[{"ddc":["581"],"status":"public","title":"Plant hormones in interactions with the environment","intvolume":" 91","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1269","oa_version":"Published Version","file":[{"file_size":297282,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-697-v1+1_s11103-016-0501-8.pdf","checksum":"0ffb7a15c5336b3a55248cc67021a825","date_created":"2018-12-12T10:18:28Z","date_updated":"2020-07-14T12:44:42Z","relation":"main_file","file_id":"5349"}],"pubrep_id":"697","type":"journal_article","abstract":[{"text":"Plants are continuously exposed to a myriad of external signals such as fluctuating nutrients availability, drought, heat, cold, high salinity, or pathogen/pest attacks that can severely affect their development, growth, and fertility. As sessile organisms, plants must therefore be able to sense and rapidly react to these external inputs, activate efficient responses, and adjust development to changing conditions. In recent years, significant progress has been made towards understanding the molecular mechanisms underlying the intricate and complex communication between plants and the environment. It is now becoming increasingly evident that hormones have an important regulatory role in plant adaptation and defense mechanisms.","lang":"eng"}],"issue":"6","page":"597","publication":"Plant Molecular Biology","citation":{"chicago":"Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant Molecular Biology. Springer, 2016. https://doi.org/10.1007/s11103-016-0501-8.","mla":"Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant Molecular Biology, vol. 91, no. 6, Springer, 2016, p. 597, doi:10.1007/s11103-016-0501-8.","short":"E. Benková, Plant Molecular Biology 91 (2016) 597.","ista":"Benková E. 2016. Plant hormones in interactions with the environment. Plant Molecular Biology. 91(6), 597.","ieee":"E. Benková, “Plant hormones in interactions with the environment,” Plant Molecular Biology, vol. 91, no. 6. Springer, p. 597, 2016.","apa":"Benková, E. (2016). Plant hormones in interactions with the environment. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-016-0501-8","ama":"Benková E. Plant hormones in interactions with the environment. Plant Molecular Biology. 2016;91(6):597. doi:10.1007/s11103-016-0501-8"},"date_published":"2016-08-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Springer","year":"2016","date_updated":"2021-01-12T06:49:31Z","date_created":"2018-12-11T11:51:03Z","volume":91,"author":[{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:44:42Z","publist_id":"6052","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11103-016-0501-8","month":"08"},{"month":"08","language":[{"iso":"eng"}],"doi":"10.1007/s11005-016-0860-8","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publist_id":"6054","file_date_updated":"2020-07-14T12:44:42Z","volume":106,"date_created":"2018-12-11T11:51:02Z","date_updated":"2021-01-12T06:49:30Z","author":[{"last_name":"Frank","first_name":"Rupert","full_name":"Frank, Rupert"},{"first_name":"Rowan","last_name":"Killip","full_name":"Killip, Rowan"},{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan"}],"department":[{"_id":"RoSe"}],"publisher":"Springer","publication_status":"published","year":"2016","acknowledgement":"Open access funding provided by Institute of Science and Technology Austria.\r\n","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2016-08-01T00:00:00Z","page":"1033 - 1036","citation":{"chicago":"Frank, Rupert, Rowan Killip, and Phan Nam. “Nonexistence of Large Nuclei in the Liquid Drop Model.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0860-8.","mla":"Frank, Rupert, et al. “Nonexistence of Large Nuclei in the Liquid Drop Model.” Letters in Mathematical Physics, vol. 106, no. 8, Springer, 2016, pp. 1033–36, doi:10.1007/s11005-016-0860-8.","short":"R. Frank, R. Killip, P. Nam, Letters in Mathematical Physics 106 (2016) 1033–1036.","ista":"Frank R, Killip R, Nam P. 2016. Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. 106(8), 1033–1036.","ieee":"R. Frank, R. Killip, and P. Nam, “Nonexistence of large nuclei in the liquid drop model,” Letters in Mathematical Physics, vol. 106, no. 8. Springer, pp. 1033–1036, 2016.","apa":"Frank, R., Killip, R., & Nam, P. (2016). Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0860-8","ama":"Frank R, Killip R, Nam P. Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. 2016;106(8):1033-1036. doi:10.1007/s11005-016-0860-8"},"publication":"Letters in Mathematical Physics","issue":"8","abstract":[{"text":"We give a simplified proof of the nonexistence of large nuclei in the liquid drop model and provide an explicit bound. Our bound is within a factor of 2.3 of the conjectured value and seems to be the first quantitative result.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"IST-2016-698-v1+1_s11005-016-0860-8.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":349464,"file_id":"4863","relation":"main_file","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:11:09Z","checksum":"d740a6a226e0f5f864f40e3e269d3cc0"}],"oa_version":"Published Version","pubrep_id":"698","intvolume":" 106","status":"public","ddc":["510","539"],"title":"Nonexistence of large nuclei in the liquid drop model","_id":"1267","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_number":"74","publist_id":"6049","file_date_updated":"2020-07-14T12:44:42Z","publisher":"BioMed Central","department":[{"_id":"CaHe"}],"publication_status":"published","year":"2016","acknowledgement":"We thank K. Lee, C. Norden, A. Webb, and the members of the Paluch lab for\r\ncomments on the manuscript. We are grateful to P. Rørth and Peter Dieterich\r\nfor discussions, S. Ares, Y. Arboleda-Estudillo and S. Schneider for technical help,\r\nM. Biro for help with programming, and the BIOTEC/MPI-CBG and IST zebrafish\r\nand imaging facilities for help and advice at various stages of this project. This work was supported by the Max Planck Society, the Medical Research Council UK (core funding to the MRC LMCB), and by grants from the Polish Ministry of Science and Higher Education (454/N-MPG/2009/0) to EKP, the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EKP, a A*Star JCO career development award (12302FG010) to WY and a Damon Runyon fellowship award to ADM (DRG 2157-12). This work was also supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001317), the UK Medical Research Council (FC001317), and the Wellcome Trust (FC001317) to GS.","volume":14,"date_updated":"2021-01-12T06:49:32Z","date_created":"2018-12-11T11:51:04Z","author":[{"last_name":"Diz Muñoz","first_name":"Alba","full_name":"Diz Muñoz, Alba"},{"first_name":"Pawel","last_name":"Romanczuk","full_name":"Romanczuk, Pawel"},{"last_name":"Yu","first_name":"Weimiao","full_name":"Yu, Weimiao"},{"full_name":"Bergert, Martin","first_name":"Martin","last_name":"Bergert"},{"last_name":"Ivanovitch","first_name":"Kenzo","full_name":"Ivanovitch, Kenzo"},{"last_name":"Salbreux","first_name":"Guillame","full_name":"Salbreux, Guillame"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"full_name":"Paluch, Ewa","first_name":"Ewa","last_name":"Paluch"}],"month":"09","project":[{"_id":"252064B8-B435-11E9-9278-68D0E5697425","grant_number":"HE_3231/6-1","name":"Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.1186/s12915-016-0294-x","type":"journal_article","issue":"1","abstract":[{"text":"Background: High directional persistence is often assumed to enhance the efficiency of chemotactic migration. Yet, cells in vivo usually display meandering trajectories with relatively low directional persistence, and the control and function of directional persistence during cell migration in three-dimensional environments are poorly understood. Results: Here, we use mesendoderm progenitors migrating during zebrafish gastrulation as a model system to investigate the control of directional persistence during migration in vivo. We show that progenitor cells alternate persistent run phases with tumble phases that result in cell reorientation. Runs are characterized by the formation of directed actin-rich protrusions and tumbles by enhanced blebbing. Increasing the proportion of actin-rich protrusions or blebs leads to longer or shorter run phases, respectively. Importantly, both reducing and increasing run phases result in larger spatial dispersion of the cells, indicative of reduced migration precision. A physical model quantitatively recapitulating the migratory behavior of mesendoderm progenitors indicates that the ratio of tumbling to run times, and thus the specific degree of directional persistence of migration, are critical for optimizing migration precision. Conclusions: Together, our experiments and model provide mechanistic insight into the control of migration directionality for cells moving in three-dimensional environments that combine different protrusion types, whereby the proportion of blebs to actin-rich protrusions determines the directional persistence and precision of movement by regulating the ratio of tumbling to run times.","lang":"eng"}],"intvolume":" 14","status":"public","title":"Steering cell migration by alternating blebs and actin-rich protrusions","ddc":["572","576"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1271","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5002","checksum":"0bfa484ac69a0a560fb9a4589aeda7f6","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:13:20Z","access_level":"open_access","file_name":"IST-2016-695-v1+1_s12915-016-0294-x.pdf","file_size":1875695,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"695","scopus_import":1,"has_accepted_license":"1","day":"02","citation":{"ama":"Diz Muñoz A, Romanczuk P, Yu W, et al. Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. 2016;14(1). doi:10.1186/s12915-016-0294-x","apa":"Diz Muñoz, A., Romanczuk, P., Yu, W., Bergert, M., Ivanovitch, K., Salbreux, G., … Paluch, E. (2016). Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. BioMed Central. https://doi.org/10.1186/s12915-016-0294-x","ieee":"A. Diz Muñoz et al., “Steering cell migration by alternating blebs and actin-rich protrusions,” BMC Biology, vol. 14, no. 1. BioMed Central, 2016.","ista":"Diz Muñoz A, Romanczuk P, Yu W, Bergert M, Ivanovitch K, Salbreux G, Heisenberg C-PJ, Paluch E. 2016. Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. 14(1), 74.","short":"A. Diz Muñoz, P. Romanczuk, W. Yu, M. Bergert, K. Ivanovitch, G. Salbreux, C.-P.J. Heisenberg, E. Paluch, BMC Biology 14 (2016).","mla":"Diz Muñoz, Alba, et al. “Steering Cell Migration by Alternating Blebs and Actin-Rich Protrusions.” BMC Biology, vol. 14, no. 1, 74, BioMed Central, 2016, doi:10.1186/s12915-016-0294-x.","chicago":"Diz Muñoz, Alba, Pawel Romanczuk, Weimiao Yu, Martin Bergert, Kenzo Ivanovitch, Guillame Salbreux, Carl-Philipp J Heisenberg, and Ewa Paluch. “Steering Cell Migration by Alternating Blebs and Actin-Rich Protrusions.” BMC Biology. BioMed Central, 2016. https://doi.org/10.1186/s12915-016-0294-x."},"publication":"BMC Biology","date_published":"2016-09-02T00:00:00Z"},{"day":"13","scopus_import":1,"date_published":"2016-09-13T00:00:00Z","publication":"Development","citation":{"mla":"Porco, Silvana, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development, vol. 143, no. 18, Company of Biologists, 2016, pp. 3340–49, doi:10.1242/dev.136283.","short":"S. Porco, A. Larrieu, Y. Du, A. Gaudinier, T. Goh, K. Swarup, R. Swarup, B. Kuempers, A. Bishopp, J. Lavenus, I. Casimiro, K. Hill, E. Benková, H. Fukaki, S. Brady, B. Scheres, B. Peéet, M. Bennett, Development 143 (2016) 3340–3349.","chicago":"Porco, Silvana, Antoine Larrieu, Yujuan Du, Allison Gaudinier, Tatsuaki Goh, Kamal Swarup, Ranjan Swarup, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.136283.","ama":"Porco S, Larrieu A, Du Y, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 2016;143(18):3340-3349. doi:10.1242/dev.136283","ista":"Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benková E, Fukaki H, Brady S, Scheres B, Peéet B, Bennett M. 2016. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 143(18), 3340–3349.","apa":"Porco, S., Larrieu, A., Du, Y., Gaudinier, A., Goh, T., Swarup, K., … Bennett, M. (2016). Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. Company of Biologists. https://doi.org/10.1242/dev.136283","ieee":"S. Porco et al., “Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3,” Development, vol. 143, no. 18. Company of Biologists, pp. 3340–3349, 2016."},"page":"3340 - 3349","abstract":[{"text":"Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence.","lang":"eng"}],"issue":"18","type":"journal_article","oa_version":"Preprint","_id":"1273","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3","status":"public","intvolume":" 143","month":"09","doi":"10.1242/dev.136283","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01595056/","open_access":"1"}],"quality_controlled":"1","publist_id":"6044","author":[{"full_name":"Porco, Silvana","last_name":"Porco","first_name":"Silvana"},{"full_name":"Larrieu, Antoine","first_name":"Antoine","last_name":"Larrieu"},{"first_name":"Yujuan","last_name":"Du","full_name":"Du, Yujuan"},{"last_name":"Gaudinier","first_name":"Allison","full_name":"Gaudinier, Allison"},{"full_name":"Goh, Tatsuaki","first_name":"Tatsuaki","last_name":"Goh"},{"full_name":"Swarup, Kamal","first_name":"Kamal","last_name":"Swarup"},{"first_name":"Ranjan","last_name":"Swarup","full_name":"Swarup, Ranjan"},{"full_name":"Kuempers, Britta","first_name":"Britta","last_name":"Kuempers"},{"full_name":"Bishopp, Anthony","first_name":"Anthony","last_name":"Bishopp"},{"last_name":"Lavenus","first_name":"Julien","full_name":"Lavenus, Julien"},{"full_name":"Casimiro, Ilda","first_name":"Ilda","last_name":"Casimiro"},{"full_name":"Hill, Kristine","first_name":"Kristine","last_name":"Hill"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hidehiro","last_name":"Fukaki","full_name":"Fukaki, Hidehiro"},{"first_name":"Siobhan","last_name":"Brady","full_name":"Brady, Siobhan"},{"full_name":"Scheres, Ben","last_name":"Scheres","first_name":"Ben"},{"last_name":"Peéet","first_name":"Benjamin","full_name":"Peéet, Benjamin"},{"first_name":"Malcolm","last_name":"Bennett","full_name":"Bennett, Malcolm"}],"date_updated":"2021-01-12T06:49:32Z","date_created":"2018-12-11T11:51:04Z","volume":143,"acknowledgement":"We acknowledge the support of glasshouse technicians at the University of\r\nNottingham for help with plant growth and the Nottingham\r\nArabidopsis\r\nStock Centre\r\n(NASC) for providing\r\nArabidopsis\r\nlines. This research was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (to A.B. and M.J.B.); the European Research Council (ERC) Advanced Grant SysArc (to B.S.) and FUTUREROOTS (to M.J.B.); The Royal Society for University and Wolfson Research Fellowship awards (to A.B. and M.J.B.); a Federation of European Biochemical Societies (FEBS) Long-Term Fellowship (to B.P.); an Intra-European Fellowship for Career Development under the 7th framework of the European Commission [IEF-2008-220506 to B.P.]; a European Molecular Biology Organization (EMBO) Long-Term Fellowship (to B.P.); and a European Reintegration Grant under the 7th framework of the European Commission [ERG-2010-276662 to B.P.]; Interuniversity Attraction Poles Programme [initiated by the Belgian Science Policy Office (Federaal Wetenschapsbeleid)] (to M.J.B.); The Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan: Grants-in-Aid for Scientific Research on Innovative Areas [25110330 to H.F.] and a JSPS Research Fellowship for Young Scientists [12J02079 to T.G.]; funds for research performed by S.M.B. and A.G. were provided by University of California, Davis startup funds.","year":"2016","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Company of Biologists"},{"day":"02","has_accepted_license":"1","scopus_import":1,"date_published":"2016-09-02T00:00:00Z","page":"712 - 721","publication":"Computer-Aided Design and Applications","citation":{"ama":"Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 2016;13(5):712-721. doi:10.1080/16864360.2016.1150718","ista":"Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 13(5), 712–721.","apa":"Held, M., Huber, S., & Palfrader, P. (2016). Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. Taylor and Francis. https://doi.org/10.1080/16864360.2016.1150718","ieee":"M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures using skeletons,” Computer-Aided Design and Applications, vol. 13, no. 5. Taylor and Francis, pp. 712–721, 2016.","mla":"Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications, vol. 13, no. 5, Taylor and Francis, 2016, pp. 712–21, doi:10.1080/16864360.2016.1150718.","short":"M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13 (2016) 712–721.","chicago":"Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications. Taylor and Francis, 2016. https://doi.org/10.1080/16864360.2016.1150718."},"abstract":[{"lang":"eng","text":"We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams."}],"issue":"5","type":"journal_article","oa_version":"Published Version","file":[{"file_size":1678369,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:20Z","date_updated":"2020-07-14T12:44:42Z","checksum":"c746f3a48edb62b588d92ea5d0fd2c0e","relation":"main_file","file_id":"5206"}],"pubrep_id":"694","status":"public","ddc":["004","516"],"title":"Generalized offsetting of planar structures using skeletons","intvolume":" 13","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1272","month":"09","language":[{"iso":"eng"}],"doi":"10.1080/16864360.2016.1150718","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:44:42Z","publist_id":"6048","date_created":"2018-12-11T11:51:04Z","date_updated":"2021-01-12T06:49:32Z","volume":13,"author":[{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","first_name":"Stefan","last_name":"Huber","full_name":"Huber, Stefan"},{"full_name":"Palfrader, Peter","first_name":"Peter","last_name":"Palfrader"}],"publication_status":"published","publisher":"Taylor and Francis","department":[{"_id":"HeEd"}],"acknowledgement":"This work was supported by Austrian Science Fund (FWF): P25816-N15.","year":"2016"},{"article_number":"e0164675","ec_funded":1,"publist_id":"6037","file_date_updated":"2020-07-14T12:44:42Z","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] via the IST FELLOWSHIP awarded to Dr. Krisztián A. Kovács and the European Research Council starting grant (acronym: HIPECMEM Project reference: 281511) awarded to Dr. Jozsef Csicsvari. We thank Lauri Viljanto for technical help in building the ripple detector.","year":"2016","publisher":"Public Library of Science","department":[{"_id":"JoCs"}],"publication_status":"published","author":[{"last_name":"Kovács","first_name":"Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","full_name":"Kovács, Krisztián"},{"last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","full_name":"O'Neill, Joseph"},{"full_name":"Schönenberger, Philipp","first_name":"Philipp","last_name":"Schönenberger","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Markku","last_name":"Penttonen","full_name":"Penttonen, Markku"},{"last_name":"Rangel Guerrero","first_name":"Dámaris K","orcid":"0000-0002-8602-4374","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","full_name":"Rangel Guerrero, Dámaris K"},{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"volume":11,"date_updated":"2021-01-12T06:49:35Z","date_created":"2018-12-11T11:51:06Z","month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"}],"quality_controlled":"1","doi":"10.1371/journal.pone.0164675","language":[{"iso":"eng"}],"type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"During hippocampal sharp wave/ripple (SWR) events, previously occurring, sensory inputdriven neuronal firing patterns are replayed. Such replay is thought to be important for plasticity- related processes and consolidation of memory traces. It has previously been shown that the electrical stimulation-induced disruption of SWR events interferes with learning in rodents in different experimental paradigms. On the other hand, the cognitive map theory posits that the plastic changes of the firing of hippocampal place cells constitute the electrophysiological counterpart of the spatial learning, observable at the behavioral level. Therefore, we tested whether intact SWR events occurring during the sleep/rest session after the first exploration of a novel environment are needed for the stabilization of the CA1 code, which process requires plasticity. We found that the newly-formed representation in the CA1 has the same level of stability with optogenetic SWR blockade as with a control manipulation that delivered the same amount of light into the brain. Therefore our results suggest that at least in the case of passive exploratory behavior, SWR-related plasticity is dispensable for the stability of CA1 ensembles."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1279","intvolume":" 11","status":"public","ddc":["570","571"],"title":"Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus","pubrep_id":"690","file":[{"file_name":"IST-2016-690-v1+1_journal.pone.0164675.PDF","access_level":"open_access","creator":"system","file_size":4353592,"content_type":"application/pdf","file_id":"5009","relation":"main_file","date_created":"2018-12-12T10:13:26Z","date_updated":"2020-07-14T12:44:42Z","checksum":"395895ecb2216e9c39135abaa56b28b3"}],"oa_version":"Published Version","scopus_import":1,"has_accepted_license":"1","day":"19","citation":{"chicago":"Kovács, Krisztián, Joseph O’Neill, Philipp Schönenberger, Markku Penttonen, Dámaris K Rangel Guerrero, and Jozsef L Csicsvari. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0164675.","short":"K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D.K. Rangel Guerrero, J.L. Csicsvari, PLoS One 11 (2016).","mla":"Kovács, Krisztián, et al. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” PLoS One, vol. 11, no. 10, e0164675, Public Library of Science, 2016, doi:10.1371/journal.pone.0164675.","ieee":"K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D. K. Rangel Guerrero, and J. L. Csicsvari, “Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus,” PLoS One, vol. 11, no. 10. Public Library of Science, 2016.","apa":"Kovács, K., O’Neill, J., Schönenberger, P., Penttonen, M., Rangel Guerrero, D. K., & Csicsvari, J. L. (2016). Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0164675","ista":"Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. 2016. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. 11(10), e0164675.","ama":"Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164675"},"publication":"PLoS One","date_published":"2016-10-19T00:00:00Z"},{"citation":{"chicago":"Matsuno, Hitomi, Moeko Kudoh, Akiya Watakabe, Tetsuo Yamamori, Ryuichi Shigemoto, and Soichi Nagao. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0164037.","mla":"Matsuno, Hitomi, et al. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One, vol. 11, no. 10, e0164037, Public Library of Science, 2016, doi:10.1371/journal.pone.0164037.","short":"H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, S. Nagao, PLoS One 11 (2016).","ista":"Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. 2016. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. 11(10), e0164037.","ieee":"H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, and S. Nagao, “Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies,” PLoS One, vol. 11, no. 10. Public Library of Science, 2016.","apa":"Matsuno, H., Kudoh, M., Watakabe, A., Yamamori, T., Shigemoto, R., & Nagao, S. (2016). Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0164037","ama":"Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164037"},"publication":"PLoS One","article_type":"original","date_published":"2016-10-06T00:00:00Z","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1278","intvolume":" 11","ddc":["570","571"],"title":"Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies","status":"public","pubrep_id":"689","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":3657084,"file_name":"IST-2016-689-v1+1_journal.pone.0164037.PDF","access_level":"open_access","date_created":"2018-12-12T10:17:16Z","date_updated":"2020-07-14T12:44:42Z","checksum":"7c0ba0ca6d79844059158059d2a38d25","file_id":"5269","relation":"main_file"}],"type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"Adaptations of vestibulo-ocular and optokinetic response eye movements have been studied as an experimental model of cerebellum-dependent motor learning. Several previous physiological and pharmacological studies have consistently suggested that the cerebellar flocculus (FL) Purkinje cells (P-cells) and the medial vestibular nucleus (MVN) neurons targeted by FL (FL-targeted MVN neurons) may respectively maintain the memory traces of short- and long-term adaptation. To study the basic structures of the FL-MVN synapses by light microscopy (LM) and electron microscopy (EM), we injected green florescence protein (GFP)-expressing lentivirus into FL to anterogradely label the FL P-cell axons in C57BL/6J mice. The FL P-cell axonal boutons were distributed in the magnocellular MVN and in the border region of parvocellular MVN and prepositus hypoglossi (PrH). In the magnocellular MVN, the FL-P cell axons mainly terminated on somata and proximal dendrites. On the other hand, in the parvocellular MVN/PrH, the FL P-cell axonal synaptic boutons mainly terminated on the relatively small-diameter (< 1 μm) distal dendrites of MVN neurons, forming symmetrical synapses. The majority of such parvocellular MVN/PrH neurons were determined to be glutamatergic by immunocytochemistry and in-situ hybridization of GFP expressing transgenic mice. To further examine the spatial relationship between the synapses of FL P-cells and those of vestibular nerve on the neurons of the parvocellular MVN/ PrH, we added injections of biotinylated dextran amine into the semicircular canal and anterogradely labeled vestibular nerve axons in some mice. The MVN dendrites receiving the FL P-cell axonal synaptic boutons often closely apposed vestibular nerve synaptic boutons in both LM and EM studies. Such a partial overlap of synaptic boutons of FL P-cell axons with those of vestibular nerve axons in the distal dendrites of MVN neurons suggests that inhibitory synapses of FL P-cells may influence the function of neighboring excitatory synapses of vestibular nerve in the parvocellular MVN/PrH neurons."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0164037","language":[{"iso":"eng"}],"month":"10","acknowledgement":"This work was supported by RIKEN [to SN]; Grant-in-Aid from the Japan Society for the Promotion of Science, https://www.jsps.go.jp/english/e-grants/ [22300112 to SN].","year":"2016","publisher":"Public Library of Science","department":[{"_id":"RySh"}],"publication_status":"published","author":[{"full_name":"Matsuno, Hitomi","last_name":"Matsuno","first_name":"Hitomi"},{"full_name":"Kudoh, Moeko","last_name":"Kudoh","first_name":"Moeko"},{"first_name":"Akiya","last_name":"Watakabe","full_name":"Watakabe, Akiya"},{"first_name":"Tetsuo","last_name":"Yamamori","full_name":"Yamamori, Tetsuo"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"full_name":"Nagao, Soichi","last_name":"Nagao","first_name":"Soichi"}],"volume":11,"date_updated":"2021-01-12T06:49:34Z","date_created":"2018-12-11T11:51:06Z","article_number":"e0164037","publist_id":"6038","file_date_updated":"2020-07-14T12:44:42Z"},{"department":[{"_id":"LeSa"}],"publisher":"Nature Publishing Group","publication_status":"published","acknowledgement":"We wish to thank CSC – IT Centre for Science (Espoo, Finland) for computational resources. For financial support, we wish to thank the Academy of Finland (TR, IV and PAP; Center of Excellence in Biomembrane Research (IV, TR)), the Finnish Doctoral Programme in Computational Sciences (KK), the Sigrid Juselius Foundation (IV), the Paulo Foundation (PAP), and the European Research Council (IV, TR; Advanced Grant project CROWDED-PRO-LIPIDS). AO acknowledges The Wellcome Trust International Senior Research Fellowship.","year":"2016","volume":6,"date_created":"2018-12-11T11:51:05Z","date_updated":"2021-01-12T06:49:34Z","author":[{"first_name":"Pekka","last_name":"Postila","full_name":"Postila, Pekka"},{"last_name":"Kaszuba","first_name":"Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","full_name":"Kaszuba, Karol"},{"full_name":"Kuleta, Patryk","first_name":"Patryk","last_name":"Kuleta"},{"full_name":"Vattulainen, Ilpo","first_name":"Ilpo","last_name":"Vattulainen"},{"full_name":"Sarewicz, Marcin","last_name":"Sarewicz","first_name":"Marcin"},{"full_name":"Osyczka, Artur","first_name":"Artur","last_name":"Osyczka"},{"full_name":"Róg, Tomasz","first_name":"Tomasz","last_name":"Róg"}],"article_number":"33607","publist_id":"6040","file_date_updated":"2020-07-14T12:44:42Z","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/srep33607","month":"09","intvolume":" 6","title":"Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex","ddc":["576"],"status":"public","_id":"1276","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2016-691-v1+1_srep33607.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1960563,"file_id":"5261","relation":"main_file","date_created":"2018-12-12T10:17:09Z","date_updated":"2020-07-14T12:44:42Z","checksum":"07c591c1250ebef266333cbc3228b4dd"}],"oa_version":"Published Version","pubrep_id":"691","type":"journal_article","abstract":[{"lang":"eng","text":"The cytochrome (cyt) bc 1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q i-site of the cyt bc 1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q i-site to facilitate binding of half-protonated semiquinone-a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q i-site."}],"citation":{"mla":"Postila, Pekka, et al. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” Scientific Reports, vol. 6, 33607, Nature Publishing Group, 2016, doi:10.1038/srep33607.","short":"P. Postila, K. Kaszuba, P. Kuleta, I. Vattulainen, M. Sarewicz, A. Osyczka, T. Róg, Scientific Reports 6 (2016).","chicago":"Postila, Pekka, Karol Kaszuba, Patryk Kuleta, Ilpo Vattulainen, Marcin Sarewicz, Artur Osyczka, and Tomasz Róg. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33607.","ama":"Postila P, Kaszuba K, Kuleta P, et al. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. 2016;6. doi:10.1038/srep33607","ista":"Postila P, Kaszuba K, Kuleta P, Vattulainen I, Sarewicz M, Osyczka A, Róg T. 2016. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. 6, 33607.","ieee":"P. Postila et al., “Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","apa":"Postila, P., Kaszuba, K., Kuleta, P., Vattulainen, I., Sarewicz, M., Osyczka, A., & Róg, T. (2016). Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep33607"},"publication":"Scientific Reports","date_published":"2016-09-26T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"26"},{"day":"27","scopus_import":1,"date_published":"2016-09-27T00:00:00Z","page":"11028 - 11033","citation":{"chicago":"Ortiz Morea, Fausto, Daniel Savatin, Wim Dejonghe, Rahul Kumar, Yu Luo, Maciek Adamowski, Jos Van Begin, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1605588113.","mla":"Ortiz Morea, Fausto, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS, vol. 113, no. 39, National Academy of Sciences, 2016, pp. 11028–33, doi:10.1073/pnas.1605588113.","short":"F. Ortiz Morea, D. Savatin, W. Dejonghe, R. Kumar, Y. Luo, M. Adamowski, J. Van Begin, K. Dressano, G. De Oliveira, X. Zhao, Q. Lu, A. Madder, J. Friml, D. De Moura, E. Russinova, PNAS 113 (2016) 11028–11033.","ista":"Ortiz Morea F, Savatin D, Dejonghe W, Kumar R, Luo Y, Adamowski M, Van Begin J, Dressano K, De Oliveira G, Zhao X, Lu Q, Madder A, Friml J, De Moura D, Russinova E. 2016. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 113(39), 11028–11033.","ieee":"F. Ortiz Morea et al., “Danger-associated peptide signaling in Arabidopsis requires clathrin,” PNAS, vol. 113, no. 39. National Academy of Sciences, pp. 11028–11033, 2016.","apa":"Ortiz Morea, F., Savatin, D., Dejonghe, W., Kumar, R., Luo, Y., Adamowski, M., … Russinova, E. (2016). Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1605588113","ama":"Ortiz Morea F, Savatin D, Dejonghe W, et al. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 2016;113(39):11028-11033. doi:10.1073/pnas.1605588113"},"publication":"PNAS","issue":"39","abstract":[{"text":"The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components.\r\n","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 113","status":"public","title":"Danger-associated peptide signaling in Arabidopsis requires clathrin","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1277","month":"09","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1605588113","quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047203/","open_access":"1"}],"oa":1,"publist_id":"6039","volume":113,"date_updated":"2021-01-12T06:49:34Z","date_created":"2018-12-11T11:51:06Z","author":[{"last_name":"Ortiz Morea","first_name":"Fausto","full_name":"Ortiz Morea, Fausto"},{"last_name":"Savatin","first_name":"Daniel","full_name":"Savatin, Daniel"},{"last_name":"Dejonghe","first_name":"Wim","full_name":"Dejonghe, Wim"},{"last_name":"Kumar","first_name":"Rahul","full_name":"Kumar, Rahul"},{"first_name":"Yu","last_name":"Luo","full_name":"Luo, Yu"},{"full_name":"Adamowski, Maciek","last_name":"Adamowski","first_name":"Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jos","last_name":"Van Begin","full_name":"Van Begin, Jos"},{"full_name":"Dressano, Keini","first_name":"Keini","last_name":"Dressano"},{"full_name":"De Oliveira, Guilherme","last_name":"De Oliveira","first_name":"Guilherme"},{"last_name":"Zhao","first_name":"Xiuyang","full_name":"Zhao, Xiuyang"},{"first_name":"Qing","last_name":"Lu","full_name":"Lu, Qing"},{"full_name":"Madder, Annemieke","last_name":"Madder","first_name":"Annemieke"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"De Moura, Daniel","first_name":"Daniel","last_name":"De Moura"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"}],"department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publication_status":"published","year":"2016","acknowledgement":"F.A.O.-M. was supported by special\r\nresearch funding from the Flemish Government for a joint doctorate fellowship\r\nat Ghent University, and funding from the Student Program\r\n–\r\nGraduate Studies\r\nPlan Program from the Coordination for the Improvement of Higher Educa-\r\ntion Personnel, Brazil, for a doctorate fellowship at the University of São Paulo.\r\nX.Z. and Q.L. are indebted to the China Science Council and G.P.d.O. to the\r\n“\r\nCiência sem Fronteiras\r\n”\r\nfor predoctoral fellowships. R.K. and Y.L. have re-\r\nceived postdoctoral fellowships from the Belgian Science Policy Office. This\r\nresearch was supported by Flanders Research Foundation Grant G008416N\r\n(to E.R.) and by the São Paulo Research Foundation and the National Council\r\nfor Scientific and Technological Development (CNPq) (D.S.d.M.). D.S.d.M. is a\r\nresearch fellow of CNPq.\r\nWe thank D. Van Damme, E. Mylle, M. Castro Silva-Filho,\r\nand J. Goeman for providing usefu\r\nl advice and technical assistance;\r\nI. Hara-Nishimura, J. Lin, G. Jürgens, M. A. Johnson, and P. Bozhkov for sharing\r\npublished materials; and M. Nowack and M. Fendrych for kindly donating the\r\npUBQ10::ATG8-YFP\r\n-expressing marker line."},{"scopus_import":1,"day":"01","publication":"Plant Physiology","citation":{"ieee":"E. Bouguyon et al., “Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1237–1248, 2016.","apa":"Bouguyon, E., Perrine Walker, F., Pervent, M., Rochette, J., Cuesta, C., Benková, E., … Nacry, P. (2016). Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01047","ista":"Bouguyon E, Perrine Walker F, Pervent M, Rochette J, Cuesta C, Benková E, Martinière A, Bach L, Krouk G, Gojon A, Nacry P. 2016. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 172(2), 1237–1248.","ama":"Bouguyon E, Perrine Walker F, Pervent M, et al. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 2016;172(2):1237-1248. doi:10.1104/pp.16.01047","chicago":"Bouguyon, Eléonore, Francine Perrine Walker, Marjorie Pervent, Juliette Rochette, Candela Cuesta, Eva Benková, Alexandre Martinière, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.01047.","short":"E. Bouguyon, F. Perrine Walker, M. Pervent, J. Rochette, C. Cuesta, E. Benková, A. Martinière, L. Bach, G. Krouk, A. Gojon, P. Nacry, Plant Physiology 172 (2016) 1237–1248.","mla":"Bouguyon, Eléonore, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1237–48, doi:10.1104/pp.16.01047."},"page":"1237 - 1248","date_published":"2016-10-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3 - through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3 -. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3 - stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue."}],"issue":"2","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1281","title":"Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor","status":"public","intvolume":" 172","oa_version":"Preprint","month":"10","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047109/","open_access":"1"}],"quality_controlled":"1","doi":"10.1104/pp.16.01047","language":[{"iso":"eng"}],"publist_id":"6035","acknowledgement":"This work was supported by the Agropolis Foundation (RHIZOPOLIS project to A.G. and P.N., and RTRA 2009-2011 project to F.P.-W.), the Knowledge Biobase Economy European project (KBBE-005-002 Root enhancement for crop improvement to M.P. and P.N.), and the European EURoot project (FP7-KBBE-2011-5 to J.R., A.G., and P.N.). We thank Carine Alcon for the help with analysis of confocal images, Xavier\r\nDumont for assistance with Arabidopsis transformations, staff members of the\r\nInstitut de Biologie Intégrative des Plantes for technical assistance with biological\r\nmaterial culture, and students and trainees for assistance with laboratory work.\r\nConfocal observations were made at the Montpellier RIO Imaging facility.","year":"2016","publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"EvBe"}],"author":[{"full_name":"Bouguyon, Eléonore","first_name":"Eléonore","last_name":"Bouguyon"},{"last_name":"Perrine Walker","first_name":"Francine","full_name":"Perrine Walker, Francine"},{"full_name":"Pervent, Marjorie","first_name":"Marjorie","last_name":"Pervent"},{"first_name":"Juliette","last_name":"Rochette","full_name":"Rochette, Juliette"},{"full_name":"Cuesta, Candela","last_name":"Cuesta","first_name":"Candela","orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"first_name":"Alexandre","last_name":"Martinière","full_name":"Martinière, Alexandre"},{"last_name":"Bach","first_name":"Lien","full_name":"Bach, Lien"},{"first_name":"Gabriel","last_name":"Krouk","full_name":"Krouk, Gabriel"},{"last_name":"Gojon","first_name":"Alain","full_name":"Gojon, Alain"},{"last_name":"Nacry","first_name":"Philippe","full_name":"Nacry, Philippe"}],"date_updated":"2021-01-12T06:49:36Z","date_created":"2018-12-11T11:51:07Z","volume":172},{"type":"journal_article","abstract":[{"lang":"eng","text":"We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of k-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the eigenvalues of the higher-dimensional Laplacian capture the notion of coboundary expansion—a higher-dimensional generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov; this question was raised, for instance, by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised k-dimensional Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn k can be taken to have vanishing integer homology in dimension less than k."}],"issue":"2","publist_id":"6034","publication_status":"published","status":"public","title":"On eigenvalues of random complexes","publisher":"Springer","intvolume":" 216","department":[{"_id":"UlWa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1282","year":"2016","date_updated":"2021-01-12T06:49:36Z","date_created":"2018-12-11T11:51:07Z","volume":216,"oa_version":"Preprint","author":[{"full_name":"Gundert, Anna","last_name":"Gundert","first_name":"Anna"},{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"day":"01","month":"10","quality_controlled":"1","page":"545 - 582","publication":"Israel Journal of Mathematics","citation":{"ieee":"A. Gundert and U. Wagner, “On eigenvalues of random complexes,” Israel Journal of Mathematics, vol. 216, no. 2. Springer, pp. 545–582, 2016.","apa":"Gundert, A., & Wagner, U. (2016). On eigenvalues of random complexes. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1419-1","ista":"Gundert A, Wagner U. 2016. On eigenvalues of random complexes. Israel Journal of Mathematics. 216(2), 545–582.","ama":"Gundert A, Wagner U. On eigenvalues of random complexes. Israel Journal of Mathematics. 2016;216(2):545-582. doi:10.1007/s11856-016-1419-1","chicago":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1419-1.","short":"A. Gundert, U. Wagner, Israel Journal of Mathematics 216 (2016) 545–582.","mla":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 545–82, doi:10.1007/s11856-016-1419-1."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.4906"}],"oa":1,"language":[{"iso":"eng"}],"date_published":"2016-10-01T00:00:00Z","doi":"10.1007/s11856-016-1419-1"},{"issue":"10","abstract":[{"lang":"eng","text":"We prove the Wigner-Dyson-Mehta conjecture at fixed energy in the bulk of the spectrum for generalized symmetric and Hermitian Wigner matrices. Previous results concerning the universality of random matrices either require an averaging in the energy parameter or they hold only for Hermitian matrices if the energy parameter is fixed. We develop a homogenization theory of the Dyson Brownian motion and show that microscopic universality follows from mesoscopic statistics."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 69","title":"Fixed energy universality for generalized wigner matrices","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1280","day":"01","scopus_import":1,"date_published":"2016-10-01T00:00:00Z","page":"1815 - 1881","citation":{"ama":"Bourgade P, Erdös L, Yau H, Yin J. Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. 2016;69(10):1815-1881. doi:10.1002/cpa.21624","apa":"Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2016). Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21624","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Fixed energy universality for generalized wigner matrices,” Communications on Pure and Applied Mathematics, vol. 69, no. 10. Wiley-Blackwell, pp. 1815–1881, 2016.","ista":"Bourgade P, Erdös L, Yau H, Yin J. 2016. Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. 69(10), 1815–1881.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Communications on Pure and Applied Mathematics 69 (2016) 1815–1881.","mla":"Bourgade, Paul, et al. “Fixed Energy Universality for Generalized Wigner Matrices.” Communications on Pure and Applied Mathematics, vol. 69, no. 10, Wiley-Blackwell, 2016, pp. 1815–81, doi:10.1002/cpa.21624.","chicago":"Bourgade, Paul, László Erdös, Horngtzer Yau, and Jun Yin. “Fixed Energy Universality for Generalized Wigner Matrices.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2016. https://doi.org/10.1002/cpa.21624."},"publication":"Communications on Pure and Applied Mathematics","publist_id":"6036","ec_funded":1,"volume":69,"date_updated":"2021-01-12T06:49:35Z","date_created":"2018-12-11T11:51:07Z","author":[{"first_name":"Paul","last_name":"Bourgade","full_name":"Bourgade, Paul"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"last_name":"Yau","first_name":"Horngtzer","full_name":"Yau, Horngtzer"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"publisher":"Wiley-Blackwell","department":[{"_id":"LaEr"}],"publication_status":"published","acknowledgement":"The work of P.B. was partially supported by National Sci-\r\nence Foundation Grant DMS-1208859. The work of L.E. was partially supported\r\nby ERC Advanced Grant RANMAT 338804. The work of H.-T. Y. was partially\r\nsupported by National Science Foundation Grant DMS-1307444 and a Simons In-\r\nvestigator award. The work of J.Y. was partially supported by National Science\r\nFoundation Grant DMS-1207961. The major part of this research was conducted\r\nwhen all authors were visiting IAS and were also supported by National Science\r\nFoundation Grant DMS-1128255.","year":"2016","month":"10","language":[{"iso":"eng"}],"doi":"10.1002/cpa.21624","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1407.5606"}]},{"month":"10","doi":"10.1103/PhysRevA.94.041601","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.06092"}],"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publist_id":"6030","ec_funded":1,"article_number":"041601","author":[{"full_name":"Midya, Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","first_name":"Bikashkali","last_name":"Midya"},{"first_name":"Michał","last_name":"Tomza","full_name":"Tomza, Michał"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"volume":94,"date_updated":"2021-01-12T06:49:37Z","date_created":"2018-12-11T11:51:09Z","acknowledgement":"The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and the Smithsonian Astrophysical Observatory. B.M. acknowledges financial support received from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 291734. M.T. acknowledges support from the EU Marie Curie COFUND action (ICFOnest), the EU Grants ERC AdG OSYRIS, FP7 SIQS and EQuaM, FETPROACT QUIC, the Spanish Ministry Grants FOQUS (FIS2013-46768-P) and Severo Ochoa (SEV-2015-0522), Generalitat de Catalunya (SGR 874), Fundacio Cellex, the National Science Centre (2015/19/D/ST4/02173), and the PL-Grid Infrastructure.","year":"2016","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","day":"13","scopus_import":1,"date_published":"2016-10-13T00:00:00Z","citation":{"ama":"Midya B, Tomza M, Schmidt R, Lemeshko M. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;94(4). doi:10.1103/PhysRevA.94.041601","apa":"Midya, B., Tomza, M., Schmidt, R., & Lemeshko, M. (2016). Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.94.041601","ieee":"B. Midya, M. Tomza, R. Schmidt, and M. Lemeshko, “Rotation of cold molecular ions inside a Bose-Einstein condensate,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 94, no. 4. American Physical Society, 2016.","ista":"Midya B, Tomza M, Schmidt R, Lemeshko M. 2016. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. 94(4), 041601.","short":"B. Midya, M. Tomza, R. Schmidt, M. Lemeshko, Physical Review A - Atomic, Molecular, and Optical Physics 94 (2016).","mla":"Midya, Bikashkali, et al. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 94, no. 4, 041601, American Physical Society, 2016, doi:10.1103/PhysRevA.94.041601.","chicago":"Midya, Bikashkali, Michał Tomza, Richard Schmidt, and Mikhail Lemeshko. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.94.041601."},"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","issue":"4","abstract":[{"text":"We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on ab initio potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the ab initio potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"1286","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 94","title":"Rotation of cold molecular ions inside a Bose-Einstein condensate","status":"public"},{"date_published":"2016-11-01T00:00:00Z","citation":{"apa":"Giuliani, A., & Seiringer, R. (2016). Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2665-0","ieee":"A. Giuliani and R. Seiringer, “Periodic striped ground states in Ising models with competing interactions,” Communications in Mathematical Physics, vol. 347, no. 3. Springer, pp. 983–1007, 2016.","ista":"Giuliani A, Seiringer R. 2016. Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. 347(3), 983–1007.","ama":"Giuliani A, Seiringer R. Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. 2016;347(3):983-1007. doi:10.1007/s00220-016-2665-0","chicago":"Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” Communications in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-016-2665-0.","short":"A. Giuliani, R. Seiringer, Communications in Mathematical Physics 347 (2016) 983–1007.","mla":"Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” Communications in Mathematical Physics, vol. 347, no. 3, Springer, 2016, pp. 983–1007, doi:10.1007/s00220-016-2665-0."},"publication":"Communications in Mathematical Physics","page":"983 - 1007","has_accepted_license":"1","day":"01","scopus_import":1,"pubrep_id":"688","file":[{"file_size":794983,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-688-v1+1_s00220-016-2665-0.pdf","checksum":"3c6e08c048fc462e312788be72874bb1","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:09:02Z","relation":"main_file","file_id":"4725"}],"oa_version":"Published Version","_id":"1291","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 347","title":"Periodic striped ground states in Ising models with competing interactions","status":"public","ddc":["510","530"],"issue":"3","abstract":[{"text":"We consider Ising models in two and three dimensions, with short range ferromagnetic and long range, power-law decaying, antiferromagnetic interactions. We let J be the ratio between the strength of the ferromagnetic to antiferromagnetic interactions. The competition between these two kinds of interactions induces the system to form domains of minus spins in a background of plus spins, or vice versa. If the decay exponent p of the long range interaction is larger than d + 1, with d the space dimension, this happens for all values of J smaller than a critical value Jc(p), beyond which the ground state is homogeneous. In this paper, we give a characterization of the infinite volume ground states of the system, for p > 2d and J in a left neighborhood of Jc(p). In particular, we prove that the quasi-one-dimensional states consisting of infinite stripes (d = 2) or slabs (d = 3), all of the same optimal width and orientation, and alternating magnetization, are infinite volume ground states. Our proof is based on localization bounds combined with reflection positivity.","lang":"eng"}],"type":"journal_article","doi":"10.1007/s00220-016-2665-0","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","month":"11","author":[{"full_name":"Giuliani, Alessandro","last_name":"Giuliani","first_name":"Alessandro"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"volume":347,"date_created":"2018-12-11T11:51:11Z","date_updated":"2021-01-12T06:49:40Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The\r\nresearch leading to these results has received funding from the European Research Council under the European\r\nUnion’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694), from\r\nthe Italian PRIN National Grant Geometric and analytic theory of Hamiltonian systems in finite and infinite\r\ndimensions, and the Austrian Science Fund (FWF), project Nr. P 27533-N27. Part of this work was completed\r\nduring a stay at the Erwin Schrödinger Institute for Mathematical Physics in Vienna (ESI program 2015\r\n“Quantum many-body systems, random matrices, and disorder”), whose hospitality and financial support is\r\ngratefully acknowledged.","year":"2016","publisher":"Springer","department":[{"_id":"RoSe"}],"publication_status":"published","publist_id":"6025","file_date_updated":"2020-07-14T12:44:42Z"},{"year":"2016","acknowledgement":"We wish to thank Alexander Engström and Bernd Sturmfels for various valuable discussions and insights. We also thank the two anonymous referees for their thoughtful feedback on the paper. CU was partially supported by the Austrian Science Fund (FWF) Y 903-N35.","publisher":"Elsevier","department":[{"_id":"CaUh"}],"publication_status":"published","author":[{"first_name":"Liam T","last_name":"Solus","id":"2AADA620-F248-11E8-B48F-1D18A9856A87","full_name":"Solus, Liam T"},{"full_name":"Uhler, Caroline","first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216"},{"first_name":"Ruriko","last_name":"Yoshida","full_name":"Yoshida, Ruriko"}],"volume":509,"date_updated":"2021-01-12T06:49:40Z","date_created":"2018-12-11T11:51:11Z","publist_id":"6024","main_file_link":[{"url":"https://arxiv.org/pdf/1506.06702.pdf","open_access":"1"}],"oa":1,"project":[{"name":"Gaussian Graphical Models: Theory and Applications","call_identifier":"FWF","grant_number":"Y 903-N35","_id":"2530CA10-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1016/j.laa.2016.07.026","language":[{"iso":"eng"}],"month":"11","_id":"1293","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 509","status":"public","title":"Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"For a graph G with p vertices the closed convex cone S⪰0(G) consists of all real positive semidefinite p×p matrices whose sparsity pattern is given by G, that is, those matrices with zeros in the off-diagonal entries corresponding to nonedges of G. The extremal rays of this cone and their associated ranks have applications to matrix completion problems, maximum likelihood estimation in Gaussian graphical models in statistics, and Gauss elimination for sparse matrices. While the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of G, has been characterized for different classes of graphs, we here study all possible extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G). For a graph G without K5 minors, we show that appropriately chosen normal vectors to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars the constant term of the linear equation of each facet-supporting hyperplane is the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show that if G is series-parallel then this gives a complete characterization of all possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for series-parallel graphs can be solved in terms of polyhedral geometry."}],"citation":{"short":"L.T. Solus, C. Uhler, R. Yoshida, Linear Algebra and Its Applications 509 (2016) 247–275.","mla":"Solus, Liam T., et al. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” Linear Algebra and Its Applications, vol. 509, Elsevier, 2016, pp. 247–75, doi:10.1016/j.laa.2016.07.026.","chicago":"Solus, Liam T, Caroline Uhler, and Ruriko Yoshida. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” Linear Algebra and Its Applications. Elsevier, 2016. https://doi.org/10.1016/j.laa.2016.07.026.","ama":"Solus LT, Uhler C, Yoshida R. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. 2016;509:247-275. doi:10.1016/j.laa.2016.07.026","ieee":"L. T. Solus, C. Uhler, and R. Yoshida, “Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors,” Linear Algebra and Its Applications, vol. 509. Elsevier, pp. 247–275, 2016.","apa":"Solus, L. T., Uhler, C., & Yoshida, R. (2016). Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2016.07.026","ista":"Solus LT, Uhler C, Yoshida R. 2016. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. 509, 247–275."},"publication":"Linear Algebra and Its Applications","page":"247 - 275","date_published":"2016-11-15T00:00:00Z","scopus_import":1,"day":"15"},{"status":"public","title":"Compounds that select against the tetracycline-resistance efflux pump","intvolume":" 12","_id":"1290","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline."}],"issue":"11","page":"902 - 904","publication":"Nature Chemical Biology","citation":{"ista":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904.","ieee":"L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” Nature Chemical Biology, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.","apa":"Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., & Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.2176","ama":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 2016;12(11):902-904. doi:10.1038/nchembio.2176","chicago":"Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/nchembio.2176.","mla":"Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:10.1038/nchembio.2176.","short":"L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904."},"date_published":"2016-11-01T00:00:00Z","scopus_import":1,"day":"01","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Nature Publishing Group","acknowledgement":"This work was supported in part by National Institute of Allergy and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to L.K.S.).\r\n","year":"2016","date_created":"2018-12-11T11:51:10Z","date_updated":"2021-01-12T06:49:39Z","volume":12,"author":[{"last_name":"Stone","first_name":"Laura","full_name":"Stone, Laura"},{"full_name":"Baym, Michael","last_name":"Baym","first_name":"Michael"},{"full_name":"Lieberman, Tami","first_name":"Tami","last_name":"Lieberman"},{"full_name":"Chait, Remy P","last_name":"Chait","first_name":"Remy P","orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jon","last_name":"Clardy","full_name":"Clardy, Jon"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"publist_id":"6026","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1038/nchembio.2176","month":"11"},{"scopus_import":1,"day":"01","page":"441 - 455","publication":"Acta Mathematica Hungarica","citation":{"ama":"Durst S, Kegel M, Klukas MD. Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. 2016;150(2):441-455. doi:10.1007/s10474-016-0648-4","ista":"Durst S, Kegel M, Klukas MD. 2016. Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. 150(2), 441–455.","ieee":"S. Durst, M. Kegel, and M. D. Klukas, “Computing the Thurston–Bennequin invariant in open books,” Acta Mathematica Hungarica, vol. 150, no. 2. Springer, pp. 441–455, 2016.","apa":"Durst, S., Kegel, M., & Klukas, M. D. (2016). Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. Springer. https://doi.org/10.1007/s10474-016-0648-4","mla":"Durst, Sebastian, et al. “Computing the Thurston–Bennequin Invariant in Open Books.” Acta Mathematica Hungarica, vol. 150, no. 2, Springer, 2016, pp. 441–55, doi:10.1007/s10474-016-0648-4.","short":"S. Durst, M. Kegel, M.D. Klukas, Acta Mathematica Hungarica 150 (2016) 441–455.","chicago":"Durst, Sebastian, Marc Kegel, and Mirko D Klukas. “Computing the Thurston–Bennequin Invariant in Open Books.” Acta Mathematica Hungarica. Springer, 2016. https://doi.org/10.1007/s10474-016-0648-4."},"date_published":"2016-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We give explicit formulas and algorithms for the computation of the Thurston–Bennequin invariant of a nullhomologous Legendrian knot on a page of a contact open book and on Heegaard surfaces in convex position. Furthermore, we extend the results to rationally nullhomologous knots in arbitrary 3-manifolds."}],"issue":"2","status":"public","title":"Computing the Thurston–Bennequin invariant in open books","intvolume":" 150","_id":"1292","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"12","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1605.00794","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/s10474-016-0648-4","publist_id":"6023","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer","acknowledgement":"The authors are veryg rateful to Hansj ̈org Geiges \r\nfor fruitful discussions and advice and Christian Evers for helpful remarks on a draft version.","year":"2016","date_created":"2018-12-11T11:51:11Z","date_updated":"2021-01-12T06:49:40Z","volume":150,"author":[{"last_name":"Durst","first_name":"Sebastian","full_name":"Durst, Sebastian"},{"full_name":"Kegel, Marc","last_name":"Kegel","first_name":"Marc"},{"full_name":"Klukas, Mirko D","id":"34927512-F248-11E8-B48F-1D18A9856A87","first_name":"Mirko D","last_name":"Klukas"}]},{"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.7554/eLife.17977","quality_controlled":"1","project":[{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"10","date_created":"2018-12-11T11:51:22Z","date_updated":"2023-02-21T10:34:24Z","volume":5,"author":[{"full_name":"Vyleta, Nicholas","last_name":"Vyleta","first_name":"Nicholas","id":"36C4978E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carolina","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"PeJo"}],"year":"2016","file_date_updated":"2020-07-14T12:44:44Z","publist_id":"5947","ec_funded":1,"article_number":"e17977","date_published":"2016-10-25T00:00:00Z","publication":"eLife","citation":{"mla":"Vyleta, Nicholas, et al. “Plasticity-Dependent, Full Detonation at Hippocampal Mossy Fiber–CA3 Pyramidal Neuron Synapses.” ELife, vol. 5, e17977, eLife Sciences Publications, 2016, doi:10.7554/eLife.17977.","short":"N. Vyleta, C. Borges Merjane, P.M. Jonas, ELife 5 (2016).","chicago":"Vyleta, Nicholas, Carolina Borges Merjane, and Peter M Jonas. “Plasticity-Dependent, Full Detonation at Hippocampal Mossy Fiber–CA3 Pyramidal Neuron Synapses.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.17977.","ama":"Vyleta N, Borges Merjane C, Jonas PM. Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. eLife. 2016;5. doi:10.7554/eLife.17977","ista":"Vyleta N, Borges Merjane C, Jonas PM. 2016. Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. eLife. 5, e17977.","ieee":"N. Vyleta, C. Borges Merjane, and P. M. Jonas, “Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses,” eLife, vol. 5. eLife Sciences Publications, 2016.","apa":"Vyleta, N., Borges Merjane, C., & Jonas, P. M. (2016). Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.17977"},"day":"25","has_accepted_license":"1","scopus_import":1,"file":[{"file_name":"IST-2016-715-v1+1_e17977-download.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1477891,"creator":"system","relation":"main_file","file_id":"5257","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:17:05Z","checksum":"a7201280c571bed88ebd459ce5ce6a47"}],"oa_version":"Published Version","pubrep_id":"715","status":"public","ddc":["571","572"],"title":"Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses","intvolume":" 5","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1323","abstract":[{"lang":"eng","text":"Mossy fiber synapses on CA3 pyramidal cells are 'conditional detonators' that reliably discharge postsynaptic targets. The 'conditional' nature implies that burst activity in dentate gyrus granule cells is required for detonation. Whether single unitary excitatory postsynaptic potentials (EPSPs) trigger spikes in CA3 neurons remains unknown. Mossy fiber synapses exhibit both pronounced short-term facilitation and uniquely large post-tetanic potentiation (PTP). We tested whether PTP could convert mossy fiber synapses from subdetonator into detonator mode, using a recently developed method to selectively and noninvasively stimulate individual presynaptic terminals in rat brain slices. Unitary EPSPs failed to initiate a spike in CA3 neurons under control conditions, but reliably discharged them after induction of presynaptic short-term plasticity. Remarkably, PTP switched mossy fiber synapses into full detonators for tens of seconds. Plasticity-dependent detonation may be critical for efficient coding, storage, and recall of information in the granule cell–CA3 cell network."}],"type":"journal_article"},{"article_number":"10","ec_funded":1,"publist_id":"5944","file_date_updated":"2020-07-14T12:44:44Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"The work has been supported by the Czech Science Foundation, grant No. 15-17564S, by EPSRC grant\r\nEP/M023656/1, and by the People Programme (Marie Curie Actions) of the European Union’s Seventh\r\nFramework Programme (FP7/2007-2013) under REA grant agreement no [291734]","year":"2016","volume":59,"date_created":"2018-12-11T11:51:23Z","date_updated":"2021-01-12T06:49:53Z","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"last_name":"Forejt","first_name":"Vojtěch","full_name":"Forejt, Vojtěch"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","first_name":"Petr","full_name":"Novotny, Petr"}],"month":"08","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.CONCUR.2016.10","conference":{"start_date":"2016-08-23","location":"Quebec City, Canada","end_date":"2016-08-26","name":"CONCUR: Concurrency Theory"},"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"We study graphs and two-player games in which rewards are assigned to states, and the goal of the players is to satisfy or dissatisfy certain property of the generated outcome, given as a mean payoff property. Since the notion of mean-payoff does not reflect possible fluctuations from the mean-payoff along a run, we propose definitions and algorithms for capturing the stability of the system, and give algorithms for deciding if a given mean payoff and stability objective can be ensured in the system."}],"intvolume":" 59","ddc":["004"],"status":"public","title":"Stability in graphs and games","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1325","file":[{"file_id":"5229","relation":"main_file","date_created":"2018-12-12T10:16:40Z","date_updated":"2020-07-14T12:44:44Z","checksum":"3c2dc6ab0358f8aa8f7aa7d6c1293159","file_name":"IST-2016-665-v1+1_Forejt_et_al__Stability_in_graphs_and_games.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":553648}],"oa_version":"Published Version","pubrep_id":"665","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"short":"T. Brázdil, V. Forejt, A. Kučera, P. Novotný, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Brázdil, Tomáš, et al. Stability in Graphs and Games. Vol. 59, 10, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.10.","chicago":"Brázdil, Tomáš, Vojtěch Forejt, Antonín Kučera, and Petr Novotný. “Stability in Graphs and Games,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.10.","ama":"Brázdil T, Forejt V, Kučera A, Novotný P. Stability in graphs and games. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.10","ieee":"T. Brázdil, V. Forejt, A. Kučera, and P. Novotný, “Stability in graphs and games,” presented at the CONCUR: Concurrency Theory, Quebec City, Canada, 2016, vol. 59.","apa":"Brázdil, T., Forejt, V., Kučera, A., & Novotný, P. (2016). Stability in graphs and games (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.10","ista":"Brázdil T, Forejt V, Kučera A, Novotný P. 2016. Stability in graphs and games. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 10."},"date_published":"2016-08-01T00:00:00Z"},{"month":"10","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"quality_controlled":"1","doi":"10.1093/gbe/evw221","language":[{"iso":"eng"}],"publist_id":"5940","file_date_updated":"2020-07-14T12:44:44Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","acknowledgement":"This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). The authors would like to thank I. Schrank, L. Theodosiou, M. Kredler, C. Laforsch, J. Wolinska, J. Griebel, R. Jaenichen, and K. Otte for providing the necessary resources and help for maintaining Daphnia cultures in the laboratory. H. Lainer supported us for the molecular laboratory work. D. Gilbert and J. K. Colbourne contributed ideas for the bioinformatics analysis, and L. Hardulak did the orthology mapping including more insect species. This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). This work benefits from and contributes to the Daphnia Genomics Consortium.","year":"2016","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"publication_status":"published","author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","first_name":"Ann K","last_name":"Huylmans","full_name":"Huylmans, Ann K"},{"first_name":"Alberto","last_name":"López Ezquerra","full_name":"López Ezquerra, Alberto"},{"last_name":"Parsch","first_name":"John","full_name":"Parsch, John"},{"full_name":"Cordellier, Mathilde","first_name":"Mathilde","last_name":"Cordellier"}],"volume":8,"date_created":"2018-12-11T11:51:24Z","date_updated":"2021-01-12T06:49:55Z","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"mla":"Huylmans, Ann K., et al. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution, vol. 8, no. 10, Oxford University Press, 2016, pp. 3120–39, doi:10.1093/gbe/evw221.","short":"A.K. Huylmans, A. López Ezquerra, J. Parsch, M. Cordellier, Genome Biology and Evolution 8 (2016) 3120–3139.","chicago":"Huylmans, Ann K, Alberto López Ezquerra, John Parsch, and Mathilde Cordellier. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/gbe/evw221.","ama":"Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 2016;8(10):3120-3139. doi:10.1093/gbe/evw221","ista":"Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. 2016. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 8(10), 3120–3139.","apa":"Huylmans, A. K., López Ezquerra, A., Parsch, J., & Cordellier, M. (2016). De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evw221","ieee":"A. K. Huylmans, A. López Ezquerra, J. Parsch, and M. Cordellier, “De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata,” Genome Biology and Evolution, vol. 8, no. 10. Oxford University Press, pp. 3120–3139, 2016."},"publication":"Genome Biology and Evolution","page":"3120 - 3139","date_published":"2016-10-01T00:00:00Z","type":"journal_article","issue":"10","abstract":[{"text":"Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species.","lang":"eng"}],"_id":"1329","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","ddc":["576"],"status":"public","title":"De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata","pubrep_id":"663","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:12:06Z","date_updated":"2020-07-14T12:44:44Z","checksum":"25c7adcb452d39d3b6343ff4b57a652d","relation":"main_file","file_id":"4924","file_size":1406265,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-663-v1+1_Genome_Biol_Evol-2016-Huylmans-3120-39.pdf","access_level":"open_access"}]},{"department":[{"_id":"KrCh"}],"publisher":"ACM","title":"Stochastic shortest path with energy constraints in POMDPs","status":"public","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1327","year":"2016","oa_version":"Preprint","date_created":"2018-12-11T11:51:23Z","date_updated":"2021-01-12T06:49:54Z","author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"full_name":"Gupta, Anchit","last_name":"Gupta","first_name":"Anchit"},{"full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny"}],"type":"conference","ec_funded":1,"publist_id":"5942","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize the expected total cost until the target set is reached. We extend the traditional framework of POMDPs to model energy consumption, which represents a hard constraint. The energy levels may increase and decrease with transitions, and the hard constraint requires that the energy level must remain positive in all steps till the target is reached. First, we present a novel algorithm for solving POMDPs with energy levels, developing on existing POMDP solvers and using RTDP as its main method. Our second contribution is related to policy representation. For larger POMDP instances the policies computed by existing solvers are too large to be understandable. We present an automated procedure based on machine learning techniques that automatically extracts important decisions of the policy allowing us to compute succinct human readable policies. Finally, we show experimentally that our algorithm performs well and computes succinct policies on a number of POMDP instances from the literature that were naturally enhanced with energy levels. ","lang":"eng"}],"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"page":"1465 - 1466","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1602.07565","open_access":"1"}],"citation":{"apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Gupta, A., & Novotný, P. (2016). Stochastic shortest path with energy constraints in POMDPs. In Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems (pp. 1465–1466). Singapore: ACM.","ieee":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, and P. Novotný, “Stochastic shortest path with energy constraints in POMDPs,” in Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, Singapore, 2016, pp. 1465–1466.","ista":"Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. 2016. Stochastic shortest path with energy constraints in POMDPs. Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. AAMAS: Autonomous Agents & Multiagent Systems, 1465–1466.","ama":"Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. Stochastic shortest path with energy constraints in POMDPs. In: Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. ACM; 2016:1465-1466.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Anchit Gupta, and Petr Novotný. “Stochastic Shortest Path with Energy Constraints in POMDPs.” In Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, 1465–66. ACM, 2016.","short":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, P. Novotný, in:, Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–1466.","mla":"Brázdil, Tomáš, et al. “Stochastic Shortest Path with Energy Constraints in POMDPs.” Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–66."},"oa":1,"publication":"Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems","language":[{"iso":"eng"}],"date_published":"2016-01-01T00:00:00Z","conference":{"location":"Singapore","start_date":"2016-05-09","end_date":"2016-05-13","name":"AAMAS: Autonomous Agents & Multiagent Systems"},"scopus_import":1,"day":"01","month":"01"},{"day":"22","scopus_import":1,"date_published":"2016-09-22T00:00:00Z","citation":{"short":"T. Brázdil, A. Kučera, P. Novotný, in:, Springer, 2016, pp. 32–49.","mla":"Brázdil, Tomáš, et al. Optimizing the Expected Mean Payoff in Energy Markov Decision Processes. Vol. 9938, Springer, 2016, pp. 32–49, doi:10.1007/978-3-319-46520-3_3.","chicago":"Brázdil, Tomáš, Antonín Kučera, and Petr Novotný. “Optimizing the Expected Mean Payoff in Energy Markov Decision Processes,” 9938:32–49. Springer, 2016. https://doi.org/10.1007/978-3-319-46520-3_3.","ama":"Brázdil T, Kučera A, Novotný P. Optimizing the expected mean payoff in Energy Markov Decision Processes. In: Vol 9938. Springer; 2016:32-49. doi:10.1007/978-3-319-46520-3_3","apa":"Brázdil, T., Kučera, A., & Novotný, P. (2016). Optimizing the expected mean payoff in Energy Markov Decision Processes (Vol. 9938, pp. 32–49). Presented at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan: Springer. https://doi.org/10.1007/978-3-319-46520-3_3","ieee":"T. Brázdil, A. Kučera, and P. Novotný, “Optimizing the expected mean payoff in Energy Markov Decision Processes,” presented at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan, 2016, vol. 9938, pp. 32–49.","ista":"Brázdil T, Kučera A, Novotný P. 2016. Optimizing the expected mean payoff in Energy Markov Decision Processes. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 9938, 32–49."},"page":"32 - 49","abstract":[{"text":"Energy Markov Decision Processes (EMDPs) are finite-state Markov decision processes where each transition is assigned an integer counter update and a rational payoff. An EMDP configuration is a pair s(n), where s is a control state and n is the current counter value. The configurations are changed by performing transitions in the standard way. We consider the problem of computing a safe strategy (i.e., a strategy that keeps the counter non-negative) which maximizes the expected mean payoff. ","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1326","status":"public","title":"Optimizing the expected mean payoff in Energy Markov Decision Processes","intvolume":" 9938","month":"09","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2016-10-20","location":"Chiba, Japan","start_date":"2016-10-17"},"doi":"10.1007/978-3-319-46520-3_3","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00678"}],"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"ec_funded":1,"publist_id":"5943","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"},{"first_name":"Petr","last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr"}],"date_updated":"2021-01-12T06:49:53Z","date_created":"2018-12-11T11:51:23Z","volume":9938,"year":"2016","acknowledgement":"The research was funded by the Czech Science Foundation Grant No. P202/12/G061 and by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}]},{"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1506.06014","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/s11856-016-1429-z","month":"10","publication_status":"published","publisher":"Springer","department":[{"_id":"HeEd"}],"acknowledgement":"Supported by People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n°[291734]. Supported by the Russian Foundation for Basic Research grant 15-31-20403 (mol a ved), by the Russian Foundation for Basic Research grant 15-01-99563 A, in part by the Moebius Contest Foundation for Young Scientists, and in part by the Simons Foundation.","year":"2016","date_created":"2018-12-11T11:51:24Z","date_updated":"2021-01-12T06:49:56Z","volume":216,"author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"full_name":"Balitskiy, Alexey","last_name":"Balitskiy","first_name":"Alexey"}],"ec_funded":1,"publist_id":"5938","page":"833 - 845","publication":"Israel Journal of Mathematics","citation":{"ista":"Akopyan A, Balitskiy A. 2016. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 216(2), 833–845.","ieee":"A. Akopyan and A. Balitskiy, “Billiards in convex bodies with acute angles,” Israel Journal of Mathematics, vol. 216, no. 2. Springer, pp. 833–845, 2016.","apa":"Akopyan, A., & Balitskiy, A. (2016). Billiards in convex bodies with acute angles. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1429-z","ama":"Akopyan A, Balitskiy A. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 2016;216(2):833-845. doi:10.1007/s11856-016-1429-z","chicago":"Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1429-z.","mla":"Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” Israel Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 833–45, doi:10.1007/s11856-016-1429-z.","short":"A. Akopyan, A. Balitskiy, Israel Journal of Mathematics 216 (2016) 833–845."},"date_published":"2016-10-15T00:00:00Z","scopus_import":1,"day":"15","status":"public","title":"Billiards in convex bodies with acute angles","intvolume":" 216","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1330","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"In this paper we investigate the existence of closed billiard trajectories in not necessarily smooth convex bodies. In particular, we show that if a body K ⊂ Rd has the property that the tangent cone of every non-smooth point q ∉ ∂K is acute (in a certain sense), then there is a closed billiard trajectory in K."}],"issue":"2"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1334","intvolume":" 7","title":"Activity dependent plasticity of hippocampal place maps","status":"public","ddc":["570"],"pubrep_id":"660","file":[{"creator":"system","file_size":1793846,"content_type":"application/pdf","file_name":"IST-2016-660-v1+1_ncomms11824.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:16:10Z","checksum":"e43307754abe65b840a21939fe163618","file_id":"5196","relation":"main_file"}],"oa_version":"Published Version","scopus_import":1,"has_accepted_license":"1","day":"10","citation":{"mla":"Schönenberger, Philipp, et al. “Activity Dependent Plasticity of Hippocampal Place Maps.” Nature Communications, vol. 7, 11824, Nature Publishing Group, 2016, doi:10.1038/ncomms11824.","short":"P. Schönenberger, J. O’Neill, J.L. Csicsvari, Nature Communications 7 (2016).","chicago":"Schönenberger, Philipp, Joseph O’Neill, and Jozsef L Csicsvari. “Activity Dependent Plasticity of Hippocampal Place Maps.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11824.","ama":"Schönenberger P, O’Neill J, Csicsvari JL. Activity dependent plasticity of hippocampal place maps. Nature Communications. 2016;7. doi:10.1038/ncomms11824","ista":"Schönenberger P, O’Neill J, Csicsvari JL. 2016. Activity dependent plasticity of hippocampal place maps. Nature Communications. 7, 11824.","ieee":"P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Activity dependent plasticity of hippocampal place maps,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","apa":"Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2016). Activity dependent plasticity of hippocampal place maps. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11824"},"publication":"Nature Communications","date_published":"2016-06-10T00:00:00Z","article_number":"11824","ec_funded":1,"publist_id":"5934","file_date_updated":"2020-07-14T12:44:44Z","year":"2016","publisher":"Nature Publishing Group","department":[{"_id":"JoCs"}],"publication_status":"published","author":[{"first_name":"Philipp","last_name":"Schönenberger","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp"},{"full_name":"O'Neill, Joseph","first_name":"Joseph","last_name":"O'Neill","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"}],"volume":7,"date_updated":"2021-01-12T06:49:57Z","date_created":"2018-12-11T11:51:26Z","month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"call_identifier":"FWF","name":"Interneuron plasticity during spatial learning","_id":"257D4372-B435-11E9-9278-68D0E5697425","grant_number":"I2072-B27"}],"quality_controlled":"1","doi":"10.1038/ncomms11824","language":[{"iso":"eng"}]},{"main_file_link":[{"url":"https://doi.org/10.1104/pp.16.00415","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1104/pp.16.00415","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"year":"2016","acknowledgement":"This work was financially supported by the following: The Alabama Agricultural Experiment Station HATCH grants 370222-310010-2055 and 370225-310006-2055 for funding to P.J.Z., E.A.K, A.M.P., and A.M.R. P.J.Z. and E.A.K were supported by an Auburn University Cellular and Molecular Biosciences Research Fellowship. I.D.C. is a postdoctoral fellow of the Research Foundation Flanders (FWO) (FWO/PDO14/043) and is also supported by FWO travel\r\ngrant 12N2415N. F.V.B. was supported by grants from the Interuniversity Attraction Poles Programme (IUAP P7/29 MARS) initiated by the Belgian Science Policy Office and Ghent University (Multidisciplinary Research Partnership Biotechnology for a Sustainable Economy, grant 01MRB510W).","publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"EvBe"}],"author":[{"full_name":"Zwack, Paul","last_name":"Zwack","first_name":"Paul"},{"full_name":"De Clercq, Inge","last_name":"De Clercq","first_name":"Inge"},{"last_name":"Howton","first_name":"Timothy","full_name":"Howton, Timothy"},{"last_name":"Hallmark","first_name":"H Tucker","full_name":"Hallmark, H Tucker"},{"full_name":"Hurny, Andrej","last_name":"Hurny","first_name":"Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Keshishian","first_name":"Erika","full_name":"Keshishian, Erika"},{"last_name":"Parish","first_name":"Alyssa","full_name":"Parish, Alyssa"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"first_name":"M Shahid","last_name":"Mukhtar","full_name":"Mukhtar, M Shahid"},{"first_name":"Frank","last_name":"Van Breusegem","full_name":"Van Breusegem, Frank"},{"full_name":"Rashotte, Aaron","last_name":"Rashotte","first_name":"Aaron"}],"date_created":"2018-12-11T11:51:25Z","date_updated":"2022-05-24T09:26:03Z","volume":172,"publist_id":"5937","publication":"Plant Physiology","citation":{"chicago":"Zwack, Paul, Inge De Clercq, Timothy Howton, H Tucker Hallmark, Andrej Hurny, Erika Keshishian, Alyssa Parish, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00415.","mla":"Zwack, Paul, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1249–58, doi:10.1104/pp.16.00415.","short":"P. Zwack, I. De Clercq, T. Howton, H.T. Hallmark, A. Hurny, E. Keshishian, A. Parish, E. Benková, M.S. Mukhtar, F. Van Breusegem, A. Rashotte, Plant Physiology 172 (2016) 1249–1258.","ista":"Zwack P, De Clercq I, Howton T, Hallmark HT, Hurny A, Keshishian E, Parish A, Benková E, Mukhtar MS, Van Breusegem F, Rashotte A. 2016. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 172(2), 1249–1258.","apa":"Zwack, P., De Clercq, I., Howton, T., Hallmark, H. T., Hurny, A., Keshishian, E., … Rashotte, A. (2016). Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00415","ieee":"P. Zwack et al., “Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1249–1258, 2016.","ama":"Zwack P, De Clercq I, Howton T, et al. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 2016;172(2):1249-1258. doi:10.1104/pp.16.00415"},"article_type":"original","page":"1249 - 1258","date_published":"2016-10-02T00:00:00Z","scopus_import":"1","day":"02","article_processing_charge":"No","_id":"1331","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress","status":"public","intvolume":" 172","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Cytokinin is a phytohormone that is well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays a key role in the inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative stress, and here we show a novel function for CRF6 in relation to oxidative stress and identify downstream transcriptional targets of CRF6 that are repressed in response to oxidative stress. Analysis of transcriptomic changes in wild-type and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially expressed transcripts, many of which were repressed rather than induced. Moreover, many repressed genes also show decreased expression in 35S:CRF6 overexpressing plants. Together, these findings suggest that CRF6 functions largely as a transcriptional repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts was a set of five genes associated with cytokinin processes: (signaling) ARR6, ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants of these cytokinin-associated target genes to reveal novel connections to oxidative stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate its targets both directly and indirectly. Together, this shows that CRF6 functions during oxidative stress as a negative regulator to control this cytokinin-associated module of CRF6- dependent genes and establishes a novel connection between cytokinin and oxidative stress response.","lang":"eng"}],"issue":"2"},{"month":"03","doi":"10.1038/ncomms10915","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","file_date_updated":"2020-07-14T12:44:44Z","publist_id":"5935","article_number":"10915","author":[{"last_name":"Milinski","first_name":"Manfred","full_name":"Milinski, Manfred"},{"full_name":"Hilbe, Christian","first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X"},{"last_name":"Semmann","first_name":"Dirk","full_name":"Semmann, Dirk"},{"full_name":"Sommerfeld, Ralf","last_name":"Sommerfeld","first_name":"Ralf"},{"full_name":"Marotzke, Jochem","last_name":"Marotzke","first_name":"Jochem"}],"date_created":"2018-12-11T11:51:25Z","date_updated":"2021-01-12T06:49:57Z","volume":7,"year":"2016","acknowledgement":"We thank the students for participation; H.-J. Krambeck for writing the software for the game; H. Arndt, T. Bakker, L. Becks, H. Brendelberger, S. Dobler and T. Reusch for support; and the Max Planck Society for the Advancement of Science for funding.","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"day":"07","has_accepted_license":"1","scopus_import":1,"date_published":"2016-03-07T00:00:00Z","publication":"Nature Communications","citation":{"short":"M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, J. Marotzke, Nature Communications 7 (2016).","mla":"Milinski, Manfred, et al. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” Nature Communications, vol. 7, 10915, Nature Publishing Group, 2016, doi:10.1038/ncomms10915.","chicago":"Milinski, Manfred, Christian Hilbe, Dirk Semmann, Ralf Sommerfeld, and Jochem Marotzke. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10915.","ama":"Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 2016;7. doi:10.1038/ncomms10915","apa":"Milinski, M., Hilbe, C., Semmann, D., Sommerfeld, R., & Marotzke, J. (2016). Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10915","ieee":"M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, and J. Marotzke, “Humans choose representatives who enforce cooperation in social dilemmas through extortion,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","ista":"Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. 2016. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 7, 10915."},"abstract":[{"lang":"eng","text":"Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the "representatives" treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most."}],"type":"journal_article","pubrep_id":"661","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4834","checksum":"9ea0d7ce59a555a1cb8353d5559407cb","date_created":"2018-12-12T10:10:44Z","date_updated":"2020-07-14T12:44:44Z","access_level":"open_access","file_name":"IST-2016-661-v1+1_ncomms10915.pdf","content_type":"application/pdf","file_size":1432577,"creator":"system"}],"_id":"1333","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["519","530","599"],"status":"public","title":"Humans choose representatives who enforce cooperation in social dilemmas through extortion","intvolume":" 7"},{"publication":"Nature Communications","citation":{"ieee":"R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","apa":"Chait, R. P., Palmer, A., Yelin, I., & Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10333","ista":"Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333.","ama":"Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 2016;7. doi:10.1038/ncomms10333","chicago":"Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10333.","short":"R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).","mla":"Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications, vol. 7, 10333, Nature Publishing Group, 2016, doi:10.1038/ncomms10333."},"date_published":"2016-01-20T00:00:00Z","scopus_import":1,"day":"20","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1332","ddc":["570","579"],"status":"public","title":"Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments","intvolume":" 7","pubrep_id":"662","file":[{"file_id":"5039","relation":"main_file","checksum":"ef147bcbb8bd37e9079cf3ce06f5815d","date_created":"2018-12-12T10:13:52Z","date_updated":"2020-07-14T12:44:44Z","access_level":"open_access","file_name":"IST-2016-662-v1+1_ncomms10333.pdf","creator":"system","file_size":1844107,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance.","lang":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1038/ncomms10333","language":[{"iso":"eng"}],"month":"01","year":"2016","acknowledgement":"This work was partially supported by US National Institutes of Health grant R01-GM081617, Israeli Centers of Research Excellence I-CORE Program ISF Grant No. 152/11, and the European Research Council FP7 ERC Grant 281891.","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"author":[{"full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","first_name":"Remy P","last_name":"Chait"},{"first_name":"Adam","last_name":"Palmer","full_name":"Palmer, Adam"},{"full_name":"Yelin, Idan","first_name":"Idan","last_name":"Yelin"},{"first_name":"Roy","last_name":"Kishony","full_name":"Kishony, Roy"}],"date_created":"2018-12-11T11:51:25Z","date_updated":"2021-01-12T06:49:57Z","volume":7,"article_number":"10333","file_date_updated":"2020-07-14T12:44:44Z","publist_id":"5936"},{"publist_id":"5932","ec_funded":1,"volume":9837,"date_created":"2018-12-11T11:51:26Z","date_updated":"2021-01-12T06:49:58Z","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","year":"2016","month":"08","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-53413-7_2","conference":{"start_date":"2016-09-08","location":"Edinburgh, United Kingdom","end_date":"2016-09-10","name":"SAS: Static Analysis Symposium"},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"oa":1,"abstract":[{"lang":"eng","text":"In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 9837","status":"public","title":"Quantitative monitor automata","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1335","day":"31","scopus_import":1,"date_published":"2016-08-31T00:00:00Z","page":"23 - 38","citation":{"short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Springer, 2016, pp. 23–38.","mla":"Chatterjee, Krishnendu, et al. Quantitative Monitor Automata. Vol. 9837, Springer, 2016, pp. 23–38, doi:10.1007/978-3-662-53413-7_2.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Monitor Automata,” 9837:23–38. Springer, 2016. https://doi.org/10.1007/978-3-662-53413-7_2.","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative monitor automata. In: Vol 9837. Springer; 2016:23-38. doi:10.1007/978-3-662-53413-7_2","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Quantitative monitor automata (Vol. 9837, pp. 23–38). Presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53413-7_2","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative monitor automata,” presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom, 2016, vol. 9837, pp. 23–38.","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative monitor automata. SAS: Static Analysis Symposium, LNCS, vol. 9837, 23–38."}},{"ddc":["581"],"title":"TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls","status":"public","intvolume":" 5","_id":"1344","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"4748","checksum":"9209541fbba00f24daad21a5d568540d","date_created":"2018-12-12T10:09:24Z","date_updated":"2020-07-14T12:44:45Z","access_level":"open_access","file_name":"IST-2016-693-v1+1_e19048-download.pdf","content_type":"application/pdf","file_size":5666343,"creator":"system"}],"oa_version":"Published Version","pubrep_id":"654","type":"journal_article","abstract":[{"text":"Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms.","lang":"eng"}],"publication":"eLife","citation":{"mla":"Fendrych, Matyas, et al. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife, vol. 5, e19048, eLife Sciences Publications, 2016, doi:10.7554/eLife.19048.","short":"M. Fendrych, J. Leung, J. Friml, ELife 5 (2016).","chicago":"Fendrych, Matyas, Jeffrey Leung, and Jiří Friml. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.19048.","ama":"Fendrych M, Leung J, Friml J. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 2016;5. doi:10.7554/eLife.19048","ista":"Fendrych M, Leung J, Friml J. 2016. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 5, e19048.","apa":"Fendrych, M., Leung, J., & Friml, J. (2016). TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.19048","ieee":"M. Fendrych, J. Leung, and J. Friml, “TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls,” eLife, vol. 5. eLife Sciences Publications, 2016."},"date_published":"2016-09-14T00:00:00Z","scopus_import":1,"day":"14","has_accepted_license":"1","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"eLife Sciences Publications","acknowledgement":"The authors express their gratitude to Veronika Bierbaum, Robert Hauschild for help with MATLAB,\r\nDaniel von Wangenheim for the gravitropism assay. We are thankful to Bill Gray, Mark Estelle,\r\nMichael Prigge, Ottoline Leyser, Claudia Oecking for sharing the seeds with us. We thank Katelyn\r\nSageman-Furnas and the members of the Friml lab for critical reading of the manuscript. The\r\nresearch leading to these results has received funding from the People Programme (Marie Curie\r\nActions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant\r\nagreement n° 291734. This work was also supported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP).","year":"2016","date_created":"2018-12-11T11:51:29Z","date_updated":"2021-01-12T06:50:01Z","volume":5,"author":[{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Leung, Jeffrey","first_name":"Jeffrey","last_name":"Leung"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"article_number":"e19048","file_date_updated":"2020-07-14T12:44:45Z","publist_id":"5908","ec_funded":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.19048","month":"09"},{"citation":{"apa":"Kaczmarczyk, J., Weimer, H., & Lemeshko, M. (2016). Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/18/9/093042","ieee":"J. Kaczmarczyk, H. Weimer, and M. Lemeshko, “Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model,” New Journal of Physics, vol. 18, no. 9. IOP Publishing Ltd., 2016.","ista":"Kaczmarczyk J, Weimer H, Lemeshko M. 2016. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. 18(9), 093042.","ama":"Kaczmarczyk J, Weimer H, Lemeshko M. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. 2016;18(9). doi:10.1088/1367-2630/18/9/093042","chicago":"Kaczmarczyk, Jan, Hendrik Weimer, and Mikhail Lemeshko. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1367-2630/18/9/093042.","short":"J. Kaczmarczyk, H. Weimer, M. Lemeshko, New Journal of Physics 18 (2016).","mla":"Kaczmarczyk, Jan, et al. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics, vol. 18, no. 9, 093042, IOP Publishing Ltd., 2016, doi:10.1088/1367-2630/18/9/093042."},"publication":"New Journal of Physics","date_published":"2016-09-22T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"22","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1343","intvolume":" 18","title":"Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model","status":"public","ddc":["530"],"pubrep_id":"655","file":[{"file_id":"5309","relation":"main_file","date_updated":"2020-07-14T12:44:45Z","date_created":"2018-12-12T10:17:52Z","checksum":"2a43e235222755e31ffbd369882c61de","file_name":"IST-2016-655-v1+1_njp_18_9_093042.pdf","access_level":"open_access","creator":"system","file_size":1076029,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"9","abstract":[{"text":"The Fermi-Hubbard model is one of the key models of condensed matter physics, which holds a\r\n\r\npotential for explaining the mystery of high-temperature superconductivity. Recent progress in\r\n\r\nultracold atoms in optical lattices has paved the way to studying the model’s phase diagram using\r\n\r\nthe tools of quantum simulation, which emerged as a promising alternative to the numerical\r\n\r\ncalculations plagued by the infamous sign problem. However, the temperatures achieved using\r\n\r\nelaborate laser cooling protocols so far have been too high to show the appearance of\r\n\r\nantiferromagnetic (AF) and superconducting quantum phases directly. In this work, we demonstrate\r\n\r\nthat using the machinery of dissipative quantum state engineering, one can observe the emergence of\r\n\r\nthe AF order in the Fermi-Hubbard model with fermions in optical lattices. The core of the approach\r\n\r\nis to add incoherent laser scattering in such a way that the AF state emerges as the dark state of\r\n\r\nthe driven-dissipative dynamics. The proposed controlled dissipation channels described in this work\r\n\r\nare straightforward to add to already existing experimental setups.","lang":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","doi":"10.1088/1367-2630/18/9/093042","language":[{"iso":"eng"}],"month":"09","year":"2016","acknowledgement":"We acknowledge stimulating discussions with Ken Brown, Tommaso Calarco, Andrew Daley, Suzanne\r\nMcEndoo, Tobias Osborne, Cindy Regal, Luis Santos, Micha\r\nł\r\nTomza, and Martin Zwierlein. The work was supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734], by the Volkswagen Foundation, and by DFG within SFB 1227 (DQ-mat).","department":[{"_id":"MiLe"}],"publisher":"IOP Publishing Ltd.","publication_status":"published","author":[{"id":"46C405DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1629-3675","first_name":"Jan","last_name":"Kaczmarczyk","full_name":"Kaczmarczyk, Jan"},{"last_name":"Weimer","first_name":"Hendrik","full_name":"Weimer, Hendrik"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"}],"volume":18,"date_created":"2018-12-11T11:51:29Z","date_updated":"2021-01-12T06:50:01Z","article_number":"093042","ec_funded":1,"publist_id":"5909","file_date_updated":"2020-07-14T12:44:45Z"},{"month":"09","conference":{"name":"SAGT: Symposium on Algorithmic Game Theory","end_date":"2016-09-21","start_date":"2016-09-19","location":"Liverpool, United Kingdom"},"doi":"10.1007/978-3-662-53354-3_6","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1604.07634","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"ec_funded":1,"publist_id":"5927","author":[{"full_name":"Hansen, Kristoffer","last_name":"Hansen","first_name":"Kristoffer"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Koucký","first_name":"Michal","full_name":"Koucký, Michal"}],"date_updated":"2021-01-12T06:50:00Z","date_created":"2018-12-11T11:51:28Z","volume":9928,"year":"2016","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","day":"01","scopus_import":1,"date_published":"2016-09-01T00:00:00Z","citation":{"ama":"Hansen K, Ibsen-Jensen R, Koucký M. The big match in small space. In: Vol 9928. Springer; 2016:64-76. doi:10.1007/978-3-662-53354-3_6","ieee":"K. Hansen, R. Ibsen-Jensen, and M. Koucký, “The big match in small space,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom, 2016, vol. 9928, pp. 64–76.","apa":"Hansen, K., Ibsen-Jensen, R., & Koucký, M. (2016). The big match in small space (Vol. 9928, pp. 64–76). Presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53354-3_6","ista":"Hansen K, Ibsen-Jensen R, Koucký M. 2016. The big match in small space. SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 64–76.","short":"K. Hansen, R. Ibsen-Jensen, M. Koucký, in:, Springer, 2016, pp. 64–76.","mla":"Hansen, Kristoffer, et al. The Big Match in Small Space. Vol. 9928, Springer, 2016, pp. 64–76, doi:10.1007/978-3-662-53354-3_6.","chicago":"Hansen, Kristoffer, Rasmus Ibsen-Jensen, and Michal Koucký. “The Big Match in Small Space,” 9928:64–76. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_6."},"page":"64 - 76","abstract":[{"text":"We study repeated games with absorbing states, a type of two-player, zero-sum concurrent mean-payoff games with the prototypical example being the Big Match of Gillete (1957). These games may not allow optimal strategies but they always have ε-optimal strategies. In this paper we design ε-optimal strategies for Player 1 in these games that use only O(log log T) space. Furthermore, we construct strategies for Player 1 that use space s(T), for an arbitrary small unbounded non-decreasing function s, and which guarantee an ε-optimal value for Player 1 in the limit superior sense. The previously known strategies use space Ω(log T) and it was known that no strategy can use constant space if it is ε-optimal even in the limit superior sense. We also give a complementary lower bound. Furthermore, we also show that no Markov strategy, even extended with finite memory, can ensure value greater than 0 in the Big Match, answering a question posed by Neyman [11].","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"1340","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The big match in small space","intvolume":" 9928"},{"publist_id":"5907","file_date_updated":"2020-07-14T12:44:45Z","article_number":"16102","author":[{"full_name":"Molnar, Gergely","first_name":"Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"volume":2,"date_created":"2018-12-11T11:51:30Z","date_updated":"2021-01-12T06:50:02Z","year":"2016","publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}],"publication_status":"published","month":"07","doi":"10.1038/nplants.2016.102","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components."}],"type":"journal_article","pubrep_id":"1007","file":[{"checksum":"9ba65f558563b287f875f48fa9f30fb2","date_updated":"2020-07-14T12:44:45Z","date_created":"2018-12-12T10:12:36Z","file_id":"4954","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":127781,"access_level":"open_access","file_name":"IST-2018-1007-v1+1_Molnar_NatPlants_2016.pdf"},{"access_level":"open_access","file_name":"IST-2018-1007-v1+2_Molnar_NatPlants_2016_editor_statement.pdf","creator":"system","file_size":430556,"content_type":"application/pdf","file_id":"4955","relation":"main_file","checksum":"550d252be808d8ca2b43e83dddb4212f","date_created":"2018-12-12T10:12:37Z","date_updated":"2020-07-14T12:44:45Z"}],"oa_version":"Published Version","_id":"1345","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 2","status":"public","ddc":["581"],"title":"Plasma membrane: Negative attraction","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2016-07-01T00:00:00Z","citation":{"mla":"Molnar, Gergely, et al. “Plasma Membrane: Negative Attraction.” Nature Plants, vol. 2, 16102, Nature Publishing Group, 2016, doi:10.1038/nplants.2016.102.","short":"G. Molnar, M. Fendrych, J. Friml, Nature Plants 2 (2016).","chicago":"Molnar, Gergely, Matyas Fendrych, and Jiří Friml. “Plasma Membrane: Negative Attraction.” Nature Plants. Nature Publishing Group, 2016. https://doi.org/10.1038/nplants.2016.102.","ama":"Molnar G, Fendrych M, Friml J. Plasma membrane: Negative attraction. Nature Plants. 2016;2. doi:10.1038/nplants.2016.102","ista":"Molnar G, Fendrych M, Friml J. 2016. Plasma membrane: Negative attraction. Nature Plants. 2, 16102.","ieee":"G. Molnar, M. Fendrych, and J. Friml, “Plasma membrane: Negative attraction,” Nature Plants, vol. 2. Nature Publishing Group, 2016.","apa":"Molnar, G., Fendrych, M., & Friml, J. (2016). Plasma membrane: Negative attraction. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2016.102"},"publication":"Nature Plants"},{"type":"journal_article","abstract":[{"lang":"eng","text":"A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front.While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front,we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate provides a versatile platformfor studying microbial adaption and directly visualizing evolutionary dynamics."}],"publist_id":"5911","issue":"6304","_id":"1342","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","status":"public","title":"Spatiotemporal microbial evolution on antibiotic landscapes","publication_status":"published","publisher":"American Association for the Advancement of Science","intvolume":" 353","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"author":[{"first_name":"Michael","last_name":"Baym","full_name":"Baym, Michael"},{"last_name":"Lieberman","first_name":"Tami","full_name":"Lieberman, Tami"},{"full_name":"Kelsic, Eric","first_name":"Eric","last_name":"Kelsic"},{"first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P"},{"full_name":"Gross, Rotem","last_name":"Gross","first_name":"Rotem"},{"first_name":"Idan","last_name":"Yelin","full_name":"Yelin, Idan"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"date_updated":"2021-01-12T06:50:01Z","date_created":"2018-12-11T11:51:29Z","volume":353,"oa_version":"Preprint","scopus_import":1,"day":"09","month":"09","publication":"Science","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/"}],"citation":{"chicago":"Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aag0822.","short":"M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151.","mla":"Baym, Michael, et al. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1147–51, doi:10.1126/science.aag0822.","apa":"Baym, M., Lieberman, T., Kelsic, E., Chait, R. P., Gross, R., Yelin, I., & Kishony, R. (2016). Spatiotemporal microbial evolution on antibiotic landscapes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag0822","ieee":"M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016.","ista":"Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304), 1147–1151.","ama":"Baym M, Lieberman T, Kelsic E, et al. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016;353(6304):1147-1151. doi:10.1126/science.aag0822"},"quality_controlled":"1","page":"1147 - 1151","doi":"10.1126/science.aag0822","date_published":"2016-09-09T00:00:00Z","language":[{"iso":"eng"}]},{"quality_controlled":"1","publication":"Applied Physics Letter","citation":{"mla":"Verbiest, Gerard, et al. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied Physics Letter, vol. 109, 143507, American Institute of Physics, 2016, doi:10.1063/1.4964122.","short":"G. Verbiest, D. Xu, M. Goldsche, T. Khodkov, S. Barzanjeh, N. Von Den Driesch, D. Buca, C. Stampfer, Applied Physics Letter 109 (2016).","chicago":"Verbiest, Gerard, Duo Xu, Matthias Goldsche, Timofiy Khodkov, Shabir Barzanjeh, Nils Von Den Driesch, Dan Buca, and Christoph Stampfer. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied Physics Letter. American Institute of Physics, 2016. https://doi.org/10.1063/1.4964122.","ama":"Verbiest G, Xu D, Goldsche M, et al. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 2016;109. doi:10.1063/1.4964122","ista":"Verbiest G, Xu D, Goldsche M, Khodkov T, Barzanjeh S, Von Den Driesch N, Buca D, Stampfer C. 2016. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 109, 143507.","ieee":"G. Verbiest et al., “Tunable mechanical coupling between driven microelectromechanical resonators,” Applied Physics Letter, vol. 109. American Institute of Physics, 2016.","apa":"Verbiest, G., Xu, D., Goldsche, M., Khodkov, T., Barzanjeh, S., Von Den Driesch, N., … Stampfer, C. (2016). Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. American Institute of Physics. https://doi.org/10.1063/1.4964122"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.04406"}],"oa":1,"language":[{"iso":"eng"}],"date_published":"2016-10-04T00:00:00Z","doi":"10.1063/1.4964122","scopus_import":1,"day":"04","month":"10","title":"Tunable mechanical coupling between driven microelectromechanical resonators","status":"public","publication_status":"published","publisher":"American Institute of Physics","intvolume":" 109","department":[{"_id":"JoFi"}],"_id":"1339","year":"2016","acknowledgement":"We acknowledge the support from the Helmholtz Nanoelectronic Facility (HNF) and funding from the ERC (GA-Nr. 280140).","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:28Z","date_updated":"2023-02-21T10:35:06Z","volume":109,"oa_version":"Preprint","author":[{"first_name":"Gerard","last_name":"Verbiest","full_name":"Verbiest, Gerard"},{"full_name":"Xu, Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87","last_name":"Xu","first_name":"Duo"},{"last_name":"Goldsche","first_name":"Matthias","full_name":"Goldsche, Matthias"},{"first_name":"Timofiy","last_name":"Khodkov","full_name":"Khodkov, Timofiy"},{"orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir"},{"full_name":"Von Den Driesch, Nils","first_name":"Nils","last_name":"Von Den Driesch"},{"first_name":"Dan","last_name":"Buca","full_name":"Buca, Dan"},{"first_name":"Christoph","last_name":"Stampfer","full_name":"Stampfer, Christoph"}],"article_number":"143507","type":"journal_article","abstract":[{"text":"We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive\r\nactuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By\r\nmeasuring the resonance frequencies of the system, we show that the comb-drive actuator and the\r\nsilicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate\r\n(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)\r\nplaced close to the silicon beam. In contrast, the effective spring constant of the system is insensitive\r\nto either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator\r\ncan be used to switch between different coupling rates with a frequency of at least 10 kHz.\r\n","lang":"eng"}],"publist_id":"5928"},{"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","year":"2016","date_updated":"2021-01-12T06:50:03Z","date_created":"2018-12-11T11:51:31Z","author":[{"full_name":"Oliveto, Pietro","first_name":"Pietro","last_name":"Oliveto"},{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"}],"file_date_updated":"2020-07-14T12:44:45Z","publist_id":"5900","ec_funded":1,"quality_controlled":"1","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"conference":{"location":"Denver, CO, USA","start_date":"2016-07-20","end_date":"2016-07-24","name":"GECCO: Genetic and evolutionary computation conference"},"doi":"10.1145/2908812.2908909","month":"07","ddc":["576"],"title":"When non-elitism outperforms elitism for crossing fitness valleys","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1349","file":[{"file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","access_level":"open_access","creator":"system","file_size":979026,"content_type":"application/pdf","file_id":"5214","relation":"main_file","date_created":"2018-12-12T10:16:27Z","date_updated":"2020-07-14T12:44:45Z","checksum":"a1896e39e4113f2711e46b435d5f3e69"}],"oa_version":"Published Version","pubrep_id":"650","type":"conference","abstract":[{"lang":"eng","text":"Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys."}],"page":"1163 - 1170","publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","citation":{"mla":"Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909.","short":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.","ama":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909","ista":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.","apa":"Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170."},"date_published":"2016-07-20T00:00:00Z","scopus_import":1,"day":"20","has_accepted_license":"1"},{"project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7"},{"grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1126/science.aaf1836","month":"09","publisher":"American Association for the Advancement of Science","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"publication_status":"published","year":"2016","volume":353,"date_updated":"2021-01-12T06:50:04Z","date_created":"2018-12-11T11:51:31Z","author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán","first_name":"José","full_name":"Guzmán, José"},{"first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"last_name":"Frotscher","first_name":"Michael","full_name":"Frotscher, Michael"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"}],"ec_funded":1,"publist_id":"5899","file_date_updated":"2020-07-14T12:44:46Z","page":"1117 - 1123","citation":{"chicago":"Guzmán, José, Alois Schlögl, Michael Frotscher, and Peter M Jonas. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aaf1836.","short":"J. Guzmán, A. Schlögl, M. Frotscher, P.M. Jonas, Science 353 (2016) 1117–1123.","mla":"Guzmán, José, et al. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1117–23, doi:10.1126/science.aaf1836.","ieee":"J. Guzmán, A. Schlögl, M. Frotscher, and P. M. Jonas, “Synaptic mechanisms of pattern completion in the hippocampal CA3 network,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1117–1123, 2016.","apa":"Guzmán, J., Schlögl, A., Frotscher, M., & Jonas, P. M. (2016). Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf1836","ista":"Guzmán J, Schlögl A, Frotscher M, Jonas PM. 2016. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 353(6304), 1117–1123.","ama":"Guzmán J, Schlögl A, Frotscher M, Jonas PM. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 2016;353(6304):1117-1123. doi:10.1126/science.aaf1836"},"publication":"Science","date_published":"2016-09-09T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"09","intvolume":" 353","ddc":["570"],"title":"Synaptic mechanisms of pattern completion in the hippocampal CA3 network","status":"public","_id":"1350","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","file":[{"creator":"system","content_type":"application/pdf","file_size":19408143,"file_name":"IST-2017-823-v1+1_aaf1836_CombinedPDF_v2-1.pdf","access_level":"open_access","date_created":"2018-12-12T10:12:27Z","date_updated":"2020-07-14T12:44:46Z","checksum":"89caefa4e181424cbf0aecc835fcc5ec","file_id":"4945","relation":"main_file"}],"pubrep_id":"823","type":"journal_article","issue":"6304","abstract":[{"text":"The hippocampal CA3 region plays a key role in learning and memory. Recurrent CA3–CA3\r\nsynapses are thought to be the subcellular substrate of pattern completion. However, the\r\nsynaptic mechanisms of this network computation remain enigmatic. To investigate these mechanisms, we combined functional connectivity analysis with network modeling.\r\nSimultaneous recording fromup to eight CA3 pyramidal neurons revealed that connectivity was sparse, spatially uniform, and highly enriched in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary connections were composed of one or two synaptic contacts, suggesting efficient use of postsynaptic space. Real-size modeling indicated that CA3 networks with sparse connectivity, disynaptic motifs, and single-contact connections robustly generated pattern completion.Thus, macro- and microconnectivity contribute to efficient\r\nmemory storage and retrieval in hippocampal networks.","lang":"eng"}]},{"month":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1103/PhysRevX.6.011012","language":[{"iso":"eng"}],"article_number":"011012","file_date_updated":"2020-07-14T12:44:45Z","publist_id":"5902","year":"2016","acknowledgement":"We are grateful to Eugene Demler, Jan Kaczmarczyk, Laleh Safari, and Hendrik Weimer for insightful discussions. The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory.","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","author":[{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"}],"date_created":"2018-12-11T11:51:30Z","date_updated":"2021-01-12T06:50:03Z","volume":6,"scopus_import":1,"day":"01","has_accepted_license":"1","publication":"Physical Review X","citation":{"chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” Physical Review X. American Physical Society, 2016. https://doi.org/10.1103/PhysRevX.6.011012.","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” Physical Review X, vol. 6, no. 1, 011012, American Physical Society, 2016, doi:10.1103/PhysRevX.6.011012.","short":"R. Schmidt, M. Lemeshko, Physical Review X 6 (2016).","ista":"Schmidt R, Lemeshko M. 2016. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 6(1), 011012.","apa":"Schmidt, R., & Lemeshko, M. (2016). Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.6.011012","ieee":"R. Schmidt and M. Lemeshko, “Deformation of a quantum many-particle system by a rotating impurity,” Physical Review X, vol. 6, no. 1. American Physical Society, 2016.","ama":"Schmidt R, Lemeshko M. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 2016;6(1). doi:10.1103/PhysRevX.6.011012"},"date_published":"2016-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"During the past 70 years, the quantum theory of angular momentum has been successfully applied to describing the properties of nuclei, atoms, and molecules, and their interactions with each other as well as with external fields. Because of the properties of quantum rotations, the angular-momentum algebra can be of tremendous complexity even for a few interacting particles, such as valence electrons of an atom, not to mention larger many-particle systems. In this work, we study an example of the latter: A rotating quantum impurity coupled to a many-body bosonic bath. In the regime of strong impurity-bath couplings, the problem involves the addition of an infinite number of angular momenta, which renders it intractable using currently available techniques. Here, we introduce a novel canonical transformation that allows us to eliminate the complex angular-momentum algebra from such a class of many-body problems. In addition, the transformation exposes the problem's constants of motion, and renders it solvable exactly in the limit of a slowly rotating impurity. We exemplify the technique by showing that there exists a critical rotational speed at which the impurity suddenly acquires one quantum of angular momentum from the many-particle bath. Such an instability is accompanied by the deformation of the phonon density in the frame rotating along with the impurity.","lang":"eng"}],"issue":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1347","title":"Deformation of a quantum many-particle system by a rotating impurity","status":"public","ddc":["530"],"intvolume":" 6","pubrep_id":"652","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1165869,"creator":"system","file_name":"IST-2016-652-v1+1_PhysRevX.6.011012.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:45Z","date_created":"2018-12-12T10:15:59Z","checksum":"6757a164d3c38905e05b2b5a188cb8ff","relation":"main_file","file_id":"5183"}]},{"citation":{"chicago":"Fulek, Radoslav. “Bounded Embeddings of Graphs in the Plane,” 9843:31–42. Springer, 2016. https://doi.org/10.1007/978-3-319-44543-4_3.","short":"R. Fulek, in:, Springer, 2016, pp. 31–42.","mla":"Fulek, Radoslav. Bounded Embeddings of Graphs in the Plane. Vol. 9843, Springer, 2016, pp. 31–42, doi:10.1007/978-3-319-44543-4_3.","ieee":"R. Fulek, “Bounded embeddings of graphs in the plane,” presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland, 2016, vol. 9843, pp. 31–42.","apa":"Fulek, R. (2016). Bounded embeddings of graphs in the plane (Vol. 9843, pp. 31–42). Presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland: Springer. https://doi.org/10.1007/978-3-319-44543-4_3","ista":"Fulek R. 2016. Bounded embeddings of graphs in the plane. IWOCA: International Workshop on Combinatorial Algorithms, LNCS, vol. 9843, 31–42.","ama":"Fulek R. Bounded embeddings of graphs in the plane. In: Vol 9843. Springer; 2016:31-42. doi:10.1007/978-3-319-44543-4_3"},"page":"31 - 42","date_published":"2016-08-09T00:00:00Z","scopus_import":1,"day":"09","_id":"1348","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 9843","title":"Bounded embeddings of graphs in the plane","status":"public","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"A drawing in the plane (ℝ2) of a graph G = (V,E) equipped with a function γ : V → ℕ is x-bounded if (i) x(u) < x(v) whenever γ(u) < γ(v) and (ii) γ(u) ≤ γ(w) ≤ γ(v), where uv ∈ E and γ(u) ≤ γ(v), whenever x(w) ∈ x(uv), where x(.) denotes the projection to the xaxis.We prove a characterization of isotopy classes of embeddings of connected graphs equipped with γ in the plane containing an x-bounded embedding.Then we present an efficient algorithm, which relies on our result, for testing the existence of an x-bounded embedding if the given graph is a forest.This partially answers a question raised recently by Angelini et al.and Chang et al., and proves that c-planarity testing of flat clustered graphs with three clusters is tractable when the underlying abstract graph is a forest.","lang":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1610.07144","open_access":"1"}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","doi":"10.1007/978-3-319-44543-4_3","conference":{"end_date":"2018-08-19","start_date":"2016-08-17","location":"Helsinki, Finland","name":"IWOCA: International Workshop on Combinatorial Algorithms"},"language":[{"iso":"eng"}],"month":"08","year":"2016","department":[{"_id":"UlWa"}],"publisher":"Springer","publication_status":"published","author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"}],"volume":9843,"date_updated":"2021-01-12T06:50:03Z","date_created":"2018-12-11T11:51:31Z","publist_id":"5901","ec_funded":1},{"file_date_updated":"2020-07-14T12:44:46Z","publist_id":"5891","article_number":"12396","date_updated":"2021-01-12T06:50:06Z","date_created":"2018-12-11T11:51:33Z","volume":7,"author":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"},{"full_name":"Kalaee, Mahmoud","first_name":"Mahmoud","last_name":"Kalaee"},{"full_name":"Pitanti, Alessandro","last_name":"Pitanti","first_name":"Alessandro"},{"last_name":"Norte","first_name":"Richard","full_name":"Norte, Richard"},{"last_name":"Heinzle","first_name":"Lukas","full_name":"Heinzle, Lukas"},{"first_name":"Marcelo","last_name":"Davanço","full_name":"Davanço, Marcelo"},{"full_name":"Srinivasan, Kartik","last_name":"Srinivasan","first_name":"Kartik"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"}],"publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"Nature Publishing Group","acknowledgement":"This work was supported by the DARPA MESO programme, the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.P. was supported by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme, NEMO (GA 298861). Certain commercial equipment and software are identified in this documentation to describe the subject adequately. Such identification does not imply recommendation or endorsement by the NIST, nor does it imply that the equipment identified is necessarily the best available for the purpose.","year":"2016","month":"08","language":[{"iso":"eng"}],"doi":"10.1038/ncomms12396","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"text":"Radiation pressure has recently been used to effectively couple the quantum motion of mechanical elements to the fields of optical or microwave light. Integration of all three degrees of freedom—mechanical, optical and microwave—would enable a quantum interconnect between microwave and optical quantum systems. We present a platform based on silicon nitride nanomembranes for integrating superconducting microwave circuits with planar acoustic and optical devices such as phononic and photonic crystals. Using planar capacitors with vacuum gaps of 60 nm and spiral inductor coils of micron pitch we realize microwave resonant circuits with large electromechanical coupling to planar acoustic structures of nanoscale dimensions and femtoFarad motional capacitance. Using this enhanced coupling, we demonstrate microwave backaction cooling of the 4.48 MHz mechanical resonance of a nanobeam to an occupancy as low as 0.32. These results indicate the viability of silicon nitride nanomembranes as an all-in-one substrate for quantum electro-opto-mechanical experiments.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"25513bd59d5bda495efa8f5920e91b22","date_created":"2018-12-12T10:13:30Z","date_updated":"2020-07-14T12:44:46Z","relation":"main_file","file_id":"5014","file_size":2139802,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-629-v1+1_ncomms12396.pdf"}],"pubrep_id":"629","ddc":["530"],"title":"Quantum electromechanics on silicon nitride nanomembranes","status":"public","intvolume":" 7","_id":"1355","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"03","has_accepted_license":"1","scopus_import":1,"date_published":"2016-08-03T00:00:00Z","publication":"Nature Communications","citation":{"chicago":"Fink, Johannes M, Mahmoud Kalaee, Alessandro Pitanti, Richard Norte, Lukas Heinzle, Marcelo Davanço, Kartik Srinivasan, and Oskar Painter. “Quantum Electromechanics on Silicon Nitride Nanomembranes.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12396.","short":"J.M. Fink, M. Kalaee, A. Pitanti, R. Norte, L. Heinzle, M. Davanço, K. Srinivasan, O. Painter, Nature Communications 7 (2016).","mla":"Fink, Johannes M., et al. “Quantum Electromechanics on Silicon Nitride Nanomembranes.” Nature Communications, vol. 7, 12396, Nature Publishing Group, 2016, doi:10.1038/ncomms12396.","apa":"Fink, J. M., Kalaee, M., Pitanti, A., Norte, R., Heinzle, L., Davanço, M., … Painter, O. (2016). Quantum electromechanics on silicon nitride nanomembranes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12396","ieee":"J. M. Fink et al., “Quantum electromechanics on silicon nitride nanomembranes,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","ista":"Fink JM, Kalaee M, Pitanti A, Norte R, Heinzle L, Davanço M, Srinivasan K, Painter O. 2016. Quantum electromechanics on silicon nitride nanomembranes. Nature Communications. 7, 12396.","ama":"Fink JM, Kalaee M, Pitanti A, et al. Quantum electromechanics on silicon nitride nanomembranes. Nature Communications. 2016;7. doi:10.1038/ncomms12396"}},{"scopus_import":1,"day":"19","article_processing_charge":"No","publication":"PNAS","citation":{"ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","apa":"Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1518830113","ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.","mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113.","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1518830113."},"article_type":"original","page":"4422 - 4427","date_published":"2016-04-19T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population."}],"issue":"16","_id":"1359","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The effect of gene interactions on the long-term response to selection","intvolume":" 113","oa_version":"Published Version","month":"04","external_id":{"pmid":["27044080"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/","open_access":"1"}],"quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1073/pnas.1518830113","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"5886","year":"2016","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"National Academy of Sciences","author":[{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"date_created":"2018-12-11T11:51:34Z","date_updated":"2021-01-12T06:50:08Z","volume":113},{"month":"08","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1512.06688"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.94.085152","article_number":"085152","publist_id":"5897","ec_funded":1,"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2016","acknowledgement":"The authors are grateful to Florian Gebhard and Mikhail Lemeshko for discussions and critical reading of the manuscript. The work was supported by the Ministry of Science and Higher Education in Poland through the Iuventus Plus Grant No. IP2012 017172, as well as by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. 291734. J.K. acknowledges hospitality of the Leibniz Universität in Hannover where a large part of the work was performed.","volume":94,"date_updated":"2021-01-12T06:50:05Z","date_created":"2018-12-11T11:51:32Z","author":[{"full_name":"Kaczmarczyk, Jan","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1629-3675","first_name":"Jan","last_name":"Kaczmarczyk"},{"last_name":"Schickling","first_name":"Tobias","full_name":"Schickling, Tobias"},{"first_name":"Jörg","last_name":"Bünemann","full_name":"Bünemann, Jörg"}],"scopus_import":1,"day":"30","citation":{"chicago":"Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.94.085152.","mla":"Kaczmarczyk, Jan, et al. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 8, 085152, American Physical Society, 2016, doi:10.1103/PhysRevB.94.085152.","short":"J. Kaczmarczyk, T. Schickling, J. Bünemann, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","ista":"Kaczmarczyk J, Schickling T, Bünemann J. 2016. Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. 94(8), 085152.","ieee":"J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Coexistence of nematic order and superconductivity in the Hubbard model,” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 8. American Physical Society, 2016.","apa":"Kaczmarczyk, J., Schickling, T., & Bünemann, J. (2016). Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.085152","ama":"Kaczmarczyk J, Schickling T, Bünemann J. Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. 2016;94(8). doi:10.1103/PhysRevB.94.085152"},"publication":"Physical Review B - Condensed Matter and Materials Physics","date_published":"2016-08-30T00:00:00Z","type":"journal_article","issue":"8","abstract":[{"text":"We study the interplay of nematic and superconducting order in the two-dimensional Hubbard model and show that they can coexist, especially when superconductivity is not the energetically dominant phase. Due to a breaking of the C4 symmetry, the coexisting phase inherently contains admixture of the s-wave pairing components. As a result, the superconducting gap exhibits nonstandard features including changed nodal directions. Our results also show that in the optimally doped regime the pure superconducting phase is typically unstable towards developing nematicity (breaking of the C4 symmetry). This has implications for the cuprate high-Tc superconductors, for which in this regime the so-called intertwined orders have recently been observed. Namely, the coexisting phase may be viewed as a precursor to such more involved patterns of symmetry breaking.","lang":"eng"}],"intvolume":" 94","title":"Coexistence of nematic order and superconductivity in the Hubbard model","status":"public","_id":"1352","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"language":[{"iso":"eng"}],"date_published":"2016-07-22T00:00:00Z","doi":"10.1103/PhysRevApplied.6.014013","quality_controlled":"1","publication":"Physical Review Applied","oa":1,"citation":{"short":"P. Dieterle, M. Kalaee, J.M. Fink, O. Painter, Physical Review Applied 6 (2016).","mla":"Dieterle, Paul, et al. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator Platform.” Physical Review Applied, vol. 6, no. 1, 014013, American Physical Society, 2016, doi:10.1103/PhysRevApplied.6.014013.","chicago":"Dieterle, Paul, Mahmoud Kalaee, Johannes M Fink, and Oskar Painter. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator Platform.” Physical Review Applied. American Physical Society, 2016. https://doi.org/10.1103/PhysRevApplied.6.014013.","ama":"Dieterle P, Kalaee M, Fink JM, Painter O. Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. 2016;6(1). doi:10.1103/PhysRevApplied.6.014013","apa":"Dieterle, P., Kalaee, M., Fink, J. M., & Painter, O. (2016). Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.6.014013","ieee":"P. Dieterle, M. Kalaee, J. M. Fink, and O. Painter, “Superconducting cavity electromechanics on a silicon-on-insulator platform,” Physical Review Applied, vol. 6, no. 1. American Physical Society, 2016.","ista":"Dieterle P, Kalaee M, Fink JM, Painter O. 2016. Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. 6(1), 014013."},"main_file_link":[{"url":"http://arxiv.org/abs/1601.04019","open_access":"1"}],"month":"07","day":"22","scopus_import":1,"date_updated":"2021-01-12T06:50:06Z","date_created":"2018-12-11T11:51:32Z","oa_version":"Preprint","volume":6,"author":[{"last_name":"Dieterle","first_name":"Paul","full_name":"Dieterle, Paul"},{"last_name":"Kalaee","first_name":"Mahmoud","full_name":"Kalaee, Mahmoud"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"},{"last_name":"Painter","first_name":"Oskar","full_name":"Painter, Oskar"}],"title":"Superconducting cavity electromechanics on a silicon-on-insulator platform","publication_status":"published","status":"public","publisher":"American Physical Society","intvolume":" 6","department":[{"_id":"JoFi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1354","year":"2016","abstract":[{"lang":"eng","text":"Fabrication processes involving anhydrous hydrofluoric vapor etching are developed to create high-Q aluminum superconducting microwave resonators on free-standing silicon membranes formed from a silicon-on-insulator wafer. Using this fabrication process, a high-impedance 8.9-GHz coil resonator is coupled capacitively with a large participation ratio to a 9.7-MHz micromechanical resonator. Two-tone microwave spectroscopy and radiation pressure backaction are used to characterize the coupled system in a dilution refrigerator down to temperatures of Tf=11 mK, yielding a measured electromechanical vacuum coupling rate of g0/2π=24.6 Hz and a mechanical resonator Q factor of Qm=1.7×107. Microwave backaction cooling of the mechanical resonator is also studied, with a minimum phonon occupancy of nm≈16 phonons being realized at an elevated fridge temperature of Tf=211 mK."}],"issue":"1","publist_id":"5892","article_number":"014013","type":"journal_article"},{"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.115.184796","month":"01","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"year":"2016","date_created":"2018-12-11T11:51:33Z","date_updated":"2021-01-12T06:50:07Z","volume":202,"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"file_date_updated":"2020-07-14T12:44:46Z","publist_id":"5889","page":"3 - 4","publication":"Genetics","citation":{"ama":"Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. 2016;202(1):3-4. doi:10.1534/genetics.115.184796","ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4.","apa":"Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184796","ieee":"N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” Genetics, vol. 202, no. 1. Genetics Society of America, pp. 3–4, 2016.","mla":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:10.1534/genetics.115.184796.","short":"N.H. Barton, Genetics 202 (2016) 3–4.","chicago":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184796."},"date_published":"2016-01-05T00:00:00Z","scopus_import":1,"day":"05","has_accepted_license":"1","status":"public","ddc":["570"],"title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","intvolume":" 202","_id":"1356","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:08:26Z","checksum":"3562b89c821a4be84edf2b6ebd870cf5","file_id":"4687","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":112674,"file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","pubrep_id":"769","type":"journal_article","issue":"1"},{"month":"03","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.116.187542","publist_id":"5888","file_date_updated":"2020-07-14T12:44:46Z","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2016","volume":202,"date_created":"2018-12-11T11:51:33Z","date_updated":"2021-01-12T06:50:07Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"scopus_import":1,"has_accepted_license":"1","day":"01","page":"865 - 866","citation":{"apa":"Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.187542","ieee":"N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” Genetics, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.","ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","ama":"Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 2016;202(3):865-866. doi:10.1534/genetics.116.187542","chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.116.187542.","short":"N.H. Barton, Genetics 202 (2016) 865–866.","mla":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:10.1534/genetics.116.187542."},"publication":"Genetics","date_published":"2016-03-01T00:00:00Z","type":"journal_article","issue":"3","intvolume":" 202","status":"public","title":"Richard Hudson and Norman Kaplan on the coalescent process","ddc":["576"],"_id":"1357","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"5127","date_created":"2018-12-12T10:15:09Z","date_updated":"2020-07-14T12:44:46Z","checksum":"b2174bab2de1d1142900062a150f35c9","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","access_level":"open_access","content_type":"application/pdf","file_size":130779,"creator":"system"}],"pubrep_id":"768"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We characterize absorption in finite idempotent algebras by means of Jónsson absorption and cube term blockers. As an application we show that it is decidable whether a given subset is an absorbing subuniverse of an algebra given by the tables of its basic operations."}],"issue":"5","status":"public","title":"Deciding absorption","intvolume":" 26","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1353","oa_version":"Preprint","scopus_import":1,"day":"20","page":"1033 - 1060","publication":"International Journal of Algebra and Computation","citation":{"chicago":"Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” International Journal of Algebra and Computation. World Scientific Publishing, 2016. https://doi.org/10.1142/S0218196716500430.","mla":"Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” International Journal of Algebra and Computation, vol. 26, no. 5, World Scientific Publishing, 2016, pp. 1033–60, doi:10.1142/S0218196716500430.","short":"L. Barto, A. Kazda, International Journal of Algebra and Computation 26 (2016) 1033–1060.","ista":"Barto L, Kazda A. 2016. Deciding absorption. International Journal of Algebra and Computation. 26(5), 1033–1060.","apa":"Barto, L., & Kazda, A. (2016). Deciding absorption. International Journal of Algebra and Computation. World Scientific Publishing. https://doi.org/10.1142/S0218196716500430","ieee":"L. Barto and A. Kazda, “Deciding absorption,” International Journal of Algebra and Computation, vol. 26, no. 5. World Scientific Publishing, pp. 1033–1060, 2016.","ama":"Barto L, Kazda A. Deciding absorption. International Journal of Algebra and Computation. 2016;26(5):1033-1060. doi:10.1142/S0218196716500430"},"date_published":"2016-07-20T00:00:00Z","publist_id":"5893","publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"World Scientific Publishing","acknowledgement":"Libor Barto and Alexandr Kazda were supported by the the Grant Agency of the Czech Republic, grant GACR 13-01832S. 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","date_created":"2018-12-11T11:51:35Z","date_updated":"2023-02-21T10:36:12Z","volume":35,"author":[{"first_name":"Morten","last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"day":"11","has_accepted_license":"1","citation":{"mla":"Bojsen-Hansen, Morten, and Chris Wojtan. Generalized Non-Reflecting Boundaries for Fluid Re-Simulation. Vol. 35, no. 4, 96, ACM, 2016, doi:10.1145/2897824.2925963.","short":"M. Bojsen-Hansen, C. Wojtan, in:, ACM, 2016.","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries for Fluid Re-Simulation,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925963.","ama":"Bojsen-Hansen M, Wojtan C. Generalized non-reflecting boundaries for fluid re-simulation. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925963","ista":"Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96.","apa":"Bojsen-Hansen, M., & Wojtan, C. (2016). Generalized non-reflecting boundaries for fluid re-simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925963","ieee":"M. Bojsen-Hansen and C. Wojtan, “Generalized non-reflecting boundaries for fluid re-simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4."},"date_published":"2016-07-11T00:00:00Z","alternative_title":["ACM Transactions on Graphics"],"type":"conference","abstract":[{"lang":"eng","text":"When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special "non-reflecting" boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation."}],"issue":"4","title":"Generalized non-reflecting boundaries for fluid re-simulation","ddc":["000"],"status":"public","intvolume":" 35","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1363","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-631-v1+2_a96-bojsen-hansen.pdf","content_type":"application/pdf","file_size":12422760,"creator":"system","relation":"main_file","file_id":"4981","checksum":"140b5532f0a2a006a0149cab7c73c17c","date_created":"2018-12-12T10:13:00Z","date_updated":"2020-07-14T12:44:47Z"}],"pubrep_id":"631"},{"article_number":"86","file_date_updated":"2020-07-14T12:44:47Z","ec_funded":1,"publist_id":"5878","publication_status":"published","publisher":"ACM","department":[{"_id":"BeBi"}],"year":"2016","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 645599.","date_updated":"2021-01-12T06:50:10Z","date_created":"2018-12-11T11:51:36Z","volume":35,"author":[{"id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder","last_name":"Miguel Villalba","full_name":"Miguel Villalba, Eder"},{"last_name":"Lepoutre","first_name":"Mathias","full_name":"Lepoutre, Mathias"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"}],"month":"07","quality_controlled":"1","project":[{"_id":"25082902-B435-11E9-9278-68D0E5697425","grant_number":"645599","call_identifier":"H2020","name":"Soft-bodied intelligence for Manipulation"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2016-07-28","start_date":"2016-07-24","location":"Anaheim, CA, USA","name":"ACM SIGGRAPH"},"doi":"10.1145/2897824.2925978","alternative_title":["ACM Transactions on Graphics"],"type":"conference","abstract":[{"lang":"eng","text":"We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated."}],"issue":"4","title":"Computational design of stable planar-rod structures","ddc":["006"],"status":"public","intvolume":" 35","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1364","oa_version":"Preprint","file":[{"file_id":"4853","relation":"main_file","checksum":"d00c2664a43d945df8876ea0193734e3","date_updated":"2020-07-14T12:44:47Z","date_created":"2018-12-12T10:11:01Z","access_level":"open_access","file_name":"IST-2017-763-v1+1_wirebending.pdf","creator":"system","file_size":44766392,"content_type":"application/pdf"}],"pubrep_id":"763","scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"ista":"Miguel Villalba E, Lepoutre M, Bickel B. 2016. Computational design of stable planar-rod structures. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 86.","ieee":"E. Miguel Villalba, M. Lepoutre, and B. 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Surface only liquids. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, a78.","apa":"Da, F., Hahn, D., Batty, C., Wojtan, C., & Grinspun, E. (2016). Surface only liquids (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925899","ieee":"F. Da, D. Hahn, C. Batty, C. Wojtan, and E. Grinspun, “Surface only liquids,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ama":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. Surface only liquids. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925899","chicago":"Da, Fang, David Hahn, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Surface Only Liquids,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925899.","mla":"Da, Fang, et al. Surface Only Liquids. Vol. 35, no. 4, a78, ACM, 2016, doi:10.1145/2897824.2925899.","short":"F. Da, D. Hahn, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2016."},"issue":"4","abstract":[{"lang":"eng","text":"We propose a novel surface-only technique for simulating incompressible, inviscid and uniform-density liquids with surface tension in three dimensions. The liquid surface is captured by a triangle mesh on which a Lagrangian velocity field is stored. Because advection of the velocity field may violate the incompressibility condition, we devise an orthogonal projection technique to remove the divergence while requiring the evaluation of only two boundary integrals. The forces of surface tension, gravity, and solid contact are all treated by a boundary element solve, allowing us to perform detailed simulations of a wide range of liquid phenomena, including waterbells, droplet and jet collisions, fluid chains, and crown splashes."}],"type":"conference","alternative_title":["ACM Transactions on Graphics"],"pubrep_id":"637","file":[{"file_name":"IST-2016-637-v1+1_2016_Da_SOL.pdf","access_level":"open_access","creator":"system","file_size":10561865,"content_type":"application/pdf","file_id":"4660","relation":"main_file","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:08:01Z","checksum":"6d662893bd447d4f575b4961a2247811"}],"oa_version":"Published Version","_id":"1361","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 35","status":"public","title":"Surface only liquids","ddc":["000"]},{"oa":1,"main_file_link":[{"url":"http://eprint.iacr.org/2016/115","open_access":"1"}],"citation":{"ista":"Alwen JF, Blocki J. 2016. Efficiently computing data-independent memory-hard functions. CRYPTO: International Cryptology Conference, LNCS, vol. 9815, 241–271.","ieee":"J. F. Alwen and J. Blocki, “Efficiently computing data-independent memory-hard functions,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA, 2016, vol. 9815, pp. 241–271.","apa":"Alwen, J. F., & Blocki, J. (2016). Efficiently computing data-independent memory-hard functions (Vol. 9815, pp. 241–271). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA: Springer. https://doi.org/10.1007/978-3-662-53008-5_9","ama":"Alwen JF, Blocki J. Efficiently computing data-independent memory-hard functions. In: Vol 9815. Springer; 2016:241-271. doi:10.1007/978-3-662-53008-5_9","chicago":"Alwen, Joel F, and Jeremiah Blocki. “Efficiently Computing Data-Independent Memory-Hard Functions,” 9815:241–71. Springer, 2016. https://doi.org/10.1007/978-3-662-53008-5_9.","mla":"Alwen, Joel F., and Jeremiah Blocki. Efficiently Computing Data-Independent Memory-Hard Functions. Vol. 9815, Springer, 2016, pp. 241–71, doi:10.1007/978-3-662-53008-5_9.","short":"J.F. Alwen, J. Blocki, in:, Springer, 2016, pp. 241–271."},"page":"241 - 271","quality_controlled":"1","date_published":"2016-08-01T00:00:00Z","doi":"10.1007/978-3-662-53008-5_9","conference":{"name":"CRYPTO: International Cryptology Conference","start_date":"2016-08-14","location":"Santa Barbara, CA, USA","end_date":"2016-08-18"},"language":[{"iso":"eng"}],"scopus_import":1,"month":"08","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1365","year":"2016","department":[{"_id":"KrPi"}],"intvolume":" 9815","publisher":"Springer","publication_status":"published","title":"Efficiently computing data-independent memory-hard functions","status":"public","author":[{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F"},{"last_name":"Blocki","first_name":"Jeremiah","full_name":"Blocki, Jeremiah"}],"oa_version":"Preprint","volume":9815,"date_updated":"2021-01-12T06:50:11Z","date_created":"2018-12-11T11:51:36Z","type":"conference","alternative_title":["LNCS"],"publist_id":"5876","abstract":[{"lang":"eng","text":"A memory-hard function (MHF) f is equipped with a space cost σ and time cost τ parameter such that repeatedly computing fσ,τ on an application specific integrated circuit (ASIC) is not economically advantageous relative to a general purpose computer. Technically we would like that any (generalized) circuit for evaluating an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent MHF (iMHF) has the added property that it can be computed with almost optimal memory and time complexity by an algorithm which accesses memory in a pattern independent of the input value. Such functions can be specified by fixing a directed acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph. In this work we develop new tools for analyzing iMHFs. First we define and motivate a new complexity measure capturing the amount of energy (i.e. electricity) required to compute a function. We argue that, in practice, this measure is at least as important as the more traditional AT-complexity. Next we describe an algorithm A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound both its energy and AT complexities per instance evaluated in terms of a certain combinatorial property of G. Next we instantiate our attack for several general classes of DAGs which include those underlying many of the most important iMHF candidates in the literature. In particular, we obtain the following results which hold for all choices of parameters σ and τ (and thread-count) such that n = σ ∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67). -The Double-Buffer and the Linear functions of [CGBS16] both have complexities in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm with complexities O(n2/ log1 −ε(n)) for all ε > 0. In particular when τ = 1 this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ ) is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness of any DAG which may prove to be of independent interest."}]},{"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We study the problem of devising provably secure PRNGs with input based on the sponge paradigm. Such constructions are very appealing, as efficient software/hardware implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES 2010), fails to achieve the security notion of robustness recently considered by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic, and thus there are high-entropy input distributions on which the construction fails to extract random bits, and (2) The construction is not forward secure, and presented solutions aiming at restoring forward security have not been rigorously analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which we prove secure in the sense of robustness, delivering in particular concrete security bounds. On the way, we make what we believe to be an important conceptual contribution, developing a variant of the security framework of Dodis et al. tailored at the ideal permutation model that captures PRNG security in settings where the weakly random inputs are provided from a large class of possible adversarial samplers which are also allowed to query the random permutation. As a further application of our techniques, we also present an efficient sponge-based key-derivation function (which can be instantiated from SHA-3 in a black-box fashion), which we also prove secure when fed with samples from permutation-dependent distributions."}],"intvolume":" 9665","status":"public","title":"Provably robust sponge-based PRNGs and KDFs","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1366","oa_version":"Preprint","scopus_import":1,"day":"01","page":"87 - 116","citation":{"chicago":"Gazi, Peter, and Stefano Tessaro. “Provably Robust Sponge-Based PRNGs and KDFs,” 9665:87–116. Springer, 2016. https://doi.org/10.1007/978-3-662-49890-3_4.","short":"P. Gazi, S. Tessaro, in:, Springer, 2016, pp. 87–116.","mla":"Gazi, Peter, and Stefano Tessaro. Provably Robust Sponge-Based PRNGs and KDFs. Vol. 9665, Springer, 2016, pp. 87–116, doi:10.1007/978-3-662-49890-3_4.","apa":"Gazi, P., & Tessaro, S. (2016). Provably robust sponge-based PRNGs and KDFs (Vol. 9665, pp. 87–116). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-662-49890-3_4","ieee":"P. Gazi and S. Tessaro, “Provably robust sponge-based PRNGs and KDFs,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria, 2016, vol. 9665, pp. 87–116.","ista":"Gazi P, Tessaro S. 2016. Provably robust sponge-based PRNGs and KDFs. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 9665, 87–116.","ama":"Gazi P, Tessaro S. Provably robust sponge-based PRNGs and KDFs. In: Vol 9665. Springer; 2016:87-116. doi:10.1007/978-3-662-49890-3_4"},"date_published":"2016-05-01T00:00:00Z","publist_id":"5872","ec_funded":1,"publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2016","volume":9665,"date_created":"2018-12-11T11:51:36Z","date_updated":"2021-01-12T06:50:11Z","author":[{"full_name":"Gazi, Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","last_name":"Gazi","first_name":"Peter"},{"last_name":"Tessaro","first_name":"Stefano","full_name":"Tessaro, Stefano"}],"month":"05","project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2016/169/20160219:201940","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-49890-3_4","conference":{"end_date":"2016-05-12","start_date":"2016-05-08","location":"Vienna, Austria","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"}},{"date_published":"2016-10-01T00:00:00Z","publication":"Proceedings of the American Mathematical Society","citation":{"mla":"Akopyan, Arseniy, et al. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” Proceedings of the American Mathematical Society, vol. 144, no. 10, American Mathematical Society, 2016, pp. 4501–13, doi:10.1090/proc/13062.","short":"A. Akopyan, A. Balitskiy, R. Karasev, A. Sharipova, Proceedings of the American Mathematical Society 144 (2016) 4501–4513.","chicago":"Akopyan, Arseniy, Alexey Balitskiy, Roman Karasev, and Anastasia Sharipova. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” Proceedings of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/13062.","ama":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 2016;144(10):4501-4513. doi:10.1090/proc/13062","ista":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. 2016. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 144(10), 4501–4513.","apa":"Akopyan, A., Balitskiy, A., Karasev, R., & Sharipova, A. (2016). Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/13062","ieee":"A. Akopyan, A. Balitskiy, R. Karasev, and A. Sharipova, “Elementary approach to closed billiard trajectories in asymmetric normed spaces,” Proceedings of the American Mathematical Society, vol. 144, no. 10. American Mathematical Society, pp. 4501–4513, 2016."},"page":"4501 - 4513","day":"01","article_processing_charge":"No","scopus_import":1,"oa_version":"Preprint","_id":"1360","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Elementary approach to closed billiard trajectories in asymmetric normed spaces","intvolume":" 144","abstract":[{"lang":"eng","text":"We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard trajectories in convex bodies, when the length is measured with a (possibly asymmetric) norm. We prove a lower bound for the length of the shortest closed billiard trajectory, related to the non-symmetric Mahler problem. With this technique we are able to give short and elementary proofs to some known results. "}],"issue":"10","type":"journal_article","doi":"10.1090/proc/13062","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1401.0442"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"month":"10","author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"first_name":"Alexey","last_name":"Balitskiy","full_name":"Balitskiy, Alexey"},{"full_name":"Karasev, Roman","last_name":"Karasev","first_name":"Roman"},{"last_name":"Sharipova","first_name":"Anastasia","full_name":"Sharipova, Anastasia"}],"date_updated":"2021-01-12T06:50:09Z","date_created":"2018-12-11T11:51:34Z","volume":144,"year":"2016","acknowledgement":"The first and third authors were supported by the Dynasty Foundation. The first, second and third authors were supported by the Russian Foundation for Basic Re- search grant 15-31-20403 (mol a ved).","publication_status":"published","publisher":"American Mathematical Society","department":[{"_id":"HeEd"}],"publist_id":"5885","ec_funded":1},{"file_date_updated":"2020-07-14T12:44:47Z","publist_id":"5839","date_updated":"2021-01-12T06:50:13Z","date_created":"2018-12-11T11:51:38Z","volume":212,"author":[{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"full_name":"Prat, Tomas","first_name":"Tomas","last_name":"Prat","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grones, Peter","first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Haruštiaková, Danka","last_name":"Haruštiaková","first_name":"Danka"},{"full_name":"Matonohova, Martina","last_name":"Matonohova","first_name":"Martina"},{"first_name":"Lukáš","last_name":"Spíchal","full_name":"Spíchal, Lukáš"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"}],"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"JiFr"}],"acknowledgement":"Funded by Ministry of Education, Youth and Sports Czech Republic. Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council. Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P","year":"2016","month":"10","language":[{"iso":"eng"}],"doi":"10.1111/nph.14049","quality_controlled":"1","oa":1,"abstract":[{"lang":"eng","text":"Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism."}],"issue":"2","type":"journal_article","file":[{"date_updated":"2020-07-14T12:44:47Z","date_created":"2018-12-12T10:14:53Z","checksum":"27fd841ceaf0403559d7048ef51500f9","relation":"main_file","file_id":"5108","content_type":"application/pdf","file_size":972763,"creator":"system","file_name":"IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","pubrep_id":"1006","ddc":["581"],"status":"public","title":"Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis","intvolume":" 212","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1372","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2016-10-01T00:00:00Z","page":"497 - 509","publication":"New Phytologist","citation":{"ama":"Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 2016;212(2):497-509. doi:10.1111/nph.14049","apa":"Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal, L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14049","ieee":"M. Pernisová et al., “Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis,” New Phytologist, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016.","ista":"Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 212(2), 497–509.","short":"M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal, T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509.","mla":"Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:10.1111/nph.14049.","chicago":"Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14049."}},{"date_published":"2016-09-15T00:00:00Z","citation":{"apa":"Kolesnikov, A., & Lampert, C. (2016). Seed, expand and constrain: Three principles for weakly-supervised image segmentation (Vol. 9908, pp. 695–711). Presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands: Springer. https://doi.org/10.1007/978-3-319-46493-0_42","ieee":"A. Kolesnikov and C. Lampert, “Seed, expand and constrain: Three principles for weakly-supervised image segmentation,” presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands, 2016, vol. 9908, pp. 695–711.","ista":"Kolesnikov A, Lampert C. 2016. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. ECCV: European Conference on Computer Vision, LNCS, vol. 9908, 695–711.","ama":"Kolesnikov A, Lampert C. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. In: Vol 9908. Springer; 2016:695-711. doi:10.1007/978-3-319-46493-0_42","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation,” 9908:695–711. Springer, 2016. https://doi.org/10.1007/978-3-319-46493-0_42.","short":"A. Kolesnikov, C. Lampert, in:, Springer, 2016, pp. 695–711.","mla":"Kolesnikov, Alexander, and Christoph Lampert. Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation. Vol. 9908, Springer, 2016, pp. 695–711, doi:10.1007/978-3-319-46493-0_42."},"page":"695 - 711","day":"15","scopus_import":1,"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1369","title":"Seed, expand and constrain: Three principles for weakly-supervised image segmentation","status":"public","intvolume":" 9908","abstract":[{"lang":"eng","text":"We introduce a new loss function for the weakly-supervised training of semantic image segmentation models based on three guiding principles: to seed with weak localization cues, to expand objects based on the information about which classes can occur in an image, and to constrain the segmentations to coincide with object boundaries. We show experimentally that training a deep convolutional neural network using the proposed loss function leads to substantially better segmentations than previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset. We furthermore give insight into the working mechanism of our method by a detailed experimental study that illustrates how the segmentation quality is affected by each term of the proposed loss function as well as their combinations."}],"type":"conference","alternative_title":["LNCS"],"conference":{"start_date":"2016-10-11","location":"Amsterdam, The Netherlands","end_date":"2016-10-14","name":"ECCV: European Conference on Computer Vision"},"doi":"10.1007/978-3-319-46493-0_42","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1603.06098","open_access":"1"}],"quality_controlled":"1","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"}],"month":"09","author":[{"full_name":"Kolesnikov, Alexander","first_name":"Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"date_updated":"2021-01-12T06:50:12Z","date_created":"2018-12-11T11:51:37Z","volume":9908,"year":"2016","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"Springer","publist_id":"5842","ec_funded":1},{"date_published":"2016-07-01T00:00:00Z","citation":{"chicago":"Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.94.024517.","mla":"Wysokiński, Marcin, et al. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 2, 024517, American Physical Society, 2016, doi:10.1103/PhysRevB.94.024517.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","ista":"Wysokiński M, Kaczmarczyk J, Spałek J. 2016. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 94(2), 024517.","apa":"Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2016). Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.024517","ieee":"M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Correlation driven d wave superconductivity in Anderson lattice model: Two gaps,” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 2. American Physical Society, 2016.","ama":"Wysokiński M, Kaczmarczyk J, Spałek J. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 2016;94(2). doi:10.1103/PhysRevB.94.024517"},"publication":"Physical Review B - Condensed Matter and Materials Physics","day":"01","scopus_import":1,"oa_version":"Preprint","intvolume":" 94","title":"Correlation driven d wave superconductivity in Anderson lattice model: Two gaps","status":"public","_id":"1368","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"2","abstract":[{"text":"Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.94.024517","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1510.00224","open_access":"1"}],"oa":1,"month":"07","volume":94,"date_created":"2018-12-11T11:51:37Z","date_updated":"2021-01-12T06:50:12Z","author":[{"first_name":"Marcin","last_name":"Wysokiński","full_name":"Wysokiński, Marcin"},{"full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarczyk","first_name":"Jan"},{"full_name":"Spałek, Jozef","first_name":"Jozef","last_name":"Spałek"}],"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"The work has been supported by the National Science Center (NCN) under the Grant MAESTRO, No.\r\nDEC-2012/04/A/ST3/00342. ","year":"2016","publist_id":"5844","ec_funded":1,"article_number":"024517"},{"month":"03","doi":"10.1103/PhysRevA.93.033846","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1601.01818"}],"oa":1,"quality_controlled":"1","publist_id":"5841","article_number":"033846","author":[{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir"},{"full_name":"Vitali, David","last_name":"Vitali","first_name":"David"}],"date_updated":"2023-02-21T10:36:32Z","date_created":"2018-12-11T11:51:38Z","volume":93,"year":"2016","acknowledgement":"The work of S.B. has been supported by the European Commission (Belgium) via the SCALEQIT program and by the Alexander von Humboldt Foundation. ","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"day":"28","scopus_import":1,"date_published":"2016-03-28T00:00:00Z","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","citation":{"chicago":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.033846.","short":"S. Barzanjeh, D. Vitali, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).","mla":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3, 033846, American Physical Society, 2016, doi:10.1103/PhysRevA.93.033846.","apa":"Barzanjeh, S., & Vitali, D. (2016). Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.93.033846","ieee":"S. Barzanjeh and D. Vitali, “Phonon Josephson junction with nanomechanical resonators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3. American Physical Society, 2016.","ista":"Barzanjeh S, Vitali D. 2016. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 033846.","ama":"Barzanjeh S, Vitali D. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3). doi:10.1103/PhysRevA.93.033846"},"abstract":[{"lang":"eng","text":"We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction."}],"issue":"3","type":"journal_article","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1370","status":"public","title":"Phonon Josephson junction with nanomechanical resonators","intvolume":" 93"},{"scopus_import":"1","article_processing_charge":"No","day":"01","month":"07","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01531698"}],"citation":{"mla":"Martin, Olivier, and Marcin P. Zagórski. “Network Architectures and Operating Principles. Reply to Comments on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 168–71, doi:10.1016/j.plrev.2016.06.006.","short":"O. Martin, M.P. Zagórski, Physics of Life Reviews 17 (2016) 168–171.","chicago":"Martin, Olivier, and Marcin P Zagórski. “Network Architectures and Operating Principles. Reply to Comments on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.006.","ama":"Martin O, Zagórski MP. Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. 2016;17:168-171. doi:10.1016/j.plrev.2016.06.006","ista":"Martin O, Zagórski MP. 2016. Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. 17, 168–171.","apa":"Martin, O., & Zagórski, M. P. (2016). Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.006","ieee":"O. Martin and M. P. Zagórski, “Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function",” Physics of Life Reviews, vol. 17. Elsevier, pp. 168–171, 2016."},"oa":1,"publication":"Physics of Life Reviews","page":"168 - 171","quality_controlled":"1","doi":"10.1016/j.plrev.2016.06.006","date_published":"2016-07-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","publist_id":"5838","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1373","year":"2016","department":[{"_id":"AnKi"}],"intvolume":" 17","publisher":"Elsevier","status":"public","title":"Network architectures and operating principles. 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We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels.","lang":"eng"}],"page":"605 - 636","citation":{"chicago":"Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M1010257.","short":"V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016) 605–636.","mla":"Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences, vol. 9, no. 2, Society for Industrial and Applied Mathematics , 2016, pp. 605–36, doi:10.1137/15M1010257.","ieee":"V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” SIAM Journal on Imaging Sciences, vol. 9, no. 2. Society for Industrial and Applied Mathematics , pp. 605–636, 2016.","apa":"Kolmogorov, V., Pock, T., & Rolinek, M. (2016). Total variation on a tree. SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/15M1010257","ista":"Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal on Imaging Sciences. 9(2), 605–636.","ama":"Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. SIAM Journal on Imaging Sciences. 2016;9(2):605-636. doi:10.1137/15M1010257"},"publication":"SIAM Journal on Imaging Sciences","date_published":"2016-05-03T00:00:00Z","scopus_import":1,"day":"03"},{"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2016.51","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2016-06-17","start_date":"2016-06-14","location":"Medford, MA, USA"},"project":[{"name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","grant_number":"PP00P2_138948","_id":"25FA3206-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"06","volume":51,"date_created":"2018-12-11T11:51:41Z","date_updated":"2021-01-12T06:50:17Z","author":[{"full_name":"Mabillard, Isaac","first_name":"Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH","publication_status":"published","year":"2016","publist_id":"5830","file_date_updated":"2020-07-14T12:44:47Z","date_published":"2016-06-01T00:00:00Z","page":"51.1 - 51.12","citation":{"chicago":"Mabillard, Isaac, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range,” 51:51.1-51.12. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.51.","mla":"Mabillard, Isaac, and Uli Wagner. Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12, doi:10.4230/LIPIcs.SoCG.2016.51.","short":"I. Mabillard, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12.","ista":"Mabillard I, Wagner U. 2016. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 51.1-51.12.","apa":"Mabillard, I., & Wagner, U. (2016). Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range (Vol. 51, p. 51.1-51.12). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH. https://doi.org/10.4230/LIPIcs.SoCG.2016.51","ieee":"I. Mabillard and U. Wagner, “Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 51.1-51.12.","ama":"Mabillard I, Wagner U. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH; 2016:51.1-51.12. doi:10.4230/LIPIcs.SoCG.2016.51"},"has_accepted_license":"1","day":"01","scopus_import":1,"file":[{"access_level":"open_access","file_name":"IST-2016-621-v1+1_LIPIcs-SoCG-2016-51.pdf","creator":"system","file_size":622969,"content_type":"application/pdf","file_id":"4791","relation":"main_file","checksum":"92c0c3735fe908f8ded6e484005cb3b1","date_created":"2018-12-12T10:10:06Z","date_updated":"2020-07-14T12:44:47Z"}],"oa_version":"Published Version","pubrep_id":"621","intvolume":" 51","ddc":["510"],"status":"public","title":"Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1381","abstract":[{"text":"Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference"},{"publist_id":"5831","issue":"3","abstract":[{"text":"We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP.","lang":"eng"}],"type":"journal_article","article_number":"23","volume":63,"oa_version":"Preprint","date_created":"2018-12-11T11:51:41Z","date_updated":"2021-01-12T06:50:17Z","author":[{"full_name":"Chonev, Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Ventsislav K","last_name":"Chonev"},{"full_name":"Ouaknine, Joël","last_name":"Ouaknine","first_name":"Joël"},{"first_name":"James","last_name":"Worrell","full_name":"Worrell, James"}],"department":[{"_id":"KrCh"}],"publisher":"ACM","intvolume":" 63","title":"On the complexity of the orbit problem","publication_status":"published","status":"public","_id":"1380","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","day":"01","month":"06","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1145/2857050","date_published":"2016-06-01T00:00:00Z","quality_controlled":"1","oa":1,"citation":{"mla":"Chonev, Ventsislav K., et al. “On the Complexity of the Orbit Problem.” Journal of the ACM, vol. 63, no. 3, 23, ACM, 2016, doi:10.1145/2857050.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, Journal of the ACM 63 (2016).","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Complexity of the Orbit Problem.” Journal of the ACM. ACM, 2016. https://doi.org/10.1145/2857050.","ama":"Chonev VK, Ouaknine J, Worrell J. On the complexity of the orbit problem. Journal of the ACM. 2016;63(3). doi:10.1145/2857050","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the complexity of the orbit problem. Journal of the ACM. 63(3), 23.","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the complexity of the orbit problem,” Journal of the ACM, vol. 63, no. 3. ACM, 2016.","apa":"Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On the complexity of the orbit problem. Journal of the ACM. ACM. https://doi.org/10.1145/2857050"},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.2981"}],"publication":"Journal of the ACM"},{"scopus_import":1,"day":"05","month":"07","quality_controlled":"1","page":"515 - 524","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"publication":"LICS '16","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.03632"}],"citation":{"mla":"Chonev, Ventsislav K., et al. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” LICS ’16, IEEE, 2016, pp. 515–24, doi:10.1145/2933575.2934548.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, LICS ’16, IEEE, 2016, pp. 515–524.","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” In LICS ’16, 515–24. IEEE, 2016. https://doi.org/10.1145/2933575.2934548.","ama":"Chonev VK, Ouaknine J, Worrell J. On recurrent reachability for continuous linear dynamical systems. In: LICS ’16. IEEE; 2016:515-524. doi:10.1145/2933575.2934548","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On recurrent reachability for continuous linear dynamical systems. LICS ’16. LICS: Logic in Computer Science, 515–524.","apa":"Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On recurrent reachability for continuous linear dynamical systems. In LICS ’16 (pp. 515–524). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934548","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On recurrent reachability for continuous linear dynamical systems,” in LICS ’16, New York, NY, USA, 2016, pp. 515–524."},"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"New York, NY, USA","start_date":"2018-07-05","end_date":"2018-07-08","name":"LICS: Logic in Computer Science"},"date_published":"2016-07-05T00:00:00Z","doi":"10.1145/2933575.2934548","type":"conference","abstract":[{"text":"The continuous evolution of a wide variety of systems, including continous-time Markov chains and linear hybrid automata, can be\r\ndescribed in terms of linear differential equations. In this paper we study the decision problem of whether the solution x(t) of a system of linear differential equations dx/dt = Ax reaches a target halfspace infinitely often. This recurrent reachability problem can\r\nequivalently be formulated as the following Infinite Zeros Problem: does a real-valued function f:R≥0 --> R satisfying a given linear\r\ndifferential equation have infinitely many zeros? Our main decidability result is that if the differential equation has order at most 7, then the Infinite Zeros Problem is decidable. On the other hand, we show that a decision procedure for the Infinite Zeros Problem at order 9 (and above) would entail a major breakthrough in Diophantine Approximation, specifically an algorithm for computing the Lagrange constants of arbitrary real algebraic numbers to arbitrary precision.","lang":"eng"}],"publist_id":"5820","ec_funded":1,"publication_status":"published","status":"public","title":"On recurrent reachability for continuous linear dynamical systems","department":[{"_id":"KrCh"}],"publisher":"IEEE","_id":"1389","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:44Z","date_updated":"2021-01-12T06:50:20Z","oa_version":"Preprint","author":[{"full_name":"Chonev, Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev","first_name":"Ventsislav K"},{"first_name":"Joël","last_name":"Ouaknine","full_name":"Ouaknine, Joël"},{"full_name":"Worrell, James","first_name":"James","last_name":"Worrell"}]},{"article_number":"036005","publist_id":"5815","ec_funded":1,"acknowledgement":"The research leading to these results has received funding from the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038.","year":"2016","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"IOP Publishing Ltd.","author":[{"full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706"},{"first_name":"Fabrizio","last_name":"Capuani","full_name":"Capuani, Fabrizio"},{"last_name":"De Martino","first_name":"Andrea","full_name":"De Martino, Andrea"}],"date_created":"2018-12-11T11:51:46Z","date_updated":"2021-01-12T06:50:23Z","volume":13,"month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.03243"}],"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"doi":"10.1088/1478-3975/13/3/036005","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The solution space of genome-scale models of cellular metabolism provides a map between physically\r\nviable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the\r\ncorresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show\r\nthat empirical growth rate distributions recently obtained in experiments at single-cell resolution can\r\nbe explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the\r\nhigher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of\r\na large bacterial population that captures this trade-off. The scaling relationships observed in\r\nexperiments encode, in such frameworks, for the same distance from the maximum achievable growth\r\nrate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being\r\ngrounded on genome-scale metabolic network reconstructions, these results allow for multiple\r\nimplications and extensions in spite of the underlying conceptual simplicity."}],"issue":"3","_id":"1394","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli","intvolume":" 13","oa_version":"Preprint","scopus_import":1,"day":"27","publication":"Physical Biology","citation":{"ama":"De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 2016;13(3). doi:10.1088/1478-3975/13/3/036005","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016.","apa":"De Martino, D., Capuani, F., & De Martino, A. (2016). Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/3/036005","ista":"De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 13(3), 036005.","short":"D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016).","mla":"De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology, vol. 13, no. 3, 036005, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/3/036005.","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1478-3975/13/3/036005."},"date_published":"2016-05-27T00:00:00Z"},{"ec_funded":1,"publist_id":"5795","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"ChWo"}],"publisher":"Wiley-Blackwell","publication_status":"published","year":"2016","acknowledgement":"This research was supported by NSERC (RGPIN-04360-2014) and IST Austria. ","volume":35,"date_created":"2018-12-11T11:51:52Z","date_updated":"2023-02-21T10:38:30Z","author":[{"first_name":"Ryan","last_name":"Goldade","full_name":"Goldade, Ryan"},{"full_name":"Batty, Christopher","first_name":"Christopher","last_name":"Batty"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"month":"05","project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/cgf.12826","type":"journal_article","issue":"2","abstract":[{"text":"Combining high-resolution level set surface tracking with lower resolution physics is an inexpensive method for achieving highly detailed liquid animations. Unfortunately, the inherent resolution mismatch introduces several types of disturbing visual artifacts. We identify the primary sources of these artifacts and present simple, efficient, and practical solutions to address them. First, we propose an unconditionally stable filtering method that selectively removes sub-grid surface artifacts not seen by the fluid physics, while preserving fine detail in dynamic splashing regions. It provides comparable results to recent error-correction techniques at lower cost, without substepping, and with better scaling behavior. Second, we show how a modified narrow-band scheme can ensure accurate free surface boundary conditions in the presence of large resolution mismatches. Our scheme preserves the efficiency of the narrow-band methodology, while eliminating objectionable stairstep artifacts observed in prior work. Third, we demonstrate that the use of linear interpolation of velocity during advection of the high-resolution level set surface is responsible for visible grid-aligned kinks; we therefore advocate higher-order velocity interpolation, and show that it dramatically reduces this artifact. While these three contributions are orthogonal, our results demonstrate that taken together they efficiently address the dominant sources of visual artifacts arising with high-resolution embedded liquid surfaces; the proposed approach offers improved visual quality, a straightforward implementation, and substantially greater scalability than competing methods.","lang":"eng"}],"intvolume":" 35","title":"A practical method for high-resolution embedded liquid surfaces","status":"public","ddc":["000"],"_id":"1412","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"creator":"system","file_size":15873858,"content_type":"application/pdf","file_name":"IST-2016-612-v1+2_Wojtan_APracticalMethod_PostPrint_2016.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:13:18Z","checksum":"8e61387ee2e3bd0e776fbe301629bfd9","file_id":"5000","relation":"main_file"}],"pubrep_id":"612","scopus_import":1,"has_accepted_license":"1","day":"27","page":"233 - 242","citation":{"chicago":"Goldade, Ryan, Christopher Batty, and Chris Wojtan. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12826.","mla":"Goldade, Ryan, et al. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 233–42, doi:10.1111/cgf.12826.","short":"R. Goldade, C. Batty, C. Wojtan, Computer Graphics Forum 35 (2016) 233–242.","ista":"Goldade R, Batty C, Wojtan C. 2016. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 35(2), 233–242.","ieee":"R. Goldade, C. Batty, and C. Wojtan, “A practical method for high-resolution embedded liquid surfaces,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 233–242, 2016.","apa":"Goldade, R., Batty, C., & Wojtan, C. (2016). A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12826","ama":"Goldade R, Batty C, Wojtan C. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 2016;35(2):233-242. doi:10.1111/cgf.12826"},"publication":"Computer Graphics Forum","date_published":"2016-05-27T00:00:00Z"},{"_id":"1410","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development","status":"public","ddc":["581"],"intvolume":" 250","pubrep_id":"1005","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:44:53Z","date_created":"2019-04-17T07:41:57Z","checksum":"ca08de036e6ddc81e6f760e0ccdebd3f","relation":"main_file","file_id":"6331","content_type":"application/pdf","file_size":4338545,"creator":"dernst","file_name":"2016_PlantScience_Ugalde.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"text":"The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis.","lang":"eng"}],"publication":"Plant Science","citation":{"ama":"Ugalde J, Rodríguez Furlán C, De Rycke R, et al. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 2016;250:10-19. doi:10.1016/j.plantsci.2016.05.014","ista":"Ugalde J, Rodríguez Furlán C, De Rycke R, Norambuena L, Friml J, León G, Tejos R. 2016. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 250, 10–19.","apa":"Ugalde, J., Rodríguez Furlán, C., De Rycke, R., Norambuena, L., Friml, J., León, G., & Tejos, R. (2016). Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2016.05.014","ieee":"J. Ugalde et al., “Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development,” Plant Science, vol. 250. Elsevier, pp. 10–19, 2016.","mla":"Ugalde, José, et al. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science, vol. 250, Elsevier, 2016, pp. 10–19, doi:10.1016/j.plantsci.2016.05.014.","short":"J. Ugalde, C. Rodríguez Furlán, R. De Rycke, L. Norambuena, J. Friml, G. León, R. Tejos, Plant Science 250 (2016) 10–19.","chicago":"Ugalde, José, Cecilia Rodríguez Furlán, Riet De Rycke, Lorena Norambuena, Jiří Friml, Gabriel León, and Ricardo Tejos. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science. Elsevier, 2016. https://doi.org/10.1016/j.plantsci.2016.05.014."},"page":"10 - 19","date_published":"2016-09-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","acknowledgement":"the Odysseus Program of the Research Foundation-Flanders [G091608] to JF.","year":"2016","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JiFr"}],"author":[{"last_name":"Ugalde","first_name":"José","full_name":"Ugalde, José"},{"first_name":"Cecilia","last_name":"Rodríguez Furlán","full_name":"Rodríguez Furlán, Cecilia"},{"last_name":"De Rycke","first_name":"Riet","full_name":"De Rycke, Riet"},{"first_name":"Lorena","last_name":"Norambuena","full_name":"Norambuena, Lorena"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"León, Gabriel","last_name":"León","first_name":"Gabriel"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"}],"date_created":"2018-12-11T11:51:51Z","date_updated":"2021-01-12T06:50:33Z","volume":250,"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5797","external_id":{"pmid":["27457979"]},"oa":1,"quality_controlled":"1","doi":"10.1016/j.plantsci.2016.05.014","language":[{"iso":"eng"}],"month":"09"},{"author":[{"full_name":"Abbott, Richard","first_name":"Richard","last_name":"Abbott"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Jeffrey","last_name":"Good","full_name":"Good, Jeffrey"}],"date_updated":"2021-01-12T06:50:33Z","date_created":"2018-12-11T11:51:51Z","volume":25,"year":"2016","publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5798","doi":"10.1111/mec.13685","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"06","pubrep_id":"772","oa_version":"Submitted Version","file":[{"file_size":226137,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","access_level":"open_access","date_created":"2018-12-12T10:10:12Z","date_updated":"2020-07-14T12:44:53Z","checksum":"ede7d0b8a471754f71f17e2b20f3135b","relation":"main_file","file_id":"4797"}],"_id":"1409","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"status":"public","title":"Genomics of hybridization and its evolutionary consequences","intvolume":" 25","issue":"11","type":"journal_article","date_published":"2016-06-08T00:00:00Z","publication":"Molecular Ecology","citation":{"apa":"Abbott, R., Barton, N. H., & Good, J. (2016). Genomics of hybridization and its evolutionary consequences. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.13685","ieee":"R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary consequences,” Molecular Ecology, vol. 25, no. 11. Wiley-Blackwell, pp. 2325–2332, 2016.","ista":"Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332.","ama":"Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 2016;25(11):2325-2332. doi:10.1111/mec.13685","chicago":"Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology. Wiley-Blackwell, 2016. https://doi.org/10.1111/mec.13685.","short":"R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332.","mla":"Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32, doi:10.1111/mec.13685."},"page":"2325 - 2332","day":"08","has_accepted_license":"1","scopus_import":1},{"month":"07","language":[{"iso":"eng"}],"doi":"10.1111/nph.14019","quality_controlled":"1","oa":1,"publist_id":"5790","file_date_updated":"2020-07-14T12:44:53Z","volume":211,"date_updated":"2021-01-12T06:50:36Z","date_created":"2018-12-11T11:51:54Z","author":[{"first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"full_name":"Skůpa, Petr","first_name":"Petr","last_name":"Skůpa"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"first_name":"Petr","last_name":"Klíma","full_name":"Klíma, Petr"},{"last_name":"Čarná","first_name":"Mária","full_name":"Čarná, Mária"},{"first_name":"Jakub","last_name":"Rolčík","full_name":"Rolčík, Jakub"},{"last_name":"De Rycke","first_name":"Riet","full_name":"De Rycke, Riet"},{"last_name":"Moreno","first_name":"Ignacio","full_name":"Moreno, Ignacio"},{"first_name":"Petre","last_name":"Dobrev","full_name":"Dobrev, Petre"},{"full_name":"Orellana, Ariel","first_name":"Ariel","last_name":"Orellana"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Wiley-Blackwell","department":[{"_id":"JiFr"}],"publication_status":"published","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, project CEITEC (CZ.1.05/1.1.00/02.0068) and the Czech Science Foundation GACR (project no. 13-4063 7S to J.F.)","year":"2016","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2016-07-01T00:00:00Z","page":"65 - 74","citation":{"chicago":"Simon, Sibu, Petr Skůpa, Tom Viaene, Marta Zwiewka, Ricardo Tejos, Petr Klíma, Mária Čarná, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14019.","short":"S. Simon, P. Skůpa, T. Viaene, M. Zwiewka, R. Tejos, P. Klíma, M. Čarná, J. Rolčík, R. De Rycke, I. Moreno, P. Dobrev, A. Orellana, E. Zažímalová, J. Friml, New Phytologist 211 (2016) 65–74.","mla":"Simon, Sibu, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist, vol. 211, no. 1, Wiley-Blackwell, 2016, pp. 65–74, doi:10.1111/nph.14019.","apa":"Simon, S., Skůpa, P., Viaene, T., Zwiewka, M., Tejos, R., Klíma, P., … Friml, J. (2016). PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14019","ieee":"S. Simon et al., “PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis,” New Phytologist, vol. 211, no. 1. Wiley-Blackwell, pp. 65–74, 2016.","ista":"Simon S, Skůpa P, Viaene T, Zwiewka M, Tejos R, Klíma P, Čarná M, Rolčík J, De Rycke R, Moreno I, Dobrev P, Orellana A, Zažímalová E, Friml J. 2016. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 211(1), 65–74.","ama":"Simon S, Skůpa P, Viaene T, et al. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 2016;211(1):65-74. doi:10.1111/nph.14019"},"publication":"New Phytologist","issue":"1","abstract":[{"lang":"eng","text":"Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf","creator":"system","file_size":3828383,"content_type":"application/pdf","file_id":"5016","relation":"main_file","checksum":"23522ced3508ffe7a4f247c4230e6493","date_created":"2018-12-12T10:13:32Z","date_updated":"2020-07-14T12:44:53Z"}],"oa_version":"Submitted Version","pubrep_id":"1004","intvolume":" 211","title":"PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis","ddc":["581"],"status":"public","_id":"1417","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"scopus_import":1,"has_accepted_license":"1","day":"01","page":"225 - 232","citation":{"ama":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 2016;35(2):225-232. doi:10.1111/cgf.12825","apa":"Ferstl, F., Ando, R., Wojtan, C., Westermann, R., & Thuerey, N. (2016). Narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12825","ieee":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, and N. Thuerey, “Narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 225–232, 2016.","ista":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. 2016. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 35(2), 225–232.","short":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, N. Thuerey, Computer Graphics Forum 35 (2016) 225–232.","mla":"Ferstl, Florian, et al. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 225–32, doi:10.1111/cgf.12825.","chicago":"Ferstl, Florian, Ryoichi Ando, Chris Wojtan, Rüdiger Westermann, and Nils Thuerey. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12825."},"publication":"Computer Graphics Forum","date_published":"2016-05-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"text":"The Fluid Implicit Particle method (FLIP) for liquid simulations uses particles to reduce numerical dissipation and provide important visual cues for events like complex splashes and small-scale features near the liquid surface. Unfortunately, FLIP simulations can be computationally expensive, because they require a dense sampling of particles to fill the entire liquid volume. Furthermore, the vast majority of these FLIP particles contribute nothing to the fluid's visual appearance, especially for larger volumes of liquid. We present a method that only uses FLIP particles within a narrow band of the liquid surface, while efficiently representing the remaining inner volume on a regular grid. We show that a naïve realization of this idea introduces unstable and uncontrollable energy fluctuations, and we propose a novel coupling scheme between FLIP particles and regular grid which overcomes this problem. Our method drastically reduces the particle count and simulation times while yielding results that are nearly indistinguishable from regular FLIP simulations. Our approach is easy to integrate into any existing FLIP implementation.","lang":"eng"}],"intvolume":" 35","status":"public","title":"Narrow band FLIP for liquid simulations","ddc":["000"],"_id":"1415","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:12:22Z","checksum":"984afbe510ed48019025dff1dcc7baad","file_id":"4940","relation":"main_file","creator":"system","file_size":5938324,"content_type":"application/pdf","file_name":"IST-2016-611-v1+3_CW_nbflip_postprint_2016.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","pubrep_id":"611","month":"05","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/cgf.12825","publist_id":"5793","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"ChWo"}],"publisher":"Wiley-Blackwell","publication_status":"published","year":"2016","volume":35,"date_updated":"2023-02-21T10:38:38Z","date_created":"2018-12-11T11:51:53Z","author":[{"first_name":"Florian","last_name":"Ferstl","full_name":"Ferstl, Florian"},{"full_name":"Ando, Ryoichi","first_name":"Ryoichi","last_name":"Ando"},{"last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"},{"first_name":"Rüdiger","last_name":"Westermann","full_name":"Westermann, Rüdiger"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"}]},{"day":"15","month":"05","scopus_import":1,"doi":"10.1103/PhysRevB.93.195145","date_published":"2016-05-15T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1603.09358"}],"citation":{"ama":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. 2016;93(19). doi:10.1103/PhysRevB.93.195145","apa":"Van Loon, E., Katsnelson, M., Chomaz, L., & Lemeshko, M. (2016). Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.93.195145","ieee":"E. Van Loon, M. Katsnelson, L. Chomaz, and M. Lemeshko, “Interaction-driven Lifshitz transition with dipolar fermions in optical lattices,” Physical Review B - Condensed Matter and Materials Physics, vol. 93, no. 19. American Physical Society, 2016.","ista":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. 2016. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. 93(19), 195145.","short":"E. Van Loon, M. Katsnelson, L. Chomaz, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 93 (2016).","mla":"Van Loon, Erik, et al. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials Physics, vol. 93, no. 19, 195145, American Physical Society, 2016, doi:10.1103/PhysRevB.93.195145.","chicago":"Van Loon, Erik, Mikhail Katsnelson, Lauriane Chomaz, and Mikhail Lemeshko. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.93.195145."},"oa":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","quality_controlled":"1","issue":"19","publist_id":"5791","abstract":[{"lang":"eng","text":"Anisotropic dipole-dipole interactions between ultracold dipolar fermions break the symmetry of the Fermi surface and thereby deform it. Here we demonstrate that such a Fermi surface deformation induces a topological phase transition - the so-called Lifshitz transition - in the regime accessible to present-day experiments. We describe the impact of the Lifshitz transition on observable quantities such as the Fermi surface topology, the density-density correlation function, and the excitation spectrum of the system. The Lifshitz transition in ultracold atoms can be controlled by tuning the dipole orientation and, in contrast to the transition studied in crystalline solids, is completely interaction driven."}],"type":"journal_article","article_number":"195145","author":[{"full_name":"Van Loon, Erik","first_name":"Erik","last_name":"Van Loon"},{"last_name":"Katsnelson","first_name":"Mikhail","full_name":"Katsnelson, Mikhail"},{"last_name":"Chomaz","first_name":"Lauriane","full_name":"Chomaz, Lauriane"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"}],"oa_version":"Preprint","volume":93,"date_updated":"2021-01-12T06:50:36Z","date_created":"2018-12-11T11:51:54Z","_id":"1416","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"intvolume":" 93","title":"Interaction-driven Lifshitz transition with dipolar fermions in optical lattices","status":"public","publication_status":"published"},{"author":[{"last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"},{"full_name":"Igler, Claudia","last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Moreno, Anaisa","first_name":"Anaisa","last_name":"Moreno"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"}],"date_updated":"2021-01-12T06:50:39Z","date_created":"2018-12-11T11:51:57Z","volume":33,"year":"2016","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"CaGu"},{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5772","ec_funded":1,"doi":"10.1093/molbev/msv269","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"month":"03","pubrep_id":"588","file":[{"creator":"system","file_size":648115,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf","checksum":"1f456ce1d2aa2f67176a1709f9702ecf","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:09:27Z","file_id":"4751","relation":"main_file"}],"oa_version":"Published Version","_id":"1427","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570","576"],"title":"Epistatic interactions in the arabinose cis-regulatory element","status":"public","intvolume":" 33","abstract":[{"text":"Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2016-03-01T00:00:00Z","publication":"Molecular Biology and Evolution","citation":{"short":"M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769.","mla":"Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University Press, 2016, pp. 761–69, doi:10.1093/molbev/msv269.","chicago":"Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msv269.","ama":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 2016;33(3):761-769. doi:10.1093/molbev/msv269","ieee":"M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic interactions in the arabinose cis-regulatory element,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016.","apa":"Lagator, M., Igler, C., Moreno, A., Guet, C. C., & Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv269","ista":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. 2016. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 33(3), 761–769."},"page":"761 - 769","day":"01","has_accepted_license":"1","scopus_import":1},{"date_published":"2016-03-07T00:00:00Z","citation":{"ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2016. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. Journal of Physics: Conference Series. 24th International Laser Physics Workshop (LPHYS’15) vol. 691, 012016.","apa":"Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2016). Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In Journal of Physics: Conference Series (Vol. 691). Shanghai, China: IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/691/1/012016","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential,” in Journal of Physics: Conference Series, Shanghai, China, 2016, vol. 691, no. 1.","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In: Journal of Physics: Conference Series. Vol 691. IOP Publishing Ltd.; 2016. doi:10.1088/1742-6596/691/1/012016","chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” In Journal of Physics: Conference Series, Vol. 691. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1742-6596/691/1/012016.","mla":"Könenberg, Martin, et al. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” Journal of Physics: Conference Series, vol. 691, no. 1, 012016, IOP Publishing Ltd., 2016, doi:10.1088/1742-6596/691/1/012016.","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, in:, Journal of Physics: Conference Series, IOP Publishing Ltd., 2016."},"publication":"Journal of Physics: Conference Series","has_accepted_license":"1","day":"07","scopus_import":1,"file":[{"file_id":"4847","relation":"main_file","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:10:55Z","checksum":"109db801749072c3f6c8f1a1848700fa","file_name":"IST-2016-585-v1+1_JPCS_691_1_012016.pdf","access_level":"open_access","creator":"system","file_size":1434688,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"585","intvolume":" 691","title":"Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential","ddc":["510","530"],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1428","issue":"1","abstract":[{"text":"We report on a mathematically rigorous analysis of the superfluid properties of a Bose- Einstein condensate in the many-body ground state of a one-dimensional model of interacting bosons in a random potential.","lang":"eng"}],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1088/1742-6596/691/1/012016","conference":{"name":"24th International Laser Physics Workshop (LPHYS'15)","location":"Shanghai, China","start_date":"2015-08-21","end_date":"2015-08-25"},"project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"03","volume":691,"date_updated":"2021-01-12T06:50:40Z","date_created":"2018-12-11T11:51:58Z","author":[{"full_name":"Könenberg, Martin","first_name":"Martin","last_name":"Könenberg"},{"last_name":"Moser","first_name":"Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","full_name":"Moser, Thomas"},{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"}],"publisher":"IOP Publishing Ltd.","department":[{"_id":"RoSe"}],"publication_status":"published","year":"2016","publist_id":"5770","file_date_updated":"2020-07-14T12:44:53Z","article_number":"012016"},{"type":"journal_article","issue":"5","abstract":[{"text":"Brood parasites exploit their host in order to increase their own fitness. Typically, this results in an arms race between parasite trickery and host defence. Thus, it is puzzling to observe hosts that accept parasitism without any resistance. The ‘mafia’ hypothesis suggests that these hosts accept parasitism to avoid retaliation. Retaliation has been shown to evolve when the hosts condition their response to mafia parasites, who use depredation as a targeted response to rejection. However, it is unclear if acceptance would also emerge when ‘farming’ parasites are present in the population. Farming parasites use depredation to synchronize the timing with the host, destroying mature clutches to force the host to re-nest. Herein, we develop an evolutionary model to analyse the interaction between depredatory parasites and their hosts. We show that coevolutionary cycles between farmers and mafia can still induce host acceptance of brood parasites. However, this equilibrium is unstable and in the long-run the dynamics of this host–parasite interaction exhibits strong oscillations: when farmers are the majority, accepters conditional to mafia (the host will reject first and only accept after retaliation by the parasite) have a higher fitness than unconditional accepters (the host always accepts parasitism). This leads to an increase in mafia parasites’ fitness and in turn induce an optimal environment for accepter hosts.","lang":"eng"}],"intvolume":" 3","title":"Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites","status":"public","ddc":["000"],"_id":"1426","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-589-v1+1_160036.full.pdf","creator":"system","content_type":"application/pdf","file_size":937002,"file_id":"5104","relation":"main_file","checksum":"bf84211b31fe87451e738ba301d729c3","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:14:49Z"}],"pubrep_id":"589","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"chicago":"Chakra, Maria, Christian Hilbe, and Arne Traulsen. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science. Royal Society, The, 2016. https://doi.org/10.1098/rsos.160036.","mla":"Chakra, Maria, et al. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science, vol. 3, no. 5, 160036, Royal Society, The, 2016, doi:10.1098/rsos.160036.","short":"M. Chakra, C. Hilbe, A. Traulsen, Royal Society Open Science 3 (2016).","ista":"Chakra M, Hilbe C, Traulsen A. 2016. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. 3(5), 160036.","apa":"Chakra, M., Hilbe, C., & Traulsen, A. (2016). Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.160036","ieee":"M. Chakra, C. Hilbe, and A. Traulsen, “Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites,” Royal Society Open Science, vol. 3, no. 5. Royal Society, The, 2016.","ama":"Chakra M, Hilbe C, Traulsen A. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. 2016;3(5). doi:10.1098/rsos.160036"},"publication":"Royal Society Open Science","date_published":"2016-05-01T00:00:00Z","article_number":"160036","publist_id":"5776","file_date_updated":"2020-07-14T12:44:53Z","publisher":"Royal Society, The","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"C.H. gratefully acknowledges funding by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","year":"2016","volume":3,"date_created":"2018-12-11T11:51:57Z","date_updated":"2021-01-12T06:50:39Z","author":[{"full_name":"Chakra, Maria","first_name":"Maria","last_name":"Chakra"},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"full_name":"Traulsen, Arne","first_name":"Arne","last_name":"Traulsen"}],"month":"05","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsos.160036"},{"article_number":"25676","file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5784","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","acknowledgement":"C.H. acknowledges generous funding from the Schrödinger scholarship of the Austrian Science Fund (FWF), J3475.","year":"2016","date_updated":"2021-01-12T06:50:38Z","date_created":"2018-12-11T11:51:56Z","volume":6,"author":[{"first_name":"Seung","last_name":"Baek","full_name":"Baek, Seung"},{"full_name":"Jeong, Hyeongchai","first_name":"Hyeongchai","last_name":"Jeong"},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"month":"05","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1038/srep25676","type":"journal_article","abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player's previous move, and memory-one strategies, which take into account the own and the co-player's previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation."}],"title":"Comparing reactive and memory-one strategies of direct reciprocity","ddc":["000"],"status":"public","intvolume":" 6","_id":"1423","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"ee17c482370d2e1b3add393710d3c696","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:18:08Z","relation":"main_file","file_id":"5327","content_type":"application/pdf","file_size":1349915,"creator":"system","access_level":"open_access","file_name":"IST-2016-590-v1+1_srep25676.pdf"}],"oa_version":"Published Version","pubrep_id":"590","scopus_import":1,"day":"10","has_accepted_license":"1","publication":"Scientific Reports","citation":{"chicago":"Baek, Seung, Hyeongchai Jeong, Christian Hilbe, and Martin Nowak. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep25676.","mla":"Baek, Seung, et al. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports, vol. 6, 25676, Nature Publishing Group, 2016, doi:10.1038/srep25676.","short":"S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016).","ista":"Baek S, Jeong H, Hilbe C, Nowak M. 2016. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 6, 25676.","apa":"Baek, S., Jeong, H., Hilbe, C., & Nowak, M. (2016). Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep25676","ieee":"S. Baek, H. Jeong, C. Hilbe, and M. Nowak, “Comparing reactive and memory-one strategies of direct reciprocity,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","ama":"Baek S, Jeong H, Hilbe C, Nowak M. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 2016;6. doi:10.1038/srep25676"},"date_published":"2016-05-10T00:00:00Z"},{"month":"07","language":[{"iso":"eng"}],"doi":"10.1007/s11005-016-0847-5","quality_controlled":"1","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5785","date_created":"2018-12-11T11:51:56Z","date_updated":"2021-01-12T06:50:38Z","volume":106,"author":[{"full_name":"Frank, Rupert","first_name":"Rupert","last_name":"Frank"},{"last_name":"Hainzl","first_name":"Christian","full_name":"Hainzl, Christian"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","year":"2016","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":1,"date_published":"2016-07-01T00:00:00Z","page":"913 - 923","publication":"Letters in Mathematical Physics","citation":{"chicago":"Frank, Rupert, Christian Hainzl, Benjamin Schlein, and Robert Seiringer. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0847-5.","short":"R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics 106 (2016) 913–923.","mla":"Frank, Rupert, et al. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics, vol. 106, no. 7, Springer, 2016, pp. 913–23, doi:10.1007/s11005-016-0847-5.","apa":"Frank, R., Hainzl, C., Schlein, B., & Seiringer, R. (2016). Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0847-5","ieee":"R. Frank, C. Hainzl, B. Schlein, and R. Seiringer, “Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations,” Letters in Mathematical Physics, vol. 106, no. 7. Springer, pp. 913–923, 2016.","ista":"Frank R, Hainzl C, Schlein B, Seiringer R. 2016. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 106(7), 913–923.","ama":"Frank R, Hainzl C, Schlein B, Seiringer R. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 2016;106(7):913-923. doi:10.1007/s11005-016-0847-5"},"abstract":[{"lang":"eng","text":"We study the time-dependent Bogoliubov–de-Gennes equations for generic translation-invariant fermionic many-body systems. For initial states that are close to thermal equilibrium states at temperatures near the critical temperature, we show that the magnitude of the order parameter stays approximately constant in time and, in particular, does not follow a time-dependent Ginzburg–Landau equation, which is often employed as a phenomenological description and predicts a decay of the order parameter in time. The full non-linear structure of the equations is necessary to understand this behavior."}],"issue":"7","type":"journal_article","file":[{"relation":"main_file","file_id":"5181","checksum":"fb404923d8ca9a1faeb949561f26cbea","date_created":"2018-12-12T10:15:57Z","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","file_name":"IST-2016-591-v1+1_s11005-016-0847-5.pdf","content_type":"application/pdf","file_size":458968,"creator":"system"}],"oa_version":"Published Version","pubrep_id":"591","ddc":["510","530"],"title":"Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations","status":"public","intvolume":" 106","_id":"1422","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"page":"1523 - 1548","publication":"Genetics","citation":{"mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127.","ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.","apa":"Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127"},"date_published":"2016-04-06T00:00:00Z","scopus_import":"1","day":"06","article_processing_charge":"No","status":"public","title":"A general approximation for the dynamics of quantitative traits","intvolume":" 202","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1420","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. ","lang":"eng"}],"issue":"4","quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"}],"external_id":{"arxiv":["1510.08344"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08344"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.115.184127","month":"04","publication_status":"published","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"Genetics Society of America","year":"2016","date_updated":"2022-08-01T10:49:55Z","date_created":"2018-12-11T11:51:55Z","volume":202,"author":[{"first_name":"Katarína","last_name":"Bod'ová","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"publist_id":"5787","ec_funded":1},{"month":"04","doi":"10.1038/ncomms11332","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","publist_id":"5769","file_date_updated":"2020-07-14T12:44:53Z","article_number":"11332 (2016)","author":[{"full_name":"Husko, Chad","last_name":"Husko","first_name":"Chad"},{"orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf","first_name":"Matthias","full_name":"Wulf, Matthias"},{"full_name":"Lefrançois, Simon","last_name":"Lefrançois","first_name":"Simon"},{"full_name":"Combrié, Sylvain","last_name":"Combrié","first_name":"Sylvain"},{"full_name":"Lehoucq, Gaëlle","last_name":"Lehoucq","first_name":"Gaëlle"},{"last_name":"De Rossi","first_name":"Alfredo","full_name":"De Rossi, Alfredo"},{"first_name":"Benjamin","last_name":"Eggleton","full_name":"Eggleton, Benjamin"},{"first_name":"Laurens","last_name":"Kuipers","full_name":"Kuipers, Laurens"}],"volume":7,"date_updated":"2021-01-12T06:50:40Z","date_created":"2018-12-11T11:51:58Z","year":"2016","acknowledgement":"This research was supported by the Australian Research Council (ARC) Center of Excellence CUDOS (CE110001018), ARC Laureate Fellowship (FL120100029), ARC Discovery Early Career Researcher Award (DECRA DE120102069), the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO). L.K. acknowledges funding from ERC Advanced Investigator Grant (no. 240438-CONSTANS). A.D.R, S.C., and G.L. acknowledge financial support from the ERC-Pharos programme lead by A. P. Mosk.","publisher":"Nature Publishing Group","department":[{"_id":"JoFi"}],"publication_status":"published","has_accepted_license":"1","day":"15","scopus_import":1,"date_published":"2016-04-15T00:00:00Z","citation":{"mla":"Husko, Chad, et al. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications, vol. 7, 11332 (2016), Nature Publishing Group, 2016, doi:10.1038/ncomms11332.","short":"C. Husko, M. Wulf, S. Lefrançois, S. Combrié, G. Lehoucq, A. De Rossi, B. Eggleton, L. Kuipers, Nature Communications 7 (2016).","chicago":"Husko, Chad, Matthias Wulf, Simon Lefrançois, Sylvain Combrié, Gaëlle Lehoucq, Alfredo De Rossi, Benjamin Eggleton, and Laurens Kuipers. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11332.","ama":"Husko C, Wulf M, Lefrançois S, et al. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 2016;7. doi:10.1038/ncomms11332","ista":"Husko C, Wulf M, Lefrançois S, Combrié S, Lehoucq G, De Rossi A, Eggleton B, Kuipers L. 2016. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 7, 11332 (2016).","ieee":"C. Husko et al., “Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","apa":"Husko, C., Wulf, M., Lefrançois, S., Combrié, S., Lehoucq, G., De Rossi, A., … Kuipers, L. (2016). Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11332"},"publication":"Nature Communications","abstract":[{"text":"Solitons are localized waves formed by a balance of focusing and defocusing effects. These nonlinear waves exist in diverse forms of matter yet exhibit similar properties including stability, periodic recurrence and particle-like trajectories. One important property is soliton fission, a process by which an energetic higher-order soliton breaks apart due to dispersive or nonlinear perturbations. Here we demonstrate through both experiment and theory that nonlinear photocarrier generation can induce soliton fission. Using near-field measurements, we directly observe the nonlinear spatial and temporal evolution of optical pulses in situ in a nanophotonic semiconductor waveguide. We develop an analytic formalism describing the free-carrier dispersion (FCD) perturbation and show the experiment exceeds the minimum threshold by an order of magnitude. We confirm these observations with a numerical nonlinear Schrödinger equation model. These results provide a fundamental explanation and physical scaling of optical pulse evolution in free-carrier media and could enable improved supercontinuum sources in gas based and integrated semiconductor waveguides.","lang":"eng"}],"type":"journal_article","pubrep_id":"583","oa_version":"Published Version","file":[{"file_name":"IST-2016-583-v1+1_ncomms11332.pdf","access_level":"open_access","creator":"system","file_size":965176,"content_type":"application/pdf","file_id":"5177","relation":"main_file","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:15:53Z","checksum":"6484fa81a2e52e4fdd7935e1ae6091d4"}],"_id":"1429","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 7","status":"public","title":"Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides","ddc":["530"]},{"pubrep_id":"584","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:17:19Z","checksum":"c27d898598a1e3d7f629607a309254e1","relation":"main_file","file_id":"5272","content_type":"application/pdf","file_size":1216360,"creator":"system","file_name":"IST-2016-584-v1+1_peerj-1865.pdf","access_level":"open_access"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1431","status":"public","title":"Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon","ddc":["570"],"intvolume":" 2016","abstract":[{"lang":"eng","text":"The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow."}],"issue":"3","type":"journal_article","date_published":"2016-01-01T00:00:00Z","publication":"PeerJ","citation":{"chicago":"Tartally, András, Andreas Kelager, Matthias Fürst, and David Nash. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” PeerJ. PeerJ, 2016. https://doi.org/10.7717/peerj.1865.","short":"A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).","mla":"Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” PeerJ, vol. 2016, no. 3, 1865, PeerJ, 2016, doi:10.7717/peerj.1865.","apa":"Tartally, A., Kelager, A., Fürst, M., & Nash, D. (2016). Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. PeerJ. https://doi.org/10.7717/peerj.1865","ieee":"A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon,” PeerJ, vol. 2016, no. 3. PeerJ, 2016.","ista":"Tartally A, Kelager A, Fürst M, Nash D. 2016. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016(3), 1865.","ama":"Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016;2016(3). doi:10.7717/peerj.1865"},"day":"01","has_accepted_license":"1","scopus_import":1,"author":[{"full_name":"Tartally, András","last_name":"Tartally","first_name":"András"},{"first_name":"Andreas","last_name":"Kelager","full_name":"Kelager, Andreas"},{"full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X","first_name":"Matthias","last_name":"Fürst"},{"full_name":"Nash, David","last_name":"Nash","first_name":"David"}],"date_updated":"2021-01-12T06:50:41Z","date_created":"2018-12-11T11:51:59Z","volume":2016,"year":"2016","publication_status":"published","publisher":"PeerJ","department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5767","article_number":"1865","doi":"10.7717/peerj.1865","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"01"},{"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1434","intvolume":" 271","title":"Local stability of the free additive convolution","status":"public","issue":"3","abstract":[{"lang":"eng","text":"We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B on scales down to N−2/3N−2/3."}],"type":"journal_article","date_published":"2016-08-01T00:00:00Z","citation":{"ama":"Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution. Journal of Functional Analysis. 2016;271(3):672-719. doi:10.1016/j.jfa.2016.04.006","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,” Journal of Functional Analysis, vol. 271, no. 3. Academic Press, pp. 672–719, 2016.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2016). Local stability of the free additive convolution. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2016.04.006","ista":"Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution. Journal of Functional Analysis. 271(3), 672–719.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016) 672–719.","mla":"Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” Journal of Functional Analysis, vol. 271, no. 3, Academic Press, 2016, pp. 672–719, doi:10.1016/j.jfa.2016.04.006.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the Free Additive Convolution.” Journal of Functional Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2016.04.006."},"publication":"Journal of Functional Analysis","page":"672 - 719","day":"01","scopus_import":1,"author":[{"full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475","first_name":"Zhigang","last_name":"Bao"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"first_name":"Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin"}],"volume":271,"date_updated":"2021-01-12T06:50:42Z","date_created":"2018-12-11T11:52:00Z","year":"2016","publisher":"Academic Press","department":[{"_id":"LaEr"}],"publication_status":"published","publist_id":"5764","ec_funded":1,"doi":"10.1016/j.jfa.2016.04.006","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1508.05905"}],"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"quality_controlled":"1","month":"08"},{"page":"1 - 30","publication":"Journal de Mathématiques Pures et Appliquées","citation":{"ista":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30.","apa":"Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., & Tzaneteas, T. (2016). Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. Elsevier. https://doi.org/10.1016/j.matpur.2015.09.003","ieee":"V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction,” Journal de Mathématiques Pures et Appliquées, vol. 105, no. 1. Elsevier, pp. 1–30, 2016.","ama":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 2016;105(1):1-30. doi:10.1016/j.matpur.2015.09.003","chicago":"Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et Appliquées. Elsevier, 2016. https://doi.org/10.1016/j.matpur.2015.09.003.","mla":"Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et Appliquées, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:10.1016/j.matpur.2015.09.003.","short":"V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques Pures et Appliquées 105 (2016) 1–30."},"date_published":"2016-01-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","title":"Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction","status":"public","ddc":["510","530"],"intvolume":" 105","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1436","file":[{"creator":"system","content_type":"application/pdf","file_size":658491,"file_name":"IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:54Z","date_created":"2018-12-12T10:10:36Z","checksum":"c5afe1f6935bc7f2b546adbde1d31a35","file_id":"4825","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"581","type":"journal_article","abstract":[{"text":"We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system.","lang":"eng"}],"issue":"1","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.matpur.2015.09.003","month":"01","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Elsevier","year":"2016","date_created":"2018-12-11T11:52:00Z","date_updated":"2021-01-12T06:50:43Z","volume":105,"author":[{"first_name":"Volker","last_name":"Bach","full_name":"Bach, Volker"},{"full_name":"Breteaux, Sébastien","first_name":"Sébastien","last_name":"Breteaux"},{"last_name":"Petrat","first_name":"Sören P","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrat, Sören P"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"},{"full_name":"Tzaneteas, Tim","last_name":"Tzaneteas","first_name":"Tim"}],"file_date_updated":"2020-07-14T12:44:54Z","ec_funded":1,"publist_id":"5763"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1155/2016/1207393","language":[{"iso":"eng"}],"month":"01","year":"2016","publication_status":"published","publisher":"Hindawi Publishing Corporation","department":[{"_id":"PeJo"}],"author":[{"last_name":"Guzmán","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José"},{"full_name":"Gerevich, Zoltan","last_name":"Gerevich","first_name":"Zoltan"}],"date_updated":"2021-01-12T06:50:43Z","date_created":"2018-12-11T11:52:00Z","volume":2016,"article_number":"1207393","file_date_updated":"2020-07-14T12:44:54Z","publist_id":"5762","publication":"Neural Plasticity","citation":{"ama":"Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016;2016. doi:10.1155/2016/1207393","ista":"Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393.","ieee":"J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction,” Neural Plasticity, vol. 2016. Hindawi Publishing Corporation, 2016.","apa":"Guzmán, J., & Gerevich, Z. (2016). P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. Hindawi Publishing Corporation. https://doi.org/10.1155/2016/1207393","mla":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity, vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:10.1155/2016/1207393.","short":"J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016).","chicago":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity. Hindawi Publishing Corporation, 2016. https://doi.org/10.1155/2016/1207393."},"date_published":"2016-01-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","_id":"1435","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction","status":"public","intvolume":" 2016","pubrep_id":"580","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4740","checksum":"8dc5c2f3d44d4775a6e7e3edb0d7a0da","date_created":"2018-12-12T10:09:17Z","date_updated":"2020-07-14T12:44:54Z","access_level":"open_access","file_name":"IST-2016-580-v1+1_1207393.pdf","file_size":1395180,"content_type":"application/pdf","creator":"system"}],"type":"journal_article","abstract":[{"text":"ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states.","lang":"eng"}]},{"ec_funded":1,"publist_id":"5759","author":[{"full_name":"Dragoi, Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","last_name":"Dragoi","first_name":"Cezara"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien"}],"date_created":"2018-12-11T11:52:01Z","date_updated":"2021-01-12T06:50:45Z","volume":"20-22","acknowledgement":"Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192 and FA8650-15-C-7564) and NSF (Grant CCF-1138967). ","year":"2016","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"ACM","month":"01","conference":{"location":"St. Petersburg, FL, USA","start_date":"2016-01-20","end_date":"2016-01-22","name":"POPL: Principles of Programming Languages"},"doi":"10.1145/2837614.2837650","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01251199/"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification.","lang":"eng"}],"type":"conference","alternative_title":["ACM SIGPLAN Notices"],"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1439","title":"PSYNC: A partially synchronous language for fault-tolerant distributed algorithms","status":"public","day":"11","scopus_import":1,"date_published":"2016-01-11T00:00:00Z","citation":{"mla":"Dragoi, Cezara, et al. PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms. Vol. 20–22, ACM, 2016, pp. 400–15, doi:10.1145/2837614.2837650.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415. ACM, 2016. https://doi.org/10.1145/2837614.2837650.","ama":"Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:10.1145/2837614.2837650","ista":"Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415.","apa":"Dragoi, C., Henzinger, T. A., & Zufferey, D. (2016). PSYNC: A partially synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp. 400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837650","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous language for fault-tolerant distributed algorithms,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415."},"page":"400 - 415"},{"page":"213 - 232","publication":"Scientometrics","citation":{"ista":"Calatrava Moreno M, Auzinger T, Werthner H. 2016. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. 107(1), 213–232.","apa":"Calatrava Moreno, M., Auzinger, T., & Werthner, H. (2016). On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. Springer. https://doi.org/10.1007/s11192-016-1842-4","ieee":"M. Calatrava Moreno, T. Auzinger, and H. Werthner, “On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data,” Scientometrics, vol. 107, no. 1. Springer, pp. 213–232, 2016.","ama":"Calatrava Moreno M, Auzinger T, Werthner H. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. 2016;107(1):213-232. doi:10.1007/s11192-016-1842-4","chicago":"Calatrava Moreno, Maria, Thomas Auzinger, and Hannes Werthner. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” Scientometrics. Springer, 2016. https://doi.org/10.1007/s11192-016-1842-4.","mla":"Calatrava Moreno, Maria, et al. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” Scientometrics, vol. 107, no. 1, Springer, 2016, pp. 213–32, doi:10.1007/s11192-016-1842-4.","short":"M. Calatrava Moreno, T. Auzinger, H. Werthner, Scientometrics 107 (2016) 213–232."},"date_published":"2016-04-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","status":"public","ddc":["000"],"title":"On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data","intvolume":" 107","_id":"1446","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"creator":"system","file_size":806035,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-530-v1+1_s11192-016-1842-4.pdf","checksum":"32d46268588b87d9b686492018e6a2b2","date_created":"2018-12-12T10:10:56Z","date_updated":"2020-07-14T12:44:55Z","file_id":"4848","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"530","type":"journal_article","abstract":[{"lang":"eng","text":"The accuracy of interdisciplinarity measurements is directly related to the quality of the underlying bibliographic data. Existing indicators of interdisciplinarity are not capable of reflecting the inaccuracies introduced by incorrect and incomplete records because correct and complete bibliographic data can rarely be obtained. This is the case for the Rao–Stirling index, which cannot handle references that are not categorized into disciplinary fields. We introduce a method that addresses this problem. It extends the Rao–Stirling index to acknowledge missing data by calculating its interval of uncertainty using computational optimization. The evaluation of our method indicates that the uncertainty interval is not only useful for estimating the inaccuracy of interdisciplinarity measurements, but it also delivers slightly more accurate aggregated interdisciplinarity measurements than the Rao–Stirling index."}],"issue":"1","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11192-016-1842-4","month":"04","publication_status":"published","publisher":"Springer","department":[{"_id":"BeBi"}],"year":"2016","date_created":"2018-12-11T11:52:04Z","date_updated":"2021-11-16T08:29:11Z","volume":107,"author":[{"full_name":"Calatrava Moreno, Maria","last_name":"Calatrava Moreno","first_name":"Maria"},{"orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87","last_name":"Auzinger","first_name":"Thomas","full_name":"Auzinger, Thomas"},{"first_name":"Hannes","last_name":"Werthner","full_name":"Werthner, Hannes"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11192-016-1902-9"}]},"file_date_updated":"2020-07-14T12:44:55Z","publist_id":"5750"},{"language":[{"iso":"eng"}],"doi":"10.1214/15-AAP1133","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.00562"}],"oa":1,"month":"06","date_updated":"2021-01-12T06:50:49Z","date_created":"2018-12-11T11:52:05Z","volume":26,"author":[{"first_name":"Max","last_name":"Fathi","full_name":"Fathi, Max"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan"}],"publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"JaMa"}],"acknowledgement":"Supported by the German Research Foundation through the Collaborative Research Center 1060\r\nThe Mathematics of Emergent Effects and the Hausdorff Center for Mathematics. Part of this work has been done while M. Fathi visited J. Maas at the University of Bonn in July 2014.We would like to thank the referees for their careful reading of the manuscript. ","year":"2016","publist_id":"5748","date_published":"2016-06-01T00:00:00Z","page":"1774 - 1806","publication":"The Annals of Applied Probability","citation":{"short":"M. Fathi, J. Maas, The Annals of Applied Probability 26 (2016) 1774–1806.","mla":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” The Annals of Applied Probability, vol. 26, no. 3, Institute of Mathematical Statistics, 2016, pp. 1774–806, doi:10.1214/15-AAP1133.","chicago":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2016. https://doi.org/10.1214/15-AAP1133.","ama":"Fathi M, Maas J. Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. 2016;26(3):1774-1806. doi:10.1214/15-AAP1133","apa":"Fathi, M., & Maas, J. (2016). Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/15-AAP1133","ieee":"M. Fathi and J. Maas, “Entropic Ricci curvature bounds for discrete interacting systems,” The Annals of Applied Probability, vol. 26, no. 3. Institute of Mathematical Statistics, pp. 1774–1806, 2016.","ista":"Fathi M, Maas J. 2016. Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. 26(3), 1774–1806."},"day":"01","scopus_import":1,"oa_version":"Preprint","title":"Entropic Ricci curvature bounds for discrete interacting systems","status":"public","intvolume":" 26","_id":"1448","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We develop a new and systematic method for proving entropic Ricci curvature lower bounds for Markov chains on discrete sets. Using different methods, such bounds have recently been obtained in several examples (e.g., 1-dimensional birth and death chains, product chains, Bernoulli–Laplace models, and random transposition models). However, a general method to obtain discrete Ricci bounds had been lacking. Our method covers all of the examples above. In addition we obtain new Ricci curvature bounds for zero-range processes on the complete graph. The method is inspired by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities."}],"issue":"3","type":"journal_article"},{"month":"01","language":[{"iso":"eng"}],"doi":"10.1242/jcs.176651","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"oa":1,"file_date_updated":"2020-07-14T12:44:56Z","ec_funded":1,"publist_id":"5720","date_created":"2018-12-11T11:52:14Z","date_updated":"2021-01-12T06:51:00Z","volume":129,"author":[{"last_name":"Toshima","first_name":"Junko","full_name":"Toshima, Junko"},{"full_name":"Horikomi, Chika","first_name":"Chika","last_name":"Horikomi"},{"full_name":"Okada, Asuka","first_name":"Asuka","last_name":"Okada"},{"first_name":"Makiko","last_name":"Hatori","full_name":"Hatori, Makiko"},{"last_name":"Nagano","first_name":"Makoto","full_name":"Nagano, Makoto"},{"full_name":"Masuda, Atsushi","last_name":"Masuda","first_name":"Atsushi"},{"first_name":"Wataru","last_name":"Yamamoto","full_name":"Yamamoto, Wataru"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus"},{"last_name":"Toshima","first_name":"Jiro","full_name":"Toshima, Jiro"}],"publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"Company of Biologists","acknowledgement":"We are grateful to Anthony Bretscher (Cornell University, NY) for providing the bni1-12 bnr1Δ (Y4135) strain. J.Y.T. was supported by a Japan Society for the Promotion of Science (JSPS) KAKENHI grant [grant number 26440067]; the Takeda Science Foundation; and the Novartis Foundation (Japan). J.T. was supported by a JSPS KAKENHI grant [grant number 25440054]; the Takeda Science Foundation; and the Kurata Memorial Hitachi Science and Technology Foundation. D.E.S. was supported by the European Union [grant number PCIG12-GA-2012-334077].","year":"2016","day":"15","has_accepted_license":"1","scopus_import":1,"date_published":"2016-01-15T00:00:00Z","page":"367 - 379","publication":"Journal of Cell Science","citation":{"apa":"Toshima, J., Horikomi, C., Okada, A., Hatori, M., Nagano, M., Masuda, A., … Toshima, J. (2016). Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.176651","ieee":"J. Toshima et al., “Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis,” Journal of Cell Science, vol. 129, no. 2. Company of Biologists, pp. 367–379, 2016.","ista":"Toshima J, Horikomi C, Okada A, Hatori M, Nagano M, Masuda A, Yamamoto W, Siekhaus DE, Toshima J. 2016. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. 129(2), 367–379.","ama":"Toshima J, Horikomi C, Okada A, et al. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. 2016;129(2):367-379. doi:10.1242/jcs.176651","chicago":"Toshima, Junko, Chika Horikomi, Asuka Okada, Makiko Hatori, Makoto Nagano, Atsushi Masuda, Wataru Yamamoto, Daria E Siekhaus, and Jiro Toshima. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2016. https://doi.org/10.1242/jcs.176651.","short":"J. Toshima, C. Horikomi, A. Okada, M. Hatori, M. Nagano, A. Masuda, W. Yamamoto, D.E. Siekhaus, J. Toshima, Journal of Cell Science 129 (2016) 367–379.","mla":"Toshima, Junko, et al. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” Journal of Cell Science, vol. 129, no. 2, Company of Biologists, 2016, pp. 367–79, doi:10.1242/jcs.176651."},"abstract":[{"lang":"eng","text":"The dynamic assembly and disassembly of actin filaments is essential for the formation and transport of vesicles during endocytosis. In yeast, two types of actin structures, namely cortical patches and cytoplasmic cables, play a direct role in endocytosis, but how their interaction is regulated remains unclear. Here, we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required for efficient endocytosis owing to its role in the formation of the actin patches that aid initial vesicle invagination and of the actin cables that these move along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented actin cables that frequently moved past actin patches, the sites of endocytosis. We find that the C-terminal CARP domain of Srv2p is vitally important for the proper assembly of actin patches and cables; we also demonstrate that the N-terminal helical folded domain of Srv2 is required for its localization to actin patches, specifically to the ADP-actin rich region through an interaction with cofilin. These results demonstrate the in vivo roles of Srv2p in the regulation of the actin cytoskeleton during clathrin-mediated endocytosis"}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:44:56Z","date_created":"2018-12-12T10:11:08Z","checksum":"2da0a09149a9ed956cdf79a95c17f08a","relation":"main_file","file_id":"4861","file_size":7176912,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-767-v1+1_367.full.pdf","access_level":"open_access"}],"pubrep_id":"767","ddc":["570","576"],"title":"Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis","status":"public","intvolume":" 129","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1476"},{"scopus_import":1,"has_accepted_license":"1","day":"25","citation":{"ama":"Toshima J, Furuya E, Nagano M, et al. Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. eLife. 2016;5(February 2016). doi:10.7554/eLife.10276","apa":"Toshima, J., Furuya, E., Nagano, M., Kanno, C., Sakamoto, Y., Ebihara, M., … Toshima, J. (2016). Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.10276","ieee":"J. Toshima et al., “Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton,” eLife, vol. 5, no. February 2016. eLife Sciences Publications, 2016.","ista":"Toshima J, Furuya E, Nagano M, Kanno C, Sakamoto Y, Ebihara M, Siekhaus DE, Toshima J. 2016. Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. eLife. 5(February 2016), e10276.","short":"J. Toshima, E. Furuya, M. Nagano, C. Kanno, Y. Sakamoto, M. Ebihara, D.E. Siekhaus, J. Toshima, ELife 5 (2016).","mla":"Toshima, Junko, et al. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” ELife, vol. 5, no. February 2016, e10276, eLife Sciences Publications, 2016, doi:10.7554/eLife.10276.","chicago":"Toshima, Junko, Eri Furuya, Makoto Nagano, Chisa Kanno, Yuta Sakamoto, Masashi Ebihara, Daria E Siekhaus, and Jiro Toshima. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.10276."},"publication":"eLife","date_published":"2016-02-25T00:00:00Z","type":"journal_article","issue":"February 2016","abstract":[{"text":"The actin cytoskeleton plays important roles in the formation and internalization of endocytic vesicles. In yeast, endocytic vesicles move towards early endosomes along actin cables, however, the molecular machinery regulating interaction between endocytic vesicles and actin cables is poorly understood. The Eps15-like protein Pan1p plays a key role in actin-mediated endocytosis and is negatively regulated by Ark1 and Prk1 kinases. Here we show that pan1 mutated to prevent phosphorylation at all 18 threonines, pan1-18TA, displayed almost the same endocytic defect as ark1Δ prk1Δ cells, and contained abnormal actin concentrations including several endocytic compartments. Early endosomes were highly localized in the actin concentrations and displayed movement along actin cables. The dephosphorylated form of Pan1p also caused stable associations between endocytic vesicles and actin cables, and between endocytic vesicles and endosomes. Thus Pan1 phosphorylation is part of a novel mechanism that regulates endocytic compartment interactions with each other and with actin cables.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1475","intvolume":" 5","ddc":["570"],"title":"Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton","status":"public","pubrep_id":"529","file":[{"content_type":"application/pdf","file_size":5198001,"creator":"system","access_level":"open_access","file_name":"IST-2016-529-v1+1_elife-10276-v1.pdf","checksum":"d1cc44870580756ba8badd8e41adfdb5","date_created":"2018-12-12T10:10:08Z","date_updated":"2020-07-14T12:44:56Z","relation":"main_file","file_id":"4793"}],"oa_version":"Published Version","month":"02","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077"}],"quality_controlled":"1","doi":"10.7554/eLife.10276","language":[{"iso":"eng"}],"article_number":"e10276","publist_id":"5721","ec_funded":1,"file_date_updated":"2020-07-14T12:44:56Z","year":"2016","department":[{"_id":"DaSi"}],"publisher":"eLife Sciences Publications","publication_status":"published","author":[{"full_name":"Toshima, Junko","last_name":"Toshima","first_name":"Junko"},{"first_name":"Eri","last_name":"Furuya","full_name":"Furuya, Eri"},{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"last_name":"Kanno","first_name":"Chisa","full_name":"Kanno, Chisa"},{"full_name":"Sakamoto, Yuta","last_name":"Sakamoto","first_name":"Yuta"},{"full_name":"Ebihara, Masashi","first_name":"Masashi","last_name":"Ebihara"},{"last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"volume":5,"date_created":"2018-12-11T11:52:14Z","date_updated":"2021-01-12T06:50:59Z"},{"volume":18,"date_created":"2018-12-11T11:52:15Z","date_updated":"2021-01-12T06:51:01Z","author":[{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"},{"first_name":"Simone","last_name":"Warzel","full_name":"Warzel, Simone"}],"publisher":"IOP Publishing Ltd.","department":[{"_id":"RoSe"}],"publication_status":"published","year":"2016","publist_id":"5716","file_date_updated":"2020-07-14T12:44:56Z","article_number":"035002","language":[{"iso":"eng"}],"doi":"10.1088/1367-2630/18/3/035002","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"02","oa_version":"Published Version","file":[{"checksum":"4f959eabc19d2a2f518318a450a4d424","date_created":"2018-12-12T10:17:22Z","date_updated":"2020-07-14T12:44:56Z","file_id":"5276","relation":"main_file","creator":"system","file_size":965607,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-579-v1+1_njp_18_3_035002.pdf"}],"pubrep_id":"579","intvolume":" 18","status":"public","title":"Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas","ddc":["510","530"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1478","issue":"3","abstract":[{"lang":"eng","text":"We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature."}],"type":"journal_article","date_published":"2016-02-29T00:00:00Z","citation":{"apa":"Seiringer, R., & Warzel, S. (2016). Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/18/3/035002","ieee":"R. Seiringer and S. Warzel, “Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas,” New Journal of Physics, vol. 18, no. 3. IOP Publishing Ltd., 2016.","ista":"Seiringer R, Warzel S. 2016. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. 18(3), 035002.","ama":"Seiringer R, Warzel S. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. 2016;18(3). doi:10.1088/1367-2630/18/3/035002","chicago":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” New Journal of Physics. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1367-2630/18/3/035002.","short":"R. Seiringer, S. Warzel, New Journal of Physics 18 (2016).","mla":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” New Journal of Physics, vol. 18, no. 3, 035002, IOP Publishing Ltd., 2016, doi:10.1088/1367-2630/18/3/035002."},"publication":"New Journal of Physics","has_accepted_license":"1","day":"29","scopus_import":1},{"author":[{"full_name":"Michałek, Mateusz","last_name":"Michałek","first_name":"Mateusz"},{"full_name":"Sturmfels, Bernd","last_name":"Sturmfels","first_name":"Bernd"},{"orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline","full_name":"Uhler, Caroline"},{"first_name":"Piotr","last_name":"Zwiernik","full_name":"Zwiernik, Piotr"}],"date_updated":"2021-01-12T06:51:02Z","date_created":"2018-12-11T11:52:16Z","volume":112,"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1480","year":"2016","publication_status":"published","status":"public","title":"Exponential varieties","department":[{"_id":"CaUh"}],"publisher":"Oxford University Press","intvolume":" 112","abstract":[{"text":"Exponential varieties arise from exponential families in statistics. These real algebraic varieties have strong positivity and convexity properties, familiar from toric varieties and their moment maps. Among them are varieties of inverses of symmetric matrices satisfying linear constraints. This class includes Gaussian graphical models. We develop a general theory of exponential varieties. These are derived from hyperbolic polynomials and their integral representations. We compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials. ","lang":"eng"}],"publist_id":"5714","issue":"1","type":"journal_article","doi":"10.1112/plms/pdv066","date_published":"2016-01-07T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the London Mathematical Society","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1412.6185","open_access":"1"}],"citation":{"short":"M. Michałek, B. Sturmfels, C. Uhler, P. Zwiernik, Proceedings of the London Mathematical Society 112 (2016) 27–56.","mla":"Michałek, Mateusz, et al. “Exponential Varieties.” Proceedings of the London Mathematical Society, vol. 112, no. 1, Oxford University Press, 2016, pp. 27–56, doi:10.1112/plms/pdv066.","chicago":"Michałek, Mateusz, Bernd Sturmfels, Caroline Uhler, and Piotr Zwiernik. “Exponential Varieties.” Proceedings of the London Mathematical Society. Oxford University Press, 2016. https://doi.org/10.1112/plms/pdv066.","ama":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. Exponential varieties. Proceedings of the London Mathematical Society. 2016;112(1):27-56. doi:10.1112/plms/pdv066","ieee":"M. Michałek, B. Sturmfels, C. Uhler, and P. Zwiernik, “Exponential varieties,” Proceedings of the London Mathematical Society, vol. 112, no. 1. Oxford University Press, pp. 27–56, 2016.","apa":"Michałek, M., Sturmfels, B., Uhler, C., & Zwiernik, P. (2016). Exponential varieties. Proceedings of the London Mathematical Society. Oxford University Press. https://doi.org/10.1112/plms/pdv066","ista":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. 2016. Exponential varieties. Proceedings of the London Mathematical Society. 112(1), 27–56."},"quality_controlled":"1","page":"27 - 56","month":"01","day":"07","scopus_import":1},{"date_created":"2018-12-11T11:52:18Z","date_updated":"2021-01-12T06:51:05Z","volume":14,"author":[{"last_name":"Grion","first_name":"Natalia","full_name":"Grion, Natalia"},{"full_name":"Akrami, Athena","first_name":"Athena","last_name":"Akrami"},{"full_name":"Zuo, Yangfang","first_name":"Yangfang","last_name":"Zuo"},{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148","first_name":"Federico","last_name":"Stella","full_name":"Stella, Federico"},{"first_name":"Mathew","last_name":"Diamond","full_name":"Diamond, Mathew"}],"publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Public Library of Science","acknowledgement":"We thank Eric Maris, Demian Battaglia, and Rodrigo Quian Quiroga for useful discussions. We are grateful to Fabrizio Manzino and Marco Gigante for construction of the behavioral apparatus, Igor Perkon for developing custom whisker tracking software and to Francesca Pulecchi for animal care and histological processing.","year":"2016","file_date_updated":"2020-07-14T12:44:57Z","publist_id":"5700","article_number":"e1002384","language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.1002384","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"02","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5129","date_created":"2018-12-12T10:15:11Z","date_updated":"2020-07-14T12:44:57Z","checksum":"3a5ce0d4e4e36bd6ceb4be761f85644a","file_name":"IST-2016-518-v1+1_journal.pbio.1002384.PDF","access_level":"open_access","file_size":2879899,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"518","ddc":["570"],"title":"Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination","status":"public","intvolume":" 14","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1487","abstract":[{"text":"Rhythms with time scales of multiple cycles per second permeate the mammalian brain, yet neuroscientists are not certain of their functional roles. One leading idea is that coherent oscillation between two brain regions facilitates the exchange of information between them. In rats, the hippocampus and the vibrissal sensorimotor system both are characterized by rhythmic oscillation in the theta range, 5–12 Hz. Previous work has been divided as to whether the two rhythms are independent or coherent. To resolve this question, we acquired three measures from rats—whisker motion, hippocampal local field potential (LFP), and barrel cortex unit firing—during a whisker-mediated texture discrimination task and during control conditions (not engaged in a whisker-mediated memory task). Compared to control conditions, the theta band of hippocampal LFP showed a marked increase in power as the rats approached and then palpated the texture. Phase synchronization between whisking and hippocampal LFP increased by almost 50% during approach and texture palpation. In addition, a greater proportion of barrel cortex neurons showed firing that was phase-locked to hippocampal theta while rats were engaged in the discrimination task. Consistent with a behavioral consequence of phase synchronization, the rats identified the texture more rapidly and with lower error likelihood on trials in which there was an increase in theta-whisking coherence at the moment of texture palpation. These results suggest that coherence between the whisking rhythm, barrel cortex firing, and hippocampal LFP is augmented selectively during epochs in which the rat collects sensory information and that such coherence enhances the efficiency of integration of stimulus information into memory and decision-making centers.","lang":"eng"}],"issue":"2","type":"journal_article","date_published":"2016-02-18T00:00:00Z","publication":"PLoS Biology","citation":{"ama":"Grion N, Akrami A, Zuo Y, Stella F, Diamond M. Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. 2016;14(2). doi:10.1371/journal.pbio.1002384","ieee":"N. Grion, A. Akrami, Y. Zuo, F. Stella, and M. Diamond, “Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination,” PLoS Biology, vol. 14, no. 2. Public Library of Science, 2016.","apa":"Grion, N., Akrami, A., Zuo, Y., Stella, F., & Diamond, M. (2016). Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002384","ista":"Grion N, Akrami A, Zuo Y, Stella F, Diamond M. 2016. Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. 14(2), e1002384.","short":"N. Grion, A. Akrami, Y. Zuo, F. Stella, M. Diamond, PLoS Biology 14 (2016).","mla":"Grion, Natalia, et al. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination.” PLoS Biology, vol. 14, no. 2, e1002384, Public Library of Science, 2016, doi:10.1371/journal.pbio.1002384.","chicago":"Grion, Natalia, Athena Akrami, Yangfang Zuo, Federico Stella, and Mathew Diamond. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.1002384."},"day":"18","has_accepted_license":"1","scopus_import":1},{"doi":"10.1371/journal.pone.0147830","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"02","author":[{"full_name":"Adibi, Milad","first_name":"Milad","last_name":"Adibi"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"last_name":"Fleck","first_name":"Christian","full_name":"Fleck, Christian"}],"volume":11,"date_created":"2018-12-11T11:52:17Z","date_updated":"2021-01-12T06:51:03Z","acknowledgement":"We thank J. Traas, B. Müller and V. Reddy for providing seed materials and Y. Deb for advice regarding the laser ablation experiments. We specially thank Thomas Laux for stimulating discussions and support in the initial phase of this project.","year":"2016","department":[{"_id":"JiFr"}],"publisher":"Public Library of Science","publication_status":"published","publist_id":"5711","file_date_updated":"2020-07-14T12:44:57Z","article_number":"e0147830","date_published":"2016-02-01T00:00:00Z","citation":{"mla":"Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:10.1371/journal.pone.0147830.","short":"M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016).","chicago":"Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0147830.","ama":"Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 2016;11(2). doi:10.1371/journal.pone.0147830","ista":"Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 11(2), e0147830.","ieee":"M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization,” PLoS One, vol. 11, no. 2. Public Library of Science, 2016.","apa":"Adibi, M., Yoshida, S., Weijers, D., & Fleck, C. (2016). Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0147830"},"publication":"PLoS One","has_accepted_license":"1","day":"01","scopus_import":1,"pubrep_id":"521","oa_version":"Published Version","file":[{"file_name":"IST-2016-521-v1+1_journal.pone.0147830.PDF","access_level":"open_access","creator":"system","file_size":4297148,"content_type":"application/pdf","file_id":"5066","relation":"main_file","date_created":"2018-12-12T10:14:16Z","date_updated":"2020-07-14T12:44:57Z","checksum":"6066146e527335030f83aa5924ab72a6"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1482","intvolume":" 11","title":"Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization","status":"public","ddc":["570"],"issue":"2","abstract":[{"text":"Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation.","lang":"eng"}],"type":"journal_article"},{"pubrep_id":"1002","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2018-1002-v1+1_Chen_TICB_2016_proofs.pdf","creator":"system","file_size":2329117,"content_type":"application/pdf","file_id":"5155","relation":"main_file","checksum":"b229e5bb4676ec3e27b7b9ea603b3a63","date_created":"2018-12-12T10:15:34Z","date_updated":"2020-07-14T12:44:57Z"}],"_id":"1484","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["581"],"title":"Environmental and endogenous control of cortical microtubule orientation","intvolume":" 26","issue":"6","type":"journal_article","date_published":"2016-06-01T00:00:00Z","publication":"Trends in Cell Biology","citation":{"ama":"Chen X, Wu S, Liu Z, Friml J. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 2016;26(6):409-419. doi:10.1016/j.tcb.2016.02.003","ista":"Chen X, Wu S, Liu Z, Friml J. 2016. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 26(6), 409–419.","ieee":"X. Chen, S. Wu, Z. Liu, and J. Friml, “Environmental and endogenous control of cortical microtubule orientation,” Trends in Cell Biology, vol. 26, no. 6. Cell Press, pp. 409–419, 2016.","apa":"Chen, X., Wu, S., Liu, Z., & Friml, J. (2016). Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2016.02.003","mla":"Chen, Xu, et al. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology, vol. 26, no. 6, Cell Press, 2016, pp. 409–19, doi:10.1016/j.tcb.2016.02.003.","short":"X. Chen, S. Wu, Z. Liu, J. Friml, Trends in Cell Biology 26 (2016) 409–419.","chicago":"Chen, Xu, Shuang Wu, Zengyu Liu, and Jiří Friml. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology. Cell Press, 2016. https://doi.org/10.1016/j.tcb.2016.02.003."},"article_type":"review","page":"409 - 419","day":"01","has_accepted_license":"1","scopus_import":1,"author":[{"first_name":"Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu"},{"full_name":"Wu, Shuang","first_name":"Shuang","last_name":"Wu"},{"first_name":"Zengyu","last_name":"Liu","full_name":"Liu, Zengyu"},{"full_name":"Friml, Jiřĺ","last_name":"Friml","first_name":"Jiřĺ","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T06:51:04Z","date_created":"2018-12-11T11:52:17Z","volume":26,"acknowledgement":"We thank Maciek Adamowski for helpful discussions and Qiang Zhu and Israel Ausin for critical reading of the manuscript. We sincerely apologize to colleagues whose work we could not include owing to space limitations.","year":"2016","publication_status":"published","publisher":"Cell Press","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:57Z","publist_id":"5704","doi":"10.1016/j.tcb.2016.02.003","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"06"},{"ec_funded":1,"publist_id":"5702","article_number":"016003","author":[{"full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","first_name":"Daniele","last_name":"De Martino"}],"volume":13,"date_updated":"2021-01-12T06:51:04Z","date_created":"2018-12-11T11:52:18Z","year":"2016","publisher":"IOP Publishing Ltd.","department":[{"_id":"GaTk"}],"publication_status":"published","month":"01","doi":"10.1088/1478-3975/13/1/016003","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1505.04613"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","issue":"1","abstract":[{"text":"In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1485","intvolume":" 13","title":"Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis","status":"public","day":"29","scopus_import":1,"date_published":"2016-01-29T00:00:00Z","citation":{"ieee":"D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” Physical Biology, vol. 13, no. 1. IOP Publishing Ltd., 2016.","apa":"De Martino, D. (2016). Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/1/016003","ista":"De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003.","ama":"De Martino D. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 2016;13(1). doi:10.1088/1478-3975/13/1/016003","chicago":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” Physical Biology. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1478-3975/13/1/016003.","short":"D. De Martino, Physical Biology 13 (2016).","mla":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” Physical Biology, vol. 13, no. 1, 016003, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/1/016003."},"publication":"Physical Biology"},{"scopus_import":1,"month":"02","day":"24","oa":1,"citation":{"chicago":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” Journal of Mathematical Physics. American Institute of Physics, 2016. https://doi.org/10.1063/1.4941723.","mla":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” Journal of Mathematical Physics, vol. 57, no. 2, 021101, American Institute of Physics, 2016, doi:10.1063/1.4941723.","short":"C. Hainzl, R. Seiringer, Journal of Mathematical Physics 57 (2016).","ista":"Hainzl C, Seiringer R. 2016. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. 57(2), 021101.","ieee":"C. Hainzl and R. Seiringer, “The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties,” Journal of Mathematical Physics, vol. 57, no. 2. American Institute of Physics, 2016.","apa":"Hainzl, C., & Seiringer, R. (2016). The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4941723","ama":"Hainzl C, Seiringer R. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. 2016;57(2). doi:10.1063/1.4941723"},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1511.01995"}],"publication":"Journal of Mathematical Physics","quality_controlled":"1","date_published":"2016-02-24T00:00:00Z","doi":"10.1063/1.4941723","language":[{"iso":"eng"}],"type":"journal_article","article_number":"021101","issue":"2","publist_id":"5701","abstract":[{"text":"We review recent results concerning the mathematical properties of the Bardeen-Cooper-Schrieffer (BCS) functional of superconductivity, which were obtained in a series of papers, partly in collaboration with R. Frank, E. Hamza, S. Naboko, and J. P. Solovej. Our discussion includes, in particular, an investigation of the critical temperature for a general class of interaction potentials, as well as a study of its dependence on external fields. We shall explain how the Ginzburg-Landau model can be derived from the BCS theory in a suitable parameter regime.","lang":"eng"}],"year":"2016","_id":"1486","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 57","department":[{"_id":"RoSe"}],"publisher":"American Institute of Physics","publication_status":"published","status":"public","title":"The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties","author":[{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"oa_version":"Preprint","volume":57,"date_created":"2018-12-11T11:52:18Z","date_updated":"2021-01-12T06:51:04Z"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis."}],"issue":"2","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1488","status":"public","ddc":["570"],"title":"Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","intvolume":" 14","pubrep_id":"517","oa_version":"Published Version","file":[{"checksum":"7f8fa1b3a29f94c0a14dd4465278cdbc","date_updated":"2020-07-14T12:44:57Z","date_created":"2018-12-12T10:13:42Z","file_id":"5027","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":5904773,"access_level":"open_access","file_name":"IST-2016-517-v1+1_journal.pbio.1002382_1_.PDF"}],"scopus_import":1,"day":"19","has_accepted_license":"1","publication":"PLoS Biology","citation":{"short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, PLoS Biology 14 (2016).","mla":"Riccio, Paul, et al. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” PLoS Biology, vol. 14, no. 2, e1002382, Public Library of Science, 2016, doi:10.1371/journal.pbio.1002382.","chicago":"Riccio, Paul, Cristina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.1002382.","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. 2016;14(2). doi:10.1371/journal.pbio.1002382","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis,” PLoS Biology, vol. 14, no. 2. Public Library of Science, 2016.","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2016). Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002382","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2016. Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. 14(2), e1002382."},"date_published":"2016-02-19T00:00:00Z","article_number":"e1002382","file_date_updated":"2020-07-14T12:44:57Z","publist_id":"5699","year":"2016","acknowledgement":"We thank Silvia Arber, Thomas Jessell, Kenneth M. Murphy, Carlton Bates, Hideki Enomoto, Liqun Luo and Andrew McMahon for mouse strains; Thomas Jessell for antibodies; and Laura Martinez Prat for experimental assistance.","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"SiHi"}],"author":[{"full_name":"Riccio, Paul","last_name":"Riccio","first_name":"Paul"},{"full_name":"Cebrián, Cristina","first_name":"Cristina","last_name":"Cebrián"},{"full_name":"Zong, Hui","last_name":"Zong","first_name":"Hui"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"},{"full_name":"Costantini, Frank","last_name":"Costantini","first_name":"Frank"}],"related_material":{"record":[{"id":"9703","status":"deleted","relation":"research_data"}]},"date_created":"2018-12-11T11:52:19Z","date_updated":"2023-02-23T10:01:08Z","volume":14,"month":"02","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pbio.1002382","language":[{"iso":"eng"}]},{"type":"journal_article","abstract":[{"text":"We prove optimal local law, bulk universality and non-trivial decay for the off-diagonal elements of the resolvent for a class of translation invariant Gaussian random matrix ensembles with correlated entries. ","lang":"eng"}],"issue":"2","status":"public","ddc":["510"],"title":"Local spectral statistics of Gaussian matrices with correlated entries","intvolume":" 163","_id":"1489","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":660602,"access_level":"open_access","file_name":"IST-2016-516-v1+1_s10955-016-1479-y.pdf","checksum":"7139598dcb1cafbe6866bd2bfd732b33","date_created":"2018-12-12T10:11:16Z","date_updated":"2020-07-14T12:44:57Z","file_id":"4869","relation":"main_file"}],"pubrep_id":"516","scopus_import":1,"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","page":"280 - 302","publication":"Journal of Statistical Physics","citation":{"chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Local Spectral Statistics of Gaussian Matrices with Correlated Entries.” Journal of Statistical Physics. Springer, 2016. https://doi.org/10.1007/s10955-016-1479-y.","mla":"Ajanki, Oskari H., et al. “Local Spectral Statistics of Gaussian Matrices with Correlated Entries.” Journal of Statistical Physics, vol. 163, no. 2, Springer, 2016, pp. 280–302, doi:10.1007/s10955-016-1479-y.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Journal of Statistical Physics 163 (2016) 280–302.","ista":"Ajanki OH, Erdös L, Krüger TH. 2016. Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. 163(2), 280–302.","apa":"Ajanki, O. H., Erdös, L., & Krüger, T. H. (2016). Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1479-y","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Local spectral statistics of Gaussian matrices with correlated entries,” Journal of Statistical Physics, vol. 163, no. 2. Springer, pp. 280–302, 2016.","ama":"Ajanki OH, Erdös L, Krüger TH. Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. 2016;163(2):280-302. doi:10.1007/s10955-016-1479-y"},"date_published":"2016-04-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:57Z","publist_id":"5698","ec_funded":1,"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Springer","year":"2016","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). Oskari H. Ajanki was Partially supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German Research Council. László Erdős was Partially supported by ERC Advanced Grant RANMAT No. 338804. Torben Krüger was Partially supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German Research Council.","date_created":"2018-12-11T11:52:19Z","date_updated":"2021-01-12T06:51:05Z","volume":163,"author":[{"first_name":"Oskari H","last_name":"Ajanki","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","full_name":"Ajanki, Oskari H"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"full_name":"Krüger, Torben H","first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297"}],"month":"04","quality_controlled":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1007/s10955-016-1479-y"},{"file":[{"access_level":"open_access","file_name":"IST-2016-515-v1+1_1-s2.0-S2211124716300262-main.pdf","creator":"system","file_size":5489897,"content_type":"application/pdf","file_id":"4948","relation":"main_file","checksum":"c98c1151d5f1e5ce1643a83d8d7f3c29","date_updated":"2020-07-14T12:44:58Z","date_created":"2018-12-12T10:12:30Z"}],"oa_version":"Published Version","pubrep_id":"515","ddc":["570"],"status":"public","title":"Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels","intvolume":" 14","_id":"1490","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"To induce adaptive immunity, dendritic cells (DCs) migrate through afferent lymphatic vessels (LVs) to draining lymph nodes (dLNs). This process occurs in several consecutive steps. Upon entry into lymphatic capillaries, DCs first actively crawl into downstream collecting vessels. From there, they are next passively and rapidly transported to the dLN by lymph flow. Here, we describe a role for the chemokine CCL21 in intralymphatic DC crawling. Performing time-lapse imaging in murine skin, we found that blockade of CCL21-but not the absence of lymph flow-completely abolished DC migration from capillaries toward collecting vessels and reduced the ability of intralymphatic DCs to emigrate from skin. Moreover, we found that in vitro low laminar flow established a CCL21 gradient along lymphatic endothelial monolayers, thereby inducing downstream-directed DC migration. These findings reveal a role for intralymphatic CCL21 in promoting DC trafficking to dLNs, through the formation of a flow-induced gradient."}],"issue":"7","type":"journal_article","date_published":"2016-02-23T00:00:00Z","page":"1723 - 1734","publication":"Cell Reports","citation":{"chicago":"Russo, Erica, Alvaro Teijeira, Kari Vaahtomeri, Ann Willrodt, Joël Bloch, Maximilian Nitschké, Laura Santambrogio, Dontscho Kerjaschki, Michael K Sixt, and Cornelia Halin. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic Cells through Afferent Lymphatic Vessels.” Cell Reports. Cell Press, 2016. https://doi.org/10.1016/j.celrep.2016.01.048.","short":"E. Russo, A. Teijeira, K. Vaahtomeri, A. Willrodt, J. Bloch, M. Nitschké, L. Santambrogio, D. Kerjaschki, M.K. Sixt, C. Halin, Cell Reports 14 (2016) 1723–1734.","mla":"Russo, Erica, et al. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic Cells through Afferent Lymphatic Vessels.” Cell Reports, vol. 14, no. 7, Cell Press, 2016, pp. 1723–34, doi:10.1016/j.celrep.2016.01.048.","apa":"Russo, E., Teijeira, A., Vaahtomeri, K., Willrodt, A., Bloch, J., Nitschké, M., … Halin, C. (2016). Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.01.048","ieee":"E. Russo et al., “Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels,” Cell Reports, vol. 14, no. 7. Cell Press, pp. 1723–1734, 2016.","ista":"Russo E, Teijeira A, Vaahtomeri K, Willrodt A, Bloch J, Nitschké M, Santambrogio L, Kerjaschki D, Sixt MK, Halin C. 2016. Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. 14(7), 1723–1734.","ama":"Russo E, Teijeira A, Vaahtomeri K, et al. Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. 2016;14(7):1723-1734. doi:10.1016/j.celrep.2016.01.048"},"day":"23","has_accepted_license":"1","scopus_import":1,"date_updated":"2021-01-12T06:51:07Z","date_created":"2018-12-11T11:52:19Z","volume":14,"author":[{"last_name":"Russo","first_name":"Erica","full_name":"Russo, Erica"},{"first_name":"Alvaro","last_name":"Teijeira","full_name":"Teijeira, Alvaro"},{"full_name":"Vaahtomeri, Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","first_name":"Kari","last_name":"Vaahtomeri"},{"full_name":"Willrodt, Ann","first_name":"Ann","last_name":"Willrodt"},{"full_name":"Bloch, Joël","first_name":"Joël","last_name":"Bloch"},{"full_name":"Nitschké, Maximilian","first_name":"Maximilian","last_name":"Nitschké"},{"first_name":"Laura","last_name":"Santambrogio","full_name":"Santambrogio, Laura"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Halin, Cornelia","first_name":"Cornelia","last_name":"Halin"}],"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Cell Press","year":"2016","file_date_updated":"2020-07-14T12:44:58Z","publist_id":"5697","language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2016.01.048","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"month":"02"},{"abstract":[{"lang":"eng","text":"We introduce a new method for deriving the time-dependent Hartree or Hartree-Fock equations as an effective mean-field dynamics from the microscopic Schrödinger equation for fermionic many-particle systems in quantum mechanics. The method is an adaption of the method used in Pickl (Lett. Math. Phys. 97 (2) 151–164 2011) for bosonic systems to fermionic systems. It is based on a Gronwall type estimate for a suitable measure of distance between the microscopic solution and an antisymmetrized product state. We use this method to treat a new mean-field limit for fermions with long-range interactions in a large volume. Some of our results hold for singular attractive or repulsive interactions. We can also treat Coulomb interaction assuming either a mild singularity cutoff or certain regularity conditions on the solutions to the Hartree(-Fock) equations. In the considered limit, the kinetic and interaction energy are of the same order, while the average force is subleading. For some interactions, we prove that the Hartree(-Fock) dynamics is a more accurate approximation than a simpler dynamics that one would expect from the subleading force. With our method we also treat the mean-field limit coupled to a semiclassical limit, which was discussed in the literature before, and we recover some of the previous results. All results hold for initial data close (but not necessarily equal) to antisymmetrized product states and we always provide explicit rates of convergence."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:16:55Z","date_updated":"2020-07-14T12:44:58Z","checksum":"eb5d2145ef0d377c4f78bf06e18f4529","file_id":"5246","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":911310,"file_name":"IST-2016-514-v1+1_s11040-016-9204-2.pdf","access_level":"open_access"}],"pubrep_id":"514","status":"public","ddc":["510","530"],"title":"A new method and a new scaling for deriving fermionic mean-field dynamics","intvolume":" 19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1493","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":1,"date_published":"2016-03-01T00:00:00Z","publication":"Mathematical Physics, Analysis and Geometry","citation":{"ama":"Petrat SP, Pickl P. A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. 2016;19(1). doi:10.1007/s11040-016-9204-2","ieee":"S. P. Petrat and P. Pickl, “A new method and a new scaling for deriving fermionic mean-field dynamics,” Mathematical Physics, Analysis and Geometry, vol. 19, no. 1. Springer, 2016.","apa":"Petrat, S. P., & Pickl, P. (2016). A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-016-9204-2","ista":"Petrat SP, Pickl P. 2016. A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. 19(1), 3.","short":"S.P. Petrat, P. Pickl, Mathematical Physics, Analysis and Geometry 19 (2016).","mla":"Petrat, Sören P., and Peter Pickl. “A New Method and a New Scaling for Deriving Fermionic Mean-Field Dynamics.” Mathematical Physics, Analysis and Geometry, vol. 19, no. 1, 3, Springer, 2016, doi:10.1007/s11040-016-9204-2.","chicago":"Petrat, Sören P, and Peter Pickl. “A New Method and a New Scaling for Deriving Fermionic Mean-Field Dynamics.” Mathematical Physics, Analysis and Geometry. Springer, 2016. https://doi.org/10.1007/s11040-016-9204-2."},"file_date_updated":"2020-07-14T12:44:58Z","publist_id":"5690","ec_funded":1,"article_number":"3","date_updated":"2021-01-12T06:51:08Z","date_created":"2018-12-11T11:52:20Z","volume":19,"author":[{"id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9166-5889","first_name":"Sören P","last_name":"Petrat","full_name":"Petrat, Sören P"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"}],"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","year":"2016","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","month":"03","language":[{"iso":"eng"}],"doi":"10.1007/s11040-016-9204-2","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"publist_id":"5691","file_date_updated":"2020-07-14T12:44:58Z","pmid":1,"acknowledgement":"This work was supported by a European Research Council Starting Inde-pendent Research grant (ERC-2007-Stg-207362-HCPO to J.D.), Research Foundation-Flanders (G033711N to A.A.), and the Austrian Science Fund (FWF01_I1774S to E.B.). P.M. is indebted to the Federation of European Biochemical Sciences for a Long-Term Fellowship. ","year":"2016","publisher":"Cold Spring Harbor Laboratory Press","department":[{"_id":"EvBe"}],"publication_status":"published","author":[{"orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","first_name":"Peter","full_name":"Marhavy, Peter"},{"first_name":"Juan C","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C"},{"first_name":"Anas","last_name":"Abuzeineh","full_name":"Abuzeineh, Anas"},{"full_name":"Van Damme, Daniël","first_name":"Daniël","last_name":"Van Damme"},{"first_name":"Joop","last_name":"Vermeer","full_name":"Vermeer, Joop"},{"last_name":"Duclercq","first_name":"Jérôme","full_name":"Duclercq, Jérôme"},{"first_name":"Hana","last_name":"Rakusova","full_name":"Rakusova, Hana"},{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","last_name":"Marhavá","full_name":"Marhavá, Petra"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Geldner, Niko","last_name":"Geldner","first_name":"Niko"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"volume":30,"date_updated":"2021-01-12T06:51:08Z","date_created":"2018-12-11T11:52:20Z","month":"03","external_id":{"pmid":[" 26883363"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1101/gad.276964.115","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"type":"journal_article","issue":"4","abstract":[{"text":"To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated cells with a preserved prolif eration capacity. The root pericycle represents a unique tissue with conditional meristematic activity, and its tight control determines initiation of lateral organs. Here we show that the meristematic activity of the pericycle is constrained by the interaction with the adjacent endodermis. Release of these restraints by elimination of endo dermal cells by single-cell ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis removal substitutes for the phytohormone auxin-dependent initiation of the pericycle meristematic activity. However, auxin is indispensable to steer the cell division plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally distinct role for auxin during lateral root initiation. In the endodermis, auxin releases constraints arising from cell-to-cell interactions that compromise the pericycle meristematic activity, whereas, in the pericycle, auxin defines the orientation of the cell division plane to initiate lateral roots.","lang":"eng"}],"_id":"1492","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 30","ddc":["570"],"title":"Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation","status":"public","oa_version":"Published Version","file":[{"creator":"kschuh","file_size":2757636,"content_type":"application/pdf","access_level":"open_access","file_name":"2016_GeneDev_Marhavy.pdf","checksum":"ea394498ee56270e021d1028a29358a0","date_updated":"2020-07-14T12:44:58Z","date_created":"2019-01-25T09:56:11Z","file_id":"5883","relation":"main_file"}],"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"ieee":"P. Marhavý et al., “Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation,” Genes and Development, vol. 30, no. 4. Cold Spring Harbor Laboratory Press, pp. 471–483, 2016.","apa":"Marhavý, P., Montesinos López, J. C., Abuzeineh, A., Van Damme, D., Vermeer, J., Duclercq, J., … Benková, E. (2016). Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.276964.115","ista":"Marhavý P, Montesinos López JC, Abuzeineh A, Van Damme D, Vermeer J, Duclercq J, Rakusova H, Marhavá P, Friml J, Geldner N, Benková E. 2016. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. 30(4), 471–483.","ama":"Marhavý P, Montesinos López JC, Abuzeineh A, et al. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. 2016;30(4):471-483. doi:10.1101/gad.276964.115","chicago":"Marhavý, Peter, Juan C Montesinos López, Anas Abuzeineh, Daniël Van Damme, Joop Vermeer, Jérôme Duclercq, Hana Rakusova, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” Genes and Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.276964.115.","short":"P. Marhavý, J.C. Montesinos López, A. Abuzeineh, D. Van Damme, J. Vermeer, J. Duclercq, H. Rakusova, P. Marhavá, J. Friml, N. Geldner, E. Benková, Genes and Development 30 (2016) 471–483.","mla":"Marhavý, Peter, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” Genes and Development, vol. 30, no. 4, Cold Spring Harbor Laboratory Press, 2016, pp. 471–83, doi:10.1101/gad.276964.115."},"publication":"Genes and Development","page":"471 - 483","date_published":"2016-03-01T00:00:00Z"},{"scopus_import":1,"day":"07","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","citation":{"ieee":"P. Amaro et al., “Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3. American Physical Society, 2016.","apa":"Amaro, P., Fratini, F., Safari, L., Machado, J., Guerra, M., Indelicato, P., & Santos, J. (2016). Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.93.032502","ista":"Amaro P, Fratini F, Safari L, Machado J, Guerra M, Indelicato P, Santos J. 2016. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 032502.","ama":"Amaro P, Fratini F, Safari L, et al. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3). doi:10.1103/PhysRevA.93.032502","chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Jorge Machado, Mauro Guerra, Paul Indelicato, and José Santos. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.032502.","short":"P. Amaro, F. Fratini, L. Safari, J. Machado, M. Guerra, P. Indelicato, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).","mla":"Amaro, Pedro, et al. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3, 032502, American Physical Society, 2016, doi:10.1103/PhysRevA.93.032502."},"date_published":"2016-03-07T00:00:00Z","type":"journal_article","abstract":[{"text":"The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is theoretically investigated within a fully relativistic framework and a second-order perturbation theory. We focus our analysis on how electron correlation, as well as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For this purpose, we include the electronic correlation via an effective local potential and within a single configuration-state model. Due to its experimental interest, evaluations of decay rates are performed for berylliumlike xenon and uranium. We find that the negative-energy contribution can be neglected at the present level of accuracy in the evaluation of the decay rate. On the other hand, if contributions of electronic correlation are not carefully taken into account, it may change the lifetime of the metastable state by up to 20%. By performing a full-relativistic jj-coupling calculation, we found a decrease of the decay rate by two orders of magnitude compared to non-relativistic LS-coupling calculations, for the selected heavy ions.","lang":"eng"}],"issue":"3","title":"Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model","status":"public","intvolume":" 93","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1496","oa_version":"Preprint","month":"03","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1508.06169","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.93.032502","article_number":"032502","publist_id":"5683","ec_funded":1,"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"year":"2016","acknowledgement":"This research was supported in part by FCT, Portugal, through Project No. PTDC/FIS/117606/2010, financed by the European Community Fund FEDER through the COMPETE. ","date_updated":"2021-01-12T06:51:09Z","date_created":"2018-12-11T11:52:21Z","volume":93,"author":[{"full_name":"Amaro, Pedro","first_name":"Pedro","last_name":"Amaro"},{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"},{"full_name":"Safari, Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","last_name":"Safari"},{"first_name":"Jorge","last_name":"Machado","full_name":"Machado, Jorge"},{"first_name":"Mauro","last_name":"Guerra","full_name":"Guerra, Mauro"},{"full_name":"Indelicato, Paul","first_name":"Paul","last_name":"Indelicato"},{"last_name":"Santos","first_name":"José","full_name":"Santos, José"}]},{"abstract":[{"lang":"eng","text":"We study the ground state of a trapped Bose gas, starting from the full many-body Schrödinger Hamiltonian, and derive the non-linear Schrödinger energy functional in the limit of a large particle number, when the interaction potential converges slowly to a Dirac delta function. Our method is based on quantitative estimates on the discrepancy between the full many-body energy and its mean-field approximation using Hartree states. These are proved using finite dimensional localization and a quantitative version of the quantum de Finetti theorem. Our approach covers the case of attractive interactions in the regime of stability. In particular, our main new result is a derivation of the 2D attractive non-linear Schrödinger ground state."}],"issue":"9","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases","intvolume":" 368","_id":"1491","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":1,"date_published":"2016-01-01T00:00:00Z","page":"6131 - 6157","publication":"Transactions of the American Mathematical Society","citation":{"ista":"Lewin M, Nam P, Rougerie N. 2016. The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. 368(9), 6131–6157.","apa":"Lewin, M., Nam, P., & Rougerie, N. (2016). The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/6537","ieee":"M. Lewin, P. Nam, and N. Rougerie, “The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases,” Transactions of the American Mathematical Society, vol. 368, no. 9. American Mathematical Society, pp. 6131–6157, 2016.","ama":"Lewin M, Nam P, Rougerie N. The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. 2016;368(9):6131-6157. doi:10.1090/tran/6537","chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “The Mean-Field Approximation and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” Transactions of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/tran/6537.","mla":"Lewin, Mathieu, et al. “The Mean-Field Approximation and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” Transactions of the American Mathematical Society, vol. 368, no. 9, American Mathematical Society, 2016, pp. 6131–57, doi:10.1090/tran/6537.","short":"M. Lewin, P. Nam, N. Rougerie, Transactions of the American Mathematical Society 368 (2016) 6131–6157."},"publist_id":"5692","date_updated":"2021-01-12T06:51:07Z","date_created":"2018-12-11T11:52:20Z","volume":368,"author":[{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"last_name":"Nam","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Nam, Phan"},{"last_name":"Rougerie","first_name":"Nicolas","full_name":"Rougerie, Nicolas"}],"publication_status":"published","publisher":"American Mathematical Society","department":[{"_id":"RoSe"}],"acknowledgement":"The authors acknowledge financial support from the European Research Council (FP7/2007-2013 Grant Agreement MNIQS 258023) and the ANR (Mathostaq project, ANR-13-JS01-0005-01). The second and third authors have benefited from the hospitality of the Institute for Mathematical Science of the National University of Singapore.","year":"2016","month":"01","language":[{"iso":"eng"}],"doi":"10.1090/tran/6537","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1405.3220"}],"oa":1},{"scopus_import":1,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","citation":{"ista":"Franek P, Krcál M. 2016. On computability and triviality of well groups. Discrete & Computational Geometry. 56(1), 126–164.","apa":"Franek, P., & Krcál, M. (2016). On computability and triviality of well groups. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9794-2","ieee":"P. Franek and M. Krcál, “On computability and triviality of well groups,” Discrete & Computational Geometry, vol. 56, no. 1. Springer, pp. 126–164, 2016.","ama":"Franek P, Krcál M. On computability and triviality of well groups. Discrete & Computational Geometry. 2016;56(1):126-164. doi:10.1007/s00454-016-9794-2","chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.” Discrete & Computational Geometry. Springer, 2016. https://doi.org/10.1007/s00454-016-9794-2.","mla":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.” Discrete & Computational Geometry, vol. 56, no. 1, Springer, 2016, pp. 126–64, doi:10.1007/s00454-016-9794-2.","short":"P. Franek, M. Krcál, Discrete & Computational Geometry 56 (2016) 126–164."},"publication":"Discrete & Computational Geometry","page":"126 - 164","date_published":"2016-07-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map (Formula presented.) on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within (Formula presented.) distance r from f for a given (Formula presented.). The main drawback of the approach is that the computability of well groups was shown only when (Formula presented.) or (Formula presented.). Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of (Formula presented.) by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and (Formula presented.), our approximation of the (Formula presented.)th well group is exact. For the second part, we find examples of maps (Formula presented.) with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1408","intvolume":" 56","title":"On computability and triviality of well groups","status":"public","ddc":["510"],"pubrep_id":"614","oa_version":"Published Version","file":[{"checksum":"e0da023abf6b72abd8c6a8c76740d53c","date_created":"2018-12-12T10:10:55Z","date_updated":"2020-07-14T12:44:53Z","file_id":"4846","relation":"main_file","creator":"system","file_size":905303,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-614-v1+1_s00454-016-9794-2.pdf"}],"month":"07","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"M01980","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Robust invariants of Nonlinear Systems"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","doi":"10.1007/s00454-016-9794-2","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"5799","file_date_updated":"2020-07-14T12:44:53Z","year":"2016","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publisher":"Springer","publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1510"}]},"author":[{"full_name":"Franek, Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Franek"},{"full_name":"Krcál, Marek","first_name":"Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87"}],"volume":56,"date_created":"2018-12-11T11:51:51Z","date_updated":"2023-02-23T10:02:11Z"},{"month":"02","language":[{"iso":"eng"}],"doi":"10.1534/genetics.115.183814","quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"oa":1,"external_id":{"pmid":["26715666"]},"file_date_updated":"2020-07-14T12:45:00Z","publist_id":"5658","ec_funded":1,"date_updated":"2022-05-24T09:16:22Z","date_created":"2018-12-11T11:52:29Z","volume":202,"author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Martin, Simon","last_name":"Martin","first_name":"Simon"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"NiBa"}],"publisher":"Genetics Society of America","acknowledgement":"We thank Lynsey Bunnefeld for discussions throughout the project and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on an earlier version of this manuscript. This work was supported by funding from the\r\nUnited Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant from the European\r\nResearch Council (250152) (to N.H.B.).","year":"2016","pmid":1,"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2016-02-01T00:00:00Z","article_type":"original","page":"775 - 786","publication":"Genetics","citation":{"chicago":"Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.183814.","mla":"Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:10.1534/genetics.115.183814.","short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.","ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.","apa":"Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.183814","ieee":"K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 775–786, 2016.","ama":"Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 2016;202(2):775-786. doi:10.1534/genetics.115.183814"},"abstract":[{"lang":"eng","text":"The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno."}],"issue":"2","type":"journal_article","oa_version":"Preprint","file":[{"file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf","access_level":"open_access","creator":"system","file_size":957466,"content_type":"application/pdf","file_id":"5241","relation":"main_file","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:16:51Z","checksum":"41c9b5d72e7fe4624dd22dfe622337d5"}],"pubrep_id":"561","title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","ddc":["570"],"status":"public","intvolume":" 202","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1518"},{"month":"01","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.00440"}],"language":[{"iso":"eng"}],"conference":{"name":"HSB: Hybrid Systems Biology","end_date":"2015-09-05","location":"Madrid, Spain","start_date":"2015-09-04"},"doi":"10.1007/978-3-319-26916-0_10","ec_funded":1,"publist_id":"5649","publication_status":"published","publisher":"Springer","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"acknowledgement":"This research was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734, and the SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2_148797.","year":"2016","date_updated":"2021-01-12T06:51:22Z","date_created":"2018-12-11T11:52:31Z","volume":9271,"author":[{"full_name":"Beica, Andreea","first_name":"Andreea","last_name":"Beica"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"first_name":"Tatjana","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana"}],"scopus_import":1,"day":"10","page":"173 - 191","citation":{"chicago":"Beica, Andreea, Calin C Guet, and Tatjana Petrov. “Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set,” 9271:173–91. Springer, 2016. https://doi.org/10.1007/978-3-319-26916-0_10.","mla":"Beica, Andreea, et al. Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set. Vol. 9271, Springer, 2016, pp. 173–91, doi:10.1007/978-3-319-26916-0_10.","short":"A. Beica, C.C. Guet, T. Petrov, in:, Springer, 2016, pp. 173–191.","ista":"Beica A, Guet CC, Petrov T. 2016. Efficient reduction of kappa models by static inspection of the rule-set. HSB: Hybrid Systems Biology, LNCS, vol. 9271, 173–191.","apa":"Beica, A., Guet, C. C., & Petrov, T. (2016). Efficient reduction of kappa models by static inspection of the rule-set (Vol. 9271, pp. 173–191). Presented at the HSB: Hybrid Systems Biology, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-26916-0_10","ieee":"A. Beica, C. C. Guet, and T. Petrov, “Efficient reduction of kappa models by static inspection of the rule-set,” presented at the HSB: Hybrid Systems Biology, Madrid, Spain, 2016, vol. 9271, pp. 173–191.","ama":"Beica A, Guet CC, Petrov T. Efficient reduction of kappa models by static inspection of the rule-set. In: Vol 9271. Springer; 2016:173-191. doi:10.1007/978-3-319-26916-0_10"},"date_published":"2016-01-10T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"When designing genetic circuits, the typical primitives used in major existing modelling formalisms are gene interaction graphs, where edges between genes denote either an activation or inhibition relation. However, when designing experiments, it is important to be precise about the low-level mechanistic details as to how each such relation is implemented. The rule-based modelling language Kappa allows to unambiguously specify mechanistic details such as DNA binding sites, dimerisation of transcription factors, or co-operative interactions. Such a detailed description comes with complexity and computationally costly executions. We propose a general method for automatically transforming a rule-based program, by eliminating intermediate species and adjusting the rate constants accordingly. To the best of our knowledge, we show the first automated reduction of rule-based models based on equilibrium approximations.\r\nOur algorithm is an adaptation of an existing algorithm, which was designed for reducing reaction-based programs; our version of the algorithm scans the rule-based Kappa model in search for those interaction patterns known to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional checks are then performed in order to verify if the reduction is meaningful in the context of the full model. The reduced model is efficiently obtained by static inspection over the rule-set. The tool is tested on a detailed rule-based model of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has 11 rules and 5 agents, and provides a dramatic reduction in simulation time of several orders of magnitude."}],"title":"Efficient reduction of kappa models by static inspection of the rule-set","status":"public","intvolume":" 9271","_id":"1524","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"}]