[{"date_updated":"2023-09-05T11:57:23Z","department":[{"_id":"MaIb"}],"_id":"8746","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0003-6951"],"eissn":["1077-3118"]},"publication_status":"published","issue":"17","volume":117,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Research in the field of colloidal semiconductor nanocrystals (NCs) has progressed tremendously, mostly because of their exceptional optoelectronic properties. Core@shell NCs, in which one or more inorganic layers overcoat individual NCs, recently received significant attention due to their remarkable optical characteristics. Reduced Auger recombination, suppressed blinking, and enhanced carrier multiplication are among the merits of core@shell NCs. Despite their importance in device development, the influence of the shell and the surface modification of the core@shell NC assemblies on the charge carrier transport remains a pertinent research objective. Type-II PbTe@PbS core@shell NCs, in which exclusive electron transport was demonstrated, still exhibit instability of their electron \r\n ransport. Here, we demonstrate the enhancement of electron transport and stability in PbTe@PbS core@shell NC assemblies using iodide as a surface passivating ligand. The combination of the PbS shelling and the use of the iodide ligand contributes to the addition of one mobile electron for each core@shell NC. Furthermore, both electron mobility and on/off current modulation ratio values of the core@shell NC field-effect transistor are steady with the usage of iodide. Excellent stability in these exclusively electron-transporting core@shell NCs paves the way for their utilization in electronic devices. "}],"month":"10","intvolume":" 117","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1063/5.0025965","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Miranti, Retno, Ricky Dwi Septianto, Maria Ibáñez, Maksym V. Kovalenko, Nobuhiro Matsushita, Yoshihiro Iwasa, and Satria Zulkarnaen Bisri. “Electron Transport in Iodide-Capped Core@shell PbTe@PbS Colloidal Nanocrystal Solids.” Applied Physics Letters. AIP Publishing, 2020. https://doi.org/10.1063/5.0025965.","ista":"Miranti R, Septianto RD, Ibáñez M, Kovalenko MV, Matsushita N, Iwasa Y, Bisri SZ. 2020. Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. 117(17), 173101.","mla":"Miranti, Retno, et al. “Electron Transport in Iodide-Capped Core@shell PbTe@PbS Colloidal Nanocrystal Solids.” Applied Physics Letters, vol. 117, no. 17, 173101, AIP Publishing, 2020, doi:10.1063/5.0025965.","apa":"Miranti, R., Septianto, R. D., Ibáñez, M., Kovalenko, M. V., Matsushita, N., Iwasa, Y., & Bisri, S. Z. (2020). Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0025965","ama":"Miranti R, Septianto RD, Ibáñez M, et al. Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. 2020;117(17). doi:10.1063/5.0025965","short":"R. Miranti, R.D. Septianto, M. Ibáñez, M.V. Kovalenko, N. Matsushita, Y. Iwasa, S.Z. Bisri, Applied Physics Letters 117 (2020).","ieee":"R. Miranti et al., “Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids,” Applied Physics Letters, vol. 117, no. 17. AIP Publishing, 2020."},"title":"Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids","author":[{"first_name":"Retno","last_name":"Miranti","full_name":"Miranti, Retno"},{"first_name":"Ricky Dwi","last_name":"Septianto","full_name":"Septianto, Ricky Dwi"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"full_name":"Kovalenko, Maksym V.","last_name":"Kovalenko","first_name":"Maksym V."},{"first_name":"Nobuhiro","last_name":"Matsushita","full_name":"Matsushita, Nobuhiro"},{"full_name":"Iwasa, Yoshihiro","last_name":"Iwasa","first_name":"Yoshihiro"},{"first_name":"Satria Zulkarnaen","full_name":"Bisri, Satria Zulkarnaen","last_name":"Bisri"}],"article_processing_charge":"No","external_id":{"isi":["000591639700001"]},"article_number":"173101","day":"26","publication":"Applied Physics Letters","isi":1,"year":"2020","date_published":"2020-10-26T00:00:00Z","doi":"10.1063/5.0025965","date_created":"2020-11-09T08:05:43Z","acknowledgement":"This work was partly supported by Grants-in-Aid for Scientific Research by Young Scientist A (KAKENHI Wakate-A) No.\r\nJP17H04802, Grants-in-Aid for Scientific Research No. JP19H05602 from the Japan Society for the Promotion of Science, and RIKEN Incentive Research Grant (Shoreikadai) 2016. M.V.K. and M.I. acknowledge financial support from the European Union (EU) via FP7 ERC Starting Grant 2012 (Project NANOSOLID, GA No. 306733) and ETH Zurich via ETH career seed grant (No. SEED-18 16-2). We acknowledge Mrs. T. Kikitsu and Dr. D. Hashizume (RIKEN-CEMS) for access to the transmission electron microscope facility.","quality_controlled":"1","publisher":"AIP Publishing","oa":1},{"abstract":[{"text":"The goal of limiting global warming to 1.5 °C requires a drastic reduction in CO2 emissions across many sectors of the world economy. Batteries are vital to this endeavor, whether used in electric vehicles, to store renewable electricity, or in aviation. Present lithium-ion technologies are preparing the public for this inevitable change, but their maximum theoretical specific capacity presents a limitation. Their high cost is another concern for commercial viability. Metal–air batteries have the highest theoretical energy density of all possible secondary battery technologies and could yield step changes in energy storage, if their practical difficulties could be overcome. The scope of this review is to provide an objective, comprehensive, and authoritative assessment of the intensive work invested in nonaqueous rechargeable metal–air batteries over the past few years, which identified the key problems and guides directions to solve them. We focus primarily on the challenges and outlook for Li–O2 cells but include Na–O2, K–O2, and Mg–O2 cells for comparison. Our review highlights the interdisciplinary nature of this field that involves a combination of materials chemistry, electrochemistry, computation, microscopy, spectroscopy, and surface science. The mechanisms of O2 reduction and evolution are considered in the light of recent findings, along with developments in positive and negative electrodes, electrolytes, electrocatalysis on surfaces and in solution, and the degradative effect of singlet oxygen, which is typically formed in Li–O2 cells.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 120","month":"03","publication_status":"published","publication_identifier":{"eissn":["1520-6890"],"issn":["0009-2665"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8060","checksum":"1a683353d46c5841c8bb2ee0a56ac7be","date_updated":"2020-07-14T12:48:06Z","file_size":8525678,"creator":"sfreunbe","date_created":"2020-06-29T16:36:01Z","file_name":"ChemRev_final.pdf"}],"volume":120,"issue":"14","_id":"7985","article_type":"review","type":"journal_article","status":"public","date_updated":"2023-09-05T12:04:28Z","ddc":["540"],"department":[{"_id":"StFr"}],"file_date_updated":"2020-07-14T12:48:06Z","acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation programme (grant agreement No 636069).","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","year":"2020","has_accepted_license":"1","isi":1,"publication":"Chemical Reviews","day":"05","page":"6626-6683","date_created":"2020-06-19T08:42:47Z","date_published":"2020-03-05T00:00:00Z","doi":"10.1021/acs.chemrev.9b00609","citation":{"ama":"Kwak W, Sharon D, Xia C, et al. Lithium-oxygen batteries and related systems: Potential, status, and future. Chemical Reviews. 2020;120(14):6626-6683. doi:10.1021/acs.chemrev.9b00609","apa":"Kwak, W., Sharon, D., Xia, C., Kim, H., Johnson, L., Bruce, P., … Aurbach, D. (2020). Lithium-oxygen batteries and related systems: Potential, status, and future. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.9b00609","short":"W. Kwak, D. Sharon, C. Xia, H. Kim, L. Johnson, P. Bruce, L. Nazar, Y. Sun, A. Frimer, M. Noked, S.A. Freunberger, D. Aurbach, Chemical Reviews 120 (2020) 6626–6683.","ieee":"W. Kwak et al., “Lithium-oxygen batteries and related systems: Potential, status, and future,” Chemical Reviews, vol. 120, no. 14. American Chemical Society, pp. 6626–6683, 2020.","mla":"Kwak, WJ, et al. “Lithium-Oxygen Batteries and Related Systems: Potential, Status, and Future.” Chemical Reviews, vol. 120, no. 14, American Chemical Society, 2020, pp. 6626–83, doi:10.1021/acs.chemrev.9b00609.","ista":"Kwak W, Sharon D, Xia C, Kim H, Johnson L, Bruce P, Nazar L, Sun Y, Frimer A, Noked M, Freunberger SA, Aurbach D. 2020. Lithium-oxygen batteries and related systems: Potential, status, and future. Chemical Reviews. 120(14), 6626–6683.","chicago":"Kwak, WJ, D Sharon, C Xia, H Kim, LR Johnson, PG Bruce, LF Nazar, et al. “Lithium-Oxygen Batteries and Related Systems: Potential, Status, and Future.” Chemical Reviews. American Chemical Society, 2020. https://doi.org/10.1021/acs.chemrev.9b00609."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"pmid":["32134255"],"isi":["000555413600008"]},"author":[{"last_name":"Kwak","full_name":"Kwak, WJ","first_name":"WJ"},{"last_name":"Sharon","full_name":"Sharon, D","first_name":"D"},{"full_name":"Xia, C","last_name":"Xia","first_name":"C"},{"first_name":"H","last_name":"Kim","full_name":"Kim, H"},{"full_name":"Johnson, LR","last_name":"Johnson","first_name":"LR"},{"last_name":"Bruce","full_name":"Bruce, PG","first_name":"PG"},{"full_name":"Nazar, LF","last_name":"Nazar","first_name":"LF"},{"full_name":"Sun, YK","last_name":"Sun","first_name":"YK"},{"full_name":"Frimer, AA","last_name":"Frimer","first_name":"AA"},{"first_name":"M","last_name":"Noked","full_name":"Noked, M"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"last_name":"Aurbach","full_name":"Aurbach, D","first_name":"D"}],"title":"Lithium-oxygen batteries and related systems: Potential, status, and future"},{"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"_id":"2699E3D2-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development"}],"author":[{"orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub"},{"first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","full_name":"Prat, Tomas","last_name":"Prat"},{"full_name":"Rydza, N","last_name":"Rydza","first_name":"N"},{"orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328"},{"last_name":"Domjan","orcid":"0000-0003-2267-106X","full_name":"Domjan, David","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","first_name":"David"},{"last_name":"Mazur","full_name":"Mazur, E","first_name":"E"},{"full_name":"Smakowska-Luzan, E","last_name":"Smakowska-Luzan","first_name":"E"},{"first_name":"W","last_name":"Smet","full_name":"Smet, W"},{"last_name":"Mor","full_name":"Mor, E","first_name":"E"},{"first_name":"J","last_name":"Nolf","full_name":"Nolf, J"},{"first_name":"B","last_name":"Yang","full_name":"Yang, B"},{"last_name":"Grunewald","full_name":"Grunewald, W","first_name":"W"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","full_name":"Molnar, Gergely","last_name":"Molnar"},{"last_name":"Belkhadir","full_name":"Belkhadir, Y","first_name":"Y"},{"first_name":"B","last_name":"De Rybel","full_name":"De Rybel, B"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"article_processing_charge":"No","external_id":{"pmid":["33122378"],"isi":["000583031800041"]},"title":"Receptor kinase module targets PIN-dependent auxin transport during canalization","citation":{"mla":"Hajny, Jakub, et al. “Receptor Kinase Module Targets PIN-Dependent Auxin Transport during Canalization.” Science, vol. 370, no. 6516, American Association for the Advancement of Science, 2020, pp. 550–57, doi:10.1126/science.aba3178.","ieee":"J. Hajny et al., “Receptor kinase module targets PIN-dependent auxin transport during canalization,” Science, vol. 370, no. 6516. American Association for the Advancement of Science, pp. 550–557, 2020.","short":"J. Hajny, T. Prat, N. Rydza, L. Rodriguez Solovey, S. Tan, I. Verstraeten, D. Domjan, E. Mazur, E. Smakowska-Luzan, W. Smet, E. Mor, J. Nolf, B. Yang, W. Grunewald, G. Molnar, Y. Belkhadir, B. De Rybel, J. Friml, Science 370 (2020) 550–557.","ama":"Hajny J, Prat T, Rydza N, et al. Receptor kinase module targets PIN-dependent auxin transport during canalization. Science. 2020;370(6516):550-557. doi:10.1126/science.aba3178","apa":"Hajny, J., Prat, T., Rydza, N., Rodriguez Solovey, L., Tan, S., Verstraeten, I., … Friml, J. (2020). Receptor kinase module targets PIN-dependent auxin transport during canalization. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba3178","chicago":"Hajny, Jakub, Tomas Prat, N Rydza, Lesia Rodriguez Solovey, Shutang Tan, Inge Verstraeten, David Domjan, et al. “Receptor Kinase Module Targets PIN-Dependent Auxin Transport during Canalization.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba3178.","ista":"Hajny J, Prat T, Rydza N, Rodriguez Solovey L, Tan S, Verstraeten I, Domjan D, Mazur E, Smakowska-Luzan E, Smet W, Mor E, Nolf J, Yang B, Grunewald W, Molnar G, Belkhadir Y, De Rybel B, Friml J. 2020. Receptor kinase module targets PIN-dependent auxin transport during canalization. Science. 370(6516), 550–557."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"acknowledgement":"We acknowledge M. Glanc and Y. Zhang for providing entryclones; Vienna Biocenter Core Facilities (VBCF) for recombinantprotein production and purification; Vienna Biocenter Massspectrometry Facility, Bioimaging, and Life Science Facilities at IST Austria and Proteomics Core Facility CEITEC for a great assistance.Funding:This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 742985) and Austrian Science Fund (FWF): I 3630-B25 to J.F.and by grants from the Austrian Academy of Science through the Gregor Mendel Institute (Y.B.) and the Austrian Agency for International Cooperation in Education and Research (D.D.); the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001) (W.S.); the Research Foundation–Flanders (FWO;Odysseus II G0D0515N) and a European Research Council grant (ERC; StG TORPEDO; 714055) to B.D.R., B.Y., and E.M.; and the Hertha Firnberg Programme postdoctoral fellowship (T-947) from the FWF Austrian Science Fund to E.S.-L.; J.H. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at IST Austria.","page":"550-557","doi":"10.1126/science.aba3178","date_published":"2020-10-30T00:00:00Z","date_created":"2020-11-02T10:04:46Z","isi":1,"year":"2020","day":"30","publication":"Science","article_type":"original","type":"journal_article","status":"public","_id":"8721","department":[{"_id":"JiFr"}],"date_updated":"2023-09-05T12:02:35Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://europepmc.org/article/MED/33122378#free-full-text"}],"month":"10","intvolume":" 370","abstract":[{"text":"Spontaneously arising channels that transport the phytohormone auxin provide positional cues for self-organizing aspects of plant development such as flexible vasculature regeneration or its patterning during leaf venation. The auxin canalization hypothesis proposes a feedback between auxin signaling and transport as the underlying mechanism, but molecular players await discovery. We identified part of the machinery that routes auxin transport. The auxin-regulated receptor CAMEL (Canalization-related Auxin-regulated Malectin-type RLK) together with CANAR (Canalization-related Receptor-like kinase) interact with and phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated PIN polarization, which macroscopically manifests as defects in leaf venation and vasculature regeneration after wounding. The CAMEL-CANAR receptor complex is part of the auxin feedback that coordinates polarization of individual cells during auxin canalization.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"pmid":1,"oa_version":"Published Version","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/molecular-compass-for-cell-orientation/","description":"News on IST Homepage"}]},"issue":"6516","volume":370,"ec_funded":1,"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"publication_status":"published","language":[{"iso":"eng"}]},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000614616200006"]},"author":[{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"full_name":"Paltiel, Yossi","last_name":"Paltiel","first_name":"Yossi"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"title":"Analytic model of chiral-induced spin selectivity","citation":{"mla":"Ghazaryan, Areg, et al. “Analytic Model of Chiral-Induced Spin Selectivity.” The Journal of Physical Chemistry C, vol. 124, no. 21, American Chemical Society, 2020, pp. 11716–21, doi:10.1021/acs.jpcc.0c02584.","ieee":"A. Ghazaryan, Y. Paltiel, and M. Lemeshko, “Analytic model of chiral-induced spin selectivity,” The Journal of Physical Chemistry C, vol. 124, no. 21. American Chemical Society, pp. 11716–11721, 2020.","short":"A. Ghazaryan, Y. Paltiel, M. Lemeshko, The Journal of Physical Chemistry C 124 (2020) 11716–11721.","ama":"Ghazaryan A, Paltiel Y, Lemeshko M. Analytic model of chiral-induced spin selectivity. The Journal of Physical Chemistry C. 2020;124(21):11716-11721. doi:10.1021/acs.jpcc.0c02584","apa":"Ghazaryan, A., Paltiel, Y., & Lemeshko, M. (2020). Analytic model of chiral-induced spin selectivity. The Journal of Physical Chemistry C. American Chemical Society. https://doi.org/10.1021/acs.jpcc.0c02584","chicago":"Ghazaryan, Areg, Yossi Paltiel, and Mikhail Lemeshko. “Analytic Model of Chiral-Induced Spin Selectivity.” The Journal of Physical Chemistry C. American Chemical Society, 2020. https://doi.org/10.1021/acs.jpcc.0c02584.","ista":"Ghazaryan A, Paltiel Y, Lemeshko M. 2020. Analytic model of chiral-induced spin selectivity. The Journal of Physical Chemistry C. 124(21), 11716–11721."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","page":"11716-11721","date_created":"2020-06-16T14:29:59Z","doi":"10.1021/acs.jpcc.0c02584","date_published":"2020-05-04T00:00:00Z","year":"2020","has_accepted_license":"1","isi":1,"publication":"The Journal of Physical Chemistry C","day":"04","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"7968","department":[{"_id":"MiLe"}],"file_date_updated":"2020-10-20T14:39:47Z","date_updated":"2023-09-05T12:07:15Z","ddc":["530"],"scopus_import":"1","intvolume":" 124","month":"05","abstract":[{"lang":"eng","text":"Organic materials are known to feature long spin-diffusion times, originating in a generally small spin–orbit coupling observed in these systems. From that perspective, chiral molecules acting as efficient spin selectors pose a puzzle that attracted a lot of attention in recent years. Here, we revisit the physical origins of chiral-induced spin selectivity (CISS) and propose a simple analytic minimal model to describe it. The model treats a chiral molecule as an anisotropic wire with molecular dipole moments aligned arbitrarily with respect to the wire’s axes and is therefore quite general. Importantly, it shows that the helical structure of the molecule is not necessary to observe CISS and other chiral nonhelical molecules can also be considered as potential candidates for the CISS effect. We also show that the suggested simple model captures the main characteristics of CISS observed in the experiment, without the need for additional constraints employed in the previous studies. The results pave the way for understanding other related physical phenomena where the CISS effect plays an essential role."}],"oa_version":"Published Version","ec_funded":1,"issue":"21","volume":124,"publication_status":"published","publication_identifier":{"eissn":["1932-7455"],"issn":["1932-7447"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"25932bb1d0b0a955be0bea4d17facd49","file_id":"8683","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_PhysChemC_Ghazaryan.pdf","date_created":"2020-10-20T14:39:47Z","creator":"kschuh","file_size":1543429,"date_updated":"2020-10-20T14:39:47Z"}]},{"_id":"10866","status":"public","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"article_type":"original","type":"journal_article","date_updated":"2023-09-05T12:05:58Z","department":[{"_id":"NanoFab"}],"pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Recent discoveries have shown that, when two layers of van der Waals (vdW) materials are superimposed with a relative twist angle between them, the electronic properties of the coupled system can be dramatically altered. Here, we demonstrate that a similar concept can be extended to the optics realm, particularly to propagating phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic phonon polaritons (PhPs), and image the propagation of the latter when launched by localized sources. Our images reveal that, under a critical angle, the PhPs isofrequency curve undergoes a topological transition, in which the propagation of PhPs is strongly guided (canalization regime) along predetermined directions without geometric spreading. These results demonstrate a new degree of freedom (twist angle) for controlling the propagation of polaritons at the nanoscale with potential for nanoimaging, (bio)-sensing, or heat management."}],"month":"07","intvolume":" 20","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.14599"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"publication_status":"published","issue":"7","volume":20,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Duan, Jiahua, Nathaniel Capote-Robayna, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Ivan Prieto Gonzalez, Javier Martín-Sánchez, Alexey Y. Nikitin, and Pablo Alonso-González. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c01673.","ista":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, Álvarez-Pérez G, Prieto Gonzalez I, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2020. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 20(7), 5323–5329.","mla":"Duan, Jiahua, et al. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” Nano Letters, vol. 20, no. 7, American Chemical Society, 2020, pp. 5323–29, doi:10.1021/acs.nanolett.0c01673.","ieee":"J. Duan et al., “Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs,” Nano Letters, vol. 20, no. 7. American Chemical Society, pp. 5323–5329, 2020.","short":"J. Duan, N. Capote-Robayna, J. Taboada-Gutiérrez, G. Álvarez-Pérez, I. Prieto Gonzalez, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Nano Letters 20 (2020) 5323–5329.","ama":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, et al. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 2020;20(7):5323-5329. doi:10.1021/acs.nanolett.0c01673","apa":"Duan, J., Capote-Robayna, N., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Prieto Gonzalez, I., Martín-Sánchez, J., … Alonso-González, P. (2020). Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01673"},"title":"Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs","author":[{"last_name":"Duan","full_name":"Duan, Jiahua","first_name":"Jiahua"},{"last_name":"Capote-Robayna","full_name":"Capote-Robayna, Nathaniel","first_name":"Nathaniel"},{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo"},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan"},{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"last_name":"Nikitin","full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y."},{"full_name":"Alonso-González, Pablo","last_name":"Alonso-González","first_name":"Pablo"}],"article_processing_charge":"No","external_id":{"arxiv":["2004.14599"],"pmid":["32530634"],"isi":["000548893200082"]},"acknowledgement":"J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the\r\nGovernment of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA20-PF-BP19-053,\r\nrespectively). J. M-S acknowledges financial support through the Ramón y Cajal Program from\r\nthe Government of Spain (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of\r\nScience, Innovation and Universities (national project no. MAT201788358-C3-3-R). P.A.-G.\r\nacknowledges support from the European Research Council under starting grant no. 715496,\r\n2DNANOPTICA.","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"day":"01","publication":"Nano Letters","isi":1,"year":"2020","doi":"10.1021/acs.nanolett.0c01673","date_published":"2020-07-01T00:00:00Z","date_created":"2022-03-18T11:37:38Z","page":"5323-5329"},{"date_created":"2020-09-30T10:33:43Z","date_published":"2020-07-21T00:00:00Z","doi":"10.1103/physrevb.102.045307","publication":"Physical Review B","day":"21","year":"2020","isi":1,"oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"We thank W. Kaganer for discussions and for comment on the manuscript. We acknowledge the financial support from the German-Israeli Foundation (GIF), grant agreement I-1277-303.10/2014. M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A.G. acknowledges support by the European Unions Horizon 2020 research and innovation\r\nprogram under the Marie Skodowska-Curie grant agreement No 754411. P.V.S acknowledges financial support\r\nfrom the Deutsche Forschungsgemeinschaft (DFG) under\r\nProject No. SA 598/12-1.","title":"Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids","external_id":{"isi":["000550579100004"],"arxiv":["1910.06015"]},"article_processing_charge":"No","author":[{"first_name":"C.","full_name":"Hubert, C.","last_name":"Hubert"},{"first_name":"K.","last_name":"Cohen","full_name":"Cohen, K."},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"first_name":"R.","last_name":"Rapaport","full_name":"Rapaport, R."},{"full_name":"Santos, P. V.","last_name":"Santos","first_name":"P. V."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Hubert, C., K. Cohen, Areg Ghazaryan, Mikhail Lemeshko, R. Rapaport, and P. V. Santos. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled Dipolar Exciton Fluids.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.102.045307.","ista":"Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. 2020. Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. 102(4), 045307.","mla":"Hubert, C., et al. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled Dipolar Exciton Fluids.” Physical Review B, vol. 102, no. 4, 045307, American Physical Society, 2020, doi:10.1103/physrevb.102.045307.","ama":"Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. 2020;102(4). doi:10.1103/physrevb.102.045307","apa":"Hubert, C., Cohen, K., Ghazaryan, A., Lemeshko, M., Rapaport, R., & Santos, P. V. (2020). Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.102.045307","ieee":"C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, and P. V. Santos, “Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids,” Physical Review B, vol. 102, no. 4. American Physical Society, 2020.","short":"C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, P.V. Santos, Physical Review B 102 (2020)."},"project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"045307","ec_funded":1,"volume":102,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"intvolume":" 102","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1910.06015","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Dipolar (or spatially indirect) excitons (IXs) in semiconductor double quantum well (DQW) subjected to an electric field are neutral species with a dipole moment oriented perpendicular to the DQW plane. Here, we theoretically study interactions between IXs in stacked DQW bilayers, where the dipolar coupling can be either attractive or repulsive depending on the relative positions of the particles. By using microscopic band structure calculations to determine the electronic states forming the excitons, we show that the attractive dipolar interaction between stacked IXs deforms their electronic wave function, thereby increasing the inter-DQW interaction energy and making the IX even more electrically polarizable. Many-particle interaction effects are addressed by considering the coupling between a single IX in one of the DQWs to a cloud of IXs in the other DQW, which is modeled either as a closed-packed lattice or as a continuum IX fluid. We find that the lattice model yields IX interlayer binding energies decreasing with increasing lattice density. This behavior is due to the dominating role of the intra-DQW dipolar repulsion, which prevents more than one exciton from entering the attractive region of the inter-DQW coupling. Finally, both models shows that the single IX distorts the distribution of IXs in the adjacent DQW, thus inducing the formation of an IX dipolar polaron (dipolaron). While the interlayer binding energy reduces with IX density for lattice dipolarons, the continuous polaron model predicts a nonmonotonous dependence on density in semiquantitative agreement with a recent experimental study [cf. Hubert et al., Phys. Rev. X 9, 021026 (2019)]."}],"department":[{"_id":"MiLe"}],"date_updated":"2023-09-05T12:12:10Z","status":"public","article_type":"original","type":"journal_article","_id":"8588"},{"publication":"Physical Review B","day":"01","year":"2020","isi":1,"date_created":"2020-11-18T07:34:17Z","date_published":"2020-10-01T00:00:00Z","doi":"10.1103/physrevb.102.144109","acknowledgement":"We are grateful to M. Correggi, A. Deuchert, and P. Schmelcher for valuable discussions. We also thank the anonymous referees for helping to clarify a few important points in the experimental realization. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement\r\nNo 754411. D.L. acknowledges financial support from the Goran Gustafsson Foundation (grant no. 1804) and LMU Munich. R.S., M.L., and N.R. gratefully acknowledge financial support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 694227, No 801770, and No 758620, respectively).","oa":1,"publisher":"American Physical Society","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Yakaboylu, Enderalp, Areg Ghazaryan, D. Lundholm, N. Rougerie, Mikhail Lemeshko, and Robert Seiringer. “Quantum Impurity Model for Anyons.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.102.144109.","ista":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. 2020. Quantum impurity model for anyons. Physical Review B. 102(14), 144109.","mla":"Yakaboylu, Enderalp, et al. “Quantum Impurity Model for Anyons.” Physical Review B, vol. 102, no. 14, 144109, American Physical Society, 2020, doi:10.1103/physrevb.102.144109.","short":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, R. Seiringer, Physical Review B 102 (2020).","ieee":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, and R. Seiringer, “Quantum impurity model for anyons,” Physical Review B, vol. 102, no. 14. American Physical Society, 2020.","apa":"Yakaboylu, E., Ghazaryan, A., Lundholm, D., Rougerie, N., Lemeshko, M., & Seiringer, R. (2020). Quantum impurity model for anyons. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.102.144109","ama":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. Quantum impurity model for anyons. Physical Review B. 2020;102(14). doi:10.1103/physrevb.102.144109"},"title":"Quantum impurity model for anyons","article_processing_charge":"No","external_id":{"isi":["000582563300001"],"arxiv":["1912.07890"]},"author":[{"first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"full_name":"Lundholm, D.","last_name":"Lundholm","first_name":"D."},{"first_name":"N.","full_name":"Rougerie, N.","last_name":"Rougerie"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"article_number":"144109","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"ec_funded":1,"volume":102,"issue":"14","oa_version":"Preprint","abstract":[{"text":"One of the hallmarks of quantum statistics, tightly entwined with the concept of topological phases of matter, is the prediction of anyons. Although anyons are predicted to be realized in certain fractional quantum Hall systems, they have not yet been unambiguously detected in experiment. Here we introduce a simple quantum impurity model, where bosonic or fermionic impurities turn into anyons as a consequence of their interaction with the surrounding many-particle bath. A cloud of phonons dresses each impurity in such a way that it effectively attaches fluxes or vortices to it and thereby converts it into an Abelian anyon. The corresponding quantum impurity model, first, provides a different approach to the numerical solution of the many-anyon problem, along with a concrete perspective of anyons as emergent quasiparticles built from composite bosons or fermions. More importantly, the model paves the way toward realizing anyons using impurities in crystal lattices as well as ultracold gases. In particular, we consider two heavy electrons interacting with a two-dimensional lattice crystal in a magnetic field, and show that when the impurity-bath system is rotated at the cyclotron frequency, impurities behave as anyons as a consequence of the angular momentum exchange between the impurities and the bath. A possible experimental realization is proposed by identifying the statistics parameter in terms of the mean-square distance of the impurities and the magnetization of the impurity-bath system, both of which are accessible to experiment. Another proposed application is impurities immersed in a two-dimensional weakly interacting Bose gas.","lang":"eng"}],"intvolume":" 102","month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.07890"}],"scopus_import":"1","date_updated":"2023-09-05T12:12:30Z","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"_id":"8769","status":"public","type":"journal_article","article_type":"original"},{"date_updated":"2023-09-05T12:11:37Z","department":[{"_id":"MaSe"}],"_id":"7971","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publication_status":"published","issue":"24","volume":101,"oa_version":"Preprint","abstract":[{"text":"Multilayer graphene lattices allow for an additional tunability of the band structure by the strong perpendicular electric field. In particular, the emergence of the new multiple Dirac points in ABA stacked trilayer graphene subject to strong transverse electric fields was proposed theoretically and confirmed experimentally. These new Dirac points dubbed “gullies” emerge from the interplay between strong electric field and trigonal warping. In this work, we first characterize the properties of new emergent Dirac points and show that the electric field can be used to tune the distance between gullies in the momentum space. We demonstrate that the band structure has multiple Lifshitz transitions and higher-order singularity of “monkey saddle” type. Following the characterization of the band structure, we consider the spectrum of Landau levels and structure of their wave functions. In the limit of strong electric fields when gullies are well separated in momentum space, they give rise to triply degenerate Landau levels. In the second part of this work, we investigate how degeneracy between three gully Landau levels is lifted in the presence of interactions. Within the Hartree-Fock approximation we show that the symmetry breaking state interpolates between the fully gully polarized state that breaks C3 symmetry at high displacement field and the gully symmetric state when the electric field is decreased. The discontinuous transition between these two states is driven by enhanced intergully tunneling and exchange. We conclude by outlining specific experimental predictions for the existence of such a symmetry-breaking state.","lang":"eng"}],"month":"06","intvolume":" 101","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.05739"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Rao, Peng, and Maksym Serbyn. “Gully Quantum Hall Ferromagnetism in Biased Trilayer Graphene.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.101.245411.","ista":"Rao P, Serbyn M. 2020. Gully quantum Hall ferromagnetism in biased trilayer graphene. Physical Review B. 101(24), 245411.","mla":"Rao, Peng, and Maksym Serbyn. “Gully Quantum Hall Ferromagnetism in Biased Trilayer Graphene.” Physical Review B, vol. 101, no. 24, 245411, American Physical Society, 2020, doi:10.1103/physrevb.101.245411.","ieee":"P. Rao and M. Serbyn, “Gully quantum Hall ferromagnetism in biased trilayer graphene,” Physical Review B, vol. 101, no. 24. American Physical Society, 2020.","short":"P. Rao, M. Serbyn, Physical Review B 101 (2020).","apa":"Rao, P., & Serbyn, M. (2020). Gully quantum Hall ferromagnetism in biased trilayer graphene. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.101.245411","ama":"Rao P, Serbyn M. Gully quantum Hall ferromagnetism in biased trilayer graphene. Physical Review B. 2020;101(24). doi:10.1103/physrevb.101.245411"},"title":"Gully quantum Hall ferromagnetism in biased trilayer graphene","author":[{"first_name":"Peng","id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB","full_name":"Rao, Peng","orcid":"0000-0003-1250-0021","last_name":"Rao"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000538715500010"]},"article_number":"245411","day":"15","publication":"Physical Review B","isi":1,"year":"2020","date_published":"2020-06-15T00:00:00Z","doi":"10.1103/physrevb.101.245411","date_created":"2020-06-17T14:52:06Z","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"year":"2020","isi":1,"publication":"Physical Review Letters","day":"05","date_created":"2020-10-08T17:27:32Z","date_published":"2020-08-05T00:00:00Z","doi":"10.1103/physrevlett.125.064501","acknowledgement":"M. F. S. and R. O. G. acknowledge funding from the National Science Foundation (CMMI-1234436, DMS1125302, CMMI-1725587) and Defense Advanced Research Projects Agency (HR0011-16-2-0033). B. S.has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007–2013/ under REA Grant Agreement No. 291734.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","citation":{"chicago":"Suri, Balachandra, Logan Kageorge, Roman O. Grigoriev, and Michael F. Schatz. “Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.064501.","ista":"Suri B, Kageorge L, Grigoriev RO, Schatz MF. 2020. Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. 125(6), 064501.","mla":"Suri, Balachandra, et al. “Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits.” Physical Review Letters, vol. 125, no. 6, 064501, American Physical Society, 2020, doi:10.1103/physrevlett.125.064501.","short":"B. Suri, L. Kageorge, R.O. Grigoriev, M.F. Schatz, Physical Review Letters 125 (2020).","ieee":"B. Suri, L. Kageorge, R. O. Grigoriev, and M. F. Schatz, “Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits,” Physical Review Letters, vol. 125, no. 6. American Physical Society, 2020.","apa":"Suri, B., Kageorge, L., Grigoriev, R. O., & Schatz, M. F. (2020). Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.064501","ama":"Suri B, Kageorge L, Grigoriev RO, Schatz MF. Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. 2020;125(6). doi:10.1103/physrevlett.125.064501"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["2008.02367"],"isi":["000555785600005"]},"article_processing_charge":"No","author":[{"full_name":"Suri, Balachandra","last_name":"Suri","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra"},{"full_name":"Kageorge, Logan","last_name":"Kageorge","first_name":"Logan"},{"full_name":"Grigoriev, Roman O.","last_name":"Grigoriev","first_name":"Roman O."},{"last_name":"Schatz","full_name":"Schatz, Michael F.","first_name":"Michael F."}],"title":"Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits","article_number":"064501","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"6","volume":125,"abstract":[{"text":"In laboratory studies and numerical simulations, we observe clear signatures of unstable time-periodic solutions in a moderately turbulent quasi-two-dimensional flow. We validate the dynamical relevance of such solutions by demonstrating that turbulent flows in both experiment and numerics transiently display time-periodic dynamics when they shadow unstable periodic orbits (UPOs). We show that UPOs we computed are also statistically significant, with turbulent flows spending a sizable fraction of the total time near these solutions. As a result, the average rates of energy input and dissipation for the turbulent flow and frequently visited UPOs differ only by a few percent.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2008.02367","open_access":"1"}],"intvolume":" 125","month":"08","date_updated":"2023-09-05T12:08:29Z","department":[{"_id":"BjHo"}],"_id":"8634","type":"journal_article","article_type":"original","keyword":["General Physics and Astronomy"],"status":"public"},{"date_created":"2020-06-08T10:10:53Z","date_published":"2020-08-01T00:00:00Z","doi":"10.1074/mcp.ra119.001826","page":"1248-1262","publication":"Molecular & Cellular Proteomics","day":"01","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"American Society for Biochemistry and Molecular Biology","acknowledgement":"We thank Maria Njo, Sarah De Cokere, Marieke Mispelaere and Darren Wells, for practical assistance, Daniël Van Damme for assistance with image analysis, Marnik Vuylsteke for advice on statistics, Catherine Perrot-Rechenmann for useful discussions, Steffen Lau for critical reading oft he manuscript, and Philip Benfey, Gerd Jürgens, Philippe Nacry, Frederik Börnke, and Frans Tax for sharing materials.","title":"The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis","article_processing_charge":"No","external_id":{"pmid":["32404488"],"isi":["000561114000001"]},"author":[{"first_name":"S","last_name":"Smith","full_name":"Smith, S"},{"full_name":"Zhu, S","last_name":"Zhu","first_name":"S"},{"first_name":"L","full_name":"Joos, L","last_name":"Joos"},{"last_name":"Roberts","full_name":"Roberts, I","first_name":"I"},{"first_name":"N","full_name":"Nikonorova, N","last_name":"Nikonorova"},{"full_name":"Vu, LD","last_name":"Vu","first_name":"LD"},{"first_name":"E","full_name":"Stes, E","last_name":"Stes"},{"first_name":"H","full_name":"Cho, H","last_name":"Cho"},{"full_name":"Larrieu, A","last_name":"Larrieu","first_name":"A"},{"last_name":"Xuan","full_name":"Xuan, W","first_name":"W"},{"first_name":"B","last_name":"Goodall","full_name":"Goodall, B"},{"full_name":"van de Cotte, B","last_name":"van de Cotte","first_name":"B"},{"full_name":"Waite, JM","last_name":"Waite","first_name":"JM"},{"first_name":"A","full_name":"Rigal, A","last_name":"Rigal"},{"first_name":"SR","full_name":"R Harborough, SR","last_name":"R Harborough"},{"first_name":"G","full_name":"Persiau, G","last_name":"Persiau"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"first_name":"GK","full_name":"Kirschner, GK","last_name":"Kirschner"},{"first_name":"E","full_name":"Vandermarliere, E","last_name":"Vandermarliere"},{"last_name":"Martens","full_name":"Martens, L","first_name":"L"},{"first_name":"Y","last_name":"Stahl","full_name":"Stahl, Y"},{"first_name":"D","last_name":"Audenaert","full_name":"Audenaert, D"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Felix, G","last_name":"Felix","first_name":"G"},{"first_name":"R","full_name":"Simon, R","last_name":"Simon"},{"last_name":"Bennett","full_name":"Bennett, M","first_name":"M"},{"first_name":"A","full_name":"Bishopp, A","last_name":"Bishopp"},{"full_name":"De Jaeger, G","last_name":"De Jaeger","first_name":"G"},{"full_name":"Ljung, K","last_name":"Ljung","first_name":"K"},{"first_name":"S","last_name":"Kepinski","full_name":"Kepinski, S"},{"first_name":"S","full_name":"Robert, S","last_name":"Robert"},{"last_name":"Nemhauser","full_name":"Nemhauser, J","first_name":"J"},{"full_name":"Hwang, I","last_name":"Hwang","first_name":"I"},{"last_name":"Gevaert","full_name":"Gevaert, K","first_name":"K"},{"first_name":"T","full_name":"Beeckman, T","last_name":"Beeckman"},{"last_name":"De Smet","full_name":"De Smet, I","first_name":"I"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Smith S, Zhu S, Joos L, Roberts I, Nikonorova N, Vu L, Stes E, Cho H, Larrieu A, Xuan W, Goodall B, van de Cotte B, Waite J, Rigal A, R Harborough S, Persiau G, Vanneste S, Kirschner G, Vandermarliere E, Martens L, Stahl Y, Audenaert D, Friml J, Felix G, Simon R, Bennett M, Bishopp A, De Jaeger G, Ljung K, Kepinski S, Robert S, Nemhauser J, Hwang I, Gevaert K, Beeckman T, De Smet I. 2020. The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Molecular & Cellular Proteomics. 19(8), 1248–1262.","chicago":"Smith, S, S Zhu, L Joos, I Roberts, N Nikonorova, LD Vu, E Stes, et al. “The CEP5 Peptide Promotes Abiotic Stress Tolerance, as Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis.” Molecular & Cellular Proteomics. American Society for Biochemistry and Molecular Biology, 2020. https://doi.org/10.1074/mcp.ra119.001826.","short":"S. Smith, S. Zhu, L. Joos, I. Roberts, N. Nikonorova, L. Vu, E. Stes, H. Cho, A. Larrieu, W. Xuan, B. Goodall, B. van de Cotte, J. Waite, A. Rigal, S. R Harborough, G. Persiau, S. Vanneste, G. Kirschner, E. Vandermarliere, L. Martens, Y. Stahl, D. Audenaert, J. Friml, G. Felix, R. Simon, M. Bennett, A. Bishopp, G. De Jaeger, K. Ljung, S. Kepinski, S. Robert, J. Nemhauser, I. Hwang, K. Gevaert, T. Beeckman, I. De Smet, Molecular & Cellular Proteomics 19 (2020) 1248–1262.","ieee":"S. Smith et al., “The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis,” Molecular & Cellular Proteomics, vol. 19, no. 8. American Society for Biochemistry and Molecular Biology, pp. 1248–1262, 2020.","apa":"Smith, S., Zhu, S., Joos, L., Roberts, I., Nikonorova, N., Vu, L., … De Smet, I. (2020). The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Molecular & Cellular Proteomics. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/mcp.ra119.001826","ama":"Smith S, Zhu S, Joos L, et al. The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Molecular & Cellular Proteomics. 2020;19(8):1248-1262. doi:10.1074/mcp.ra119.001826","mla":"Smith, S., et al. “The CEP5 Peptide Promotes Abiotic Stress Tolerance, as Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis.” Molecular & Cellular Proteomics, vol. 19, no. 8, American Society for Biochemistry and Molecular Biology, 2020, pp. 1248–62, doi:10.1074/mcp.ra119.001826."},"issue":"8","volume":19,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9373","checksum":"3f3f37b4a1ba2cfd270fc7733dd89680","success":1,"creator":"kschuh","date_updated":"2021-05-05T10:10:14Z","file_size":1632311,"date_created":"2021-05-05T10:10:14Z","file_name":"2020_MCP_Smith.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1535-9484"]},"intvolume":" 19","month":"08","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Peptides derived from non-functional precursors play important roles in various developmental processes, but also in (a)biotic stress signaling. Our (phospho)proteome-wide analyses of C-terminally encoded peptide 5 (CEP5)-mediated changes revealed an impact on abiotic stress-related processes. Drought has a dramatic impact on plant growth, development and reproduction, and the plant hormone auxin plays a role in drought responses. Our genetic, physiological, biochemical and pharmacological results demonstrated that CEP5-mediated signaling is relevant for osmotic and drought stress tolerance in Arabidopsis, and that CEP5 specifically counteracts auxin effects. Specifically, we found that CEP5 signaling stabilizes AUX/IAA transcriptional repressors, suggesting the existence of a novel peptide-dependent control mechanism that tunes auxin signaling. These observations align with the recently described role of AUX/IAAs in stress tolerance and provide a novel role for CEP5 in osmotic and drought stress tolerance.","lang":"eng"}],"department":[{"_id":"JiFr"}],"file_date_updated":"2021-05-05T10:10:14Z","ddc":["580"],"date_updated":"2023-09-05T12:17:46Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"7949"},{"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"title":"Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters","article_processing_charge":"No","external_id":{"isi":["000545741500030"],"pmid":["32193204"]},"author":[{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","last_name":"Zhang","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627"},{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski"},{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","full_name":"Marhavá, Petra","last_name":"Marhavá"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","last_name":"Zhang","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237"},{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"full_name":"Pukyšová, Vendula","last_name":"Pukyšová","first_name":"Vendula"},{"first_name":"Adrià Sans","full_name":"Sánchez, Adrià Sans","last_name":"Sánchez"},{"full_name":"Raxwal, Vivek Kumar","last_name":"Raxwal","first_name":"Vivek Kumar"},{"full_name":"Hardtke, Christian S.","last_name":"Hardtke","first_name":"Christian S."},{"first_name":"Tomasz","full_name":"Nodzynski, Tomasz","last_name":"Nodzynski"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Zhang X, Adamowski M, Marhavá P, et al. Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. 2020;32(5):1644-1664. doi:10.1105/tpc.19.00869","apa":"Zhang, X., Adamowski, M., Marhavá, P., Tan, S., Zhang, Y., Rodriguez Solovey, L., … Friml, J. (2020). Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.19.00869","ieee":"X. Zhang et al., “Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters,” The Plant Cell, vol. 32, no. 5. American Society of Plant Biologists, pp. 1644–1664, 2020.","short":"X. Zhang, M. Adamowski, P. Marhavá, S. Tan, Y. Zhang, L. Rodriguez Solovey, M. Zwiewka, V. Pukyšová, A.S. Sánchez, V.K. Raxwal, C.S. Hardtke, T. Nodzynski, J. Friml, The Plant Cell 32 (2020) 1644–1664.","mla":"Zhang, Xixi, et al. “Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters.” The Plant Cell, vol. 32, no. 5, American Society of Plant Biologists, 2020, pp. 1644–64, doi:10.1105/tpc.19.00869.","ista":"Zhang X, Adamowski M, Marhavá P, Tan S, Zhang Y, Rodriguez Solovey L, Zwiewka M, Pukyšová V, Sánchez AS, Raxwal VK, Hardtke CS, Nodzynski T, Friml J. 2020. Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. 32(5), 1644–1664.","chicago":"Zhang, Xixi, Maciek Adamowski, Petra Marhavá, Shutang Tan, Yuzhou Zhang, Lesia Rodriguez Solovey, Marta Zwiewka, et al. “Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters.” The Plant Cell. American Society of Plant Biologists, 2020. https://doi.org/10.1105/tpc.19.00869."},"oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","date_created":"2020-03-28T07:39:22Z","doi":"10.1105/tpc.19.00869","date_published":"2020-05-01T00:00:00Z","page":"1644-1664","publication":"The Plant Cell","day":"01","year":"2020","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"7619","department":[{"_id":"JiFr"}],"date_updated":"2023-09-05T12:21:06Z","intvolume":" 32","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.19.00869"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Cell polarity is a fundamental feature of all multicellular organisms. In plants, prominent cell polarity markers are PIN auxin transporters crucial for plant development. To identify novel components involved in cell polarity establishment and maintenance, we carried out a forward genetic screening with PIN2:PIN1-HA;pin2 Arabidopsis plants, which ectopically express predominantly basally localized PIN1 in the root epidermal cells leading to agravitropic root growth. From the screen, we identified the regulator of PIN polarity 12 (repp12) mutation, which restored gravitropic root growth and caused PIN1-HA polarity switch from basal to apical side of root epidermal cells. Complementation experiments established the repp12 causative mutation as an amino acid substitution in Aminophospholipid ATPase3 (ALA3), a phospholipid flippase with predicted function in vesicle formation. ala3 T-DNA mutants show defects in many auxin-regulated processes, in asymmetric auxin distribution and in PIN trafficking. Analysis of quintuple and sextuple mutants confirmed a crucial role of ALA proteins in regulating plant development and in PIN trafficking and polarity. Genetic and physical interaction studies revealed that ALA3 functions together with GNOM and BIG3 ARF GEFs. Taken together, our results identified ALA3 flippase as an important interactor and regulator of ARF GEF functioning in PIN polarity, trafficking and auxin-mediated development."}],"acknowledged_ssus":[{"_id":"Bio"}],"ec_funded":1,"volume":32,"issue":"5","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]}},{"oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","date_created":"2020-10-05T12:45:16Z","doi":"10.1105/tpc.20.00384","date_published":"2020-11-01T00:00:00Z","page":"3598-3612","publication":"Plant Cell","day":"01","year":"2020","isi":1,"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"title":"Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif","external_id":{"pmid":["32958564"],"isi":["000600226800021"]},"article_processing_charge":"No","author":[{"first_name":"D","last_name":"Liu","full_name":"Liu, D"},{"full_name":"Kumar, R","last_name":"Kumar","first_name":"R"},{"last_name":"LAN","full_name":"LAN, Claus","first_name":"Claus"},{"last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"W","full_name":"Siao, W","last_name":"Siao"},{"first_name":"I","full_name":"Vanhoutte, I","last_name":"Vanhoutte"},{"last_name":"Wang","full_name":"Wang, P","first_name":"P"},{"first_name":"KW","last_name":"Bender","full_name":"Bender, KW"},{"full_name":"Yperman, K","last_name":"Yperman","first_name":"K"},{"first_name":"S","full_name":"Martins, S","last_name":"Martins"},{"last_name":"Zhao","full_name":"Zhao, X","first_name":"X"},{"first_name":"G","last_name":"Vert","full_name":"Vert, G"},{"first_name":"D","full_name":"Van Damme, D","last_name":"Van Damme"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Russinova, E","last_name":"Russinova","first_name":"E"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Liu, D., Kumar, R., LAN, C., Johnson, A. J., Siao, W., Vanhoutte, I., … Russinova, E. (2020). Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.20.00384","ama":"Liu D, Kumar R, LAN C, et al. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. 2020;32(11):3598-3612. doi:10.1105/tpc.20.00384","ieee":"D. Liu et al., “Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif,” Plant Cell, vol. 32, no. 11. American Society of Plant Biologists, pp. 3598–3612, 2020.","short":"D. Liu, R. Kumar, C. LAN, A.J. Johnson, W. Siao, I. Vanhoutte, P. Wang, K. Bender, K. Yperman, S. Martins, X. Zhao, G. Vert, D. Van Damme, J. Friml, E. Russinova, Plant Cell 32 (2020) 3598–3612.","mla":"Liu, D., et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyrosine-Based Motif.” Plant Cell, vol. 32, no. 11, American Society of Plant Biologists, 2020, pp. 3598–612, doi:10.1105/tpc.20.00384.","ista":"Liu D, Kumar R, LAN C, Johnson AJ, Siao W, Vanhoutte I, Wang P, Bender K, Yperman K, Martins S, Zhao X, Vert G, Van Damme D, Friml J, Russinova E. 2020. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. 32(11), 3598–3612.","chicago":"Liu, D, R Kumar, Claus LAN, Alexander J Johnson, W Siao, I Vanhoutte, P Wang, et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyrosine-Based Motif.” Plant Cell. American Society of Plant Biologists, 2020. https://doi.org/10.1105/tpc.20.00384."},"intvolume":" 32","month":"11","main_file_link":[{"open_access":"1","url":"https://europepmc.org/article/MED/32958564"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles through the recognition of motifs based on tyrosine or di-leucine in their cytoplasmic tails. However, in plants, very little is known on how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis thaliana, the brassinosteroid (BR) receptor, BR INSENSITIVE1 (BRI1), undergoes endocytosis that depends on clathrin and AP-2. Here we demonstrate that BRI1 binds directly to the medium AP-2 subunit, AP2M. The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed tyrosine-based endocytic motifs. The tyrosine-to-phenylalanine substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2-dependent internalization of PM proteins via the recognition of functional tyrosine motifs also operates in plants."}],"ec_funded":1,"volume":32,"issue":"11","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"status":"public","type":"journal_article","article_type":"original","_id":"8607","department":[{"_id":"JiFr"}],"date_updated":"2023-09-05T12:21:32Z"},{"title":"High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits","article_processing_charge":"No","external_id":{"pmid":["32321842"],"isi":["000550682000018"]},"author":[{"first_name":"J","last_name":"Wang","full_name":"Wang, J"},{"first_name":"E","full_name":"Mylle, E","last_name":"Mylle"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"first_name":"N","last_name":"Besbrugge","full_name":"Besbrugge, N"},{"last_name":"De Jaeger","full_name":"De Jaeger, G","first_name":"G"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"R","full_name":"Pleskot, R","last_name":"Pleskot"},{"last_name":"van Damme","full_name":"van Damme, D","first_name":"D"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Wang, J., et al. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” Plant Physiology, vol. 183, no. 3, American Society of Plant Biologists, 2020, pp. 986–97, doi:10.1104/pp.20.00178.","short":"J. Wang, E. Mylle, A.J. Johnson, N. Besbrugge, G. De Jaeger, J. Friml, R. Pleskot, D. van Damme, Plant Physiology 183 (2020) 986–997.","ieee":"J. Wang et al., “High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits,” Plant Physiology, vol. 183, no. 3. American Society of Plant Biologists, pp. 986–997, 2020.","ama":"Wang J, Mylle E, Johnson AJ, et al. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 2020;183(3):986-997. doi:10.1104/pp.20.00178","apa":"Wang, J., Mylle, E., Johnson, A. J., Besbrugge, N., De Jaeger, G., Friml, J., … van Damme, D. (2020). High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00178","chicago":"Wang, J, E Mylle, Alexander J Johnson, N Besbrugge, G De Jaeger, Jiří Friml, R Pleskot, and D van Damme. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00178.","ista":"Wang J, Mylle E, Johnson AJ, Besbrugge N, De Jaeger G, Friml J, Pleskot R, van Damme D. 2020. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 183(3), 986–997."},"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"date_created":"2020-04-29T15:23:00Z","doi":"10.1104/pp.20.00178","date_published":"2020-07-01T00:00:00Z","page":"986-997","publication":"Plant Physiology","day":"01","year":"2020","isi":1,"oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"date_updated":"2023-09-05T12:20:02Z","status":"public","article_type":"original","type":"journal_article","_id":"7695","volume":183,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"intvolume":" 183","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.13.948109"}],"scopus_import":"1","pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The TPLATE complex (TPC) is a key endocytic adaptor protein complex in plants. TPC in Arabidopsis (Arabidopsis thaliana) contains six evolutionarily conserved subunits and two plant-specific subunits, AtEH1/Pan1 and AtEH2/Pan1, although cytoplasmic proteins are not associated with the hexameric subcomplex in the cytoplasm. To investigate the dynamic assembly of the octameric TPC at the plasma membrane (PM), we performed state-of-the-art dual-color live cell imaging at physiological and lowered temperatures. Lowering the temperature slowed down endocytosis, thereby enhancing the temporal resolution of the differential recruitment of endocytic components. Under both normal and lowered temperature conditions, the core TPC subunit TPLATE and the AtEH/Pan1 proteins exhibited simultaneous recruitment at the PM. These results, together with co-localization analysis of different TPC subunits, allow us to conclude that TPC in plant cells is not recruited to the PM sequentially but as an octameric complex."}]},{"year":"2020","publication":"Proceedings of the AAAI Conference on Artificial Intelligence","day":"03","page":"1798-1805","date_created":"2021-02-25T09:05:18Z","date_published":"2020-04-03T00:00:00Z","doi":"10.1609/aaai.v34i02.5546","acknowledgement":"This research was supported by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE), Z211-N23 (Wittgenstein Award), and M 2369-N33 (Meitner fellowship).","publisher":"Association for the Advancement of Artificial Intelligence","quality_controlled":"1","citation":{"mla":"Avni, Guy, et al. “All-Pay Bidding Games on Graphs.” Proceedings of the AAAI Conference on Artificial Intelligence, vol. 34, no. 02, Association for the Advancement of Artificial Intelligence, 2020, pp. 1798–805, doi:10.1609/aaai.v34i02.5546.","short":"G. Avni, R. Ibsen-Jensen, J. Tkadlec, Proceedings of the AAAI Conference on Artificial Intelligence 34 (2020) 1798–1805.","ieee":"G. Avni, R. Ibsen-Jensen, and J. Tkadlec, “All-pay bidding games on graphs,” Proceedings of the AAAI Conference on Artificial Intelligence, vol. 34, no. 02. Association for the Advancement of Artificial Intelligence, pp. 1798–1805, 2020.","ama":"Avni G, Ibsen-Jensen R, Tkadlec J. All-pay bidding games on graphs. Proceedings of the AAAI Conference on Artificial Intelligence. 2020;34(02):1798-1805. doi:10.1609/aaai.v34i02.5546","apa":"Avni, G., Ibsen-Jensen, R., & Tkadlec, J. (2020). All-pay bidding games on graphs. Proceedings of the AAAI Conference on Artificial Intelligence. New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i02.5546","chicago":"Avni, Guy, Rasmus Ibsen-Jensen, and Josef Tkadlec. “All-Pay Bidding Games on Graphs.” Proceedings of the AAAI Conference on Artificial Intelligence. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i02.5546.","ista":"Avni G, Ibsen-Jensen R, Tkadlec J. 2020. All-pay bidding games on graphs. Proceedings of the AAAI Conference on Artificial Intelligence. 34(02), 1798–1805."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"arxiv":["1911.08360"]},"author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"}],"title":"All-pay bidding games on graphs","project":[{"grant_number":"S11402-N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory"}],"publication_status":"published","publication_identifier":{"eissn":["2374-3468"],"isbn":["9781577358350"],"issn":["2159-5399"]},"language":[{"iso":"eng"}],"issue":"02","volume":34,"abstract":[{"lang":"eng","text":"In this paper we introduce and study all-pay bidding games, a class of two player, zero-sum games on graphs. The game proceeds as follows. We place a token on some vertex in the graph and assign budgets to the two players. Each turn, each player submits a sealed legal bid (non-negative and below their remaining budget), which is deducted from their budget and the highest bidder moves the token onto an adjacent vertex. The game ends once a sink is reached, and Player 1 pays Player 2 the outcome that is associated with the sink. The players attempt to maximize their expected outcome. Our games model settings where effort (of no inherent value) needs to be invested in an ongoing and stateful manner. On the negative side, we show that even in simple games on DAGs, optimal strategies may require a distribution over bids with infinite support. A central quantity in bidding games is the ratio of the players budgets. On the positive side, we show a simple FPTAS for DAGs, that, for each budget ratio, outputs an approximation for the optimal strategy for that ratio. We also implement it, show that it performs well, and suggests interesting properties of these games. Then, given an outcome c, we show an algorithm for finding the necessary and sufficient initial ratio for guaranteeing outcome c with probability 1 and a strategy ensuring such. Finally, while the general case has not previously been studied, solving the specific game in which Player 1 wins iff he wins the first two auctions, has been long stated as an open question, which we solve."}],"oa_version":"Preprint","scopus_import":"1","intvolume":" 34","month":"04","date_updated":"2023-09-05T12:40:00Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"_id":"9197","conference":{"name":"AAAI: Conference on Artificial Intelligence","location":"New York, NY, United States","end_date":"2020-02-12","start_date":"2020-02-07"},"type":"journal_article","article_type":"original","status":"public"},{"volume":39,"issue":"17","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"43d2b36598708e6ab05c69074e191d57","file_id":"8827","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_EMBO_Montesinos.pdf","date_created":"2020-12-02T09:13:23Z","file_size":3497156,"date_updated":"2020-12-02T09:13:23Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"intvolume":" 39","month":"09","scopus_import":"1","pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.","lang":"eng"}],"file_date_updated":"2020-12-02T09:13:23Z","department":[{"_id":"MiSi"},{"_id":"EvBe"}],"ddc":["580"],"date_updated":"2023-09-05T13:05:47Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"8142","date_created":"2020-07-21T09:08:38Z","date_published":"2020-09-01T00:00:00Z","doi":"10.15252/embj.2019104238","publication":"The Embo Journal","day":"01","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Embo Press","acknowledgement":"We thank Takashi Aoyama, David Alabadi, and Bert De Rybel for sharing material, Jiří Friml, Maciek Adamowski, and Katerina Schwarzerová for inspiring discussions, and Martine De Cock for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Bioimaging Facility (BIF), especially to Robert Hauschild; and the Life Science Facility (LSF). J.C.M. is the recipient of a EMBO Long‐Term Fellowship (ALTF number 710‐2016). This work was supported with MEYS CR, project no.CZ.02.1.01/0.0/0.0/16_019/0000738 to J.P., and by the Austrian Science Fund (FWF01_I1774S) to E.B.","title":"Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage","external_id":{"isi":["000548311800001"],"pmid":["32667089"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099"},{"full_name":"Abuzeineh, A","last_name":"Abuzeineh","first_name":"A"},{"full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","last_name":"Kopf","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"},{"id":"40F05888-F248-11E8-B48F-1D18A9856A87","first_name":"Alba","last_name":"Juanes Garcia","orcid":"0000-0002-1009-9652","full_name":"Juanes Garcia, Alba"},{"first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","last_name":"Ötvös","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina"},{"first_name":"J","last_name":"Petrášek","full_name":"Petrášek, J"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Montesinos López JC, Abuzeineh A, Kopf A, Juanes Garcia A, Ötvös K, Petrášek J, Sixt MK, Benková E. 2020. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 39(17), e104238.","chicago":"Montesinos López, Juan C, A Abuzeineh, Aglaja Kopf, Alba Juanes Garcia, Krisztina Ötvös, J Petrášek, Michael K Sixt, and Eva Benková. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” The Embo Journal. Embo Press, 2020. https://doi.org/10.15252/embj.2019104238.","ieee":"J. C. Montesinos López et al., “Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage,” The Embo Journal, vol. 39, no. 17. Embo Press, 2020.","short":"J.C. Montesinos López, A. Abuzeineh, A. Kopf, A. Juanes Garcia, K. Ötvös, J. Petrášek, M.K. Sixt, E. Benková, The Embo Journal 39 (2020).","apa":"Montesinos López, J. C., Abuzeineh, A., Kopf, A., Juanes Garcia, A., Ötvös, K., Petrášek, J., … Benková, E. (2020). Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. Embo Press. https://doi.org/10.15252/embj.2019104238","ama":"Montesinos López JC, Abuzeineh A, Kopf A, et al. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 2020;39(17). doi:10.15252/embj.2019104238","mla":"Montesinos López, Juan C., et al. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” The Embo Journal, vol. 39, no. 17, e104238, Embo Press, 2020, doi:10.15252/embj.2019104238."},"project":[{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"},{"grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425"}],"article_number":"e104238"},{"date_published":"2020-01-02T00:00:00Z","doi":"10.1523/jneurosci.1278-19.2019","date_created":"2020-07-05T15:24:51Z","page":"171-190","day":"02","publication":"Journal of Neuroscience","has_accepted_license":"1","isi":1,"year":"2020","quality_controlled":"1","publisher":"Society for Neuroscience","oa":1,"title":"Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake","author":[{"orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","last_name":"Lombardi","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"last_name":"Gómez-Extremera","full_name":"Gómez-Extremera, Manuel","first_name":"Manuel"},{"full_name":"Bernaola-Galván, Pedro","last_name":"Bernaola-Galván","first_name":"Pedro"},{"last_name":"Vetrivelan","full_name":"Vetrivelan, Ramalingam","first_name":"Ramalingam"},{"full_name":"Saper, Clifford B.","last_name":"Saper","first_name":"Clifford B."},{"first_name":"Thomas E.","last_name":"Scammell","full_name":"Scammell, Thomas E."},{"last_name":"Ivanov","full_name":"Ivanov, Plamen Ch.","first_name":"Plamen Ch."}],"article_processing_charge":"No","external_id":{"isi":["000505167600016"],"pmid":["31694962"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Lombardi, F., Gómez-Extremera, M., Bernaola-Galván, P., Vetrivelan, R., Saper, C. B., Scammell, T. E., & Ivanov, P. C. (2020). Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.1278-19.2019","ama":"Lombardi F, Gómez-Extremera M, Bernaola-Galván P, et al. Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. 2020;40(1):171-190. doi:10.1523/jneurosci.1278-19.2019","ieee":"F. Lombardi et al., “Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake,” Journal of Neuroscience, vol. 40, no. 1. Society for Neuroscience, pp. 171–190, 2020.","short":"F. Lombardi, M. Gómez-Extremera, P. Bernaola-Galván, R. Vetrivelan, C.B. Saper, T.E. Scammell, P.C. Ivanov, Journal of Neuroscience 40 (2020) 171–190.","mla":"Lombardi, Fabrizio, et al. “Critical Dynamics and Coupling in Bursts of Cortical Rhythms Indicate Non-Homeostatic Mechanism for Sleep-Stage Transitions and Dual Role of VLPO Neurons in Both Sleep and Wake.” Journal of Neuroscience, vol. 40, no. 1, Society for Neuroscience, 2020, pp. 171–90, doi:10.1523/jneurosci.1278-19.2019.","ista":"Lombardi F, Gómez-Extremera M, Bernaola-Galván P, Vetrivelan R, Saper CB, Scammell TE, Ivanov PC. 2020. Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. 40(1), 171–190.","chicago":"Lombardi, Fabrizio, Manuel Gómez-Extremera, Pedro Bernaola-Galván, Ramalingam Vetrivelan, Clifford B. Saper, Thomas E. Scammell, and Plamen Ch. Ivanov. “Critical Dynamics and Coupling in Bursts of Cortical Rhythms Indicate Non-Homeostatic Mechanism for Sleep-Stage Transitions and Dual Role of VLPO Neurons in Both Sleep and Wake.” Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/jneurosci.1278-19.2019."},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"issue":"1","volume":40,"ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8150","file_size":6646046,"date_updated":"2020-07-22T11:44:48Z","creator":"dernst","file_name":"2020_JournNeuroscience_Lombardi.pdf","date_created":"2020-07-22T11:44:48Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"publication_status":"published","month":"01","intvolume":" 40","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Origin and functions of intermittent transitions among sleep stages, including brief awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation.","lang":"eng"}],"department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-22T11:44:48Z","ddc":["570"],"date_updated":"2023-09-05T14:02:55Z","status":"public","article_type":"original","type":"journal_article","_id":"8084"},{"_id":"7650","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"date_updated":"2023-09-05T14:18:49Z","file_date_updated":"2020-11-20T13:17:42Z","department":[{"_id":"RoSe"}],"oa_version":"Published Version","abstract":[{"text":"We consider a dilute, homogeneous Bose gas at positive temperature. The system is investigated in the Gross–Pitaevskii limit, where the scattering length a is so small that the interaction energy is of the same order of magnitude as the spectral gap of the Laplacian, and for temperatures that are comparable to the critical temperature of the ideal gas. We show that the difference between the specific free energy of the interacting system and the one of the ideal gas is to leading order given by 4πa(2ϱ2−ϱ20). Here ϱ denotes the density of the system and ϱ0 is the expected condensate density of the ideal gas. Additionally, we show that the one-particle density matrix of any approximate minimizer of the Gibbs free energy functional is to leading order given by the one of the ideal gas. This in particular proves Bose–Einstein condensation with critical temperature given by the one of the ideal gas to leading order. One key ingredient of our proof is a novel use of the Gibbs variational principle that goes hand in hand with the c-number substitution.","lang":"eng"}],"month":"03","intvolume":" 236","scopus_import":"1","file":[{"file_name":"2020_ArchRatMechanicsAnalysis_Deuchert.pdf","date_created":"2020-11-20T13:17:42Z","file_size":704633,"date_updated":"2020-11-20T13:17:42Z","creator":"dernst","success":1,"file_id":"8785","checksum":"b645fb64bfe95bbc05b3eea374109a9c","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"publication_status":"published","volume":236,"issue":"6","ec_funded":1,"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-020-01489-4.","ista":"Deuchert A, Seiringer R. 2020. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. 236(6), 1217–1271.","mla":"Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis, vol. 236, no. 6, Springer Nature, 2020, pp. 1217–71, doi:10.1007/s00205-020-01489-4.","short":"A. Deuchert, R. Seiringer, Archive for Rational Mechanics and Analysis 236 (2020) 1217–1271.","ieee":"A. Deuchert and R. Seiringer, “Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature,” Archive for Rational Mechanics and Analysis, vol. 236, no. 6. Springer Nature, pp. 1217–1271, 2020.","apa":"Deuchert, A., & Seiringer, R. (2020). Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-020-01489-4","ama":"Deuchert A, Seiringer R. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. 2020;236(6):1217-1271. doi:10.1007/s00205-020-01489-4"},"title":"Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature","author":[{"last_name":"Deuchert","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas","first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1901.11363"],"isi":["000519415000001"]},"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). It is a pleasure to thank Jakob Yngvason for helpful discussions. Financial support by the European Research Council (ERC) under the European Union’sHorizon 2020 research and innovation programme (Grant Agreement No. 694227) is gratefully acknowledged. A. D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 836146.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"09","publication":"Archive for Rational Mechanics and Analysis","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.1007/s00205-020-01489-4","date_published":"2020-03-09T00:00:00Z","date_created":"2020-04-08T15:18:03Z","page":"1217-1271"},{"_id":"8130","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-05T14:19:06Z","ddc":["510"],"department":[{"_id":"RoSe"}],"file_date_updated":"2020-12-02T08:50:38Z","abstract":[{"text":"We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 238","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"publication_status":"published","file":[{"checksum":"cc67a79a67bef441625fcb1cd031db3d","file_id":"8826","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-12-02T08:50:38Z","file_name":"2020_ArchiveRatMech_Bossmann.pdf","date_updated":"2020-12-02T08:50:38Z","file_size":942343,"creator":"dernst"}],"language":[{"iso":"eng"}],"volume":238,"issue":"11","ec_funded":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"citation":{"ama":"Bossmann L. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 2020;238(11):541-606. doi:10.1007/s00205-020-01548-w","apa":"Bossmann, L. (2020). Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-020-01548-w","ieee":"L. Bossmann, “Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons,” Archive for Rational Mechanics and Analysis, vol. 238, no. 11. Springer Nature, pp. 541–606, 2020.","short":"L. Bossmann, Archive for Rational Mechanics and Analysis 238 (2020) 541–606.","mla":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis, vol. 238, no. 11, Springer Nature, 2020, pp. 541–606, doi:10.1007/s00205-020-01548-w.","ista":"Bossmann L. 2020. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 238(11), 541–606.","chicago":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-020-01548-w."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","last_name":"Bossmann","orcid":"0000-0002-6854-1343","full_name":"Bossmann, Lea"}],"external_id":{"isi":["000550164400001"],"arxiv":["1907.04547"]},"article_processing_charge":"Yes (via OA deal)","title":"Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). I thank Stefan Teufel for helpful remarks and for his involvement in the closely related joint project [10]. Helpful discussions with Serena Cenatiempo and Nikolai Leopold are gratefully acknowledged. This work was supported by the German Research Foundation within the Research Training Group 1838 “Spectral Theory and Dynamics of Quantum Systems” and has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Archive for Rational Mechanics and Analysis","page":"541-606","date_published":"2020-11-01T00:00:00Z","doi":"10.1007/s00205-020-01548-w","date_created":"2020-07-18T15:06:35Z"},{"month":"09","intvolume":" 180","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We consider the Fröhlich model of a polaron, and show that its effective mass diverges in thestrong coupling limit.","lang":"eng"}],"volume":180,"ec_funded":1,"file":[{"creator":"dernst","date_updated":"2020-11-19T11:13:55Z","file_size":279749,"date_created":"2020-11-19T11:13:55Z","file_name":"2020_JourStatPhysics_Lieb.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8774","checksum":"1e67bee6728592f7bdcea2ad2d9366dc","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1572-9613"],"issn":["0022-4715"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7235","department":[{"_id":"RoSe"}],"file_date_updated":"2020-11-19T11:13:55Z","ddc":["510","530"],"date_updated":"2023-09-05T14:57:29Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227; R.S.) is gratefully acknowledged.","date_published":"2020-09-01T00:00:00Z","doi":"10.1007/s10955-019-02322-3","date_created":"2020-01-07T09:42:03Z","page":"23-33","day":"01","publication":"Journal of Statistical Physics","isi":1,"has_accepted_license":"1","year":"2020","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"title":"Divergence of the effective mass of a polaron in the strong coupling limit","author":[{"last_name":"Lieb","full_name":"Lieb, Elliott H.","first_name":"Elliott H."},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000556199700003"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Lieb EH, Seiringer R. 2020. Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. 180, 23–33.","chicago":"Lieb, Elliott H., and Robert Seiringer. “Divergence of the Effective Mass of a Polaron in the Strong Coupling Limit.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-019-02322-3.","short":"E.H. Lieb, R. Seiringer, Journal of Statistical Physics 180 (2020) 23–33.","ieee":"E. H. Lieb and R. Seiringer, “Divergence of the effective mass of a polaron in the strong coupling limit,” Journal of Statistical Physics, vol. 180. Springer Nature, pp. 23–33, 2020.","apa":"Lieb, E. H., & Seiringer, R. (2020). Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-019-02322-3","ama":"Lieb EH, Seiringer R. Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. 2020;180:23-33. doi:10.1007/s10955-019-02322-3","mla":"Lieb, Elliott H., and Robert Seiringer. “Divergence of the Effective Mass of a Polaron in the Strong Coupling Limit.” Journal of Statistical Physics, vol. 180, Springer Nature, 2020, pp. 23–33, doi:10.1007/s10955-019-02322-3."}},{"type":"conference","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","start_date":"2020-05-11","end_date":"2020-05-15"},"status":"public","_id":"7966","department":[{"_id":"KrPi"}],"date_updated":"2023-09-05T15:06:40Z","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/364"}],"month":"05","intvolume":" 12107","abstract":[{"lang":"eng","text":"For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters).\r\n\r\nFor Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario.\r\n\r\nAs our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem."}],"oa_version":"Submitted Version","volume":12107,"ec_funded":1,"publication_identifier":{"issn":["0302-9743"],"isbn":["9783030457266","9783030457273"],"eissn":["1611-3349"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Auerbach","full_name":"Auerbach, Benedikt","orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","first_name":"Benedikt"},{"last_name":"Giacon","full_name":"Giacon, Federico","first_name":"Federico"},{"first_name":"Eike","full_name":"Kiltz, Eike","last_name":"Kiltz"}],"external_id":{"isi":["000828688000016"]},"article_processing_charge":"No","title":"Everybody’s a target: Scalability in public-key encryption","citation":{"ista":"Auerbach B, Giacon F, Kiltz E. 2020. Everybody’s a target: Scalability in public-key encryption. Advances in Cryptology – EUROCRYPT 2020. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 12107, 475–506.","chicago":"Auerbach, Benedikt, Federico Giacon, and Eike Kiltz. “Everybody’s a Target: Scalability in Public-Key Encryption.” In Advances in Cryptology – EUROCRYPT 2020, 12107:475–506. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45727-3_16.","ama":"Auerbach B, Giacon F, Kiltz E. Everybody’s a target: Scalability in public-key encryption. In: Advances in Cryptology – EUROCRYPT 2020. Vol 12107. Springer Nature; 2020:475-506. doi:10.1007/978-3-030-45727-3_16","apa":"Auerbach, B., Giacon, F., & Kiltz, E. (2020). Everybody’s a target: Scalability in public-key encryption. In Advances in Cryptology – EUROCRYPT 2020 (Vol. 12107, pp. 475–506). Springer Nature. https://doi.org/10.1007/978-3-030-45727-3_16","ieee":"B. Auerbach, F. Giacon, and E. Kiltz, “Everybody’s a target: Scalability in public-key encryption,” in Advances in Cryptology – EUROCRYPT 2020, 2020, vol. 12107, pp. 475–506.","short":"B. Auerbach, F. Giacon, E. Kiltz, in:, Advances in Cryptology – EUROCRYPT 2020, Springer Nature, 2020, pp. 475–506.","mla":"Auerbach, Benedikt, et al. “Everybody’s a Target: Scalability in Public-Key Encryption.” Advances in Cryptology – EUROCRYPT 2020, vol. 12107, Springer Nature, 2020, pp. 475–506, doi:10.1007/978-3-030-45727-3_16."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"475-506","date_published":"2020-05-01T00:00:00Z","doi":"10.1007/978-3-030-45727-3_16","date_created":"2020-06-15T07:13:37Z","isi":1,"year":"2020","day":"01","publication":"Advances in Cryptology – EUROCRYPT 2020"},{"ddc":["000"],"date_updated":"2023-09-05T15:08:26Z","file_date_updated":"2020-10-15T14:28:06Z","department":[{"_id":"ToHe"}],"_id":"8623","status":"public","conference":{"name":"RV: Runtime Verification","location":"Los Angeles, CA, United States","end_date":"2020-10-09","start_date":"2020-10-06"},"type":"conference","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8665","checksum":"00661f9b7034f52e18bf24fa552b8194","file_size":478148,"date_updated":"2020-10-15T14:28:06Z","creator":"esarac","file_name":"monitorability.pdf","date_created":"2020-10-15T14:28:06Z"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030605070","9783030605087"],"issn":["0302-9743"]},"volume":12399,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We introduce the monitoring of trace properties under assumptions. An assumption limits the space of possible traces that the monitor may encounter. An assumption may result from knowledge about the system that is being monitored, about the environment, or about another, connected monitor. We define monitorability under assumptions and study its theoretical properties. In particular, we show that for every assumption A, the boolean combinations of properties that are safe or co-safe relative to A are monitorable under A. We give several examples and constructions on how an assumption can make a non-monitorable property monitorable, and how an assumption can make a monitorable property monitorable with fewer resources, such as integer registers."}],"intvolume":" 12399","month":"10","alternative_title":["LNCS"],"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"T.A. Henzinger, N.E. Sarac, in:, Runtime Verification, Springer Nature, 2020, pp. 3–18.","ieee":"T. A. Henzinger and N. E. Sarac, “Monitorability under assumptions,” in Runtime Verification, Los Angeles, CA, United States, 2020, vol. 12399, pp. 3–18.","ama":"Henzinger TA, Sarac NE. Monitorability under assumptions. In: Runtime Verification. Vol 12399. Springer Nature; 2020:3-18. doi:10.1007/978-3-030-60508-7_1","apa":"Henzinger, T. A., & Sarac, N. E. (2020). Monitorability under assumptions. In Runtime Verification (Vol. 12399, pp. 3–18). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-030-60508-7_1","mla":"Henzinger, Thomas A., and Naci E. Sarac. “Monitorability under Assumptions.” Runtime Verification, vol. 12399, Springer Nature, 2020, pp. 3–18, doi:10.1007/978-3-030-60508-7_1.","ista":"Henzinger TA, Sarac NE. 2020. Monitorability under assumptions. Runtime Verification. RV: Runtime Verification, LNCS, vol. 12399, 3–18.","chicago":"Henzinger, Thomas A, and Naci E Sarac. “Monitorability under Assumptions.” In Runtime Verification, 12399:3–18. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-60508-7_1."},"title":"Monitorability under assumptions","article_processing_charge":"No","external_id":{"isi":["000728160600001"]},"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","last_name":"Sarac"}],"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"publication":"Runtime Verification","day":"02","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-10-07T15:05:37Z","date_published":"2020-10-02T00:00:00Z","doi":"10.1007/978-3-030-60508-7_1","page":"3-18","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"conference":{"location":"Leeds, United Kingdom","end_date":"2020-06-26","start_date":"2020-06-24","name":"WG: Workshop on Graph-Theoretic Concepts in Computer Science"},"type":"conference","status":"public","_id":"8732","department":[{"_id":"UlWa"}],"date_updated":"2023-09-05T15:09:16Z","alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 12301","month":"10","abstract":[{"text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP -complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ , it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.","lang":"eng"}],"oa_version":"None","ec_funded":1,"volume":12301,"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030604394","9783030604400"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M","last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670"},{"full_name":"Klute, Fabian","last_name":"Klute","first_name":"Fabian"},{"first_name":"Irene","last_name":"Parada","full_name":"Parada, Irene"},{"first_name":"Raimund","full_name":"Seidel, Raimund","last_name":"Seidel"},{"first_name":"Birgit","full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber"},{"full_name":"Wiedera, Tilo","last_name":"Wiedera","first_name":"Tilo"}],"title":"Inserting one edge into a simple drawing is hard","citation":{"ama":"Arroyo Guevara AM, Klute F, Parada I, Seidel R, Vogtenhuber B, Wiedera T. Inserting one edge into a simple drawing is hard. In: Graph-Theoretic Concepts in Computer Science. Vol 12301. Springer Nature; 2020:325-338. doi:10.1007/978-3-030-60440-0_26","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Seidel, R., Vogtenhuber, B., & Wiedera, T. (2020). Inserting one edge into a simple drawing is hard. In Graph-Theoretic Concepts in Computer Science (Vol. 12301, pp. 325–338). Leeds, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-60440-0_26","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, R. Seidel, B. Vogtenhuber, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” in Graph-Theoretic Concepts in Computer Science, Leeds, United Kingdom, 2020, vol. 12301, pp. 325–338.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, R. Seidel, B. Vogtenhuber, T. Wiedera, in:, Graph-Theoretic Concepts in Computer Science, Springer Nature, 2020, pp. 325–338.","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Graph-Theoretic Concepts in Computer Science, vol. 12301, Springer Nature, 2020, pp. 325–38, doi:10.1007/978-3-030-60440-0_26.","ista":"Arroyo Guevara AM, Klute F, Parada I, Seidel R, Vogtenhuber B, Wiedera T. 2020. Inserting one edge into a simple drawing is hard. Graph-Theoretic Concepts in Computer Science. WG: Workshop on Graph-Theoretic Concepts in Computer Science, LNCS, vol. 12301, 325–338.","chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Raimund Seidel, Birgit Vogtenhuber, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” In Graph-Theoretic Concepts in Computer Science, 12301:325–38. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-60440-0_26."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","quality_controlled":"1","page":"325-338","date_created":"2020-11-06T08:45:03Z","doi":"10.1007/978-3-030-60440-0_26","date_published":"2020-10-09T00:00:00Z","year":"2020","publication":"Graph-Theoretic Concepts in Computer Science","day":"09"},{"date_updated":"2023-09-05T15:10:02Z","type":"book_chapter","status":"public","_id":"10865","series_title":"LNCS","volume":12110,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030453732","9783030453749"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/090"}],"month":"04","place":"Cham","intvolume":" 12110","abstract":[{"lang":"eng","text":"We introduce the notion of Witness Maps as a cryptographic notion of a proof system. A Unique Witness Map (UWM) deterministically maps all witnesses for an NP statement to a single representative witness, resulting in a computationally sound, deterministic-prover, non-interactive witness independent proof system. A relaxation of UWM, called Compact Witness Map (CWM), maps all the witnesses to a small number of witnesses, resulting in a “lossy” deterministic-prover, non-interactive proof-system. We also define a Dual Mode Witness Map (DMWM) which adds an “extractable” mode to a CWM.\r\nOur main construction is a DMWM for all NP relations, assuming sub-exponentially secure indistinguishability obfuscation ( iO ), along with standard cryptographic assumptions. The DMWM construction relies on a CWM and a new primitive called Cumulative All-Lossy-But-One Trapdoor Functions (C-ALBO-TDF), both of which are in turn instantiated based on iO and other primitives. Our instantiation of a CWM is in fact a UWM; in turn, we show that a UWM implies Witness Encryption. Along the way to constructing UWM and C-ALBO-TDF, we also construct, from standard assumptions, Puncturable Digital Signatures and a new primitive called Cumulative Lossy Trapdoor Functions (C-LTDF). The former improves up on a construction of Bellare et al. (Eurocrypt 2016), who relied on sub-exponentially secure iO and sub-exponentially secure OWF.\r\nAs an application of our constructions, we show how to use a DMWM to construct the first leakage and tamper-resilient signatures with a deterministic signer, thereby solving a decade old open problem posed by Katz and Vaikunthanathan (Asiacrypt 2009), by Boyle, Segev and Wichs (Eurocrypt 2011), as well as by Faonio and Venturi (Asiacrypt 2016). Our construction achieves the optimal leakage rate of 1−o(1) ."}],"oa_version":"Preprint","author":[{"last_name":"Chakraborty","full_name":"Chakraborty, Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425","first_name":"Suvradip"},{"full_name":"Prabhakaran, Manoj","last_name":"Prabhakaran","first_name":"Manoj"},{"last_name":"Wichs","full_name":"Wichs, Daniel","first_name":"Daniel"}],"article_processing_charge":"No","title":"Witness maps and applications","editor":[{"full_name":"Kiayias, A","last_name":"Kiayias","first_name":"A"}],"citation":{"mla":"Chakraborty, Suvradip, et al. “Witness Maps and Applications.” Public-Key Cryptography, edited by A Kiayias, vol. 12110, Springer Nature, 2020, pp. 220–46, doi:10.1007/978-3-030-45374-9_8.","apa":"Chakraborty, S., Prabhakaran, M., & Wichs, D. (2020). Witness maps and applications. In A. Kiayias (Ed.), Public-Key Cryptography (Vol. 12110, pp. 220–246). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-45374-9_8","ama":"Chakraborty S, Prabhakaran M, Wichs D. Witness maps and applications. In: Kiayias A, ed. Public-Key Cryptography. Vol 12110. LNCS. Cham: Springer Nature; 2020:220-246. doi:10.1007/978-3-030-45374-9_8","ieee":"S. Chakraborty, M. Prabhakaran, and D. Wichs, “Witness maps and applications,” in Public-Key Cryptography, vol. 12110, A. Kiayias, Ed. Cham: Springer Nature, 2020, pp. 220–246.","short":"S. Chakraborty, M. Prabhakaran, D. Wichs, in:, A. Kiayias (Ed.), Public-Key Cryptography, Springer Nature, Cham, 2020, pp. 220–246.","chicago":"Chakraborty, Suvradip, Manoj Prabhakaran, and Daniel Wichs. “Witness Maps and Applications.” In Public-Key Cryptography, edited by A Kiayias, 12110:220–46. LNCS. Cham: Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45374-9_8.","ista":"Chakraborty S, Prabhakaran M, Wichs D. 2020.Witness maps and applications. In: Public-Key Cryptography. vol. 12110, 220–246."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"220-246","date_published":"2020-04-29T00:00:00Z","doi":"10.1007/978-3-030-45374-9_8","date_created":"2022-03-18T11:35:51Z","year":"2020","day":"29","publication":"Public-Key Cryptography","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank the anonymous reviewers of PKC 2019 for their useful comments and suggestions. We thank Omer Paneth for pointing out to us the connection between Unique Witness Maps (UWM) and Witness encryption (WE). The first author would like to acknowledge Pandu Rangan for his involvement during the initial discussion phase of the project."},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Rademacher, Simone Anna Elvira. “Central Limit Theorem for Bose Gases Interacting through Singular Potentials.” Letters in Mathematical Physics, vol. 110, Springer Nature, 2020, pp. 2143–74, doi:10.1007/s11005-020-01286-w.","short":"S.A.E. Rademacher, Letters in Mathematical Physics 110 (2020) 2143–2174.","ieee":"S. A. E. Rademacher, “Central limit theorem for Bose gases interacting through singular potentials,” Letters in Mathematical Physics, vol. 110. Springer Nature, pp. 2143–2174, 2020.","ama":"Rademacher SAE. Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. 2020;110:2143-2174. doi:10.1007/s11005-020-01286-w","apa":"Rademacher, S. A. E. (2020). Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-020-01286-w","chicago":"Rademacher, Simone Anna Elvira. “Central Limit Theorem for Bose Gases Interacting through Singular Potentials.” Letters in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s11005-020-01286-w.","ista":"Rademacher SAE. 2020. Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. 110, 2143–2174."},"title":"Central limit theorem for Bose gases interacting through singular potentials","author":[{"last_name":"Rademacher","full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira"}],"external_id":{"isi":["000551556000006"]},"article_processing_charge":"Yes (via OA deal)","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"day":"12","publication":"Letters in Mathematical Physics","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.1007/s11005-020-01286-w","date_published":"2020-03-12T00:00:00Z","date_created":"2020-03-23T11:11:47Z","page":"2143-2174","acknowledgement":"Simone Rademacher acknowledges partial support from the NCCR SwissMAP. This project has received\r\nfunding from the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).\r\nS.R. would like to thank Benjamin Schlein for many fruitful discussions.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"ddc":["510"],"date_updated":"2023-09-05T15:14:50Z","department":[{"_id":"RoSe"}],"file_date_updated":"2020-11-20T12:04:26Z","_id":"7611","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"8784","checksum":"3bdd41f10ad947b67a45b98f507a7d4a","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-11-20T12:04:26Z","file_name":"2020_LettersMathPhysics_Rademacher.pdf","date_updated":"2020-11-20T12:04:26Z","file_size":478683,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"publication_status":"published","volume":110,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"We consider a system of N bosons in the limit N→∞, interacting through singular potentials. For initial data exhibiting Bose–Einstein condensation, the many-body time evolution is well approximated through a quadratic fluctuation dynamics around a cubic nonlinear Schrödinger equation of the condensate wave function. We show that these fluctuations satisfy a (multi-variate) central limit theorem.","lang":"eng"}],"month":"03","intvolume":" 110","scopus_import":"1"},{"month":"02","intvolume":" 90","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study."}],"issue":"1","volume":90,"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7469","checksum":"ab8130c6e68101f5a091d05324c36f08","file_size":537941,"date_updated":"2020-07-14T12:47:54Z","creator":"dernst","file_name":"2020_EcologMono_Baskett.pdf","date_created":"2020-02-10T08:18:14Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1557-7015"],"issn":["0012-9615"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"7236","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:54Z","ddc":["570"],"date_updated":"2023-09-05T15:43:19Z","quality_controlled":"1","publisher":"Wiley","oa":1,"doi":"10.1002/ecm.1397","date_published":"2020-02-01T00:00:00Z","date_created":"2020-01-07T12:47:07Z","day":"01","publication":"Ecological Monographs","isi":1,"has_accepted_license":"1","year":"2020","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_number":"e01397","title":"Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair","author":[{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina"},{"first_name":"Lucy","last_name":"Schroeder","full_name":"Schroeder, Lucy"},{"first_name":"Marjorie G.","last_name":"Weber","full_name":"Weber, Marjorie G."},{"full_name":"Schemske, Douglas W.","last_name":"Schemske","first_name":"Douglas W."}],"external_id":{"isi":["000508511600001"]},"article_processing_charge":"Yes (via OA deal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Baskett, Carina, et al. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs, vol. 90, no. 1, e01397, Wiley, 2020, doi:10.1002/ecm.1397.","apa":"Baskett, C., Schroeder, L., Weber, M. G., & Schemske, D. W. (2020). Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. Wiley. https://doi.org/10.1002/ecm.1397","ama":"Baskett C, Schroeder L, Weber MG, Schemske DW. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 2020;90(1). doi:10.1002/ecm.1397","short":"C. Baskett, L. Schroeder, M.G. Weber, D.W. Schemske, Ecological Monographs 90 (2020).","ieee":"C. Baskett, L. Schroeder, M. G. Weber, and D. W. Schemske, “Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair,” Ecological Monographs, vol. 90, no. 1. Wiley, 2020.","chicago":"Baskett, Carina, Lucy Schroeder, Marjorie G. Weber, and Douglas W. Schemske. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs. Wiley, 2020. https://doi.org/10.1002/ecm.1397.","ista":"Baskett C, Schroeder L, Weber MG, Schemske DW. 2020. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 90(1), e01397."}},{"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"Y. Zhang, C. Hartinger, X. Wang, J. Friml, New Phytologist 227 (2020) 1406–1416.","ieee":"Y. Zhang, C. Hartinger, X. Wang, and J. Friml, “Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters,” New Phytologist, vol. 227, no. 5. Wiley, pp. 1406–1416, 2020.","apa":"Zhang, Y., Hartinger, C., Wang, X., & Friml, J. (2020). Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. Wiley. https://doi.org/10.1111/nph.16629","ama":"Zhang Y, Hartinger C, Wang X, Friml J. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 2020;227(5):1406-1416. doi:10.1111/nph.16629","mla":"Zhang, Yuzhou, et al. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” New Phytologist, vol. 227, no. 5, Wiley, 2020, pp. 1406–16, doi:10.1111/nph.16629.","ista":"Zhang Y, Hartinger C, Wang X, Friml J. 2020. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 227(5), 1406–1416.","chicago":"Zhang, Yuzhou, Corinna Hartinger, Xiaojuan Wang, and Jiří Friml. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16629."},"title":"Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters","author":[{"first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang"},{"last_name":"Hartinger","full_name":"Hartinger, Corinna","orcid":"0000-0003-1618-2737","id":"AEFB2266-8ABF-11EA-AA39-812C3623CBE4","first_name":"Corinna"},{"full_name":"Wang, Xiaojuan","last_name":"Wang","first_name":"Xiaojuan"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"external_id":{"pmid":["32350870"],"isi":["000534092400001"]},"article_processing_charge":"Yes (via OA deal)","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"01","publication":"New Phytologist","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1111/nph.16629","date_published":"2020-09-01T00:00:00Z","date_created":"2020-04-30T08:43:29Z","page":"1406-1416","_id":"7697","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"date_updated":"2023-09-05T15:46:04Z","file_date_updated":"2020-11-24T12:19:38Z","department":[{"_id":"JiFr"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"* Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane‐based PIN‐FORMED (PIN) auxin transporters. PINs localize to a particular side of the plasma membrane (PM) or to the endoplasmic reticulum (ER) to directionally transport auxin and maintain intercellular and intracellular auxin homeostasis, respectively. However, the molecular cues that confer their diverse cellular localizations remain largely unknown.\r\n* In this study, we systematically swapped the domains between ER‐ and PM‐localized PIN proteins, as well as between apical and basal PM‐localized PINs from Arabidopsis thaliana , to shed light on why PIN family members with similar topological structures reside at different membrane compartments within cells.\r\n* Our results show that not only do the N‐ and C‐terminal transmembrane domains (TMDs) and central hydrophilic loop contribute to their differential subcellular localizations and cellular polarity, but that the pairwise‐matched N‐ and C‐terminal TMDs resulting from intramolecular domain–domain coevolution are also crucial for their divergent patterns of localization.\r\n* These findings illustrate the complexity of the evolutionary path of PIN proteins in acquiring their plethora of developmental functions and adaptive growth in plants.","lang":"eng"}],"month":"09","intvolume":" 227","scopus_import":"1","file":[{"creator":"dernst","date_updated":"2020-11-24T12:19:38Z","file_size":3643395,"date_created":"2020-11-24T12:19:38Z","file_name":"2020_09_NewPhytologist_Zhang.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"8e8150dbbba8cb65b72f81d1f0864b8b","file_id":"8799","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"publication_status":"published","issue":"5","volume":227,"ec_funded":1},{"type":"journal_article","article_type":"original","status":"public","keyword":["Computer Networks and Communications"],"_id":"8765","department":[{"_id":"ChWo"}],"file_date_updated":"2020-11-23T09:05:13Z","date_updated":"2023-09-05T16:00:13Z","ddc":["000"],"scopus_import":"1","month":"05","intvolume":" 39","abstract":[{"lang":"eng","text":"This paper introduces a simple method for simulating highly anisotropic elastoplastic material behaviors like the dissolution of fibrous phenomena (splintering wood, shredding bales of hay) and materials composed of large numbers of irregularly‐shaped bodies (piles of twigs, pencils, or cards). We introduce a simple transformation of the anisotropic problem into an equivalent isotropic one, and we solve this new “fictitious” isotropic problem using an existing simulator based on the material point method. Our approach results in minimal changes to existing simulators, and it allows us to re‐use popular isotropic plasticity models like the Drucker‐Prager yield criterion instead of inventing new anisotropic plasticity models for every phenomenon we wish to simulate."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","volume":39,"issue":"2","ec_funded":1,"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-11-23T09:05:13Z","file_size":38969122,"date_created":"2020-11-23T09:05:13Z","file_name":"2020_poff_revisited.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7605f605acd84d0942b48bc7a1c2d72e","file_id":"8796","success":1}],"language":[{"iso":"eng"}],"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille","full_name":"Schreck, Camille","last_name":"Schreck"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"article_processing_charge":"No","external_id":{"isi":["000548709600008"]},"title":"A practical method for animating anisotropic elastoplastic materials","citation":{"ista":"Schreck C, Wojtan C. 2020. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 39(2), 89–99.","chicago":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” Computer Graphics Forum. Wiley, 2020. https://doi.org/10.1111/cgf.13914.","apa":"Schreck, C., & Wojtan, C. (2020). A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13914","ama":"Schreck C, Wojtan C. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 2020;39(2):89-99. doi:10.1111/cgf.13914","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 39 (2020) 89–99.","ieee":"C. Schreck and C. Wojtan, “A practical method for animating anisotropic elastoplastic materials,” Computer Graphics Forum, vol. 39, no. 2. Wiley, pp. 89–99, 2020.","mla":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” Computer Graphics Forum, vol. 39, no. 2, Wiley, 2020, pp. 89–99, doi:10.1111/cgf.13914."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would also like to thank Joseph Teran and Chenfanfu Jiang for the helpful discussions.\r\nThis project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 638176.","page":"89-99","date_published":"2020-05-01T00:00:00Z","doi":"10.1111/cgf.13914","date_created":"2020-11-17T09:35:10Z","isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Computer Graphics Forum"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Bouchal R, Li Z, Bongu C, Le Vot S, Berthelot R, Rotenberg B, Favier F, Freunberger SA, Salanne M, Fontaine O. 2020. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. 132(37), 16047–16051.","chicago":"Bouchal, Roza, Zhujie Li, Chandra Bongu, Steven Le Vot, Romain Berthelot, Benjamin Rotenberg, Frederic Favier, Stefan Alexander Freunberger, Mathieu Salanne, and Olivier Fontaine. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie. Wiley, 2020. https://doi.org/10.1002/ange.202005378.","ieee":"R. Bouchal et al., “Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte,” Angewandte Chemie, vol. 132, no. 37. Wiley, pp. 16047–16051, 2020.","short":"R. Bouchal, Z. Li, C. Bongu, S. Le Vot, R. Berthelot, B. Rotenberg, F. Favier, S.A. Freunberger, M. Salanne, O. Fontaine, Angewandte Chemie 132 (2020) 16047–16051.","ama":"Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. 2020;132(37):16047-16051. doi:10.1002/ange.202005378","apa":"Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., … Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.202005378","mla":"Bouchal, Roza, et al. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie, vol. 132, no. 37, Wiley, 2020, pp. 16047–51, doi:10.1002/ange.202005378."},"title":"Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte","article_processing_charge":"No","author":[{"full_name":"Bouchal, Roza","last_name":"Bouchal","first_name":"Roza"},{"last_name":"Li","full_name":"Li, Zhujie","first_name":"Zhujie"},{"first_name":"Chandra","full_name":"Bongu, Chandra","last_name":"Bongu"},{"full_name":"Le Vot, Steven","last_name":"Le Vot","first_name":"Steven"},{"last_name":"Berthelot","full_name":"Berthelot, Romain","first_name":"Romain"},{"full_name":"Rotenberg, Benjamin","last_name":"Rotenberg","first_name":"Benjamin"},{"first_name":"Frederic","full_name":"Favier, Frederic","last_name":"Favier"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger"},{"first_name":"Mathieu","last_name":"Salanne","full_name":"Salanne, Mathieu"},{"first_name":"Olivier","full_name":"Fontaine, Olivier","last_name":"Fontaine"}],"oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"Angewandte Chemie","day":"07","year":"2020","has_accepted_license":"1","date_created":"2020-06-29T16:15:49Z","date_published":"2020-09-07T00:00:00Z","doi":"10.1002/ange.202005378","page":"16047-16051","_id":"8057","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["540","541"],"date_updated":"2023-09-05T15:47:50Z","department":[{"_id":"StFr"}],"file_date_updated":"2020-09-17T08:59:43Z","oa_version":"Published Version","abstract":[{"text":"Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities approaching 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of ‘free’ and ‘bound’ water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability.","lang":"eng"}],"intvolume":" 132","month":"09","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":1904552,"date_updated":"2020-09-17T08:59:43Z","creator":"dernst","file_name":"2020_AngChemieDE_Bouchal.pdf","date_created":"2020-09-17T08:59:43Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"7dd0a56f6bd5de08ea75b1ec388c91bc","file_id":"8401"}],"publication_status":"published","publication_identifier":{"eissn":["1521-3757"],"issn":["0044-8249"]},"issue":"37","volume":132},{"scopus_import":"1","intvolume":" 23","month":"03","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"text":"Coinfections with multiple pathogens can result in complex within‐host dynamics affecting virulence and transmission. While multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defences of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different‐species coinfections. Here, it decreased overall pathogen sporulation success while increasing co‐sporulation on individual cadavers and maintaining a higher pathogen diversity at the community level. Mathematical modelling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast‐germinating, thus less grooming‐sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host level and population level.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"status":"public","id":"13060","relation":"research_data"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/social-ants-shapes-disease-outcome/"}]},"issue":"3","volume":23,"publication_status":"published","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8776","checksum":"0cd8be386fa219db02845b7c3991ce04","success":1,"date_updated":"2020-11-19T11:27:10Z","file_size":561749,"creator":"dernst","date_created":"2020-11-19T11:27:10Z","file_name":"2020_EcologyLetters_Milutinovic.pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"letter_note","type":"journal_article","status":"public","_id":"7343","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"file_date_updated":"2020-11-19T11:27:10Z","date_updated":"2023-09-05T16:04:49Z","ddc":["570"],"oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"We thank Bernhardt Steinwender and Jorgen Eilenberg for the fungal strains, Xavier Espadaler, Mireia Diaz, Christiane Wanke, Lumi Viljakainen and the Social Immunity Team at IST Austria, for help with ant collection, and Wanda Gorecka and Gertraud Stift of the IST Austria Life Science Facility for technical support. We are thankful to Dieter Ebert for input at all stages of the project, Roger Mundry for statistical advice, Hinrich Schulenburg, Paul Schmid-Hempel, Yuko\r\nUlrich and Joachim Kurtz for project discussion, Bor Kavcic for advice on growth curves, Marcus Roper for advice on modelling work and comments on the manuscript, as well as Marjon de Vos, Weini Huang and the Social Immunity Team for comments on the manuscript.\r\nThis study was funded by the German Research Foundation (DFG) within the Priority Programme 1399 Host-parasite Coevolution (CR 118/3 to S.C.) and the People Programme\r\n(Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no 291734 (ISTFELLOW to B.M.). ","page":"565-574","date_created":"2020-01-20T13:32:12Z","date_published":"2020-03-01T00:00:00Z","doi":"10.1111/ele.13458","year":"2020","isi":1,"has_accepted_license":"1","publication":"Ecology Letters","day":"01","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000507515900001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara"},{"id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Stock","full_name":"Stock, Miriam"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse"},{"full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","first_name":"Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"title":"Social immunity modulates competition between coinfecting pathogens","citation":{"mla":"Milutinovic, Barbara, et al. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Ecology Letters, vol. 23, no. 3, Wiley, 2020, pp. 565–74, doi:10.1111/ele.13458.","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, Ecology Letters 23 (2020) 565–574.","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens,” Ecology Letters, vol. 23, no. 3. Wiley, pp. 565–574, 2020.","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. Ecology Letters. 2020;23(3):565-574. doi:10.1111/ele.13458","apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Ecology Letters. Wiley. https://doi.org/10.1111/ele.13458","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Ecology Letters. Wiley, 2020. https://doi.org/10.1111/ele.13458.","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens. Ecology Letters. 23(3), 565–574."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"8099","file_date_updated":"2020-11-26T11:46:43Z","department":[{"_id":"BeVi"}],"ddc":["570"],"date_updated":"2023-09-05T16:07:08Z","intvolume":" 20","month":"11","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.","lang":"eng"}],"ec_funded":1,"issue":"6","volume":20,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-11-26T11:46:43Z","file_size":820428,"creator":"dernst","date_created":"2020-11-26T11:46:43Z","file_name":"2020_MolecularEcologyRes_Gammerdinger.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3d87ebb8757dcd504f20c618b72e6575","file_id":"8814","success":1}],"publication_status":"published","publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"title":"Disagreement in FST estimators: A case study from sex chromosomes","external_id":{"pmid":["32543001"],"isi":["000545451200001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"orcid":"0000-0001-9638-1220","full_name":"Gammerdinger, William J","last_name":"Gammerdinger","first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources, vol. 20, no. 6, Wiley, 2020, pp. 1517–25, doi:10.1111/1755-0998.13210.","apa":"Gammerdinger, W. J., Toups, M. A., & Vicoso, B. (2020). Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13210","ama":"Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 2020;20(6):1517-1525. doi:10.1111/1755-0998.13210","short":"W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20 (2020) 1517–1525.","ieee":"W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators: A case study from sex chromosomes,” Molecular Ecology Resources, vol. 20, no. 6. Wiley, pp. 1517–1525, 2020.","chicago":"Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources. Wiley, 2020. https://doi.org/10.1111/1755-0998.13210.","ista":"Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525."},"oa":1,"quality_controlled":"1","publisher":"Wiley","date_created":"2020-07-07T08:56:16Z","doi":"10.1111/1755-0998.13210","date_published":"2020-11-01T00:00:00Z","page":"1517-1525","publication":"Molecular Ecology Resources","day":"01","year":"2020","isi":1,"has_accepted_license":"1"},{"oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"Angewandte Chemie International Edition","day":"07","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-05-14T21:00:30Z","date_published":"2020-09-07T00:00:00Z","doi":"10.1002/anie.202005378","page":"15913-1591","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Bouchal, Roza, Zhujie Li, Chandra Bongu, Steven Le Vot, Romain Berthelot, Benjamin Rotenberg, Fréderic Favier, Stefan Alexander Freunberger, Mathieu Salanne, and Olivier Fontaine. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie International Edition. Wiley, 2020. https://doi.org/10.1002/anie.202005378.","ista":"Bouchal R, Li Z, Bongu C, Le Vot S, Berthelot R, Rotenberg B, Favier F, Freunberger SA, Salanne M, Fontaine O. 2020. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. 59(37), 15913–1591.","mla":"Bouchal, Roza, et al. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie International Edition, vol. 59, no. 37, Wiley, 2020, pp. 15913–1591, doi:10.1002/anie.202005378.","ieee":"R. Bouchal et al., “Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte,” Angewandte Chemie International Edition, vol. 59, no. 37. Wiley, pp. 15913–1591, 2020.","short":"R. Bouchal, Z. Li, C. Bongu, S. Le Vot, R. Berthelot, B. Rotenberg, F. Favier, S.A. Freunberger, M. Salanne, O. Fontaine, Angewandte Chemie International Edition 59 (2020) 15913–1591.","ama":"Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. 2020;59(37):15913-1591. doi:10.1002/anie.202005378","apa":"Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., … Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202005378"},"title":"Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte","external_id":{"isi":["000541488700001"],"pmid":["32390281"]},"article_processing_charge":"No","author":[{"first_name":"Roza","full_name":"Bouchal, Roza","last_name":"Bouchal"},{"full_name":"Li, Zhujie","last_name":"Li","first_name":"Zhujie"},{"last_name":"Bongu","full_name":"Bongu, Chandra","first_name":"Chandra"},{"first_name":"Steven","full_name":"Le Vot, Steven","last_name":"Le Vot"},{"first_name":"Romain","full_name":"Berthelot, Romain","last_name":"Berthelot"},{"last_name":"Rotenberg","full_name":"Rotenberg, Benjamin","first_name":"Benjamin"},{"last_name":"Favier","full_name":"Favier, Fréderic","first_name":"Fréderic"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Salanne, Mathieu","last_name":"Salanne","first_name":"Mathieu"},{"last_name":"Fontaine","full_name":"Fontaine, Olivier","first_name":"Olivier"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities nearing 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of 'free' and 'bound' water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability. "}],"intvolume":" 59","month":"09","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2020-09-17T08:57:16Z","file_name":"2020_AngChemieINT_Buchal.pdf","date_updated":"2020-09-17T08:57:16Z","file_size":1966184,"creator":"dernst","file_id":"8400","checksum":"7b6c2fc20e9b0ff4353352f7a7004e2d","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"issue":"37","volume":59,"_id":"7847","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["540","546"],"date_updated":"2023-09-05T16:02:53Z","file_date_updated":"2020-09-17T08:57:16Z","department":[{"_id":"StFr"}]},{"publication_status":"published","publication_identifier":{"eissn":["1461-0248"],"issn":["1461-023X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7486","checksum":"372f67f2744f4b6049e9778364766c22","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_EcologyLetters_Rybicki.pdf","date_created":"2020-02-14T12:02:50Z","file_size":3005474,"date_updated":"2020-07-14T12:47:54Z","creator":"dernst"}],"ec_funded":1,"volume":23,"issue":"3","abstract":[{"text":"Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. In contrast, empirical studies report contrasting patterns: some find positive and others negative effects of fragmentation per se on species richness. To explain this apparent disparity, we devise a stochastic, spatially explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have complex effects on species diversity in competitive communities. When the total amount of habitat is large, fragmentation per se tends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentation per se decreases species diversity.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 23","month":"03","date_updated":"2023-09-05T16:04:30Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:54Z","department":[{"_id":"DaAl"}],"_id":"7224","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","year":"2020","isi":1,"has_accepted_license":"1","publication":"Ecology Letters","day":"01","page":"506-517","date_created":"2020-01-04T11:04:30Z","date_published":"2020-03-01T00:00:00Z","doi":"10.1111/ele.13450","oa":1,"publisher":"Wiley","quality_controlled":"1","citation":{"mla":"Rybicki, Joel, et al. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters, vol. 23, no. 3, Wiley, 2020, pp. 506–17, doi:10.1111/ele.13450.","ieee":"J. Rybicki, N. Abrego, and O. Ovaskainen, “Habitat fragmentation and species diversity in competitive communities,” Ecology Letters, vol. 23, no. 3. Wiley, pp. 506–517, 2020.","short":"J. Rybicki, N. Abrego, O. Ovaskainen, Ecology Letters 23 (2020) 506–517.","apa":"Rybicki, J., Abrego, N., & Ovaskainen, O. (2020). Habitat fragmentation and species diversity in competitive communities. Ecology Letters. Wiley. https://doi.org/10.1111/ele.13450","ama":"Rybicki J, Abrego N, Ovaskainen O. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 2020;23(3):506-517. doi:10.1111/ele.13450","chicago":"Rybicki, Joel, Nerea Abrego, and Otso Ovaskainen. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters. Wiley, 2020. https://doi.org/10.1111/ele.13450.","ista":"Rybicki J, Abrego N, Ovaskainen O. 2020. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 23(3), 506–517."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000503625200001"]},"author":[{"full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"},{"full_name":"Abrego, Nerea","last_name":"Abrego","first_name":"Nerea"},{"full_name":"Ovaskainen, Otso","last_name":"Ovaskainen","first_name":"Otso"}],"title":"Habitat fragmentation and species diversity in competitive communities","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"840605","name":"Coordination in constrained and natural distributed systems"}]},{"author":[{"first_name":"Werner","full_name":"Schlemmer, Werner","last_name":"Schlemmer"},{"last_name":"Nothdurft","full_name":"Nothdurft, Philipp","first_name":"Philipp"},{"first_name":"Alina","full_name":"Petzold, Alina","last_name":"Petzold"},{"first_name":"Philipp","full_name":"Frühwirt, Philipp","last_name":"Frühwirt"},{"first_name":"Max","last_name":"Schmallegger","full_name":"Schmallegger, Max"},{"last_name":"Gescheidt-Demner","full_name":"Gescheidt-Demner, Georg","first_name":"Georg"},{"last_name":"Fischer","full_name":"Fischer, Roland","first_name":"Roland"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"last_name":"Kern","full_name":"Kern, Wolfgang","first_name":"Wolfgang"},{"last_name":"Spirk","full_name":"Spirk, Stefan","first_name":"Stefan"}],"article_processing_charge":"No","external_id":{"isi":["000576148700001"]},"title":"2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries","citation":{"chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, Roland Fischer, Stefan Alexander Freunberger, Wolfgang Kern, and Stefan Spirk. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition. Wiley, 2020. https://doi.org/10.1002/anie.202008253.","ista":"Schlemmer W, Nothdurft P, Petzold A, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 59(51), 22943–22946.","mla":"Schlemmer, Werner, et al. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition, vol. 59, no. 51, Wiley, 2020, pp. 22943–46, doi:10.1002/anie.202008253.","short":"W. Schlemmer, P. Nothdurft, A. Petzold, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, Angewandte Chemie International Edition 59 (2020) 22943–22946.","ieee":"W. Schlemmer et al., “2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries,” Angewandte Chemie International Edition, vol. 59, no. 51. Wiley, pp. 22943–22946, 2020.","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 2020;59(51):22943-22946. doi:10.1002/anie.202008253","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Frühwirt, P., Schmallegger, M., Gescheidt-Demner, G., … Spirk, S. (2020). 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202008253"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"22943-22946","date_published":"2020-12-14T00:00:00Z","doi":"10.1002/anie.202008253","date_created":"2020-09-03T16:10:56Z","isi":1,"year":"2020","day":"14","publication":"Angewandte Chemie International Edition","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"The Austrian Research Promotion Agency (FFG) is gratefully acknowledged for financial support of the project LignoBatt (860429).","department":[{"_id":"StFr"}],"date_updated":"2023-09-05T16:03:47Z","type":"journal_article","article_type":"original","status":"public","_id":"8329","issue":"51","volume":59,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9780"}]},"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/anie.202008253"}],"month":"12","intvolume":" 59","abstract":[{"lang":"eng","text":"We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone (MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous redox flow batteries. We identified semiquinone intermediates at insufficiently low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO 4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds of cycles."}],"oa_version":"Published Version"},{"month":"12","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.crjdfn318","open_access":"1"}],"oa":1,"oa_version":"Published Version","abstract":[{"text":"Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level.","lang":"eng"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7343"}]},"doi":"10.5061/DRYAD.CRJDFN318","date_published":"2020-12-19T00:00:00Z","date_created":"2023-05-23T16:11:22Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"19","year":"2020","status":"public","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"13060","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"title":"Social immunity modulates competition between coinfecting pathogens","author":[{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic"},{"id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Stock","full_name":"Stock, Miriam"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2023-09-05T16:04:48Z","citation":{"apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. https://doi.org/10.5061/DRYAD.CRJDFN318","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:10.5061/DRYAD.CRJDFN318","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020.","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020).","mla":"Milutinovic, Barbara, et al. Social Immunity Modulates Competition between Coinfecting Pathogens. Dryad, 2020, doi:10.5061/DRYAD.CRJDFN318.","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, 10.5061/DRYAD.CRJDFN318.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. https://doi.org/10.5061/DRYAD.CRJDFN318."}},{"citation":{"mla":"Schlemmer, Werner, et al. CCDC 1991959: Experimental Crystal Structure Determination. CCDC, 2020, doi:10.5517/ccdc.csd.cc24vsrk.","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal Structure Determination. 2020. doi:10.5517/ccdc.csd.cc24vsrk","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger, M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination. CCDC. https://doi.org/10.5517/ccdc.csd.cc24vsrk","short":"W. Schlemmer, P. Nothdurft, A. Petzold, G. Riess, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, (2020).","ieee":"W. Schlemmer et al., “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020.","chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020. https://doi.org/10.5517/ccdc.csd.cc24vsrk.","ista":"Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. CCDC 1991959: Experimental Crystal Structure Determination, CCDC, 10.5517/ccdc.csd.cc24vsrk."},"date_updated":"2023-09-05T16:03:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Werner","full_name":"Schlemmer, Werner","last_name":"Schlemmer"},{"first_name":"Philipp","last_name":"Nothdurft","full_name":"Nothdurft, Philipp"},{"first_name":"Alina","full_name":"Petzold, Alina","last_name":"Petzold"},{"full_name":"Riess, Gisbert","last_name":"Riess","first_name":"Gisbert"},{"last_name":"Frühwirt","full_name":"Frühwirt, Philipp","first_name":"Philipp"},{"first_name":"Max","full_name":"Schmallegger, Max","last_name":"Schmallegger"},{"first_name":"Georg","last_name":"Gescheidt-Demner","full_name":"Gescheidt-Demner, Georg"},{"last_name":"Fischer","full_name":"Fischer, Roland","first_name":"Roland"},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"first_name":"Wolfgang","last_name":"Kern","full_name":"Kern, Wolfgang"},{"first_name":"Stefan","full_name":"Spirk, Stefan","last_name":"Spirk"}],"department":[{"_id":"StFr"}],"title":"CCDC 1991959: Experimental Crystal Structure Determination","_id":"9780","type":"research_data_reference","status":"public","year":"2020","day":"22","date_created":"2021-08-06T07:41:07Z","related_material":{"record":[{"relation":"used_in_publication","id":"8329","status":"public"}]},"doi":"10.5517/ccdc.csd.cc24vsrk","date_published":"2020-03-22T00:00:00Z","abstract":[{"text":"PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°","lang":"eng"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk","open_access":"1"}],"publisher":"CCDC","month":"03"},{"year":"2020","has_accepted_license":"1","isi":1,"publication":"Brain Pathology","day":"01","page":"554-575","date_created":"2019-12-22T23:00:43Z","date_published":"2020-05-01T00:00:00Z","doi":"10.1111/bpa.12802","oa":1,"quality_controlled":"1","publisher":"Wiley","citation":{"chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology. Wiley, 2020. https://doi.org/10.1111/bpa.12802.","ista":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Früh S, Bettler B, Shigemoto R, Fukazawa Y, Luján R. 2020. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 30(3), 554–575.","mla":"Martín-Belmonte, Alejandro, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology, vol. 30, no. 3, Wiley, 2020, pp. 554–75, doi:10.1111/bpa.12802.","short":"A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, S. Früh, B. Bettler, R. Shigemoto, Y. Fukazawa, R. Luján, Brain Pathology 30 (2020) 554–575.","ieee":"A. Martín-Belmonte et al., “Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease,” Brain Pathology, vol. 30, no. 3. Wiley, pp. 554–575, 2020.","ama":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 2020;30(3):554-575. doi:10.1111/bpa.12802","apa":"Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. Wiley. https://doi.org/10.1111/bpa.12802"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000502270900001"],"pmid":["31729777"]},"author":[{"full_name":"Martín-Belmonte, Alejandro","last_name":"Martín-Belmonte","first_name":"Alejandro"},{"last_name":"Aguado","full_name":"Aguado, Carolina","first_name":"Carolina"},{"first_name":"Rocío","full_name":"Alfaro-Ruíz, Rocío","last_name":"Alfaro-Ruíz"},{"last_name":"Moreno-Martínez","full_name":"Moreno-Martínez, Ana Esther","first_name":"Ana Esther"},{"full_name":"De La Ossa, Luis","last_name":"De La Ossa","first_name":"Luis"},{"last_name":"Martínez-Hernández","full_name":"Martínez-Hernández, José","first_name":"José"},{"first_name":"Alain","full_name":"Buisson, Alain","last_name":"Buisson"},{"last_name":"Früh","full_name":"Früh, Simon","first_name":"Simon"},{"last_name":"Bettler","full_name":"Bettler, Bernhard","first_name":"Bernhard"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"last_name":"Fukazawa","full_name":"Fukazawa, Yugo","first_name":"Yugo"},{"first_name":"Rafael","full_name":"Luján, Rafael","last_name":"Luján"}],"title":"Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer's disease","project":[{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270"},{"call_identifier":"H2020","_id":"26436750-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","grant_number":"785907"}],"publication_status":"published","publication_identifier":{"eissn":["17503639"],"issn":["10156305"]},"language":[{"iso":"eng"}],"file":[{"checksum":"549cc1b18f638a21d17a939ba5563fa9","file_id":"8554","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-09-22T09:47:19Z","file_name":"2020_BrainPathology_MartinBelmonte.pdf","date_updated":"2020-09-22T09:47:19Z","file_size":4220935,"creator":"dernst"}],"ec_funded":1,"volume":30,"issue":"3","abstract":[{"lang":"eng","text":"The hippocampus plays key roles in learning and memory and is a main target of Alzheimer's disease (AD), which causes progressive memory impairments. Despite numerous investigations about the processes required for the normal hippocampal functions, the neurotransmitter receptors involved in the synaptic deficits by which AD disables the hippocampus are not yet characterized. By combining histoblots, western blots, immunohistochemistry and high‐resolution immunoelectron microscopic methods for GABAB receptors, this study provides a quantitative description of the expression and the subcellular localization of GABAB1 in the hippocampus in a mouse model of AD at 1, 6 and 12 months of age. Western blots and histoblots showed that the total amount of protein and the laminar expression pattern of GABAB1 were similar in APP/PS1 mice and in age‐matched wild‐type mice. In contrast, immunoelectron microscopic techniques showed that the subcellular localization of GABAB1 subunit did not change significantly in APP/PS1 mice at 1 month of age, was significantly reduced in the stratum lacunosum‐moleculare of CA1 pyramidal cells at 6 months of age and significantly reduced at the membrane surface of CA1 pyramidal cells at 12 months of age. This reduction of plasma membrane GABAB1 was paralleled by a significant increase of the subunit at the intracellular sites. We further observed a decrease of membrane‐targeted GABAB receptors in axon terminals contacting CA1 pyramidal cells. Our data demonstrate compartment‐ and age‐dependent reduction of plasma membrane‐targeted GABAB receptors in the CA1 region of the hippocampus, suggesting that this decrease might be enough to alter the GABAB‐mediated synaptic transmission taking place in AD."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 30","month":"05","date_updated":"2023-09-06T14:48:01Z","ddc":["570"],"file_date_updated":"2020-09-22T09:47:19Z","department":[{"_id":"RySh"}],"_id":"7207","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public"},{"related_material":{"record":[{"status":"public","id":"13067","relation":"research_data"}]},"issue":"3","volume":33,"publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"publication_status":"published","file":[{"date_created":"2020-09-22T09:42:18Z","file_name":"2020_EvolBiology_Johannesson.pdf","date_updated":"2020-09-22T09:42:18Z","file_size":885611,"creator":"dernst","file_id":"8553","checksum":"7534ff0839709c0c5265c12d29432f03","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 33","abstract":[{"lang":"eng","text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females."}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"NiBa"}],"file_date_updated":"2020-09-22T09:42:18Z","date_updated":"2023-09-06T14:48:57Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7205","page":"342-351","doi":"10.1111/jeb.13570","date_published":"2020-03-01T00:00:00Z","date_created":"2019-12-22T23:00:43Z","isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Journal of Evolutionary Biology","quality_controlled":"1","publisher":"Wiley","oa":1,"author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Zuzanna","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"article_processing_charge":"No","external_id":{"pmid":["31724256"],"isi":["000500954800001"]},"title":"Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?","citation":{"mla":"Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology, vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:10.1111/jeb.13570.","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,” Journal of Evolutionary Biology, vol. 33, no. 3. Wiley, pp. 342–351, 2020.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 2020;33(3):342-351. doi:10.1111/jeb.13570","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13570","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology. Wiley, 2020. https://doi.org/10.1111/jeb.13570.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 33(3), 342–351."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"oa_version":"None","pmid":1,"abstract":[{"text":"Gastrulation entails specification and formation of three embryonic germ layers—ectoderm, mesoderm and endoderm—thereby establishing the basis for the future body plan. In zebrafish embryos, germ layer specification occurs during blastula and early gastrula stages (Ho & Kimmel, 1993), a period when the main morphogenetic movements underlying gastrulation are initiated. Hence, the signals driving progenitor cell fate specification, such as Nodal ligands from the TGF-β family, also play key roles in regulating germ layer progenitor cell segregation (Carmany-Rampey & Schier, 2001; David & Rosa, 2001; Feldman et al., 2000; Gritsman et al., 1999; Keller et al., 2008). In this review, we summarize and discuss the main signaling pathways involved in germ layer progenitor cell fate specification and segregation, specifically focusing on recent advances in understanding the interplay between mesoderm and endoderm specification and the internalization movements at the onset of zebrafish gastrulation.","lang":"eng"}],"intvolume":" 136","month":"06","scopus_import":"1","alternative_title":["Current Topics in Developmental Biology"],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00702153"]},"ec_funded":1,"volume":136,"_id":"7227","status":"public","type":"book_chapter","date_updated":"2023-09-06T14:54:36Z","department":[{"_id":"CaHe"}],"acknowledgement":"We thank Alexandra Schauer, Nicoletta Petridou and Feyza Nur Arslan for comments on the manuscript. Research in the Heisenberg laboratory is supported by an ERC Advanced Grant (MECSPEC 742573), ANR/FWF (I03601) and FWF/DFG (I03196) International Cooperation Grants. D. Pinheiro acknowledges a fellowship from EMBO ALTF (850-2017) and is currently supported by HFSP LTF (LT000429/2018-L2).","publisher":"Elsevier","quality_controlled":"1","publication":"Gastrulation: From Embryonic Pattern to Form","day":"01","year":"2020","isi":1,"date_created":"2020-01-05T23:00:46Z","date_published":"2020-06-01T00:00:00Z","doi":"10.1016/bs.ctdb.2019.10.009","page":"343-375","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"2646861A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Control of embryonic cleavage pattern","grant_number":"I03601"},{"_id":"2608FC64-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Control of epithelial cell layer spreading in zebrafish","grant_number":"I03196"},{"name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Nunes Pinheiro, Diana C., and Carl-Philipp J. Heisenberg. “Zebrafish Gastrulation: Putting Fate in Motion.” Gastrulation: From Embryonic Pattern to Form, vol. 136, Elsevier, 2020, pp. 343–75, doi:10.1016/bs.ctdb.2019.10.009.","apa":"Nunes Pinheiro, D. C., & Heisenberg, C.-P. J. (2020). Zebrafish gastrulation: Putting fate in motion. In Gastrulation: From Embryonic Pattern to Form (Vol. 136, pp. 343–375). Elsevier. https://doi.org/10.1016/bs.ctdb.2019.10.009","ama":"Nunes Pinheiro DC, Heisenberg C-PJ. Zebrafish gastrulation: Putting fate in motion. In: Gastrulation: From Embryonic Pattern to Form. Vol 136. Elsevier; 2020:343-375. doi:10.1016/bs.ctdb.2019.10.009","ieee":"D. C. Nunes Pinheiro and C.-P. J. Heisenberg, “Zebrafish gastrulation: Putting fate in motion,” in Gastrulation: From Embryonic Pattern to Form, vol. 136, Elsevier, 2020, pp. 343–375.","short":"D.C. Nunes Pinheiro, C.-P.J. Heisenberg, in:, Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 343–375.","chicago":"Nunes Pinheiro, Diana C, and Carl-Philipp J Heisenberg. “Zebrafish Gastrulation: Putting Fate in Motion.” In Gastrulation: From Embryonic Pattern to Form, 136:343–75. Elsevier, 2020. https://doi.org/10.1016/bs.ctdb.2019.10.009.","ista":"Nunes Pinheiro DC, Heisenberg C-PJ. 2020.Zebrafish gastrulation: Putting fate in motion. In: Gastrulation: From Embryonic Pattern to Form. Current Topics in Developmental Biology, vol. 136, 343–375."},"title":"Zebrafish gastrulation: Putting fate in motion","article_processing_charge":"No","external_id":{"isi":["000611830600013"],"pmid":["31959295"]},"author":[{"full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","last_name":"Nunes Pinheiro","first_name":"Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}]},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1559-2324"]},"publication_status":"published","volume":15,"issue":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development.","lang":"eng"}],"month":"01","intvolume":" 15","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154","open_access":"1"}],"date_updated":"2023-09-06T15:23:04Z","department":[{"_id":"JiFr"}],"_id":"7417","status":"public","article_type":"original","type":"journal_article","day":"01","publication":"Plant Signaling & Behavior","isi":1,"year":"2020","date_published":"2020-01-01T00:00:00Z","doi":"10.1080/15592324.2019.1687185","date_created":"2020-01-30T10:14:14Z","quality_controlled":"1","publisher":"Informa UK Limited","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior. Informa UK Limited, 2020. https://doi.org/10.1080/15592324.2019.1687185.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 15(1), e1687185.","mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:10.1080/15592324.2019.1687185.","apa":"Sinclair, S. A., Gille, S., Pauly, M., & Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. Informa UK Limited. https://doi.org/10.1080/15592324.2019.1687185","ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687185","short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling & Behavior 15 (2020).","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” Plant Signaling & Behavior, vol. 15, no. 1. Informa UK Limited, 2020."},"title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","author":[{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A","orcid":"0000-0002-4566-0593","full_name":"Sinclair, Scott A","last_name":"Sinclair"},{"first_name":"S.","full_name":"Gille, S.","last_name":"Gille"},{"first_name":"M.","last_name":"Pauly","full_name":"Pauly, M."},{"first_name":"U.","last_name":"Krämer","full_name":"Krämer, U."}],"article_processing_charge":"No","external_id":{"pmid":["31696770"],"isi":["000494907500001"]},"article_number":"e1687185"},{"file_date_updated":"2020-11-18T11:14:37Z","department":[{"_id":"LaEr"}],"ddc":["530","510"],"date_updated":"2023-09-07T12:54:12Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"6185","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6179"}]},"volume":378,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8771","checksum":"c3a683e2afdcea27afa6880b01e53dc2","file_size":2904574,"date_updated":"2020-11-18T11:14:37Z","creator":"dernst","file_name":"2020_CommMathPhysics_Erdoes.pdf","date_created":"2020-11-18T11:14:37Z"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"intvolume":" 378","month":"09","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969)."}],"title":"Cusp universality for random matrices I: Local law and the complex Hermitian case","external_id":{"isi":["000529483000001"],"arxiv":["1809.03971"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Erdös, László, et al. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics, vol. 378, Springer Nature, 2020, pp. 1203–78, doi:10.1007/s00220-019-03657-4.","ama":"Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 2020;378:1203-1278. doi:10.1007/s00220-019-03657-4","apa":"Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03657-4","short":"L. Erdös, T.H. Krüger, D.J. Schröder, Communications in Mathematical Physics 378 (2020) 1203–1278.","ieee":"L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices I: Local law and the complex Hermitian case,” Communications in Mathematical Physics, vol. 378. Springer Nature, pp. 1203–1278, 2020.","chicago":"Erdös, László, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-019-03657-4.","ista":"Erdös L, Krüger TH, Schröder DJ. 2020. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 378, 1203–1278."},"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"date_created":"2019-03-28T10:21:15Z","date_published":"2020-09-01T00:00:00Z","doi":"10.1007/s00220-019-03657-4","page":"1203-1278","publication":"Communications in Mathematical Physics","day":"01","year":"2020","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to Johannes Alt for numerous discussions on the Dyson equation and for his invaluable help in adjusting [10] to the needs of the present work."},{"file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"JaMa"}],"ddc":["510"],"date_updated":"2023-09-07T13:03:12Z","supervisor":[{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas"}],"status":"public","type":"dissertation","_id":"7629","ec_funded":1,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","file_id":"7657","date_updated":"2020-07-14T12:48:01Z","file_size":3297129,"creator":"dernst","date_created":"2020-04-14T10:47:59Z","file_name":"Thesis_Forkert_PDFA.pdf"},{"checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","file_id":"7658","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","date_created":"2020-04-14T10:47:59Z","file_name":"Thesis_Forkert_source.zip","date_updated":"2020-07-14T12:48:01Z","file_size":1063908,"creator":"dernst"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"03","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals.","lang":"eng"}],"title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","article_processing_charge":"No","author":[{"id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L","full_name":"Forkert, Dominik L","last_name":"Forkert"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629.","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629","apa":"Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629","mla":"Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629."},"project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-04-02T06:40:23Z","doi":"10.15479/AT:ISTA:7629","date_published":"2020-03-31T00:00:00Z","page":"154","day":"31","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria"},{"department":[{"_id":"NiBa"}],"file_date_updated":"2020-09-28T07:25:37Z","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"date_updated":"2023-09-07T13:11:39Z","ddc":["570"],"type":"dissertation","status":"public","_id":"8574","publication_identifier":{"eissn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"checksum":"20e71f015fbbd78fea708893ad634ed0","file_id":"8575","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-09-28T07:25:35Z","file_name":"thesis_EnikoSzep_final.pdf","date_updated":"2020-09-28T07:25:35Z","file_size":6354833,"creator":"dernst"},{"file_size":23020401,"date_updated":"2020-09-28T07:25:37Z","creator":"dernst","file_name":"thesisFiles_EnikoSzep.zip","date_created":"2020-09-28T07:25:37Z","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"a8de2c14a1bb4e53c857787efbb289e1","file_id":"8576"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. ","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","full_name":"Szep, Eniko"}],"article_processing_charge":"No","title":"Local adaptation in metapopulations","citation":{"chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574","apa":"Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"158","doi":"10.15479/AT:ISTA:8574","date_published":"2020-09-20T00:00:00Z","date_created":"2020-09-28T07:33:38Z","has_accepted_license":"1","year":"2020","day":"20","publisher":"Institute of Science and Technology Austria","oa":1},{"ddc":["510"],"supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:12:42Z","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:59Z","_id":"7514","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","file_id":"7515","creator":"dernst","file_size":1563429,"date_updated":"2020-07-14T12:47:59Z","file_name":"thesis.pdf","date_created":"2020-02-24T09:15:06Z"},{"checksum":"ad7425867b52d7d9e72296e87bc9cb67","file_id":"7516","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","date_created":"2020-02-24T09:15:16Z","file_name":"thesis_source.zip","date_updated":"2020-07-14T12:47:59Z","file_size":2028038,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"7524","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks.","lang":"eng"}],"month":"02","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","apa":"Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514","mla":"Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.","ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514."},"title":"The free energy of a dilute two-dimensional Bose gas","author":[{"id":"30C4630A-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Mayer","full_name":"Mayer, Simon"}],"article_processing_charge":"No","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"day":"24","has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:7514","date_published":"2020-02-24T00:00:00Z","date_created":"2020-02-24T09:17:27Z","page":"148","publisher":"Institute of Science and Technology Austria","oa":1},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"8284","status":"public"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"Thesis_Julia_Steiner_pdfA.pdf","date_created":"2020-09-09T14:22:35Z","file_size":117547589,"date_updated":"2021-09-16T12:40:56Z","creator":"jsteiner","checksum":"2388d7e6e7a4d364c096fa89f305c3de","file_id":"8354","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8355","checksum":"ba112f957b7145462d0ab79044873ee9","creator":"jsteiner","file_size":223328668,"date_updated":"2020-09-15T08:48:37Z","file_name":"Thesis_Julia_Steiner.docx","date_created":"2020-09-09T14:23:25Z"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"oa_version":"None","department":[{"_id":"LeSa"}],"file_date_updated":"2021-09-16T12:40:56Z","date_updated":"2023-09-07T13:14:09Z","supervisor":[{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"ddc":["572"],"type":"dissertation","status":"public","_id":"8353","page":"191","date_created":"2020-09-09T14:27:01Z","date_published":"2020-09-09T00:00:00Z","doi":"10.15479/AT:ISTA:8353","year":"2020","has_accepted_license":"1","day":"09","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","article_processing_charge":"No","author":[{"first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","full_name":"Steiner, Julia","orcid":"0000-0003-0493-3775","last_name":"Steiner"}],"title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","citation":{"mla":"Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8353.","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353","apa":"Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8353.","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","grant_number":"24741"}]},{"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-09-30T14:50:20Z","file_name":"2020_Han_Thesis.docx","date_updated":"2020-09-30T14:50:20Z","file_size":49198118,"creator":"dernst","file_id":"8590","checksum":"c4bda1947d4c09c428ac9ce667b02327","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"},{"creator":"dernst","date_updated":"2021-10-01T13:33:02Z","file_size":15513963,"date_created":"2020-09-30T14:49:59Z","file_name":"2020_Han_Thesis.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8591","checksum":"3f4f5d1718c2230adf30639ecaf8a00b"}],"related_material":{"record":[{"status":"public","id":"7643","relation":"part_of_dissertation"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","date_updated":"2023-09-07T13:13:05Z","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"ddc":["580"],"department":[{"_id":"JiFr"}],"file_date_updated":"2021-10-01T13:33:02Z","_id":"8589","type":"dissertation","status":"public","year":"2020","has_accepted_license":"1","day":"30","page":"164","date_created":"2020-09-30T14:50:51Z","date_published":"2020-09-30T00:00:00Z","doi":"10.15479/AT:ISTA:8589","acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589.","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589","apa":"Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","mla":"Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han"}],"title":"Novel insights into PIN polarity regulation during Arabidopsis development"},{"acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"31","publication":"eLife","date_published":"2020-07-31T00:00:00Z","doi":"10.7554/eLife.59407","date_created":"2020-08-24T06:24:04Z","article_number":"e59407","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"citation":{"chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.59407.","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407.","mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife Sciences Publications, 2020, doi:10.7554/eLife.59407.","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications, 2020.","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","apa":"Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.59407","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Steiner","full_name":"Steiner, Julia","orcid":"0000-0003-0493-3775","first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000562123600001"],"pmid":["32735215"]},"article_processing_charge":"No","title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"abstract":[{"text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 9","publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","file":[{"file_size":7320493,"date_updated":"2020-08-24T13:31:53Z","creator":"cziletti","file_name":"2020_eLife_Steiner.pdf","date_created":"2020-08-24T13:31:53Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8289","checksum":"b3656d14d5ddbb9d26e3074eea2d0c15"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8353"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage"}]},"volume":9,"_id":"8284","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-07T13:14:08Z","ddc":["570"],"department":[{"_id":"LeSa"}],"file_date_updated":"2020-08-24T13:31:53Z"},{"_id":"8155","type":"dissertation","status":"public","date_updated":"2023-09-07T13:13:27Z","supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"ddc":["530","570"],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-30T13:04:55Z","abstract":[{"text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8176","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","date_created":"2020-07-27T12:00:07Z","creator":"rgrah","file_size":16638998,"date_updated":"2020-07-27T12:00:07Z"},{"file_id":"8177","content_type":"application/zip","access_level":"closed","relation":"main_file","date_created":"2020-07-27T12:02:23Z","file_name":"Thesis_new.zip","date_updated":"2020-07-30T13:04:55Z","file_size":347459978,"creator":"rgrah"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7675","status":"public"},{"relation":"part_of_dissertation","id":"7569","status":"public"},{"status":"public","id":"7652","relation":"part_of_dissertation"}]},"project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"citation":{"short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155","ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","mla":"Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"}],"title":"Gene regulation across scales – how biophysical constraints shape evolution","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2020","has_accepted_license":"1","day":"24","page":"310","date_created":"2020-07-23T09:51:28Z","doi":"10.15479/AT:ISTA:8155","date_published":"2020-07-24T00:00:00Z"},{"department":[{"_id":"JiFr"}],"date_updated":"2023-09-07T13:13:04Z","status":"public","article_type":"letter_note","type":"journal_article","_id":"7643","ec_funded":1,"issue":"5","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8589"}]},"volume":183,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"intvolume":" 183","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.20.00212"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","title":"SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism","article_processing_charge":"No","external_id":{"pmid":["32107280"],"isi":["000536641800018"]},"author":[{"full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana","last_name":"Rakusova","full_name":"Rakusova, Hana"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten"},{"orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Han, Huibin, Hana Rakusova, Inge Verstraeten, Yuzhou Zhang, and Jiří Friml. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00212.","ista":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. 2020. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 183(5), 37–40.","mla":"Han, Huibin, et al. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology, vol. 183, no. 5, American Society of Plant Biologists, 2020, pp. 37–40, doi:10.1104/pp.20.00212.","ama":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 2020;183(5):37-40. doi:10.1104/pp.20.00212","apa":"Han, H., Rakusova, H., Verstraeten, I., Zhang, Y., & Friml, J. (2020). SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00212","ieee":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, and J. Friml, “SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism,” Plant Physiology, vol. 183, no. 5. American Society of Plant Biologists, pp. 37–40, 2020.","short":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40."},"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"date_created":"2020-04-06T10:06:40Z","date_published":"2020-05-08T00:00:00Z","doi":"10.1104/pp.20.00212","page":"37-40","publication":"Plant Physiology","day":"08","year":"2020","isi":1,"oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship). "},{"month":"04","main_file_link":[{"url":"https://doi.org/10.1101/2020.04.08.029405 ","open_access":"1"}],"oa":1,"publisher":"Cold Spring Harbor Laboratory","oa_version":"Preprint","abstract":[{"text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.","lang":"eng"}],"date_created":"2020-04-23T10:12:51Z","date_published":"2020-04-09T00:00:00Z","doi":"10.1101/2020.04.08.029405","related_material":{"record":[{"relation":"dissertation_contains","id":"8155","status":"public"}]},"publication":"bioRxiv","language":[{"iso":"eng"}],"day":"09","year":"2020","publication_status":"published","project":[{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"status":"public","type":"preprint","_id":"7675","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Normative models of enhancer function","article_processing_charge":"No","author":[{"last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.","ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.08.029405","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405.","ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, 10.1101/2020.04.08.029405."},"date_updated":"2023-09-07T13:13:26Z"},{"month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"record":[{"status":"public","id":"6608","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"file_id":"7461","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"thesis_ist-final_noack.pdf","date_created":"2020-02-06T14:43:54Z","creator":"koelsboe","file_size":76195184,"date_updated":"2020-07-14T12:47:58Z"},{"file_id":"7462","checksum":"7a52383c812b0be64d3826546509e5a4","description":"latex source files, figures","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","date_created":"2020-02-06T14:52:45Z","file_name":"latex-files.zip","date_updated":"2020-07-14T12:47:58Z","file_size":122103715,"creator":"koelsboe"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","_id":"7460","file_date_updated":"2020-07-14T12:47:58Z","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"ddc":["514"],"date_updated":"2023-09-07T13:15:30Z","supervisor":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2020-02-06T14:56:53Z","date_published":"2020-02-10T00:00:00Z","doi":"10.15479/AT:ISTA:7460","page":"155","day":"10","year":"2020","has_accepted_license":"1","title":"The hole system of triangulated shapes","article_processing_charge":"No","author":[{"first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4672-8297","full_name":"Ölsböck, Katharina","last_name":"Ölsböck"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460."}}]