[{"month":"02","external_id":{"pmid":["25643149"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/"}],"oa":1,"quality_controlled":"1","doi":"10.1038/nmeth.3279","language":[{"iso":"eng"}],"publist_id":"5617","year":"2015","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","author":[{"first_name":"Cheyang","last_name":"Liao","full_name":"Liao, Cheyang"},{"full_name":"Smet, Wouter","last_name":"Smet","first_name":"Wouter"},{"first_name":"Géraldine","last_name":"Brunoud","full_name":"Brunoud, Géraldine"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida","full_name":"Yoshida, Saiko"},{"full_name":"Vernoux, Teva","first_name":"Teva","last_name":"Vernoux"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"}],"date_created":"2018-12-11T11:52:41Z","date_updated":"2021-01-12T06:51:34Z","volume":12,"scopus_import":1,"day":"26","publication":"Nature Methods","citation":{"chicago":"Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279.","mla":"Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:10.1038/nmeth.3279.","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210.","apa":"Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279","ieee":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” Nature Methods, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.","ama":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210. doi:10.1038/nmeth.3279"},"page":"207 - 210","date_published":"2015-02-26T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species."}],"issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1554","title":"Reporters for sensitive and quantitative measurement of auxin response","status":"public","intvolume":" 12","oa_version":"Submitted Version"},{"page":"338 - 340","quality_controlled":"1","citation":{"ista":"Hons M, Sixt MK. 2015. The lymph node filter revealed. Nature Immunology. 16(4), 338–340.","ieee":"M. Hons and M. K. Sixt, “The lymph node filter revealed,” Nature Immunology, vol. 16, no. 4. Nature Publishing Group, pp. 338–340, 2015.","apa":"Hons, M., & Sixt, M. K. (2015). The lymph node filter revealed. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3126","ama":"Hons M, Sixt MK. The lymph node filter revealed. Nature Immunology. 2015;16(4):338-340. doi:10.1038/ni.3126","chicago":"Hons, Miroslav, and Michael K Sixt. “The Lymph Node Filter Revealed.” Nature Immunology. Nature Publishing Group, 2015. https://doi.org/10.1038/ni.3126.","mla":"Hons, Miroslav, and Michael K. Sixt. “The Lymph Node Filter Revealed.” Nature Immunology, vol. 16, no. 4, Nature Publishing Group, 2015, pp. 338–40, doi:10.1038/ni.3126.","short":"M. Hons, M.K. Sixt, Nature Immunology 16 (2015) 338–340."},"publication":"Nature Immunology","language":[{"iso":"eng"}],"date_published":"2015-03-19T00:00:00Z","doi":"10.1038/ni.3126","scopus_import":1,"month":"03","day":"19","intvolume":" 16","department":[{"_id":"MiSi"}],"publisher":"Nature Publishing Group","title":"The lymph node filter revealed","status":"public","publication_status":"published","_id":"1560","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":16,"oa_version":"None","date_updated":"2021-01-12T06:51:36Z","date_created":"2018-12-11T11:52:43Z","author":[{"first_name":"Miroslav","last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"type":"journal_article","issue":"4","publist_id":"5611","abstract":[{"text":"Stromal cells in the subcapsular sinus of the lymph node 'decide' which cells and molecules are allowed access to the deeper parenchyma. The glycoprotein PLVAP is a crucial component of this selector function.","lang":"eng"}]},{"abstract":[{"text":"Leptin is an adipokine produced by the adipose tissue regulating body weight through its appetite-suppressing effect. Besides being expressed in the hypothalamus and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells of the adrenal medulla. In the present study, we report the effect of leptin on mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused a slowly developing membrane hyperpolarization followed by complete blockade of action potential (AP) firing. This inhibitory effect at rest was abolished by the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium channels. Single-channel recordings in 'perforated microvesicles' confirmed that leptin increased BK channel open probability without altering its unitary conductance. BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K) signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully prevented BK current increase. We also tested the effect of leptin on evoked AP firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains of lower frequency, APs are broader and depolarization-evoked exocytosis is increased as a result of the larger size of the ready-releasable pool and higher frequency of vesicle release. The kinetics and quantal size of single secretory events remained unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual action on MCC activity. It dampens AP firing at rest but preserves AP firing and increases catecholamine secretion during sustained stimulation, highlighting the importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic tone and catecholamine release.","lang":"eng"}],"issue":"22","type":"journal_article","oa_version":"Submitted Version","title":"Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells","status":"public","intvolume":" 593","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1565","day":"15","scopus_import":1,"date_published":"2015-11-15T00:00:00Z","page":"4835 - 4853","publication":"Journal of Physiology","citation":{"ieee":"D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” Journal of Physiology, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015.","apa":"Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., & Carabelli, V. (2015). Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP271078","ista":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 593(22), 4835–4853.","ama":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 2015;593(22):4835-4853. doi:10.1113/JP271078","chicago":"Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2015. https://doi.org/10.1113/JP271078.","short":"D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853.","mla":"Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology, vol. 593, no. 22, Wiley-Blackwell, 2015, pp. 4835–53, doi:10.1113/JP271078."},"publist_id":"5606","date_created":"2018-12-11T11:52:45Z","date_updated":"2021-01-12T06:51:38Z","volume":593,"author":[{"full_name":"Gavello, Daniela","last_name":"Gavello","first_name":"Daniela"},{"full_name":"Vandael, David H","last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sara","last_name":"Gosso","full_name":"Gosso, Sara"},{"last_name":"Carbone","first_name":"Emilio","full_name":"Carbone, Emilio"},{"full_name":"Carabelli, Valentina","last_name":"Carabelli","first_name":"Valentina"}],"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Wiley-Blackwell","year":"2015","acknowledgement":"This work was supported by the Compagnia di San Paolo Foundation ‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank Dr Claudio Franchino for cell preparation and for providing excellent technical support.","pmid":1,"month":"11","language":[{"iso":"eng"}],"doi":"10.1113/JP271078","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/","open_access":"1"}],"external_id":{"pmid":["26282459"]}},{"month":"08","doi":"10.1093/jxb/erv177","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"publist_id":"5609","ec_funded":1,"author":[{"first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Xu"},{"first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"last_name":"De Rycke","first_name":"Riet","full_name":"De Rycke, Riet"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:52:44Z","date_updated":"2023-02-23T10:04:26Z","volume":66,"acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG- 20101109-PSDP to JF); the European Social Fund and the state budget of the Czech Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR) [project 13-40637S to JF].","year":"2015","publication_status":"published","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publisher":"Oxford University Press","day":"01","scopus_import":1,"date_published":"2015-08-01T00:00:00Z","publication":"Journal of Experimental Botany","citation":{"ama":"Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 2015;66(16):5055-5065. doi:10.1093/jxb/erv177","ieee":"P. Grones et al., “Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015.","apa":"Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T., … Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv177","ista":"Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065.","short":"P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E. Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065.","mla":"Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:10.1093/jxb/erv177.","chicago":"Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv177."},"article_type":"original","page":"5055 - 5065","abstract":[{"lang":"eng","text":"The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor."}],"issue":"16","type":"journal_article","oa_version":"None","_id":"1562","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles","status":"public","intvolume":" 66"},{"ec_funded":1,"publist_id":"5607","file_date_updated":"2020-07-14T12:45:02Z","article_number":"145","volume":9,"date_created":"2018-12-11T11:52:45Z","date_updated":"2021-01-12T06:51:37Z","author":[{"last_name":"Gilson","first_name":"Matthieu","full_name":"Gilson, Matthieu"},{"full_name":"Savin, Cristina","first_name":"Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zenke, Friedemann","first_name":"Friedemann","last_name":"Zenke"}],"publisher":"Frontiers Research Foundation","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2015","month":"11","language":[{"iso":"eng"}],"doi":"10.3389/fncom.2015.00145","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"issue":"11","type":"journal_article","file":[{"content_type":"application/pdf","file_size":187038,"creator":"system","file_name":"IST-2016-479-v1+1_fncom-09-00145.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:12:09Z","checksum":"cea73b6d3ef1579f32da10b82f4de4fd","relation":"main_file","file_id":"4927"}],"oa_version":"Published Version","pubrep_id":"479","intvolume":" 9","title":"Editorial: Emergent neural computation from the interaction of different forms of plasticity","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1564","has_accepted_license":"1","day":"30","scopus_import":1,"date_published":"2015-11-30T00:00:00Z","citation":{"chicago":"Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.","mla":"Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.","short":"M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015).","ista":"Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.","apa":"Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145","ieee":"M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.","ama":"Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 2015;9(11). doi:10.3389/fncom.2015.00145"},"publication":"Frontiers in Computational Neuroscience"},{"language":[{"iso":"eng"}],"date_published":"2015-02-05T00:00:00Z","doi":"10.1109/SYNASC.2014.81","conference":{"end_date":"2014-09-25","start_date":"2014-09-22","location":"Timisoara, Romania","name":"SYNASC: Symbolic and Numeric Algorithms for Scientific Computing"},"page":"7034731","quality_controlled":"1","citation":{"short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, in:, Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731.","mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731, doi:10.1109/SYNASC.2014.81.","chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, and Daria Malkova. “The Classification of Endoscopy Images with Persistent Homology.” In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, 7034731. IEEE, 2015. https://doi.org/10.1109/SYNASC.2014.81.","ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. The classification of endoscopy images with persistent homology. In: Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. IEEE; 2015:7034731. doi:10.1109/SYNASC.2014.81","apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., & Malkova, D. (2015). The classification of endoscopy images with persistent homology. In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (p. 7034731). Timisoara, Romania: IEEE. https://doi.org/10.1109/SYNASC.2014.81","ieee":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, and D. Malkova, “The classification of endoscopy images with persistent homology,” in Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, Timisoara, Romania, 2015, p. 7034731.","ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. 2015. The classification of endoscopy images with persistent homology. Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC: Symbolic and Numeric Algorithms for Scientific Computing, 7034731."},"publication":"Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing","day":"05","month":"02","scopus_import":1,"oa_version":"None","date_updated":"2023-02-21T16:57:29Z","date_created":"2018-12-11T11:52:46Z","related_material":{"record":[{"id":"1289","relation":"later_version","status":"public"}]},"author":[{"last_name":"Dunaeva","first_name":"Olga","full_name":"Dunaeva, Olga"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Lukyanov, Anton","last_name":"Lukyanov","first_name":"Anton"},{"first_name":"Michael","last_name":"Machin","full_name":"Machin, Michael"},{"first_name":"Daria","last_name":"Malkova","full_name":"Malkova, Daria"}],"department":[{"_id":"HeEd"}],"publisher":"IEEE","title":"The classification of endoscopy images with persistent homology","status":"public","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1568","year":"2015","acknowledgement":"This research is supported by the project No. 477 of P.G. Demidov Yaroslavl State University within State Assignment for Research.","publist_id":"5603","abstract":[{"lang":"eng","text":"Aiming at the automatic diagnosis of tumors from narrow band imaging (NBI) magnifying endoscopy (ME) images of the stomach, we combine methods from image processing, computational topology, and machine learning to classify patterns into normal, tubular, vessel. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions."}],"type":"conference"},{"oa_version":"None","volume":9411,"date_created":"2018-12-11T11:52:46Z","date_updated":"2022-01-28T08:25:00Z","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"intvolume":" 9411","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"title":"Shape, homology, persistence, and stability","status":"public","publication_status":"published","_id":"1567","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2015","publist_id":"5604","abstract":[{"lang":"eng","text":"My personal journey to the fascinating world of geometric forms started more than 30 years ago with the invention of alpha shapes in the plane. It took about 10 years before we generalized the concept to higher dimensions, we produced working software with a graphics interface for the three-dimensional case. At the same time, we added homology to the computations. Needless to say that this foreshadowed the inception of persistent homology, because it suggested the study of filtrations to capture the scale of a shape or data set. Importantly, this method has fast algorithms. The arguably most useful result on persistent homology is the stability of its diagrams under perturbations."}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"date_published":"2015-01-01T00:00:00Z","conference":{"end_date":"2015-09-26","location":"Los Angeles, CA, United States","start_date":"2015-09-24","name":"GD: Graph Drawing and Network Visualization"},"quality_controlled":"1","citation":{"ista":"Edelsbrunner H. 2015. Shape, homology, persistence, and stability. 23rd International Symposium. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411.","ieee":"H. Edelsbrunner, “Shape, homology, persistence, and stability,” in 23rd International Symposium, Los Angeles, CA, United States, 2015, vol. 9411.","apa":"Edelsbrunner, H. (2015). Shape, homology, persistence, and stability. In 23rd International Symposium (Vol. 9411). Los Angeles, CA, United States: Springer Nature.","ama":"Edelsbrunner H. Shape, homology, persistence, and stability. In: 23rd International Symposium. Vol 9411. Springer Nature; 2015.","chicago":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” In 23rd International Symposium, Vol. 9411. Springer Nature, 2015.","mla":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” 23rd International Symposium, vol. 9411, Springer Nature, 2015.","short":"H. Edelsbrunner, in:, 23rd International Symposium, Springer Nature, 2015."},"publication":"23rd International Symposium","article_processing_charge":"No","month":"01","day":"01","scopus_import":"1"},{"oa_version":"None","volume":45,"date_updated":"2021-01-12T06:51:37Z","date_created":"2018-12-11T11:52:44Z","author":[{"full_name":"Graff, Grzegorz","first_name":"Grzegorz","last_name":"Graff"},{"last_name":"Pilarczyk","first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel"}],"department":[{"_id":"HeEd"}],"intvolume":" 45","publisher":"Juliusz Schauder Center for Nonlinear Studies","status":"public","publication_status":"published","title":"An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds","_id":"1563","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","publist_id":"5608","issue":"1","abstract":[{"text":"For a given self-map $f$ of $M$, a closed smooth connected and simply-connected manifold of dimension $m\\geq 4$, we provide an algorithm for estimating the values of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic points in the smooth homotopy class of $f$. Our results are based on the combinatorial scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm programmed in C++ is publicly available at {\\tt http://www.pawelpilarczyk.com/combtop/}.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.12775/TMNA.2015.014","date_published":"2015-03-01T00:00:00Z","page":"273 - 286","quality_controlled":"1","citation":{"apa":"Graff, G., & Pilarczyk, P. (2015). An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. Juliusz Schauder Center for Nonlinear Studies. https://doi.org/10.12775/TMNA.2015.014","ieee":"G. Graff and P. Pilarczyk, “An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds,” Topological Methods in Nonlinear Analysis, vol. 45, no. 1. Juliusz Schauder Center for Nonlinear Studies, pp. 273–286, 2015.","ista":"Graff G, Pilarczyk P. 2015. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 45(1), 273–286.","ama":"Graff G, Pilarczyk P. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 2015;45(1):273-286. doi:10.12775/TMNA.2015.014","chicago":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” Topological Methods in Nonlinear Analysis. Juliusz Schauder Center for Nonlinear Studies, 2015. https://doi.org/10.12775/TMNA.2015.014.","short":"G. Graff, P. Pilarczyk, Topological Methods in Nonlinear Analysis 45 (2015) 273–286.","mla":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” Topological Methods in Nonlinear Analysis, vol. 45, no. 1, Juliusz Schauder Center for Nonlinear Studies, 2015, pp. 273–86, doi:10.12775/TMNA.2015.014."},"publication":"Topological Methods in Nonlinear Analysis","month":"03","day":"01","scopus_import":1},{"title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development","ddc":["580"],"status":"public","intvolume":" 6","_id":"1574","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2016-477-v1+1_ncomms9821.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1701815,"file_id":"5085","relation":"main_file","date_created":"2018-12-12T10:14:32Z","date_updated":"2020-07-14T12:45:02Z","checksum":"8ff5c108899b548806e1cb7a302fe76d"}],"oa_version":"Published Version","pubrep_id":"477","type":"journal_article","abstract":[{"lang":"eng","text":"Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level."}],"publication":"Nature Communications","citation":{"chicago":"Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821.","short":"Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015).","mla":"Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821.","apa":"Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821","ieee":"Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","ista":"Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821.","ama":"Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821"},"date_published":"2015-11-18T00:00:00Z","scopus_import":1,"day":"18","has_accepted_license":"1","publication_status":"published","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"Nature Publishing Group","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","year":"2015","date_created":"2018-12-11T11:52:48Z","date_updated":"2021-01-12T06:51:42Z","volume":6,"author":[{"last_name":"Chen","first_name":"Qian","full_name":"Chen, Qian"},{"last_name":"Liu","first_name":"Yang","full_name":"Liu, Yang"},{"full_name":"Maere, Steven","last_name":"Maere","first_name":"Steven"},{"first_name":"Eunkyoung","last_name":"Lee","full_name":"Lee, Eunkyoung"},{"full_name":"Van Isterdael, Gert","first_name":"Gert","last_name":"Van Isterdael"},{"full_name":"Xie, Zidian","first_name":"Zidian","last_name":"Xie"},{"first_name":"Wei","last_name":"Xuan","full_name":"Xuan, Wei"},{"full_name":"Lucas, Jessica","first_name":"Jessica","last_name":"Lucas"},{"full_name":"Vassileva, Valya","first_name":"Valya","last_name":"Vassileva"},{"last_name":"Kitakura","first_name":"Saeko","full_name":"Kitakura, Saeko"},{"full_name":"Marhavy, Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","first_name":"Peter","last_name":"Marhavy"},{"full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","last_name":"Wabnik"},{"full_name":"Geldner, Niko","last_name":"Geldner","first_name":"Niko"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"full_name":"Le, Jie","last_name":"Le","first_name":"Jie"},{"first_name":"Hidehiro","last_name":"Fukaki","full_name":"Fukaki, Hidehiro"},{"first_name":"Erich","last_name":"Grotewold","full_name":"Grotewold, Erich"},{"last_name":"Li","first_name":"Chuanyou","full_name":"Li, Chuanyou"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sack","first_name":"Fred","full_name":"Sack, Fred"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"}],"article_number":"8821","file_date_updated":"2020-07-14T12:45:02Z","publist_id":"5597","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms9821","month":"11"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1038/ncomms8526","language":[{"iso":"eng"}],"month":"06","year":"2015","acknowledgement":"M.C. and M.L.H. were supported by fellowships from the Fondation pour la Recherche Médicale and the Association pour la Recherche contre le Cancer, respectively. This work was funded by grants from the City of Paris and the European Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico) to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL* and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934, Institut Curie).","department":[{"_id":"MiSi"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"full_name":"Chabaud, Mélanie","first_name":"Mélanie","last_name":"Chabaud"},{"full_name":"Heuzé, Mélina","last_name":"Heuzé","first_name":"Mélina"},{"full_name":"Bretou, Marine","last_name":"Bretou","first_name":"Marine"},{"first_name":"Pablo","last_name":"Vargas","full_name":"Vargas, Pablo"},{"full_name":"Maiuri, Paolo","first_name":"Paolo","last_name":"Maiuri"},{"first_name":"Paola","last_name":"Solanes","full_name":"Solanes, Paola"},{"full_name":"Maurin, Mathieu","first_name":"Mathieu","last_name":"Maurin"},{"first_name":"Emmanuel","last_name":"Terriac","full_name":"Terriac, Emmanuel"},{"last_name":"Le Berre","first_name":"Maël","full_name":"Le Berre, Maël"},{"full_name":"Lankar, Danielle","first_name":"Danielle","last_name":"Lankar"},{"last_name":"Piolot","first_name":"Tristan","full_name":"Piolot, Tristan"},{"full_name":"Adelstein, Robert","last_name":"Adelstein","first_name":"Robert"},{"full_name":"Zhang, Yingfan","first_name":"Yingfan","last_name":"Zhang"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Jordan","last_name":"Jacobelli","full_name":"Jacobelli, Jordan"},{"first_name":"Olivier","last_name":"Bénichou","full_name":"Bénichou, Olivier"},{"first_name":"Raphaël","last_name":"Voituriez","full_name":"Voituriez, Raphaël"},{"last_name":"Piel","first_name":"Matthieu","full_name":"Piel, Matthieu"},{"first_name":"Ana","last_name":"Lennon Duménil","full_name":"Lennon Duménil, Ana"}],"volume":6,"date_created":"2018-12-11T11:52:48Z","date_updated":"2021-01-12T06:51:42Z","article_number":"7526","publist_id":"5596","file_date_updated":"2020-07-14T12:45:02Z","citation":{"short":"M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin, E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt, J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications 6 (2015).","mla":"Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications, vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526.","chicago":"Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri, Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526.","ama":"Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 2015;6. doi:10.1038/ncomms8526","apa":"Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., … Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms8526","ieee":"M. Chabaud et al., “Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","ista":"Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J, Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 6, 7526."},"publication":"Nature Communications","date_published":"2015-06-25T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1575","intvolume":" 6","ddc":["570"],"status":"public","title":"Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells","pubrep_id":"476","file":[{"file_id":"4915","relation":"main_file","checksum":"bae12e86be2adb28253f890b8bba8315","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:11:58Z","access_level":"open_access","file_name":"IST-2016-476-v1+1_ncomms8526.pdf","creator":"system","content_type":"application/pdf","file_size":4530215}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space.","lang":"eng"}]},{"month":"02","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"doi":"10.1073/pnas.1424856112","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"5602","acknowledgement":"This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). ","year":"2015","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","author":[{"full_name":"Doyle, Siamsa","first_name":"Siamsa","last_name":"Doyle"},{"last_name":"Haegera","first_name":"Ash","full_name":"Haegera, Ash"},{"first_name":"Thomas","last_name":"Vain","full_name":"Vain, Thomas"},{"full_name":"Rigala, Adeline","last_name":"Rigala","first_name":"Adeline"},{"full_name":"Viotti, Corrado","first_name":"Corrado","last_name":"Viotti"},{"full_name":"Łangowskaa, Małgorzata","last_name":"Łangowskaa","first_name":"Małgorzata"},{"full_name":"Maa, Qian","first_name":"Qian","last_name":"Maa"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Raikhel","first_name":"Natasha","full_name":"Raikhel, Natasha"},{"last_name":"Hickse","first_name":"Glenn","full_name":"Hickse, Glenn"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"}],"date_created":"2018-12-11T11:52:46Z","date_updated":"2021-01-12T06:51:39Z","volume":112,"scopus_import":1,"day":"17","publication":"PNAS","citation":{"ama":"Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112","ista":"Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815.","apa":"Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112","ieee":"S. Doyle et al., “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015.","mla":"Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112.","short":"S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.","chicago":"Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112."},"page":"E806 - E815","date_published":"2015-02-17T00:00:00Z","type":"journal_article","abstract":[{"text":"Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.","lang":"eng"}],"issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1569","status":"public","title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","intvolume":" 112","oa_version":"Published Version"},{"publication_status":"published","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publisher":"National Academy of Sciences","year":"2015","pmid":1,"date_created":"2018-12-11T11:52:47Z","date_updated":"2021-01-12T06:51:40Z","volume":112,"author":[{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"},{"first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S"}],"ec_funded":1,"publist_id":"5601","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/","open_access":"1"}],"external_id":{"pmid":["26504200"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1508400112","month":"11","status":"public","title":"Novel plasticity rule can explain the development of sensorimotor intelligence","intvolume":" 112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1570","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution.","lang":"eng"}],"issue":"45","page":"E6224 - E6232","publication":"PNAS","citation":{"ieee":"R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015.","apa":"Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1508400112","ista":"Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.","ama":"Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112","chicago":"Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1508400112.","short":"R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.","mla":"Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112."},"date_published":"2015-11-10T00:00:00Z","scopus_import":1,"day":"10"},{"type":"journal_article","abstract":[{"text":"Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that crossenvironmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance.","lang":"eng"}],"publist_id":"5600","issue":"48","publication_status":"published","title":"Breaking evolutionary constraint with a tradeoff ratchet","status":"public","publisher":"National Academy of Sciences","intvolume":" 112","department":[{"_id":"ToBo"}],"_id":"1571","acknowledgement":"This work is part of the research program of the Foundation for Fundamental Research on Matter, which is part of the Netherlands Organization for Scientific Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences (ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão, J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for discussions and suggestions on the Markov computation. Furthermore, we thank F. J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial version of the manuscript.","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:40Z","date_created":"2018-12-11T11:52:47Z","volume":112,"oa_version":"None","author":[{"full_name":"De Vos, Marjon","first_name":"Marjon","last_name":"De Vos","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dawid","first_name":"Alexandre","full_name":"Dawid, Alexandre"},{"full_name":"Šunderlíková, Vanda","last_name":"Šunderlíková","first_name":"Vanda"},{"full_name":"Tans, Sander","last_name":"Tans","first_name":"Sander"}],"scopus_import":1,"month":"12","day":"01","quality_controlled":"1","page":"14906 - 14911","publication":"PNAS","citation":{"ama":"de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 2015;112(48):14906-14911. doi:10.1073/pnas.1510282112","ieee":"M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary constraint with a tradeoff ratchet,” PNAS, vol. 112, no. 48. National Academy of Sciences, pp. 14906–14911, 2015.","apa":"de Vos, M., Dawid, A., Šunderlíková, V., & Tans, S. (2015). Breaking evolutionary constraint with a tradeoff ratchet. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510282112","ista":"de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 112(48), 14906–14911.","short":"M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911.","mla":"de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11, doi:10.1073/pnas.1510282112.","chicago":"Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510282112."},"language":[{"iso":"eng"}],"date_published":"2015-12-01T00:00:00Z","doi":"10.1073/pnas.1510282112"},{"day":"23","month":"06","scopus_import":1,"date_published":"2015-06-23T00:00:00Z","doi":"10.1007/s00220-015-2402-0","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1312.7873","open_access":"1"}],"oa":1,"citation":{"ista":"Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 339(1), 279–307.","ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet,” Communications in Mathematical Physics, vol. 339, no. 1. Springer, pp. 279–307, 2015.","apa":"Correggi, M., Giuliani, A., & Seiringer, R. (2015). Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2402-0","ama":"Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 2015;339(1):279-307. doi:10.1007/s00220-015-2402-0","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-015-2402-0.","mla":"Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:10.1007/s00220-015-2402-0.","short":"M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics 339 (2015) 279–307."},"publication":"Communications in Mathematical Physics","page":"279 - 307","quality_controlled":"1","issue":"1","publist_id":"5599","abstract":[{"lang":"eng","text":"We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice.\r\n"}],"type":"journal_article","author":[{"full_name":"Correggi, Michele","first_name":"Michele","last_name":"Correggi"},{"full_name":"Giuliani, Alessandro","last_name":"Giuliani","first_name":"Alessandro"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"volume":339,"oa_version":"Preprint","date_created":"2018-12-11T11:52:47Z","date_updated":"2021-01-12T06:51:41Z","year":"2015","_id":"1572","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"intvolume":" 339","publisher":"Springer","status":"public","publication_status":"published","title":"Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet"},{"type":"journal_article","abstract":[{"text":"We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau.","lang":"eng"}],"issue":"10","title":"Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti","status":"public","intvolume":" 68","_id":"1573","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":1,"day":"01","page":"1845 - 1884","publication":"Communications on Pure and Applied Mathematics","citation":{"chicago":"Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics. Wiley, 2015. https://doi.org/10.1002/cpa.21552.","mla":"Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics, vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:10.1002/cpa.21552.","short":"T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and Applied Mathematics 68 (2015) 1845–1884.","ista":"Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 68(10), 1845–1884.","apa":"Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2015). Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21552","ieee":"T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti,” Communications on Pure and Applied Mathematics, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015.","ama":"Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 2015;68(10):1845-1884. doi:10.1002/cpa.21552"},"date_published":"2015-10-01T00:00:00Z","publist_id":"5598","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Wiley","year":"2015","date_updated":"2021-01-12T06:51:41Z","date_created":"2018-12-11T11:52:48Z","volume":68,"author":[{"last_name":"Chen","first_name":"Thomas","full_name":"Chen, Thomas"},{"last_name":"Hainzl","first_name":"Christian","full_name":"Hainzl, Christian"},{"last_name":"Pavlović","first_name":"Nataša","full_name":"Pavlović, Nataša"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"month":"10","quality_controlled":"1","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"http://arxiv.org/abs/1307.3168","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/cpa.21552"},{"file":[{"relation":"main_file","file_id":"7849","checksum":"af2c4c994718c7be417eba0dc746aac9","date_updated":"2020-07-14T12:45:02Z","date_created":"2020-05-15T06:50:20Z","access_level":"open_access","file_name":"2015_Neuroscience_Brenes.pdf","file_size":5563015,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Submitted Version","_id":"1580","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons","ddc":["570"],"intvolume":" 311","abstract":[{"text":"Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins crucial for the fine-tuning of synaptic function. A large amount of experimental evidences has shown that Syns are involved in the development of epileptic phenotypes and several mutations in Syn genes have been associated with epilepsy in humans and animal models. Syn mutations induce alterations in circuitry and neurotransmitter release, differentially affecting excitatory and inhibitory synapses, thus causing an excitation/inhibition imbalance in network excitability toward hyperexcitability that may be a determinant with regard to the development of epilepsy. Another approach to investigate epileptogenic mechanisms is to understand how silencing Syn affects the cellular behavior of single neurons and is associated with the hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional effects of antisense-RNA inhibition of Syn expression on individually identified and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin silencing increases cell excitability characterized by a slightly depolarized resting membrane potential, decreases the rheobase, reduces the threshold for action potential (AP) firing and increases the mean and instantaneous firing rates, with respect to control cells. The observed increase of Ca2+ and BK currents in Syn-silenced cells seems to be related to changes in the shape of the AP waveform. These currents sustain the faster spiking in Syn-deficient cells by increasing the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation during repetitive firing. This in turn speeds up the depolarization phase by reaching the AP threshold faster. Our results provide evidence that Syn silencing increases intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent BK currents in the absence of excitatory or inhibitory inputs.","lang":"eng"}],"type":"journal_article","date_published":"2015-12-17T00:00:00Z","publication":"Neuroscience","citation":{"mla":"Brenes, Oscar, et al. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience, vol. 311, Elsevier, 2015, pp. 430–43, doi:10.1016/j.neuroscience.2015.10.046.","short":"O. Brenes, D.H. Vandael, E. Carbone, P. Montarolo, M. Ghirardi, Neuroscience 311 (2015) 430–443.","chicago":"Brenes, Oscar, David H Vandael, Emilio Carbone, Pier Montarolo, and Mirella Ghirardi. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience. Elsevier, 2015. https://doi.org/10.1016/j.neuroscience.2015.10.046.","ama":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 2015;311:430-443. doi:10.1016/j.neuroscience.2015.10.046","ista":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. 2015. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 311, 430–443.","apa":"Brenes, O., Vandael, D. H., Carbone, E., Montarolo, P., & Ghirardi, M. (2015). Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2015.10.046","ieee":"O. Brenes, D. H. Vandael, E. Carbone, P. Montarolo, and M. Ghirardi, “Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons,” Neuroscience, vol. 311. Elsevier, pp. 430–443, 2015."},"article_type":"original","page":"430 - 443","day":"17","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"author":[{"full_name":"Brenes, Oscar","last_name":"Brenes","first_name":"Oscar"},{"full_name":"Vandael, David H","first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676"},{"first_name":"Emilio","last_name":"Carbone","full_name":"Carbone, Emilio"},{"full_name":"Montarolo, Pier","first_name":"Pier","last_name":"Montarolo"},{"full_name":"Ghirardi, Mirella","last_name":"Ghirardi","first_name":"Mirella"}],"date_updated":"2021-01-12T06:51:44Z","date_created":"2018-12-11T11:52:50Z","volume":311,"year":"2015","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Elsevier","file_date_updated":"2020-07-14T12:45:02Z","publist_id":"5591","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.1016/j.neuroscience.2015.10.046","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","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"},"quality_controlled":"1","month":"12"},{"volume":112,"date_updated":"2021-01-12T06:51:43Z","date_created":"2018-12-11T11:52:49Z","author":[{"first_name":"Antonio","last_name":"Carvalho","full_name":"Carvalho, Antonio"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"},{"full_name":"Russo, Claudia","last_name":"Russo","first_name":"Claudia"},{"full_name":"Swenor, Bonnielin","first_name":"Bonnielin","last_name":"Swenor"},{"first_name":"Andrew","last_name":"Clark","full_name":"Clark, Andrew"}],"department":[{"_id":"BeVi"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2015","acknowledgement":"This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski, C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski, B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments on the manuscript.","publist_id":"5594","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1516543112","quality_controlled":"1","external_id":{"pmid":["26385968"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/"}],"month":"10","oa_version":"Published Version","intvolume":" 112","title":"Birth of a new gene on the Y chromosome of Drosophila melanogaster","status":"public","_id":"1577","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"40","abstract":[{"lang":"eng","text":"Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes."}],"type":"journal_article","date_published":"2015-10-06T00:00:00Z","page":"12450 - 12455","article_type":"original","citation":{"short":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455.","mla":"Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015, pp. 12450–55, doi:10.1073/pnas.1516543112.","chicago":"Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112.","ama":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455. doi:10.1073/pnas.1516543112","apa":"Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1516543112","ieee":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no. 40. National Academy of Sciences, pp. 12450–12455, 2015.","ista":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455."},"publication":"PNAS","article_processing_charge":"No","day":"06","scopus_import":1},{"article_processing_charge":"No","day":"01","scopus_import":1,"date_published":"2015-06-01T00:00:00Z","citation":{"chicago":"Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/S0002-9947-2014-06192-8.","mla":"Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society, vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:10.1090/S0002-9947-2014-06192-8.","short":"C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American Mathematical Society 367 (2015) 4183–4206.","ista":"Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 367(6), 4183–4206.","ieee":"C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of Schubert problems of lines are at least alternating,” Transactions of the American Mathematical Society, vol. 367, no. 6. American Mathematical Society, pp. 4183–4206, 2015.","apa":"Brooks, C., Martin del Campo Sanchez, A., & Sottile, F. (2015). Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0002-9947-2014-06192-8","ama":"Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 2015;367(6):4183-4206. doi:10.1090/S0002-9947-2014-06192-8"},"publication":"Transactions of the American Mathematical Society","page":"4183 - 4206","issue":"6","abstract":[{"text":"We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. This constitutes the largest family of enumerative problems whose Galois groups have been largely determined. Using a criterion of Vakil and a special position argument due to Schubert, our result follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, a combinatorial injection proves the inequality. For the remaining cases, we use the Weyl integral formulas to obtain an integral formula for these Kostka numbers. This rewrites the inequality as an integral, which we estimate to establish the inequality.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1579","intvolume":" 367","title":"Galois groups of Schubert problems of lines are at least alternating","status":"public","month":"06","doi":"10.1090/S0002-9947-2014-06192-8","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.4280"}],"quality_controlled":"1","publist_id":"5592","author":[{"first_name":"Christopher","last_name":"Brooks","full_name":"Brooks, Christopher"},{"id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","last_name":"Martin Del Campo Sanchez","first_name":"Abraham","full_name":"Martin Del Campo Sanchez, Abraham"},{"first_name":"Frank","last_name":"Sottile","full_name":"Sottile, Frank"}],"volume":367,"date_updated":"2021-01-12T06:51:43Z","date_created":"2018-12-11T11:52:50Z","year":"2015","acknowledgement":"This research was supported in part by NSF grant DMS-915211 and the Institut Mittag-Leffler.\r\n","publisher":"American Mathematical Society","department":[{"_id":"CaUh"}],"publication_status":"published"},{"month":"08","day":"01","scopus_import":1,"date_published":"2015-08-01T00:00:00Z","doi":"10.1016/j.comgeo.2015.04.001","language":[{"iso":"eng"}],"citation":{"chicago":"Cao, Thanhtung, Herbert Edelsbrunner, and Tiowseng Tan. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.04.001.","mla":"Cao, Thanhtung, et al. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry, vol. 48, no. 7, Elsevier, 2015, pp. 507–19, doi:10.1016/j.comgeo.2015.04.001.","short":"T. Cao, H. Edelsbrunner, T. Tan, Computational Geometry 48 (2015) 507–519.","ista":"Cao T, Edelsbrunner H, Tan T. 2015. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 48(7), 507–519.","ieee":"T. Cao, H. Edelsbrunner, and T. Tan, “Triangulations from topologically correct digital Voronoi diagrams,” Computational Geometry, vol. 48, no. 7. Elsevier, pp. 507–519, 2015.","apa":"Cao, T., Edelsbrunner, H., & Tan, T. (2015). Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. Elsevier. https://doi.org/10.1016/j.comgeo.2015.04.001","ama":"Cao T, Edelsbrunner H, Tan T. Triangulations from topologically correct digital Voronoi diagrams. 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This provides the proof of correctness for recently developed GPU algorithms that outperform traditional CPU algorithms for constructing two-dimensional Delaunay triangulations.","lang":"eng"}],"type":"journal_article","author":[{"full_name":"Cao, Thanhtung","last_name":"Cao","first_name":"Thanhtung"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"first_name":"Tiowseng","last_name":"Tan","full_name":"Tan, Tiowseng"}],"oa_version":"None","volume":48,"date_updated":"2021-01-12T06:51:43Z","date_created":"2018-12-11T11:52:49Z","year":"2015","_id":"1578","acknowledgement":"The research of the second author is partially supported by NSF under grant DBI-0820624 and by DARPA under grants HR011-05-1-0057 and HR0011-09-006\r\n","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","department":[{"_id":"HeEd"}],"intvolume":" 48","publication_status":"published","status":"public","title":"Triangulations from topologically correct digital Voronoi diagrams"},{"publication_status":"published","title":"Gradients are shaping up","status":"public","publisher":"Cell Press","department":[{"_id":"ToBo"},{"_id":"CaHe"}],"intvolume":" 161","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1581","year":"2015","date_updated":"2022-08-25T13:56:10Z","date_created":"2018-12-11T11:52:50Z","oa_version":"None","volume":161,"author":[{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"type":"journal_article","abstract":[{"text":"In animal embryos, morphogen gradients determine tissue patterning and morphogenesis. Shyer et al. provide evidence that, during vertebrate gut formation, tissue folding generates graded activity of signals required for subsequent steps of gut growth and differentiation, thereby revealing an intriguing link between tissue morphogenesis and morphogen gradient formation.","lang":"eng"}],"publist_id":"5590","issue":"3","quality_controlled":"1","page":"431 - 432","publication":"Cell","citation":{"short":"M.T. Bollenbach, C.-P.J. Heisenberg, Cell 161 (2015) 431–432.","mla":"Bollenbach, Mark Tobias, and Carl-Philipp J. Heisenberg. “Gradients Are Shaping Up.” Cell, vol. 161, no. 3, Cell Press, 2015, pp. 431–32, doi:10.1016/j.cell.2015.04.009.","chicago":"Bollenbach, Mark Tobias, and Carl-Philipp J Heisenberg. “Gradients Are Shaping Up.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.04.009.","ama":"Bollenbach MT, Heisenberg C-PJ. Gradients are shaping up. Cell. 2015;161(3):431-432. doi:10.1016/j.cell.2015.04.009","ieee":"M. T. Bollenbach and C.-P. J. Heisenberg, “Gradients are shaping up,” Cell, vol. 161, no. 3. Cell Press, pp. 431–432, 2015.","apa":"Bollenbach, M. T., & Heisenberg, C.-P. J. (2015). Gradients are shaping up. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.04.009","ista":"Bollenbach MT, Heisenberg C-PJ. 2015. Gradients are shaping up. Cell. 161(3), 431–432."},"language":[{"iso":"eng"}],"date_published":"2015-04-23T00:00:00Z","doi":"10.1016/j.cell.2015.04.009","scopus_import":"1","day":"23","month":"04","article_processing_charge":"No"},{"day":"21","has_accepted_license":"1","scopus_import":1,"date_published":"2015-12-21T00:00:00Z","article_type":"original","publication":"Scientific Reports","citation":{"apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep18589","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","ista":"Altmeyer S, Do Y, Lai Y. 2015. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 5, 18589.","ama":"Altmeyer S, Do Y, Lai Y. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 2015;5. doi:10.1038/srep18589","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep18589.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","mla":"Altmeyer, Sebastian, et al. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports, vol. 5, 18589, Nature Publishing Group, 2015, doi:10.1038/srep18589."},"abstract":[{"text":"We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant azimuthal modes. Without external magnetic field flows are stable and pro-grade with respect to the rotation of the inner cylinder. More complex behaviors can arise when an axial or a transverse magnetic field is applied. Depending on the direction and strength of the field, multi-stable wavy states and bifurcations can occur. We uncover the phenomenon of flow pattern reversal as the strength of the magnetic field is increased through a critical value. In between the regimes of pro-grade and retrograde flow rotations, standing waves with zero angular velocities can emerge. A striking finding is that, under a transverse magnetic field, a second reversal in the flow pattern direction can occur, where the flow pattern evolves into pro-grade rotation again from a retrograde state. Flow reversal is relevant to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic field in a controlled manner, which can be realized in laboratory experiments with potential applications in the development of modern fluid devices.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:13:49Z","date_updated":"2020-07-14T12:45:03Z","checksum":"927e151674347661ce36eae2818dafdc","file_id":"5036","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":2771236,"file_name":"IST-2016-472-v1+1_srep18589.pdf","access_level":"open_access"}],"pubrep_id":"472","status":"public","title":"Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system","ddc":["530","540"],"intvolume":" 5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1589","month":"12","language":[{"iso":"eng"}],"doi":"10.1038/srep18589","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:45:03Z","publist_id":"5582","article_number":"18589","date_updated":"2021-01-12T06:51:48Z","date_created":"2018-12-11T11:52:53Z","volume":5,"author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","first_name":"Sebastian","last_name":"Altmeyer","full_name":"Altmeyer, Sebastian"},{"full_name":"Do, Younghae","first_name":"Younghae","last_name":"Do"},{"first_name":"Ying","last_name":"Lai","full_name":"Lai, Ying"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"BjHo"}],"year":"2015"},{"month":"07","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.comgeo.2015.01.004","file_date_updated":"2020-07-14T12:45:03Z","publist_id":"5587","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Elsevier","year":"2015","date_updated":"2023-02-23T10:05:22Z","date_created":"2018-12-11T11:52:51Z","volume":48,"author":[{"full_name":"Biedl, Therese","first_name":"Therese","last_name":"Biedl"},{"full_name":"Held, Martin","first_name":"Martin","last_name":"Held"},{"full_name":"Huber, Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","first_name":"Stefan","last_name":"Huber"},{"full_name":"Kaaser, Dominik","first_name":"Dominik","last_name":"Kaaser"},{"full_name":"Palfrader, Peter","first_name":"Peter","last_name":"Palfrader"}],"related_material":{"record":[{"id":"1582","status":"public","relation":"other"}]},"scopus_import":1,"day":"01","has_accepted_license":"1","page":"429 - 442","publication":"Computational Geometry: Theory and Applications","citation":{"ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 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Elsevier, pp. 429–442, 2015.","mla":"Biedl, Therese, et al. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 5, Elsevier, 2015, pp. 429–42, doi:10.1016/j.comgeo.2015.01.004.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 429–442.","chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.01.004."},"date_published":"2015-07-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights."}],"issue":"5","status":"public","ddc":["000"],"title":"Reprint of: Weighted straight skeletons in the plane","intvolume":" 48","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1584","oa_version":"Published Version","file":[{"file_id":"5292","relation":"main_file","date_updated":"2020-07-14T12:45:03Z","date_created":"2018-12-12T10:17:36Z","checksum":"5b33719a86f7f4c8e5dc62c1b6893f49","file_name":"IST-2016-475-v1+1_1-s2.0-S092577211500005X-main.pdf","access_level":"open_access","creator":"system","file_size":508379,"content_type":"application/pdf"}],"pubrep_id":"475"},{"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights."}],"intvolume":" 48","ddc":["000"],"status":"public","title":"Weighted straight skeletons in the plane","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1582","file":[{"file_id":"5215","relation":"main_file","checksum":"c1ef67f6ec925e12f73a96b8fe285ab4","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:16:28Z","access_level":"open_access","file_name":"IST-2016-474-v1+1_1-s2.0-S0925772114000807-main.pdf","creator":"system","file_size":505987,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"474","scopus_import":1,"has_accepted_license":"1","day":"01","page":"120 - 133","citation":{"chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.006.","mla":"Biedl, Therese, et al. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 2, Elsevier, 2015, pp. 120–33, doi:10.1016/j.comgeo.2014.08.006.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 120–133.","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(2), 120–133.","ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 2. Elsevier, pp. 120–133, 2015.","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 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A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 2015;115(2):243-247. doi:10.1016/j.ipl.2014.09.021","ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “A simple algorithm for computing positively weighted straight skeletons of monotone polygons,” Information Processing Letters, vol. 115, no. 2. Elsevier, pp. 243–247, 2015.","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.021","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 115(2), 243–247.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Information Processing Letters 115 (2015) 243–247.","mla":"Biedl, Therese, et al. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters, vol. 115, no. 2, Elsevier, 2015, pp. 243–47, doi:10.1016/j.ipl.2014.09.021.","chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.021."},"publication":"Information Processing Letters","page":"243 - 247","date_published":"2015-02-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1583","intvolume":" 115","title":"A simple algorithm for computing positively weighted straight skeletons of monotone polygons","status":"public","ddc":["000"],"pubrep_id":"473","oa_version":"Published Version","file":[{"checksum":"2779a648610c9b5c86d0b51a62816d23","date_created":"2018-12-12T10:18:45Z","date_updated":"2020-07-14T12:45:03Z","relation":"main_file","file_id":"5367","content_type":"application/pdf","file_size":270137,"creator":"system","access_level":"open_access","file_name":"IST-2016-473-v1+1_1-s2.0-S0020019014001987-main.pdf"}],"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We study the characteristics of straight skeletons of monotone polygonal chains and use them to devise an algorithm for computing positively weighted straight skeletons of monotone polygons. Our algorithm runs in O(nlogn) time and O(n) space, where n denotes the number of vertices of the polygon."}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1016/j.ipl.2014.09.021","language":[{"iso":"eng"}],"month":"02","year":"2015","publisher":"Elsevier","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"last_name":"Biedl","first_name":"Therese","full_name":"Biedl, Therese"},{"full_name":"Held, Martin","first_name":"Martin","last_name":"Held"},{"full_name":"Huber, Stefan","first_name":"Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814"},{"full_name":"Kaaser, Dominik","last_name":"Kaaser","first_name":"Dominik"},{"last_name":"Palfrader","first_name":"Peter","full_name":"Palfrader, Peter"}],"volume":115,"date_updated":"2021-01-12T06:51:45Z","date_created":"2018-12-11T11:52:51Z","publist_id":"5588","file_date_updated":"2020-07-14T12:45:03Z"},{"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1511.03585"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03585"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.92.062506","month":"12","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2015","date_updated":"2021-01-12T06:51:47Z","date_created":"2018-12-11T11:52:53Z","volume":92,"author":[{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"},{"id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","first_name":"Laleh","full_name":"Safari, Laleh"},{"full_name":"Antognini, Aldo","last_name":"Antognini","first_name":"Aldo"},{"last_name":"Indelicato","first_name":"Paul","full_name":"Indelicato, Paul"},{"first_name":"Randolf","last_name":"Pohl","full_name":"Pohl, Randolf"},{"full_name":"Santos, José","last_name":"Santos","first_name":"José"}],"article_number":"062506","publist_id":"5584","ec_funded":1,"article_type":"original","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","citation":{"chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Aldo Antognini, Paul Indelicato, Randolf Pohl, and José Santos. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.062506.","mla":"Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:10.1103/PhysRevA.92.062506.","short":"P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 92 (2015).","ista":"Amaro P, Fratini F, Safari L, Antognini A, Indelicato P, Pohl R, Santos J. 2015. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 92(6), 062506.","ieee":"P. Amaro et al., “Quantum interference shifts in laser spectroscopy with elliptical polarization,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6. American Physical Society, 2015.","apa":"Amaro, P., Fratini, F., Safari, L., Antognini, A., Indelicato, P., Pohl, R., & Santos, J. (2015). Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.92.062506","ama":"Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 2015;92(6). doi:10.1103/PhysRevA.92.062506"},"date_published":"2015-12-31T00:00:00Z","scopus_import":1,"day":"31","article_processing_charge":"No","status":"public","title":"Quantum interference shifts in laser spectroscopy with elliptical polarization","intvolume":" 92","_id":"1587","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme."}],"issue":"6"},{"year":"2015","_id":"1588","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows","publication_status":"published","department":[{"_id":"BjHo"}],"intvolume":" 92","publisher":"American Physical Society","author":[{"full_name":"Altmeyer, Sebastian","first_name":"Sebastian","last_name":"Altmeyer","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203"},{"first_name":"Younghae","last_name":"Do","full_name":"Do, Younghae"},{"full_name":"Lai, Ying","last_name":"Lai","first_name":"Ying"}],"date_updated":"2021-01-12T06:51:47Z","date_created":"2018-12-11T11:52:53Z","volume":92,"oa_version":"None","article_number":"053018","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate the Taylor-Couette system where the radius ratio is close to unity. Systematically increasing the Reynolds number, we observe a number of previously known transitions, such as one from the classical Taylor vortex flow (TVF) to wavy vortex flow (WVF) and the transition to fully developed turbulence. Prior to the onset of turbulence, we observe intermittent bursting patterns of localized turbulent patches, confirming the experimentally observed pattern of very short wavelength bursts (VSWBs). A striking finding is that, for a Reynolds number larger than that for the onset of VSWBs, a new type of intermittently bursting behavior emerges: patterns of azimuthally closed rings of various orders. We call them ring-bursting patterns, which surround the cylinder completely but remain localized and separated in the axial direction through nonturbulent wavy structures. We employ a number of quantitative measures including the cross-flow energy to characterize the ring-bursting patterns and to distinguish them from the background flow. These patterns are interesting because they do not occur in the wide-gap Taylor-Couette flow systems. The narrow-gap regime is less studied but certainly deserves further attention to gain deeper insights into complex flow dynamics in fluids."}],"publist_id":"5583","issue":"5","publication":"Physical Review E","citation":{"chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.92.053018.","short":"S. Altmeyer, Y. Do, Y. Lai, Physical Review E 92 (2015).","mla":"Altmeyer, Sebastian, et al. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review E, vol. 92, no. 5, 053018, American Physical Society, 2015, doi:10.1103/PhysRevE.92.053018.","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows,” Physical Review E, vol. 92, no. 5. American Physical Society, 2015.","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.92.053018","ista":"Altmeyer S, Do Y, Lai Y. 2015. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 92(5), 053018.","ama":"Altmeyer S, Do Y, Lai Y. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 2015;92(5). doi:10.1103/PhysRevE.92.053018"},"quality_controlled":"1","date_published":"2015-11-24T00:00:00Z","doi":"10.1103/PhysRevE.92.053018","language":[{"iso":"eng"}],"scopus_import":1,"day":"24","month":"11"},{"doi":"10.1016/j.tibtech.2015.03.009","date_published":"2015-06-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Angermayr, Andreas, Aleix Gorchs, and Klaas Hellingwerf. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology. Elsevier, 2015. https://doi.org/10.1016/j.tibtech.2015.03.009.","short":"A. Angermayr, A. Gorchs, K. Hellingwerf, Trends in Biotechnology 33 (2015) 352–361.","mla":"Angermayr, Andreas, et al. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology, vol. 33, no. 6, Elsevier, 2015, pp. 352–61, doi:10.1016/j.tibtech.2015.03.009.","apa":"Angermayr, A., Gorchs, A., & Hellingwerf, K. (2015). Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. Elsevier. https://doi.org/10.1016/j.tibtech.2015.03.009","ieee":"A. Angermayr, A. Gorchs, and K. Hellingwerf, “Metabolic engineering of cyanobacteria for the synthesis of commodity products,” Trends in Biotechnology, vol. 33, no. 6. Elsevier, pp. 352–361, 2015.","ista":"Angermayr A, Gorchs A, Hellingwerf K. 2015. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 33(6), 352–361.","ama":"Angermayr A, Gorchs A, Hellingwerf K. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 2015;33(6):352-361. doi:10.1016/j.tibtech.2015.03.009"},"publication":"Trends in Biotechnology","page":"352 - 361","quality_controlled":"1","month":"06","day":"01","scopus_import":1,"author":[{"last_name":"Angermayr","first_name":"Andreas","orcid":"0000-0001-8619-2223","id":"4677C796-F248-11E8-B48F-1D18A9856A87","full_name":"Angermayr, Andreas"},{"full_name":"Gorchs, Aleix","first_name":"Aleix","last_name":"Gorchs"},{"last_name":"Hellingwerf","first_name":"Klaas","full_name":"Hellingwerf, Klaas"}],"volume":33,"oa_version":"None","date_updated":"2021-01-12T06:51:46Z","date_created":"2018-12-11T11:52:52Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1586","year":"2015","publisher":"Elsevier","intvolume":" 33","department":[{"_id":"ToBo"}],"title":"Metabolic engineering of cyanobacteria for the synthesis of commodity products","publication_status":"published","status":"public","issue":"6","publist_id":"5585","abstract":[{"text":"Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO2, light, and water directly. Such cyanobacterial 'cell factories' are constructed to produce biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers and synthetic biologists allow the modification of the intermediary metabolism at various branching points, expanding the product range. The new biosynthesis routes 'tap' the metabolism ever more efficiently, particularly through the engineering of driving forces and utilization of cofactors generated during the light reactions of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling ultimately allow an almost-complete allocation of fixed carbon to product above biomass.","lang":"eng"}],"type":"journal_article"},{"type":"journal_article","publist_id":"5586","issue":"6","abstract":[{"lang":"eng","text":"In this paper, we consider the fluctuation of mutual information statistics of a multiple input multiple output channel communication systems without assuming that the entries of the channel matrix have zero pseudovariance. To this end, we also establish a central limit theorem of the linear spectral statistics for sample covariance matrices under general moment conditions by removing the restrictions imposed on the second moment and fourth moment on the matrix entries in Bai and Silverstein (2004)."}],"publisher":"IEEE","intvolume":" 61","department":[{"_id":"LaEr"}],"title":"Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices","publication_status":"published","status":"public","_id":"1585","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"G. Pan was supported by MOE Tier 2 under Grant 2014-T2-2-060 and in part by Tier 1 under Grant RG25/14 through the Nanyang Technological University, Singapore. W. Zhou was supported by the National University of Singapore, Singapore, under Grant R-155-000-131-112.\r\n","oa_version":"None","volume":61,"date_updated":"2021-01-12T06:51:46Z","date_created":"2018-12-11T11:52:52Z","author":[{"orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","first_name":"Zhigang","full_name":"Bao, Zhigang"},{"last_name":"Pan","first_name":"Guangming","full_name":"Pan, Guangming"},{"first_name":"Wang","last_name":"Zhou","full_name":"Zhou, Wang"}],"scopus_import":1,"day":"01","month":"06","page":"3413 - 3426","quality_controlled":"1","citation":{"chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory. IEEE, 2015. https://doi.org/10.1109/TIT.2015.2421894.","short":"Z. Bao, G. Pan, W. Zhou, IEEE Transactions on Information Theory 61 (2015) 3413–3426.","mla":"Bao, Zhigang, et al. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory, vol. 61, no. 6, IEEE, 2015, pp. 3413–26, doi:10.1109/TIT.2015.2421894.","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2015.2421894","ieee":"Z. Bao, G. Pan, and W. Zhou, “Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices,” IEEE Transactions on Information Theory, vol. 61, no. 6. IEEE, pp. 3413–3426, 2015.","ista":"Bao Z, Pan G, Zhou W. 2015. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 61(6), 3413–3426.","ama":"Bao Z, Pan G, Zhou W. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 2015;61(6):3413-3426. doi:10.1109/TIT.2015.2421894"},"publication":"IEEE Transactions on Information Theory","language":[{"iso":"eng"}],"date_published":"2015-06-01T00:00:00Z","doi":"10.1109/TIT.2015.2421894"},{"author":[{"last_name":"Žádníková","first_name":"Petra","full_name":"Žádníková, Petra"},{"full_name":"Smet, Dajo","last_name":"Smet","first_name":"Dajo"},{"full_name":"Zhu, Qiang","last_name":"Zhu","first_name":"Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van Der Straeten, Dominique","first_name":"Dominique","last_name":"Van Der Straeten"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"volume":6,"date_created":"2018-12-11T11:52:55Z","date_updated":"2021-01-12T06:51:50Z","year":"2015","department":[{"_id":"EvBe"}],"publisher":"Frontiers Research Foundation","publication_status":"published","publist_id":"5578","ec_funded":1,"file_date_updated":"2020-07-14T12:45:03Z","doi":"10.3389/fpls.2015.00218","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"04","pubrep_id":"471","oa_version":"Published Version","file":[{"checksum":"c454d642e18dfa86820b97a86cd6d3cc","date_updated":"2020-07-14T12:45:03Z","date_created":"2018-12-12T10:15:23Z","file_id":"5142","relation":"main_file","creator":"system","file_size":965690,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-471-v1+1_fpls-06-00218.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1593","intvolume":" 6","status":"public","ddc":["570"],"title":"Strategies of seedlings to overcome their sessile nature: Auxin in mobility control","issue":"4","abstract":[{"text":"Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component.","lang":"eng"}],"type":"journal_article","date_published":"2015-04-14T00:00:00Z","citation":{"chicago":"Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fpls.2015.00218.","short":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers in Plant Science 6 (2015).","mla":"Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science, vol. 6, no. 4, Frontiers Research Foundation, 2015, doi:10.3389/fpls.2015.00218.","apa":"Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., & Benková, E. (2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.00218","ieee":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies of seedlings to overcome their sessile nature: Auxin in mobility control,” Frontiers in Plant Science, vol. 6, no. 4. Frontiers Research Foundation, 2015.","ista":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 6(4).","ama":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 2015;6(4). doi:10.3389/fpls.2015.00218"},"publication":"Frontiers in Plant Science","has_accepted_license":"1","day":"14","scopus_import":1},{"oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:03Z","date_created":"2018-12-12T10:08:36Z","checksum":"685f91bd077a951ba067d42cce75409e","relation":"main_file","file_id":"4697","content_type":"application/pdf","file_size":330135,"creator":"system","file_name":"IST-2016-594-v1+1_HTCylinder_GD_Revision.pdf","access_level":"open_access"}],"pubrep_id":"594","intvolume":" 9411","title":"Hanani-Tutte for radial planarity","ddc":["510"],"status":"public","_id":"1595","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2015-11-27T00:00:00Z","page":"99 - 110","citation":{"ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. In: Vol 9411. Springer; 2015:99-110. doi:10.1007/978-3-319-27261-0_9","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2015). Hanani-Tutte for radial planarity (Vol. 9411, pp. 99–110). Presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA: Springer. https://doi.org/10.1007/978-3-319-27261-0_9","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA, 2015, vol. 9411, pp. 99–110.","ista":"Fulek R, Pelsmajer M, Schaefer M. 2015. Hanani-Tutte for radial planarity. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411, 99–110.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2015, pp. 99–110.","mla":"Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity. Vol. 9411, Springer, 2015, pp. 99–110, doi:10.1007/978-3-319-27261-0_9.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity,” 9411:99–110. Springer, 2015. https://doi.org/10.1007/978-3-319-27261-0_9."},"has_accepted_license":"1","day":"27","scopus_import":1,"volume":9411,"date_updated":"2023-02-21T16:23:36Z","date_created":"2018-12-11T11:52:55Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"1113"},{"status":"public","relation":"later_version","id":"1164"}]},"author":[{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav","full_name":"Fulek, Radoslav"},{"last_name":"Pelsmajer","first_name":"Michael","full_name":"Pelsmajer, Michael"},{"full_name":"Schaefer, Marcus","last_name":"Schaefer","first_name":"Marcus"}],"publisher":"Springer","department":[{"_id":"UlWa"}],"publication_status":"published","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].","year":"2015","publist_id":"5576","ec_funded":1,"file_date_updated":"2020-07-14T12:45:03Z","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-27261-0_9","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2015-09-26","start_date":"2015-09-24","location":"Los Angeles, CA, USA"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"month":"11"},{"author":[{"last_name":"Aichholzer","first_name":"Oswin","full_name":"Aichholzer, Oswin"},{"full_name":"Biedl, Therese","first_name":"Therese","last_name":"Biedl"},{"full_name":"Hackl, Thomas","last_name":"Hackl","first_name":"Thomas"},{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","first_name":"Stefan","last_name":"Huber","full_name":"Huber, Stefan"},{"first_name":"Peter","last_name":"Palfrader","full_name":"Palfrader, Peter"},{"full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber","first_name":"Birgit"}],"date_created":"2018-12-11T11:52:54Z","date_updated":"2022-01-28T09:10:37Z","volume":9411,"year":"2015","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publist_id":"5581","conference":{"end_date":"2015-09-26","start_date":"2015-09-24","location":"Los Angeles, CA, United States","name":"GD: International Symposium on Graph Drawing"},"doi":"10.1007/978-3-319-27261-0_28","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1508.01076","open_access":"1"}],"oa":1,"quality_controlled":"1","month":"11","publication_identifier":{"isbn":["978-3-319-27260-3"],"eisbn":["978-3-319-27261-0"]},"oa_version":"Preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1590","title":"Representing directed trees as straight skeletons","status":"public","intvolume":" 9411","abstract":[{"text":"The straight skeleton of a polygon is the geometric graph obtained by tracing the vertices during a mitered offsetting process. It is known that the straight skeleton of a simple polygon is a tree, and one can naturally derive directions on the edges of the tree from the propagation of the shrinking process. In this paper, we ask the reverse question: Given a tree with directed edges, can it be the straight skeleton of a polygon? And if so, can we find a suitable simple polygon? We answer these questions for all directed trees where the order of edges around each node is fixed.","lang":"eng"}],"type":"book_chapter","alternative_title":["LNCS"],"date_published":"2015-11-27T00:00:00Z","publication":"Graph Drawing and Network Visualization","citation":{"ama":"Aichholzer O, Biedl T, Hackl T, et al. Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:335-347. doi:10.1007/978-3-319-27261-0_28","ista":"Aichholzer O, Biedl T, Hackl T, Held M, Huber S, Palfrader P, Vogtenhuber B. 2015.Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 335–347.","apa":"Aichholzer, O., Biedl, T., Hackl, T., Held, M., Huber, S., Palfrader, P., & Vogtenhuber, B. (2015). Representing directed trees as straight skeletons. In Graph Drawing and Network Visualization (Vol. 9411, pp. 335–347). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_28","ieee":"O. Aichholzer et al., “Representing directed trees as straight skeletons,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–347.","mla":"Aichholzer, Oswin, et al. “Representing Directed Trees as Straight Skeletons.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–47, doi:10.1007/978-3-319-27261-0_28.","short":"O. Aichholzer, T. Biedl, T. Hackl, M. Held, S. Huber, P. Palfrader, B. Vogtenhuber, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 335–347.","chicago":"Aichholzer, Oswin, Therese Biedl, Thomas Hackl, Martin Held, Stefan Huber, Peter Palfrader, and Birgit Vogtenhuber. “Representing Directed Trees as Straight Skeletons.” In Graph Drawing and Network Visualization, 9411:335–47. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_28."},"page":"335 - 347","day":"27","article_processing_charge":"No","scopus_import":"1"},{"author":[{"first_name":"Vojtěch","last_name":"Forejt","full_name":"Forejt, Vojtěch"},{"full_name":"Krčál, Jan","first_name":"Jan","last_name":"Krčál"},{"full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:52:55Z","date_updated":"2021-01-12T06:51:50Z","volume":9450,"year":"2015","acknowledgement":"This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the Czech Science Foundation under grant agreement P202/12/G061, by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the CDZ project 1023 (CAP), by the CAS/SAFEA International Partnership Program for Creative Research Teams, by the EPSRC grant EP/M023656/1, by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734, by the Austrian Science Fund (FWF) S11407-N23 (RiSE/SHiNE), and by the ERC Start Grant (279307: Graph Games).\r\n","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Springer","publist_id":"5577","ec_funded":1,"conference":{"name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning","start_date":"2015-11-24","location":"Suva, Fiji","end_date":"2015-11-28"},"doi":"10.1007/978-3-662-48899-7_12","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"month":"11","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1594","status":"public","title":"Controller synthesis for MDPs and frequency LTL\\GU","intvolume":" 9450","abstract":[{"text":"Quantitative extensions of temporal logics have recently attracted significant attention. In this work, we study frequency LTL (fLTL), an extension of LTL which allows to speak about frequencies of events along an execution. Such an extension is particularly useful for probabilistic systems that often cannot fulfil strict qualitative guarantees on the behaviour. It has been recently shown that controller synthesis for Markov decision processes and fLTL is decidable when all the bounds on frequencies are 1. As a step towards a complete quantitative solution, we show that the problem is decidable for the fragment fLTL\\GU, where U does not occur in the scope of G (but still F can). Our solution is based on a novel translation of such quantitative formulae into equivalent deterministic automata.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2015-11-22T00:00:00Z","citation":{"ama":"Forejt V, Krčál J, Kretinsky J. Controller synthesis for MDPs and frequency LTL\\GU. In: Vol 9450. Springer; 2015:162-177. doi:10.1007/978-3-662-48899-7_12","ieee":"V. Forejt, J. Krčál, and J. Kretinsky, “Controller synthesis for MDPs and frequency LTL\\GU,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji, 2015, vol. 9450, pp. 162–177.","apa":"Forejt, V., Krčál, J., & Kretinsky, J. (2015). Controller synthesis for MDPs and frequency LTL\\GU (Vol. 9450, pp. 162–177). Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji: Springer. https://doi.org/10.1007/978-3-662-48899-7_12","ista":"Forejt V, Krčál J, Kretinsky J. 2015. Controller synthesis for MDPs and frequency LTL\\GU. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 9450, 162–177.","short":"V. Forejt, J. Krčál, J. Kretinsky, in:, Springer, 2015, pp. 162–177.","mla":"Forejt, Vojtěch, et al. Controller Synthesis for MDPs and Frequency LTL\\GU. Vol. 9450, Springer, 2015, pp. 162–77, doi:10.1007/978-3-662-48899-7_12.","chicago":"Forejt, Vojtěch, Jan Krčál, and Jan Kretinsky. “Controller Synthesis for MDPs and Frequency LTL\\GU,” 9450:162–77. Springer, 2015. https://doi.org/10.1007/978-3-662-48899-7_12."},"page":"162 - 177","day":"22","scopus_import":1},{"alternative_title":["LNCS"],"type":"book_chapter","abstract":[{"lang":"eng","text":"Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon in the plane with the stacking order. The collection C forms a visibility clique if for everyi < j the intersection Ci and (Ci ∩ Cj)\\⋃i<l<jCl =∅.elements that are stacked between them, i.e., We show that if C forms a visibility clique its size is bounded from above by O(k4) thereby improving the upper bound of 22k from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the size of a visibility clique for homothetes of a convex (not necessarily regular) k-gon."}],"status":"public","title":"Vertical visibility among parallel polygons in three dimensions","ddc":["510"],"intvolume":" 9411","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1596","oa_version":"Submitted Version","file":[{"date_created":"2018-12-12T10:17:06Z","date_updated":"2020-07-14T12:45:04Z","checksum":"eec04f86c5921d04f025d5791db9b965","file_id":"5258","relation":"main_file","creator":"system","file_size":312992,"content_type":"application/pdf","file_name":"IST-2016-595-v1+1_VerticalVisibilityGDRevision.pdf","access_level":"open_access"}],"pubrep_id":"595","scopus_import":"1","day":"27","article_processing_charge":"No","has_accepted_license":"1","page":"373 - 379","publication":"Graph Drawing and Network Visualization","citation":{"chicago":"Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” In Graph Drawing and Network Visualization, 9411:373–79. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_31.","short":"R. Fulek, R. Radoičić, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 373–379.","mla":"Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–79, doi:10.1007/978-3-319-27261-0_31.","apa":"Fulek, R., & Radoičić, R. (2015). Vertical visibility among parallel polygons in three dimensions. In Graph Drawing and Network Visualization (Vol. 9411, pp. 373–379). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_31","ieee":"R. Fulek and R. Radoičić, “Vertical visibility among parallel polygons in three dimensions,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–379.","ista":"Fulek R, Radoičić R. 2015.Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 373–379.","ama":"Fulek R, Radoičić R. Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:373-379. doi:10.1007/978-3-319-27261-0_31"},"date_published":"2015-11-27T00:00:00Z","file_date_updated":"2020-07-14T12:45:04Z","ec_funded":1,"publist_id":"5575","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"year":"2015","date_updated":"2022-01-28T09:20:50Z","date_created":"2018-12-11T11:52:56Z","volume":9411,"author":[{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav","full_name":"Fulek, Radoslav"},{"first_name":"Radoš","last_name":"Radoičić","full_name":"Radoičić, Radoš"}],"month":"11","publication_identifier":{"isbn":["978-3-319-27260-3"]},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2015-09-26","start_date":"2015-09-24","location":"Los Angeles, CA, United States"},"doi":"10.1007/978-3-319-27261-0_31"},{"language":[{"iso":"eng"}],"conference":{"name":"CAV: Computer Aided Verification","end_date":"2015-07-24","start_date":"2015-07-18","location":"San Francisco, CA, United States"},"doi":"10.1007/978-3-319-21690-4_31","quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"oa":1,"month":"07","date_updated":"2021-01-12T06:51:54Z","date_created":"2018-12-11T11:52:57Z","volume":9206,"author":[{"last_name":"Babiak","first_name":"Tomáš","full_name":"Babiak, Tomáš"},{"full_name":"Blahoudek, František","first_name":"František","last_name":"Blahoudek"},{"last_name":"Duret Lutz","first_name":"Alexandre","full_name":"Duret Lutz, Alexandre"},{"first_name":"Joachim","last_name":"Klein","full_name":"Klein, Joachim"},{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan","full_name":"Kretinsky, Jan"},{"full_name":"Mueller, Daniel","first_name":"Daniel","last_name":"Mueller"},{"last_name":"Parker","first_name":"David","full_name":"Parker, David"},{"full_name":"Strejček, Jan","first_name":"Jan","last_name":"Strejček"}],"publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Springer","year":"2015","file_date_updated":"2020-07-14T12:45:04Z","publist_id":"5566","ec_funded":1,"date_published":"2015-07-16T00:00:00Z","page":"479 - 486","citation":{"short":"T. Babiak, F. Blahoudek, A. Duret Lutz, J. Klein, J. Kretinsky, D. Mueller, D. Parker, J. Strejček, in:, Springer, 2015, pp. 479–486.","mla":"Babiak, Tomáš, et al. The Hanoi Omega-Automata Format. Vol. 9206, Springer, 2015, pp. 479–86, doi:10.1007/978-3-319-21690-4_31.","chicago":"Babiak, Tomáš, František Blahoudek, Alexandre Duret Lutz, Joachim Klein, Jan Kretinsky, Daniel Mueller, David Parker, and Jan Strejček. “The Hanoi Omega-Automata Format,” 9206:479–86. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_31.","ama":"Babiak T, Blahoudek F, Duret Lutz A, et al. The Hanoi omega-automata format. In: Vol 9206. Springer; 2015:479-486. doi:10.1007/978-3-319-21690-4_31","ieee":"T. Babiak et al., “The Hanoi omega-automata format,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 479–486.","apa":"Babiak, T., Blahoudek, F., Duret Lutz, A., Klein, J., Kretinsky, J., Mueller, D., … Strejček, J. (2015). The Hanoi omega-automata format (Vol. 9206, pp. 479–486). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_31","ista":"Babiak T, Blahoudek F, Duret Lutz A, Klein J, Kretinsky J, Mueller D, Parker D, Strejček J. 2015. The Hanoi omega-automata format. CAV: Computer Aided Verification, LNCS, vol. 9206, 479–486."},"day":"16","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"file":[{"date_updated":"2020-07-14T12:45:04Z","date_created":"2020-05-15T08:38:12Z","checksum":"5885236fa88a439baba9ac6f3e801e93","relation":"main_file","file_id":"7850","content_type":"application/pdf","file_size":1651779,"creator":"dernst","file_name":"2015_CAV_Babiak.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","ddc":["000"],"title":"The Hanoi omega-automata format","status":"public","intvolume":" 9206","_id":"1601","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We propose a flexible exchange format for ω-automata, as typically used in formal verification, and implement support for it in a range of established tools. Our aim is to simplify the interaction of tools, helping the research community to build upon other people’s work. A key feature of the format is the use of very generic acceptance conditions, specified by Boolean combinations of acceptance primitives, rather than being limited to common cases such as Büchi, Streett, or Rabin. Such flexibility in the choice of acceptance conditions can be exploited in applications, for example in probabilistic model checking, and furthermore encourages the development of acceptance-agnostic tools for automata manipulations. The format allows acceptance conditions that are either state-based or transition-based, and also supports alternating automata."}],"alternative_title":["LNCS"],"type":"conference"},{"oa_version":"Submitted Version","file":[{"file_name":"2015_LNCS_Bogomolov.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1053207,"file_id":"7851","relation":"main_file","date_created":"2020-05-15T08:43:19Z","date_updated":"2020-07-14T12:45:05Z","checksum":"3aab260f3f34641d622030ba22645b3e"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1605","intvolume":" 9434","status":"public","ddc":["000"],"title":"Abstraction-based parameter synthesis for multiaffine systems","abstract":[{"text":"Multiaffine hybrid automata (MHA) represent a powerful formalism to model complex dynamical systems. This formalism is particularly suited for the representation of biological systems which often exhibit highly non-linear behavior. In this paper, we consider the problem of parameter identification for MHA. We present an abstraction of MHA based on linear hybrid automata, which can be analyzed by the SpaceEx model checker. This abstraction enables a precise handling of time-dependent properties. We demonstrate the potential of our approach on a model of a genetic regulatory network and a myocyte model.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2015-11-28T00:00:00Z","citation":{"ista":"Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference, LNCS, vol. 9434, 19–35.","ieee":"S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu, “Abstraction-based parameter synthesis for multiaffine systems,” presented at the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35.","apa":"Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., & Grosu, R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol. 9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_2","ama":"Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35. doi:10.1007/978-3-319-26287-1_2","chicago":"Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,” 9434:19–35. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_2.","mla":"Bogomolov, Sergiy, et al. Abstraction-Based Parameter Synthesis for Multiaffine Systems. Vol. 9434, Springer, 2015, pp. 19–35, doi:10.1007/978-3-319-26287-1_2.","short":"S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:, Springer, 2015, pp. 19–35."},"page":"19 - 35","article_processing_charge":"No","has_accepted_license":"1","day":"28","scopus_import":1,"author":[{"full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy"},{"orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"last_name":"Batt","first_name":"Grégory","full_name":"Batt, Grégory"},{"first_name":"Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui"},{"full_name":"Grosu, Radu","first_name":"Radu","last_name":"Grosu"}],"volume":9434,"date_updated":"2021-01-12T06:51:56Z","date_created":"2018-12-11T11:52:59Z","year":"2015","acknowledgement":"This work was partly supported by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS, http://www.avacs.org/).","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","publist_id":"5561","ec_funded":1,"file_date_updated":"2020-07-14T12:45:05Z","doi":"10.1007/978-3-319-26287-1_2","conference":{"end_date":"2015-11-19","start_date":"2015-11-17","location":"Haifa, Israel","name":"HVC: Haifa Verification Conference"},"language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","month":"11"},{"department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","year":"2015","volume":9333,"date_created":"2018-12-11T11:52:59Z","date_updated":"2022-02-01T14:52:59Z","author":[{"first_name":"Luan","last_name":"Nguyen","full_name":"Nguyen, Luan"},{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling"},{"first_name":"Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"full_name":"Johnson, Taylor","last_name":"Johnson","first_name":"Taylor"}],"ec_funded":1,"publist_id":"5562","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-23820-3_19","conference":{"name":"RV: Runtime Verification","end_date":"2015-09-25","location":"Vienna, Austria","start_date":"2015-09-22"},"publication_identifier":{"isbn":["978-3-319-23819-7"]},"month":"11","intvolume":" 9333","status":"public","title":"Runtime verification for hybrid analysis tools","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1606","oa_version":"None","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"In this paper, we present the first steps toward a runtime verification framework for monitoring hybrid and cyber-physical systems (CPS) development tools based on randomized differential testing. The development tools include hybrid systems reachability analysis tools, model-based development environments like Simulink/Stateflow (SLSF), etc. First, hybrid automaton models are randomly generated. Next, these hybrid automaton models are translated to a number of different tools (currently, SpaceEx, dReach, Flow*, HyCreate, and the MathWorks’ Simulink/Stateflow) using the HyST source transformation and translation tool. Then, the hybrid automaton models are executed in the different tools and their outputs are parsed. The final step is the differential comparison: the outputs of the different tools are compared. If the results do not agree (in the sense that an analysis or verification result from one tool does not match that of another tool, ignoring timeouts, etc.), a candidate bug is flagged and the model is saved for future analysis by the user. The process then repeats and the monitoring continues until the user terminates the process. We present preliminary results that have been useful in identifying a few bugs in the analysis methods of different development tools, and in an earlier version of HyST.","lang":"eng"}],"page":"281 - 286","citation":{"ama":"Nguyen L, Schilling C, Bogomolov S, Johnson T. Runtime verification for hybrid analysis tools. In: 6th International Conference. Vol 9333. Springer Nature; 2015:281-286. doi:10.1007/978-3-319-23820-3_19","ieee":"L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, “Runtime verification for hybrid analysis tools,” in 6th International Conference, Vienna, Austria, 2015, vol. 9333, pp. 281–286.","apa":"Nguyen, L., Schilling, C., Bogomolov, S., & Johnson, T. (2015). Runtime verification for hybrid analysis tools. In 6th International Conference (Vol. 9333, pp. 281–286). Vienna, Austria: Springer Nature. https://doi.org/10.1007/978-3-319-23820-3_19","ista":"Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Runtime verification for hybrid analysis tools. 6th International Conference. RV: Runtime Verification, LNCS, vol. 9333, 281–286.","short":"L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, in:, 6th International Conference, Springer Nature, 2015, pp. 281–286.","mla":"Nguyen, Luan, et al. “Runtime Verification for Hybrid Analysis Tools.” 6th International Conference, vol. 9333, Springer Nature, 2015, pp. 281–86, doi:10.1007/978-3-319-23820-3_19.","chicago":"Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson. “Runtime Verification for Hybrid Analysis Tools.” In 6th International Conference, 9333:281–86. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-23820-3_19."},"publication":"6th International Conference","date_published":"2015-11-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15"},{"conference":{"start_date":"2015-07-06","location":"Kyoto, Japan","end_date":"2015-07-10","name":"ICALP: Automata, Languages and Programming"},"doi":"10.1007/978-3-662-47666-6_9","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.04844"}],"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"month":"06","publication_identifier":{"isbn":["978-3-662-47665-9"]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"last_name":"Vardi","first_name":"Moshe","full_name":"Vardi, Moshe"}],"date_created":"2018-12-11T11:53:00Z","date_updated":"2022-02-01T15:04:44Z","volume":9135,"year":"2015","acknowledgement":"This research was supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","publist_id":"5557","ec_funded":1,"date_published":"2015-06-20T00:00:00Z","publication":"42nd International Colloquium","citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity of Synthesis from Probabilistic Components.” In 42nd International Colloquium, 9135:108–20. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_9.","short":"K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer Nature, 2015, pp. 108–120.","mla":"Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic Components.” 42nd International Colloquium, vol. 9135, Springer Nature, 2015, pp. 108–20, doi:10.1007/978-3-662-47666-6_9.","ieee":"K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic components,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol. 9135, pp. 108–120.","apa":"Chatterjee, K., Doyen, L., & Vardi, M. (2015). The complexity of synthesis from probabilistic components. In 42nd International Colloquium (Vol. 9135, pp. 108–120). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_9","ista":"Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic components. 42nd International Colloquium. ICALP: Automata, Languages and Programming, LNCS, vol. 9135, 108–120.","ama":"Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic components. In: 42nd International Colloquium. Vol 9135. Springer Nature; 2015:108-120. doi:10.1007/978-3-662-47666-6_9"},"page":"108 - 120","day":"20","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1609","status":"public","title":"The complexity of synthesis from probabilistic components","intvolume":" 9135","abstract":[{"lang":"eng","text":"The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is “constructed from scratch” rather than composed from reusable components. However, this is rare in practice, and almost every non-trivial software system relies heavily on the use of libraries of reusable components. Recently, Lustig and Vardi introduced dataflow and controlflow synthesis from libraries of reusable components. They proved that dataflow synthesis is undecidable, while controlflow synthesis is decidable. The problem of controlflow synthesis from libraries of probabilistic components was considered by Nain, Lustig and Vardi, and was shown to be decidable for qualitative analysis (that asks that the specification be satisfied with probability 1). Our main contribution for controlflow synthesis from probabilistic components is to establish better complexity bounds for the qualitative analysis problem, and to show that the more general quantitative problem is undecidable. For the qualitative analysis, we show that the problem (i) is EXPTIME-complete when the specification is given as a deterministic parity word automaton, improving the previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games hard, when the specification is given directly as a parity condition on the components, improving the previously known EXPTIME upper bound."}],"type":"conference","alternative_title":["LNCS"]},{"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Cell Press","year":"2015","acknowledgement":"This work was supported by the Max Planck Society (N.B. and H.E.), the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.), the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody. We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler for valuable advice and excellent technical support. We are grateful to the staff at the animal facility of the Max Planck Institute of Experimental Medicine for mouse husbandry.","date_created":"2018-12-11T11:53:02Z","date_updated":"2021-01-12T06:52:01Z","volume":13,"author":[{"full_name":"Hammer, Matthieu","first_name":"Matthieu","last_name":"Hammer"},{"full_name":"Krueger Burg, Dilja","last_name":"Krueger Burg","first_name":"Dilja"},{"full_name":"Tuffy, Liam","first_name":"Liam","last_name":"Tuffy"},{"last_name":"Cooper","first_name":"Benjamin","full_name":"Cooper, Benjamin"},{"full_name":"Taschenberger, Holger","last_name":"Taschenberger","first_name":"Holger"},{"full_name":"Goswami, Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","last_name":"Goswami","first_name":"Sarit"},{"last_name":"Ehrenreich","first_name":"Hannelore","full_name":"Ehrenreich, Hannelore"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"full_name":"Varoqueaux, Frederique","first_name":"Frederique","last_name":"Varoqueaux"},{"first_name":"Jeong","last_name":"Rhee","full_name":"Rhee, Jeong"},{"last_name":"Brose","first_name":"Nils","full_name":"Brose, Nils"}],"file_date_updated":"2020-07-14T12:45:07Z","publist_id":"5551","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2015.09.011","month":"10","ddc":["570"],"title":"Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism","status":"public","intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1615","oa_version":"Published Version","file":[{"creator":"system","file_size":2314406,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf","checksum":"44d30fbb543774b076b4938bd36af9d7","date_created":"2018-12-12T10:13:23Z","date_updated":"2020-07-14T12:45:07Z","file_id":"5005","relation":"main_file"}],"pubrep_id":"470","type":"journal_article","abstract":[{"lang":"eng","text":"Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches."}],"issue":"3","page":"516 - 523","publication":"Cell Reports","citation":{"mla":"Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports, vol. 13, no. 3, Cell Press, 2015, pp. 516–23, doi:10.1016/j.celrep.2015.09.011.","short":"M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami, H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015) 516–523.","chicago":"Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports. Cell Press, 2015. https://doi.org/10.1016/j.celrep.2015.09.011.","ama":"Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 2015;13(3):516-523. doi:10.1016/j.celrep.2015.09.011","ista":"Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 13(3), 516–523.","ieee":"M. Hammer et al., “Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism,” Cell Reports, vol. 13, no. 3. Cell Press, pp. 516–523, 2015.","apa":"Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami, S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2015.09.011"},"date_published":"2015-10-20T00:00:00Z","scopus_import":1,"day":"20","has_accepted_license":"1"},{"has_accepted_license":"1","day":"27","scopus_import":1,"date_published":"2015-01-27T00:00:00Z","citation":{"ama":"Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 2015;112(4):1220-1225. doi:10.1073/pnas.1412996112","ieee":"M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells,” PNAS, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.","apa":"Strüber, M., Jonas, P. M., & Bartos, M. (2015). Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1412996112","ista":"Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 112(4), 1220–1225.","short":"M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.","mla":"Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS, vol. 112, no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:10.1073/pnas.1412996112.","chicago":"Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1412996112."},"publication":"PNAS","page":"1220 - 1225","issue":"4","abstract":[{"lang":"eng","text":"GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. "}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":1280860,"content_type":"application/pdf","access_level":"open_access","file_name":"2015_PNAS_Strueber.pdf","checksum":"6703309a1f58493cf5a704211fb6ebed","date_created":"2019-01-17T07:52:40Z","date_updated":"2020-07-14T12:45:07Z","file_id":"5838","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1614","intvolume":" 112","title":"Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells","ddc":["570"],"status":"public","month":"01","doi":"10.1073/pnas.1412996112","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["25583495"]},"project":[{"call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publist_id":"5552","ec_funded":1,"file_date_updated":"2020-07-14T12:45:07Z","author":[{"full_name":"Strüber, Michael","first_name":"Michael","last_name":"Strüber"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"},{"first_name":"Marlene","last_name":"Bartos","full_name":"Bartos, Marlene"}],"volume":112,"date_updated":"2021-01-12T06:52:01Z","date_created":"2018-12-11T11:53:02Z","pmid":1,"year":"2015","department":[{"_id":"PeJo"}],"publisher":"National Academy of Sciences","publication_status":"published"},{"title":"Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction","status":"public","intvolume":" 24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1611","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue.","lang":"eng"}],"issue":"9","page":"1412 - 1422","publication":"Protein Science","citation":{"mla":"Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science, vol. 24, no. 9, Wiley, 2015, pp. 1412–22, doi:10.1002/pro.2721.","short":"J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak, C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.","chicago":"Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski, Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science. Wiley, 2015. https://doi.org/10.1002/pro.2721.","ama":"Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 2015;24(9):1412-1422. doi:10.1002/pro.2721","ista":"Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.","ieee":"J. Whitfield et al., “Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction,” Protein Science, vol. 24, no. 9. Wiley, pp. 1412–1422, 2015.","apa":"Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak, H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. Wiley. https://doi.org/10.1002/pro.2721"},"date_published":"2015-09-01T00:00:00Z","scopus_import":1,"day":"01","publication_status":"published","publisher":"Wiley","department":[{"_id":"HaJa"}],"year":"2015","pmid":1,"date_created":"2018-12-11T11:53:01Z","date_updated":"2021-01-12T06:52:00Z","volume":24,"author":[{"full_name":"Whitfield, Jason","first_name":"Jason","last_name":"Whitfield"},{"full_name":"Zhang, William","last_name":"Zhang","first_name":"William"},{"full_name":"Herde, Michel","first_name":"Michel","last_name":"Herde"},{"first_name":"Ben","last_name":"Clifton","full_name":"Clifton, Ben"},{"full_name":"Radziejewski, Johanna","first_name":"Johanna","last_name":"Radziejewski"},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"publist_id":"5555","quality_controlled":"1","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"pmid":["26061224"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/"}],"language":[{"iso":"eng"}],"doi":"10.1002/pro.2721","month":"09"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","doi":"10.1038/srep17147","language":[{"iso":"eng"}],"month":"11","acknowledgement":"The research was supported by the Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft Faculty Fellows award. Support from the John Templeton foundation is gratefully acknowledged.","year":"2015","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Ben","last_name":"Adlam","full_name":"Adlam, Ben"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"volume":5,"date_created":"2018-12-11T11:53:06Z","date_updated":"2021-01-12T06:52:05Z","article_number":"17147","publist_id":"5536","ec_funded":1,"file_date_updated":"2020-07-14T12:45:07Z","citation":{"ama":"Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. Cellular cooperation with shift updating and repulsion. Scientific Reports. 2015;5. doi:10.1038/srep17147","ieee":"A. Pavlogiannis, K. Chatterjee, B. Adlam, and M. Nowak, “Cellular cooperation with shift updating and repulsion,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","apa":"Pavlogiannis, A., Chatterjee, K., Adlam, B., & Nowak, M. (2015). Cellular cooperation with shift updating and repulsion. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep17147","ista":"Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. 2015. Cellular cooperation with shift updating and repulsion. Scientific Reports. 5, 17147.","short":"A. Pavlogiannis, K. Chatterjee, B. Adlam, M. Nowak, Scientific Reports 5 (2015).","mla":"Pavlogiannis, Andreas, et al. “Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports, vol. 5, 17147, Nature Publishing Group, 2015, doi:10.1038/srep17147.","chicago":"Pavlogiannis, Andreas, Krishnendu Chatterjee, Ben Adlam, and Martin Nowak. “Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep17147."},"publication":"Scientific Reports","date_published":"2015-11-25T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1624","intvolume":" 5","ddc":["000"],"status":"public","title":"Cellular cooperation with shift updating and repulsion","pubrep_id":"466","file":[{"relation":"main_file","file_id":"4947","checksum":"38e06d8310d2087cae5f6d4d4bfe082b","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-12T10:12:29Z","access_level":"open_access","file_name":"IST-2016-466-v1+1_srep17147.pdf","content_type":"application/pdf","file_size":1021931,"creator":"system"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Population structure can facilitate evolution of cooperation. In a structured population, cooperators can form clusters which resist exploitation by defectors. Recently, it was observed that a shift update rule is an extremely strong amplifier of cooperation in a one dimensional spatial model. For the shift update rule, an individual is chosen for reproduction proportional to fecundity; the offspring is placed next to the parent; a random individual dies. Subsequently, the population is rearranged (shifted) until all individual cells are again evenly spaced out. For large population size and a one dimensional population structure, the shift update rule favors cooperation for any benefit-to-cost ratio greater than one. But every attempt to generalize shift updating to higher dimensions while maintaining its strong effect has failed. The reason is that in two dimensions the clusters are fragmented by the movements caused by rearranging the cells. Here we introduce the natural phenomenon of a repulsive force between cells of different types. After a birth and death event, the cells are being rearranged minimizing the overall energy expenditure. If the repulsive force is sufficiently high, shift becomes a strong promoter of cooperation in two dimensions.","lang":"eng"}]},{"scopus_import":1,"day":"25","has_accepted_license":"1","publication":"Biotechnology for Biofuels","citation":{"chicago":"Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer, Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology for Biofuels. BioMed Central, 2015. https://doi.org/10.1186/s13068-015-0380-2.","short":"P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E. Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015).","mla":"Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology for Biofuels, vol. 8, no. 1, 193, BioMed Central, 2015, doi:10.1186/s13068-015-0380-2.","ieee":"P. Hammar et al., “Single-cell screening of photosynthetic growth and lactate production by cyanobacteria,” Biotechnology for Biofuels, vol. 8, no. 1. BioMed Central, 2015.","apa":"Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K., Hudson, E., & Joensson, H. (2015). Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. BioMed Central. https://doi.org/10.1186/s13068-015-0380-2","ista":"Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E, Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 8(1), 193.","ama":"Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 2015;8(1). doi:10.1186/s13068-015-0380-2"},"date_published":"2015-11-25T00:00:00Z","type":"journal_article","abstract":[{"text":"Background\r\nPhotosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology.\r\n","lang":"eng"}],"issue":"1","_id":"1623","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Single-cell screening of photosynthetic growth and lactate production by cyanobacteria","ddc":["570"],"intvolume":" 8","pubrep_id":"467","file":[{"creator":"system","content_type":"application/pdf","file_size":2914089,"file_name":"IST-2016-467-v1+1_s13068-015-0380-2.pdf","access_level":"open_access","date_created":"2018-12-12T10:10:11Z","date_updated":"2020-07-14T12:45:07Z","checksum":"172b0b6f4eb2e5c22b7cec1d57dc0107","file_id":"4796","relation":"main_file"}],"oa_version":"Published Version","month":"11","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1186/s13068-015-0380-2","language":[{"iso":"eng"}],"article_number":"193","file_date_updated":"2020-07-14T12:45:07Z","publist_id":"5537","year":"2015","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"ToBo"}],"author":[{"full_name":"Hammar, Petter","last_name":"Hammar","first_name":"Petter"},{"orcid":"0000-0001-8619-2223","id":"4677C796-F248-11E8-B48F-1D18A9856A87","last_name":"Angermayr","first_name":"Andreas","full_name":"Angermayr, Andreas"},{"last_name":"Sjostrom","first_name":"Staffan","full_name":"Sjostrom, Staffan"},{"last_name":"Van Der Meer","first_name":"Josefin","full_name":"Van Der Meer, Josefin"},{"full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf","first_name":"Klaas"},{"first_name":"Elton","last_name":"Hudson","full_name":"Hudson, Elton"},{"first_name":"Hakaan","last_name":"Joensson","full_name":"Joensson, Hakaan"}],"date_created":"2018-12-11T11:53:05Z","date_updated":"2021-01-12T06:52:04Z","volume":8},{"scopus_import":1,"month":"07","day":"27","quality_controlled":"1","citation":{"mla":"Bermano, Amit, et al. Detailed Spatio-Temporal Reconstruction of Eyelids. Vol. 34, no. 4, 44, ACM, 2015, doi:10.1145/2766924.","short":"A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, M. Gross, in:, ACM, 2015.","chicago":"Bermano, Amit, Thabo Beeler, Yeara Kozlov, Derek Bradley, Bernd Bickel, and Markus Gross. “Detailed Spatio-Temporal Reconstruction of Eyelids,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766924.","ama":"Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. Detailed spatio-temporal reconstruction of eyelids. In: Vol 34. ACM; 2015. doi:10.1145/2766924","ista":"Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. 2015. Detailed spatio-temporal reconstruction of eyelids. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 44.","apa":"Bermano, A., Beeler, T., Kozlov, Y., Bradley, D., Bickel, B., & Gross, M. (2015). Detailed spatio-temporal reconstruction of eyelids (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766924","ieee":"A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, and M. Gross, “Detailed spatio-temporal reconstruction of eyelids,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4."},"language":[{"iso":"eng"}],"conference":{"end_date":"2015-08-13","location":"Los Angeles, CA, United States","start_date":"2015-08-09","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"doi":"10.1145/2766924","date_published":"2015-07-27T00:00:00Z","article_number":"44","type":"conference","abstract":[{"lang":"eng","text":"In recent years we have seen numerous improvements on 3D scanning and tracking of human faces, greatly advancing the creation of digital doubles for film and video games. However, despite the high-resolution quality of the reconstruction approaches available, current methods are unable to capture one of the most important regions of the face - the eye region. In this work we present the first method for detailed spatio-temporal reconstruction of eyelids. Tracking and reconstructing eyelids is extremely challenging, as this region exhibits very complex and unique skin deformation where skin is folded under while opening the eye. Furthermore, eyelids are often only partially visible and obstructed due to selfocclusion and eyelashes. Our approach is to combine a geometric deformation model with image data, leveraging multi-view stereo, optical flow, contour tracking and wrinkle detection from local skin appearance. Our deformation model serves as a prior that enables reconstruction of eyelids even under strong self-occlusions caused by rolling and folding skin as the eye opens and closes. The output is a person-specific, time-varying eyelid reconstruction with anatomically plausible deformations. Our high-resolution detailed eyelids couple naturally with current facial performance capture approaches. As a result, our method can largely increase the fidelity of facial capture and the creation of digital doubles."}],"publist_id":"5535","issue":"4","title":"Detailed spatio-temporal reconstruction of eyelids","status":"public","publication_status":"published","department":[{"_id":"BeBi"}],"intvolume":" 34","publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1625","year":"2015","date_updated":"2021-01-12T06:52:05Z","date_created":"2018-12-11T11:53:06Z","volume":34,"oa_version":"None","author":[{"first_name":"Amit","last_name":"Bermano","full_name":"Bermano, Amit"},{"full_name":"Beeler, Thabo","first_name":"Thabo","last_name":"Beeler"},{"first_name":"Yeara","last_name":"Kozlov","full_name":"Kozlov, Yeara"},{"full_name":"Bradley, Derek","last_name":"Bradley","first_name":"Derek"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"},{"full_name":"Gross, Markus","first_name":"Markus","last_name":"Gross"}]},{"oa_version":"None","volume":34,"date_updated":"2021-01-12T06:52:05Z","date_created":"2018-12-11T11:53:06Z","author":[{"full_name":"Martin, Tobias","last_name":"Martin","first_name":"Tobias"},{"first_name":"Nobuyuki","last_name":"Umetani","full_name":"Umetani, Nobuyuki"},{"full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"}],"department":[{"_id":"BeBi"}],"publisher":"ACM","intvolume":" 34","title":"OmniAD: Data-driven omni-directional aerodynamics","status":"public","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1626","year":"2015","publist_id":"5532","issue":"4","abstract":[{"lang":"eng","text":"This paper introduces "OmniAD," a novel data-driven pipeline to model and acquire the aerodynamics of three-dimensional rigid objects. Traditionally, aerodynamics are examined through elaborate wind tunnel experiments or expensive fluid dynamics computations, and are only measured for a small number of discrete wind directions. OmniAD allows the evaluation of aerodynamic forces, such as drag and lift, for any incoming wind direction using a novel representation based on spherical harmonics. Our datadriven technique acquires the aerodynamic properties of an object simply by capturing its falling motion using a single camera. Once model parameters are estimated, OmniAD enables realistic realtime simulation of rigid bodies, such as the tumbling and gliding of leaves, without simulating the surrounding air. In addition, we propose an intuitive user interface based on OmniAD to interactively design three-dimensional kites that actually fly. Various nontraditional kites were designed to demonstrate the physical validity of our model."}],"alternative_title":["ACM Transactions on Graphics"],"type":"conference","article_number":"113","language":[{"iso":"eng"}],"date_published":"2015-07-27T00:00:00Z","doi":"10.1145/2766919","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2015-08-13","start_date":"2015-08-09","location":"Los Angeles, CA, United States"},"quality_controlled":"1","citation":{"chicago":"Martin, Tobias, Nobuyuki Umetani, and Bernd Bickel. “OmniAD: Data-Driven Omni-Directional Aerodynamics,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766919.","short":"T. Martin, N. Umetani, B. Bickel, in:, ACM, 2015.","mla":"Martin, Tobias, et al. OmniAD: Data-Driven Omni-Directional Aerodynamics. Vol. 34, no. 4, 113, ACM, 2015, doi:10.1145/2766919.","apa":"Martin, T., Umetani, N., & Bickel, B. (2015). OmniAD: Data-driven omni-directional aerodynamics (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766919","ieee":"T. Martin, N. Umetani, and B. Bickel, “OmniAD: Data-driven omni-directional aerodynamics,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","ista":"Martin T, Umetani N, Bickel B. 2015. OmniAD: Data-driven omni-directional aerodynamics. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 113.","ama":"Martin T, Umetani N, Bickel B. OmniAD: Data-driven omni-directional aerodynamics. In: Vol 34. ACM; 2015. doi:10.1145/2766919"},"day":"27","month":"07","scopus_import":1},{"issue":"4","abstract":[{"lang":"eng","text":"We propose a method for fabricating deformable objects with spatially varying elasticity using 3D printing. Using a single, relatively stiff printer material, our method designs an assembly of smallscale microstructures that have the effect of a softer material at the object scale, with properties depending on the microstructure used in each part of the object. We build on work in the area of metamaterials, using numerical optimization to design tiled microstructures with desired properties, but with the key difference that our method designs families of related structures that can be interpolated to smoothly vary the material properties over a wide range. To create an object with spatially varying elastic properties, we tile the object's interior with microstructures drawn from these families, generating a different microstructure for each cell using an efficient algorithm to select compatible structures for neighboring cells. We show results computed for both 2D and 3D objects, validating several 2D and 3D printed structures using standard material tests as well as demonstrating various example applications."}],"type":"conference","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1628","intvolume":" 34","status":"public","title":"Microstructures to control elasticity in 3D printing","article_processing_charge":"No","day":"01","scopus_import":1,"date_published":"2015-08-01T00:00:00Z","citation":{"short":"C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, M. Gross, in:, ACM, 2015.","mla":"Schumacher, Christian, et al. Microstructures to Control Elasticity in 3D Printing. Vol. 34, no. 4, 136, ACM, 2015, doi:10.1145/2766926.","chicago":"Schumacher, Christian, Bernd Bickel, Jan Rys, Steve Marschner, Chiara Daraio, and Markus Gross. “Microstructures to Control Elasticity in 3D Printing,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766926.","ama":"Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. Microstructures to control elasticity in 3D printing. In: Vol 34. ACM; 2015. doi:10.1145/2766926","ieee":"C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, and M. Gross, “Microstructures to control elasticity in 3D printing,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.","apa":"Schumacher, C., Bickel, B., Rys, J., Marschner, S., Daraio, C., & Gross, M. (2015). Microstructures to control elasticity in 3D printing (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766926","ista":"Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. 2015. Microstructures to control elasticity in 3D printing. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 136."},"publist_id":"5529","article_number":"136","author":[{"first_name":"Christian","last_name":"Schumacher","full_name":"Schumacher, Christian"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"},{"full_name":"Rys, Jan","first_name":"Jan","last_name":"Rys"},{"full_name":"Marschner, Steve","last_name":"Marschner","first_name":"Steve"},{"full_name":"Daraio, Chiara","last_name":"Daraio","first_name":"Chiara"},{"last_name":"Gross","first_name":"Markus","full_name":"Gross, Markus"}],"volume":34,"date_created":"2018-12-11T11:53:07Z","date_updated":"2021-01-12T06:52:06Z","year":"2015","publisher":"ACM","department":[{"_id":"BeBi"}],"publication_status":"published","month":"08","doi":"10.1145/2766926","conference":{"location":"Los Angeles, CA, USA","start_date":"2015-08-09","end_date":"2015-08-13","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/2766926"}],"quality_controlled":"1"},{"scopus_import":1,"month":"07","day":"27","citation":{"ama":"Pérez J, Thomaszewski B, Coros S, et al. Design and fabrication of flexible rod meshes. In: Vol 34. ACM; 2015. doi:10.1145/2766998","ista":"Pérez J, Thomaszewski B, Coros S, Bickel B, Canabal J, Sumner R, Otaduy M. 2015. Design and fabrication of flexible rod meshes. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 138.","apa":"Pérez, J., Thomaszewski, B., Coros, S., Bickel, B., Canabal, J., Sumner, R., & Otaduy, M. (2015). Design and fabrication of flexible rod meshes (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766998","ieee":"J. Pérez et al., “Design and fabrication of flexible rod meshes,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","mla":"Pérez, Jesús, et al. Design and Fabrication of Flexible Rod Meshes. Vol. 34, no. 4, 138, ACM, 2015, doi:10.1145/2766998.","short":"J. Pérez, B. Thomaszewski, S. Coros, B. Bickel, J. Canabal, R. Sumner, M. Otaduy, in:, ACM, 2015.","chicago":"Pérez, Jesús, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, José Canabal, Robert Sumner, and Miguel Otaduy. “Design and Fabrication of Flexible Rod Meshes,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766998."},"quality_controlled":"1","date_published":"2015-07-27T00:00:00Z","doi":"10.1145/2766998","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2015-08-13","location":"Los Angeles, CA, United States","start_date":"2015-08-09"},"language":[{"iso":"eng"}],"type":"conference","article_number":"138","issue":"4","publist_id":"5530","abstract":[{"text":"We present a computational tool for fabrication-oriented design of flexible rod meshes. Given a deformable surface and a set of deformed poses as input, our method automatically computes a printable rod mesh that, once manufactured, closely matches the input poses under the same boundary conditions. The core of our method is formed by an optimization scheme that adjusts the cross-sectional profiles of the rods and their rest centerline in order to best approximate the target deformations. This approach allows us to locally control the bending and stretching resistance of the surface with a single material, yielding high design flexibility and low fabrication cost.","lang":"eng"}],"_id":"1627","acknowledgement":"This work was supported in part by grants from the Spanish Ministry of Economy (TIN2012-35840), and the European Research Council (ERC Starting Grant no. 280135 Animetrics).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","publisher":"ACM","intvolume":" 34","department":[{"_id":"BeBi"}],"publication_status":"published","title":"Design and fabrication of flexible rod meshes","status":"public","author":[{"full_name":"Pérez, Jesús","last_name":"Pérez","first_name":"Jesús"},{"full_name":"Thomaszewski, Bernhard","last_name":"Thomaszewski","first_name":"Bernhard"},{"full_name":"Coros, Stelian","first_name":"Stelian","last_name":"Coros"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"},{"last_name":"Canabal","first_name":"José","full_name":"Canabal, José"},{"first_name":"Robert","last_name":"Sumner","full_name":"Sumner, Robert"},{"first_name":"Miguel","last_name":"Otaduy","full_name":"Otaduy, Miguel"}],"oa_version":"None","volume":34,"date_created":"2018-12-11T11:53:07Z","date_updated":"2021-01-12T06:52:06Z"},{"language":[{"iso":"eng"}],"conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2015-08-13","start_date":"2015-08-09","location":"Los Angeles, CA, United States"},"doi":"10.1145/2767003","quality_controlled":"1","project":[{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"oa":1,"month":"07","date_updated":"2023-02-23T10:07:42Z","date_created":"2018-12-11T11:53:09Z","volume":34,"author":[{"last_name":"Da","first_name":"Fang","full_name":"Da, Fang"},{"full_name":"Batty, Christopher","first_name":"Christopher","last_name":"Batty"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"},{"last_name":"Grinspun","first_name":"Eitan","full_name":"Grinspun, Eitan"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"year":"2015","file_date_updated":"2020-07-14T12:45:07Z","publist_id":"5521","ec_funded":1,"article_number":"149","date_published":"2015-07-27T00:00:00Z","citation":{"mla":"Da, Fang, et al. Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams. Vol. 34, no. 4, 149, ACM, 2015, doi:10.1145/2767003.","short":"F. Da, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2015.","chicago":"Da, Fang, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2767003.","ama":"Da F, Batty C, Wojtan C, Grinspun E. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. In: Vol 34. ACM; 2015. doi:10.1145/2767003","ista":"Da F, Batty C, Wojtan C, Grinspun E. 2015. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 149.","apa":"Da, F., Batty, C., Wojtan, C., & Grinspun, E. (2015). Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2767003","ieee":"F. Da, C. Batty, C. Wojtan, and E. Grinspun, “Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4."},"day":"27","has_accepted_license":"1","scopus_import":1,"oa_version":"Submitted Version","file":[{"creator":"system","file_size":8973215,"content_type":"application/pdf","file_name":"IST-2016-608-v1+1_doublebubbles.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-12T10:11:14Z","checksum":"57b07d78d2d612a8052744b37d4a71fa","file_id":"4867","relation":"main_file"}],"pubrep_id":"608","title":"Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams","ddc":["000"],"status":"public","intvolume":" 34","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1634","abstract":[{"lang":"eng","text":"Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally required the use of a fully three-dimensional many-phase Navier-Stokes solver, even though their visual appearance is completely dominated by the thin liquid surface. We depart from earlier work on soap bubbles and foams by noting that their dynamics are naturally described by a Lagrangian vortex sheet model in which circulation is the primary variable. This leads us to derive a novel circulation-preserving surface-only discretization of foam dynamics driven by surface tension on a non-manifold triangle mesh. We represent the surface using a mesh-based multimaterial surface tracker which supports complex bubble topology changes, and evolve the surface according to the ambient air flow induced by a scalar circulation field stored on the mesh. Surface tension forces give rise to a simple update rule for circulation, even at non-manifold Plateau borders, based on a discrete measure of signed scalar mean curvature. We further incorporate vertex constraints to enable the interaction of soap films with wires. The result is a method that is at once simple, robust, and efficient, yet able to capture an array of soap films behaviors including foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being pulled apart."}],"issue":"4","type":"conference"},{"ec_funded":1,"publist_id":"5519","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"},{"first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"},{"full_name":"Takhanov, Rustem","first_name":"Rustem","last_name":"Takhanov"}],"volume":9472,"date_updated":"2022-02-01T15:12:35Z","date_created":"2018-12-11T11:53:10Z","year":"2015","publisher":"Springer Nature","department":[{"_id":"VlKo"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-662-48970-3"]},"month":"12","doi":"10.1007/978-3-662-48971-0_48","conference":{"end_date":"2015-12-11","location":"Nagoya, Japan","start_date":"2015-12-09","name":"ISAAC: International Symposium on Algorithms and Computation"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1504.07067"]},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1504.07067","open_access":"1"}],"project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Constraint Satisfaction Problem (CSP) is a fundamental algorithmic problem that appears in many areas of Computer Science. It can be equivalently stated as computing a homomorphism R→ΓΓ between two relational structures, e.g. between two directed graphs. Analyzing its complexity has been a prominent research direction, especially for the fixed template CSPs where the right side ΓΓ is fixed and the left side R is unconstrained.\r\n\r\nFar fewer results are known for the hybrid setting that restricts both sides simultaneously. It assumes that R belongs to a certain class of relational structures (called a structural restriction in this paper). We study which structural restrictions are effective, i.e. there exists a fixed template ΓΓ (from a certain class of languages) for which the problem is tractable when R is restricted, and NP-hard otherwise. We provide a characterization for structural restrictions that are closed under inverse homomorphisms. The criterion is based on the chromatic number of a relational structure defined in this paper; it generalizes the standard chromatic number of a graph.\r\n\r\nAs our main tool, we use the algebraic machinery developed for fixed template CSPs. To apply it to our case, we introduce a new construction called a “lifted language”. We also give a characterization for structural restrictions corresponding to minor-closed families of graphs, extend results to certain Valued CSPs (namely conservative valued languages), and state implications for (valued) CSPs with ordered variables and for the maximum weight independent set problem on some restricted families of graphs."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"1636","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 9472","status":"public","title":"Effectiveness of structural restrictions for hybrid CSPs","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2015-12-01T00:00:00Z","citation":{"chicago":"Kolmogorov, Vladimir, Michal Rolinek, and Rustem Takhanov. “Effectiveness of Structural Restrictions for Hybrid CSPs.” In 26th International Symposium, 9472:566–77. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-48971-0_48.","mla":"Kolmogorov, Vladimir, et al. “Effectiveness of Structural Restrictions for Hybrid CSPs.” 26th International Symposium, vol. 9472, Springer Nature, 2015, pp. 566–77, doi:10.1007/978-3-662-48971-0_48.","short":"V. Kolmogorov, M. Rolinek, R. Takhanov, in:, 26th International Symposium, Springer Nature, 2015, pp. 566–577.","ista":"Kolmogorov V, Rolinek M, Takhanov R. 2015. Effectiveness of structural restrictions for hybrid CSPs. 26th International Symposium. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 9472, 566–577.","apa":"Kolmogorov, V., Rolinek, M., & Takhanov, R. (2015). Effectiveness of structural restrictions for hybrid CSPs. In 26th International Symposium (Vol. 9472, pp. 566–577). Nagoya, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-48971-0_48","ieee":"V. Kolmogorov, M. Rolinek, and R. Takhanov, “Effectiveness of structural restrictions for hybrid CSPs,” in 26th International Symposium, Nagoya, Japan, 2015, vol. 9472, pp. 566–577.","ama":"Kolmogorov V, Rolinek M, Takhanov R. Effectiveness of structural restrictions for hybrid CSPs. In: 26th International Symposium. Vol 9472. Springer Nature; 2015:566-577. doi:10.1007/978-3-662-48971-0_48"},"publication":"26th International Symposium","page":"566 - 577"},{"month":"07","language":[{"iso":"eng"}],"doi":"10.1145/2766935","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2015-08-13","location":"Los Angeles, CA, USA","start_date":"2015-08-09"},"quality_controlled":"1","oa":1,"publist_id":"5523","file_date_updated":"2020-07-14T12:45:07Z","article_number":"53","volume":34,"date_updated":"2023-02-23T10:07:37Z","date_created":"2018-12-11T11:53:09Z","author":[{"full_name":"Ando, Ryoichi","first_name":"Ryoichi","last_name":"Ando"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","year":"2015","acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad. This work was also supported by the ERC projects ERC-2014-StG-637014 realFlow and ERC-2014- StG-638176 BigSplash.","has_accepted_license":"1","day":"27","scopus_import":1,"date_published":"2015-07-27T00:00:00Z","citation":{"ista":"Ando R, Thuerey N, Wojtan C. 2015. A stream function solver for liquid simulations. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 53.","ieee":"R. Ando, N. Thuerey, and C. Wojtan, “A stream function solver for liquid simulations,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.","apa":"Ando, R., Thuerey, N., & Wojtan, C. (2015). A stream function solver for liquid simulations (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766935","ama":"Ando R, Thuerey N, Wojtan C. A stream function solver for liquid simulations. In: Vol 34. ACM; 2015. doi:10.1145/2766935","chicago":"Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “A Stream Function Solver for Liquid Simulations,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766935.","mla":"Ando, Ryoichi, et al. A Stream Function Solver for Liquid Simulations. Vol. 34, no. 4, 53, ACM, 2015, doi:10.1145/2766935.","short":"R. Ando, N. Thuerey, C. Wojtan, in:, ACM, 2015."},"issue":"4","abstract":[{"text":"This paper presents a liquid simulation technique that enforces the incompressibility condition using a stream function solve instead of a pressure projection. Previous methods have used stream function techniques for the simulation of detailed single-phase flows, but a formulation for liquid simulation has proved elusive in part due to the free surface boundary conditions. In this paper, we introduce a stream function approach to liquid simulations with novel boundary conditions for free surfaces, solid obstacles, and solid-fluid coupling.\r\n\r\nAlthough our approach increases the dimension of the linear system necessary to enforce incompressibility, it provides interesting and surprising benefits. First, the resulting flow is guaranteed to be divergence-free regardless of the accuracy of the solve. Second, our free-surface boundary conditions guarantee divergence-free motion even in the un-simulated air phase, which enables two-phase flow simulation by only computing a single phase. We implemented this method using a variant of FLIP simulation which only samples particles within a narrow band of the liquid surface, and we illustrate the effectiveness of our method for detailed two-phase flow simulations with complex boundaries, detailed bubble interactions, and two-way solid-fluid coupling.","lang":"eng"}],"alternative_title":["ACM Transactions on Graphics"],"type":"conference","file":[{"content_type":"application/pdf","file_size":21831121,"creator":"system","file_name":"IST-2016-610-v1+1_vecpotential.pdf","access_level":"open_access","date_created":"2018-12-12T10:11:52Z","date_updated":"2020-07-14T12:45:07Z","checksum":"7a9afdfaba9209157ce19376e15bc90b","relation":"main_file","file_id":"4909"}],"oa_version":"Submitted Version","pubrep_id":"610","intvolume":" 34","ddc":["000"],"title":"A stream function solver for liquid simulations","status":"public","_id":"1632","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Learning shape placements by example","status":"public","ddc":["000"],"intvolume":" 34","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1630","file":[{"file_id":"4647","relation":"main_file","checksum":"8b05a51e372c9b0b5af9a00098a9538b","date_created":"2018-12-12T10:07:49Z","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access","file_name":"IST-2016-576-v1+1_guerrero-2015-lsp-paper.pdf","creator":"system","file_size":11902290,"content_type":"application/pdf"}],"oa_version":"Submitted Version","pubrep_id":"576","type":"conference","abstract":[{"text":"We present a method to learn and propagate shape placements in 2D polygonal scenes from a few examples provided by a user. The placement of a shape is modeled as an oriented bounding box. Simple geometric relationships between this bounding box and nearby scene polygons define a feature set for the placement. The feature sets of all example placements are then used to learn a probabilistic model over all possible placements and scenes. With this model, we can generate a new set of placements with similar geometric relationships in any given scene. We introduce extensions that enable propagation and generation of shapes in 3D scenes, as well as the application of a learned modeling session to large scenes without additional user interaction. These concepts allow us to generate complex scenes with thousands of objects with relatively little user interaction.","lang":"eng"}],"issue":"4","citation":{"ama":"Guerrero P, Jeschke S, Wimmer M, Wonka P. Learning shape placements by example. In: Vol 34. ACM; 2015. doi:10.1145/2766933","ista":"Guerrero P, Jeschke S, Wimmer M, Wonka P. 2015. Learning shape placements by example. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 108.","ieee":"P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Learning shape placements by example,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","apa":"Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2015). Learning shape placements by example (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766933","mla":"Guerrero, Paul, et al. Learning Shape Placements by Example. Vol. 34, no. 4, 108, ACM, 2015, doi:10.1145/2766933.","short":"P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, in:, ACM, 2015.","chicago":"Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Learning Shape Placements by Example,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766933."},"date_published":"2015-07-27T00:00:00Z","scopus_import":1,"day":"27","has_accepted_license":"1","publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"year":"2015","acknowledgement":"This publication is based upon work supported by the KAUST Office of Competitive Research Funds (OCRF) under Award No. 62140401, the KAUST Visual Computing Center and the Austrian Science Fund (FWF) projects DEEP PICTURES (no. P24352-N23) and Data-Driven Procedural Modeling of Interiors (no. P24600-N23).","date_created":"2018-12-11T11:53:08Z","date_updated":"2021-01-12T06:52:07Z","volume":34,"author":[{"last_name":"Guerrero","first_name":"Paul","full_name":"Guerrero, Paul"},{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wimmer, Michael","first_name":"Michael","last_name":"Wimmer"},{"first_name":"Peter","last_name":"Wonka","full_name":"Wonka, Peter"}],"article_number":"108","file_date_updated":"2020-07-14T12:45:07Z","publist_id":"5525","quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images","_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Los Angeles, CA, United States","start_date":"2015-08-09","end_date":"2015-08-13","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"doi":"10.1145/2766933","month":"07"}]