[{"oa":1,"oa_version":"Preprint","month":"01","date_updated":"2024-11-06T12:20:24Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.10932"}],"conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2019-01-06","location":"San Diego, CA, United States","end_date":"2019-01-09"},"day":"01","author":[{"last_name":"Bernstein","first_name":"Aaron","full_name":"Bernstein, Aaron"},{"first_name":"Sebastian","full_name":"Forster, Sebastian","last_name":"Forster"},{"first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"}],"_id":"11871","publication_status":"published","external_id":{"arxiv":["1810.10932"]},"publisher":"Society for Industrial and Applied Mathematics","extern":"1","doi":"10.1137/1.9781611975482.115","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Many dynamic graph algorithms have an amortized update time, rather than a stronger worst-case guarantee. But amortized data structures are not suitable for real-time systems, where each individual operation has to be executed quickly. For this reason, there exist many recent randomized results that aim to provide a guarantee stronger than amortized expected. The strongest possible guarantee for a randomized algorithm is that it is always correct (Las Vegas), and has high-probability worst-case update time, which gives a bound on the time for each individual operation that holds with high probability.\r\n\r\nIn this paper we present the first polylogarithmic high-probability worst-case time bounds for the dynamic spanner and the dynamic maximal matching problem.\r\n\r\n1.\t\r\nFor dynamic spanner, the only known o(n) worst-case bounds were O(n3/4) high-probability worst-case update time for maintaining a 3-spanner, and O(n5/9) for maintaining a 5-spanner. We give a O(1)k log3(n) high-probability worst-case time bound for maintaining a (2k – 1)-spanner, which yields the first worst-case polylog update time for all constant k. (All the results above maintain the optimal tradeoff of stretch 2k – 1 and Õ(n1+1/k) edges.)\r\n\r\n2.\t\r\nFor dynamic maximal matching, or dynamic 2-approximate maximum matching, no algorithm with o(n) worst-case time bound was known and we present an algorithm with O(log5 (n)) high-probability worst-case time; similar worst-case bounds existed only for maintaining a matching that was (2 + ∊)-approximate, and hence not maximal.\r\n\r\nOur results are achieved using a new approach for converting amortized guarantees to worst-case ones for randomized data structures by going through a third type of guarantee, which is a middle ground between the two above: an algorithm is said to have worst-case expected update time α if for every update σ, the expected time to process σ is at most α. Although stronger than amortized expected, the worst-case expected guarantee does not resolve the fundamental problem of amortization: a worst-case expected update time of O(1) still allows for the possibility that every 1/f(n) updates requires Θ(f(n)) time to process, for arbitrarily high f(n). In this paper we present a black-box reduction that converts any data structure with worst-case expected update time into one with a high-probability worst-case update time: the query time remains the same, while the update time increases by a factor of O(log2(n)).\r\n\r\nThus we achieve our results in two steps: (1) First we show how to convert existing dynamic graph algorithms with amortized expected polylogarithmic running times into algorithms with worst-case expected polylogarithmic running times. (2) Then we use our black-box reduction to achieve the polylogarithmic high-probability worst-case time bound. All our algorithms are Las-Vegas-type algorithms."}],"publication_identifier":{"eisbn":["978-1-61197-548-2"]},"date_published":"2019-01-01T00:00:00Z","page":"1899-1918","arxiv":1,"type":"conference","year":"2019","publication":"30th Annual ACM-SIAM Symposium on Discrete Algorithms","title":"A deamortization approach for dynamic spanner and dynamic maximal matching","language":[{"iso":"eng"}],"scopus_import":"1","quality_controlled":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"11871"}]},"date_created":"2022-08-16T09:50:33Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bernstein A, Forster S, Henzinger M. 2019. A deamortization approach for dynamic spanner and dynamic maximal matching. 30th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1899–1918.","short":"A. Bernstein, S. Forster, M. Henzinger, in:, 30th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2019, pp. 1899–1918.","mla":"Bernstein, Aaron, et al. “A Deamortization Approach for Dynamic Spanner and Dynamic Maximal Matching.” <i>30th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2019, pp. 1899–918, doi:<a href=\"https://doi.org/10.1137/1.9781611975482.115\">10.1137/1.9781611975482.115</a>.","ama":"Bernstein A, Forster S, Henzinger M. A deamortization approach for dynamic spanner and dynamic maximal matching. In: <i>30th Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2019:1899-1918. doi:<a href=\"https://doi.org/10.1137/1.9781611975482.115\">10.1137/1.9781611975482.115</a>","apa":"Bernstein, A., Forster, S., &#38; Henzinger, M. (2019). A deamortization approach for dynamic spanner and dynamic maximal matching. In <i>30th Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 1899–1918). San Diego, CA, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611975482.115\">https://doi.org/10.1137/1.9781611975482.115</a>","ieee":"A. Bernstein, S. Forster, and M. Henzinger, “A deamortization approach for dynamic spanner and dynamic maximal matching,” in <i>30th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, San Diego, CA, United States, 2019, pp. 1899–1918.","chicago":"Bernstein, Aaron, Sebastian Forster, and Monika Henzinger. “A Deamortization Approach for Dynamic Spanner and Dynamic Maximal Matching.” In <i>30th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 1899–1918. Society for Industrial and Applied Mathematics, 2019. <a href=\"https://doi.org/10.1137/1.9781611975482.115\">https://doi.org/10.1137/1.9781611975482.115</a>."}},{"oa":1,"article_type":"letter_note","oa_version":"Published Version","date_updated":"2023-02-21T10:10:23Z","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.oprd.9b00456"}],"extern":"1","_id":"11984","publisher":"American Chemical Society","publication_status":"published","author":[{"last_name":"Guberman","full_name":"Guberman, Mónica","first_name":"Mónica"},{"last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"},{"first_name":"Peter H.","full_name":"Seeberger, Peter H.","last_name":"Seeberger"}],"day":"20","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Differentially protected galactosamine building blocks are key components for the synthesis of human and bacterial oligosaccharides. The azidophenylselenylation of 3,4,6-tri-O-acetyl-d-galactal provides straightforward access to the corresponding 2-nitrogenated glycoside. Poor reproducibility and the use of azides that lead to the formation of potentially explosive and toxic species limit the scalability of this reaction and render it a bottleneck for carbohydrate synthesis. Here, we present a method for the safe, efficient, and reliable azidophenylselenylation of 3,4,6-tri-O-acetyl-d-galactal at room temperature, using continuous flow chemistry. Careful analysis of the transformation resulted in reaction conditions that produce minimal side products while the reaction time was reduced drastically when compared to batch reactions. The flow setup is readily scalable to process 5 mmol of galactal in 3 h, producing 1.2 mmol/h of product."}],"doi":"10.1021/acs.oprd.9b00456","publication_identifier":{"issn":["1083-6160"],"eissn":["1520-586X"]},"intvolume":"        23","page":"2764-2770","date_published":"2019-12-20T00:00:00Z","year":"2019","issue":"12","type":"journal_article","language":[{"iso":"eng"}],"title":"Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks","publication":"Organic Process Research and Development","date_created":"2022-08-25T11:30:33Z","scopus_import":"1","quality_controlled":"1","citation":{"short":"M. Guberman, B. Pieber, P.H. Seeberger, Organic Process Research and Development 23 (2019) 2764–2770.","ista":"Guberman M, Pieber B, Seeberger PH. 2019. Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks. Organic Process Research and Development. 23(12), 2764–2770.","ama":"Guberman M, Pieber B, Seeberger PH. Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks. <i>Organic Process Research and Development</i>. 2019;23(12):2764-2770. doi:<a href=\"https://doi.org/10.1021/acs.oprd.9b00456\">10.1021/acs.oprd.9b00456</a>","mla":"Guberman, Mónica, et al. “Safe and Scalable Continuous Flow Azidophenylselenylation of Galactal to Prepare Galactosamine Building Blocks.” <i>Organic Process Research and Development</i>, vol. 23, no. 12, American Chemical Society, 2019, pp. 2764–70, doi:<a href=\"https://doi.org/10.1021/acs.oprd.9b00456\">10.1021/acs.oprd.9b00456</a>.","ieee":"M. Guberman, B. Pieber, and P. H. Seeberger, “Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks,” <i>Organic Process Research and Development</i>, vol. 23, no. 12. American Chemical Society, pp. 2764–2770, 2019.","apa":"Guberman, M., Pieber, B., &#38; Seeberger, P. H. (2019). Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks. <i>Organic Process Research and Development</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.oprd.9b00456\">https://doi.org/10.1021/acs.oprd.9b00456</a>","chicago":"Guberman, Mónica, Bartholomäus Pieber, and Peter H. Seeberger. “Safe and Scalable Continuous Flow Azidophenylselenylation of Galactal to Prepare Galactosamine Building Blocks.” <i>Organic Process Research and Development</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/acs.oprd.9b00456\">https://doi.org/10.1021/acs.oprd.9b00456</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":23,"status":"public"},{"intvolume":"       190","date_published":"2019-07-05T00:00:00Z","arxiv":1,"page":"249-305","publication_identifier":{"issn":["0003-486X"]},"OA_place":"repository","scopus_import":"1","quality_controlled":"1","date_created":"2026-06-19T07:37:37Z","status":"public","volume":190,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Killip R, Vişan M. KdV is well-posed in H^-1. <i>Annals of Mathematics</i>. 2019;190(1):249-305. doi:<a href=\"https://doi.org/10.4007/annals.2019.190.1.4\">10.4007/annals.2019.190.1.4</a>","mla":"Killip, Rowan, and Monica Vişan. “KdV Is Well-Posed in H^-1.” <i>Annals of Mathematics</i>, vol. 190, no. 1, Annals of Mathematics, 2019, pp. 249–305, doi:<a href=\"https://doi.org/10.4007/annals.2019.190.1.4\">10.4007/annals.2019.190.1.4</a>.","short":"R. Killip, M. Vişan, Annals of Mathematics 190 (2019) 249–305.","ista":"Killip R, Vişan M. 2019. KdV is well-posed in H^-1. Annals of Mathematics. 190(1), 249–305.","chicago":"Killip, Rowan, and Monica Vişan. “KdV Is Well-Posed in H^-1.” <i>Annals of Mathematics</i>. Annals of Mathematics, 2019. <a href=\"https://doi.org/10.4007/annals.2019.190.1.4\">https://doi.org/10.4007/annals.2019.190.1.4</a>.","ieee":"R. Killip and M. Vişan, “KdV is well-posed in H^-1,” <i>Annals of Mathematics</i>, vol. 190, no. 1. Annals of Mathematics, pp. 249–305, 2019.","apa":"Killip, R., &#38; Vişan, M. (2019). KdV is well-posed in H^-1. <i>Annals of Mathematics</i>. Annals of Mathematics. <a href=\"https://doi.org/10.4007/annals.2019.190.1.4\">https://doi.org/10.4007/annals.2019.190.1.4</a>"},"year":"2019","type":"journal_article","issue":"1","publication":"Annals of Mathematics","title":"KdV is well-posed in H^-1","language":[{"iso":"eng"}],"month":"07","date_updated":"2026-06-22T11:12:40Z","OA_type":"green","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1802.04851","open_access":"1"}],"article_type":"original","oa":1,"oa_version":"Preprint","das_tickbox":"1","day":"05","_id":"22028","author":[{"full_name":"Killip, Rowan","first_name":"Rowan","last_name":"Killip"},{"last_name":"Visan","id":"056daca0-b8d1-11f0-964f-f91054abf8ca","first_name":"Monica","full_name":"Visan, Monica"}],"publication_status":"published","publisher":"Annals of Mathematics","external_id":{"arxiv":["1802.04851"]},"extern":"1","doi":"10.4007/annals.2019.190.1.4","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We prove global well-posedness of the Korteweg–de Vries equation for\r\ninitial data in the space H^−1(R). This is sharp in the class of H^s(R) spaces.\r\nEven local well-posedness was previously unknown for s < −3/4. The proof\r\nis based on the introduction of a new method of general applicability for the\r\nstudy of low-regularity well-posedness for integrable PDE, informed by the\r\nexistence of commuting flows. In particular, as we will show, completely\r\nparallel arguments give a new proof of global well-posedness for KdV with\r\nperiodic H−1 data, shown previously by Kappeler and Topalov, as well as\r\nglobal well-posedness for the fifth order KdV equation in L^2(R).\r\nAdditionally, we give a new proof of the a priori local smoothing bound\r\nof Buckmaster and Koch for KdV on the line. Moreover, we upgrade this\r\nestimate to show that convergence of initial data in H^−1(R) guarantees\r\nconvergence of the resulting solutions in L^2loc(R × R). Thus, solutions with\r\nH^−1(R) initial data are distributional solutions."}]},{"article_processing_charge":"No","abstract":[{"lang":"eng","text":"We consider the mass-subcritical NLS in dimensions d>=3 with radial initial data. In the defocusing case, we prove that any solution that remains bounded in the critical Sobolev space throughout its lifespan must be global and scatter. In the focusing case, we prove the existence of a threshold solution that has a compact flow."}],"doi":"10.3934/dcds.2019023","extern":"1","publisher":"American Institute of Mathematical Sciences","_id":"22030","author":[{"first_name":"Rowan","full_name":"Killip, Rowan","last_name":"Killip"},{"last_name":"Masaki","full_name":"Masaki, Satoshi","first_name":"Satoshi"},{"last_name":"Murphy","full_name":"Murphy, Jason","first_name":"Jason"},{"last_name":"Visan","id":"056daca0-b8d1-11f0-964f-f91054abf8ca","full_name":"Visan, Monica","first_name":"Monica"}],"publication_status":"published","external_id":{"arxiv":["1804.06753"]},"day":"01","das_tickbox":"1","oa_version":"Preprint","oa":1,"article_type":"original","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1804.06753","open_access":"1"}],"OA_type":"green","date_updated":"2026-06-22T11:06:54Z","month":"01","language":[{"iso":"eng"}],"title":"The radial mass-subcritical NLS in negative order Sobolev spaces","publication":"Discrete and Continuous Dynamical Systems","issue":"1","year":"2019","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Killip R, Masaki S, Murphy J, Vişan M. The radial mass-subcritical NLS in negative order Sobolev spaces. <i>Discrete and Continuous Dynamical Systems</i>. 2019;39(1):553-583. doi:<a href=\"https://doi.org/10.3934/dcds.2019023\">10.3934/dcds.2019023</a>","mla":"Killip, Rowan, et al. “The Radial Mass-Subcritical NLS in Negative Order Sobolev Spaces.” <i>Discrete and Continuous Dynamical Systems</i>, vol. 39, no. 1, American Institute of Mathematical Sciences, 2019, pp. 553–83, doi:<a href=\"https://doi.org/10.3934/dcds.2019023\">10.3934/dcds.2019023</a>.","ista":"Killip R, Masaki S, Murphy J, Vişan M. 2019. The radial mass-subcritical NLS in negative order Sobolev spaces. Discrete and Continuous Dynamical Systems. 39(1), 553–583.","short":"R. Killip, S. Masaki, J. Murphy, M. Vişan, Discrete and Continuous Dynamical Systems 39 (2019) 553–583.","chicago":"Killip, Rowan, Satoshi Masaki, Jason Murphy, and Monica Vişan. “The Radial Mass-Subcritical NLS in Negative Order Sobolev Spaces.” <i>Discrete and Continuous Dynamical Systems</i>. American Institute of Mathematical Sciences, 2019. <a href=\"https://doi.org/10.3934/dcds.2019023\">https://doi.org/10.3934/dcds.2019023</a>.","ieee":"R. Killip, S. Masaki, J. Murphy, and M. Vişan, “The radial mass-subcritical NLS in negative order Sobolev spaces,” <i>Discrete and Continuous Dynamical Systems</i>, vol. 39, no. 1. American Institute of Mathematical Sciences, pp. 553–583, 2019.","apa":"Killip, R., Masaki, S., Murphy, J., &#38; Vişan, M. (2019). The radial mass-subcritical NLS in negative order Sobolev spaces. <i>Discrete and Continuous Dynamical Systems</i>. American Institute of Mathematical Sciences. <a href=\"https://doi.org/10.3934/dcds.2019023\">https://doi.org/10.3934/dcds.2019023</a>"},"volume":39,"status":"public","date_created":"2026-06-19T07:41:46Z","quality_controlled":"1","scopus_import":"1","OA_place":"repository","publication_identifier":{"issn":["1078-0947"],"eissn":["1553-5231"]},"page":"553-583","arxiv":1,"date_published":"2019-01-01T00:00:00Z","intvolume":"        39"},{"volume":7,"status":"public","citation":{"chicago":"Wijngaard, René R., Jakob F. Steiner, Philip D. A. Kraaijenbrink, Christoph Klug, Surendra Adhikari, Argha Banerjee, Francesca Pellicciotti, et al. “Modeling the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate since the Little Ice Age.” <i>Frontiers in Earth Science</i>. Frontiers Media, 2019. <a href=\"https://doi.org/10.3389/feart.2019.00143\">https://doi.org/10.3389/feart.2019.00143</a>.","ieee":"R. R. Wijngaard <i>et al.</i>, “Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age,” <i>Frontiers in Earth Science</i>, vol. 7. Frontiers Media, 2019.","apa":"Wijngaard, R. R., Steiner, J. F., Kraaijenbrink, P. D. A., Klug, C., Adhikari, S., Banerjee, A., … Immerzeel, W. W. (2019). Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. <i>Frontiers in Earth Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/feart.2019.00143\">https://doi.org/10.3389/feart.2019.00143</a>","ama":"Wijngaard RR, Steiner JF, Kraaijenbrink PDA, et al. Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. <i>Frontiers in Earth Science</i>. 2019;7. doi:<a href=\"https://doi.org/10.3389/feart.2019.00143\">10.3389/feart.2019.00143</a>","mla":"Wijngaard, René R., et al. “Modeling the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate since the Little Ice Age.” <i>Frontiers in Earth Science</i>, vol. 7, 143, Frontiers Media, 2019, doi:<a href=\"https://doi.org/10.3389/feart.2019.00143\">10.3389/feart.2019.00143</a>.","ista":"Wijngaard RR, Steiner JF, Kraaijenbrink PDA, Klug C, Adhikari S, Banerjee A, Pellicciotti F, van Beek LPH, Bierkens MFP, Lutz AF, Immerzeel WW. 2019. Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. 7, 143.","short":"R.R. Wijngaard, J.F. Steiner, P.D.A. Kraaijenbrink, C. Klug, S. Adhikari, A. Banerjee, F. Pellicciotti, L.P.H. van Beek, M.F.P. Bierkens, A.F. Lutz, W.W. Immerzeel, Frontiers in Earth Science 7 (2019)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","scopus_import":"1","date_created":"2023-02-20T08:13:08Z","title":"Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age","publication":"Frontiers in Earth Science","language":[{"iso":"eng"}],"type":"journal_article","year":"2019","date_published":"2019-06-04T00:00:00Z","article_number":"143","intvolume":"         7","publication_identifier":{"issn":["2296-6463"]},"abstract":[{"text":"This study aims at developing and applying a spatially-distributed coupled glacier mass balance and ice-flow model to attribute the response of glaciers to natural and anthropogenic climate change. We focus on two glaciers with contrasting surface characteristics: a debris-covered glacier (Langtang Glacier in Nepal) and a clean-ice glacier (Hintereisferner in Austria). The model is applied from the end of the Little Ice Age (1850) to the present-day (2016) and is forced with four bias-corrected General Circulation Models (GCMs) from the historical experiment of the CMIP5 archive. The selected GCMs represent region-specific warm-dry, warm-wet, cold-dry, and cold-wet climate conditions. To isolate the effects of anthropogenic climate change on glacier mass balance and flow runs from these GCMs with and without further anthropogenic forcing after 1970 until 2016 are selected. The outcomes indicate that both glaciers experience the largest reduction in area and volume under warm climate conditions, whereas area and volume reductions are smaller under cold climate conditions. Simultaneously with changes in glacier area and volume, surface velocities generally decrease over time. Without further anthropogenic forcing the results reveal a 3% (9%) smaller decline in glacier area (volume) for the debris-covered glacier and a 18% (39%) smaller decline in glacier area (volume) for the clean-ice glacier. The difference in the magnitude between the two glaciers can mainly be attributed to differences in the response time of the glaciers, where the clean-ice glacier shows a much faster response to climate change. We conclude that the response of the two glaciers can mainly be attributed to anthropogenic climate change and that the impact is larger on the clean-ice glacier. The outcomes show that the model performs well under different climate conditions and that the developed approach can be used for regional-scale glacio-hydrological modeling.","lang":"eng"}],"article_processing_charge":"No","doi":"10.3389/feart.2019.00143","day":"04","extern":"1","author":[{"full_name":"Wijngaard, René R.","first_name":"René R.","last_name":"Wijngaard"},{"last_name":"Steiner","first_name":"Jakob F.","full_name":"Steiner, Jakob F."},{"last_name":"Kraaijenbrink","full_name":"Kraaijenbrink, Philip D. A.","first_name":"Philip D. A."},{"first_name":"Christoph","full_name":"Klug, Christoph","last_name":"Klug"},{"full_name":"Adhikari, Surendra","first_name":"Surendra","last_name":"Adhikari"},{"first_name":"Argha","full_name":"Banerjee, Argha","last_name":"Banerjee"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca","full_name":"Pellicciotti, Francesca"},{"last_name":"van Beek","full_name":"van Beek, Ludovicus P. H.","first_name":"Ludovicus P. H."},{"last_name":"Bierkens","full_name":"Bierkens, Marc F. P.","first_name":"Marc F. P."},{"full_name":"Lutz, Arthur F.","first_name":"Arthur F.","last_name":"Lutz"},{"first_name":"Walter W.","full_name":"Immerzeel, Walter W.","last_name":"Immerzeel"}],"publication_status":"published","publisher":"Frontiers Media","_id":"12602","main_file_link":[{"url":"https://doi.org/10.3389/feart.2019.00143","open_access":"1"}],"month":"06","date_updated":"2023-02-28T12:04:48Z","oa_version":"Published Version","oa":1,"article_type":"original"},{"day":"20","extern":"1","_id":"13468","publication_status":"published","author":[{"last_name":"Zapartas","full_name":"Zapartas, Emmanouil","first_name":"Emmanouil"},{"last_name":"de Mink","full_name":"de Mink, Selma E.","first_name":"Selma E."},{"full_name":"Justham, Stephen","first_name":"Stephen","last_name":"Justham"},{"first_name":"Nathan","full_name":"Smith, Nathan","last_name":"Smith"},{"last_name":"de Koter","full_name":"de Koter, Alex","first_name":"Alex"},{"full_name":"Renzo, Mathieu","first_name":"Mathieu","last_name":"Renzo"},{"full_name":"Arcavi, Iair","first_name":"Iair","last_name":"Arcavi"},{"first_name":"Rob","full_name":"Farmer, Rob","last_name":"Farmer"},{"last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","first_name":"Ylva Louise Linsdotter"},{"last_name":"Toonen","first_name":"Silvia","full_name":"Toonen, Silvia"}],"publisher":"EDP Sciences","external_id":{"arxiv":["1907.06687"]},"article_processing_charge":"No","abstract":[{"text":"Hydrogen-rich supernovae, known as Type II (SNe II), are the most common class of explosions observed following the collapse of the core of massive stars. We used analytical estimates and population synthesis simulations to assess the fraction of SNe II progenitors that are expected to have exchanged mass with a companion prior to explosion. We estimate that 1/3 to 1/2 of SN II progenitors have a history of mass exchange with a binary companion before exploding. The dominant binary channels leading to SN II progenitors involve the merger of binary stars. Mergers are expected to produce a diversity of SN II progenitor characteristics, depending on the evolutionary timing and properties of the merger. Alternatively, SN II progenitors from interacting binaries may have accreted mass from their companion, and subsequently been ejected from the binary system after their companion exploded. We show that the overall fraction of SN II progenitors that are predicted to have experienced binary interaction is robust against the main physical uncertainties in our models. However, the relative importance of different binary evolutionary channels is affected by changing physical assumptions. We further discuss ways in which binarity might contribute to the observed diversity of SNe II by considering potential observational signatures arising from each binary channel. For supernovae which have a substantial H-rich envelope at explosion (i.e., excluding Type IIb SNe), a surviving non-compact companion would typically indicate that the supernova progenitor star was in a wide, non-interacting binary. We argue that a significant fraction of even Type II-P SNe are expected to have gained mass from a companion prior to explosion.","lang":"eng"}],"doi":"10.1051/0004-6361/201935854","month":"11","date_updated":"2023-08-09T12:36:09Z","main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/201935854","open_access":"1"}],"article_type":"original","oa":1,"oa_version":"Published Version","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","quality_controlled":"1","date_created":"2023-08-03T10:13:52Z","volume":631,"status":"public","citation":{"short":"E. Zapartas, S.E. de Mink, S. Justham, N. Smith, A. de Koter, M. Renzo, I. Arcavi, R. Farmer, Y.L.L. Götberg, S. Toonen, Astronomy &#38; Astrophysics 631 (2019).","ista":"Zapartas E, de Mink SE, Justham S, Smith N, de Koter A, Renzo M, Arcavi I, Farmer R, Götberg YLL, Toonen S. 2019. The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy &#38; Astrophysics. 631, A5.","mla":"Zapartas, Emmanouil, et al. “The Diverse Lives of Progenitors of Hydrogen-Rich Core-Collapse Supernovae: The Role of Binary Interaction.” <i>Astronomy &#38; Astrophysics</i>, vol. 631, A5, EDP Sciences, 2019, doi:<a href=\"https://doi.org/10.1051/0004-6361/201935854\">10.1051/0004-6361/201935854</a>.","ama":"Zapartas E, de Mink SE, Justham S, et al. The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. <i>Astronomy &#38; Astrophysics</i>. 2019;631. doi:<a href=\"https://doi.org/10.1051/0004-6361/201935854\">10.1051/0004-6361/201935854</a>","apa":"Zapartas, E., de Mink, S. E., Justham, S., Smith, N., de Koter, A., Renzo, M., … Toonen, S. (2019). The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/201935854\">https://doi.org/10.1051/0004-6361/201935854</a>","ieee":"E. Zapartas <i>et al.</i>, “The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction,” <i>Astronomy &#38; Astrophysics</i>, vol. 631. EDP Sciences, 2019.","chicago":"Zapartas, Emmanouil, Selma E. de Mink, Stephen Justham, Nathan Smith, Alex de Koter, Mathieu Renzo, Iair Arcavi, Rob Farmer, Ylva Louise Linsdotter Götberg, and Silvia Toonen. “The Diverse Lives of Progenitors of Hydrogen-Rich Core-Collapse Supernovae: The Role of Binary Interaction.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2019. <a href=\"https://doi.org/10.1051/0004-6361/201935854\">https://doi.org/10.1051/0004-6361/201935854</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","type":"journal_article","title":"The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction","publication":"Astronomy & Astrophysics","language":[{"iso":"eng"}],"intvolume":"       631","date_published":"2019-11-20T00:00:00Z","article_number":"A5","arxiv":1,"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]}},{"publication_identifier":{"eisbn":["9781728104690"],"isbn":["9781728104706"]},"oa_version":"None","date_updated":"2023-08-22T09:32:56Z","month":"10","article_number":"8871819","date_published":"2019-10-17T00:00:00Z","type":"conference","year":"2019","language":[{"iso":"eng"}],"publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","title":"Probing molecular influence on photoemission delays","date_created":"2023-08-09T13:10:49Z","_id":"14002","publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","author":[{"first_name":"Shubhadeep","full_name":"Biswas, Shubhadeep","last_name":"Biswas"},{"last_name":"Liontos","first_name":"I.","full_name":"Liontos, I."},{"last_name":"Kamal","full_name":"Kamal, A. M.","first_name":"A. M."},{"last_name":"Kling","full_name":"Kling, N. G.","first_name":"N. G."},{"full_name":"Alharbi, A. F.","first_name":"A. F.","last_name":"Alharbi"},{"full_name":"Alharbi, M.","first_name":"M.","last_name":"Alharbi"},{"last_name":"Azzeer","full_name":"Azzeer, A. M.","first_name":"A. M."},{"full_name":"Worner, H. J.","first_name":"H. J.","last_name":"Worner"},{"first_name":"A. S.","full_name":"Landsman, A. S.","last_name":"Landsman"},{"first_name":"M. F.","full_name":"Kling, M. F.","last_name":"Kling"},{"first_name":"B.","full_name":"Forg, B.","last_name":"Forg"},{"first_name":"J.","full_name":"Schotz, J.","last_name":"Schotz"},{"last_name":"Schweinberger","full_name":"Schweinberger, W.","first_name":"W."},{"last_name":"Ortmann","first_name":"L.","full_name":"Ortmann, L."},{"first_name":"T.","full_name":"Zimmermann, T.","last_name":"Zimmermann"},{"last_name":"Pi","full_name":"Pi, L.-W.","first_name":"L.-W."},{"first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva"},{"first_name":"H. A.","full_name":"Masood, H. A.","last_name":"Masood"}],"extern":"1","quality_controlled":"1","scopus_import":"1","day":"17","conference":{"location":"Munich, Germany","start_date":"2019-06-23","name":"CLEO: European Conference on Lasers and Electro-Optics","end_date":"2019-06-27"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Biswas, Shubhadeep, I. Liontos, A. M. Kamal, N. G. Kling, A. F. Alharbi, M. Alharbi, A. M. Azzeer, et al. “Probing Molecular Influence on Photoemission Delays.” In <i>2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference</i>. Institute of Electrical and Electronics Engineers, 2019. <a href=\"https://doi.org/10.1109/cleoe-eqec.2019.8871819\">https://doi.org/10.1109/cleoe-eqec.2019.8871819</a>.","ieee":"S. Biswas <i>et al.</i>, “Probing molecular influence on photoemission delays,” in <i>2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference</i>, Munich, Germany, 2019.","apa":"Biswas, S., Liontos, I., Kamal, A. M., Kling, N. G., Alharbi, A. F., Alharbi, M., … Masood, H. A. (2019). Probing molecular influence on photoemission delays. In <i>2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference</i>. Munich, Germany: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/cleoe-eqec.2019.8871819\">https://doi.org/10.1109/cleoe-eqec.2019.8871819</a>","ama":"Biswas S, Liontos I, Kamal AM, et al. Probing molecular influence on photoemission delays. In: <i>2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference</i>. Institute of Electrical and Electronics Engineers; 2019. doi:<a href=\"https://doi.org/10.1109/cleoe-eqec.2019.8871819\">10.1109/cleoe-eqec.2019.8871819</a>","mla":"Biswas, Shubhadeep, et al. “Probing Molecular Influence on Photoemission Delays.” <i>2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference</i>, 8871819, Institute of Electrical and Electronics Engineers, 2019, doi:<a href=\"https://doi.org/10.1109/cleoe-eqec.2019.8871819\">10.1109/cleoe-eqec.2019.8871819</a>.","ista":"Biswas S, Liontos I, Kamal AM, Kling NG, Alharbi AF, Alharbi M, Azzeer AM, Worner HJ, Landsman AS, Kling MF, Forg B, Schotz J, Schweinberger W, Ortmann L, Zimmermann T, Pi L-W, Baykusheva DR, Masood HA. 2019. Probing molecular influence on photoemission delays. 2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference. CLEO: European Conference on Lasers and Electro-Optics, 8871819.","short":"S. Biswas, I. Liontos, A.M. Kamal, N.G. Kling, A.F. Alharbi, M. Alharbi, A.M. Azzeer, H.J. Worner, A.S. Landsman, M.F. Kling, B. Forg, J. Schotz, W. Schweinberger, L. Ortmann, T. Zimmermann, L.-W. Pi, D.R. Baykusheva, H.A. Masood, in:, 2019 Conference on Lasers and Electro-Optics Europe &#38; European Quantum Electronics Conference, Institute of Electrical and Electronics Engineers, 2019."},"status":"public","doi":"10.1109/cleoe-eqec.2019.8871819","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The advancement of attosecond chronoscopy has made it possible to reveal ultrashort time dynamics of photoionization [1]. Ionization delay measurements in atomic targets provide a wealth of information about the timing of the photoelectric effect [2], resonances, electron correlations and transport. The extension of this approach to molecules, however, presents great challenges. In addition to the difficulty of identifying correct ionization channels, it is hard to disentangle the role of the anisotropic molecular landscape from the delays inherent to the excitation process itself. Here, we present the measurements of ionization delays from ethyl iodide around the 4d giant dipole resonance of iodine. We employ attosecond streaking spectroscopy, which enables to disentangle the contribution to the delay from the functional ethyl group, being responsible for the characteristic chemical reactivity of the molecule. An attosecond extreme ultraviolet (XUV) pulse ionizes the molecule around the energy of the giant resonance and the released electron is exposed to the ponderomotive force of a synchronized near-infrared (NIR) field, which yields a streaking spectrogram (see figure). Comparative phase analysis of the spectrograms corresponding to iodine 4d and neon 2p emission permits extracting overall photoemission delays for ethyl iodide. The data is recorded for multiple photon energies around the iodine 4d resonance and compared to classical Wigner propagation [3] and quantum scattering [4] calculations. Here the outgoing electron, produced via inner shell ionization of the iodine atom in ethyl iodide, and thereby hardly influenced by the molecular potential during the birth process, acquires the necessary information about the influence of the functional ethyl group during its propagation. We find significant delay contributions that can distinguish between different functional groups, providing a sensitive probe of the local molecular environment [5]. This would stimulate to perform further angle resolved measurements in molecules to probe the potential landscape in three dimension."}]},{"title":"Stochastic Frank-Wolfe for composite convex minimization","publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"type":"conference","year":"2019","volume":32,"status":"public","citation":{"ista":"Locatello F, Yurtsever A, Fercoq O, Cevher V. 2019. Stochastic Frank-Wolfe for composite convex minimization. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14291–14301.","short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301.","ama":"Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite convex minimization. In: <i>Advances in Neural Information Processing Systems</i>. Vol 32. ; 2019:14291–14301.","mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” <i>Advances in Neural Information Processing Systems</i>, vol. 32, 2019, pp. 14291–14301.","ieee":"F. Locatello, A. Yurtsever, O. Fercoq, and V. Cevher, “Stochastic Frank-Wolfe for composite convex minimization,” in <i>Advances in Neural Information Processing Systems</i>, Vancouver, Canada, 2019, vol. 32, pp. 14291–14301.","apa":"Locatello, F., Yurtsever, A., Fercoq, O., &#38; Cevher, V. (2019). Stochastic Frank-Wolfe for composite convex minimization. In <i>Advances in Neural Information Processing Systems</i> (Vol. 32, pp. 14291–14301). Vancouver, Canada.","chicago":"Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher. “Stochastic Frank-Wolfe for Composite Convex Minimization.” In <i>Advances in Neural Information Processing Systems</i>, 32:14291–14301, 2019."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","quality_controlled":"1","date_created":"2023-08-22T14:09:35Z","department":[{"_id":"FrLo"}],"publication_identifier":{"isbn":["9781713807933"]},"date_published":"2019-12-29T00:00:00Z","page":"14291–14301","arxiv":1,"intvolume":"        32","abstract":[{"lang":"eng","text":"A broad class of convex optimization problems can be formulated as a semidefinite program (SDP), minimization of a convex function over the positive-semidefinite cone subject to some affine constraints. The majority of classical SDP solvers are designed for the deterministic setting where problem data is readily available. In this setting, generalized conditional gradient methods (aka Frank-Wolfe-type methods) provide scalable solutions by leveraging the so-called linear minimization oracle instead of the projection onto the semidefinite cone. Most problems in machine learning and modern engineering applications, however, contain some degree of stochasticity. In this work, we propose the first conditional-gradient-type method for solving stochastic optimization problems under affine constraints. Our method guarantees O(k−1/3) convergence rate in expectation on the objective residual and O(k−5/12) on the feasibility gap."}],"article_processing_charge":"No","day":"29","conference":{"end_date":"2019-12-14","start_date":"2019-12-08","location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems"},"extern":"1","external_id":{"arxiv":["1901.10348"]},"_id":"14191","author":[{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco"},{"last_name":"Yurtsever","full_name":"Yurtsever, Alp","first_name":"Alp"},{"last_name":"Fercoq","first_name":"Olivier","full_name":"Fercoq, Olivier"},{"last_name":"Cevher","first_name":"Volkan","full_name":"Cevher, Volkan"}],"publication_status":"published","oa_version":"Preprint","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10348"}],"month":"12","date_updated":"2023-09-12T08:48:45Z"},{"day":"23","_id":"5907","external_id":{"isi":["000456392400012"]},"author":[{"first_name":"Réka","full_name":"Mócsai, Réka","last_name":"Mócsai"},{"last_name":"Figl","full_name":"Figl, Rudolf","first_name":"Rudolf"},{"last_name":"Troschl","full_name":"Troschl, Clemens","first_name":"Clemens"},{"last_name":"Strasser","full_name":"Strasser, Richard","first_name":"Richard"},{"full_name":"Svehla, Elisabeth","first_name":"Elisabeth","last_name":"Svehla"},{"last_name":"Windwarder","first_name":"Markus","full_name":"Windwarder, Markus"},{"first_name":"Andreas","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader"},{"last_name":"Altmann","first_name":"Friedrich","full_name":"Altmann, Friedrich"}],"publication_status":"published","publisher":"Nature Publishing Group","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins."}],"doi":"10.1038/s41598-018-36884-1","ddc":["580"],"month":"01","date_updated":"2023-08-24T14:33:16Z","has_accepted_license":"1","oa":1,"file_date_updated":"2020-07-14T12:47:13Z","oa_version":"Published Version","quality_controlled":"1","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2019-02-03T22:59:13Z","volume":9,"status":"public","citation":{"apa":"Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M., … Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-36884-1\">https://doi.org/10.1038/s41598-018-36884-1</a>","ieee":"R. Mócsai <i>et al.</i>, “N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated,” <i>Scientific Reports</i>, vol. 9, no. 1. Nature Publishing Group, 2019.","chicago":"Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” <i>Scientific Reports</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41598-018-36884-1\">https://doi.org/10.1038/s41598-018-36884-1</a>.","ista":"Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A, Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 9(1), 331.","short":"R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019).","mla":"Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” <i>Scientific Reports</i>, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-018-36884-1\">10.1038/s41598-018-36884-1</a>.","ama":"Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. <i>Scientific Reports</i>. 2019;9(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-36884-1\">10.1038/s41598-018-36884-1</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","issue":"1","type":"journal_article","title":"N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated","publication":"Scientific Reports","language":[{"iso":"eng"}],"file":[{"checksum":"4129c7d7663d1f8a1edf8c4232372f66","file_name":"2019_ScientificReports_Mocsai.pdf","file_size":2124292,"relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-05T13:10:02Z","file_id":"5923","access_level":"open_access","creator":"dernst"}],"intvolume":"         9","article_number":"331","date_published":"2019-01-23T00:00:00Z","department":[{"_id":"FlSc"}],"isi":1,"license":"https://creativecommons.org/licenses/by/4.0/"},{"abstract":[{"lang":"eng","text":"We study the termination problem for nondeterministic probabilistic programs. We consider the bounded termination problem that asks whether the supremum of the expected termination time over all schedulers is bounded. First, we show that ranking supermartingales (RSMs) are both sound and complete for proving bounded termination over nondeterministic probabilistic programs. For nondeterministic probabilistic programs a previous result claimed that RSMs are not complete for bounded termination, whereas our result corrects the previous flaw and establishes completeness with a rigorous proof. Second, we present the first sound approach to establish lower bounds on expected termination time through RSMs."}],"article_processing_charge":"No","doi":"10.1007/978-3-030-11245-5_22","day":"11","conference":{"location":"Cascais, Portugal","start_date":"2019-01-13","name":"VMCAI: Verification, Model Checking, and Abstract Interpretation","end_date":"2019-01-15"},"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"_id":"5948","external_id":{"arxiv":["1701.02944"],"isi":["000931943000022"]},"publication_status":"published","author":[{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"}],"publisher":"Springer Nature","oa_version":"Preprint","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1701.02944"}],"OA_type":"green","month":"01","date_updated":"2025-07-03T11:45:45Z","title":"Termination of nondeterministic probabilistic programs","publication":"International Conference on Verification, Model Checking, and Abstract Interpretation","language":[{"iso":"eng"}],"type":"conference","year":"2019","volume":11388,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” In <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, 11388:468–90. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">https://doi.org/10.1007/978-3-030-11245-5_22</a>.","apa":"Fu, H., &#38; Chatterjee, K. (2019). Termination of nondeterministic probabilistic programs. In <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i> (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">https://doi.org/10.1007/978-3-030-11245-5_22</a>","ieee":"H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,” in <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, Cascais, Portugal, 2019, vol. 11388, pp. 468–490.","mla":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:<a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">10.1007/978-3-030-11245-5_22</a>.","ama":"Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs. In: <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>. Vol 11388. Springer Nature; 2019:468-490. doi:<a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">10.1007/978-3-030-11245-5_22</a>","short":"H. Fu, K. Chatterjee, in:, International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490.","ista":"Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs. International Conference on Verification, Model Checking, and Abstract Interpretation. VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388, 468–490."},"scopus_import":"1","quality_controlled":"1","date_created":"2019-02-10T22:59:17Z","OA_place":"repository","department":[{"_id":"KrCh"}],"isi":1,"date_published":"2019-01-11T00:00:00Z","alternative_title":["LNCS"],"arxiv":1,"page":"468-490","intvolume":"     11388"},{"ec_funded":1,"abstract":[{"lang":"eng","text":"Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain."}],"article_processing_charge":"No","doi":"10.1038/s41477-019-0363-6","day":"08","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer Nature","_id":"6023","external_id":{"isi":["000460479600014"]},"publication_status":"published","author":[{"last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko","first_name":"Saiko"},{"last_name":"Van Der Schuren","full_name":"Van Der Schuren, Alja","first_name":"Alja"},{"first_name":"Maritza","full_name":"Van Dop, Maritza","last_name":"Van Dop"},{"last_name":"Van Galen","first_name":"Luc","full_name":"Van Galen, Luc"},{"last_name":"Saiga","full_name":"Saiga, Shunsuke","first_name":"Shunsuke"},{"first_name":"Milad","full_name":"Adibi, Milad","last_name":"Adibi"},{"full_name":"Möller, Barbara","first_name":"Barbara","last_name":"Möller"},{"last_name":"Ten Hove","first_name":"Colette A.","full_name":"Ten Hove, Colette A."},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741","first_name":"Peter"},{"full_name":"Smith, Richard","first_name":"Richard","last_name":"Smith"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"}],"oa_version":"Submitted Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/479113v1.abstract"}],"month":"02","date_updated":"2025-04-15T06:50:24Z","title":"A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis","publication":"Nature Plants","language":[{"iso":"eng"}],"issue":"2","type":"journal_article","year":"2019","volume":5,"status":"public","citation":{"apa":"Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi, M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-019-0363-6\">https://doi.org/10.1038/s41477-019-0363-6</a>","ieee":"S. Yoshida <i>et al.</i>, “A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis,” <i>Nature Plants</i>, vol. 5, no. 2. Springer Nature, pp. 160–166, 2019.","chicago":"Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” <i>Nature Plants</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41477-019-0363-6\">https://doi.org/10.1038/s41477-019-0363-6</a>.","ista":"Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166.","short":"S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi, B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants 5 (2019) 160–166.","mla":"Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” <i>Nature Plants</i>, vol. 5, no. 2, Springer Nature, 2019, pp. 160–66, doi:<a href=\"https://doi.org/10.1038/s41477-019-0363-6\">10.1038/s41477-019-0363-6</a>.","ama":"Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. <i>Nature Plants</i>. 2019;5(2):160-166. doi:<a href=\"https://doi.org/10.1038/s41477-019-0363-6\">10.1038/s41477-019-0363-6</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","quality_controlled":"1","date_created":"2019-02-17T22:59:21Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"isi":1,"date_published":"2019-02-08T00:00:00Z","page":"160-166","intvolume":"         5"},{"publication_status":"published","_id":"6028","external_id":{"isi":["000475465000003"]},"publisher":"Wiley","author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate"},{"first_name":"Martin","full_name":"Hairer, Martin","last_name":"Hairer"}],"day":"08","doi":"10.1002/cpa.21816","article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small."}],"ddc":["500"],"has_accepted_license":"1","date_updated":"2024-10-09T20:58:47Z","month":"02","oa":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:17Z","date_created":"2019-02-17T22:59:24Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","scopus_import":"1","citation":{"ieee":"M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” <i>Communications on Pure and Applied Mathematics</i>, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019.","apa":"Gerencser, M., &#38; Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21816\">https://doi.org/10.1002/cpa.21816</a>","chicago":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cpa.21816\">https://doi.org/10.1002/cpa.21816</a>.","short":"M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005.","ista":"Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005.","ama":"Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. <i>Communications on Pure and Applied Mathematics</i>. 2019;72(9):1983-2005. doi:<a href=\"https://doi.org/10.1002/cpa.21816\">10.1002/cpa.21816</a>","mla":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” <i>Communications on Pure and Applied Mathematics</i>, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:<a href=\"https://doi.org/10.1002/cpa.21816\">10.1002/cpa.21816</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","volume":72,"type":"journal_article","year":"2019","issue":"9","file":[{"file_id":"7237","access_level":"open_access","creator":"kschuh","file_name":"2019_Wiley_Gerencser.pdf","checksum":"09aec427eb48c0f96a1cce9ff53f013b","relation":"main_file","file_size":381350,"content_type":"application/pdf","date_created":"2020-01-07T13:25:55Z","date_updated":"2020-07-14T12:47:17Z"}],"language":[{"iso":"eng"}],"corr_author":"1","publication":"Communications on Pure and Applied Mathematics","title":"A solution theory for quasilinear singular SPDEs","intvolume":"        72","page":"1983-2005","date_published":"2019-02-08T00:00:00Z","isi":1,"department":[{"_id":"JaMa"}]},{"_id":"6042","publication_status":"published","external_id":{"isi":["000681166500013"]},"author":[{"last_name":"Christakis","full_name":"Christakis, Maria","first_name":"Maria"},{"first_name":"Matthias","full_name":"Heizmann, Matthias","last_name":"Heizmann"},{"last_name":"Mansur","full_name":"Mansur, Muhammad Numair","first_name":"Muhammad Numair"},{"last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"},{"last_name":"Wüstholz","first_name":"Valentin","full_name":"Wüstholz, Valentin"}],"publisher":"Springer Nature","day":"04","conference":{"location":"Prague, Czech Republic","start_date":"2019-04-06","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2019-04-11"},"project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"abstract":[{"text":"Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1007/978-3-030-17462-0_13","ddc":["000"],"ec_funded":1,"date_updated":"2025-04-15T06:26:12Z","has_accepted_license":"1","month":"04","oa":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:17Z","date_created":"2019-02-18T16:44:06Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","scopus_import":"1","citation":{"ama":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault localization and suspiciousness ranking. In: <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>. Vol 11427. Springer Nature; 2019:226-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">10.1007/978-3-030-17462-0_13</a>","mla":"Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.” <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, vol. 11427, Springer Nature, 2019, pp. 226–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">10.1007/978-3-030-17462-0_13</a>.","short":"M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:, 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2019, pp. 226–243.","ista":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic fault localization and suspiciousness ranking. 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427, 226–243.","chicago":"Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness Ranking.” In <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, 11427:226–43. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">https://doi.org/10.1007/978-3-030-17462-0_13</a>.","ieee":"M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic fault localization and suspiciousness ranking,” in <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, Prague, Czech Republic, 2019, vol. 11427, pp. 226–243.","apa":"Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., &#38; Wüstholz, V. (2019). Semantic fault localization and suspiciousness ranking. In <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i> (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">https://doi.org/10.1007/978-3-030-17462-0_13</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":11427,"status":"public","year":"2019","type":"conference","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","file_id":"6408","creator":"dernst","file_name":"2019_LNCS_Christakis.pdf","checksum":"9998496f6fe202c0a19124b4209154c6","relation":"main_file","file_size":773083,"content_type":"application/pdf","date_created":"2019-05-10T14:16:05Z","date_updated":"2020-07-14T12:47:17Z"}],"title":"Semantic fault localization and suspiciousness ranking","publication":"25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ","intvolume":"     11427","page":"226-243","date_published":"2019-04-04T00:00:00Z","alternative_title":["LNCS"],"department":[{"_id":"ToHe"}],"isi":1},{"month":"03","date_updated":"2025-04-14T07:44:00Z","has_accepted_license":"1","oa_version":"Submitted Version","file_date_updated":"2021-06-29T14:41:46Z","oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis."}],"article_processing_charge":"No","doi":"10.1038/s41596-018-0117-3","day":"01","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03600","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["30778205"],"isi":["000459890700008"]},"_id":"6052","publication_status":"published","publisher":"Nature Publishing Group","author":[{"last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","full_name":"Truckenbrodt, Sven M"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"first_name":"Silvio O","full_name":"Rizzoli, Silvio O","last_name":"Rizzoli"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"}],"ec_funded":1,"ddc":["570"],"date_published":"2019-03-01T00:00:00Z","page":"832–863","intvolume":"        14","department":[{"_id":"JoDa"},{"_id":"Bio"}],"isi":1,"volume":14,"status":"public","citation":{"ieee":"S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” <i>Nature Protocols</i>, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019.","apa":"Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., &#38; Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. <i>Nature Protocols</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41596-018-0117-3\">https://doi.org/10.1038/s41596-018-0117-3</a>","chicago":"Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” <i>Nature Protocols</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41596-018-0117-3\">https://doi.org/10.1038/s41596-018-0117-3</a>.","short":"S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863.","ista":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863.","ama":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization in X10 expansion microscopy. <i>Nature Protocols</i>. 2019;14(3):832–863. doi:<a href=\"https://doi.org/10.1038/s41596-018-0117-3\">10.1038/s41596-018-0117-3</a>","mla":"Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion Microscopy.” <i>Nature Protocols</i>, vol. 14, no. 3, Nature Publishing Group, 2019, pp. 832–863, doi:<a href=\"https://doi.org/10.1038/s41596-018-0117-3\">10.1038/s41596-018-0117-3</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","quality_controlled":"1","date_created":"2019-02-24T22:59:20Z","title":"A practical guide to optimization in X10 expansion microscopy","publication":"Nature Protocols","language":[{"iso":"eng"}],"file":[{"checksum":"7efb9951e7ddf3e3dcc2fb92b859c623","file_name":"181031_Truckenbrodt_ExM_NatProtoc.docx","file_size":84478958,"relation":"main_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2021-06-29T14:41:46Z","date_created":"2021-06-29T14:41:46Z","success":1,"access_level":"open_access","file_id":"9619","creator":"kschuh"}],"pmid":1,"type":"journal_article","year":"2019","issue":"3"},{"ddc":["570"],"type":"research_data","year":"2019","title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","file":[{"content_type":"application/zip","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-07T13:37:19Z","checksum":"bc1b285edca9e98a2c63d153c79bb75b","file_name":"Setd5_paper.zip","relation":"supplementary_material","file_size":33202743,"creator":"dernst","file_id":"6084","access_level":"open_access"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"3"}]},"day":"09","publisher":"Institute of Science and Technology Austria","_id":"6074","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","first_name":"Christoph"},{"first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"}],"date_created":"2019-03-07T13:32:35Z","status":"public","doi":"10.15479/AT:ISTA:6074","article_processing_charge":"No","abstract":[{"text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"C. Dotter, G. Novarino, (2019).","ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:6074\">10.15479/AT:ISTA:6074</a>.","mla":"Dotter, Christoph, and Gaia Novarino. <i>Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.”</i> Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6074\">10.15479/AT:ISTA:6074</a>.","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6074\">10.15479/AT:ISTA:6074</a>","apa":"Dotter, C., &#38; Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6074\">https://doi.org/10.15479/AT:ISTA:6074</a>","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6074\">https://doi.org/10.15479/AT:ISTA:6074</a>."},"department":[{"_id":"GaNo"}],"oa":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:18Z","month":"01","has_accepted_license":"1","date_updated":"2025-04-15T07:50:27Z","date_published":"2019-01-09T00:00:00Z"},{"isi":1,"department":[{"_id":"JoFi"}],"publication_identifier":{"issn":["2095-5545"],"eissn":["2047-7538"]},"date_published":"2019-03-06T00:00:00Z","article_number":"28","arxiv":1,"intvolume":"         8","publication":"Light: Science and Applications","title":"A full vectorial mapping of nanophotonic light fields","file":[{"access_level":"open_access","file_id":"6108","creator":"dernst","checksum":"d71e528cff9c56f70ccc29dd7005257f","file_name":"2019_Light_LeFeber.pdf","relation":"main_file","file_size":1119947,"content_type":"application/pdf","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-18T08:08:22Z"}],"language":[{"iso":"eng"}],"year":"2019","issue":"1","type":"journal_article","status":"public","volume":8,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. 2019. A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. 8(1), 28.","short":"B. Le Feber, J.E. Sipe, M. Wulf, L. Kuipers, N. Rotenberg, Light: Science and Applications 8 (2019).","ama":"Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. A full vectorial mapping of nanophotonic light fields. <i>Light: Science and Applications</i>. 2019;8(1). doi:<a href=\"https://doi.org/10.1038/s41377-019-0124-3\">10.1038/s41377-019-0124-3</a>","mla":"Le Feber, B., et al. “A Full Vectorial Mapping of Nanophotonic Light Fields.” <i>Light: Science and Applications</i>, vol. 8, no. 1, 28, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41377-019-0124-3\">10.1038/s41377-019-0124-3</a>.","ieee":"B. Le Feber, J. E. Sipe, M. Wulf, L. Kuipers, and N. Rotenberg, “A full vectorial mapping of nanophotonic light fields,” <i>Light: Science and Applications</i>, vol. 8, no. 1. Springer Nature, 2019.","apa":"Le Feber, B., Sipe, J. E., Wulf, M., Kuipers, L., &#38; Rotenberg, N. (2019). A full vectorial mapping of nanophotonic light fields. <i>Light: Science and Applications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41377-019-0124-3\">https://doi.org/10.1038/s41377-019-0124-3</a>","chicago":"Le Feber, B., J. E. Sipe, Matthias Wulf, L. Kuipers, and N. Rotenberg. “A Full Vectorial Mapping of Nanophotonic Light Fields.” <i>Light: Science and Applications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41377-019-0124-3\">https://doi.org/10.1038/s41377-019-0124-3</a>."},"quality_controlled":"1","scopus_import":"1","date_created":"2019-03-17T22:59:13Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:19Z","oa":1,"month":"03","has_accepted_license":"1","date_updated":"2025-07-10T11:53:10Z","ddc":["530"],"doi":"10.1038/s41377-019-0124-3","abstract":[{"text":"Light is a union of electric and magnetic fields, and nowhere is the complex relationship between these fields more evident than in the near fields of nanophotonic structures. There, complicated electric and magnetic fields varying over subwavelength scales are generally present, which results in photonic phenomena such as extraordinary optical momentum, superchiral fields, and a complex spatial evolution of optical singularities. An understanding of such phenomena requires nanoscale measurements of the complete optical field vector. Although the sensitivity of near- field scanning optical microscopy to the complete electromagnetic field was recently demonstrated, a separation of different components required a priori knowledge of the sample. Here, we introduce a robust algorithm that can disentangle all six electric and magnetic field components from a single near-field measurement without any numerical modeling of the structure. As examples, we unravel the fields of two prototypical nanophotonic structures: a photonic crystal waveguide and a plasmonic nanowire. These results pave the way for new studies of complex photonic phenomena at the nanoscale and for the design of structures that optimize their optical behavior.","lang":"eng"}],"article_processing_charge":"No","day":"06","publisher":"Springer Nature","_id":"6102","author":[{"first_name":"B.","full_name":"Le Feber, B.","last_name":"Le Feber"},{"last_name":"Sipe","first_name":"J. E.","full_name":"Sipe, J. E."},{"last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","first_name":"Matthias"},{"last_name":"Kuipers","full_name":"Kuipers, L.","first_name":"L."},{"last_name":"Rotenberg","full_name":"Rotenberg, N.","first_name":"N."}],"publication_status":"published","external_id":{"arxiv":["1803.10145"],"isi":["000460470700004"]}},{"conference":{"end_date":"2019-03-28","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","start_date":"2019-03-26","location":"Marne-la-Vallée, France"},"day":"23","quality_controlled":"1","extern":"1","date_created":"2019-03-21T12:12:19Z","_id":"6163","author":[{"first_name":"Ranita","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Largeteau-Skapin","full_name":"Largeteau-Skapin, Gaëlle","first_name":"Gaëlle"},{"full_name":"Zrour, Rita","first_name":"Rita","last_name":"Zrour"},{"last_name":"Andres","first_name":"Eric","full_name":"Andres, Eric"}],"publication_status":"published","publisher":"Springer Berlin Heidelberg","abstract":[{"text":"We propose a new non-orthogonal basis to express the 3D Euclidean space in terms of a regular grid. Every grid point, each represented by integer 3-coordinates, corresponds to rhombic dodecahedron centroid. Rhombic dodecahedron is a space filling polyhedron which represents the close packing of spheres in 3D space and the Voronoi structures of the face centered cubic (FCC) lattice. In order to illustrate the interest of the new coordinate system, we propose the characterization of 3D digital plane with its topological features, such as the interrelation between the thickness of the digital plane and the separability constraint we aim to obtain. A characterization of a 3D digital sphere with relevant topological features is proposed as well with the help of a 48 symmetry that comes with the new coordinate system.","lang":"eng"}],"article_processing_charge":"No","volume":11414,"doi":"10.1007/978-3-030-14085-4_3","status":"public","citation":{"chicago":"Biswas, Ranita, Gaëlle Largeteau-Skapin, Rita Zrour, and Eric Andres. “Rhombic Dodecahedron Grid—Coordinate System and 3D Digital Object Definitions.” In <i>21st IAPR International Conference on Discrete Geometry for Computer Imagery</i>, 11414:27–37. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. <a href=\"https://doi.org/10.1007/978-3-030-14085-4_3\">https://doi.org/10.1007/978-3-030-14085-4_3</a>.","ieee":"R. Biswas, G. Largeteau-Skapin, R. Zrour, and E. Andres, “Rhombic dodecahedron grid—coordinate system and 3D digital object definitions,” in <i>21st IAPR International Conference on Discrete Geometry for Computer Imagery</i>, Marne-la-Vallée, France, 2019, vol. 11414, pp. 27–37.","apa":"Biswas, R., Largeteau-Skapin, G., Zrour, R., &#38; Andres, E. (2019). Rhombic dodecahedron grid—coordinate system and 3D digital object definitions. In <i>21st IAPR International Conference on Discrete Geometry for Computer Imagery</i> (Vol. 11414, pp. 27–37). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-030-14085-4_3\">https://doi.org/10.1007/978-3-030-14085-4_3</a>","ama":"Biswas R, Largeteau-Skapin G, Zrour R, Andres E. Rhombic dodecahedron grid—coordinate system and 3D digital object definitions. In: <i>21st IAPR International Conference on Discrete Geometry for Computer Imagery</i>. Vol 11414. Berlin, Heidelberg: Springer Berlin Heidelberg; 2019:27-37. doi:<a href=\"https://doi.org/10.1007/978-3-030-14085-4_3\">10.1007/978-3-030-14085-4_3</a>","mla":"Biswas, Ranita, et al. “Rhombic Dodecahedron Grid—Coordinate System and 3D Digital Object Definitions.” <i>21st IAPR International Conference on Discrete Geometry for Computer Imagery</i>, vol. 11414, Springer Berlin Heidelberg, 2019, pp. 27–37, doi:<a href=\"https://doi.org/10.1007/978-3-030-14085-4_3\">10.1007/978-3-030-14085-4_3</a>.","short":"R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, in:, 21st IAPR International Conference on Discrete Geometry for Computer Imagery, Springer Berlin Heidelberg, Berlin, Heidelberg, 2019, pp. 27–37.","ista":"Biswas R, Largeteau-Skapin G, Zrour R, Andres E. 2019. Rhombic dodecahedron grid—coordinate system and 3D digital object definitions. 21st IAPR International Conference on Discrete Geometry for Computer Imagery. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 11414, 27–37."},"place":"Berlin, Heidelberg","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"conference","year":"2019","title":"Rhombic dodecahedron grid—coordinate system and 3D digital object definitions","publication":"21st IAPR International Conference on Discrete Geometry for Computer Imagery","language":[{"iso":"eng"}],"intvolume":"     11414","month":"02","date_updated":"2022-01-27T14:25:17Z","date_published":"2019-02-23T00:00:00Z","alternative_title":["LNCS"],"page":"27-37","publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["978-3-6624-6446-5","978-3-6624-6447-2"]},"oa_version":"None"},{"intvolume":"       568","page":"240-243","date_published":"2019-04-11T00:00:00Z","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"department":[{"_id":"JiFr"}],"isi":1,"date_created":"2019-04-09T08:37:05Z","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/","description":"News on IST Homepage"}]},"scopus_import":"1","quality_controlled":"1","citation":{"ama":"Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential growth of the apical hook. <i>Nature</i>. 2019;568:240-243. doi:<a href=\"https://doi.org/10.1038/s41586-019-1069-7\">10.1038/s41586-019-1069-7</a>","mla":"Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” <i>Nature</i>, vol. 568, Springer Nature, 2019, pp. 240–43, doi:<a href=\"https://doi.org/10.1038/s41586-019-1069-7\">10.1038/s41586-019-1069-7</a>.","ista":"Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z, Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 568, 240–243.","short":"M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu, Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243.","chicago":"Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1069-7\">https://doi.org/10.1038/s41586-019-1069-7</a>.","ieee":"M. Cao <i>et al.</i>, “TMK1-mediated auxin signalling regulates differential growth of the apical hook,” <i>Nature</i>, vol. 568. Springer Nature, pp. 240–243, 2019.","apa":"Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated auxin signalling regulates differential growth of the apical hook. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1069-7\">https://doi.org/10.1038/s41586-019-1069-7</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":568,"status":"public","year":"2019","type":"journal_article","pmid":1,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","file_id":"8751","success":1,"creator":"dernst","relation":"main_file","file_size":4321328,"file_name":"2019_Nature _Cao_accepted.pdf","checksum":"6b84ab602a34382cf0340a37a1378c75","date_created":"2020-11-13T07:37:41Z","date_updated":"2020-11-13T07:37:41Z","content_type":"application/pdf"}],"title":"TMK1-mediated auxin signalling regulates differential growth of the apical hook","publication":"Nature","date_updated":"2025-04-14T07:45:04Z","has_accepted_license":"1","month":"04","article_type":"original","oa":1,"oa_version":"Submitted Version","file_date_updated":"2020-11-13T07:37:41Z","_id":"6259","author":[{"last_name":"Cao","full_name":"Cao, Min","first_name":"Min"},{"full_name":"Chen, Rong","first_name":"Rong","last_name":"Chen"},{"last_name":"Li","first_name":"Pan","full_name":"Li, Pan"},{"full_name":"Yu, Yongqiang","first_name":"Yongqiang","last_name":"Yu"},{"first_name":"Rui","full_name":"Zheng, Rui","last_name":"Zheng"},{"last_name":"Ge","full_name":"Ge, Danfeng","first_name":"Danfeng"},{"last_name":"Zheng","full_name":"Zheng, Wei","first_name":"Wei"},{"full_name":"Wang, Xuhui","first_name":"Xuhui","last_name":"Wang"},{"first_name":"Yangtao","full_name":"Gu, Yangtao","last_name":"Gu"},{"first_name":"Zuzana","orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Zhang","first_name":"Heng","full_name":"Zhang, Heng"},{"last_name":"Liu","first_name":"Renyi","full_name":"Liu, Renyi"},{"last_name":"He","full_name":"He, Jun","first_name":"Jun"},{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"}],"publisher":"Springer Nature","external_id":{"pmid":["30944466"],"isi":["000464412700050"]},"publication_status":"published","day":"11","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"}],"abstract":[{"lang":"eng","text":"The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes."}],"article_processing_charge":"No","doi":"10.1038/s41586-019-1069-7","ddc":["580"],"ec_funded":1},{"date_published":"2019-05-01T00:00:00Z","page":"47-59","isi":1,"department":[{"_id":"MaLo"}],"publication_identifier":{"issn":["0945-053X"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","quality_controlled":"1","date_created":"2019-04-11T20:55:01Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"status":"public","volume":"78-79","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">https://doi.org/10.1016/j.matbio.2018.12.002</a>.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. <i>Matrix Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">https://doi.org/10.1016/j.matbio.2018.12.002</a>","ieee":"H. S. Davies <i>et al.</i>, “An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments,” <i>Matrix Biology</i>, vol. 78–79. Elsevier, pp. 47–59, 2019.","mla":"Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:<a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">10.1016/j.matbio.2018.12.002</a>.","ama":"Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. <i>Matrix Biology</i>. 2019;78-79:47-59. doi:<a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">10.1016/j.matbio.2018.12.002</a>","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 78–79, 47–59."},"year":"2019","type":"journal_article","publication":"Matrix Biology","title":"An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments","file":[{"file_id":"7825","access_level":"open_access","creator":"dernst","file_size":4444339,"relation":"main_file","file_name":"2018_MatrixBiology_Davies.pdf","checksum":"790878cd78bfc54a147ddcc7c8f286a0","date_created":"2020-05-14T09:02:07Z","date_updated":"2020-07-14T12:47:27Z","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"month":"05","has_accepted_license":"1","date_updated":"2023-08-25T10:11:28Z","article_type":"original","oa":1,"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:47:27Z","day":"01","external_id":{"isi":["000468707600005"]},"_id":"6297","author":[{"last_name":"Davies","full_name":"Davies, Heather S.","first_name":"Heather S."},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","first_name":"Natalia S.","full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124"},{"last_name":"El Amri","first_name":"Nouha","full_name":"El Amri, Nouha"},{"full_name":"Coche-Guérente, Liliane","first_name":"Liliane","last_name":"Coche-Guérente"},{"last_name":"Verdier","full_name":"Verdier, Claude","first_name":"Claude"},{"last_name":"Bureau","first_name":"Lionel","full_name":"Bureau, Lionel"},{"full_name":"Richter, Ralf P.","first_name":"Ralf P.","last_name":"Richter"},{"last_name":"Débarre","full_name":"Débarre, Delphine","first_name":"Delphine"}],"publisher":"Elsevier","publication_status":"published","doi":"10.1016/j.matbio.2018.12.002","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow."}],"ddc":["570"]},{"type":"book_chapter","year":"2019","language":[{"iso":"eng"}],"publication":"2017 MATRIX Annals","title":"How to Sheafify an Elliptic Quantum Group","date_created":"2025-07-10T13:31:38Z","quality_controlled":"1","series_title":"MXBS","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"Y. Yang and G. Zhao, “How to Sheafify an Elliptic Quantum Group,” in <i>2017 MATRIX Annals</i>, vol. 2, Cham: Springer International Publishing, 2019, pp. 675–691.","apa":"Yang, Y., &#38; Zhao, G. (2019). How to Sheafify an Elliptic Quantum Group. In <i>2017 MATRIX Annals</i> (Vol. 2, pp. 675–691). Cham: Springer International Publishing. <a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">https://doi.org/10.1007/978-3-030-04161-8_54</a>","chicago":"Yang, Yaping, and Gufang Zhao. “How to Sheafify an Elliptic Quantum Group.” In <i>2017 MATRIX Annals</i>, 2:675–91. MXBS. Cham: Springer International Publishing, 2019. <a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">https://doi.org/10.1007/978-3-030-04161-8_54</a>.","short":"Y. Yang, G. Zhao, in:, 2017 MATRIX Annals, Springer International Publishing, Cham, 2019, pp. 675–691.","ista":"Yang Y, Zhao G. 2019.How to Sheafify an Elliptic Quantum Group. In: 2017 MATRIX Annals. MATRIX Book Series, vol. 2, 675–691.","ama":"Yang Y, Zhao G. How to Sheafify an Elliptic Quantum Group. In: <i>2017 MATRIX Annals</i>. Vol 2. MXBS. Cham: Springer International Publishing; 2019:675-691. doi:<a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">10.1007/978-3-030-04161-8_54</a>","mla":"Yang, Yaping, and Gufang Zhao. “How to Sheafify an Elliptic Quantum Group.” <i>2017 MATRIX Annals</i>, vol. 2, Springer International Publishing, 2019, pp. 675–91, doi:<a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">10.1007/978-3-030-04161-8_54</a>."},"status":"public","volume":2,"department":[{"_id":"TaHa"}],"publication_identifier":{"eisbn":["9783030041618"],"eissn":["2523-305X"],"issn":["2523-3041"],"isbn":["9783030041601"]},"OA_place":"repository","intvolume":"         2","page":"675-691","arxiv":1,"alternative_title":["MATRIX Book Series"],"date_published":"2019-03-25T00:00:00Z","_id":"19987","publication_status":"published","author":[{"last_name":"Yang","id":"360D8648-F248-11E8-B48F-1D18A9856A87","full_name":"Yang, Yaping","first_name":"Yaping"},{"id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","last_name":"Zhao","full_name":"Zhao, Gufang","first_name":"Gufang"}],"external_id":{"arxiv":["1803.06627"]},"publisher":"Springer International Publishing","day":"25","place":"Cham","doi":"10.1007/978-3-030-04161-8_54","abstract":[{"text":"These lecture notes are based on Yang’s talk at the MATRIX program Geometric R-Matrices: from Geometry to Probability, at the University of Melbourne, Dec. 18–22, 2017, and Zhao’s talk at Perimeter Institute for Theoretical Physics in January 2018. We give an introductory survey of the results in Yang and Zhao (Quiver varieties and elliptic quantum groups, 2017. arxiv1708.01418). We discuss a sheafified elliptic quantum group associated to any symmetric Kac-Moody Lie algebra. The sheafification is obtained by applying the equivariant elliptic cohomological theory to the moduli space of representations of a preprojective algebra. By construction, the elliptic quantum group naturally acts on the equivariant elliptic cohomology of Nakajima quiver varieties. As an application, we obtain a relation between the sheafified elliptic quantum group and the global affine Grassmannian over an elliptic curve.","lang":"eng"}],"article_processing_charge":"No","oa":1,"oa_version":"Preprint","date_updated":"2025-09-23T11:59:52Z","month":"03","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1803.06627","open_access":"1"}],"OA_type":"green","acknowledgement":"Y.Y. would like to thank the organizers of the MATRIX program Geometric R-Matrices: from Geometry to Probability for their kind invitation, and many participants of the program for useful discussions, including Vassily Gorbounov, Andrei Okounkov, Allen Knutson, Hitoshi Konno, Paul Zinn-Justin. Proposition 1 and Sect. 3.3 are new, for which we thank Hitoshi Konno for interesting discussions and communications. These notes were written when both authors were visiting the Perimeter Institute for Theoretical Physics (PI). We are grateful to PI for the hospitality."}]