[{"related_material":{"record":[{"status":"public","relation":"research_data","id":"13075"}]},"_id":"2968","date_updated":"2023-05-30T13:07:47Z","title":"A likelihood based comparison of population histories in a parasitoid guild","oa":1,"has_accepted_license":"1","acknowledgement":"This work was supported by funding from the UK Natural Environment Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1, NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on earlier versions of the manuscript. ","year":"2012","project":[{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"volume":21,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:00:36Z","doi":"10.1111/j.1365-294X.2012.05700.x","status":"public","author":[{"full_name":"Lohse, Konrad","first_name":"Konrad","last_name":"Lohse"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"full_name":"Melika, George","first_name":"George","last_name":"Melika"},{"full_name":"Stone, Graham","first_name":"Graham","last_name":"Stone"}],"oa_version":"Submitted Version","date_published":"2012-09-01T00:00:00Z","day":"01","type":"journal_article","ddc":["570","579"],"issue":"18","ec_funded":1,"page":"4605 - 4617","month":"09","intvolume":"        21","pubrep_id":"296","publication_status":"published","citation":{"chicago":"Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05700.x\">https://doi.org/10.1111/j.1365-294X.2012.05700.x</a>.","apa":"Lohse, K., Barton, N. H., Melika, G., &#38; Stone, G. (2012). A likelihood based comparison of population histories in a parasitoid guild. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05700.x\">https://doi.org/10.1111/j.1365-294X.2012.05700.x</a>","ama":"Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population histories in a parasitoid guild. <i>Molecular Ecology</i>. 2012;21(18):4605-4617. doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05700.x\">10.1111/j.1365-294X.2012.05700.x</a>","mla":"Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” <i>Molecular Ecology</i>, vol. 21, no. 18, Wiley-Blackwell, 2012, pp. 4605–17, doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05700.x\">10.1111/j.1365-294X.2012.05700.x</a>.","short":"K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617.","ieee":"K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison of population histories in a parasitoid guild,” <i>Molecular Ecology</i>, vol. 21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012.","ista":"Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617."},"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:57Z","file":[{"relation":"main_file","file_name":"IST-2014-296-v1+1_4_wasps_revised3.pdf","date_updated":"2020-07-14T12:45:57Z","date_created":"2018-12-12T10:17:47Z","file_size":235820,"creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"c14ee4cb2a8ba9575bfd8a9bb7a883bb","file_id":"5304"},{"relation":"main_file","file_name":"IST-2014-296-v1+2_4_wasps_Supporting2.pdf","date_updated":"2020-07-14T12:45:57Z","file_size":41975,"date_created":"2018-12-12T10:17:48Z","creator":"system","access_level":"open_access","checksum":"f00afc5b887c8222014b57375b8caece","content_type":"application/pdf","file_id":"5305"}],"publication":"Molecular Ecology","scopus_import":1,"publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"publist_id":"3746","abstract":[{"text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd.","lang":"eng"}]},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632771/","open_access":"1"}],"type":"journal_article","intvolume":"        32","month":"10","page":"14294 - 14304","issue":"41","quality_controlled":"1","citation":{"short":"S. Goswami, I. Bucurenciu, P.M. Jonas, Journal of Neuroscience 32 (2012) 14294–14304.","mla":"Goswami, Sarit, et al. “Miniature IPSCs in Hippocampal Granule Cells Are Triggered by Voltage-Gated Ca^(2+) Channels via Microdomain Coupling.” <i>Journal of Neuroscience</i>, vol. 32, no. 41, Society for Neuroscience, 2012, pp. 14294–304, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.6104-11.2012\">10.1523/JNEUROSCI.6104-11.2012</a>.","ieee":"S. Goswami, I. Bucurenciu, and P. M. Jonas, “Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling,” <i>Journal of Neuroscience</i>, vol. 32, no. 41. Society for Neuroscience, pp. 14294–14304, 2012.","ista":"Goswami S, Bucurenciu I, Jonas PM. 2012. Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal of Neuroscience. 32(41), 14294–14304.","apa":"Goswami, S., Bucurenciu, I., &#38; Jonas, P. M. (2012). Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.6104-11.2012\">https://doi.org/10.1523/JNEUROSCI.6104-11.2012</a>","chicago":"Goswami, Sarit, Iancu Bucurenciu, and Peter M Jonas. “Miniature IPSCs in Hippocampal Granule Cells Are Triggered by Voltage-Gated Ca^(2+) Channels via Microdomain Coupling.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2012. <a href=\"https://doi.org/10.1523/JNEUROSCI.6104-11.2012\">https://doi.org/10.1523/JNEUROSCI.6104-11.2012</a>.","ama":"Goswami S, Bucurenciu I, Jonas PM. Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. <i>Journal of Neuroscience</i>. 2012;32(41):14294-14304. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.6104-11.2012\">10.1523/JNEUROSCI.6104-11.2012</a>"},"publication_status":"published","abstract":[{"lang":"eng","text":"The coupling between presynaptic Ca^(2+) channels and Ca^(2+) sensors of exocytosis is a key determinant of synaptic transmission. Evoked release from parvalbumin (PV)-expressing interneurons is triggered by nanodomain coupling of P/Q-type Ca^(2+) channels, whereas release from cholecystokinin (CCK)-containing interneurons is generated by microdomain coupling of N-type channels. Nanodomain coupling has several functional advantages, including speed and efficacy of transmission. One potential disadvantage is that stochastic\r\nopening of presynaptic Ca^(2+) channels may trigger spontaneous transmitter release. We addressed this possibility in rat hippocampal\r\ngranule cells, which receive converging inputs from different inhibitory sources. Both reduction of extracellular Ca^(2+) concentration and the unselective Ca^(2+) channel blocker Cd^(2+) reduced the frequency of miniature IPSCs (mIPSCs) in granule cells by ~50%, suggesting that the opening of presynaptic Ca^(2+) channels contributes to spontaneous release. Application of the selective P/Q-type Ca^(2+) channel blocker\r\nω-agatoxin IVa had no detectable effects, whereas both the N-type blocker ω-conotoxin GVIa and the L-type blocker nimodipine reduced\r\nmIPSC frequency. Furthermore, both the fast Ca^(2+) chelator BAPTA-AM and the slow chelator EGTA-AM reduced the mIPSC frequency,\r\nsuggesting that Ca^(2+)-dependent spontaneous release is triggered by microdomain rather than nanodomain coupling. The CB_(1) receptor\r\nagonist WIN 55212-2 also decreased spontaneous release; this effect was occluded by prior application of ω-conotoxin GVIa, suggesting that a major fraction of Ca^(2+)-dependent spontaneous release was generated at the terminals of CCK-expressing interneurons. Tonic inhibition generated by spontaneous opening of presynaptic N- and L-type Ca^(2+) channels may be important for hippocampal information processing.\r\n"}],"language":[{"iso":"eng"}],"publist_id":"3744","department":[{"_id":"PeJo"}],"publisher":"Society for Neuroscience","publication":"Journal of Neuroscience","scopus_import":1,"title":"Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling","date_updated":"2021-01-12T07:40:08Z","_id":"2969","acknowledgement":"This work was supported by grants from the Deutsche Forschungsgemeinschaft (TR 3/B10, Leibniz program, GSC-4 Spemann Graduate School) and the European Union (European Research Council Advanced Grant).","year":"2012","project":[{"_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","grant_number":"SFB-TR3-TP10B"}],"oa":1,"oa_version":"Submitted Version","status":"public","author":[{"full_name":"Goswami, Sarit","first_name":"Sarit","last_name":"Goswami","id":"3A578F32-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Iancu","full_name":"Bucurenciu, Iancu","last_name":"Bucurenciu"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1523/JNEUROSCI.6104-11.2012","pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:00:36Z","volume":32,"external_id":{"pmid":["23055500"]},"day":"10","date_published":"2012-10-10T00:00:00Z"},{"title":"Investigating the principles of morphogen gradient formation: from tissues to cells","date_updated":"2021-01-12T07:40:09Z","_id":"2970","type":"journal_article","month":"12","year":"2012","acknowledgement":"AK is currently supported by an MRC CDF. MGG and OW were supported by the Swiss National Science Foundation, grants from the Swiss SystemsX.ch initiative, LipidX-2008/011, an ERC advanced investigator grant and the Polish-Swiss research program.","intvolume":"        22","issue":"6","page":"527 - 532","status":"public","author":[{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X"},{"first_name":"Ortrud","full_name":"Wartlick, Ortrud","last_name":"Wartlick"},{"last_name":"Julicher","first_name":"Frank","full_name":"Julicher, Frank"},{"full_name":"Gonzalez Gaitan, Marcos","first_name":"Marcos","last_name":"Gonzalez Gaitan"}],"quality_controlled":"1","citation":{"ista":"Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. 2012. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics &#38; Development. 22(6), 527–532.","ieee":"A. Kicheva, M. T. Bollenbach, O. Wartlick, F. Julicher, and M. Gonzalez Gaitan, “Investigating the principles of morphogen gradient formation: from tissues to cells,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 22, no. 6. Elsevier, pp. 527–532, 2012.","mla":"Kicheva, Anna, et al. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 22, no. 6, Elsevier, 2012, pp. 527–32, doi:<a href=\"https://doi.org/10.1016/j.gde.2012.08.004\">10.1016/j.gde.2012.08.004</a>.","short":"A. Kicheva, M.T. Bollenbach, O. Wartlick, F. Julicher, M. Gonzalez Gaitan, Current Opinion in Genetics &#38; Development 22 (2012) 527–532.","ama":"Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. Investigating the principles of morphogen gradient formation: from tissues to cells. <i>Current Opinion in Genetics &#38; Development</i>. 2012;22(6):527-532. doi:<a href=\"https://doi.org/10.1016/j.gde.2012.08.004\">10.1016/j.gde.2012.08.004</a>","chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ortrud Wartlick, Frank Julicher, and Marcos Gonzalez Gaitan. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.gde.2012.08.004\">https://doi.org/10.1016/j.gde.2012.08.004</a>.","apa":"Kicheva, A., Bollenbach, M. T., Wartlick, O., Julicher, F., &#38; Gonzalez Gaitan, M. (2012). Investigating the principles of morphogen gradient formation: from tissues to cells. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2012.08.004\">https://doi.org/10.1016/j.gde.2012.08.004</a>"},"oa_version":"None","date_created":"2018-12-11T12:00:37Z","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":22,"doi":"10.1016/j.gde.2012.08.004","language":[{"iso":"eng"}],"publist_id":"3739","department":[{"_id":"ToBo"}],"abstract":[{"text":"Morphogen gradients regulate the patterning and growth of many tissues, hence a key question is how they are established and maintained during development. Theoretical descriptions have helped to explain how gradient shape is controlled by the rates of morphogen production, spreading and degradation. These effective rates have been measured using fluorescence recovery after photobleaching (FRAP) and photoactivation. To unravel which molecular events determine the effective rates, such tissue-level assays have been combined with genetic analysis, high-resolution assays, and models that take into account interactions with receptors, extracellular components and trafficking. Nevertheless, because of the natural and experimental data variability, and the underlying assumptions of transport models, it remains challenging to conclusively distinguish between cellular mechanisms.","lang":"eng"}],"date_published":"2012-12-01T00:00:00Z","scopus_import":1,"publication":"Current Opinion in Genetics & Development","day":"01","publisher":"Elsevier"},{"page":"11 - 20","year":"2012","intvolume":"      7476","month":"01","date_updated":"2021-01-12T07:40:10Z","_id":"2971","type":"conference","conference":{"name":"Pattern Recognition","location":"Graz, Austria","start_date":"2012-08-28","end_date":"2012-08-31"},"title":"Interactive labeling of image segmentation hierarchies","publisher":"Springer","day":"01","date_published":"2012-01-01T00:00:00Z","scopus_import":1,"abstract":[{"lang":"eng","text":"We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. "}],"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publist_id":"3737","doi":"10.1007/978-3-642-32717-9_2","date_created":"2018-12-11T12:00:37Z","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":7476,"oa_version":"None","quality_controlled":"1","author":[{"full_name":"Zankl, Georg","first_name":"Georg","last_name":"Zankl"},{"first_name":"Yll","full_name":"Haxhimusa, Yll","last_name":"Haxhimusa"},{"id":"29F89302-F248-11E8-B48F-1D18A9856A87","last_name":"Ion","full_name":"Ion, Adrian","first_name":"Adrian"}],"status":"public","citation":{"chicago":"Zankl, Georg, Yll Haxhimusa, and Adrian Ion. “Interactive Labeling of Image Segmentation Hierarchies,” 7476:11–20. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-32717-9_2\">https://doi.org/10.1007/978-3-642-32717-9_2</a>.","apa":"Zankl, G., Haxhimusa, Y., &#38; Ion, A. (2012). Interactive labeling of image segmentation hierarchies (Vol. 7476, pp. 11–20). Presented at the Pattern Recognition, Graz, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-642-32717-9_2\">https://doi.org/10.1007/978-3-642-32717-9_2</a>","ama":"Zankl G, Haxhimusa Y, Ion A. Interactive labeling of image segmentation hierarchies. In: Vol 7476. Springer; 2012:11-20. doi:<a href=\"https://doi.org/10.1007/978-3-642-32717-9_2\">10.1007/978-3-642-32717-9_2</a>","short":"G. Zankl, Y. Haxhimusa, A. Ion, in:, Springer, 2012, pp. 11–20.","mla":"Zankl, Georg, et al. <i>Interactive Labeling of Image Segmentation Hierarchies</i>. Vol. 7476, Springer, 2012, pp. 11–20, doi:<a href=\"https://doi.org/10.1007/978-3-642-32717-9_2\">10.1007/978-3-642-32717-9_2</a>.","ista":"Zankl G, Haxhimusa Y, Ion A. 2012. Interactive labeling of image segmentation hierarchies. Pattern Recognition vol. 7476, 11–20.","ieee":"G. Zankl, Y. Haxhimusa, and A. Ion, “Interactive labeling of image segmentation hierarchies,” presented at the Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 11–20."}},{"oa":1,"year":"2012","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","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"}],"has_accepted_license":"1","date_updated":"2023-02-23T11:45:29Z","_id":"2972","related_material":{"record":[{"status":"public","id":"3851","relation":"earlier_version"}]},"title":"Energy parity games","day":"02","date_published":"2012-11-02T00:00:00Z","external_id":{"arxiv":["1001.5183"]},"doi":"10.1016/j.tcs.2012.07.038","date_created":"2018-12-11T12:00:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":458,"oa_version":"Published Version","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"status":"public","page":"49 - 60","ec_funded":1,"intvolume":"       458","pubrep_id":"935","month":"11","ddc":["004"],"type":"journal_article","arxiv":1,"publisher":"Elsevier","file":[{"creator":"kschuh","access_level":"open_access","content_type":"application/pdf","checksum":"719e4a5af5a01ad3f2f7f7f05b3c2b09","file_id":"5935","relation":"main_file","file_name":"2012_Elsevier_Chatterjee.pdf","date_updated":"2020-07-14T12:45:57Z","file_size":351271,"date_created":"2019-02-06T11:56:22Z"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:45:57Z","publication":"Theoretical Computer Science","abstract":[{"lang":"eng","text":"Energy parity games are infinite two-player turn-based games played on weighted graphs. The objective of the game combines a (qualitative) parity condition with the (quantitative) requirement that the sum of the weights (i.e., the level of energy in the game) must remain positive. Beside their own interest in the design and synthesis of resource-constrained omega-regular specifications, energy parity games provide one of the simplest model of games with combined qualitative and quantitative objectives. Our main results are as follows: (a) exponential memory is sufficient and may be necessary for winning strategies in energy parity games; (b) the problem of deciding the winner in energy parity games can be solved in NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to energy games. We also show that the problem of deciding the winner in energy parity games is logspace-equivalent to the problem of deciding the winner in mean-payoff parity games, which can thus be solved in NP ∩ coNP. As a consequence we also obtain a conceptually simple algorithm to solve mean-payoff parity games."}],"publist_id":"3736","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_status":"published","quality_controlled":"1","citation":{"ieee":"K. Chatterjee and L. Doyen, “Energy parity games,” <i>Theoretical Computer Science</i>, vol. 458. Elsevier, pp. 49–60, 2012.","ista":"Chatterjee K, Doyen L. 2012. Energy parity games. Theoretical Computer Science. 458, 49–60.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games.” <i>Theoretical Computer Science</i>, vol. 458, Elsevier, 2012, pp. 49–60, doi:<a href=\"https://doi.org/10.1016/j.tcs.2012.07.038\">10.1016/j.tcs.2012.07.038</a>.","short":"K. Chatterjee, L. Doyen, Theoretical Computer Science 458 (2012) 49–60.","ama":"Chatterjee K, Doyen L. Energy parity games. <i>Theoretical Computer Science</i>. 2012;458:49-60. doi:<a href=\"https://doi.org/10.1016/j.tcs.2012.07.038\">10.1016/j.tcs.2012.07.038</a>","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games.” <i>Theoretical Computer Science</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.tcs.2012.07.038\">https://doi.org/10.1016/j.tcs.2012.07.038</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2012). Energy parity games. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2012.07.038\">https://doi.org/10.1016/j.tcs.2012.07.038</a>"}},{"publisher":"Springer","file_date_updated":"2020-07-14T12:45:58Z","file":[{"date_updated":"2020-07-14T12:45:58Z","file_name":"IST-2016-721-v1+1_513.pdf","file_size":482570,"date_created":"2018-12-12T10:14:00Z","relation":"main_file","file_id":"5048","access_level":"open_access","creator":"system","checksum":"ab879537385efc4cb4203e7ef0fea17b","content_type":"application/pdf"}],"scopus_import":1,"abstract":[{"text":"We construct a perfectly binding string commitment scheme whose security is based on the learning parity with noise (LPN) assumption, or equivalently, the hardness of decoding random linear codes. Our scheme not only allows for a simple and efficient zero-knowledge proof of knowledge for committed values (essentially a Σ-protocol), but also for such proofs showing any kind of relation amongst committed values, i.e. proving that messages m_0,...,m_u, are such that m_0=C(m_1,...,m_u) for any circuit C.\r\n\r\nTo get soundness which is exponentially small in a security parameter t, and when the zero-knowledge property relies on the LPN problem with secrets of length l, our 3 round protocol has communication complexity O(t|C|l log(l)) and computational complexity of O(t|C|l) bit operations. The hidden constants are small, and the computation consists mostly of computing inner products of bit-vectors.","lang":"eng"}],"editor":[{"last_name":"Wang","full_name":"Wang, Xiaoyun","first_name":"Xiaoyun"},{"first_name":"Kazue","full_name":"Sako, Kazue","last_name":"Sako"}],"language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"publist_id":"3730","publication_status":"published","citation":{"ama":"Jain A, Krenn S, Pietrzak KZ, Tentes A. Commitments and efficient zero knowledge proofs from learning parity with noise. In: Wang X, Sako K, eds. Vol 7658. Springer; 2012:663-680. doi:<a href=\"https://doi.org/10.1007/978-3-642-34961-4_40\">10.1007/978-3-642-34961-4_40</a>","chicago":"Jain, Abhishek, Stephan Krenn, Krzysztof Z Pietrzak, and Aris Tentes. “Commitments and Efficient Zero Knowledge Proofs from Learning Parity with Noise.” edited by Xiaoyun Wang and Kazue Sako, 7658:663–80. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-34961-4_40\">https://doi.org/10.1007/978-3-642-34961-4_40</a>.","apa":"Jain, A., Krenn, S., Pietrzak, K. Z., &#38; Tentes, A. (2012). Commitments and efficient zero knowledge proofs from learning parity with noise. In X. Wang &#38; K. Sako (Eds.) (Vol. 7658, pp. 663–680). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-642-34961-4_40\">https://doi.org/10.1007/978-3-642-34961-4_40</a>","ista":"Jain A, Krenn S, Pietrzak KZ, Tentes A. 2012. Commitments and efficient zero knowledge proofs from learning parity with noise. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 7658, 663–680.","ieee":"A. Jain, S. Krenn, K. Z. Pietrzak, and A. Tentes, “Commitments and efficient zero knowledge proofs from learning parity with noise,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Beijing, China, 2012, vol. 7658, pp. 663–680.","short":"A. Jain, S. Krenn, K.Z. Pietrzak, A. Tentes, in:, X. Wang, K. Sako (Eds.), Springer, 2012, pp. 663–680.","mla":"Jain, Abhishek, et al. <i>Commitments and Efficient Zero Knowledge Proofs from Learning Parity with Noise</i>. Edited by Xiaoyun Wang and Kazue Sako, vol. 7658, Springer, 2012, pp. 663–80, doi:<a href=\"https://doi.org/10.1007/978-3-642-34961-4_40\">10.1007/978-3-642-34961-4_40</a>."},"alternative_title":["LNCS"],"ec_funded":1,"page":"663 - 680","intvolume":"      7658","pubrep_id":"721","month":"12","type":"conference","ddc":["004","005"],"day":"01","date_published":"2012-12-01T00:00:00Z","doi":"10.1007/978-3-642-34961-4_40","volume":7658,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:00:38Z","oa_version":"Submitted Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"last_name":"Jain","first_name":"Abhishek","full_name":"Jain, Abhishek"},{"id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","last_name":"Krenn","first_name":"Stephan","full_name":"Krenn, Stephan","orcid":"0000-0003-2835-9093"},{"first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"},{"last_name":"Tentes","first_name":"Aris","full_name":"Tentes, Aris"}],"oa":1,"acknowledgement":"We are grateful to Petros Mol for helpful discussions on the reduction for the hardness of the xLPN problem.\r\n","year":"2012","project":[{"grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","_id":"2974","date_updated":"2021-01-12T07:40:11Z","conference":{"start_date":"2012-12-02","end_date":"2012-12-06","name":"ASIACRYPT: Theory and Application of Cryptology and Information Security","location":"Beijing, China"},"title":"Commitments and efficient zero knowledge proofs from learning parity with noise"},{"author":[{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"full_name":"De Smet, Ive","first_name":"Ive","last_name":"De Smet"},{"full_name":"Lewis, Daniel R","first_name":"Daniel","last_name":"Lewis"},{"first_name":"Christian","full_name":"Löfke, Christian","last_name":"Löfke"},{"last_name":"Jansen","full_name":"Jansen, Leentje","first_name":"Leentje"},{"first_name":"Geert","full_name":"Goeminne, Geert","last_name":"Goeminne"},{"full_name":"Vanden Bossche, Robin","first_name":"Robin","last_name":"Vanden Bossche"},{"full_name":"Karimi, Mansour","first_name":"Mansour","last_name":"Karimi"},{"last_name":"De Rybel","full_name":"De Rybel, Bert","first_name":"Bert"},{"first_name":"Bartel","full_name":"Vanholme, Bartel","last_name":"Vanholme"},{"last_name":"Teichmann","full_name":"Teichmann, Thomas","first_name":"Thomas"},{"first_name":"Wout","full_name":"Boerjan, Wout","last_name":"Boerjan"},{"full_name":"Van Montagu, Marc C","first_name":"Marc","last_name":"Van Montagu"},{"last_name":"Gheysen","full_name":"Gheysen, Godelieve","first_name":"Godelieve"},{"last_name":"Muday","full_name":"Muday, Gloria K","first_name":"Gloria"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Jirí Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"}],"status":"public","quality_controlled":0,"extern":1,"citation":{"ista":"Grunewald W, De Smet I, Lewis D, Löfke C, Jansen L, Goeminne G, Vanden Bossche R, Karimi M, De Rybel B, Vanholme B, Teichmann T, Boerjan W, Van Montagu M, Gheysen G, Muday G, Friml J, Beeckman T. 2012. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 109(5), 1554–1559.","ieee":"W. Grunewald <i>et al.</i>, “Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis,” <i>PNAS</i>, vol. 109, no. 5. National Academy of Sciences, pp. 1554–1559, 2012.","short":"W. Grunewald, I. De Smet, D. Lewis, C. Löfke, L. Jansen, G. Goeminne, R. Vanden Bossche, M. Karimi, B. De Rybel, B. Vanholme, T. Teichmann, W. Boerjan, M. Van Montagu, G. Gheysen, G. Muday, J. Friml, T. Beeckman, PNAS 109 (2012) 1554–1559.","mla":"Grunewald, Wim, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” <i>PNAS</i>, vol. 109, no. 5, National Academy of Sciences, 2012, pp. 1554–59, doi:<a href=\"https://doi.org/10.1073/pnas.1121134109\">10.1073/pnas.1121134109</a>.","ama":"Grunewald W, De Smet I, Lewis D, et al. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. <i>PNAS</i>. 2012;109(5):1554-1559. doi:<a href=\"https://doi.org/10.1073/pnas.1121134109\">10.1073/pnas.1121134109</a>","apa":"Grunewald, W., De Smet, I., Lewis, D., Löfke, C., Jansen, L., Goeminne, G., … Beeckman, T. (2012). Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1121134109\">https://doi.org/10.1073/pnas.1121134109</a>","chicago":"Grunewald, Wim, Ive De Smet, Daniel Lewis, Christian Löfke, Leentje Jansen, Geert Goeminne, Robin Vanden Bossche, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” <i>PNAS</i>. National Academy of Sciences, 2012. <a href=\"https://doi.org/10.1073/pnas.1121134109\">https://doi.org/10.1073/pnas.1121134109</a>."},"publication_status":"published","date_created":"2018-12-11T12:01:24Z","volume":109,"doi":"10.1073/pnas.1121134109","publist_id":"3595","abstract":[{"lang":"eng","text":"\nGradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds knownasflavonols have beenshownto act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis."}],"date_published":"2012-01-31T00:00:00Z","publication":"PNAS","day":"31","publisher":"National Academy of Sciences","title":"Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis","date_updated":"2021-01-12T07:41:05Z","type":"journal_article","_id":"3104","month":"01","intvolume":"       109","year":"2012","issue":"5","page":"1554 - 1559"},{"type":"journal_article","_id":"3105","date_updated":"2021-01-12T07:41:06Z","title":"GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses","page":"678 - 685","issue":"3","intvolume":"        22","year":"2012","month":"03","doi":"10.1016/j.devcel.2012.02.002","volume":22,"date_created":"2018-12-11T12:01:25Z","publication_status":"published","extern":1,"citation":{"chicago":"Whitford, Ryan, Ana Fernandez, Ricardo Tejos, Amparo Pérez, Jürgen Kleine Vehn, Steffen Vanneste, Andrzej Drozdzecki, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” <i>Developmental Cell</i>. Cell Press, 2012. <a href=\"https://doi.org/10.1016/j.devcel.2012.02.002\">https://doi.org/10.1016/j.devcel.2012.02.002</a>.","apa":"Whitford, R., Fernandez, A., Tejos, R., Pérez, A., Kleine Vehn, J., Vanneste, S., … Hilson, P. (2012). GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2012.02.002\">https://doi.org/10.1016/j.devcel.2012.02.002</a>","ama":"Whitford R, Fernandez A, Tejos R, et al. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. <i>Developmental Cell</i>. 2012;22(3):678-685. doi:<a href=\"https://doi.org/10.1016/j.devcel.2012.02.002\">10.1016/j.devcel.2012.02.002</a>","short":"R. Whitford, A. Fernandez, R. Tejos, A. Pérez, J. Kleine Vehn, S. Vanneste, A. Drozdzecki, J. Leitner, L. Abas, M. Aerts, K. Hoogewijs, P. Baster, R. De Groodt, Y. Lin, V. Storme, Y. Van De Peer, T. Beeckman, A. Madder, B. Devreese, C. Luschnig, J. Friml, P. Hilson, Developmental Cell 22 (2012) 678–685.","mla":"Whitford, Ryan, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” <i>Developmental Cell</i>, vol. 22, no. 3, Cell Press, 2012, pp. 678–85, doi:<a href=\"https://doi.org/10.1016/j.devcel.2012.02.002\">10.1016/j.devcel.2012.02.002</a>.","ista":"Whitford R, Fernandez A, Tejos R, Pérez A, Kleine Vehn J, Vanneste S, Drozdzecki A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin Y, Storme V, Van De Peer Y, Beeckman T, Madder A, Devreese B, Luschnig C, Friml J, Hilson P. 2012. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 22(3), 678–685.","ieee":"R. Whitford <i>et al.</i>, “GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses,” <i>Developmental Cell</i>, vol. 22, no. 3. Cell Press, pp. 678–685, 2012."},"quality_controlled":0,"author":[{"first_name":"Ryan","full_name":"Whitford, Ryan","last_name":"Whitford"},{"last_name":"Fernandez","first_name":"Ana","full_name":"Fernandez, Ana"},{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"first_name":"Amparo","full_name":"Pérez, Amparo Cuéllar","last_name":"Pérez"},{"last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"full_name":"Drozdzecki, Andrzej","first_name":"Andrzej","last_name":"Drozdzecki"},{"last_name":"Leitner","full_name":"Leitner, Johannes","first_name":"Johannes"},{"last_name":"Abas","first_name":"Lindy","full_name":"Abas, Lindy"},{"full_name":"Aerts, Maarten","first_name":"Maarten","last_name":"Aerts"},{"first_name":"Kurt","full_name":"Hoogewijs, Kurt","last_name":"Hoogewijs"},{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","full_name":"Pawel Baster","first_name":"Pawel"},{"full_name":"De Groodt, Ruth","first_name":"Ruth","last_name":"De Groodt"},{"first_name":"Yao","full_name":"Lin, Yao-Cheng","last_name":"Lin"},{"last_name":"Storme","full_name":"Storme, Véronique","first_name":"Véronique"},{"last_name":"Van De Peer","full_name":"Van de Peer, Yves","first_name":"Yves"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"first_name":"Annemieke","full_name":"Madder, Annemieke","last_name":"Madder"},{"first_name":"Bart","full_name":"Devreese, Bart","last_name":"Devreese"},{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"},{"full_name":"Jirí Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Hilson","first_name":"Pierre","full_name":"Hilson, Pierre"}],"status":"public","day":"13","publisher":"Cell Press","publication":"Developmental Cell","date_published":"2012-03-13T00:00:00Z","abstract":[{"text":"Growth and development are coordinated by an array of intercellular communications. Known plant signaling molecules include phytohormones and hormone peptides. Although both classes can be implicated in the same developmental processes, little is known about the interplay between phytohormone action and peptide signaling within the cellular microenvironment. We show that genes coding for small secretory peptides, designated GOLVEN (GLV), modulate the distribution of the phytohormone auxin. The deregulation of the GLV function impairs the formation of auxin gradients and alters the reorientation of shoots and roots after a gravity stimulus. Specifically, the GLV signal modulates the trafficking dynamics of the auxin efflux carrier PIN-FORMED2 involved in root tropic responses and meristem organization. Our work links the local action of secretory peptides with phytohormone transport. Root growth factor (RGF) or GOLVEN (GLV) secreted peptides have previously been implicated in meristem regulation. Whitford et al. now show that RGF/GLV peptides induce rapid relocalization of the auxin efflux regulator PIN2, regulate auxin gradients, and modulate auxin-dependent root responses to specific stimuli.","lang":"eng"}],"publist_id":"3594"},{"abstract":[{"text":"Cell polarization via asymmetrical distribution of structures or molecules is essential for diverse cellular functions and development of organisms, but how polarity is developmentally controlled has been poorly understood. In plants, the asymmetrical distribution of the PIN-FORMED (PIN) proteins involved in the cellular efflux of the quintessential phytohormone auxin plays a central role in developmental patterning, morphogenesis, and differential growth. Recently we showed that auxin promotes cell interdigitation by activating the Rho family ROP GTPases in leaf epidermal pavement cells. Here we found that auxin activation of the ROP2 signaling pathway regulates the asymmetric distribution of PIN1 by inhibiting its endocytosis. ROP2 inhibits PIN1 endocytosis via the accumulation of cortical actin microfilaments induced by the ROP2 effector protein RIC4. Our findings suggest a link between the developmental auxin signal and polar PIN1 distribution via Rho-dependent cytoskeletal reorganization and reveal the conservation of a design principle for cell polarization that is based on Rho GTPase-mediated inhibition of endocytosis.","lang":"eng"}],"publist_id":"3593","publisher":"Public Library of Science","day":"01","date_published":"2012-04-01T00:00:00Z","publication":"PLoS Biology","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":0,"author":[{"last_name":"Nagawa","first_name":"Shingo","full_name":"Nagawa, Shingo"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"},{"full_name":"Lin, Deshu","first_name":"Deshu","last_name":"Lin"},{"first_name":"Pankaj","full_name":"Dhonukshe, Pankaj","last_name":"Dhonukshe"},{"last_name":"Zhang","full_name":"Zhang, Xingxing","first_name":"Xingxing"},{"full_name":"Jirí Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Scheres","full_name":"Scheres, Ben","first_name":"Ben"},{"last_name":"Fu","first_name":"Ying","full_name":"Fu, Ying"},{"last_name":"Yang","full_name":"Yang, Zhenbiao","first_name":"Zhenbiao"}],"citation":{"apa":"Nagawa, S., Xu, T., Lin, D., Dhonukshe, P., Zhang, X., Friml, J., … Yang, Z. (2012). ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1001299\">https://doi.org/10.1371/journal.pbio.1001299</a>","chicago":"Nagawa, Shingo, Tongda Xu, Deshu Lin, Pankaj Dhonukshe, Xingxing Zhang, Jiří Friml, Ben Scheres, Ying Fu, and Zhenbiao Yang. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” <i>PLoS Biology</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pbio.1001299\">https://doi.org/10.1371/journal.pbio.1001299</a>.","ama":"Nagawa S, Xu T, Lin D, et al. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. <i>PLoS Biology</i>. 2012;10(4). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001299\">10.1371/journal.pbio.1001299</a>","short":"S. Nagawa, T. Xu, D. Lin, P. Dhonukshe, X. Zhang, J. Friml, B. Scheres, Y. Fu, Z. Yang, PLoS Biology 10 (2012).","mla":"Nagawa, Shingo, et al. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” <i>PLoS Biology</i>, vol. 10, no. 4, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001299\">10.1371/journal.pbio.1001299</a>.","ieee":"S. Nagawa <i>et al.</i>, “ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis,” <i>PLoS Biology</i>, vol. 10, no. 4. Public Library of Science, 2012.","ista":"Nagawa S, Xu T, Lin D, Dhonukshe P, Zhang X, Friml J, Scheres B, Fu Y, Yang Z. 2012. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 10(4)."},"extern":1,"doi":"10.1371/journal.pbio.1001299","publication_status":"published","date_created":"2018-12-11T12:01:25Z","volume":10,"year":"2012","intvolume":"        10","month":"04","issue":"4","title":"ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis","date_updated":"2021-01-12T07:41:06Z","type":"journal_article","_id":"3106"},{"month":"05","year":"2012","intvolume":"         8","issue":"5","page":"415 - 416","title":"Plant signaling: Deconstructing auxin sensing","type":"other_academic_publication","_id":"3107","date_updated":"2021-01-12T07:41:06Z","language":[{"iso":"eng"}],"publist_id":"3592","publication":"Nature Chemical Biology","date_published":"2012-05-01T00:00:00Z","day":"01","publisher":"Nature Publishing Group","citation":{"ieee":"S. Vanneste and J. Friml, <i>Plant signaling: Deconstructing auxin sensing</i>, vol. 8, no. 5. Nature Publishing Group, 2012, pp. 415–416.","ista":"Vanneste S, Friml J. 2012. Plant signaling: Deconstructing auxin sensing, Nature Publishing Group,p.","mla":"Vanneste, Steffen, and Jiří Friml. “Plant Signaling: Deconstructing Auxin Sensing.” <i>Nature Chemical Biology</i>, vol. 8, no. 5, Nature Publishing Group, 2012, pp. 415–16, doi:<a href=\"https://doi.org/10.1038/nchembio.943\">10.1038/nchembio.943</a>.","short":"S. Vanneste, J. Friml, Plant Signaling: Deconstructing Auxin Sensing, Nature Publishing Group, 2012.","ama":"Vanneste S, Friml J. <i>Plant Signaling: Deconstructing Auxin Sensing</i>. Vol 8. Nature Publishing Group; 2012:415-416. doi:<a href=\"https://doi.org/10.1038/nchembio.943\">10.1038/nchembio.943</a>","apa":"Vanneste, S., &#38; Friml, J. (2012). <i>Plant signaling: Deconstructing auxin sensing</i>. <i>Nature Chemical Biology</i> (Vol. 8, pp. 415–416). Nature Publishing Group. <a href=\"https://doi.org/10.1038/nchembio.943\">https://doi.org/10.1038/nchembio.943</a>","chicago":"Vanneste, Steffen, and Jiří Friml. <i>Plant Signaling: Deconstructing Auxin Sensing</i>. <i>Nature Chemical Biology</i>. Vol. 8. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nchembio.943\">https://doi.org/10.1038/nchembio.943</a>."},"extern":"1","status":"public","quality_controlled":"1","author":[{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","volume":8,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:01:26Z","publication_status":"published","doi":"10.1038/nchembio.943"},{"date_updated":"2021-01-12T07:41:07Z","_id":"3108","type":"journal_article","title":"A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants","issue":"7396","page":"119 - 122","month":"05","year":"2012","intvolume":"       485","date_created":"2018-12-11T12:01:26Z","publication_status":"published","volume":485,"doi":"10.1038/nature11001","author":[{"first_name":"Elke","full_name":"Barbez, Elke","last_name":"Barbez"},{"last_name":"Kubeš","full_name":"Kubeš, Martin","first_name":"Martin"},{"full_name":"Rolčík, Jakub","first_name":"Jakub","last_name":"Rolčík"},{"last_name":"Béziat","full_name":"Béziat, Chloe","first_name":"Chloe"},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"last_name":"Wang","full_name":"Wang, Bangjun","first_name":"Bangjun"},{"full_name":"Rosquete, Michel Ruiz","first_name":"Michel","last_name":"Rosquete"},{"first_name":"Jinsheng","full_name":"Zhu, Jinsheng","last_name":"Zhu"},{"first_name":"Petre","full_name":"Dobrev, Petre I","last_name":"Dobrev"},{"last_name":"Lee","first_name":"Yuree","full_name":"Lee, Yuree"},{"first_name":"Eva","full_name":"Zašímalová, Eva","last_name":"Zašímalová"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Jirí Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"}],"quality_controlled":0,"status":"public","extern":1,"citation":{"apa":"Barbez, E., Kubeš, M., Rolčík, J., Béziat, C., Pěnčík, A., Wang, B., … Kleine Vehn, J. (2012). A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature11001\">https://doi.org/10.1038/nature11001</a>","chicago":"Barbez, Elke, Martin Kubeš, Jakub Rolčík, Chloe Béziat, Aleš Pěnčík, Bangjun Wang, Michel Rosquete, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” <i>Nature</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nature11001\">https://doi.org/10.1038/nature11001</a>.","ama":"Barbez E, Kubeš M, Rolčík J, et al. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. <i>Nature</i>. 2012;485(7396):119-122. doi:<a href=\"https://doi.org/10.1038/nature11001\">10.1038/nature11001</a>","mla":"Barbez, Elke, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” <i>Nature</i>, vol. 485, no. 7396, Nature Publishing Group, 2012, pp. 119–22, doi:<a href=\"https://doi.org/10.1038/nature11001\">10.1038/nature11001</a>.","short":"E. Barbez, M. Kubeš, J. Rolčík, C. Béziat, A. Pěnčík, B. Wang, M. Rosquete, J. Zhu, P. Dobrev, Y. Lee, E. Zašímalová, J. Petrášek, M. Geisler, J. Friml, J. Kleine Vehn, Nature 485 (2012) 119–122.","ieee":"E. Barbez <i>et al.</i>, “A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants,” <i>Nature</i>, vol. 485, no. 7396. Nature Publishing Group, pp. 119–122, 2012.","ista":"Barbez E, Kubeš M, Rolčík J, Béziat C, Pěnčík A, Wang B, Rosquete M, Zhu J, Dobrev P, Lee Y, Zašímalová E, Petrášek J, Geisler M, Friml J, Kleine Vehn J. 2012. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 485(7396), 119–122."},"date_published":"2012-05-03T00:00:00Z","publication":"Nature","day":"03","publisher":"Nature Publishing Group","publist_id":"3591","abstract":[{"text":"The phytohormone auxin acts as a prominent signal, providing, by its local accumulation or depletion in selected cells, a spatial and temporal reference for changes in the developmental program. The distribution of auxin depends on both auxin metabolism (biosynthesis, conjugation and degradation) and cellular auxin transport. We identified in silico a novel putative auxin transport facilitator family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required for auxin-dependent regulation of plant growth by determining the cellular sensitivity to auxin. PILS proteins regulate intracellular auxin accumulation at the endoplasmic reticulum and thus auxin availability for nuclear auxin signalling. PILS activity affects the level of endogenous auxin indole-3-acetic acid (IAA), presumably via intracellular accumulation and metabolism. Our findings reveal that the transport machinery to compartmentalize auxin within the cell is of an unexpected molecular complexity and demonstrate this compartmentalization to be functionally important for a number of developmental processes.","lang":"eng"}]},{"intvolume":"         8","year":"2012","month":"06","page":"583 - 589","issue":"6","title":"Fluorescent castasterone reveals BRI1 signaling from the plasma membrane","_id":"3109","type":"journal_article","date_updated":"2021-01-12T07:41:07Z","abstract":[{"lang":"eng","text":"Receptor-mediated endocytosis is an integral part of signal transduction as it mediates signal attenuation and provides spatial and temporal dimensions to signaling events. One of the best-studied leucine-rich repeat receptor-like kinases in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid (BR) hormone, at the cell surface and is constitutively endocytosed. However, the importance of endocytosis for BR signaling remains unclear. Here we developed a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment of endocytosis dependent on clathrin and the guanine nucleotide exchange factor for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what is to our knowledge the first visualization of receptor-ligand complexes in plants and reveal clathrin-and ARF-GEF-dependent endocytic regulation of BR signaling from the plasma membrane."}],"publist_id":"3590","publisher":"Nature Publishing Group","day":"01","publication":"Nature Chemical Biology","date_published":"2012-06-01T00:00:00Z","extern":1,"citation":{"chicago":"Irani, Niloufer, Simone Di Rubbo, Evelien Mylle, Jos Van Den Begin, Joanna Schneider Pizoń, Jaroslava Hniliková, Miroslav Šíša, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nchembio.958\">https://doi.org/10.1038/nchembio.958</a>.","apa":"Irani, N., Di Rubbo, S., Mylle, E., Van Den Begin, J., Schneider Pizoń, J., Hniliková, J., … Russinova, E. (2012). Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nchembio.958\">https://doi.org/10.1038/nchembio.958</a>","ama":"Irani N, Di Rubbo S, Mylle E, et al. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. <i>Nature Chemical Biology</i>. 2012;8(6):583-589. doi:<a href=\"https://doi.org/10.1038/nchembio.958\">10.1038/nchembio.958</a>","short":"N. Irani, S. Di Rubbo, E. Mylle, J. Van Den Begin, J. Schneider Pizoń, J. Hniliková, M. Šíša, D. Buyst, J. Vilarrasa Blasi, A. Szatmári, D. Van Damme, K. Mishev, M. Codreanu, L. Kohout, M. Strnad, A. Caño Delgado, J. Friml, A. Madder, E. Russinova, Nature Chemical Biology 8 (2012) 583–589.","mla":"Irani, Niloufer, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” <i>Nature Chemical Biology</i>, vol. 8, no. 6, Nature Publishing Group, 2012, pp. 583–89, doi:<a href=\"https://doi.org/10.1038/nchembio.958\">10.1038/nchembio.958</a>.","ista":"Irani N, Di Rubbo S, Mylle E, Van Den Begin J, Schneider Pizoń J, Hniliková J, Šíša M, Buyst D, Vilarrasa Blasi J, Szatmári A, Van Damme D, Mishev K, Codreanu M, Kohout L, Strnad M, Caño Delgado A, Friml J, Madder A, Russinova E. 2012. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 8(6), 583–589.","ieee":"N. Irani <i>et al.</i>, “Fluorescent castasterone reveals BRI1 signaling from the plasma membrane,” <i>Nature Chemical Biology</i>, vol. 8, no. 6. Nature Publishing Group, pp. 583–589, 2012."},"quality_controlled":0,"status":"public","author":[{"first_name":"Niloufer","full_name":"Irani, Niloufer G","last_name":"Irani"},{"first_name":"Simone","full_name":"Di Rubbo, Simone","last_name":"Di Rubbo"},{"first_name":"Evelien","full_name":"Mylle, Evelien","last_name":"Mylle"},{"last_name":"Van Den Begin","first_name":"Jos","full_name":"Van Den Begin, Jos"},{"first_name":"Joanna","full_name":"Schneider-Pizoń, Joanna","last_name":"Schneider Pizoń"},{"full_name":"Hniliková, Jaroslava","first_name":"Jaroslava","last_name":"Hniliková"},{"first_name":"Miroslav","full_name":"Šíša, Miroslav","last_name":"Šíša"},{"first_name":"Dieter","full_name":"Buyst, Dieter","last_name":"Buyst"},{"full_name":"Vilarrasa-Blasi, Josep","first_name":"Josep","last_name":"Vilarrasa Blasi"},{"last_name":"Szatmári","full_name":"Szatmári, Anna-Maria","first_name":"Anna"},{"full_name":"Van Damme, Daniël","first_name":"Daniël","last_name":"Van Damme"},{"last_name":"Mishev","first_name":"Kiril","full_name":"Mishev, Kiril"},{"full_name":"Codreanu, Mirela-Corina","first_name":"Mirela","last_name":"Codreanu"},{"last_name":"Kohout","full_name":"Kohout, Ladislav","first_name":"Ladislav"},{"first_name":"Miroslav","full_name":"Strnad, Miroslav","last_name":"Strnad"},{"last_name":"Caño Delgado","first_name":"Ana","full_name":"Caño-Delgado, Ana I"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Jirí Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Madder","full_name":"Madder, Annemieke","first_name":"Annemieke"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"}],"doi":"10.1038/nchembio.958","volume":8,"date_created":"2018-12-11T12:01:26Z","publication_status":"published"},{"date_created":"2018-12-11T12:01:27Z","publication_status":"published","volume":24,"doi":"10.1105/tpc.112.098905","status":"public","author":[{"last_name":"Dai","first_name":"Mingqiu","full_name":"Dai, Mingqiu"},{"last_name":"Zhang","full_name":"Zhang, Chen","first_name":"Chen"},{"first_name":"Urszula","full_name":"Urszula Kania","last_name":"Kania","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chen, Fang","first_name":"Fang","last_name":"Chen"},{"first_name":"Qin","full_name":"Xue, Qin","last_name":"Xue"},{"last_name":"Mccray","full_name":"McCray, Tyra","first_name":"Tyra"},{"first_name":"Gang","full_name":"Li, Gang","last_name":"Li"},{"last_name":"Qin","first_name":"Genji","full_name":"Qin, Genji"},{"last_name":"Wakeley","first_name":"Michelle","full_name":"Wakeley, Michelle"},{"last_name":"Terzaghi","first_name":"William","full_name":"Terzaghi, William"},{"last_name":"Wan","full_name":"Wan, Jianmin","first_name":"Jianmin"},{"first_name":"Yunde","full_name":"Zhao, Yunde","last_name":"Zhao"},{"full_name":"Xu, Jian","first_name":"Jian","last_name":"Xu"},{"first_name":"Jirí","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Deng","first_name":"Xing","full_name":"Deng, Xing W"},{"last_name":"Wang","full_name":"Wang, Haiyang","first_name":"Haiyang"}],"quality_controlled":0,"citation":{"mla":"Dai, Mingqiu, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.” <i>Plant Cell</i>, vol. 24, no. 6, American Society of Plant Biologists, 2012, pp. 2497–514, doi:<a href=\"https://doi.org/10.1105/tpc.112.098905\">10.1105/tpc.112.098905</a>.","short":"M. Dai, C. Zhang, U. Kania, F. Chen, Q. Xue, T. Mccray, G. Li, G. Qin, M. Wakeley, W. Terzaghi, J. Wan, Y. Zhao, J. Xu, J. Friml, X. Deng, H. Wang, Plant Cell 24 (2012) 2497–2514.","ieee":"M. Dai <i>et al.</i>, “A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis,” <i>Plant Cell</i>, vol. 24, no. 6. American Society of Plant Biologists, pp. 2497–2514, 2012.","ista":"Dai M, Zhang C, Kania U, Chen F, Xue Q, Mccray T, Li G, Qin G, Wakeley M, Terzaghi W, Wan J, Zhao Y, Xu J, Friml J, Deng X, Wang H. 2012. A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. 24(6), 2497–2514.","chicago":"Dai, Mingqiu, Chen Zhang, Urszula Kania, Fang Chen, Qin Xue, Tyra Mccray, Gang Li, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2012. <a href=\"https://doi.org/10.1105/tpc.112.098905\">https://doi.org/10.1105/tpc.112.098905</a>.","apa":"Dai, M., Zhang, C., Kania, U., Chen, F., Xue, Q., Mccray, T., … Wang, H. (2012). A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.112.098905\">https://doi.org/10.1105/tpc.112.098905</a>","ama":"Dai M, Zhang C, Kania U, et al. A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. <i>Plant Cell</i>. 2012;24(6):2497-2514. doi:<a href=\"https://doi.org/10.1105/tpc.112.098905\">10.1105/tpc.112.098905</a>"},"extern":1,"date_published":"2012-06-01T00:00:00Z","publication":"Plant Cell","publisher":"American Society of Plant Biologists","day":"01","publist_id":"3589","abstract":[{"text":"The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate that mutations simultaneously disrupting the function of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN proteins, correlating with a basal-to-apical shift in subcellular PIN localization. The changes in PIN polarity result in increased root basipetal auxin transport and severe defects, including shorter roots, fewer lateral roots, defective columella cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins (RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3) physically interact to form a novel PP6-type heterotrimeric holoenzyme complex. We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins and that for SAL the strength of the interaction depends on the PIN phosphorylation status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically with PID to direct auxin transport polarity and plant development by directly regulating PIN phosphorylation. ","lang":"eng"}],"date_updated":"2021-01-12T07:41:08Z","type":"journal_article","_id":"3110","title":"A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis","issue":"6","page":"2497 - 2514","month":"06","year":"2012","intvolume":"        24"},{"date_updated":"2021-01-12T07:41:08Z","_id":"3111","type":"journal_article","title":"A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots","page":"1319 - 1325","issue":"14","year":"2012","intvolume":"        22","month":"07","doi":"10.1016/j.cub.2012.05.019","date_created":"2018-12-11T12:01:27Z","publication_status":"published","volume":22,"author":[{"full_name":"Lin, Deshu","first_name":"Deshu","last_name":"Lin"},{"first_name":"Shingo","full_name":"Nagawa, Shingo","last_name":"Nagawa"},{"last_name":"Chen","first_name":"Jisheng","full_name":"Chen, Jisheng"},{"last_name":"Cao","full_name":"Cao, Lingyan","first_name":"Lingyan"},{"last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Xu Chen","first_name":"Xu"},{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"full_name":"Hongjiang Li","first_name":"Hongjiang","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"last_name":"Dhonukshe","full_name":"Dhonukshe, Pankaj","first_name":"Pankaj"},{"last_name":"Yamamuro","first_name":"Chizuko","full_name":"Yamamuro, Chizuko"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Jirí Friml","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Scheres","full_name":"Scheres, Ben","first_name":"Ben"},{"full_name":"Fu, Ying","first_name":"Ying","last_name":"Fu"},{"first_name":"Zhenbiao","full_name":"Yang, Zhenbiao","last_name":"Yang"}],"status":"public","quality_controlled":0,"citation":{"mla":"Lin, Deshu, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates the Subcellular Distribution of PIN2 in Arabidopsis Roots.” <i>Current Biology</i>, vol. 22, no. 14, Cell Press, 2012, pp. 1319–25, doi:<a href=\"https://doi.org/10.1016/j.cub.2012.05.019\">10.1016/j.cub.2012.05.019</a>.","short":"D. Lin, S. Nagawa, J. Chen, L. Cao, X. Chen, T. Xu, H. Li, P. Dhonukshe, C. Yamamuro, J. Friml, B. Scheres, Y. Fu, Z. Yang, Current Biology 22 (2012) 1319–1325.","ista":"Lin D, Nagawa S, Chen J, Cao L, Chen X, Xu T, Li H, Dhonukshe P, Yamamuro C, Friml J, Scheres B, Fu Y, Yang Z. 2012. A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology. 22(14), 1319–1325.","ieee":"D. Lin <i>et al.</i>, “A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots,” <i>Current Biology</i>, vol. 22, no. 14. Cell Press, pp. 1319–1325, 2012.","apa":"Lin, D., Nagawa, S., Chen, J., Cao, L., Chen, X., Xu, T., … Yang, Z. (2012). A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2012.05.019\">https://doi.org/10.1016/j.cub.2012.05.019</a>","chicago":"Lin, Deshu, Shingo Nagawa, Jisheng Chen, Lingyan Cao, Xu Chen, Tongda Xu, Hongjiang Li, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates the Subcellular Distribution of PIN2 in Arabidopsis Roots.” <i>Current Biology</i>. Cell Press, 2012. <a href=\"https://doi.org/10.1016/j.cub.2012.05.019\">https://doi.org/10.1016/j.cub.2012.05.019</a>.","ama":"Lin D, Nagawa S, Chen J, et al. A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. <i>Current Biology</i>. 2012;22(14):1319-1325. doi:<a href=\"https://doi.org/10.1016/j.cub.2012.05.019\">10.1016/j.cub.2012.05.019</a>"},"extern":1,"publisher":"Cell Press","day":"24","date_published":"2012-07-24T00:00:00Z","publication":"Current Biology","abstract":[{"text":"PIN-FORMED (PIN) protein-mediated auxin polar transport is critically important for development, pattern formation, and morphogenesis in plants. Auxin has been implicated in the regulation of polar auxin transport by inhibiting PIN endocytosis [1, 2], but how auxin regulates this process is poorly understood. Our genetic screen identified the Arabidopsis SPIKE1 (SPK1) gene whose loss-of-function mutations increased lateral root density and retarded gravitropic responses, as do pin2 knockout mutations [3]. SPK1 belongs to the conserved DHR2-Dock family of Rho guanine nucleotide exchange factors [4-6]. The spk1 mutations induced PIN2 internalization that was not suppressed by auxin, as did the loss-of-function mutations for Rho-like GTPase from Plants 6 (ROP6)-GTPase or its effector RIC1. Furthermore, SPK1 was required for auxin induction of ROP6 activation. Our results have established a Rho GTPase-based auxin signaling pathway that maintains PIN2 polar distribution to the plasma membrane via inhibition of its internalization in Arabidopsis roots. Our findings provide new insights into signaling mechanisms that underlie the regulation of the dynamic trafficking of PINs required for long-distance auxin transport and that link auxin signaling to PIN-mediated pattern formation and morphogenesis.","lang":"eng"}],"publist_id":"3588"},{"month":"07","year":"2012","intvolume":"        22","issue":"14","page":"1326 - 1332","title":"ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots","date_updated":"2021-01-12T07:41:08Z","_id":"3112","type":"journal_article","publist_id":"3587","abstract":[{"text":"The dynamic spatial and temporal distribution of the crucial plant signaling molecule auxin is achieved by feedback coordination of auxin signaling and intercellular auxin transport pathways [1, 2]. Developmental roles of auxin have been attributed predominantly to its effect on transcription; however, an alternative pathway involving AUXIN BINDING PROTEIN1 (ABP1) has been proposed to regulate clathrin-mediated endocytosis in roots and Rho-like GTPase (ROP)-dependent pavement cell interdigitation in leaves [3, 4]. In this study, we show that ROP6 and its downstream effector RIC1 regulate clathrin association with the plasma membrane for clathrin-mediated endocytosis, as well as for its feedback regulation by auxin. Genetic analysis revealed that ROP6/RIC1 acts downstream of ABP1 to regulate endocytosis. This signaling circuit is also involved in the feedback regulation of PIN-FORMED 1 (PIN1) and PIN2 auxin transporters activity (via its constitutive endocytosis) and corresponding auxin transport-mediated processes, including root gravitropism and leave vascular tissue patterning. Our findings suggest that the signaling module auxin-ABP1-ROP6/RIC1-clathrin-PIN1/PIN2 is a shared component of the feedback regulation of auxin transport during both root and aerial development.","lang":"eng"}],"date_published":"2012-07-24T00:00:00Z","publication":"Current Biology","publisher":"Cell Press","day":"24","author":[{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Xu","full_name":"Xu Chen"},{"last_name":"Naramoto","full_name":"Naramoto, Satoshi","first_name":"Satoshi"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"first_name":"Ricardo","full_name":"Tejos, Ricardo","last_name":"Tejos"},{"first_name":"Christian","full_name":"Löfke, Christian","last_name":"Löfke"},{"full_name":"Lin, Deshu","first_name":"Deshu","last_name":"Lin"},{"full_name":"Yang, Zhenbiao","first_name":"Zhenbiao","last_name":"Yang"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","first_name":"Jirí"}],"quality_controlled":0,"status":"public","citation":{"ista":"Chen X, Naramoto S, Robert S, Tejos R, Löfke C, Lin D, Yang Z, Friml J. 2012. ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. Current Biology. 22(14), 1326–1332.","ieee":"X. Chen <i>et al.</i>, “ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots,” <i>Current Biology</i>, vol. 22, no. 14. Cell Press, pp. 1326–1332, 2012.","mla":"Chen, Xu, et al. “ABP1 and ROP6 GTPase Signaling Regulate Clathrin Mediated Endocytosis in Arabidopsis Roots.” <i>Current Biology</i>, vol. 22, no. 14, Cell Press, 2012, pp. 1326–32, doi:<a href=\"https://doi.org/10.1016/j.cub.2012.05.020\">10.1016/j.cub.2012.05.020</a>.","short":"X. Chen, S. Naramoto, S. Robert, R. Tejos, C. Löfke, D. Lin, Z. Yang, J. Friml, Current Biology 22 (2012) 1326–1332.","ama":"Chen X, Naramoto S, Robert S, et al. ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. <i>Current Biology</i>. 2012;22(14):1326-1332. doi:<a href=\"https://doi.org/10.1016/j.cub.2012.05.020\">10.1016/j.cub.2012.05.020</a>","apa":"Chen, X., Naramoto, S., Robert, S., Tejos, R., Löfke, C., Lin, D., … Friml, J. (2012). ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2012.05.020\">https://doi.org/10.1016/j.cub.2012.05.020</a>","chicago":"Chen, Xu, Satoshi Naramoto, Stéphanie Robert, Ricardo Tejos, Christian Löfke, Deshu Lin, Zhenbiao Yang, and Jiří Friml. “ABP1 and ROP6 GTPase Signaling Regulate Clathrin Mediated Endocytosis in Arabidopsis Roots.” <i>Current Biology</i>. Cell Press, 2012. <a href=\"https://doi.org/10.1016/j.cub.2012.05.020\">https://doi.org/10.1016/j.cub.2012.05.020</a>."},"extern":1,"date_created":"2018-12-11T12:01:27Z","publication_status":"published","volume":22,"doi":"10.1016/j.cub.2012.05.020"},{"title":"Cell wall constrains lateral diffusion of plant plasma membrane proteins","_id":"3113","type":"journal_article","date_updated":"2021-01-12T07:41:09Z","month":"07","year":"2012","intvolume":"       109","issue":"31","page":"12805 - 12810","extern":1,"citation":{"ama":"Martinière A, Lavagi I, Nageswaran G, et al. Cell wall constrains lateral diffusion of plant plasma membrane proteins. <i>PNAS</i>. 2012;109(31):12805-12810. doi:<a href=\"https://doi.org/10.1073/pnas.1202040109\">10.1073/pnas.1202040109</a>","chicago":"Martinière, Alexandre, Irene Lavagi, Gayathri Nageswaran, Daniel Rolfe, Lilly Maneta Peyret, Doan Luu, Stanley Botchway, et al. “Cell Wall Constrains Lateral Diffusion of Plant Plasma Membrane Proteins.” <i>PNAS</i>. National Academy of Sciences, 2012. <a href=\"https://doi.org/10.1073/pnas.1202040109\">https://doi.org/10.1073/pnas.1202040109</a>.","apa":"Martinière, A., Lavagi, I., Nageswaran, G., Rolfe, D., Maneta Peyret, L., Luu, D., … Runions, J. (2012). Cell wall constrains lateral diffusion of plant plasma membrane proteins. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1202040109\">https://doi.org/10.1073/pnas.1202040109</a>","ista":"Martinière A, Lavagi I, Nageswaran G, Rolfe D, Maneta Peyret L, Luu D, Botchway S, Webb S, Mongrand S, Maurel C, Martin Fernandez M, Kleine Vehn J, Friml J, Moreau P, Runions J. 2012. Cell wall constrains lateral diffusion of plant plasma membrane proteins. PNAS. 109(31), 12805–12810.","ieee":"A. Martinière <i>et al.</i>, “Cell wall constrains lateral diffusion of plant plasma membrane proteins,” <i>PNAS</i>, vol. 109, no. 31. National Academy of Sciences, pp. 12805–12810, 2012.","short":"A. Martinière, I. Lavagi, G. Nageswaran, D. Rolfe, L. Maneta Peyret, D. Luu, S. Botchway, S. Webb, S. Mongrand, C. Maurel, M. Martin Fernandez, J. Kleine Vehn, J. Friml, P. Moreau, J. Runions, PNAS 109 (2012) 12805–12810.","mla":"Martinière, Alexandre, et al. “Cell Wall Constrains Lateral Diffusion of Plant Plasma Membrane Proteins.” <i>PNAS</i>, vol. 109, no. 31, National Academy of Sciences, 2012, pp. 12805–10, doi:<a href=\"https://doi.org/10.1073/pnas.1202040109\">10.1073/pnas.1202040109</a>."},"author":[{"last_name":"Martinière","full_name":"Martinière, Alexandre","first_name":"Alexandre"},{"last_name":"Lavagi","full_name":"Lavagi, Irene","first_name":"Irene"},{"full_name":"Nageswaran, Gayathri","first_name":"Gayathri","last_name":"Nageswaran"},{"full_name":"Rolfe, Daniel J","first_name":"Daniel","last_name":"Rolfe"},{"last_name":"Maneta Peyret","full_name":"Maneta-Peyret, Lilly","first_name":"Lilly"},{"first_name":"Doan","full_name":"Luu, Doan-Trung","last_name":"Luu"},{"last_name":"Botchway","first_name":"Stanley","full_name":"Botchway, Stanley W"},{"last_name":"Webb","first_name":"Stephen","full_name":"Webb, Stephen E"},{"last_name":"Mongrand","full_name":"Mongrand, Sebastien","first_name":"Sebastien"},{"last_name":"Maurel","full_name":"Maurel, Christophe","first_name":"Christophe"},{"first_name":"Marisa","full_name":"Martin-Fernandez, Marisa L","last_name":"Martin Fernandez"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"first_name":"Patrick","full_name":"Moreau, Patrick","last_name":"Moreau"},{"first_name":"John","full_name":"Runions, John","last_name":"Runions"}],"status":"public","quality_controlled":0,"volume":109,"publication_status":"published","date_created":"2018-12-11T12:01:28Z","doi":"10.1073/pnas.1202040109","publist_id":"3586","abstract":[{"text":"A cell membrane can be considered a liquid-phase plane in which lipids and proteins theoretically are free to diffuse. Numerous reports,however, describe retarded diffusion ofmembrane proteins in animal cells. This anomalous diffusion results from a combination of structuring factors including protein-protein interactions, cytoskeleton corralling, and lipid organization into microdomains. In plant cells, plasma-membrane (PM) proteins have been described as relatively immobile, but the control mechanisms that structure the PM have not been studied. Here, we use fluorescence recovery after photobleaching to estimate mobility of a set of minimal PM proteins. These proteins consist only of a PM-anchoring domain fused to a fluorescent protein, but their mobilities remained limited, as is the case for many full-length proteins. Neither the cytoskeleton nor membrane microdomain structure was involved in constraining the diffusion of these proteins. The cell wall, however, was shown to have a crucial role in immobilizing PM proteins. In addition, by single-molecule fluorescence imaging we confirmed that the pattern of cellulose deposition in the cell wall affects the trajectory and speed ofPMprotein diffusion. Regulation ofPMprotein dynamics by the plant cell wall can be interpreted as a mechanism for regulating protein interactions in processes such as trafficking and signal transduction.","lang":"eng"}],"publication":"PNAS","date_published":"2012-07-31T00:00:00Z","publisher":"National Academy of Sciences","day":"31"},{"publication":"Nature Communications","date_published":"2012-07-03T00:00:00Z","publisher":"Nature Publishing Group","day":"03","publist_id":"3585","abstract":[{"text":"Auxin is a key coordinative signal required for many aspects of plant development and its levels are controlled by auxin metabolism and intercellular auxin transport. Here we find that a member of PIN auxin transporter family, PIN8 is expressed in male gametophyte of Arabidopsis thaliana and has a crucial role in pollen development and functionality. Ectopic expression in sporophytic tissues establishes a role of PIN8 in regulating auxin homoeostasis and metabolism. PIN8 co-localizes with PIN5 to the endoplasmic reticulum (ER) where it acts as an auxin transporter. Genetic analyses reveal an antagonistic action of PIN5 and PIN8 in the regulation of intracellular auxin homoeostasis and gametophyte as well as sporophyte development. Our results reveal a role of the auxin transport in male gametophyte development in which the distinct actions of ER-localized PIN transporters regulate cellular auxin homoeostasis and maintain the auxin levels optimal for pollen development and pollen tube growth.","lang":"eng"}],"volume":3,"date_created":"2018-12-11T12:01:28Z","publication_status":"published","doi":"10.1038/ncomms1941","extern":1,"citation":{"ama":"Ding Z, Wang B, Moreno I, et al. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. <i>Nature Communications</i>. 2012;3(AN 941). doi:<a href=\"https://doi.org/10.1038/ncomms1941\">10.1038/ncomms1941</a>","chicago":"Ding, Zhaojun, Bangjun Wang, Ignacio Moreno, Nikoleta Dupláková, Sibu Simon, Nicola Carraro, Jesica Reemmer, et al. “ER-Localized Auxin Transporter PIN8 Regulates Auxin Homeostasis and Male Gametophyte Development in Arabidopsis.” <i>Nature Communications</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/ncomms1941\">https://doi.org/10.1038/ncomms1941</a>.","apa":"Ding, Z., Wang, B., Moreno, I., Dupláková, N., Simon, S., Carraro, N., … Friml, J. (2012). ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms1941\">https://doi.org/10.1038/ncomms1941</a>","ista":"Ding Z, Wang B, Moreno I, Dupláková N, Simon S, Carraro N, Reemmer J, Pěnčík A, Chen X, Tejos R, Skůpa P, Pollmann S, Mravec J, Petrášek J, Zažímalová E, Honys D, Rolčík J, Murphy A, Orellana A, Geisler M, Friml J. 2012. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications. 3(AN 941).","ieee":"Z. Ding <i>et al.</i>, “ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis,” <i>Nature Communications</i>, vol. 3, no. AN 941. Nature Publishing Group, 2012.","mla":"Ding, Zhaojun, et al. “ER-Localized Auxin Transporter PIN8 Regulates Auxin Homeostasis and Male Gametophyte Development in Arabidopsis.” <i>Nature Communications</i>, vol. 3, no. AN 941, Nature Publishing Group, 2012, doi:<a href=\"https://doi.org/10.1038/ncomms1941\">10.1038/ncomms1941</a>.","short":"Z. Ding, B. Wang, I. Moreno, N. Dupláková, S. Simon, N. Carraro, J. Reemmer, A. Pěnčík, X. Chen, R. Tejos, P. Skůpa, S. Pollmann, J. Mravec, J. Petrášek, E. Zažímalová, D. Honys, J. Rolčík, A. Murphy, A. Orellana, M. Geisler, J. Friml, Nature Communications 3 (2012)."},"quality_controlled":0,"status":"public","author":[{"first_name":"Zhaojun","full_name":"Ding, Zhaojun","last_name":"Ding"},{"first_name":"Bangjun","full_name":"Wang, Bangjun","last_name":"Wang"},{"last_name":"Moreno","full_name":"Moreno, Ignacio","first_name":"Ignacio"},{"last_name":"Dupláková","first_name":"Nikoleta","full_name":"Dupláková, Nikoleta"},{"last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","full_name":"Sibu Simon","first_name":"Sibu"},{"full_name":"Carraro, Nicola","first_name":"Nicola","last_name":"Carraro"},{"full_name":"Reemmer, Jesica","first_name":"Jesica","last_name":"Reemmer"},{"last_name":"Pěnčík","full_name":"Pěnčík, Aleš","first_name":"Aleš"},{"full_name":"Xu Chen","first_name":"Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tejos","full_name":"Tejos, Ricardo I","first_name":"Ricardo"},{"last_name":"Skůpa","first_name":"Petr","full_name":"Skůpa, Petr"},{"full_name":"Pollmann, Stephan","first_name":"Stephan","last_name":"Pollmann"},{"first_name":"Jozef","full_name":"Mravec, Jozef","last_name":"Mravec"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"last_name":"Honys","first_name":"David","full_name":"Honys, David"},{"last_name":"Rolčík","full_name":"Rolčík, Jakub","first_name":"Jakub"},{"last_name":"Murphy","full_name":"Murphy, Angus S","first_name":"Angus"},{"last_name":"Orellana","first_name":"Ariel","full_name":"Orellana, Ariel"},{"full_name":"Geisler, Markus","first_name":"Markus","last_name":"Geisler"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Jirí Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"issue":"AN 941","month":"07","year":"2012","intvolume":"         3","_id":"3114","type":"journal_article","date_updated":"2021-01-12T07:41:09Z","title":"ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis"},{"type":"journal_article","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.2158"}],"arxiv":1,"issue":"4","page":"964 - 989","month":"12","intvolume":"        48","publication_status":"published","quality_controlled":"1","citation":{"ama":"Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate offsets. <i>Discrete &#38; Computational Geometry</i>. 2012;48(4):964-989. doi:<a href=\"https://doi.org/10.1007/s00454-012-9441-5\">10.1007/s00454-012-9441-5</a>","chicago":"Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing Approximate Offsets.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s00454-012-9441-5\">https://doi.org/10.1007/s00454-012-9441-5</a>.","apa":"Berberich, E., Halperin, D., Kerber, M., &#38; Pogalnikova, R. (2012). Deconstructing approximate offsets. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-012-9441-5\">https://doi.org/10.1007/s00454-012-9441-5</a>","ieee":"E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing approximate offsets,” <i>Discrete &#38; Computational Geometry</i>, vol. 48, no. 4. Springer, pp. 964–989, 2012.","ista":"Berberich E, Halperin D, Kerber M, Pogalnikova R. 2012. Deconstructing approximate offsets. Discrete &#38; Computational Geometry. 48(4), 964–989.","short":"E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, Discrete &#38; Computational Geometry 48 (2012) 964–989.","mla":"Berberich, Eric, et al. “Deconstructing Approximate Offsets.” <i>Discrete &#38; Computational Geometry</i>, vol. 48, no. 4, Springer, 2012, pp. 964–89, doi:<a href=\"https://doi.org/10.1007/s00454-012-9441-5\">10.1007/s00454-012-9441-5</a>."},"scopus_import":1,"publication":"Discrete & Computational Geometry","publisher":"Springer","language":[{"iso":"eng"}],"publist_id":"3584","department":[{"_id":"HeEd"}],"abstract":[{"text":"We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution P; then, P's offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(nlogn)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. A variant of the algorithm, which we have implemented using the cgal library, is based on rational arithmetic and answers the same deconstruction problem up to an uncertainty parameter δ its running time additionally depends on δ. If the input shape is found to be approximable, this algorithm also computes an approximate solution for the problem. It also allows us to solve parameter-optimization problems induced by the offset-deconstruction problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution P with at most one more vertex than a vertex-minimal one.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3329"}]},"date_updated":"2023-02-23T11:22:30Z","_id":"3115","title":"Deconstructing approximate offsets","oa":1,"acknowledgement":"We thank Eyal Flato (Plataine Ltd.) for raising the offset-deconstruction problem in connection with wood cutting. We also thank Tim Bretl (UIUC) for suggesting the digital-pen offset-deconstruction problem. This work has been supported in part by the Israel Science Foundation (grant no. 1102/11), by the German–Israeli Foundation (grant no. 969/07), by the Hermann Minkowski–Minerva Center for Geometry at Tel Aviv University, and by the EU Project under Contract No. 255827 (CGL—Computational Geometry Learning).\r\n","year":"2012","date_created":"2018-12-11T12:01:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":48,"doi":"10.1007/s00454-012-9441-5","status":"public","author":[{"last_name":"Berberich","full_name":"Berberich, Eric","first_name":"Eric"},{"last_name":"Halperin","first_name":"Dan","full_name":"Halperin, Dan"},{"last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","first_name":"Michael","full_name":"Kerber, Michael"},{"full_name":"Pogalnikova, Roza","first_name":"Roza","last_name":"Pogalnikova"}],"oa_version":"Preprint","date_published":"2012-12-01T00:00:00Z","day":"01","external_id":{"arxiv":["1109.2158"]}},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1006.1990"}],"title":"Minimizing a sum of submodular functions","date_updated":"2021-01-12T07:41:11Z","type":"journal_article","_id":"3117","intvolume":"       160","year":"2012","month":"10","page":"2246 - 2258","oa":1,"issue":"15","oa_version":"Preprint","author":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","status":"public","citation":{"ama":"Kolmogorov V. Minimizing a sum of submodular functions. <i>Discrete Applied Mathematics</i>. 2012;160(15):2246-2258. doi:<a href=\"https://doi.org/10.1016/j.dam.2012.05.025\">10.1016/j.dam.2012.05.025</a>","apa":"Kolmogorov, V. (2012). Minimizing a sum of submodular functions. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dam.2012.05.025\">https://doi.org/10.1016/j.dam.2012.05.025</a>","chicago":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” <i>Discrete Applied Mathematics</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.dam.2012.05.025\">https://doi.org/10.1016/j.dam.2012.05.025</a>.","ista":"Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 160(15), 2246–2258.","ieee":"V. Kolmogorov, “Minimizing a sum of submodular functions,” <i>Discrete Applied Mathematics</i>, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012.","mla":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” <i>Discrete Applied Mathematics</i>, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:<a href=\"https://doi.org/10.1016/j.dam.2012.05.025\">10.1016/j.dam.2012.05.025</a>.","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258."},"doi":"10.1016/j.dam.2012.05.025","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:01:29Z","publication_status":"published","volume":160,"abstract":[{"text":"We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"VlKo"}],"publist_id":"3582","day":"01","publisher":"Elsevier","date_published":"2012-10-01T00:00:00Z","publication":"Discrete Applied Mathematics","scopus_import":1},{"language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"publist_id":"3581","abstract":[{"text":"We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process.","lang":"eng"}],"file":[{"content_type":"application/pdf","checksum":"1e219c5bf4e5552c1290c62eefa5cd60","access_level":"open_access","creator":"system","file_id":"5359","relation":"main_file","file_size":44538518,"date_created":"2018-12-12T10:18:37Z","date_updated":"2020-07-14T12:46:00Z","file_name":"IST-2016-602-v1+1_topoReg.pdf"}],"publication":"ACM Transactions on Graphics","file_date_updated":"2020-07-14T12:46:00Z","scopus_import":"1","publisher":"ACM","alternative_title":["SIGGRAPH"],"quality_controlled":"1","citation":{"mla":"Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” <i>ACM Transactions on Graphics</i>, vol. 31, no. 4, 53, ACM, 2012, doi:<a href=\"https://doi.org/10.1145/2185520.2185549\">10.1145/2185520.2185549</a>.","short":"M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012).","ista":"Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 31(4), 53.","ieee":"M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,” <i>ACM Transactions on Graphics</i>, vol. 31, no. 4. ACM, 2012.","apa":"Bojsen-Hansen, M., Li, H., &#38; Wojtan, C. (2012). Tracking surfaces with evolving topology. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2185520.2185549\">https://doi.org/10.1145/2185520.2185549</a>","chicago":"Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with Evolving Topology.” <i>ACM Transactions on Graphics</i>. ACM, 2012. <a href=\"https://doi.org/10.1145/2185520.2185549\">https://doi.org/10.1145/2185520.2185549</a>.","ama":"Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology. <i>ACM Transactions on Graphics</i>. 2012;31(4). doi:<a href=\"https://doi.org/10.1145/2185520.2185549\">10.1145/2185520.2185549</a>"},"publication_status":"published","article_type":"original","month":"07","intvolume":"        31","pubrep_id":"602","article_number":"53","issue":"4","ddc":["000"],"type":"journal_article","date_published":"2012-07-01T00:00:00Z","day":"01","status":"public","author":[{"orcid":"0000-0002-4417-3224","first_name":"Morten","full_name":"Bojsen-Hansen, Morten","last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Li","full_name":"Li, Hao","first_name":"Hao"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"oa_version":"Submitted Version","date_created":"2018-12-11T12:01:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":31,"doi":"10.1145/2185520.2185549","has_accepted_license":"1","acknowledgement":"This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu Ceylan for helping with the rendering, and Art Tevs for the human performance data comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. ","year":"2012","oa":1,"article_processing_charge":"No","title":"Tracking surfaces with evolving topology","date_updated":"2022-05-24T08:21:11Z","_id":"3118"}]