - lang: eng text: 'Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root-root interaction strength was calculated using quantitative metrics that characterize the extent towhich the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes.' article_processing_charge: No article_type: original author: - first_name: Suqin full_name: Fang, Suqin last_name: Fang - first_name: Randy full_name: Clark, Randy last_name: Clark - first_name: Ying full_name: Zheng, Ying last_name: Zheng - first_name: Anjali full_name: Iyer Pascuzzi, Anjali last_name: Iyer Pascuzzi - first_name: Joshua full_name: Weitz, Joshua last_name: Weitz - first_name: Leon full_name: Kochian, Leon last_name: Kochian - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Hong full_name: Liao, Hong last_name: Liao - first_name: Philip full_name: Benfey, Philip last_name: Benfey citation: ama: Fang S, Clark R, Zheng Y, et al. Genotypic recognition and spatial responses by rice roots. PNAS. 2013;110(7):2670-2675. doi:10.1073/pnas.1222821110 apa: Fang, S., Clark, R., Zheng, Y., Iyer Pascuzzi, A., Weitz, J., Kochian, L., … Benfey, P. (2013). Genotypic recognition and spatial responses by rice roots. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1222821110 chicago: Fang, Suqin, Randy Clark, Ying Zheng, Anjali Iyer Pascuzzi, Joshua Weitz, Leon Kochian, Herbert Edelsbrunner, Hong Liao, and Philip Benfey. “Genotypic Recognition and Spatial Responses by Rice Roots.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1222821110. ieee: S. Fang et al., “Genotypic recognition and spatial responses by rice roots,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675, 2013. ista: Fang S, Clark R, Zheng Y, Iyer Pascuzzi A, Weitz J, Kochian L, Edelsbrunner H, Liao H, Benfey P. 2013. Genotypic recognition and spatial responses by rice roots. PNAS. 110(7), 2670–2675. mla: Fang, Suqin, et al. “Genotypic Recognition and Spatial Responses by Rice Roots.” PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2670–75, doi:10.1073/pnas.1222821110. short: S. Fang, R. Clark, Y. Zheng, A. Iyer Pascuzzi, J. Weitz, L. Kochian, H. Edelsbrunner, H. Liao, P. Benfey, PNAS 110 (2013) 2670–2675. date_created: 2018-12-11T12:00:09Z date_published: 2013-02-12T00:00:00Z date_updated: 2021-01-12T07:00:29Z day: '12' department: - _id: HeEd doi: 10.1073/pnas.1222821110 external_id: pmid: - '23362379' intvolume: ' 110' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/ month: '02' oa: 1 oa_version: Published Version page: 2670 - 2675 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3872' quality_controlled: '1' scopus_import: 1 status: public title: Genotypic recognition and spatial responses by rice roots type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2901' abstract: - lang: eng text: ' We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data. ' alternative_title: - ' JMLR: W&CP' author: - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Zhu full_name: Yan, Zhu last_name: Yan - first_name: Dimitris full_name: Metaxas, Dimitris last_name: Metaxas - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. Computing the M most probable modes of a graphical model. In: Vol 31. JMLR; 2013:161-169.' apa: 'Chen, C., Kolmogorov, V., Yan, Z., Metaxas, D., & Lampert, C. (2013). Computing the M most probable modes of a graphical model (Vol. 31, pp. 161–169). Presented at the AISTATS: Conference on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States: JMLR.' chicago: Chen, Chao, Vladimir Kolmogorov, Zhu Yan, Dimitris Metaxas, and Christoph Lampert. “Computing the M Most Probable Modes of a Graphical Model,” 31:161–69. JMLR, 2013. ieee: 'C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, and C. Lampert, “Computing the M most probable modes of a graphical model,” presented at the AISTATS: Conference on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States, 2013, vol. 31, pp. 161–169.' ista: 'Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. 2013. Computing the M most probable modes of a graphical model. AISTATS: Conference on Uncertainty in Artificial Intelligence, JMLR: W&CP, vol. 31, 161–169.' mla: Chen, Chao, et al. Computing the M Most Probable Modes of a Graphical Model. Vol. 31, JMLR, 2013, pp. 161–69. short: C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, JMLR, 2013, pp. 161–169. conference: end_date: 2013-05-01 location: Scottsdale, AZ, United States name: ' AISTATS: Conference on Uncertainty in Artificial Intelligence' start_date: 2013-04-29 date_created: 2018-12-11T12:00:14Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:00:35Z day: '01' department: - _id: HeEd - _id: VlKo - _id: ChLa intvolume: ' 31' language: - iso: eng main_file_link: - open_access: '1' url: http://jmlr.org/proceedings/papers/v31/chen13a.html month: '01' oa: 1 oa_version: None page: 161 - 169 publication_status: published publisher: JMLR publist_id: '3846' quality_controlled: '1' scopus_import: 1 status: public title: Computing the M most probable modes of a graphical model type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2013' ...