[{"day":"01","quality_controlled":"1","month":"06","publist_id":"4072","publication_status":"published","publication":"Proceedings of the 29th annual symposium on Computational Geometry","title":"Homological reconstruction and simplification in R3","language":[{"iso":"eng"}],"status":"public","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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/2462356.2462373","_id":"2812","oa":1,"date_published":"2013-06-01T00:00:00Z","conference":{"location":"Rio de Janeiro, Brazil","name":"SoCG: Symposium on Computational Geometry","start_date":"2013-06-17","end_date":"2013-06-20"},"date_created":"2018-12-11T11:59:44Z","scopus_import":1,"citation":{"mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>, ACM, 2013, pp. 117–25, doi:<a href=\"https://doi.org/10.1145/2462356.2462373\">10.1145/2462356.2462373</a>.","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.","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” in <i>Proceedings of the 29th annual symposium on Computational Geometry</i>, Rio de Janeiro, Brazil, 2013, pp. 117–125.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” In <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>, 117–25. ACM, 2013. <a href=\"https://doi.org/10.1145/2462356.2462373\">https://doi.org/10.1145/2462356.2462373</a>.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., &#38; Lieutier, A. (2013). Homological reconstruction and simplification in R3. In <i>Proceedings of the 29th annual symposium on Computational Geometry</i> (pp. 117–125). Rio de Janeiro, Brazil: ACM. <a href=\"https://doi.org/10.1145/2462356.2462373\">https://doi.org/10.1145/2462356.2462373</a>","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.","ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. In: <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>. ACM; 2013:117-125. doi:<a href=\"https://doi.org/10.1145/2462356.2462373\">10.1145/2462356.2462373</a>"},"main_file_link":[{"open_access":"1","url":"http://hal.archives-ouvertes.fr/hal-00833791/"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1805"}]},"page":"117 - 125","publisher":"ACM","oa_version":"Submitted Version","type":"conference","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."}],"date_updated":"2025-09-23T09:18:30Z","department":[{"_id":"HeEd"}],"author":[{"full_name":"Attali, Dominique","first_name":"Dominique","last_name":"Attali"},{"id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer"},{"full_name":"Devillers, Olivier","first_name":"Olivier","last_name":"Devillers"},{"last_name":"Glisse","first_name":"Marc","full_name":"Glisse, Marc"},{"full_name":"Lieutier, André","first_name":"André","last_name":"Lieutier"}],"year":"2013"},{"day":"25","publication_status":"published","publication":"PNAS","language":[{"iso":"eng"}],"date_published":"2013-06-25T00:00:00Z","oa":1,"doi":"10.1073/pnas.1219666110","date_created":"2018-12-11T11:59:44Z","citation":{"mla":"Samanta, Devranjan, et al. “Elasto-Inertial Turbulence.” <i>PNAS</i>, vol. 110, no. 26, National Academy of Sciences, 2013, pp. 10557–62, doi:<a href=\"https://doi.org/10.1073/pnas.1219666110\">10.1073/pnas.1219666110</a>.","ista":"Samanta D, Dubief Y, Holzner M, Schäfer C, Morozov A, Wagner C, Hof B. 2013. Elasto-inertial turbulence. PNAS. 110(26), 10557–10562.","ieee":"D. Samanta <i>et al.</i>, “Elasto-inertial turbulence,” <i>PNAS</i>, vol. 110, no. 26. National Academy of Sciences, pp. 10557–10562, 2013.","chicago":"Samanta, Devranjan, Yves Dubief, Markus Holzner, Christof Schäfer, Alexander Morozov, Christian Wagner, and Björn Hof. “Elasto-Inertial Turbulence.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1219666110\">https://doi.org/10.1073/pnas.1219666110</a>.","short":"D. Samanta, Y. Dubief, M. Holzner, C. Schäfer, A. Morozov, C. Wagner, B. Hof, PNAS 110 (2013) 10557–10562.","ama":"Samanta D, Dubief Y, Holzner M, et al. Elasto-inertial turbulence. <i>PNAS</i>. 2013;110(26):10557-10562. doi:<a href=\"https://doi.org/10.1073/pnas.1219666110\">10.1073/pnas.1219666110</a>","apa":"Samanta, D., Dubief, Y., Holzner, M., Schäfer, C., Morozov, A., Wagner, C., &#38; Hof, B. (2013). Elasto-inertial turbulence. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1219666110\">https://doi.org/10.1073/pnas.1219666110</a>"},"intvolume":"       110","isi":1,"publisher":"National Academy of Sciences","type":"journal_article","department":[{"_id":"BjHo"}],"month":"06","quality_controlled":"1","publist_id":"4073","volume":110,"title":"Elasto-inertial turbulence","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2813","external_id":{"isi":["000321503700035"],"pmid":["23757498"]},"issue":"26","scopus_import":"1","corr_author":"1","page":"10557 - 10562","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696777/","open_access":"1"}],"oa_version":"Submitted Version","pmid":1,"year":"2013","article_processing_charge":"No","author":[{"last_name":"Samanta","full_name":"Samanta, Devranjan","first_name":"Devranjan"},{"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"},{"last_name":"Morozov","full_name":"Morozov, Alexander","first_name":"Alexander"},{"full_name":"Wagner, Christian","first_name":"Christian","last_name":"Wagner"},{"first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"date_updated":"2025-09-29T14:03:43Z","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 &quot;maximum drag reduction&quot; asymptote, which is exhibited by a wide range of viscoelastic fluids."}]},{"language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publication":"International Journal of Foundations of Computer Science","oa":1,"date_published":"2013-02-01T00:00:00Z","doi":"10.1142/S0129054113400066","day":"01","publication_status":"published","citation":{"chicago":"Chatterjee, Krishnendu, Luca Alfaro, and Ritankar Majumdar. “The Complexity of Coverage.” <i>International Journal of Foundations of Computer Science</i>. World Scientific Publishing, 2013. <a href=\"https://doi.org/10.1142/S0129054113400066\">https://doi.org/10.1142/S0129054113400066</a>.","ieee":"K. Chatterjee, L. Alfaro, and R. Majumdar, “The complexity of coverage,” <i>International Journal of Foundations of Computer Science</i>, vol. 24, no. 2. World Scientific Publishing, pp. 165–185, 2013.","ista":"Chatterjee K, Alfaro L, Majumdar R. 2013. The complexity of coverage. International Journal of Foundations of Computer Science. 24(2), 165–185.","mla":"Chatterjee, Krishnendu, et al. “The Complexity of Coverage.” <i>International Journal of Foundations of Computer Science</i>, vol. 24, no. 2, World Scientific Publishing, 2013, pp. 165–85, doi:<a href=\"https://doi.org/10.1142/S0129054113400066\">10.1142/S0129054113400066</a>.","apa":"Chatterjee, K., Alfaro, L., &#38; Majumdar, R. (2013). The complexity of coverage. <i>International Journal of Foundations of Computer Science</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129054113400066\">https://doi.org/10.1142/S0129054113400066</a>","ama":"Chatterjee K, Alfaro L, Majumdar R. The complexity of coverage. <i>International Journal of Foundations of Computer Science</i>. 2013;24(2):165-185. doi:<a href=\"https://doi.org/10.1142/S0129054113400066\">10.1142/S0129054113400066</a>","short":"K. Chatterjee, L. Alfaro, R. Majumdar, International Journal of Foundations of Computer Science 24 (2013) 165–185."},"type":"journal_article","department":[{"_id":"KrCh"}],"isi":1,"intvolume":"        24","publisher":"World Scientific Publishing","date_created":"2018-12-11T11:59:44Z","status":"public","volume":24,"title":"The complexity of coverage","_id":"2814","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"4070","month":"02","quality_controlled":"1","page":"165 - 185","main_file_link":[{"url":"https://arxiv.org/abs/0804.4525","open_access":"1"}],"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luca","full_name":"Alfaro, Luca","last_name":"Alfaro"},{"full_name":"Majumdar, Ritankar","first_name":"Ritankar","last_name":"Majumdar"}],"article_processing_charge":"No","year":"2013","ec_funded":1,"date_updated":"2025-09-29T14:02:41Z","abstract":[{"lang":"eng","text":"We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing &quot;reset&quot; action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies. We also discuss the memory requirement for deterministic strategies and extensions of our results to other models, such as pushdown systems and timed systems."}],"arxiv":1,"oa_version":"Preprint","external_id":{"isi":["000319838100002"],"arxiv":["0804.4525"]},"issue":"2","scopus_import":"1"},{"date_created":"2018-12-11T11:59:44Z","citation":{"ama":"Edelsbrunner H, Fasy BT, Rote G. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. <i>Discrete &#38; Computational Geometry</i>. 2013;49(4):797-822. doi:<a href=\"https://doi.org/10.1007/s00454-013-9517-x\">10.1007/s00454-013-9517-x</a>","short":"H. Edelsbrunner, B.T. Fasy, G. Rote, Discrete &#38; Computational Geometry 49 (2013) 797–822.","apa":"Edelsbrunner, H., Fasy, B. T., &#38; Rote, G. (2013). Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-013-9517-x\">https://doi.org/10.1007/s00454-013-9517-x</a>","chicago":"Edelsbrunner, Herbert, Brittany Terese Fasy, and Günter Rote. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s00454-013-9517-x\">https://doi.org/10.1007/s00454-013-9517-x</a>.","ieee":"H. Edelsbrunner, B. T. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” <i>Discrete &#38; Computational Geometry</i>, vol. 49, no. 4. Springer, pp. 797–822, 2013.","mla":"Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” <i>Discrete &#38; Computational Geometry</i>, vol. 49, no. 4, Springer, 2013, pp. 797–822, doi:<a href=\"https://doi.org/10.1007/s00454-013-9517-x\">10.1007/s00454-013-9517-x</a>.","ista":"Edelsbrunner H, Fasy BT, Rote G. 2013. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Discrete &#38; Computational Geometry. 49(4), 797–822."},"department":[{"_id":"HeEd"}],"type":"journal_article","publisher":"Springer","isi":1,"intvolume":"        49","day":"01","publication_status":"published","language":[{"iso":"eng"}],"publication":"Discrete & Computational Geometry","doi":"10.1007/s00454-013-9517-x","date_published":"2013-06-01T00:00:00Z","oa":1,"external_id":{"isi":["000320672400005"]},"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"corr_author":"1","issue":"4","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1007/s00454-013-9517-x","open_access":"1"}],"related_material":{"record":[{"id":"3134","relation":"earlier_version","status":"public"}]},"page":"797 - 822","article_type":"original","date_updated":"2025-09-29T14:02:00Z","abstract":[{"text":"The fact that a sum of isotropic Gaussian kernels can have more modes than kernels is surprising. Extra (ghost) modes do not exist in ℝ1 and are generally not well studied in higher dimensions. We study a configuration of n+1 Gaussian kernels for which there are exactly n+2 modes. We show that all modes lie on a finite set of lines, which we call axes, and study the restriction of the Gaussian mixture to these axes in order to discover that there are an exponential number of critical points in this configuration. Although the existence of ghost modes remained unknown due to the difficulty of finding examples in ℝ2, we show that the resilience of ghost modes grows like the square root of the dimension. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes.","lang":"eng"}],"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"},{"last_name":"Fasy","id":"F65D502E-E68D-11E9-9252-C644099818F6","first_name":"Brittany Terese","full_name":"Fasy, Brittany Terese"},{"full_name":"Rote, Günter","first_name":"Günter","last_name":"Rote"}],"year":"2013","article_processing_charge":"No","oa_version":"Published Version","publist_id":"3991","quality_controlled":"1","month":"06","status":"public","title":"Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions","volume":49,"_id":"2815","acknowledgement":"This research is partially supported by the National Science Foundation (NSF) under Grant DBI-0820624, by the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"pubrep_id":"134","date_created":"2018-12-11T11:59:45Z","publisher":"eLife Sciences Publications","intvolume":"         2","isi":1,"department":[{"_id":"KrCh"}],"type":"journal_article","citation":{"short":"I. Božić, J. Reiter, B. Allen, T. Antal, K. Chatterjee, P. Shah, Y. Moon, A. Yaqubie, N. Kelly, D. Le, E. Lipson, P. Chapman, L. Diaz, B. Vogelstein, M. Nowak, ELife 2 (2013).","ama":"Božić I, Reiter J, Allen B, et al. Evolutionary dynamics of cancer in response to targeted combination therapy. <i>eLife</i>. 2013;2. doi:<a href=\"https://doi.org/10.7554/eLife.00747\">10.7554/eLife.00747</a>","apa":"Božić, I., Reiter, J., Allen, B., Antal, T., Chatterjee, K., Shah, P., … Nowak, M. (2013). Evolutionary dynamics of cancer in response to targeted combination therapy. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.00747\">https://doi.org/10.7554/eLife.00747</a>","ista":"Božić I, Reiter J, Allen B, Antal T, Chatterjee K, Shah P, Moon Y, Yaqubie A, Kelly N, Le D, Lipson E, Chapman P, Diaz L, Vogelstein B, Nowak M. 2013. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife. 2, e00747.","mla":"Božić, Ivana, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” <i>ELife</i>, vol. 2, e00747, eLife Sciences Publications, 2013, doi:<a href=\"https://doi.org/10.7554/eLife.00747\">10.7554/eLife.00747</a>.","chicago":"Božić, Ivana, Johannes Reiter, Benjamin Allen, Tibor Antal, Krishnendu Chatterjee, Preya Shah, Yo Moon, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” <i>ELife</i>. eLife Sciences Publications, 2013. <a href=\"https://doi.org/10.7554/eLife.00747\">https://doi.org/10.7554/eLife.00747</a>.","ieee":"I. Božić <i>et al.</i>, “Evolutionary dynamics of cancer in response to targeted combination therapy,” <i>eLife</i>, vol. 2. eLife Sciences Publications, 2013."},"article_number":"e00747","publication_status":"published","day":"25","doi":"10.7554/eLife.00747","oa":1,"date_published":"2013-06-25T00:00:00Z","publication":"eLife","file_date_updated":"2020-07-14T12:45:49Z","file":[{"content_type":"application/pdf","file_size":3358321,"date_created":"2018-12-12T10:12:48Z","checksum":"2c38c47815eacd8fa66cb8b404cf7c61","relation":"main_file","file_name":"IST-2013-134-v1+1_e00747.full.pdf","file_id":"4967","creator":"system","date_updated":"2020-07-14T12:45:49Z","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"external_id":{"isi":["000328619300005"]},"oa_version":"Published Version","has_accepted_license":"1","date_updated":"2025-09-29T14:00:58Z","abstract":[{"lang":"eng","text":"In solid tumors, targeted treatments can lead to dramatic regressions, but responses are often short-lived because resistant cancer cells arise. The major strategy proposed for overcoming resistance is combination therapy. We present a mathematical model describing the evolutionary dynamics of lesions in response to treatment. We first studied 20 melanoma patients receiving vemurafenib. We then applied our model to an independent set of pancreatic, colorectal, and melanoma cancer patients with metastatic disease. We find that dual therapy results in long-term disease control for most patients, if there are no single mutations that cause cross-resistance to both drugs; in patients with large disease burden, triple therapy is needed. We also find that simultaneous therapy with two drugs is much more effective than sequential therapy. Our results provide realistic expectations for the efficacy of new drug combinations and inform the design of trials for new cancer therapeutics."}],"year":"2013","article_processing_charge":"No","author":[{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"first_name":"Johannes","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","last_name":"Reiter"},{"full_name":"Allen, Benjamin","first_name":"Benjamin","last_name":"Allen"},{"full_name":"Antal, Tibor","first_name":"Tibor","last_name":"Antal"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Shah","full_name":"Shah, Preya","first_name":"Preya"},{"last_name":"Moon","full_name":"Moon, Yo","first_name":"Yo"},{"first_name":"Amin","full_name":"Yaqubie, Amin","last_name":"Yaqubie"},{"first_name":"Nicole","full_name":"Kelly, Nicole","last_name":"Kelly"},{"last_name":"Le","first_name":"Dung","full_name":"Le, Dung"},{"first_name":"Evan","full_name":"Lipson, Evan","last_name":"Lipson"},{"full_name":"Chapman, Paul","first_name":"Paul","last_name":"Chapman"},{"last_name":"Diaz","full_name":"Diaz, Luis","first_name":"Luis"},{"last_name":"Vogelstein","full_name":"Vogelstein, Bert","first_name":"Bert"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"related_material":{"record":[{"status":"public","id":"1400","relation":"dissertation_contains"}]},"quality_controlled":"1","month":"06","ddc":["570","610"],"publist_id":"3985","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2816","title":"Evolutionary dynamics of cancer in response to targeted combination therapy","volume":2,"status":"public"},{"status":"public","volume":334,"title":"Density games","_id":"2817","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3984","ddc":["000"],"month":"10","quality_controlled":"1","page":"26 - 34","year":"2013","author":[{"last_name":"Novak","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"article_processing_charge":"No","ec_funded":1,"abstract":[{"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.","lang":"eng"}],"date_updated":"2025-09-29T13:59:11Z","oa_version":"Published Version","has_accepted_license":"1","external_id":{"isi":["000323629500003"]},"corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf","checksum":"3c29059ab03a4b8f97a07646b817ddbb","relation":"main_file","file_size":834604,"date_created":"2018-12-12T10:14:54Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:49Z","creator":"system","file_id":"5110"}],"file_date_updated":"2020-07-14T12:45:49Z","publication":"Journal of Theoretical Biology","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"oa":1,"date_published":"2013-10-07T00:00:00Z","doi":"10.1016/j.jtbi.2013.05.029","day":"07","publication_status":"published","citation":{"apa":"Novak, S., Chatterjee, K., &#38; Nowak, M. (2013). Density games. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">https://doi.org/10.1016/j.jtbi.2013.05.029</a>","short":"S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34.","ama":"Novak S, Chatterjee K, Nowak M. Density games. <i>Journal of Theoretical Biology</i>. 2013;334:26-34. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">10.1016/j.jtbi.2013.05.029</a>","mla":"Novak, Sebastian, et al. “Density Games.” <i>Journal of Theoretical Biology</i>, vol. 334, Elsevier, 2013, pp. 26–34, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">10.1016/j.jtbi.2013.05.029</a>.","ista":"Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34.","ieee":"S. Novak, K. Chatterjee, and M. Nowak, “Density games,” <i>Journal of Theoretical Biology</i>, vol. 334. Elsevier, pp. 26–34, 2013.","chicago":"Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” <i>Journal of Theoretical Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">https://doi.org/10.1016/j.jtbi.2013.05.029</a>."},"type":"journal_article","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"intvolume":"       334","isi":1,"publisher":"Elsevier","date_created":"2018-12-11T11:59:45Z","pubrep_id":"400"},{"publist_id":"3983","month":"07","quality_controlled":"1","_id":"2818","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","volume":25,"title":"Learning quadratic receptive fields from neural responses to natural stimuli","scopus_import":"1","issue":"7","external_id":{"isi":["000319903700001"],"arxiv":["1209.0121"]},"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"}],"article_processing_charge":"No","year":"2013","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."}],"date_updated":"2025-09-29T13:58:36Z","oa_version":"Preprint","arxiv":1,"page":"1661 - 1692","main_file_link":[{"url":"http://arxiv.org/abs/1209.0121","open_access":"1"}],"publication_status":"published","day":"01","oa":1,"date_published":"2013-07-01T00:00:00Z","doi":"10.1162/NECO_a_00463","language":[{"iso":"eng"}],"publication":"Neural Computation","date_created":"2018-12-11T11:59:45Z","type":"journal_article","department":[{"_id":"GaTk"}],"isi":1,"intvolume":"        25","publisher":"MIT Press ","citation":{"apa":"Rajan, K., Marre, O., &#38; Tkačik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. <i>Neural Computation</i>. MIT Press . <a href=\"https://doi.org/10.1162/NECO_a_00463\">https://doi.org/10.1162/NECO_a_00463</a>","short":"K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.","ama":"Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. <i>Neural Computation</i>. 2013;25(7):1661-1692. doi:<a href=\"https://doi.org/10.1162/NECO_a_00463\">10.1162/NECO_a_00463</a>","mla":"Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” <i>Neural Computation</i>, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:<a href=\"https://doi.org/10.1162/NECO_a_00463\">10.1162/NECO_a_00463</a>.","ista":"Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692.","chicago":"Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” <i>Neural Computation</i>. MIT Press , 2013. <a href=\"https://doi.org/10.1162/NECO_a_00463\">https://doi.org/10.1162/NECO_a_00463</a>.","ieee":"K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” <i>Neural Computation</i>, vol. 25, no. 7. MIT Press , pp. 1661–1692, 2013."}},{"doi":"10.1145/2461328.2461370","conference":{"start_date":"2013-04-08","end_date":"2013-04-11","location":"Philadelphia, PA USA","name":"HSCC: Hybrid Systems - Computation and Control"},"oa":1,"date_published":"2013-04-01T00:00:00Z","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publication":"Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control","language":[{"iso":"eng"}],"publication_status":"published","day":"01","publisher":"Springer","intvolume":"         1","type":"conference","department":[{"_id":"KrCh"}],"citation":{"apa":"Chatterjee, K., &#38; Prabhu, V. (2013). Quantitative timed simulation functions and refinement metrics for real-time systems. In <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i> (Vol. 1, pp. 273–282). Philadelphia, PA USA: Springer. <a href=\"https://doi.org/10.1145/2461328.2461370\">https://doi.org/10.1145/2461328.2461370</a>","short":"K. Chatterjee, V. Prabhu, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Springer, 2013, pp. 273–282.","ama":"Chatterjee K, Prabhu V. Quantitative timed simulation functions and refinement metrics for real-time systems. In: <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>. Vol 1. Springer; 2013:273-282. doi:<a href=\"https://doi.org/10.1145/2461328.2461370\">10.1145/2461328.2461370</a>","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, vol. 1, Springer, 2013, pp. 273–82, doi:<a href=\"https://doi.org/10.1145/2461328.2461370\">10.1145/2461328.2461370</a>.","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.","chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” In <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, 1:273–82. Springer, 2013. <a href=\"https://doi.org/10.1145/2461328.2461370\">https://doi.org/10.1145/2461328.2461370</a>.","ieee":"K. Chatterjee and V. Prabhu, “Quantitative timed simulation functions and refinement metrics for real-time systems,” in <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, Philadelphia, PA USA, 2013, vol. 1, pp. 273–282."},"date_created":"2018-12-11T11:59:46Z","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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2819","title":"Quantitative timed simulation functions and refinement metrics for real-time systems","volume":1,"status":"public","quality_controlled":"1","month":"04","publist_id":"3982","arxiv":1,"oa_version":"Preprint","abstract":[{"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 &quot;steady-state&quot; 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. ","lang":"eng"}],"date_updated":"2025-06-11T08:04:41Z","ec_funded":1,"year":"2013","article_processing_charge":"No","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prabhu","full_name":"Prabhu, Vinayak","first_name":"Vinayak"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1212.6556"}],"page":"273 - 282","scopus_import":"1","external_id":{"arxiv":["1212.6556"]}},{"scopus_import":1,"publication_identifier":{"isbn":["978-1-4503-1567-8 "]},"date_created":"2018-12-11T11:59:46Z","publisher":"ACM","oa_version":"None","date_updated":"2025-04-15T08:12:28Z","type":"conference","ec_funded":1,"department":[{"_id":"KrCh"}],"abstract":[{"text":"In this paper, we introduce the powerful framework of graph games for the analysis of real-time scheduling with firm deadlines. We introduce a novel instance of a partial-observation game that is suitable for this purpose, and prove decidability of all the involved decision problems. We derive a graph game that allows the automated computation of the competitive ratio (along with an optimal witness algorithm for the competitive ratio) and establish an NP-completeness proof for the graph game problem. For a given on-line algorithm, we present polynomial time solution for computing (i) the worst-case utility; (ii) the worst-case utility ratio w.r.t. a clairvoyant off-line algorithm; and (iii) the competitive ratio. A major strength of the proposed approach lies in its flexibility w.r.t. incorporating additional constraints on the adversary and/or the algorithm, including limited maximum or average load, finiteness of periods of overload, etc., which are easily added by means of additional instances of standard objective functions for graph games. ","lang":"eng"}],"year":"2013","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Kößler","full_name":"Kößler, Alexander","first_name":"Alexander"},{"last_name":"Schmid","first_name":"Ulrich","full_name":"Schmid, Ulrich"}],"citation":{"ama":"Chatterjee K, Kößler A, Schmid U. Automated analysis of real-time scheduling using graph games. In: <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>. ACM; 2013:163-172. doi:<a href=\"https://doi.org/10.1145/2461328.2461356\">10.1145/2461328.2461356</a>","short":"K. Chatterjee, A. Kößler, U. Schmid, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, ACM, 2013, pp. 163–172.","apa":"Chatterjee, K., Kößler, A., &#38; Schmid, U. (2013). Automated analysis of real-time scheduling using graph games. In <i>Proceedings of the 16th International conference on Hybrid systems: Computation and control</i> (pp. 163–172). Philadelphia, PA, United States: ACM. <a href=\"https://doi.org/10.1145/2461328.2461356\">https://doi.org/10.1145/2461328.2461356</a>","chicago":"Chatterjee, Krishnendu, Alexander Kößler, and Ulrich Schmid. “Automated Analysis of Real-Time Scheduling Using Graph Games.” In <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, 163–72. ACM, 2013. <a href=\"https://doi.org/10.1145/2461328.2461356\">https://doi.org/10.1145/2461328.2461356</a>.","ieee":"K. Chatterjee, A. Kößler, and U. Schmid, “Automated analysis of real-time scheduling using graph games,” in <i>Proceedings of the 16th International conference on Hybrid systems: Computation and control</i>, Philadelphia, PA, United States, 2013, pp. 163–172.","ista":"Chatterjee K, Kößler A, Schmid U. 2013. Automated analysis of real-time scheduling using graph games. Proceedings of the 16th International conference on Hybrid systems: Computation and control. HSCC: Hybrid Systems - Computation and Control, 163–172.","mla":"Chatterjee, Krishnendu, et al. “Automated Analysis of Real-Time Scheduling Using Graph Games.” <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, ACM, 2013, pp. 163–72, doi:<a href=\"https://doi.org/10.1145/2461328.2461356\">10.1145/2461328.2461356</a>."},"related_material":{"record":[{"id":"738","relation":"later_version","status":"public"}]},"page":"163 - 172","quality_controlled":"1","month":"04","publist_id":"3981","publication_status":"published","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/2461328.2461356","_id":"2820","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","location":"Philadelphia, PA, United States","end_date":"2013-04-11","start_date":"2013-04-08"},"date_published":"2013-04-01T00:00:00Z","publication":"Proceedings of the 16th International conference on Hybrid systems: Computation and control","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"title":"Automated analysis of real-time scheduling using graph games","status":"public","language":[{"iso":"eng"}]},{"doi":"10.1105/tpc.113.110353","date_published":"2013-04-24T00:00:00Z","oa":1,"language":[{"iso":"eng"}],"publication":"Plant Cell","publication_status":"published","day":"24","type":"journal_article","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","intvolume":"        25","isi":1,"citation":{"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.” <i>Plant Cell</i>, vol. 25, no. 3, American Society of Plant Biologists, 2013, pp. 901–26, doi:<a href=\"https://doi.org/10.1105/tpc.113.110353\">10.1105/tpc.113.110353</a>.","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.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.110353\">https://doi.org/10.1105/tpc.113.110353</a>.","ieee":"E. Remy <i>et al.</i>, “A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 3. American Society of Plant Biologists, pp. 901–926, 2013.","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. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.110353\">https://doi.org/10.1105/tpc.113.110353</a>","short":"E. Remy, T. Cabrito, P. Baster, R. Batista, M. Teixeira, J. Friml, I. Sá Correia, P. Duque, Plant Cell 25 (2013) 901–926.","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. <i>Plant Cell</i>. 2013;25(3):901-926. doi:<a href=\"https://doi.org/10.1105/tpc.113.110353\">10.1105/tpc.113.110353</a>"},"date_created":"2018-12-11T11:59:46Z","_id":"2821","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","title":"A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis","volume":25,"publist_id":"3980","quality_controlled":"1","month":"04","date_updated":"2025-09-29T13:57:58Z","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."}],"year":"2013","article_processing_charge":"No","author":[{"full_name":"Remy, Estelle","first_name":"Estelle","last_name":"Remy"},{"last_name":"Cabrito","first_name":"Tânia","full_name":"Cabrito, Tânia"},{"last_name":"Baster","first_name":"Pawel","full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Batista","first_name":"Rita","full_name":"Batista, Rita"},{"last_name":"Teixeira","full_name":"Teixeira, Miguel","first_name":"Miguel"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sá Correia","first_name":"Isabel","full_name":"Sá Correia, Isabel"},{"full_name":"Duque, Paula","first_name":"Paula","last_name":"Duque"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634696/","open_access":"1"}],"page":"901 - 926","scopus_import":"1","issue":"3","external_id":{"pmid":["23524662"],"isi":["000318157100012"]}},{"scopus_import":"1","issue":"18","external_id":{"isi":["000318682300008"],"pmid":["25673779"]},"oa_version":"Submitted Version","pmid":1,"author":[{"last_name":"Topp","first_name":"Christopher","full_name":"Topp, Christopher"},{"last_name":"Iyer Pascuzzi","full_name":"Iyer Pascuzzi, Anjali","first_name":"Anjali"},{"full_name":"Anderson, Jill","first_name":"Jill","last_name":"Anderson"},{"full_name":"Lee, Cheng","first_name":"Cheng","last_name":"Lee"},{"last_name":"Zurek","full_name":"Zurek, Paul","first_name":"Paul"},{"last_name":"Symonova","orcid":"0000-0003-2012-9947","full_name":"Symonova, Olga","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zheng","first_name":"Ying","full_name":"Zheng, Ying"},{"full_name":"Bucksch, Alexander","first_name":"Alexander","last_name":"Bucksch"},{"last_name":"Mileyko","first_name":"Yuriy","full_name":"Mileyko, Yuriy"},{"first_name":"Taras","full_name":"Galkovskyi, Taras","last_name":"Galkovskyi"},{"full_name":"Moore, Brad","first_name":"Brad","last_name":"Moore"},{"first_name":"John","full_name":"Harer, John","last_name":"Harer"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"full_name":"Mitchell Olds, Thomas","first_name":"Thomas","last_name":"Mitchell Olds"},{"first_name":"Joshua","full_name":"Weitz, Joshua","last_name":"Weitz"},{"last_name":"Benfey","full_name":"Benfey, Philip","first_name":"Philip"}],"year":"2013","article_processing_charge":"No","date_updated":"2025-09-29T13:57:21Z","abstract":[{"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 &gt;1,400 3D root models and &gt;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.","lang":"eng"}],"page":"E1695 - E1704","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378147/","open_access":"1"}],"month":"04","quality_controlled":"1","publist_id":"3979","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2822","volume":110,"title":"3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture","status":"public","date_created":"2018-12-11T11:59:47Z","intvolume":"       110","isi":1,"publisher":"National Academy of Sciences","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"type":"journal_article","citation":{"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. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1304354110\">https://doi.org/10.1073/pnas.1304354110</a>","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.","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. <i>PNAS</i>. 2013;110(18):E1695-E1704. doi:<a href=\"https://doi.org/10.1073/pnas.1304354110\">10.1073/pnas.1304354110</a>","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.” <i>PNAS</i>, vol. 110, no. 18, National Academy of Sciences, 2013, pp. E1695–704, doi:<a href=\"https://doi.org/10.1073/pnas.1304354110\">10.1073/pnas.1304354110</a>.","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.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1304354110\">https://doi.org/10.1073/pnas.1304354110</a>.","ieee":"C. Topp <i>et al.</i>, “3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture,” <i>PNAS</i>, vol. 110, no. 18. National Academy of Sciences, pp. E1695–E1704, 2013."},"publication_status":"published","day":"30","oa":1,"date_published":"2013-04-30T00:00:00Z","doi":"10.1073/pnas.1304354110","publication":"PNAS","language":[{"iso":"eng"}]},{"status":"public","title":"Post-fire recovery of revegetated woodland communities in south-eastern Australia","volume":38,"_id":"2823","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3978","quality_controlled":"1","month":"05","page":"300 - 312","date_updated":"2025-09-29T13:56:47Z","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 (&gt;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 &lt;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":[{"full_name":"Pickup, Melinda","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","orcid":"0000-0001-6118-0541"},{"last_name":"Wilson","full_name":"Wilson, Susie","first_name":"Susie"},{"last_name":"Freudenberger","first_name":"David","full_name":"Freudenberger, David"},{"first_name":"Nick","full_name":"Nicholls, Nick","last_name":"Nicholls"},{"full_name":"Gould, Lori","first_name":"Lori","last_name":"Gould"},{"last_name":"Hnatiuk","full_name":"Hnatiuk, Sarah","first_name":"Sarah"},{"full_name":"Delandre, Jeni","first_name":"Jeni","last_name":"Delandre"}],"year":"2013","article_processing_charge":"No","oa_version":"None","external_id":{"isi":["000318188200007"]},"issue":"3","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Austral Ecology","doi":"10.1111/j.1442-9993.2012.02404.x","date_published":"2013-05-01T00:00:00Z","day":"01","publication_status":"published","citation":{"apa":"Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., &#38; Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. <i>Austral Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">https://doi.org/10.1111/j.1442-9993.2012.02404.x</a>","short":"M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312.","ama":"Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. <i>Austral Ecology</i>. 2013;38(3):300-312. doi:<a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">10.1111/j.1442-9993.2012.02404.x</a>","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.” <i>Austral Ecology</i>, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:<a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">10.1111/j.1442-9993.2012.02404.x</a>.","ieee":"M. Pickup <i>et al.</i>, “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” <i>Austral Ecology</i>, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013.","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.” <i>Austral Ecology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">https://doi.org/10.1111/j.1442-9993.2012.02404.x</a>."},"department":[{"_id":"NiBa"}],"type":"journal_article","publisher":"Wiley-Blackwell","intvolume":"        38","isi":1,"date_created":"2018-12-11T11:59:47Z"},{"status":"public","volume":"228-229","title":"Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems","_id":"2824","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3977","month":"04","quality_controlled":"1","page":"83-119","article_processing_charge":"No","year":"2013","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Prabhu, Vinayak","first_name":"Vinayak","last_name":"Prabhu"}],"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."}],"ec_funded":1,"date_updated":"2025-09-29T13:56:16Z","oa_version":"None","external_id":{"isi":["000322295300005"]},"scopus_import":"1","language":[{"iso":"eng"}],"publication":"Information and Computation","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"date_published":"2013-04-24T00:00:00Z","doi":"10.1016/j.ic.2013.04.003","day":"24","publication_status":"published","citation":{"short":"K. Chatterjee, V. Prabhu, Information and Computation 228–229 (2013) 83–119.","ama":"Chatterjee K, Prabhu V. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. <i>Information and Computation</i>. 2013;228-229:83-119. doi:<a href=\"https://doi.org/10.1016/j.ic.2013.04.003\">10.1016/j.ic.2013.04.003</a>","apa":"Chatterjee, K., &#38; Prabhu, V. (2013). Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2013.04.003\">https://doi.org/10.1016/j.ic.2013.04.003</a>","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.” <i>Information and Computation</i>, vol. 228–229, Elsevier, 2013, pp. 83–119, doi:<a href=\"https://doi.org/10.1016/j.ic.2013.04.003\">10.1016/j.ic.2013.04.003</a>.","ieee":"K. Chatterjee and V. Prabhu, “Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems,” <i>Information and Computation</i>, vol. 228–229. Elsevier, pp. 83–119, 2013.","chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” <i>Information and Computation</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.ic.2013.04.003\">https://doi.org/10.1016/j.ic.2013.04.003</a>."},"type":"journal_article","department":[{"_id":"KrCh"}],"isi":1,"publisher":"Elsevier","date_created":"2018-12-11T11:59:47Z"},{"publication_status":"published","day":"02","doi":"10.1016/j.ajhg.2013.04.005","date_published":"2013-05-02T00:00:00Z","oa":1,"language":[{"iso":"eng"}],"publication":"American Journal of Human Genetics","date_created":"2018-12-11T11:59:48Z","type":"journal_article","department":[{"_id":"MD"}],"publisher":"Cell Press","isi":1,"intvolume":"        92","citation":{"mla":"Tran Viet, Khanh, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia.” <i>American Journal of Human Genetics</i>, vol. 92, no. 5, Cell Press, 2013, pp. 820–26, doi:<a href=\"https://doi.org/10.1016/j.ajhg.2013.04.005\">10.1016/j.ajhg.2013.04.005</a>.","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.","ieee":"K. Tran Viet <i>et al.</i>, “Mutations in SCO2 are associated with autosomal-dominant high-grade myopia,” <i>American Journal of Human Genetics</i>, vol. 92, no. 5. Cell Press, pp. 820–826, 2013.","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.” <i>American Journal of Human Genetics</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.ajhg.2013.04.005\">https://doi.org/10.1016/j.ajhg.2013.04.005</a>.","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.","ama":"Tran Viet K, Powell C, Barathi V, et al. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. <i>American Journal of Human Genetics</i>. 2013;92(5):820-826. doi:<a href=\"https://doi.org/10.1016/j.ajhg.2013.04.005\">10.1016/j.ajhg.2013.04.005</a>","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. <i>American Journal of Human Genetics</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.ajhg.2013.04.005\">https://doi.org/10.1016/j.ajhg.2013.04.005</a>"},"publist_id":"3974","quality_controlled":"1","month":"05","_id":"2826","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","title":"Mutations in SCO2 are associated with autosomal-dominant high-grade myopia","volume":92,"scopus_import":"1","issue":"5","external_id":{"isi":["000318582800017"],"pmid":["23643385"]},"date_updated":"2025-09-29T13:54:47Z","abstract":[{"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&gt;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&gt;A, c.418G&gt;A, and c.776C&gt;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.","lang":"eng"}],"author":[{"last_name":"Tran Viet","first_name":"Khanh","full_name":"Tran Viet, Khanh"},{"first_name":"Caldwell","full_name":"Powell, Caldwell","last_name":"Powell"},{"full_name":"Barathi, Veluchamy","first_name":"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"},{"full_name":"Limviphuvadh, Vachiranee","first_name":"Vachiranee","last_name":"Limviphuvadh"},{"full_name":"Soler, Vincent","first_name":"Vincent","last_name":"Soler"},{"last_name":"Ho","first_name":"Candice","full_name":"Ho, Candice"},{"first_name":"Tammy","full_name":"Yanovitch, Tammy","last_name":"Yanovitch"},{"last_name":"Schneider","full_name":"Schneider, Georg","first_name":"Georg","id":"329095A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Li, Yi","first_name":"Yi","last_name":"Li"},{"full_name":"Nading, Erica","first_name":"Erica","last_name":"Nading"},{"first_name":"Ravikanth","full_name":"Metlapally, Ravikanth","last_name":"Metlapally"},{"last_name":"Saw","first_name":"Seang","full_name":"Saw, Seang"},{"last_name":"Goh","first_name":"Liang","full_name":"Goh, Liang"},{"first_name":"Steve","full_name":"Rozen, Steve","last_name":"Rozen"},{"last_name":"Young","full_name":"Young, Terri","first_name":"Terri"}],"article_processing_charge":"No","year":"2013","pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644634/","open_access":"1"}],"page":"820 - 826"},{"date_published":"2013-05-07T00:00:00Z","oa":1,"doi":"10.1073/pnas.1220205110","project":[{"name":"Koerber Prize","_id":"2574781E-B435-11E9-9278-68D0E5697425"}],"publication":"PNAS","language":[{"iso":"eng"}],"publication_status":"published","day":"07","isi":1,"intvolume":"       110","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"type":"journal_article","citation":{"mla":"Du, Yunlong, et al. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic Protein Trafficking.” <i>PNAS</i>, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7946–51, doi:<a href=\"https://doi.org/10.1073/pnas.1220205110\">10.1073/pnas.1220205110</a>.","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.","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.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1220205110\">https://doi.org/10.1073/pnas.1220205110</a>.","ieee":"Y. Du <i>et al.</i>, “Salicylic acid interferes with clathrin-mediated endocytic protein trafficking,” <i>PNAS</i>, vol. 110, no. 19. National Academy of Sciences, pp. 7946–7951, 2013.","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. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1220205110\">https://doi.org/10.1073/pnas.1220205110</a>","short":"Y. Du, R. Tejos, M. Beck, E. Himschoot, H. Li, S. Robatzek, S. Vanneste, J. Friml, PNAS 110 (2013) 7946–7951.","ama":"Du Y, Tejos R, Beck M, et al. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. <i>PNAS</i>. 2013;110(19):7946-7951. doi:<a href=\"https://doi.org/10.1073/pnas.1220205110\">10.1073/pnas.1220205110</a>"},"date_created":"2018-12-11T11:59:48Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2827","volume":110,"title":"Salicylic acid interferes with clathrin-mediated endocytic protein trafficking","status":"public","month":"05","quality_controlled":"1","publist_id":"3972","oa_version":"Submitted Version","pmid":1,"author":[{"first_name":"Yunlong","full_name":"Du, Yunlong","last_name":"Du"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"first_name":"Martina","full_name":"Beck, Martina","last_name":"Beck"},{"first_name":"Ellie","full_name":"Himschoot, Ellie","last_name":"Himschoot"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Hongjiang","first_name":"Hongjiang","last_name":"Li","orcid":"0000-0001-5039-9660"},{"first_name":"Silke","full_name":"Robatzek, Silke","last_name":"Robatzek"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"year":"2013","article_processing_charge":"No","date_updated":"2025-09-29T13:52:38Z","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."}],"page":"7946 - 7951","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651428/"}],"issue":"19","scopus_import":"1","corr_author":"1","external_id":{"pmid":["23613581"],"isi":["000319327700089"]}},{"department":[{"_id":"VlKo"}],"type":"journal_article","intvolume":"        60","isi":1,"publisher":"ACM","citation":{"ieee":"V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,” <i>Journal of the ACM</i>, vol. 60, no. 2. ACM, 2013.","chicago":"Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs.” <i>Journal of the ACM</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2450142.2450146\">https://doi.org/10.1145/2450142.2450146</a>.","mla":"Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs.” <i>Journal of the ACM</i>, vol. 60, no. 2, 10, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2450142.2450146\">10.1145/2450142.2450146</a>.","ista":"Kolmogorov V, Živný S. 2013. The complexity of conservative valued CSPs. Journal of the ACM. 60(2), 10.","apa":"Kolmogorov, V., &#38; Živný, S. (2013). The complexity of conservative valued CSPs. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/2450142.2450146\">https://doi.org/10.1145/2450142.2450146</a>","ama":"Kolmogorov V, Živný S. The complexity of conservative valued CSPs. <i>Journal of the ACM</i>. 2013;60(2). doi:<a href=\"https://doi.org/10.1145/2450142.2450146\">10.1145/2450142.2450146</a>","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","oa":1,"doi":"10.1145/2450142.2450146","language":[{"iso":"eng"}],"publication":"Journal of the ACM","publication_status":"published","article_number":"10","day":"02","year":"2013","article_processing_charge":"No","author":[{"last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"},{"full_name":"Živný, Stanislav","first_name":"Stanislav","last_name":"Živný"}],"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."}],"date_updated":"2025-09-29T13:52:07Z","oa_version":"Preprint","arxiv":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1110.2809"}],"issue":"2","scopus_import":"1","external_id":{"arxiv":["1110.2809"],"isi":["000318628500004"]},"_id":"2828","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","volume":60,"title":"The complexity of conservative valued CSPs","publist_id":"3971","month":"04","quality_controlled":"1"},{"status":"public","title":"Scale invariance at the onset of turbulence in couette flow","volume":110,"_id":"2829","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3970","quality_controlled":"1","month":"05","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.5446"}],"ec_funded":1,"date_updated":"2025-09-29T13:51:32Z","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","year":"2013","author":[{"last_name":"Shi","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","first_name":"Liang","full_name":"Shi, Liang"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"arxiv":1,"oa_version":"Preprint","external_id":{"arxiv":["1304.5446"],"isi":["000319062300011"]},"issue":"20","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Physical Review Letters","project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","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"}],"doi":"10.1103/PhysRevLett.110.204502","oa":1,"date_published":"2013-05-13T00:00:00Z","day":"13","publication_status":"published","article_number":"204502","citation":{"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.” <i>Physical Review Letters</i>, vol. 110, no. 20, 204502, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.204502\">10.1103/PhysRevLett.110.204502</a>.","ieee":"L. Shi, M. Avila, and B. Hof, “Scale invariance at the onset of turbulence in couette flow,” <i>Physical Review Letters</i>, vol. 110, no. 20. American Physical Society, 2013.","chicago":"Shi, Liang, Marc Avila, and Björn Hof. “Scale Invariance at the Onset of Turbulence in Couette Flow.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.204502\">https://doi.org/10.1103/PhysRevLett.110.204502</a>.","apa":"Shi, L., Avila, M., &#38; Hof, B. (2013). Scale invariance at the onset of turbulence in couette flow. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.204502\">https://doi.org/10.1103/PhysRevLett.110.204502</a>","short":"L. Shi, M. Avila, B. Hof, Physical Review Letters 110 (2013).","ama":"Shi L, Avila M, Hof B. Scale invariance at the onset of turbulence in couette flow. <i>Physical Review Letters</i>. 2013;110(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.204502\">10.1103/PhysRevLett.110.204502</a>"},"type":"journal_article","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","isi":1,"intvolume":"       110","date_created":"2018-12-11T11:59:49Z"},{"date_published":"2013-05-23T00:00:00Z","doi":"10.1016/j.immuni.2013.05.005","publication":"Immunity","language":[{"iso":"eng"}],"publication_status":"published","day":"23","intvolume":"        38","isi":1,"publisher":"Cell Press","department":[{"_id":"MiSi"}],"type":"journal_article","citation":{"mla":"Moussion, Christine, and Michael K. Sixt. “A Conduit to Amplify Innate Immunity.” <i>Immunity</i>, vol. 38, no. 5, Cell Press, 2013, pp. 853–54, doi:<a href=\"https://doi.org/10.1016/j.immuni.2013.05.005\">10.1016/j.immuni.2013.05.005</a>.","ista":"Moussion C, Sixt MK. 2013. A conduit to amplify innate immunity. Immunity. 38(5), 853–854.","chicago":"Moussion, Christine, and Michael K Sixt. “A Conduit to Amplify Innate Immunity.” <i>Immunity</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.immuni.2013.05.005\">https://doi.org/10.1016/j.immuni.2013.05.005</a>.","ieee":"C. Moussion and M. K. Sixt, “A conduit to amplify innate immunity,” <i>Immunity</i>, vol. 38, no. 5. Cell Press, pp. 853–854, 2013.","short":"C. Moussion, M.K. Sixt, Immunity 38 (2013) 853–854.","ama":"Moussion C, Sixt MK. A conduit to amplify innate immunity. <i>Immunity</i>. 2013;38(5):853-854. doi:<a href=\"https://doi.org/10.1016/j.immuni.2013.05.005\">10.1016/j.immuni.2013.05.005</a>","apa":"Moussion, C., &#38; Sixt, M. K. (2013). A conduit to amplify innate immunity. <i>Immunity</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.immuni.2013.05.005\">https://doi.org/10.1016/j.immuni.2013.05.005</a>"},"date_created":"2018-12-11T11:59:49Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2830","volume":38,"title":"A conduit to amplify innate immunity","status":"public","month":"05","quality_controlled":"1","publist_id":"3969","oa_version":"None","article_processing_charge":"No","author":[{"last_name":"Moussion","id":"3356F664-F248-11E8-B48F-1D18A9856A87","full_name":"Moussion, Christine","first_name":"Christine"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"year":"2013","date_updated":"2025-09-29T13:51:00Z","page":"853 - 854","scopus_import":"1","issue":"5","corr_author":"1","external_id":{"isi":["000330942500005"]}},{"day":"01","publication_status":"published","language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publication":"Formal Methods in System Design","date_published":"2013-06-01T00:00:00Z","oa":1,"doi":"10.1007/s10703-012-0180-2","date_created":"2018-12-11T11:59:49Z","citation":{"ieee":"K. Chatterjee, M. Henzinger, M. Joglekar, and N. Shah, “Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives,” <i>Formal Methods in System Design</i>, vol. 42, no. 3. Springer, pp. 301–327, 2013.","chicago":"Chatterjee, Krishnendu, Monika Henzinger, Manas Joglekar, and Nisarg Shah. “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with Büchi Objectives.” <i>Formal Methods in System Design</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s10703-012-0180-2\">https://doi.org/10.1007/s10703-012-0180-2</a>.","mla":"Chatterjee, Krishnendu, et al. “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with Büchi Objectives.” <i>Formal Methods in System Design</i>, vol. 42, no. 3, Springer, 2013, pp. 301–27, doi:<a href=\"https://doi.org/10.1007/s10703-012-0180-2\">10.1007/s10703-012-0180-2</a>.","ista":"Chatterjee K, Henzinger M, Joglekar M, Shah N. 2013. Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. Formal Methods in System Design. 42(3), 301–327.","ama":"Chatterjee K, Henzinger M, Joglekar M, Shah N. Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. <i>Formal Methods in System Design</i>. 2013;42(3):301-327. doi:<a href=\"https://doi.org/10.1007/s10703-012-0180-2\">10.1007/s10703-012-0180-2</a>","short":"K. Chatterjee, M. Henzinger, M. Joglekar, N. Shah, Formal Methods in System Design 42 (2013) 301–327.","apa":"Chatterjee, K., Henzinger, M., Joglekar, M., &#38; Shah, N. (2013). Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-012-0180-2\">https://doi.org/10.1007/s10703-012-0180-2</a>"},"type":"journal_article","department":[{"_id":"KrCh"}],"intvolume":"        42","isi":1,"publisher":"Springer","publist_id":"3968","month":"06","quality_controlled":"1","status":"public","volume":42,"title":"Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives","_id":"2831","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000319151400003"],"arxiv":["1104.3348"]},"corr_author":"1","issue":"3","scopus_import":"1","page":"301 - 327","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3342"}]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.3348"}],"year":"2013","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530"},{"first_name":"Manas","full_name":"Joglekar, Manas","last_name":"Joglekar"},{"full_name":"Shah, Nisarg","first_name":"Nisarg","last_name":"Shah"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with Büchi (liveness) objectives. We consider the problem of computing the set of almost-sure winning states from where the objective can be ensured with probability 1. Our contributions are as follows: First, we present the first subquadratic symbolic algorithm to compute the almost-sure winning set for MDPs with Büchi objectives; our algorithm takes O(n · √ m) symbolic steps as compared to the previous known algorithm that takes O(n 2) symbolic steps, where n is the number of states and m is the number of edges of the MDP. In practice MDPs have constant out-degree, and then our symbolic algorithm takes O(n · √ n) symbolic steps, as compared to the previous known O(n 2) symbolic steps algorithm. Second, we present a new algorithm, namely win-lose algorithm, with the following two properties: (a) the algorithm iteratively computes subsets of the almost-sure winning set and its complement, as compared to all previous algorithms that discover the almost-sure winning set upon termination; and (b) requires O(n · √ K) symbolic steps, where K is the maximal number of edges of strongly connected components (scc's) of the MDP. The win-lose algorithm requires symbolic computation of scc's. Third, we improve the algorithm for symbolic scc computation; the previous known algorithm takes linear symbolic steps, and our new algorithm improves the constants associated with the linear number of steps. In the worst case the previous known algorithm takes 5×n symbolic steps, whereas our new algorithm takes 4×n symbolic steps."}],"ec_funded":1,"date_updated":"2025-09-29T13:50:32Z","arxiv":1,"oa_version":"Preprint"},{"pubrep_id":"411","date_created":"2018-12-11T11:59:50Z","publisher":"Public Library of Science","intvolume":"         9","isi":1,"department":[{"_id":"JiFr"}],"type":"journal_article","citation":{"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. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1003540\">https://doi.org/10.1371/journal.pgen.1003540</a>","short":"H. Tanaka, S. Kitakura, H. Rakusová, T. Uemura, M. Feraru, R. De Rycke, S. Robert, T. Kakimoto, J. Friml, PLoS Genetics 9 (2013).","ama":"Tanaka H, Kitakura S, Rakusová H, et al. Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. <i>PLoS Genetics</i>. 2013;9(5). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003540\">10.1371/journal.pgen.1003540</a>","mla":"Tanaka, Hirokazu, et al. “Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis Thaliana.” <i>PLoS Genetics</i>, vol. 9, no. 5, e1003540, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003540\">10.1371/journal.pgen.1003540</a>.","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.","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.” <i>PLoS Genetics</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pgen.1003540\">https://doi.org/10.1371/journal.pgen.1003540</a>.","ieee":"H. Tanaka <i>et al.</i>, “Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana,” <i>PLoS Genetics</i>, vol. 9, no. 5. Public Library of Science, 2013."},"article_number":"e1003540","publication_status":"published","day":"05","doi":"10.1371/journal.pgen.1003540","date_published":"2013-05-05T00:00:00Z","oa":1,"publication":"PLoS Genetics","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"file_date_updated":"2020-07-14T12:45:50Z","file":[{"access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:45:50Z","file_id":"4957","file_name":"IST-2016-411-v1+1_journal.pgen.1003540.pdf","checksum":"050237d6c53e8d1601b26808ee1dd6d8","relation":"main_file","content_type":"application/pdf","file_size":3813091,"date_created":"2018-12-12T10:12:39Z"}],"language":[{"iso":"eng"}],"issue":"5","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"corr_author":"1","external_id":{"isi":["000320030000043"]},"has_accepted_license":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"date_updated":"2025-09-29T13:50:00Z","ec_funded":1,"year":"2013","author":[{"full_name":"Tanaka, Hirokazu","first_name":"Hirokazu","last_name":"Tanaka"},{"last_name":"Kitakura","full_name":"Kitakura, Saeko","first_name":"Saeko"},{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"},{"full_name":"Uemura, Tomohiro","first_name":"Tomohiro","last_name":"Uemura"},{"last_name":"Feraru","full_name":"Feraru, Mugurel","first_name":"Mugurel"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"},{"last_name":"Kakimoto","first_name":"Tatsuo","full_name":"Kakimoto, Tatsuo"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","quality_controlled":"1","month":"05","ddc":["570"],"publist_id":"3967","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2832","title":"Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana","volume":9,"status":"public"}]