[{"arxiv":1,"oa_version":"Preprint","doi":"10.48550/arXiv.2306.07109","day":"13","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"GeKa"},{"_id":"M-Shop"}],"author":[{"full_name":"Valentini, Marco","last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","full_name":"Sagi, Oliver","last_name":"Sagi"},{"last_name":"Baghumyan","full_name":"Baghumyan, Levon","first_name":"Levon"},{"last_name":"Gijsel","full_name":"Gijsel, Thijs de","first_name":"Thijs de"},{"first_name":"Jason","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","full_name":"Jung, Jason","last_name":"Jung"},{"last_name":"Calcaterra","full_name":"Calcaterra, Stefano","first_name":"Stefano"},{"last_name":"Ballabio","full_name":"Ballabio, Andrea","first_name":"Andrea"},{"first_name":"Juan Aguilera","last_name":"Servin","full_name":"Servin, Juan Aguilera"},{"first_name":"Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","orcid":"0000-0001-9985-9293","full_name":"Aggarwal, Kushagra","last_name":"Aggarwal"},{"id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","full_name":"Janik, Marian","last_name":"Janik"},{"first_name":"Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","full_name":"Adletzberger, Thomas","last_name":"Adletzberger"},{"last_name":"Souto","full_name":"Souto, Rubén Seoane","first_name":"Rubén Seoane"},{"first_name":"Martin","full_name":"Leijnse, Martin","last_name":"Leijnse"},{"first_name":"Jeroen","last_name":"Danon","full_name":"Danon, Jeroen"},{"full_name":"Schrade, Constantin","last_name":"Schrade","first_name":"Constantin"},{"first_name":"Erik","last_name":"Bakkers","full_name":"Bakkers, Erik"},{"last_name":"Chrastina","full_name":"Chrastina, Daniel","first_name":"Daniel"},{"last_name":"Isella","full_name":"Isella, Giovanni","first_name":"Giovanni"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"year":"2023","type":"preprint","citation":{"short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.A. Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.S. Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","apa":"Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra, S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2306.07109\">https://doi.org/10.48550/arXiv.2306.07109</a>","ieee":"M. Valentini <i>et al.</i>, “Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas,” <i>arXiv</i>. .","ama":"Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2306.07109\">10.48550/arXiv.2306.07109</a>","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving  Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2306.07109\">https://doi.org/10.48550/arXiv.2306.07109</a>.","mla":"Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving  Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” <i>ArXiv</i>, 2306.07109, doi:<a href=\"https://doi.org/10.48550/arXiv.2306.07109\">10.48550/arXiv.2306.07109</a>.","ista":"Valentini M, Sagi O, Baghumyan L, Gijsel T de, Jung J, Calcaterra S, Ballabio A, Servin JA, Aggarwal K, Janik M, Adletzberger T, Souto RS, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas. arXiv, 2306.07109."},"ddc":["530"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"status":"public","publication_status":"submitted","abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing\r\ninterest in the past years. Superconducting electronics aims to complement\r\nsemiconductor technology, while hybrid architectures are at the forefront of\r\nnew ideas such as topological superconductivity and protected qubits. In this\r\nwork, we engineer the induced superconductivity in two-dimensional germanium\r\nhole gas by varying the distance between the quantum well and the aluminum. We\r\ndemonstrate a hard superconducting gap and realize an electrically and flux\r\ntunable superconducting diode using a superconducting quantum interference\r\ndevice (SQUID). This allows to tune the current phase relation (CPR), to a\r\nregime where single Cooper pair tunneling is suppressed, creating a $ \\sin\r\n\\left( 2 \\varphi \\right)$ CPR. Shapiro experiments complement this\r\ninterpretation and the microwave drive allows to create a diode with $ \\approx\r\n100 \\%$ efficiency. The reported results open up the path towards monolithic\r\nintegration of spin qubit devices, microwave resonators and (protected)\r\nsuperconducting qubits on a silicon technology compatible platform.","lang":"eng"}],"publication":"arXiv","date_created":"2023-07-26T11:17:20Z","external_id":{"arxiv":["2306.07109"]},"project":[{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices"},{"name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507"},{"grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","name":"Conventional and unconventional topological superconductors"},{"_id":"bd5b4ec5-d553-11ed-ba76-a6eedb083344","name":"Protected states of quantum matter"}],"_id":"13312","month":"06","date_updated":"2024-02-07T07:52:32Z","title":"Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas","ec_funded":1,"date_published":"2023-06-13T00:00:00Z","article_processing_charge":"No","keyword":["Mesoscale and Nanoscale Physics"],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13286"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.07109"}],"acknowledgement":"The authors acknowledge Alexander Brinkmann, Alessandro Crippa, Andrew Higginbotham, Andrea Iorio, Giordano\r\nScappucci and Christian Schonenberger for helpful discussions. We thank Marcel Verheijen for the support in the\r\nTEM analysis. This research and related results were made\r\npossible with the support of the NOMIS Foundation. It was\r\nsupported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the\r\nnanofabrication facility, the European Union’s Horizon 2020\r\nresearch and innovation programme under Grant Agreement\r\nNo 862046, the HORIZON-RIA 101069515 project and the\r\nFWF Projects #P-32235, #P-36507 and #F-8606. R.S.S.\r\nacknowledges Spanish CM “Talento Program” Project No.\r\n2022-T1/IND-24070.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"article_number":"2306.07109"},{"quality_controlled":"1","abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division."}],"publication_status":"published","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ddc":["530"],"article_type":"original","file":[{"date_created":"2024-01-30T14:28:30Z","creator":"dernst","file_id":"14916","access_level":"open_access","success":1,"file_name":"2023_NaturePhysics_Dunajova.pdf","file_size":22471673,"date_updated":"2024-01-30T14:28:30Z","content_type":"application/pdf","checksum":"bc7673ca07d37309013a86166577b2f7","relation":"main_file"}],"type":"journal_article","citation":{"ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments. Nature Physics. 19, 1916–1926.","mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:<a href=\"https://doi.org/10.1038/s41567-023-02218-w\">10.1038/s41567-023-02218-w</a>.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. <i>Nature Physics</i>. 2023;19:1916-1926. doi:<a href=\"https://doi.org/10.1038/s41567-023-02218-w\">10.1038/s41567-023-02218-w</a>","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02218-w\">https://doi.org/10.1038/s41567-023-02218-w</a>.","ieee":"Z. Dunajova <i>et al.</i>, “Chiral and nematic phases of flexible active filaments,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1916–1926, 2023.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02218-w\">https://doi.org/10.1038/s41567-023-02218-w</a>"},"author":[{"full_name":"Dunajova, Zuzana","last_name":"Dunajova","first_name":"Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87"},{"id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze","last_name":"Prats Mateu","full_name":"Prats Mateu, Batirtze"},{"last_name":"Radler","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Keesiang","full_name":"Lim, Keesiang","last_name":"Lim"},{"id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","first_name":"Dörte","full_name":"Brandis, Dörte","last_name":"Brandis"},{"last_name":"Velicky","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"},{"first_name":"Richard W.","full_name":"Wong, Richard W.","last_name":"Wong"},{"full_name":"Elgeti, Jens","last_name":"Elgeti","first_name":"Jens"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"year":"2023","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","day":"01","doi":"10.1038/s41567-023-02218-w","oa_version":"Published Version","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        19","oa":1,"volume":19,"related_material":{"record":[{"id":"13116","relation":"research_data","status":"public"}]},"scopus_import":"1","date_published":"2023-12-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"title":"Chiral and nematic phases of flexible active filaments","date_updated":"2024-02-21T12:19:08Z","month":"12","_id":"13314","project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360","name":"Motile active matter models of migrating cells and chiral filaments"}],"date_created":"2023-07-27T14:44:45Z","external_id":{"pmid":["38075437"]},"file_date_updated":"2024-01-30T14:28:30Z","publication":"Nature Physics","page":"1916-1926"},{"day":"25","publisher":"National Academy of Sciences","oa_version":"Published Version","doi":"10.1073/pnas.2302028120","year":"2023","author":[{"last_name":"Barbier","full_name":"Barbier, Jean","first_name":"Jean"},{"first_name":"Francesco","last_name":"Camilli","full_name":"Camilli, Francesco"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"last_name":"Sáenz","full_name":"Sáenz, Manuel","first_name":"Manuel"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"MaMo"}],"publication_identifier":{"eissn":["1091-6490"]},"article_type":"original","ddc":["000"],"type":"journal_article","citation":{"ieee":"J. Barbier, F. Camilli, M. Mondelli, and M. Sáenz, “Fundamental limits in structured principal component analysis and how to reach them,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 30. National Academy of Sciences, 2023.","short":"J. Barbier, F. Camilli, M. Mondelli, M. Sáenz, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","apa":"Barbier, J., Camilli, F., Mondelli, M., &#38; Sáenz, M. (2023). Fundamental limits in structured principal component analysis and how to reach them. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2302028120\">https://doi.org/10.1073/pnas.2302028120</a>","mla":"Barbier, Jean, et al. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 30, e2302028120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2302028120\">10.1073/pnas.2302028120</a>.","ista":"Barbier J, Camilli F, Mondelli M, Sáenz M. 2023. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 120(30), e2302028120.","chicago":"Barbier, Jean, Francesco Camilli, Marco Mondelli, and Manuel Sáenz. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2302028120\">https://doi.org/10.1073/pnas.2302028120</a>.","ama":"Barbier J, Camilli F, Mondelli M, Sáenz M. Fundamental limits in structured principal component analysis and how to reach them. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(30). doi:<a href=\"https://doi.org/10.1073/pnas.2302028120\">10.1073/pnas.2302028120</a>"},"file":[{"checksum":"1fc06228afdb3aa80cf8e7766bcf9dc5","relation":"main_file","file_size":995933,"content_type":"application/pdf","date_updated":"2023-07-31T07:30:48Z","file_name":"2023_PNAS_Barbier.pdf","access_level":"open_access","success":1,"file_id":"13323","creator":"dernst","date_created":"2023-07-31T07:30:48Z"}],"quality_controlled":"1","pmid":1,"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"text":"How do statistical dependencies in measurement noise influence high-dimensional inference? To answer this, we study the paradigmatic spiked matrix model of principal components analysis (PCA), where a rank-one matrix is corrupted by additive noise. We go beyond the usual independence assumption on the noise entries, by drawing the noise from a low-order polynomial orthogonal matrix ensemble. The resulting noise correlations make the setting relevant for applications but analytically challenging. We provide characterization of the Bayes optimal limits of inference in this model. If the spike is rotation invariant, we show that standard spectral PCA is optimal. However, for more general priors, both PCA and the existing approximate message-passing algorithm (AMP) fall short of achieving the information-theoretic limits, which we compute using the replica method from statistical physics. We thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer equations, which is empirically observed to saturate the conjectured theoretical limit. This AMP comes with a rigorous state evolution analysis tracking its performance. Although we focus on specific noise distributions, our methodology can be generalized to a wide class of trace matrix ensembles at the cost of more involved expressions. Finally, despite the seemingly strong assumption of rotation-invariant noise, our theory empirically predicts algorithmic performance on real data, pointing at strong universality properties.","lang":"eng"}],"external_id":{"pmid":["37463204"]},"date_created":"2023-07-30T22:01:02Z","_id":"13315","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","file_date_updated":"2023-07-31T07:30:48Z","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-07-25T00:00:00Z","month":"07","title":"Fundamental limits in structured principal component analysis and how to reach them","date_updated":"2024-09-10T13:03:18Z","scopus_import":"1","intvolume":"       120","oa":1,"issue":"30","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"J.B. was funded by the European Union (ERC, CHORAL, project number 101039794). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. M.M. was supported by the 2019 Lopez-Loreta Prize. We would like to thank the reviewers for the insightful comments and, in particular, for suggesting the BAMP-inspired denoisers leading to AMP-AP.","article_number":"e2302028120","related_material":{"link":[{"relation":"software","url":"https://github.com/fcamilli95/Structured-PCA-"}]},"volume":120},{"year":"2023","author":[{"last_name":"Toshima","full_name":"Toshima, Junko Y.","first_name":"Junko Y."},{"first_name":"Ayana","last_name":"Tsukahara","full_name":"Tsukahara, Ayana"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"first_name":"Takuro","last_name":"Tojima","full_name":"Tojima, Takuro"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nakano, Akihiko","last_name":"Nakano","first_name":"Akihiko"},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"isi":1,"department":[{"_id":"DaSi"}],"publication_identifier":{"eissn":["2050-084X"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"eLife Sciences Publications","day":"21","doi":"10.7554/eLife.84850","oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN.","lang":"eng"}],"publication_status":"published","status":"public","pmid":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"ddc":["570"],"article_type":"original","file":[{"checksum":"2af111a00cf5e3a956f7f0fd13199b15","relation":"main_file","content_type":"application/pdf","date_updated":"2023-07-31T07:43:00Z","file_size":11980913,"file_name":"2023_eLife_Toshima.pdf","success":1,"access_level":"open_access","file_id":"13324","date_created":"2023-07-31T07:43:00Z","creator":"dernst"}],"citation":{"apa":"Toshima, J. Y., Tsukahara, A., Nagano, M., Tojima, T., Siekhaus, D. E., Nakano, A., &#38; Toshima, J. (2023). The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.84850\">https://doi.org/10.7554/eLife.84850</a>","short":"J.Y. Toshima, A. Tsukahara, M. Nagano, T. Tojima, D.E. Siekhaus, A. Nakano, J. Toshima, ELife 12 (2023).","ieee":"J. Y. Toshima <i>et al.</i>, “The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2023.","chicago":"Toshima, Junko Y., Ayana Tsukahara, Makoto Nagano, Takuro Tojima, Daria E Siekhaus, Akihiko Nakano, and Jiro Toshima. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” <i>ELife</i>. eLife Sciences Publications, 2023. <a href=\"https://doi.org/10.7554/eLife.84850\">https://doi.org/10.7554/eLife.84850</a>.","ama":"Toshima JY, Tsukahara A, Nagano M, et al. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. <i>eLife</i>. 2023;12. doi:<a href=\"https://doi.org/10.7554/eLife.84850\">10.7554/eLife.84850</a>","ista":"Toshima JY, Tsukahara A, Nagano M, Tojima T, Siekhaus DE, Nakano A, Toshima J. 2023. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 12, e84850.","mla":"Toshima, Junko Y., et al. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” <i>ELife</i>, vol. 12, e84850, eLife Sciences Publications, 2023, doi:<a href=\"https://doi.org/10.7554/eLife.84850\">10.7554/eLife.84850</a>."},"type":"journal_article","article_processing_charge":"Yes","date_published":"2023-07-21T00:00:00Z","title":"The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network","date_updated":"2023-12-13T11:37:36Z","month":"07","_id":"13316","external_id":{"pmid":["37477116"],"isi":["001035372800001"]},"date_created":"2023-07-30T22:01:02Z","publication":"eLife","file_date_updated":"2023-07-31T07:43:00Z","article_number":"e84850","intvolume":"        12","oa":1,"acknowledgement":"This work was supported by JSPS KAKENHI grant #18K062291, and the Takeda Science Foundation to JYT., as well as JSPS KAKENHI grant #19K065710, the Takeda Science Foundation, and Life Science Foundation of Japan to JT.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":12,"scopus_import":"1"},{"scopus_import":"1","oa":1,"intvolume":"       190","issue":"7","acknowledgement":"LE, JH, and VR were supported by ERC Advanced Grant “RMTBeyond” No. 101020331. SS was supported by KAKENHI Grant Number JP22J14935 from the Japan Society for the Promotion of Science (JSPS) and Forefront Physics and Mathematics Program to Drive Transformation (FoPM), a World-leading Innovative Graduate Study (WINGS) Program, the University of Tokyo.\r\nOpen access funding provided by The University of Tokyo.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"128","volume":190,"external_id":{"isi":["001035677200002"],"arxiv":["2304.04213"]},"date_created":"2023-07-30T22:01:02Z","_id":"13317","project":[{"call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"publication":"Journal of Statistical Physics","file_date_updated":"2023-07-31T07:49:31Z","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","date_published":"2023-07-21T00:00:00Z","month":"07","date_updated":"2023-12-13T11:38:44Z","title":"Eigenstate thermalisation hypothesis for translation invariant spin systems","article_type":"original","ddc":["510","530"],"type":"journal_article","citation":{"short":"S. Sugimoto, S.J. Henheik, V. Riabov, L. Erdös, Journal of Statistical Physics 190 (2023).","apa":"Sugimoto, S., Henheik, S. J., Riabov, V., &#38; Erdös, L. (2023). Eigenstate thermalisation hypothesis for translation invariant spin systems. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-023-03132-4\">https://doi.org/10.1007/s10955-023-03132-4</a>","ieee":"S. Sugimoto, S. J. Henheik, V. Riabov, and L. Erdös, “Eigenstate thermalisation hypothesis for translation invariant spin systems,” <i>Journal of Statistical Physics</i>, vol. 190, no. 7. Springer Nature, 2023.","chicago":"Sugimoto, Shoki, Sven Joscha Henheik, Volodymyr Riabov, and László Erdös. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” <i>Journal of Statistical Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s10955-023-03132-4\">https://doi.org/10.1007/s10955-023-03132-4</a>.","ama":"Sugimoto S, Henheik SJ, Riabov V, Erdös L. Eigenstate thermalisation hypothesis for translation invariant spin systems. <i>Journal of Statistical Physics</i>. 2023;190(7). doi:<a href=\"https://doi.org/10.1007/s10955-023-03132-4\">10.1007/s10955-023-03132-4</a>","mla":"Sugimoto, Shoki, et al. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” <i>Journal of Statistical Physics</i>, vol. 190, no. 7, 128, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s10955-023-03132-4\">10.1007/s10955-023-03132-4</a>.","ista":"Sugimoto S, Henheik SJ, Riabov V, Erdös L. 2023. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 190(7), 128."},"file":[{"checksum":"c2ef6b2aecfee1ad6d03fab620507c2c","relation":"main_file","file_size":612755,"content_type":"application/pdf","date_updated":"2023-07-31T07:49:31Z","file_name":"2023_JourStatPhysics_Sugimoto.pdf","access_level":"open_access","success":1,"file_id":"13325","date_created":"2023-07-31T07:49:31Z","creator":"dernst"}],"quality_controlled":"1","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"abstract":[{"text":"We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction.","lang":"eng"}],"publication_status":"published","day":"21","publisher":"Springer Nature","oa_version":"Published Version","arxiv":1,"doi":"10.1007/s10955-023-03132-4","year":"2023","author":[{"full_name":"Sugimoto, Shoki","last_name":"Sugimoto","first_name":"Shoki"},{"first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X","last_name":"Henheik"},{"first_name":"Volodymyr","id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","last_name":"Riabov","full_name":"Riabov, Volodymyr"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"}],"isi":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"department":[{"_id":"LaEr"}]},{"project":[{"_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","grant_number":"M03337","name":"Curvature-dimension in noncommutative analysis"}],"_id":"13318","external_id":{"arxiv":["2210.14468"],"isi":["001035665500001"]},"date_created":"2023-07-30T22:01:03Z","publication":"Mathematische Annalen","article_processing_charge":"No","date_published":"2023-07-24T00:00:00Z","date_updated":"2023-12-13T11:36:20Z","title":"Noncommutative Bohnenblust–Hille inequalities","month":"07","scopus_import":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The research of A.V. is supported by NSF DMS-1900286, DMS-2154402 and by Hausdorff Center for Mathematics. H.Z. is supported by the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. This work is partially supported by NSF DMS-1929284 while both authors were in residence at the Institute for Computational and Experimental Research in Mathematics in Providence, RI, during the Harmonic Analysis and Convexity program.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00208-023-02680-0"}],"publisher":"Springer Nature","day":"24","doi":"10.1007/s00208-023-02680-0","oa_version":"Published Version","arxiv":1,"year":"2023","author":[{"first_name":"Alexander","full_name":"Volberg, Alexander","last_name":"Volberg"},{"id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","first_name":"Haonan","full_name":"Zhang, Haonan","last_name":"Zhang"}],"isi":1,"department":[{"_id":"JaMa"}],"publication_identifier":{"issn":["0025-5831"],"eissn":["1432-1807"]},"article_type":"original","type":"journal_article","citation":{"ieee":"A. Volberg and H. Zhang, “Noncommutative Bohnenblust–Hille inequalities,” <i>Mathematische Annalen</i>. Springer Nature, 2023.","short":"A. Volberg, H. Zhang, Mathematische Annalen (2023).","apa":"Volberg, A., &#38; Zhang, H. (2023). Noncommutative Bohnenblust–Hille inequalities. <i>Mathematische Annalen</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00208-023-02680-0\">https://doi.org/10.1007/s00208-023-02680-0</a>","ista":"Volberg A, Zhang H. 2023. Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen.","mla":"Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.” <i>Mathematische Annalen</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00208-023-02680-0\">10.1007/s00208-023-02680-0</a>.","chicago":"Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.” <i>Mathematische Annalen</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00208-023-02680-0\">https://doi.org/10.1007/s00208-023-02680-0</a>.","ama":"Volberg A, Zhang H. Noncommutative Bohnenblust–Hille inequalities. <i>Mathematische Annalen</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s00208-023-02680-0\">10.1007/s00208-023-02680-0</a>"},"quality_controlled":"1","publication_status":"epub_ahead","abstract":[{"lang":"eng","text":"Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free constants that grow subexponentially in the degree (Defant et al. in Math Ann 374(1):653–680, 2019). Such inequalities have found great applications in learning low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum Boolean functions, 2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894). In this paper, we give a new proof of these Bohnenblust–Hille inequalities for qubit system with constants that are dimension-free and of exponential growth in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials. Using similar ideas, we also study learning problems of low degree quantum observables and Bohr’s radius phenomenon on quantum Boolean cubes."}],"status":"public","language":[{"iso":"eng"}]},{"author":[{"full_name":"Vernooij, Matthijs","last_name":"Vernooij","first_name":"Matthijs"},{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","first_name":"Melchior","last_name":"Wirth","full_name":"Wirth, Melchior","orcid":"0000-0002-0519-4241"}],"isi":1,"year":"2023","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"JaMa"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"day":"01","publisher":"Springer Nature","arxiv":1,"oa_version":"Published Version","doi":"10.1007/s00220-023-04795-6","quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"We prove that the generator of the L2 implementation of a KMS-symmetric quantum Markov semigroup can be expressed as the square of a derivation with values in a Hilbert bimodule, extending earlier results by Cipriani and Sauvageot for tracially symmetric semigroups and the second-named author for GNS-symmetric semigroups. This result hinges on the introduction of a new completely positive map on the algebra of bounded operators on the GNS Hilbert space. This transformation maps symmetric Markov operators to symmetric Markov operators and is essential to obtain the required inner product on the Hilbert bimodule."}],"publication_status":"published","article_type":"original","ddc":["510"],"type":"journal_article","citation":{"ieee":"M. Vernooij and M. Wirth, “Derivations and KMS-symmetric quantum Markov semigroups,” <i>Communications in Mathematical Physics</i>, vol. 403. Springer Nature, pp. 381–416, 2023.","apa":"Vernooij, M., &#38; Wirth, M. (2023). Derivations and KMS-symmetric quantum Markov semigroups. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-023-04795-6\">https://doi.org/10.1007/s00220-023-04795-6</a>","short":"M. Vernooij, M. Wirth, Communications in Mathematical Physics 403 (2023) 381–416.","ista":"Vernooij M, Wirth M. 2023. Derivations and KMS-symmetric quantum Markov semigroups. Communications in Mathematical Physics. 403, 381–416.","mla":"Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric Quantum Markov Semigroups.” <i>Communications in Mathematical Physics</i>, vol. 403, Springer Nature, 2023, pp. 381–416, doi:<a href=\"https://doi.org/10.1007/s00220-023-04795-6\">10.1007/s00220-023-04795-6</a>.","chicago":"Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric Quantum Markov Semigroups.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00220-023-04795-6\">https://doi.org/10.1007/s00220-023-04795-6</a>.","ama":"Vernooij M, Wirth M. Derivations and KMS-symmetric quantum Markov semigroups. <i>Communications in Mathematical Physics</i>. 2023;403:381-416. doi:<a href=\"https://doi.org/10.1007/s00220-023-04795-6\">10.1007/s00220-023-04795-6</a>"},"file":[{"file_name":"2023_CommMathPhysics_Vernooij.pdf","success":1,"access_level":"open_access","relation":"main_file","checksum":"cca204e81891270216a0c84eb8bcd398","content_type":"application/pdf","date_updated":"2024-01-30T12:15:11Z","file_size":481209,"date_created":"2024-01-30T12:15:11Z","creator":"dernst","file_id":"14905"}],"date_published":"2023-10-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","month":"10","date_updated":"2024-01-30T12:16:32Z","title":"Derivations and KMS-symmetric quantum Markov semigroups","date_created":"2023-07-30T22:01:03Z","external_id":{"arxiv":["2303.15949"],"isi":["001033655400002"]},"project":[{"name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","grant_number":"ESP156_N"}],"_id":"13319","page":"381-416","file_date_updated":"2024-01-30T12:15:11Z","publication":"Communications in Mathematical Physics","acknowledgement":"The authors are grateful to Martijn Caspers for helpful comments on a preliminary version of this manuscript. M. V. was supported by the NWO Vidi grant VI.Vidi.192.018 ‘Non-commutative harmonic analysis and rigidity of operator algebras’. M. W. was funded by the Austrian Science Fund (FWF) under the Esprit Programme [ESP 156]. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Open access funding provided by Austrian Science Fund (FWF).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"       403","volume":403,"scopus_import":"1"},{"date_created":"2023-07-30T22:01:04Z","external_id":{"isi":["001031733100053"],"arxiv":["2212.01572"]},"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"_id":"13321","page":"294-298","publication":"2023 IEEE Information Theory Workshop","date_published":"2023-05-01T00:00:00Z","article_processing_charge":"No","month":"05","title":"Approximate message passing for multi-layer estimation in rotationally invariant models","date_updated":"2024-09-10T13:03:19Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Marco Mondelli was partially supported by the 2019 Lopez-Loreta prize.","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.01572"}],"day":"01","publisher":"Institute of Electrical and Electronics Engineers","oa_version":"Preprint","arxiv":1,"doi":"10.1109/ITW55543.2023.10160238","author":[{"last_name":"Xu","full_name":"Xu, Yizhou","first_name":"Yizhou"},{"last_name":"Hou","full_name":"Hou, Tian Qi","first_name":"Tian Qi"},{"first_name":"Shan Suo","last_name":"Liang","full_name":"Liang, Shan Suo"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli"}],"isi":1,"year":"2023","conference":{"name":"ITW: Information Theory Workshop","end_date":"2023-04-28","location":"Saint-Malo, France","start_date":"2023-04-23"},"publication_identifier":{"eissn":["2475-4218"],"isbn":["9798350301496"]},"department":[{"_id":"MaMo"}],"type":"conference","citation":{"mla":"Xu, Yizhou, et al. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” <i>2023 IEEE Information Theory Workshop</i>, Institute of Electrical and Electronics Engineers, 2023, pp. 294–98, doi:<a href=\"https://doi.org/10.1109/ITW55543.2023.10160238\">10.1109/ITW55543.2023.10160238</a>.","ista":"Xu Y, Hou TQ, Liang SS, Mondelli M. 2023. Approximate message passing for multi-layer estimation in rotationally invariant models. 2023 IEEE Information Theory Workshop. ITW: Information Theory Workshop, 294–298.","chicago":"Xu, Yizhou, Tian Qi Hou, Shan Suo Liang, and Marco Mondelli. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” In <i>2023 IEEE Information Theory Workshop</i>, 294–98. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/ITW55543.2023.10160238\">https://doi.org/10.1109/ITW55543.2023.10160238</a>.","ama":"Xu Y, Hou TQ, Liang SS, Mondelli M. Approximate message passing for multi-layer estimation in rotationally invariant models. In: <i>2023 IEEE Information Theory Workshop</i>. Institute of Electrical and Electronics Engineers; 2023:294-298. doi:<a href=\"https://doi.org/10.1109/ITW55543.2023.10160238\">10.1109/ITW55543.2023.10160238</a>","ieee":"Y. Xu, T. Q. Hou, S. S. Liang, and M. Mondelli, “Approximate message passing for multi-layer estimation in rotationally invariant models,” in <i>2023 IEEE Information Theory Workshop</i>, Saint-Malo, France, 2023, pp. 294–298.","short":"Y. Xu, T.Q. Hou, S.S. Liang, M. Mondelli, in:, 2023 IEEE Information Theory Workshop, Institute of Electrical and Electronics Engineers, 2023, pp. 294–298.","apa":"Xu, Y., Hou, T. Q., Liang, S. S., &#38; Mondelli, M. (2023). Approximate message passing for multi-layer estimation in rotationally invariant models. In <i>2023 IEEE Information Theory Workshop</i> (pp. 294–298). Saint-Malo, France: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/ITW55543.2023.10160238\">https://doi.org/10.1109/ITW55543.2023.10160238</a>"},"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm.","lang":"eng"}],"publication_status":"published"},{"related_material":{"record":[{"id":"12680","status":"public","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Master's Thesis"],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"26","supervisor":[{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"file_date_updated":"2023-08-03T15:28:55Z","date_created":"2023-07-31T10:20:55Z","_id":"13331","month":"07","title":"Exterior algebra and combinatorics","date_updated":"2023-10-04T11:54:56Z","article_processing_charge":"No","date_published":"2023-07-31T00:00:00Z","citation":{"ieee":"S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology Austria, 2023.","apa":"Köse, S. (2023). <i>Exterior algebra and combinatorics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13331\">https://doi.org/10.15479/at:ista:13331</a>","short":"S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology Austria, 2023.","ista":"Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and Technology Austria.","mla":"Köse, Seyda. <i>Exterior Algebra and Combinatorics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13331\">10.15479/at:ista:13331</a>.","chicago":"Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13331\">https://doi.org/10.15479/at:ista:13331</a>.","ama":"Köse S. Exterior algebra and combinatorics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13331\">10.15479/at:ista:13331</a>"},"type":"dissertation","file":[{"creator":"skoese","date_created":"2023-07-31T10:16:32Z","file_id":"13333","file_name":"Exterior Algebra and Combinatorics.zip","access_level":"closed","relation":"source_file","checksum":"96ee518d796d02af71395622c45de03c","file_size":28684,"content_type":"application/x-zip-compressed","date_updated":"2023-07-31T10:16:32Z"},{"access_level":"open_access","success":1,"file_name":"thesis-pdfa.pdf","file_size":4953418,"date_updated":"2023-08-03T15:28:55Z","content_type":"application/pdf","checksum":"f610f4713f88bc477de576aaa46b114e","relation":"main_file","creator":"skoese","date_created":"2023-08-03T15:28:55Z","file_id":"13480"}],"ddc":["510","516"],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"abstract":[{"text":"The extension of extremal combinatorics to the setting of exterior algebra is a work\r\nin progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.\r\n","lang":"eng"}],"publication_status":"published","oa_version":"Published Version","doi":"10.15479/at:ista:13331","day":"31","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2791-4585"]},"department":[{"_id":"GradSch"},{"_id":"UlWa"}],"degree_awarded":"MS","year":"2023","author":[{"full_name":"Köse, Seyda","last_name":"Köse","first_name":"Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb"}]},{"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"13258"}]},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8059564","open_access":"1"}],"ddc":["000"],"citation":{"mla":"Kleshnina, Maria. <i>Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8059564\">10.5281/ZENODO.8059564</a>.","ista":"Kleshnina M. 2023. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8059564\">10.5281/ZENODO.8059564</a>.","ama":"Kleshnina M. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8059564\">10.5281/ZENODO.8059564</a>","chicago":"Kleshnina, Maria. “Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8059564\">https://doi.org/10.5281/ZENODO.8059564</a>.","ieee":"M. Kleshnina, “kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games.” Zenodo, 2023.","short":"M. Kleshnina, (2023).","apa":"Kleshnina, M. (2023). kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8059564\">https://doi.org/10.5281/ZENODO.8059564</a>"},"type":"research_data_reference","article_processing_charge":"No","year":"2023","date_published":"2023-06-20T00:00:00Z","author":[{"first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","last_name":"Kleshnina","full_name":"Kleshnina, Maria"}],"month":"06","department":[{"_id":"KrCh"}],"date_updated":"2025-07-14T09:09:53Z","title":"kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games","day":"20","date_created":"2023-07-31T11:30:46Z","publisher":"Zenodo","_id":"13336","oa_version":"Published Version","doi":"10.5281/ZENODO.8059564"},{"article_type":"original","citation":{"ama":"Gemen J, Church JR, Ruoko T-P, et al. Disequilibrating azoarenes by visible-light sensitization under confinement. <i>Science</i>. 2023;381(6664):1357-1363. doi:<a href=\"https://doi.org/10.1126/science.adh9059\">10.1126/science.adh9059</a>","chicago":"Gemen, Julius, Jonathan R. Church, Tero-Petri Ruoko, Nikita Durandin, Michał J. Białek, Maren Weissenfels, Moran Feller, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adh9059\">https://doi.org/10.1126/science.adh9059</a>.","ista":"Gemen J, Church JR, Ruoko T-P, Durandin N, Białek MJ, Weissenfels M, Feller M, Kazes M, Borin VA, Odaybat M, Kalepu R, Diskin-Posner Y, Oron D, Fuchter MJ, Priimagi A, Schapiro I, Klajn R. 2023. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 381(6664), 1357–1363.","mla":"Gemen, Julius, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” <i>Science</i>, vol. 381, no. 6664, American Association for the Advancement of Science, 2023, pp. 1357–63, doi:<a href=\"https://doi.org/10.1126/science.adh9059\">10.1126/science.adh9059</a>.","short":"J. Gemen, J.R. Church, T.-P. Ruoko, N. Durandin, M.J. Białek, M. Weissenfels, M. Feller, M. Kazes, V.A. Borin, M. Odaybat, R. Kalepu, Y. Diskin-Posner, D. Oron, M.J. Fuchter, A. Priimagi, I. Schapiro, R. Klajn, Science 381 (2023) 1357–1363.","apa":"Gemen, J., Church, J. R., Ruoko, T.-P., Durandin, N., Białek, M. J., Weissenfels, M., … Klajn, R. (2023). Disequilibrating azoarenes by visible-light sensitization under confinement. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adh9059\">https://doi.org/10.1126/science.adh9059</a>","ieee":"J. Gemen <i>et al.</i>, “Disequilibrating azoarenes by visible-light sensitization under confinement,” <i>Science</i>, vol. 381, no. 6664. American Association for the Advancement of Science, pp. 1357–1363, 2023."},"type":"journal_article","quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host–photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation."}],"status":"public","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","day":"22","doi":"10.1126/science.adh9059","oa_version":"Preprint","year":"2023","author":[{"last_name":"Gemen","full_name":"Gemen, Julius","first_name":"Julius"},{"last_name":"Church","full_name":"Church, Jonathan R.","first_name":"Jonathan R."},{"first_name":"Tero-Petri","full_name":"Ruoko, Tero-Petri","last_name":"Ruoko"},{"first_name":"Nikita","full_name":"Durandin, Nikita","last_name":"Durandin"},{"full_name":"Białek, Michał J.","last_name":"Białek","first_name":"Michał J."},{"last_name":"Weissenfels","full_name":"Weissenfels, Maren","first_name":"Maren"},{"first_name":"Moran","last_name":"Feller","full_name":"Feller, Moran"},{"first_name":"Miri","full_name":"Kazes, Miri","last_name":"Kazes"},{"last_name":"Borin","full_name":"Borin, Veniamin A.","first_name":"Veniamin A."},{"full_name":"Odaybat, Magdalena","last_name":"Odaybat","first_name":"Magdalena"},{"first_name":"Rishir","last_name":"Kalepu","full_name":"Kalepu, Rishir"},{"first_name":"Yael","last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael"},{"last_name":"Oron","full_name":"Oron, Dan","first_name":"Dan"},{"last_name":"Fuchter","full_name":"Fuchter, Matthew J.","first_name":"Matthew J."},{"first_name":"Arri","full_name":"Priimagi, Arri","last_name":"Priimagi"},{"first_name":"Igor","last_name":"Schapiro","full_name":"Schapiro, Igor"},{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"publication_identifier":{"eissn":["1095-9203"]},"department":[{"_id":"RaKl"}],"scopus_import":"1","oa":1,"intvolume":"       381","acknowledgement":"We acknowledge funding from the European Union’s Horizon 2020 Research and Innovation Program [European Research Council grants 820008 (Ra.K.) and 101045223 (A.P.) and Marie Skłodowska-Curie grants 812868 (J.G.) and 101022777 (T.-P.R.)], the Academy of Finland [Center of Excellence Programme LIBER grant 346107 (A.P.), Flagship Programme PREIN grant 320165 (A.P.), and Postdoctoral Researcher grant 340103 (T.-P.R.)], Zuckerman STEM Leadership Program Fellowship (J.R.C.), President’s PhD Scholarship (M.O.), and the EPSRC [Established Career Fellowship grant EP/R00188X/1 (M.J.F.)].","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6664","main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv-2023-gq2h0","open_access":"1"}],"volume":381,"_id":"13340","date_created":"2023-08-01T08:26:15Z","publication":"Science","page":"1357-1363","article_processing_charge":"No","date_published":"2023-09-22T00:00:00Z","date_updated":"2023-10-03T08:11:26Z","title":"Disequilibrating azoarenes by visible-light sensitization under confinement","month":"09"},{"article_number":"e114557","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Christoph Mayr and Bingzhi Wang for initial experiments on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry, EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry, and the Animal Core Facility of the Biomedical Center (BMC) for excellent support. This study was supported by the Peter Hans Hofschneider Professorship of the foundation “Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to JR), and the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled and organized by Projekt DEAL.","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","date_published":"2023-11-21T00:00:00Z","title":"Adaptive pathfinding by nucleokinesis during amoeboid migration","date_updated":"2023-11-27T08:47:45Z","month":"11","_id":"13342","external_id":{"pmid":["37987147"]},"date_created":"2023-08-01T08:59:06Z","publication":"EMBO Journal","file_date_updated":"2023-11-27T08:45:56Z","quality_controlled":"1","abstract":[{"text":"Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoeba<jats:italic>Dictyostelium discoideum</jats:italic>, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease.","lang":"eng"}],"publication_status":"published","pmid":1,"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"ddc":["570"],"article_type":"original","file":[{"checksum":"6261d0041c7e8d284c39712c40079730","relation":"main_file","file_size":4862497,"date_updated":"2023-11-27T08:45:56Z","content_type":"application/pdf","file_name":"2023_EmboJournal_Kroll.pdf","access_level":"open_access","success":1,"file_id":"14611","date_created":"2023-11-27T08:45:56Z","creator":"dernst"}],"citation":{"mla":"Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” <i>EMBO Journal</i>, e114557, Embo Press, 2023, doi:<a href=\"https://doi.org/10.15252/embj.2023114557\">10.15252/embj.2023114557</a>.","ista":"Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal., e114557.","chicago":"Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” <i>EMBO Journal</i>. Embo Press, 2023. <a href=\"https://doi.org/10.15252/embj.2023114557\">https://doi.org/10.15252/embj.2023114557</a>.","ama":"Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis during amoeboid migration. <i>EMBO Journal</i>. 2023. doi:<a href=\"https://doi.org/10.15252/embj.2023114557\">10.15252/embj.2023114557</a>","ieee":"J. Kroll <i>et al.</i>, “Adaptive pathfinding by nucleokinesis during amoeboid migration,” <i>EMBO Journal</i>. Embo Press, 2023.","short":"J. Kroll, R. Hauschild, A. Kuznetcov, K. Stefanowski, M.D. Hermann, J. Merrin, L.B. Shafeek, A. Müller-Taubenberger, J. Renkawitz, EMBO Journal (2023).","apa":"Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin, J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid migration. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2023114557\">https://doi.org/10.15252/embj.2023114557</a>"},"type":"journal_article","year":"2023","author":[{"full_name":"Kroll, Janina","last_name":"Kroll","first_name":"Janina"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"full_name":"Kuznetcov, Arthur","last_name":"Kuznetcov","first_name":"Arthur"},{"full_name":"Stefanowski, Kasia","last_name":"Stefanowski","first_name":"Kasia"},{"first_name":"Monika D.","full_name":"Hermann, Monika D.","last_name":"Hermann"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"last_name":"Shafeek","orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B","first_name":"Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Müller-Taubenberger, Annette","last_name":"Müller-Taubenberger","first_name":"Annette"},{"last_name":"Renkawitz","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"department":[{"_id":"NanoFab"},{"_id":"Bio"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"Embo Press","day":"21","doi":"10.15252/embj.2023114557","oa_version":"Published Version"},{"main_file_link":[{"url":"https://arxiv.org/abs/2006.02356","open_access":"1"}],"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/when-is-necessary-sufficient/","relation":"press_release"}]},"volume":197,"oa":1,"intvolume":"       197","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","publication":"Annals of Mathematics","page":"1115-1203","_id":"8682","external_id":{"isi":["000966611000003"],"arxiv":["2006.02356"],"oaworkID":["w3033938593"]},"date_created":"2020-10-19T14:28:50Z","title":"The Hasse principle for random Fano hypersurfaces","date_updated":"2025-08-11T11:59:49Z","month":"05","article_processing_charge":"No","date_published":"2023-05-01T00:00:00Z","type":"journal_article","citation":{"ama":"Browning TD, Boudec PL, Sawin W. The Hasse principle for random Fano hypersurfaces. <i>Annals of Mathematics</i>. 2023;197(3):1115-1203. doi:<a href=\"https://doi.org/10.4007/annals.2023.197.3.3\">10.4007/annals.2023.197.3.3</a>","chicago":"Browning, Timothy D, Pierre Le Boudec, and Will Sawin. “The Hasse Principle for Random Fano Hypersurfaces.” <i>Annals of Mathematics</i>. Princeton University, 2023. <a href=\"https://doi.org/10.4007/annals.2023.197.3.3\">https://doi.org/10.4007/annals.2023.197.3.3</a>.","ista":"Browning TD, Boudec PL, Sawin W. 2023. The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. 197(3), 1115–1203.","mla":"Browning, Timothy D., et al. “The Hasse Principle for Random Fano Hypersurfaces.” <i>Annals of Mathematics</i>, vol. 197, no. 3, Princeton University, 2023, pp. 1115–203, doi:<a href=\"https://doi.org/10.4007/annals.2023.197.3.3\">10.4007/annals.2023.197.3.3</a>.","short":"T.D. Browning, P.L. Boudec, W. Sawin, Annals of Mathematics 197 (2023) 1115–1203.","apa":"Browning, T. D., Boudec, P. L., &#38; Sawin, W. (2023). The Hasse principle for random Fano hypersurfaces. <i>Annals of Mathematics</i>. Princeton University. <a href=\"https://doi.org/10.4007/annals.2023.197.3.3\">https://doi.org/10.4007/annals.2023.197.3.3</a>","ieee":"T. D. Browning, P. L. Boudec, and W. Sawin, “The Hasse principle for random Fano hypersurfaces,” <i>Annals of Mathematics</i>, vol. 197, no. 3. Princeton University, pp. 1115–1203, 2023."},"article_type":"original","abstract":[{"text":"It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces.","lang":"eng"}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.4007/annals.2023.197.3.3","oa_version":"Preprint","arxiv":1,"publisher":"Princeton University","day":"01","department":[{"_id":"TiBr"}],"publication_identifier":{"issn":["0003-486X"]},"year":"2023","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning"},{"last_name":"Boudec","full_name":"Boudec, Pierre Le","first_name":"Pierre Le"},{"last_name":"Sawin","full_name":"Sawin, Will","first_name":"Will"}],"isi":1},{"_id":"9034","date_created":"2021-01-22T09:31:09Z","external_id":{"arxiv":["1901.08503"],"isi":["000773116000001"]},"publication":"International Mathematics Research Notices","page":"6780-6808","date_published":"2023-04-01T00:00:00Z","article_processing_charge":"No","title":"Integral points of bounded height on a log Fano threefold","date_updated":"2023-08-01T12:23:55Z","month":"04","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","issue":"8","oa":1,"intvolume":"      2023","volume":2023,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.08503"}],"publisher":"Oxford Academic","day":"01","doi":"10.1093/imrn/rnac048","arxiv":1,"oa_version":"Preprint","isi":1,"author":[{"first_name":"Florian Alexander","id":"560601DA-8D36-11E9-A136-7AC1E5697425","orcid":"0000-0001-7302-8256","full_name":"Wilsch, Florian Alexander","last_name":"Wilsch"}],"year":"2023","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"department":[{"_id":"TiBr"}],"article_type":"original","type":"journal_article","citation":{"short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. <i>International Mathematics Research Notices</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/imrn/rnac048\">https://doi.org/10.1093/imrn/rnac048</a>","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” <i>International Mathematics Research Notices</i>, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023.","ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. <i>International Mathematics Research Notices</i>. 2023;2023(8):6780-6808. doi:<a href=\"https://doi.org/10.1093/imrn/rnac048\">10.1093/imrn/rnac048</a>","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” <i>International Mathematics Research Notices</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/imrn/rnac048\">https://doi.org/10.1093/imrn/rnac048</a>.","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” <i>International Mathematics Research Notices</i>, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:<a href=\"https://doi.org/10.1093/imrn/rnac048\">10.1093/imrn/rnac048</a>.","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808."},"quality_controlled":"1","abstract":[{"lang":"eng","text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors."}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public"},{"quality_controlled":"1","publication_status":"published","abstract":[{"text":"Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic astroglial processes and plays major roles in synaptic transmission. We have previously found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent glutamine release to sustain physiological synaptic transmissions and cognitiogns. However, whether Cx43 is important for the release of synaptic vesicles, which is a critical component of synaptic efficacy, remains unanswered. Here, using transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate whether and how astrocytes regulate the release of synaptic vesicles from hippocampal synapses. We report that CA1 pyramidal neurons and their synapses develop normally in the absence of astroglial Cx43. However, a significant impairment in synaptic vesicle distribution and release dynamics were observed. In particular, the FM1-43 assays performed using two-photon live imaging and combined with multi-electrode array stimulation in acute hippocampal slices, revealed a slower rate of synaptic vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that synaptic vesicle release probability was also reduced and is dependent on glutamine supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for Cx43 in regulating presynaptic functions by controlling the rate and probability of synaptic vesicle release. Our findings further highlight the significance of astroglial Cx43 in synaptic transmission and efficacy.","lang":"eng"}],"language":[{"iso":"eng"}],"pmid":1,"has_accepted_license":"1","status":"public","ddc":["570"],"article_type":"original","file":[{"date_created":"2024-01-16T09:26:52Z","creator":"dernst","file_id":"14808","file_name":"2023_Cells_Cheung.pdf","access_level":"open_access","success":1,"checksum":"6798cd75d8857976fbc58a43fd173d68","relation":"main_file","file_size":7931643,"content_type":"application/pdf","date_updated":"2024-01-16T09:26:52Z"}],"type":"journal_article","citation":{"ama":"Cheung GT, Chever O, Rollenhagen A, et al. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. <i>Cells</i>. 2023;12(8). doi:<a href=\"https://doi.org/10.3390/cells12081133\">10.3390/cells12081133</a>","chicago":"Cheung, Giselle T, Oana Chever, Astrid Rollenhagen, Nicole Quenech’du, Pascal Ezan, Joachim H. R. Lübke, and Nathalie Rouach. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” <i>Cells</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/cells12081133\">https://doi.org/10.3390/cells12081133</a>.","ista":"Cheung GT, Chever O, Rollenhagen A, Quenech’du N, Ezan P, Lübke JHR, Rouach N. 2023. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 12(8), 1133.","mla":"Cheung, Giselle T., et al. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” <i>Cells</i>, vol. 12, no. 8, 1133, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/cells12081133\">10.3390/cells12081133</a>.","apa":"Cheung, G. T., Chever, O., Rollenhagen, A., Quenech’du, N., Ezan, P., Lübke, J. H. R., &#38; Rouach, N. (2023). Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells12081133\">https://doi.org/10.3390/cells12081133</a>","short":"G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke, N. Rouach, Cells 12 (2023).","ieee":"G. T. Cheung <i>et al.</i>, “Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses,” <i>Cells</i>, vol. 12, no. 8. MDPI, 2023."},"isi":1,"author":[{"orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T"},{"first_name":"Oana","last_name":"Chever","full_name":"Chever, Oana"},{"last_name":"Rollenhagen","full_name":"Rollenhagen, Astrid","first_name":"Astrid"},{"full_name":"Quenech’du, Nicole","last_name":"Quenech’du","first_name":"Nicole"},{"last_name":"Ezan","full_name":"Ezan, Pascal","first_name":"Pascal"},{"full_name":"Lübke, Joachim H. R.","last_name":"Lübke","first_name":"Joachim H. R."},{"last_name":"Rouach","full_name":"Rouach, Nathalie","first_name":"Nathalie"}],"year":"2023","publication_identifier":{"issn":["2073-4409"]},"department":[{"_id":"SiHi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"MDPI","day":"11","doi":"10.3390/cells12081133","oa_version":"Published Version","article_number":"1133","acknowledgement":"This research was funded by grants from the European Research Council (Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R., as well as from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development (grant #622289) to G.C. We thank Elena Dossi, Grégory Ghézali, and Jérémie Teillon for support with setting up the MEA system for the two-photon microscope. We would also like to thank Tayfun Palaz for their technical assistance with the EM preparations.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"8","intvolume":"        12","oa":1,"volume":12,"date_published":"2023-04-11T00:00:00Z","article_processing_charge":"Yes","keyword":["General Medicine"],"title":"Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses","date_updated":"2024-01-16T09:29:35Z","month":"04","_id":"14783","date_created":"2024-01-10T09:46:35Z","external_id":{"pmid":["37190042"],"isi":["000977445700001"]},"file_date_updated":"2024-01-16T09:26:52Z","publication":"Cells"},{"keyword":["Multidisciplinary"],"article_processing_charge":"Yes","date_published":"2023-08-25T00:00:00Z","date_updated":"2024-01-16T09:38:58Z","title":"Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells","month":"08","_id":"14784","external_id":{"pmid":["37624890"],"isi":["001054596800007"]},"date_created":"2024-01-10T09:48:01Z","publication":"Science Advances","file_date_updated":"2024-01-16T09:35:28Z","article_number":"adg1610","intvolume":"         9","oa":1,"issue":"34","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by a postdoctoral fellowship from the Swedish Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W., a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the program of fundamental research (theme 65.1) of the Institute for Biomedical Problems of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K., D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB) to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation, and Karolinska Institutet to L.S.W.","volume":9,"year":"2023","isi":1,"author":[{"last_name":"Gallardo-Dodd","full_name":"Gallardo-Dodd, Carlos J.","first_name":"Carlos J."},{"first_name":"Christian","full_name":"Oertlin, Christian","last_name":"Oertlin"},{"first_name":"Julien","full_name":"Record, Julien","last_name":"Record"},{"last_name":"Galvani","full_name":"Galvani, Rômulo G.","first_name":"Rômulo G."},{"last_name":"Sommerauer","full_name":"Sommerauer, Christian","first_name":"Christian"},{"last_name":"Kuznetsov","full_name":"Kuznetsov, Nikolai V.","first_name":"Nikolai V."},{"full_name":"Doukoumopoulos, Evangelos","last_name":"Doukoumopoulos","first_name":"Evangelos"},{"last_name":"Ali","full_name":"Ali, Liaqat","first_name":"Liaqat"},{"last_name":"Oliveira","full_name":"Oliveira, Mariana M. S.","first_name":"Mariana M. S."},{"full_name":"Seitz, Christina","last_name":"Seitz","first_name":"Christina"},{"full_name":"Percipalle, Mathias","last_name":"Percipalle","first_name":"Mathias","id":"45adb726-eb97-11eb-a6c2-c7c3d3caabe9"},{"first_name":"Tijana","full_name":"Nikić, Tijana","last_name":"Nikić"},{"first_name":"Anastasia A.","last_name":"Sadova","full_name":"Sadova, Anastasia A."},{"first_name":"Sofia M.","full_name":"Shulgina, Sofia M.","last_name":"Shulgina"},{"first_name":"Vjacheslav A.","last_name":"Shmarov","full_name":"Shmarov, Vjacheslav A."},{"last_name":"Kutko","full_name":"Kutko, Olga V.","first_name":"Olga V."},{"last_name":"Vlasova","full_name":"Vlasova, Daria D.","first_name":"Daria D."},{"first_name":"Kseniya D.","full_name":"Orlova, Kseniya D.","last_name":"Orlova"},{"first_name":"Marina P.","last_name":"Rykova","full_name":"Rykova, Marina P."},{"full_name":"Andersson, John","last_name":"Andersson","first_name":"John"},{"last_name":"Percipalle","full_name":"Percipalle, Piergiorgio","first_name":"Piergiorgio"},{"first_name":"Claudia","full_name":"Kutter, Claudia","last_name":"Kutter"},{"first_name":"Sergey A.","last_name":"Ponomarev","full_name":"Ponomarev, Sergey A."},{"last_name":"Westerberg","full_name":"Westerberg, Lisa S.","first_name":"Lisa S."}],"publication_identifier":{"issn":["2375-2548"]},"department":[{"_id":"FlSc"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"American Association for the Advancement of Science","day":"25","doi":"10.1126/sciadv.adg1610","oa_version":"Published Version","quality_controlled":"1","publication_status":"published","abstract":[{"text":"The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.","lang":"eng"}],"has_accepted_license":"1","status":"public","pmid":1,"language":[{"iso":"eng"}],"ddc":["570"],"article_type":"original","file":[{"date_created":"2024-01-16T09:35:28Z","creator":"dernst","file_id":"14809","file_name":"2023_ScienceAdvances_GallardoDodd.pdf","success":1,"access_level":"open_access","relation":"main_file","checksum":"b9072e20e2d5d9d34d2c53319bafee41","content_type":"application/pdf","date_updated":"2024-01-16T09:35:28Z","file_size":1596639}],"citation":{"ieee":"C. J. Gallardo-Dodd <i>et al.</i>, “Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells,” <i>Science Advances</i>, vol. 9, no. 34. American Association for the Advancement of Science, 2023.","apa":"Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer, C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adg1610\">https://doi.org/10.1126/sciadv.adg1610</a>","short":"C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V. Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova, K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev, L.S. Westerberg, Science Advances 9 (2023).","ista":"Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 9(34), adg1610.","mla":"Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” <i>Science Advances</i>, vol. 9, no. 34, adg1610, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.adg1610\">10.1126/sciadv.adg1610</a>.","ama":"Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. <i>Science Advances</i>. 2023;9(34). doi:<a href=\"https://doi.org/10.1126/sciadv.adg1610\">10.1126/sciadv.adg1610</a>","chicago":"Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani, Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.adg1610\">https://doi.org/10.1126/sciadv.adg1610</a>."},"type":"journal_article"},{"language":[{"iso":"eng"}],"pmid":1,"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid‐encoded genes is similar to that of chromosome‐encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two <jats:italic>Synechocystis</jats:italic> sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited."}],"publication_status":"published","quality_controlled":"1","type":"journal_article","citation":{"chicago":"Nies, Fabian, Tanita Wein, Dustin M. Hanke, Benjamin L Springstein, Jaime Alcorta, Claudia Taubenheim, and Tal Dagan. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” <i>Environmental Microbiology Reports</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/1758-2229.13203\">https://doi.org/10.1111/1758-2229.13203</a>.","ama":"Nies F, Wein T, Hanke DM, et al. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. <i>Environmental Microbiology Reports</i>. 2023;15(6):656-668. doi:<a href=\"https://doi.org/10.1111/1758-2229.13203\">10.1111/1758-2229.13203</a>","mla":"Nies, Fabian, et al. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” <i>Environmental Microbiology Reports</i>, vol. 15, no. 6, Wiley, 2023, pp. 656–68, doi:<a href=\"https://doi.org/10.1111/1758-2229.13203\">10.1111/1758-2229.13203</a>.","ista":"Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. 2023. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 15(6), 656–668.","short":"F. Nies, T. Wein, D.M. Hanke, B.L. Springstein, J. Alcorta, C. Taubenheim, T. Dagan, Environmental Microbiology Reports 15 (2023) 656–668.","apa":"Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim, C., &#38; Dagan, T. (2023). Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. <i>Environmental Microbiology Reports</i>. Wiley. <a href=\"https://doi.org/10.1111/1758-2229.13203\">https://doi.org/10.1111/1758-2229.13203</a>","ieee":"F. Nies <i>et al.</i>, “Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803,” <i>Environmental Microbiology Reports</i>, vol. 15, no. 6. Wiley, pp. 656–668, 2023."},"file":[{"creator":"dernst","date_created":"2024-01-16T09:42:10Z","file_id":"14810","success":1,"access_level":"open_access","file_name":"2023_EnvirMicroBiolReports_Nies.pdf","date_updated":"2024-01-16T09:42:10Z","content_type":"application/pdf","file_size":1518350,"relation":"main_file","checksum":"d09ebb68fee61f4e2e09ec286c9cf1d3"}],"article_type":"original","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["1758-2229"]},"department":[{"_id":"MaLo"}],"author":[{"full_name":"Nies, Fabian","last_name":"Nies","first_name":"Fabian"},{"first_name":"Tanita","last_name":"Wein","full_name":"Wein, Tanita"},{"full_name":"Hanke, Dustin M.","last_name":"Hanke","first_name":"Dustin M."},{"last_name":"Springstein","orcid":"0000-0002-3461-5391","full_name":"Springstein, Benjamin L","first_name":"Benjamin L","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083"},{"first_name":"Jaime","full_name":"Alcorta, Jaime","last_name":"Alcorta"},{"first_name":"Claudia","last_name":"Taubenheim","full_name":"Taubenheim, Claudia"},{"first_name":"Tal","last_name":"Dagan","full_name":"Dagan, Tal"}],"isi":1,"year":"2023","oa_version":"Published Version","doi":"10.1111/1758-2229.13203","day":"01","publisher":"Wiley","volume":15,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank the lab of Francisco Javier Florencio Bel-lido, Sevilla, Spain for supplying theSynechocystislabtype Sevilla used in this work and the lab of MartinHagemann, Rostock, Germany for supplying the pIGAplasmidusedinthiswork.WethankNilsHülterforfruitful discussions. We thank Fenna Stücker forgraphical illustrations and Katrin Schumann, FennaStücker,  and  Lidusha  Manivannan  for  technicalsupport.\r\nChilean National Agency for Research andDevelopment (ANID), Grant/Award Number:21191763; DeutscheForschungsgemeinschaft, Grant/AwardNumbers: 456882089, RTG2501; EuropeanResearch Council (ERC), Grant/AwardNumber: 101043835","issue":"6","oa":1,"intvolume":"        15","month":"12","date_updated":"2024-01-16T09:46:12Z","title":"Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803","date_published":"2023-12-01T00:00:00Z","keyword":["Agricultural and Biological Sciences (miscellaneous)","Ecology","Evolution","Behavior and Systematics"],"article_processing_charge":"Yes (in subscription journal)","page":"656-668","file_date_updated":"2024-01-16T09:42:10Z","publication":"Environmental Microbiology Reports","date_created":"2024-01-10T10:41:07Z","external_id":{"pmid":["37794696"],"isi":["001080203100001"]},"_id":"14785"},{"article_processing_charge":"No","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"date_published":"2023-08-20T00:00:00Z","title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS","date_updated":"2024-01-16T10:04:57Z","month":"08","_id":"14786","external_id":{"isi":["001002645100001"],"pmid":["37169189"]},"date_created":"2024-01-10T10:43:08Z","publication":"Science of The Total Environment","article_number":"164010","intvolume":"       887","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors thank the Czech Science Foundation (project No. 19-28399X) and the Czech Academy of Sciences (RVO: 60077344) and are sincerely grateful to the Bordeaux Imaging Centre (member of the France BioImaging national infrastructure, ANR-10-INBS-04) for help with TEM and to members of the Laboratory of Biological Effects of Metals and Laboratory of Aquaculture and Pathology of Aquatic Organisms (Ruđer Bošković Institute, Croatia) for the assistance with fieldwork.","volume":887,"year":"2023","isi":1,"author":[{"first_name":"Vlatka","full_name":"Filipović Marijić, Vlatka","last_name":"Filipović Marijić"},{"full_name":"Subirana, Maria Angels","last_name":"Subirana","first_name":"Maria Angels"},{"full_name":"Schaumlöffel, Dirk","last_name":"Schaumlöffel","first_name":"Dirk"},{"last_name":"Barišić","full_name":"Barišić, Josip","first_name":"Josip"},{"full_name":"Gontier, Etienne","last_name":"Gontier","first_name":"Etienne"},{"full_name":"Krasnici, Nesrete","last_name":"Krasnici","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","first_name":"Nesrete"},{"full_name":"Mijošek, Tatjana","last_name":"Mijošek","first_name":"Tatjana"},{"first_name":"Jesús S.","last_name":"Hernández-Orts","full_name":"Hernández-Orts, Jesús S."},{"full_name":"Scholz, Tomáš","last_name":"Scholz","first_name":"Tomáš"},{"full_name":"Erk, Marijana","last_name":"Erk","first_name":"Marijana"}],"department":[{"_id":"LifeSc"}],"publication_identifier":{"issn":["0048-9697"]},"publisher":"Elsevier","day":"20","doi":"10.1016/j.scitotenv.2023.164010","oa_version":"None","quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species."}],"pmid":1,"status":"public","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Filipović Marijić, Vlatka, Maria Angels Subirana, Dirk Schaumlöffel, Josip Barišić, Etienne Gontier, Nesrete Krasnici, Tatjana Mijošek, Jesús S. Hernández-Orts, Tomáš Scholz, and Marijana Erk. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” <i>Science of The Total Environment</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">https://doi.org/10.1016/j.scitotenv.2023.164010</a>.","ama":"Filipović Marijić V, Subirana MA, Schaumlöffel D, et al. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. <i>Science of The Total Environment</i>. 2023;887. doi:<a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">10.1016/j.scitotenv.2023.164010</a>","mla":"Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” <i>Science of The Total Environment</i>, vol. 887, 164010, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">10.1016/j.scitotenv.2023.164010</a>.","ista":"Filipović Marijić V, Subirana MA, Schaumlöffel D, Barišić J, Gontier E, Krasnici N, Mijošek T, Hernández-Orts JS, Scholz T, Erk M. 2023. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 887, 164010.","apa":"Filipović Marijić, V., Subirana, M. A., Schaumlöffel, D., Barišić, J., Gontier, E., Krasnici, N., … Erk, M. (2023). First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. <i>Science of The Total Environment</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">https://doi.org/10.1016/j.scitotenv.2023.164010</a>","short":"V. Filipović Marijić, M.A. Subirana, D. Schaumlöffel, J. Barišić, E. Gontier, N. Krasnici, T. Mijošek, J.S. Hernández-Orts, T. Scholz, M. Erk, Science of The Total Environment 887 (2023).","ieee":"V. Filipović Marijić <i>et al.</i>, “First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS,” <i>Science of The Total Environment</i>, vol. 887. Elsevier, 2023."},"type":"journal_article"},{"year":"2023","isi":1,"author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Madeline A.","full_name":"Chase, Madeline A.","last_name":"Chase"},{"full_name":"McIntosh, Hanna","last_name":"McIntosh","first_name":"Hanna"},{"last_name":"Streisfeld","full_name":"Streisfeld, Matthew A.","first_name":"Matthew A."}],"department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"day":"01","publisher":"Wiley","oa_version":"Preprint","doi":"10.1111/mec.16849","quality_controlled":"1","status":"public","pmid":1,"language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes of<jats:italic>Mimulus aurantiacus</jats:italic>. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system."}],"article_type":"original","type":"journal_article","citation":{"ama":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. <i>Molecular Ecology</i>. 2023;32(8):2041-2054. doi:<a href=\"https://doi.org/10.1111/mec.16849\">10.1111/mec.16849</a>","chicago":"Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16849\">https://doi.org/10.1111/mec.16849</a>.","ista":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.","mla":"Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” <i>Molecular Ecology</i>, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:<a href=\"https://doi.org/10.1111/mec.16849\">10.1111/mec.16849</a>.","apa":"Stankowski, S., Chase, M. A., McIntosh, H., &#38; Streisfeld, M. A. (2023). Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16849\">https://doi.org/10.1111/mec.16849</a>","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054.","ieee":"S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone,” <i>Molecular Ecology</i>, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023."},"article_processing_charge":"No","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"date_published":"2023-04-01T00:00:00Z","month":"04","date_updated":"2024-01-16T10:10:00Z","title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","external_id":{"isi":["000919244600001"],"pmid":["36651268"]},"date_created":"2024-01-10T10:44:45Z","_id":"14787","page":"2041-2054","publication":"Molecular Ecology","oa":1,"intvolume":"        32","acknowledgement":"We thank Julian Catchen for making modifications to Stacks to aid this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and Nicholas H. Barton provided advice, stimulating discussion and critical feedback. The project was supported by National Science Foundation grant DEB-1258199.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"8","main_file_link":[{"url":"https://doi.org/10.1101/2022.01.28.478139","open_access":"1"}],"volume":32},{"doi":"10.1083/jcb.202206038","oa_version":"Published Version","publisher":"Rockefeller University Press","day":"03","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"department":[{"_id":"AnSa"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023","isi":1,"author":[{"last_name":"Mund","full_name":"Mund, Markus","first_name":"Markus"},{"last_name":"Tschanz","full_name":"Tschanz, Aline","first_name":"Aline"},{"full_name":"Wu, Yu-Le","last_name":"Wu","first_name":"Yu-Le"},{"full_name":"Frey, Felix F","orcid":"0000-0001-8501-6017","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","first_name":"Felix F"},{"first_name":"Johanna L.","full_name":"Mehl, Johanna L.","last_name":"Mehl"},{"full_name":"Kaksonen, Marko","last_name":"Kaksonen","first_name":"Marko"},{"first_name":"Ori","full_name":"Avinoam, Ori","last_name":"Avinoam"},{"full_name":"Schwarz, Ulrich S.","last_name":"Schwarz","first_name":"Ulrich S."},{"full_name":"Ries, Jonas","last_name":"Ries","first_name":"Jonas"}],"file":[{"file_id":"14811","date_created":"2024-01-16T10:15:09Z","creator":"dernst","relation":"main_file","checksum":"505d5cac36c14b073b68c7fed1a92bd3","content_type":"application/pdf","date_updated":"2024-01-16T10:15:09Z","file_size":5678069,"file_name":"2023_JCB_Mund.pdf","success":1,"access_level":"open_access"}],"citation":{"mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>.","ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038.","ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. 2023;222(3). doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2023. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>.","ieee":"M. Mund <i>et al.</i>, “Clathrin coats partially preassemble and subsequently bend during endocytosis,” <i>Journal of Cell Biology</i>, vol. 222, no. 3. Rockefeller University Press, 2023.","short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>"},"type":"journal_article","ddc":["570"],"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane."}],"status":"public","has_accepted_license":"1","pmid":1,"language":[{"iso":"eng"}],"quality_controlled":"1","publication":"Journal of Cell Biology","file_date_updated":"2024-01-16T10:15:09Z","_id":"14788","external_id":{"isi":["000978065000001"],"pmid":["36734980"]},"date_created":"2024-01-10T10:45:55Z","date_updated":"2024-01-16T10:17:05Z","title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","month":"02","article_processing_charge":"No","keyword":["Cell Biology"],"date_published":"2023-02-03T00:00:00Z","volume":222,"article_number":"e202206038","intvolume":"       222","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair."}]