[{"month":"08","intvolume":" 46","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments."}],"issue":"3","volume":46,"file":[{"file_id":"5694","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-17T10:49:49Z","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","date_updated":"2020-07-14T12:44:43Z","file_size":8948384,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"132","department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:44:43Z","ddc":["570"],"date_updated":"2023-09-11T12:52:41Z","publisher":"Cell Press","quality_controlled":"1","oa":1,"acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","date_published":"2018-08-06T00:00:00Z","doi":"10.1016/j.devcel.2018.06.028","date_created":"2018-12-11T11:44:48Z","page":"360 - 375","day":"06","publication":"Developmental Cell","has_accepted_license":"1","isi":1,"year":"2018","title":"Defining lineage potential and fate behavior of precursors during pancreas development","publist_id":"7791","author":[{"full_name":"Sznurkowska, Magdalena","last_name":"Sznurkowska","first_name":"Magdalena"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roberta","last_name":"Azzarelli","full_name":"Azzarelli, Roberta"},{"last_name":"Rulands","full_name":"Rulands, Steffen","first_name":"Steffen"},{"first_name":"Sonia","full_name":"Nestorowa, Sonia","last_name":"Nestorowa"},{"first_name":"Christopher","full_name":"Hindley, Christopher","last_name":"Hindley"},{"first_name":"Jennifer","full_name":"Nichols, Jennifer","last_name":"Nichols"},{"first_name":"Berthold","last_name":"Göttgens","full_name":"Göttgens, Berthold"},{"first_name":"Meritxell","full_name":"Huch, Meritxell","last_name":"Huch"},{"full_name":"Philpott, Anna","last_name":"Philpott","first_name":"Anna"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"}],"external_id":{"isi":["000441327300012"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"M. Sznurkowska et al., “Defining lineage potential and fate behavior of precursors during pancreas development,” Developmental Cell, vol. 46, no. 3. Cell Press, pp. 360–375, 2018.","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 2018;46(3):360-375. doi:10.1016/j.devcel.2018.06.028","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.06.028","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:10.1016/j.devcel.2018.06.028.","ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.06.028."}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176.","chicago":"Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák, and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery281.","ieee":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo, “Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis,” Journal of Experimental Botany, vol. 69, no. 21. Oxford University Press, pp. 5169–5176, 2018.","short":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal of Experimental Botany 69 (2018) 5169–5176.","apa":"Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., & Colombo, L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery281","ama":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 2018;69(21):5169-5176. doi:10.1093/jxb/ery281","mla":"Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:10.1093/jxb/ery281."},"title":"Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis","author":[{"full_name":"Cucinotta, Mara","last_name":"Cucinotta","first_name":"Mara"},{"last_name":"Manrique","full_name":"Manrique, Silvia","first_name":"Silvia"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","last_name":"Cuesta"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"first_name":"Lucia","last_name":"Colombo","full_name":"Colombo, Lucia"}],"publist_id":"8012","article_processing_charge":"No","external_id":{"isi":["000448163900015"]},"acknowledgement":"This work was funded by the Ministry of Education, Youth and Sports of the Czech Republic through the National Program of Sustainability (grant no. LO1204).","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"day":"26","publication":"Journal of Experimental Botany","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-07-26T00:00:00Z","doi":"10.1093/jxb/ery281","date_created":"2018-12-11T11:44:19Z","page":"5169 - 5176","_id":"42","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["575"],"date_updated":"2023-09-11T12:52:03Z","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:46:25Z","oa_version":"Published Version","abstract":[{"text":"Seeds derive from ovules upon fertilization and therefore the total number of ovules determines the final seed yield, a fundamental trait in crop plants. Among the factors that co-ordinate the process of ovule formation, the transcription factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK) have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2 causes a severe reduction in ovule number, a phenotype that can be rescued by CK treatment. In this study, we combined CK quantification with an integrative genome-wide target identification approach to select Arabidopsis genes regulated by CUCs that are also involved in CK metabolism. We focused our attention on the functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1, which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance of CUCs and CKs in the determination of seed yield.","lang":"eng"}],"month":"07","intvolume":" 69","scopus_import":"1","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"ca3b6711040b1662488aeb3d1f961f13","file_id":"5691","creator":"dernst","date_updated":"2020-07-14T12:46:25Z","file_size":1292128,"date_created":"2018-12-17T10:44:16Z","file_name":"2018_JournalExperimBotany_Cucinotta.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"21","volume":69},{"publication_status":"published","language":[{"iso":"eng"}],"volume":150,"abstract":[{"text":"Isoprenoid cytokinins play a number of crucial roles in the regulation of plant growth and development. To study cytokinin receptor properties in plants, we designed and prepared fluorescent derivatives of 6-[(3-methylbut-2-en-1-yl)amino]purine (N6-isopentenyladenine, iP) with several fluorescent labels attached to the C2 or N9 atom of the purine moiety via a 2- or 6-carbon linker. The fluorescent labels included dansyl (DS), fluorescein (FC), 7-nitrobenzofurazan (NBD), rhodamine B (RhoB), coumarin (Cou), 7-(diethylamino)coumarin (DEAC) and cyanine 5 dye (Cy5). All prepared compounds were screened for affinity for the Arabidopsis thaliana cytokinin receptor (CRE1/AHK4). Although the attachment of the fluorescent labels to iP via the linkers mostly disrupted binding to the receptor, several fluorescent derivatives interacted well. For this reason, three derivatives, two rhodamine B and one 4-chloro-7-nitrobenzofurazan labeled iP were tested for their interaction with CRE1/AHK4 and Zea mays cytokinin receptors in detail. We further showed that the three derivatives were able to activate transcription of cytokinin response regulator ARR5 in Arabidopsis seedlings. The activity of fluorescently labeled cytokinins was compared with corresponding 6-dimethylaminopurine fluorescently labeled negative controls. Selected rhodamine B C2-labeled compounds 17, 18 and 4-chloro-7-nitrobenzofurazan N9-labeled compound 28 and their respective negative controls (19, 20 and 29, respectively) were used for in planta staining experiments in Arabidopsis thaliana cell suspension culture using live cell confocal microscopy.","lang":"eng"}],"oa_version":"None","scopus_import":"1","month":"06","intvolume":" 150","date_updated":"2023-09-11T12:53:11Z","department":[{"_id":"EvBe"}],"_id":"407","type":"journal_article","status":"public","isi":1,"year":"2018","day":"01","publication":"Phytochemistry","page":"1-11","doi":"10.1016/j.phytochem.2018.02.015","date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:46:18Z","acknowledgement":"This work was supported by the Ministry of Education Youth and Sports, Czech Republic (grant LO1204 from the National Program of Sustainability I and Agricultural Research ) and by Czech Science Foundation grants 16-04184S , 501/10/1450 and 13-39982S and by IGA projects IGA_PrF_2018_033 and IGA_PrF_2018_023 . We would like to thank Jarmila Balonová, Olga Hustáková and Miroslava Šubová for their skillful technical assistance and Mgr. Tomáš Pospíšil, Ph.D. for his measurement of 1 H NMR and analysis of some 2D NMR spectral data. \r\n","quality_controlled":"1","publisher":"Elsevier","citation":{"ama":"Kubiasová K, Mik V, Nisler J, et al. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 2018;150:1-11. doi:10.1016/j.phytochem.2018.02.015","apa":"Kubiasová, K., Mik, V., Nisler, J., Hönig, M., Husičková, A., Spíchal, L., … Plíhalová, L. (2018). Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. Elsevier. https://doi.org/10.1016/j.phytochem.2018.02.015","ieee":"K. Kubiasová et al., “Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins,” Phytochemistry, vol. 150. Elsevier, pp. 1–11, 2018.","short":"K. Kubiasová, V. Mik, J. Nisler, M. Hönig, A. Husičková, L. Spíchal, Z. Pěkná, O. Šamajová, K. Doležal, O. Plíhal, E. Benková, M. Strnad, L. Plíhalová, Phytochemistry 150 (2018) 1–11.","mla":"Kubiasová, Karolina, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry, vol. 150, Elsevier, 2018, pp. 1–11, doi:10.1016/j.phytochem.2018.02.015.","ista":"Kubiasová K, Mik V, Nisler J, Hönig M, Husičková A, Spíchal L, Pěkná Z, Šamajová O, Doležal K, Plíhal O, Benková E, Strnad M, Plíhalová L. 2018. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 150, 1–11.","chicago":"Kubiasová, Karolina, Václav Mik, Jaroslav Nisler, Martin Hönig, Alexandra Husičková, Lukáš Spíchal, Zuzana Pěkná, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry. Elsevier, 2018. https://doi.org/10.1016/j.phytochem.2018.02.015."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Karolina","last_name":"Kubiasová","full_name":"Kubiasová, Karolina"},{"first_name":"Václav","full_name":"Mik, Václav","last_name":"Mik"},{"first_name":"Jaroslav","last_name":"Nisler","full_name":"Nisler, Jaroslav"},{"full_name":"Hönig, Martin","last_name":"Hönig","first_name":"Martin"},{"full_name":"Husičková, Alexandra","last_name":"Husičková","first_name":"Alexandra"},{"first_name":"Lukáš","last_name":"Spíchal","full_name":"Spíchal, Lukáš"},{"first_name":"Zuzana","full_name":"Pěkná, Zuzana","last_name":"Pěkná"},{"first_name":"Olga","last_name":"Šamajová","full_name":"Šamajová, Olga"},{"first_name":"Karel","full_name":"Doležal, Karel","last_name":"Doležal"},{"last_name":"Plíhal","full_name":"Plíhal, Ondřej","first_name":"Ondřej"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"last_name":"Strnad","full_name":"Strnad, Miroslav","first_name":"Miroslav"},{"last_name":"Plíhalová","full_name":"Plíhalová, Lucie","first_name":"Lucie"}],"publist_id":"7422","external_id":{"isi":["000435623400001"]},"article_processing_charge":"No","title":"Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins"},{"article_number":"161122","author":[{"last_name":"Hetterich","full_name":"Hetterich, Daniel","first_name":"Daniel"},{"last_name":"Yao","full_name":"Yao, Norman","first_name":"Norman"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pollmann, Frank","last_name":"Pollmann","first_name":"Frank"},{"last_name":"Trauzettel","full_name":"Trauzettel, Björn","first_name":"Björn"}],"publist_id":"8008","external_id":{"isi":["000448596500002"],"arxiv":["1806.08316"]},"article_processing_charge":"No","title":"Detection and characterization of many-body localization in central spin models","citation":{"ista":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and characterization of many-body localization in central spin models. Physical Review B. 98(16), 161122.","chicago":"Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn Trauzettel. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.161122.","ieee":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection and characterization of many-body localization in central spin models,” Physical Review B, vol. 98, no. 16. American Physical Society, 2018.","short":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review B 98 (2018).","ama":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization of many-body localization in central spin models. Physical Review B. 2018;98(16). doi:10.1103/PhysRevB.98.161122","apa":"Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., & Trauzettel, B. (2018). Detection and characterization of many-body localization in central spin models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.161122","mla":"Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B, vol. 98, no. 16, 161122, American Physical Society, 2018, doi:10.1103/PhysRevB.98.161122."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"F.P. acknowledges the sup- port of the DFG Research Unit FOR 1807 through Grants No. PO 1370/2-1 and No. TRR80, the Nanosystems Initiative Munich (NIM) by the German Excellence Initiative, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 771537). N.Y.Y. acknowledges support from the NSF (PHY-1654740), the ARO STIR program, and a Google research award.","date_published":"2018-10-15T00:00:00Z","doi":"10.1103/PhysRevB.98.161122","date_created":"2018-12-11T11:44:20Z","isi":1,"year":"2018","day":"15","publication":"Physical Review B","type":"journal_article","article_type":"original","status":"public","_id":"46","department":[{"_id":"MaSe"}],"date_updated":"2023-09-11T12:55:03Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.08316","open_access":"1"}],"month":"10","intvolume":" 98","abstract":[{"lang":"eng","text":"We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase."}],"oa_version":"Preprint","issue":"16","volume":98,"publication_status":"published","language":[{"iso":"eng"}]},{"oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Developmental Cell","day":"07","year":"2018","isi":1,"date_created":"2018-12-11T11:45:44Z","date_published":"2018-05-07T00:00:00Z","doi":"10.1016/j.devcel.2018.04.002","page":"331 - 346","project":[{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Drosophila TNFa´s Funktion in Immunzellen","grant_number":"P29638"},{"grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell, vol. 45, no. 3, Elsevier, 2018, pp. 331–46, doi:10.1016/j.devcel.2018.04.002.","short":"A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W. Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018) 331–346.","ieee":"A. Ratheesh et al., “Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration,” Developmental Cell, vol. 45, no. 3. Elsevier, pp. 331–346, 2018.","apa":"Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G., … Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2018.04.002","ama":"Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 2018;45(3):331-346. doi:10.1016/j.devcel.2018.04.002","chicago":"Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano, and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell. Elsevier, 2018. https://doi.org/10.1016/j.devcel.2018.04.002.","ista":"Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W, György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 45(3), 331–346."},"title":"Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration","article_processing_charge":"No","external_id":{"isi":["000432461400009"],"pmid":["29738712"]},"author":[{"first_name":"Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","last_name":"Ratheesh","orcid":"0000-0001-7190-0776","full_name":"Ratheesh, Aparna"},{"first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","full_name":"Biebl, Julia","last_name":"Biebl"},{"full_name":"Smutny, Michael","last_name":"Smutny","first_name":"Michael"},{"first_name":"Jana","id":"433253EE-F248-11E8-B48F-1D18A9856A87","full_name":"Veselá, Jana","last_name":"Veselá"},{"full_name":"Papusheva, Ekaterina","last_name":"Papusheva","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"György","orcid":"0000-0002-1819-198X","full_name":"György, Attila","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Casano, Alessandra M","orcid":"0000-0002-6009-6804","last_name":"Casano","first_name":"Alessandra M","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo."}],"acknowledged_ssus":[{"_id":"SSU"}],"intvolume":" 45","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2018.04.002"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"3","volume":45,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/"}]},"_id":"308","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-11T13:22:13Z","department":[{"_id":"DaSi"},{"_id":"CaHe"},{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"MiSi"}]},{"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"103302 ","publist_id":"8038","author":[{"last_name":"Varshney","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul"},{"full_name":"Steinberg, Victor","last_name":"Steinberg","first_name":"Victor"}],"external_id":{"isi":["000447311500001"]},"article_processing_charge":"No","title":"Drag enhancement and drag reduction in viscoelastic flow","citation":{"chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103302.","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302.","mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103302.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018.","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103302","apa":"Varshney, A., & Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103302"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"American Physical Society","quality_controlled":"1","oa":1,"date_published":"2018-10-15T00:00:00Z","doi":"10.1103/PhysRevFluids.3.103302","date_created":"2018-12-11T11:44:11Z","has_accepted_license":"1","isi":1,"year":"2018","day":"15","publication":"Physical Review Fluids","type":"journal_article","status":"public","pubrep_id":"1061","_id":"17","file_date_updated":"2020-07-14T12:45:12Z","department":[{"_id":"BjHo"}],"date_updated":"2023-09-11T12:59:28Z","ddc":["532"],"scopus_import":"1","month":"10","intvolume":" 3","abstract":[{"lang":"eng","text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow."}],"oa_version":"Published Version","volume":3,"issue":"10","ec_funded":1,"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e1445be33e8165114e96246275600750","file_id":"4800","date_updated":"2020-07-14T12:45:12Z","file_size":1409040,"creator":"system","date_created":"2018-12-12T10:10:14Z","file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf"}],"language":[{"iso":"eng"}]},{"year":"2018","isi":1,"publication":"PNAS","day":"05","page":"6088 - 6093","date_created":"2018-12-11T11:45:35Z","date_published":"2018-06-05T00:00:00Z","doi":"10.1073/pnas.1716659115","acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","citation":{"ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.","chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1716659115.","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000434114900071"],"pmid":["29784812"]},"article_processing_charge":"No","publist_id":"7618","author":[{"full_name":"Granados, Alejandro","last_name":"Granados","first_name":"Alejandro"},{"full_name":"Pietsch, Julian","last_name":"Pietsch","first_name":"Julian"},{"first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A"},{"first_name":"Isebail","last_name":"Farquhar","full_name":"Farquhar, Isebail"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Swain, Peter","last_name":"Swain","first_name":"Peter"}],"title":"Distributed and dynamic intracellular organization of extracellular information","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"publication_status":"published","language":[{"iso":"eng"}],"volume":115,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6473"}]},"issue":"23","abstract":[{"text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.","lang":"eng"}],"pmid":1,"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/09/21/192039"}],"scopus_import":"1","intvolume":" 115","month":"06","date_updated":"2023-09-11T12:58:24Z","department":[{"_id":"GaTk"}],"_id":"281","article_type":"original","type":"journal_article","status":"public"},{"publication_status":"published","language":[{"iso":"eng"}],"volume":131,"issue":"1","abstract":[{"text":"Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062","open_access":"1"}],"scopus_import":"1","intvolume":" 131","month":"01","date_updated":"2023-09-11T12:57:13Z","department":[{"_id":"DaSi"}],"_id":"620","type":"journal_article","status":"public","year":"2018","isi":1,"publication":"Journal of Cell Science","day":"04","date_created":"2018-12-11T11:47:32Z","date_published":"2018-01-04T00:00:00Z","doi":"10.1242/jcs.207696","oa":1,"publisher":"Company of Biologists","quality_controlled":"1","citation":{"chicago":"Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.","ista":"Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696.","mla":"Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.","ieee":"W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018.","short":"W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018).","ama":"Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696","apa":"Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000424786900012"],"pmid":["29192062"]},"article_processing_charge":"No","author":[{"last_name":"Yamamoto","full_name":"Yamamoto, Wataru","first_name":"Wataru"},{"first_name":"Suguru","last_name":"Wada","full_name":"Wada, Suguru"},{"first_name":"Makoto","full_name":"Nagano, Makoto","last_name":"Nagano"},{"first_name":"Kaito","last_name":"Aoshima","full_name":"Aoshima, Kaito"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"publist_id":"7184","title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","article_number":"jcs207696"},{"type":"conference","conference":{"start_date":"2018-04-11","location":"Porto, Portugal","end_date":"2018-04-13","name":"HSCC: Hybrid Systems: Computation and Control"},"status":"public","_id":"182","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"ToHe"}],"date_updated":"2023-09-11T13:30:51Z","ddc":["000"],"scopus_import":"1","alternative_title":["HSCC Proceedings"],"month":"04","abstract":[{"lang":"eng","text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice."}],"oa_version":"Submitted Version","publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7833","checksum":"81eabc96430e84336ea88310ac0a1ad0","creator":"dernst","file_size":5900421,"date_updated":"2020-07-14T12:45:17Z","file_name":"2018_HSCC_Bakhirkin.pdf","date_created":"2020-05-14T12:18:29Z"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey","first_name":"Alexey"},{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Oded","full_name":"Maler, Oded","last_name":"Maler"}],"publist_id":"7739","article_processing_charge":"No","external_id":{"isi":["000474781600020"]},"title":"Efficient parametric identification for STL","citation":{"chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In Proceedings of the 21st International Conference on Hybrid Systems, 177–86. ACM, 2018. https://doi.org/10.1145/3178126.3178132.","ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186.","mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–86, doi:10.1145/3178126.3178132.","apa":"Bakhirkin, A., Ferrere, T., & Maler, O. (2018). Efficient parametric identification for STL. In Proceedings of the 21st International Conference on Hybrid Systems (pp. 177–186). Porto, Portugal: ACM. https://doi.org/10.1145/3178126.3178132","ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: Proceedings of the 21st International Conference on Hybrid Systems. ACM; 2018:177-186. doi:10.1145/3178126.3178132","ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in Proceedings of the 21st International Conference on Hybrid Systems, Porto, Portugal, 2018, pp. 177–186.","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"ACM","quality_controlled":"1","oa":1,"page":"177 - 186","date_published":"2018-04-11T00:00:00Z","doi":"10.1145/3178126.3178132","date_created":"2018-12-11T11:45:04Z","isi":1,"has_accepted_license":"1","year":"2018","day":"11","publication":"Proceedings of the 21st International Conference on Hybrid Systems"},{"department":[{"_id":"KrCh"}],"date_updated":"2023-09-11T13:23:42Z","conference":{"name":"LICS: Logic in Computer Science","start_date":"2018-07-09","location":"Oxford, United Kingdom","end_date":"2018-07-12"},"type":"conference","status":"public","_id":"143","ec_funded":1,"volume":"F138033","publication_status":"published","publication_identifier":{"isbn":["978-1-4503-5583-4"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1804.10985","open_access":"1"}],"scopus_import":"1","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"month":"07","abstract":[{"lang":"eng","text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis."}],"oa_version":"Preprint","article_processing_charge":"No","external_id":{"isi":["000545262800020"]},"author":[{"last_name":"Brázdil","full_name":"Brázdil, Tomáš","first_name":"Tomáš"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Kučera","full_name":"Kučera, Antonín","first_name":"Antonín"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny","full_name":"Novotny, Petr"},{"first_name":"Dominik","last_name":"Velan","full_name":"Velan, Dominik"},{"first_name":"Florian","full_name":"Zuleger, Florian","last_name":"Zuleger"}],"publist_id":"7780","title":"Efficient algorithms for asymptotic bounds on termination time in VASS","citation":{"mla":"Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191.","apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191","ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:10.1145/3209108.3209191","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194.","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191.","ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"185 - 194","date_created":"2018-12-11T11:44:51Z","doi":"10.1145/3209108.3209191","date_published":"2018-07-09T00:00:00Z","year":"2018","isi":1,"day":"09","oa":1,"publisher":"IEEE","quality_controlled":"1"},{"publisher":"IEEE","quality_controlled":"1","oa":1,"day":"28","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","isi":1,"year":"2018","doi":"10.1109/cvpr.2018.00389","date_published":"2018-06-28T00:00:00Z","date_created":"2018-12-11T11:45:33Z","page":"3693-3701","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, 2018, pp. 3693–3701.","short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:3693-3701. doi:10.1109/cvpr.2018.00389","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., & Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. https://doi.org/10.1109/cvpr.2018.00389","mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–701, doi:10.1109/cvpr.2018.00389.","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 3693–3701. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00389."},"title":"Efficient optimization for rank-based loss functions","author":[{"first_name":"Pritish","last_name":"Mohapatra","full_name":"Mohapatra, Pritish"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rolinek","full_name":"Rolinek, Michal"},{"last_name":"Jawahar","full_name":"Jawahar, C V","first_name":"C V"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"first_name":"M Pawan","full_name":"Kumar, M Pawan","last_name":"Kumar"}],"article_processing_charge":"No","external_id":{"arxiv":["1604.08269"],"isi":["000457843603087"]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time."}],"month":"06","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08269"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781538664209"]},"publication_status":"published","ec_funded":1,"_id":"273","status":"public","type":"conference","conference":{"start_date":"2018-06-18","end_date":"2018-06-22","location":"Salt Lake City, UT, USA","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"date_updated":"2023-09-11T13:24:43Z","department":[{"_id":"VlKo"}]},{"publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"The experimental work at UCSB was funded by the National Science Foundation under Grant No. DMR- 1654186. Work at Columbia was supported by the National Science Foundation under Grant No. DMR- 1507788. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Japan Society for the Promotion of Science KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Fellowship from the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard foundation and the Sloan Foundation. Measurements made use of a dilution refrigerator funded through the Major Research Instrumentation program of the U.S. National Science Foundation under Grant No. DMR- 1531389, and the MRL Shared Experimental Facilities, which are supported by the MRSEC Program of the U.S. National Science Foundation under Grant No. DMR- 1720256.","date_published":"2018-10-19T00:00:00Z","doi":"10.1103/PhysRevLett.121.167601","date_created":"2018-12-11T11:45:38Z","day":"19","publication":"Physical Review Letters","isi":1,"year":"2018","article_number":"167601","title":"Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene","author":[{"full_name":"Zibrov, Alexander","last_name":"Zibrov","first_name":"Alexander"},{"last_name":"Peng","orcid":"0000-0003-1250-0021","full_name":"Peng, Rao","id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB","first_name":"Rao"},{"full_name":"Kometter, Carlos","last_name":"Kometter","first_name":"Carlos"},{"first_name":"Jia","last_name":"Li","full_name":"Li, Jia"},{"last_name":"Dean","full_name":"Dean, Cory","first_name":"Cory"},{"first_name":"Takashi","last_name":"Taniguchi","full_name":"Taniguchi, Takashi"},{"full_name":"Watanabe, Kenji","last_name":"Watanabe","first_name":"Kenji"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"last_name":"Young","full_name":"Young, Andrea","first_name":"Andrea"}],"external_id":{"arxiv":["1805.01038"],"isi":["000447307500007"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Zibrov, Alexander, Peng Rao, Carlos Kometter, Jia Li, Cory Dean, Takashi Taniguchi, Kenji Watanabe, Maksym Serbyn, and Andrea Young. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.167601.","ista":"Zibrov A, Rao P, Kometter C, Li J, Dean C, Taniguchi T, Watanabe K, Serbyn M, Young A. 2018. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 121(16), 167601.","mla":"Zibrov, Alexander, et al. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters, vol. 121, no. 16, 167601, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.167601.","ieee":"A. Zibrov et al., “Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","short":"A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe, M. Serbyn, A. Young, Physical Review Letters 121 (2018).","apa":"Zibrov, A., Rao, P., Kometter, C., Li, J., Dean, C., Taniguchi, T., … Young, A. (2018). Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.167601","ama":"Zibrov A, Rao P, Kometter C, et al. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.167601"},"month":"10","intvolume":" 121","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1805.01038","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We report on quantum capacitance measurements of high quality, graphite- and hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices. At zero applied magnetic field, we observe a number of electron density- and electrical displacement-tuned features in the electronic compressibility associated with changes in Fermi surface topology. At high displacement field and low density, strong trigonal warping gives rise to emergent Dirac gullies centered near the corners of the hexagonal Brillouin and related by three fold rotation symmetry. At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy of the Landau levels from two to three. Weak incompressible states are also observed at integer filling within these triplets Landau levels, which a Hartree-Fock analysis indicates are associated with Coulomb-driven nematic phases that spontaneously break rotation symmetry.","lang":"eng"}],"volume":121,"issue":"16","language":[{"iso":"eng"}],"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"289","department":[{"_id":"MaSe"}],"date_updated":"2023-09-11T13:39:50Z"},{"acknowledgement":"The work of SB has been supported by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska Curie grant agreement No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC (Canada) for his research. MC acknowledges support from the Czech Science Foundation, projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211 and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.","quality_controlled":"1","publisher":"Frontiers in Bioscience","oa":1,"day":"01","publication":"Frontiers in Bioscience - Landmark","isi":1,"year":"2018","date_published":"2018-03-01T00:00:00Z","doi":"10.2741/4651","date_created":"2018-12-11T11:45:37Z","page":"1391 - 1406","project":[{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark, vol. 23, no. 8, Frontiers in Bioscience, 2018, pp. 1391–406, doi:10.2741/4651.","short":"V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406.","ieee":"V. Salari et al., “Electromagnetic fields and optomechanics In cancer diagnostics and treatment,” Frontiers in Bioscience - Landmark, vol. 23, no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.","apa":"Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei, Z., & Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. Frontiers in Bioscience. https://doi.org/10.2741/4651","ama":"Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 2018;23(8):1391-1406. doi:10.2741/4651","chicago":"Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann, Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark. Frontiers in Bioscience, 2018. https://doi.org/10.2741/4651.","ista":"Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 23(8), 1391–1406."},"title":"Electromagnetic fields and optomechanics In cancer diagnostics and treatment","author":[{"first_name":"Vahid","full_name":"Salari, Vahid","last_name":"Salari"},{"last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cifra, Michal","last_name":"Cifra","first_name":"Michal"},{"full_name":"Simon, Christoph","last_name":"Simon","first_name":"Christoph"},{"first_name":"Felix","full_name":"Scholkmann, Felix","last_name":"Scholkmann"},{"first_name":"Zahra","full_name":"Alirezaei, Zahra","last_name":"Alirezaei"},{"first_name":"Jack","last_name":"Tuszynski","full_name":"Tuszynski, Jack"}],"external_id":{"pmid":["29293441"],"isi":["000439042800001"]},"article_processing_charge":"No","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy."}],"month":"03","intvolume":" 23","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.bioscience.org/2018/v23/af/4651/fulltext.htm"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"8","volume":23,"ec_funded":1,"_id":"287","status":"public","type":"journal_article","date_updated":"2023-09-11T13:38:14Z","department":[{"_id":"JoFi"}]},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.0815"}],"month":"01","intvolume":" 65","abstract":[{"lang":"eng","text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in R3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, that is, an essential curve in the boundary of X bounding a disk in S3 \\ X with length bounded by a computable function of the number of tetrahedra of X."}],"oa_version":"Preprint","related_material":{"record":[{"id":"2157","status":"public","relation":"earlier_version"}]},"issue":"1","volume":65,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"425","department":[{"_id":"UlWa"}],"date_updated":"2023-09-11T13:38:49Z","quality_controlled":"1","publisher":"ACM","oa":1,"date_published":"2018-01-01T00:00:00Z","doi":"10.1145/3078632","date_created":"2018-12-11T11:46:24Z","isi":1,"year":"2018","day":"01","publication":"Journal of the ACM","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_number":"5","author":[{"first_name":"Jiří","last_name":"Matoušek","full_name":"Matoušek, Jiří"},{"first_name":"Eric","full_name":"Sedgwick, Eric","last_name":"Sedgwick"},{"first_name":"Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","last_name":"Tancer","full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"publist_id":"7398","external_id":{"arxiv":["1402.0815"],"isi":["000425685900006"]},"article_processing_charge":"No","title":"Embeddability in the 3-Sphere is decidable","citation":{"ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 65(1), 5.","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3078632.","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2018). Embeddability in the 3-Sphere is decidable. Journal of the ACM. ACM. https://doi.org/10.1145/3078632","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 2018;65(1). doi:10.1145/3078632","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3-Sphere is decidable,” Journal of the ACM, vol. 65, no. 1. ACM, 2018.","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018).","mla":"Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM, vol. 65, no. 1, 5, ACM, 2018, doi:10.1145/3078632."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007."},"title":"Establishment in a new habitat by polygenic adaptation","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"}],"publist_id":"7250","article_processing_charge":"No","external_id":{"isi":["000440392900014"]},"quality_controlled":"1","publisher":"Academic Press","oa":1,"day":"01","publication":"Theoretical Population Biology","isi":1,"has_accepted_license":"1","year":"2018","date_published":"2018-07-01T00:00:00Z","doi":"10.1016/j.tpb.2017.11.007","date_created":"2018-12-11T11:47:12Z","page":"110-127","_id":"564","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"ddc":["519","576"],"date_updated":"2023-09-11T13:41:22Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:09Z","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population."}],"month":"07","intvolume":" 122","scopus_import":"1","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7199","checksum":"0b96f6db47e3e91b5e7d103b847c239d","file_size":2287682,"date_updated":"2020-07-14T12:47:09Z","creator":"nbarton","file_name":"bartonetheridge.pdf","date_created":"2019-12-21T09:36:39Z"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"id":"9842","status":"public","relation":"research_data"}]},"issue":"7","volume":122,"ec_funded":1},{"status":"public","type":"journal_article","_id":"157","file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-09-11T13:43:22Z","month":"07","intvolume":" 559","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas."}],"issue":"7713","volume":559,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/engineering-cooperation/","relation":"press_release","description":"News on IST Homepage"}]},"ec_funded":1,"file":[{"file_name":"2018_Nature_Hilbe.pdf","date_created":"2019-11-19T08:09:57Z","creator":"dernst","file_size":2834442,"date_updated":"2020-07-14T12:45:02Z","checksum":"011ab905cf9a410bc2b96f15174d654d","file_id":"7049","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Evolution of cooperation in stochastic games","author":[{"orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"first_name":"Štepán","last_name":"Šimsa","full_name":"Šimsa, Štepán"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"publist_id":"7764","article_processing_charge":"No","external_id":{"isi":["000438240900054"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” Nature, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:10.1038/s41586-018-0277-x.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. Nature. 2018;559(7713):246-249. doi:10.1038/s41586-018-0277-x","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., & Nowak, M. (2018). Evolution of cooperation in stochastic games. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0277-x","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” Nature, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0277-x.","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249."},"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","date_published":"2018-07-04T00:00:00Z","doi":"10.1038/s41586-018-0277-x","date_created":"2018-12-11T11:44:56Z","page":"246 - 249","day":"04","publication":"Nature","isi":1,"has_accepted_license":"1","year":"2018"},{"file_date_updated":"2020-07-14T12:46:16Z","department":[{"_id":"FyKo"}],"date_updated":"2023-09-11T13:56:52Z","ddc":["576"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"999","_id":"384","issue":"3","volume":10,"publication_status":"published","file":[{"file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","date_created":"2018-12-12T10:08:07Z","file_size":691602,"date_updated":"2020-07-14T12:46:16Z","creator":"system","file_id":"4667","checksum":"458a7c2c2e79528567edfeb0f326cbe0","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 10","abstract":[{"text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification.","lang":"eng"}],"oa_version":"Published Version","author":[{"last_name":"Hönigschmid","full_name":"Hönigschmid, Peter","first_name":"Peter"},{"last_name":"Bykova","full_name":"Bykova, Nadya","first_name":"Nadya"},{"last_name":"Schneider","full_name":"Schneider, René","first_name":"René"},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry"},{"last_name":"Frishman","full_name":"Frishman, Dmitrij","first_name":"Dmitrij"}],"publist_id":"7445","article_processing_charge":"No","external_id":{"isi":["000429483700022"]},"title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","citation":{"chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049.","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy049","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"928 - 938","doi":"10.1093/gbe/evy049","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:46:10Z","isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Genome Biology and Evolution","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft (grant number FR 1411/9-1). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.","ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245. doi:10.1534/genetics.117.300638","apa":"Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300638","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” Genetics, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638."},"title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","author":[{"full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","last_name":"Ringbauer","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald"},{"first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander"},{"full_name":"Field, David","last_name":"Field","first_name":"David"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7251","article_processing_charge":"No","external_id":{"isi":["000426219600025"]},"day":"01","publication":"Genetics","isi":1,"year":"2018","doi":"10.1534/genetics.117.300638","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:47:12Z","page":"1231-1245","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"date_updated":"2023-09-11T13:42:38Z","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"_id":"563","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"3","related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"volume":208,"oa_version":"Preprint","abstract":[{"text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.","lang":"eng"}],"month":"03","intvolume":" 208","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/205484v1"}]},{"article_type":"original","type":"journal_article","status":"public","_id":"135","department":[{"_id":"ChWo"}],"file_date_updated":"2020-10-08T08:38:23Z","date_updated":"2023-09-11T14:00:26Z","ddc":["006"],"alternative_title":["Eurographics"],"scopus_import":"1","month":"05","intvolume":" 37","abstract":[{"lang":"eng","text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion."}],"oa_version":"Submitted Version","volume":37,"issue":"2","ec_funded":1,"publication_identifier":{"issn":["0167-7055"]},"publication_status":"published","file":[{"success":1,"checksum":"8edb90da8a72395eb5d970580e0925b6","file_id":"8627","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"exnbflip.pdf","date_created":"2020-10-08T08:38:23Z","file_size":54309947,"date_updated":"2020-10-08T08:38:23Z","creator":"wojtan"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Takahiro","last_name":"Sato","full_name":"Sato, Takahiro"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"first_name":"Takeo","last_name":"Igarashi","full_name":"Igarashi, Takeo"},{"first_name":"Ryoichi","full_name":"Ando, Ryoichi","last_name":"Ando"}],"article_processing_charge":"No","external_id":{"isi":["000434085600016"]},"title":"Extended narrow band FLIP for liquid simulations","citation":{"apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13351","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no. 2. Wiley, pp. 169–177, 2018.","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351.","ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Wiley","oa":1,"page":"169 - 177","doi":"10.1111/cgf.13351","date_published":"2018-05-22T00:00:00Z","date_created":"2018-12-11T11:44:49Z","isi":1,"has_accepted_license":"1","year":"2018","day":"22","publication":"Computer Graphics Forum"},{"date_updated":"2023-09-11T13:57:43Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"_id":"316","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","id":"9813","relation":"research_data"}]},"volume":209,"issue":"3","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants."}],"intvolume":" 209","month":"07","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/node/80098.abstract"}],"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748."},"title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","external_id":{"isi":["000437171700017"]},"article_processing_charge":"No","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Bodova","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina"},{"first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas","last_name":"Priklopil"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"}],"project":[{"name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960","call_identifier":"FP7","_id":"25B36484-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication":"Genetics","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:45:47Z","doi":"10.1534/genetics.118.300748","date_published":"2018-07-01T00:00:00Z","page":"861-883","oa":1,"quality_controlled":"1","publisher":"Genetics Society of America"}]