[{"volume":22,"language":[{"iso":"eng"}],"scopus_import":"1","citation":{"ieee":"N. Mishra, Y. I. Li, E. B. Hannezo, and C.-P. J. Heisenberg, “Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo,” <i>Nature Physics</i>, vol. 22. Springer Nature, pp. 139–150, 2026.","ista":"Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. 2026. Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. Nature Physics. 22, 139–150.","ama":"Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. <i>Nature Physics</i>. 2026;22:139-150. doi:<a href=\"https://doi.org/10.1038/s41567-025-03122-1\">10.1038/s41567-025-03122-1</a>","chicago":"Mishra, Nikhil, Yuting I Li, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” <i>Nature Physics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41567-025-03122-1\">https://doi.org/10.1038/s41567-025-03122-1</a>.","apa":"Mishra, N., Li, Y. I., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2026). Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-03122-1\">https://doi.org/10.1038/s41567-025-03122-1</a>","mla":"Mishra, Nikhil, et al. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” <i>Nature Physics</i>, vol. 22, Springer Nature, 2026, pp. 139–50, doi:<a href=\"https://doi.org/10.1038/s41567-025-03122-1\">10.1038/s41567-025-03122-1</a>.","short":"N. Mishra, Y.I. Li, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 22 (2026) 139–150."},"oa_version":"Published Version","file":[{"access_level":"open_access","success":1,"date_created":"2026-01-21T08:21:11Z","checksum":"0ab7ac2fbcb61a364dba57152db64ed7","file_size":7335694,"date_updated":"2026-01-21T08:21:11Z","file_name":"2026_NaturePhysics_Mishra.pdf","file_id":"21026","content_type":"application/pdf","creator":"dernst","relation":"main_file"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"_id":"917c023a-16d5-11f0-9cad-eb5cafc52090","name":"Cytoplasmic self-organization into cell-like compartments as a common guiding principle in early animal development"}],"fulldoi":"https://doi.org/10.1038/s41567-025-03122-1","OA_place":"publisher","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"year":"2026","external_id":{"oaworkid":["W7118187193"]},"title":"Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo","publication_status":"published","publication":"Nature Physics","publication_identifier":{"eissn":["1745-2481"],"issnl":[" 1745-2473"],"issn":["1745-2473"]},"ec_funded":1,"department":[{"_id":"EdHa"},{"_id":"CaHe"}],"has_accepted_license":"1","ddc":["570"],"doi":"10.1038/s41567-025-03122-1","related_material":{"link":[{"url":"https://ista.ac.at/en/news/geometry-shapes-life/","relation":"research_data","description":"News on ISTA website"}]},"_id":"21015","date_created":"2026-01-20T10:12:19Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"Yes (via OA deal)","status":"public","type":"journal_article","author":[{"full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788","last_name":"Mishra","first_name":"Nikhil","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E"},{"id":"ee7a5ca8-8b71-11ed-b662-b3341c05b7eb","first_name":"Yuting I","full_name":"Li, Yuting I","last_name":"Li"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"page":"139-150","article_type":"original","corr_author":"1","OA_type":"hybrid","abstract":[{"lang":"eng","text":"Early embryo geometry is one of the most invariant species-specific traits, yet its role in ensuring developmental reproducibility and robustness remains underexplored. Here we show that in zebrafish, the geometry of the fertilized egg—specifically its curvature and volume—serves as a critical initial condition triggering a cascade of events that influence development. The embryo geometry guides patterned asymmetric cell divisions in the blastoderm, generating radial gradients of cell volume and nucleocytoplasmic ratio. These gradients generate mitotic phase waves, with the nucleocytoplasmic ratio determining individual cell cycle periods independently of other cells. We demonstrate that reducing cell autonomy reshapes these waves, emphasizing the instructive role of geometry-derived volume patterns in setting the intrinsic period of the cell cycle oscillator. In addition to organizing cell cycles, early embryo geometry spatially patterns zygotic genome activation at the midblastula transition, a key step in establishing embryonic autonomy. Disrupting the embryo shape alters the zygotic genome activation pattern and causes ectopic germ layer specification, underscoring the developmental significance of geometry. Together, our findings reveal a symmetry-breaking function of early embryo geometry in coordinating cell cycle and transcriptional patterning."}],"file_date_updated":"2026-01-21T08:21:11Z","intvolume":"        22","acknowledgement":"We thank N. Petridou (EMBL) for sharing results before publication. N.M. was supported by funding from the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie COFUND Actions ISTplus grant agreement number 754411. Y.I.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 101034413. The research was supported by funding to C.-P.H. from the NOMIS Foundation, Project ID 1.844. We would like to thank past and present members of the Heisenberg and Hannezo groups for discussions, particularly S. Shamipour, V. Doddihal, M. Jovic, N. Hino, F. N. Arslan, R. Kobylinska and C. Camelo for feedback on the draft manuscript. This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria through resources provided by the Aquatics Facility, Imaging & Optics Facility (IOF), Scientific Computing (SciComp) facility and Lab Support Facility (LSF). Open access funding provided by Institute of Science and Technology (IST Austria).","oaworkid":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","day":"05","date_published":"2026-01-05T00:00:00Z","date_updated":"2026-04-28T12:55:30Z","month":"01","PlanS_conform":"1"},{"author":[{"last_name":"Grosjean","full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M"},{"first_name":"Markus","full_name":"Ostermann, Markus","last_name":"Ostermann"},{"first_name":"Markus","full_name":"Sauer, Markus","last_name":"Sauer"},{"first_name":"Michael","last_name":"Hahn","full_name":"Hahn, Michael"},{"full_name":"Pichler, Christian M.","last_name":"Pichler","first_name":"Christian M."},{"last_name":"Fahrnberger","full_name":"Fahrnberger, Florian","first_name":"Florian"},{"first_name":"Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","last_name":"Pertl","orcid":"0000-0003-0463-5794","full_name":"Pertl, Felix"},{"full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"last_name":"Link","full_name":"Link, Mason M.","first_name":"Mason M."},{"full_name":"Kim, Seong H.","last_name":"Kim","first_name":"Seong H."},{"full_name":"Schrader, Devin L.","last_name":"Schrader","first_name":"Devin L."},{"first_name":"Adriana","full_name":"Blanco, Adriana","last_name":"Blanco"},{"first_name":"Francisco","last_name":"Gracia","full_name":"Gracia, Francisco"},{"first_name":"Nicolás","last_name":"Mujica","full_name":"Mujica, Nicolás"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"page":"626-631","corr_author":"1","article_type":"original","issue":"8106","type":"journal_article","article_processing_charge":"Yes (via OA deal)","status":"public","related_material":{"link":[{"url":"https://ista.ac.at/en/news/colliding-dust-and-the-sparks-of-creation/","relation":"press_release","description":"News on ISTA website"}]},"_id":"21485","date_created":"2026-03-23T15:04:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-28T12:06:01Z","PlanS_conform":"1","month":"03","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","day":"18","date_published":"2026-03-18T00:00:00Z","file_date_updated":"2026-03-24T06:57:08Z","abstract":[{"lang":"eng","text":"Insulating oxides are among the most abundant solid materials in the universe1,2,3. Of the many ways in which they influence natural phenomena, perhaps the most consequential is their capacity to transfer electrical charge during contact4,5,6,7,8,9,10—which occurs even between samples of the same oxide—yet the symmetry-breaking parameter that causes this remains unidentified11,12. Here we show that adventitious carbonaceous molecules adsorbed from the environment are the symmetry-breaking factor in same-material oxide contact electrification (CE). We use acoustic levitation to measure charge exchange between a sphere and a plate composed of identical amorphous silicon dioxide (SiO2). Although charging polarity is random for co-prepared samples, we control it with baking or plasma treatment. Observing the charge-exchange relaxation afterwards, we see dynamics over a timescale of hours and connect this directly to the presence of adventitious carbon with time-of-flight mass spectrometry, low-energy ion scattering and infrared spectroscopy. Going further, we confirm that adventitious carbon can even determine charge exchange among different oxides. Our results identify the symmetry-breaking parameter that causes insulating oxides to exchange charge in settings ranging from desert sands4 to volcanic plumes5,6, while simultaneously highlighting an overlooked factor in CE more broadly."}],"intvolume":"       651","acknowledgement":"This project has received support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 949120) and from the Marie Skłodowska-Curie programme (grant agreement no. 754411). We acknowledge the state of Lower Austria and the European Regional Development Fund under grant no. WST3-F-542638/004-2021. N.M. acknowledges support from grant Fondecyt 1221597. G.G. is a Serra Húnter fellow. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing facility and Lab Support Facility. We thank the Modic group for the use of the Laue camera, T. Zauner for the photography of the experimental set-up and R. Möller for insightful discussions. Open access funding provided by Institute of Science and Technology (IST Austria).","OA_type":"hybrid","publisher":"Springer Nature","year":"2026","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"OA_place":"publisher","pmid":1,"citation":{"mla":"Grosjean, Galien M., et al. “Adventitious Carbon Breaks Symmetry in Oxide Contact Electrification.” <i>Nature</i>, vol. 651, no. 8106, Springer Nature, 2026, pp. 626–31, doi:<a href=\"https://doi.org/10.1038/s41586-025-10088-w\">10.1038/s41586-025-10088-w</a>.","apa":"Grosjean, G. M., Ostermann, M., Sauer, M., Hahn, M., Pichler, C. M., Fahrnberger, F., … Waitukaitis, S. R. (2026). Adventitious carbon breaks symmetry in oxide contact electrification. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-10088-w\">https://doi.org/10.1038/s41586-025-10088-w</a>","short":"G.M. Grosjean, M. Ostermann, M. Sauer, M. Hahn, C.M. Pichler, F. Fahrnberger, F. Pertl, D. Balazs, M.M. Link, S.H. Kim, D.L. Schrader, A. Blanco, F. Gracia, N. Mujica, S.R. Waitukaitis, Nature 651 (2026) 626–631.","chicago":"Grosjean, Galien M, Markus Ostermann, Markus Sauer, Michael Hahn, Christian M. Pichler, Florian Fahrnberger, Felix Pertl, et al. “Adventitious Carbon Breaks Symmetry in Oxide Contact Electrification.” <i>Nature</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41586-025-10088-w\">https://doi.org/10.1038/s41586-025-10088-w</a>.","ama":"Grosjean GM, Ostermann M, Sauer M, et al. Adventitious carbon breaks symmetry in oxide contact electrification. <i>Nature</i>. 2026;651(8106):626-631. doi:<a href=\"https://doi.org/10.1038/s41586-025-10088-w\">10.1038/s41586-025-10088-w</a>","ista":"Grosjean GM, Ostermann M, Sauer M, Hahn M, Pichler CM, Fahrnberger F, Pertl F, Balazs D, Link MM, Kim SH, Schrader DL, Blanco A, Gracia F, Mujica N, Waitukaitis SR. 2026. Adventitious carbon breaks symmetry in oxide contact electrification. Nature. 651(8106), 626–631.","ieee":"G. M. Grosjean <i>et al.</i>, “Adventitious carbon breaks symmetry in oxide contact electrification,” <i>Nature</i>, vol. 651, no. 8106. Springer Nature, pp. 626–631, 2026."},"oa_version":"Published Version","file":[{"creator":"dernst","relation":"main_file","file_id":"21494","content_type":"application/pdf","file_size":12245694,"checksum":"dafef9ed575b44be4263e948a47ae056","date_updated":"2026-03-24T06:57:08Z","file_name":"2026_Nature_Grosjean.pdf","date_created":"2026-03-24T06:57:08Z","success":1,"access_level":"open_access"}],"project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"fulldoi":"https://doi.org/10.1038/s41586-025-10088-w","volume":651,"language":[{"iso":"eng"}],"has_accepted_license":"1","ddc":["540"],"doi":"10.1038/s41586-025-10088-w","ec_funded":1,"department":[{"_id":"ScWa"},{"_id":"GradSch"},{"_id":"LifeSc"}],"publication":"Nature","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"external_id":{"pmid":["41851325"]},"title":"Adventitious carbon breaks symmetry in oxide contact electrification","publication_status":"published"},{"department":[{"_id":"JuFi"}],"arxiv":1,"ec_funded":1,"doi":"10.1214/25-aop1763","ddc":["510"],"APC_amount":"1352,08 EUR","has_accepted_license":"1","publication_status":"published","title":"Density fluctuations in weakly interacting particle systems via the Dean–Kawasaki equation","external_id":{"arxiv":["2303.00429"]},"publication_identifier":{"eissn":["2168-894X"],"issn":["0091-1798"]},"publication":"The Annals of Probability","OA_place":"publisher","keyword":["Weakly interacting particle systems","fluctuating hydrodynamics","Dean-Kawasaki equation","stochastic PDEs","numerical approximation"],"year":"2026","publisher":"Institute of Mathematical Statistics","language":[{"iso":"eng"}],"volume":54,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"fulldoi":"https://doi.org/10.1214/25-aop1763","file":[{"access_level":"open_access","success":1,"date_created":"2026-05-21T07:11:27Z","file_size":865745,"checksum":"3e60c0e25a1c96342029a7d2b031505f","file_name":"2026_AnnalsProbability_Cornalba.pdf","date_updated":"2026-05-21T07:11:27Z","file_id":"21906","content_type":"application/pdf","relation":"main_file","creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","citation":{"ieee":"F. Cornalba, J. L. Fischer, J. Ingmanns, and C. Raithel, “Density fluctuations in weakly interacting particle systems via the Dean–Kawasaki equation,” <i>The Annals of Probability</i>, vol. 54, no. 1. Institute of Mathematical Statistics, pp. 155–215, 2026.","ista":"Cornalba F, Fischer JL, Ingmanns J, Raithel C. 2026. Density fluctuations in weakly interacting particle systems via the Dean–Kawasaki equation. The Annals of Probability. 54(1), 155–215.","chicago":"Cornalba, Federico, Julian L Fischer, Jonas Ingmanns, and Claudia Raithel. “Density Fluctuations in Weakly Interacting Particle Systems via the Dean–Kawasaki Equation.” <i>The Annals of Probability</i>. Institute of Mathematical Statistics, 2026. <a href=\"https://doi.org/10.1214/25-aop1763\">https://doi.org/10.1214/25-aop1763</a>.","ama":"Cornalba F, Fischer JL, Ingmanns J, Raithel C. Density fluctuations in weakly interacting particle systems via the Dean–Kawasaki equation. <i>The Annals of Probability</i>. 2026;54(1):155-215. doi:<a href=\"https://doi.org/10.1214/25-aop1763\">10.1214/25-aop1763</a>","apa":"Cornalba, F., Fischer, J. L., Ingmanns, J., &#38; Raithel, C. (2026). Density fluctuations in weakly interacting particle systems via the Dean–Kawasaki equation. <i>The Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/25-aop1763\">https://doi.org/10.1214/25-aop1763</a>","mla":"Cornalba, Federico, et al. “Density Fluctuations in Weakly Interacting Particle Systems via the Dean–Kawasaki Equation.” <i>The Annals of Probability</i>, vol. 54, no. 1, Institute of Mathematical Statistics, 2026, pp. 155–215, doi:<a href=\"https://doi.org/10.1214/25-aop1763\">10.1214/25-aop1763</a>.","short":"F. Cornalba, J.L. Fischer, J. Ingmanns, C. Raithel, The Annals of Probability 54 (2026) 155–215."},"date_published":"2026-01-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"01","quality_controlled":"1","oa":1,"PlanS_conform":"1","month":"01","date_updated":"2026-05-21T07:21:25Z","OA_type":"hybrid","intvolume":"        54","acknowledgement":"All authors gratefully acknowledge funding from the Austrian Science Fund (FWF) through the project F65. CR gratefully acknowledges support from the Austrian Science Fund (FWF), grants P30000, P33010, W1245. FC gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","file_date_updated":"2026-05-21T07:11:27Z","abstract":[{"lang":"eng","text":"The Dean–Kawasaki equation—one of the most fundamental SPDEs of\r\nfluctuating hydrodynamics—has been proposed as a model for density fluctuations in weakly interacting particle systems. In its original form, it is highly\r\nsingular and fails to be renormalizable, even by approaches such as regularity structures and paracontrolled distributions, hindering mathematical approaches to its rigorous justification. It has been understood recently that it is\r\nnatural to introduce a suitable regularization, for example, by applying a formal spatial discretization or by truncating high-frequency noise: This yields\r\nwell-posed equations that should still precisely approximate the law of the\r\nparticle density fluctuations.\r\nIn the present work, we prove that a regularization in the form of a formal\r\ndiscretization of the Dean–Kawasaki equation indeed accurately describes\r\ndensity fluctuations in systems of weakly interacting diffusing particles: We\r\nshow that, in suitable weak metrics, the law of fluctuations as predicted by\r\nthe discretized Dean–Kawasaki SPDE approximates the law of fluctuations\r\nof the original particle system, up to an error that is of arbitrarily high order in\r\nthe inverse particle number and a discretization error. In particular, the Dean–\r\nKawasaki equation provides a means for efficient and accurate simulations of\r\ndensity fluctuations in weakly interacting particle systems."}],"type":"journal_article","issue":"1","corr_author":"1","article_type":"original","page":"155-215","author":[{"full_name":"Cornalba, Federico","last_name":"Cornalba","first_name":"Federico"},{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"first_name":"Jonas","id":"71523d30-15b2-11ec-abd3-f80aa909d6b0","last_name":"Ingmanns","orcid":"0009-0008-1310-7946","full_name":"Ingmanns, Jonas"},{"first_name":"Claudia","last_name":"Raithel","full_name":"Raithel, Claudia"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-05-20T08:25:25Z","_id":"21894","status":"public","article_processing_charge":"Yes (in subscription journal)"},{"title":"Developmental emergence of sparse and structured synaptic connectivity in the hippocampal CA3 memory circuit","publication_status":"published","das_tickbox":"1","external_id":{"pmid":["42014695"]},"article_number":"5540","publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"ec_funded":1,"ddc":["570"],"doi":"10.1038/s41467-026-71914-x","has_accepted_license":"1","language":[{"iso":"eng"}],"volume":17,"file":[{"access_level":"open_access","date_created":"2026-07-01T06:46:06Z","success":1,"date_updated":"2026-07-01T06:46:06Z","file_name":"2026_NatureComm_VargasBarroso.pdf","checksum":"d0b0093493926985b4c268662ff4d556","file_size":18304997,"creator":"dernst","relation":"main_file","content_type":"application/pdf","file_id":"22231"}],"project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"_id":"e62b56fe-ab3c-11f0-94c7-d181dd352b3b","grant_number":"101199096","name":"Synaptic mechanisms of engram storage and retrieval in CA3 hippocampal microcircuits"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits"},{"_id":"8d9195e9-16d5-11f0-9cad-d075be887a1e","grant_number":"PAT 4178023","name":"Synaptic networks of human brain"},{"name":"Reglas de Conectividad funcional en el hipocampo","_id":"26366136-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1038/s41467-026-71914-x","citation":{"apa":"Vargas Barroso, V. M., Watson, J., Navas Olivé, A. C., Schlögl, A., &#38; Jonas, P. M. (2026). Developmental emergence of sparse and structured synaptic connectivity in the hippocampal CA3 memory circuit. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-71914-x\">https://doi.org/10.1038/s41467-026-71914-x</a>","mla":"Vargas Barroso, Victor M., et al. “Developmental Emergence of Sparse and Structured Synaptic Connectivity in the Hippocampal CA3 Memory Circuit.” <i>Nature Communications</i>, vol. 17, 5540, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-71914-x\">10.1038/s41467-026-71914-x</a>.","short":"V.M. Vargas Barroso, J. Watson, A.C. Navas Olivé, A. Schlögl, P.M. Jonas, Nature Communications 17 (2026).","ista":"Vargas Barroso VM, Watson J, Navas Olivé AC, Schlögl A, Jonas PM. 2026. Developmental emergence of sparse and structured synaptic connectivity in the hippocampal CA3 memory circuit. Nature Communications. 17, 5540.","ieee":"V. M. Vargas Barroso, J. Watson, A. C. Navas Olivé, A. Schlögl, and P. M. Jonas, “Developmental emergence of sparse and structured synaptic connectivity in the hippocampal CA3 memory circuit,” <i>Nature Communications</i>, vol. 17. Springer Nature, 2026.","chicago":"Vargas Barroso, Victor M, Jake Watson, Andrea C Navas Olivé, Alois Schlögl, and Peter M Jonas. “Developmental Emergence of Sparse and Structured Synaptic Connectivity in the Hippocampal CA3 Memory Circuit.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-71914-x\">https://doi.org/10.1038/s41467-026-71914-x</a>.","ama":"Vargas Barroso VM, Watson J, Navas Olivé AC, Schlögl A, Jonas PM. Developmental emergence of sparse and structured synaptic connectivity in the hippocampal CA3 memory circuit. <i>Nature Communications</i>. 2026;17. doi:<a href=\"https://doi.org/10.1038/s41467-026-71914-x\">10.1038/s41467-026-71914-x</a>"},"oa_version":"Published Version","scopus_import":"1","OA_place":"publisher","pmid":1,"DOAJ_listed":"1","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"year":"2026","researchdata_availability":"yes","dataavailabilitystatement":"Source data are provided with this paper. Additional original data are available from the corresponding author upon request. Code is available from https://doi.org/10.15479/AT-ISTA-21442 under the link https://research-explorer.ista.ac.at/download/21442/21443/ca3simu-vargas2026v1.tar.gz","OA_type":"gold","file_date_updated":"2026-07-01T06:46:06Z","abstract":[{"lang":"eng","text":"Hippocampal CA3 pyramidal neurons (PNs) form the largest autoassociative network in the mammalian brain. Whether CA3–CA3 recurrent connectivity is genetically preconfigured or environmentally shaped during ongoing memory storage is currently unknown. To address this question, we performed multicellular patch-clamp-based circuit mapping of up to eight CA3 PNs in the mouse hippocampus at multiple postnatal time points (P7–8, P18–25, and P45–50). Here, we show that the hippocampal CA3 network undergoes a developmental transformation from local, dense, and random connectivity to a distributed, sparse, and structured configuration. Thus, sparse and structured connectivity may emerge via experience-dependent mechanisms. In parallel, the strength of single synapses is downregulated; single synaptic events are sufficient to trigger postsynaptic spiking early in development, whereas spatial summation of several inputs is required at later time points. Biologically inspired models of memory storage by Hebbian synaptic plasticity and retrieval via pattern completion suggest that developmental changes improve specific aspects of memory storage and retrieval. Our results imply a developmental transformation of the neuronal code and the memory functions in the hippocampal CA3 network.</jats:p>"}],"acknowledgement":"We thank Jose Guzman, Simon Hippenmeyer, and Tim Vogels for critically reading the manuscript, Jozsef Csicsvari for useful discussions, Florian Marr for technical assistance, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA: the preclinical facility (PCF) provided housing and breeding of the animals, the imaging and optics facility (IOF) offered technical training and state of the art equipment, the Miba machine shop contributed to the construction and maintenance of multicellular recording setups, and the scientific computing unit helped with the large-scale simulations. The project received funding from the European Union’s Horizon 2020 research and innovation programme (ERC Advanced Grants No 692692 GIANTSYN and 101199096 CA3-SYNGRAM to P.J.; Marie Skłodowska-Curie Grant 754411 to V.V.B.; Marie Skłodowska-Curie Grant 101026635 to J.F.W.), the Fond zur Förderung der Wissenschaftlichen Forschung (P 36232-B, PAT4178023, and 10.55776/CoE16 to P.J.), and the Nomis Foundation (fellowship to A.N.-O.). V.V.B. received funding from a CONACyT fellowship (289638).","intvolume":"        17","date_published":"2026-06-23T00:00:00Z","oa":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"23","PlanS_conform":"1","month":"06","date_updated":"2026-07-01T06:47:49Z","date_created":"2026-06-30T13:05:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"research_data","id":"21442"}]},"_id":"22229","status":"public","supplementarymaterial":"yes","article_processing_charge":"Yes","type":"journal_article","corr_author":"1","article_type":"original","author":[{"full_name":"Vargas Barroso, Victor M","last_name":"Vargas Barroso","first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"last_name":"Navas Olivé","orcid":"0000-0002-9280-8597","full_name":"Navas Olivé, Andrea C","id":"739d26c9-52e8-11ee-8d72-f14d3893b4ce","first_name":"Andrea C"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}]},{"ddc":["540"],"doi":"10.1021/acs.chemmater.6c01284","has_accepted_license":"1","department":[{"_id":"MaIb"},{"_id":"GradSch"},{"_id":"NanoFab"}],"ec_funded":1,"publication":"Chemistry of Materials","publication_identifier":{"eissn":["1520-5002"],"issn":["0897-4756"]},"title":"Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe","das_tickbox":"0","publication_status":"published","external_id":{"pmid":["42787739"]},"publisher":"American Chemical Society","year":"2026","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"pmid":1,"OA_place":"publisher","file":[{"access_level":"open_access","success":1,"date_created":"2026-10-06T12:11:04Z","checksum":"15e7866ca4fd57f5526737945651a6f2","file_size":7461570,"date_updated":"2026-10-06T12:11:04Z","file_name":"2026_ChemistryMaterials_Fiedler.pdf","content_type":"application/pdf","file_id":"23063","relation":"main_file","creator":"dernst"}],"fulldoi":"https://doi.org/10.1021/acs.chemmater.6c01284","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"},{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"citation":{"short":"C. Fiedler, S. Horta, N. Jakhar, K. Maji, T. Kleinhanns, J. Llorca, Q. Wang, M.G. Ramon, S. Das, V. Gavini, Y. Liu, M. Ibáñez, Chemistry of Materials 38 (2026) 9323–9332.","mla":"Fiedler, Christine, et al. “Alkali Ions Retained from Synthesis Govern Microstructure and Transport in Solution-Processed SnSe.” <i>Chemistry of Materials</i>, vol. 38, no. 18, American Chemical Society, 2026, pp. 9323–9332, doi:<a href=\"https://doi.org/10.1021/acs.chemmater.6c01284\">10.1021/acs.chemmater.6c01284</a>.","apa":"Fiedler, C., Horta, S., Jakhar, N., Maji, K., Kleinhanns, T., Llorca, J., … Ibáñez, M. (2026). Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe. <i>Chemistry of Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.chemmater.6c01284\">https://doi.org/10.1021/acs.chemmater.6c01284</a>","chicago":"Fiedler, Christine, Sharona Horta, Navita Jakhar, Krishnendu Maji, Tobias Kleinhanns, Jordi Llorca, Qi Wang, et al. “Alkali Ions Retained from Synthesis Govern Microstructure and Transport in Solution-Processed SnSe.” <i>Chemistry of Materials</i>. American Chemical Society, 2026. <a href=\"https://doi.org/10.1021/acs.chemmater.6c01284\">https://doi.org/10.1021/acs.chemmater.6c01284</a>.","ama":"Fiedler C, Horta S, Jakhar N, et al. Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe. <i>Chemistry of Materials</i>. 2026;38(18):9323–9332. doi:<a href=\"https://doi.org/10.1021/acs.chemmater.6c01284\">10.1021/acs.chemmater.6c01284</a>","ista":"Fiedler C, Horta S, Jakhar N, Maji K, Kleinhanns T, Llorca J, Wang Q, Ramon MG, Das S, Gavini V, Liu Y, Ibáñez M. 2026. Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe. Chemistry of Materials. 38(18), 9323–9332.","ieee":"C. Fiedler <i>et al.</i>, “Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe,” <i>Chemistry of Materials</i>, vol. 38, no. 18. American Chemical Society, pp. 9323–9332, 2026."},"scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":38,"PlanS_conform":"1","month":"09","date_updated":"2026-10-06T12:16:03Z","date_published":"2026-09-22T00:00:00Z","oa":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"22","file_date_updated":"2026-10-06T12:11:04Z","abstract":[{"text":"Alkali salts are widely used in solution processing, yet the corresponding cations are often assumed to remain in the liquid phase. Here, we show that alkali ions introduced during the solution synthesis of SnSe are retained through particle isolation and continue to influence the material during subsequent thermal processing, where they shape the evolution of the final polycrystalline material. Different SnSe powders were prepared using Li+, Na+, and K+ precursors, as well as tetramethylammonium (TMA+) precursors as a nonalkali reference for comparison, and all samples were consolidated under identical conditions. Although all three alkali ions were found in the matrix, at grain boundaries, and in segregated nanoscale regions, they partitioned differently and resulted in distinct grain sizes, defect distributions, and therefore transport properties. Li induced the strongest grain size heterogeneity and the lowest energy barriers, Na the best overall balance between carrier concentration and mobility, and K the broadest alkali-rich grain boundary regions along with the strongest interfacial penalty to charge carrier transport. These results show that residual alkali ions are not just remnants of solution synthesis but active determinants of microstructure and thermoelectric performance in SnSe.","lang":"eng"}],"intvolume":"        38","acknowledgement":"ISTA and the Werner Siemens Foundation financially supported this work. The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), Juan Aguilera Servin from the Nanofabrication facility (NNF). Special acknowledgments to the Ibá\r\nez group for their fruitful discussions and insights. K.M. acknowledges the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413 and PETRAIII at DESY for the synchrotron X-ray measurements under proposal No. I-20241048 EC. JL is a Serra Húnter Fellow and is grateful to the Academia Excellence program (Generalitat de Catalunya), project PID2024-156765OB-C21 funded by MICIU/AEI/10.13039/501100011033 and the European Regional Development Fund (FEDER), and María de Maeztu Units of Excellence Programme CEX2023-001300 M, funded by MCIN/AEI 10.13039/501100011033. VG and SD acknowledge the use of resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411, the National Natural Science Foundation of China (NSFC) (Grants No. 22209034).","researchdata_availability":"no","OA_type":"hybrid","corr_author":"1","article_type":"original","page":"9323–9332","author":[{"first_name":"Christine","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","full_name":"Fiedler, Christine","last_name":"Fiedler"},{"full_name":"Horta, Sharona","last_name":"Horta","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"orcid":"0000-0001-7408-8197","full_name":"Navita, Navita","last_name":"Navita","id":"6ebe278d-ba0b-11ee-8184-f34cdc671de4","first_name":"Navita"},{"first_name":"Krishnendu","id":"76bc9e9f-ba0b-11ee-8184-90edabd17a58","last_name":"Maji","full_name":"Maji, Krishnendu"},{"orcid":"0000-0003-1537-7436","full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","first_name":"Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425"},{"last_name":"Llorca","full_name":"Llorca, Jordi","first_name":"Jordi"},{"first_name":"Qi","id":"0d37923a-aca1-11ef-951f-fd411b71d5f0","full_name":"Wang, Qi","last_name":"Wang"},{"last_name":"Ramon","full_name":"Ramon, Maria Garcia","first_name":"Maria Garcia","id":"1ffff7cd-ed76-11ed-8d5f-be5e7c364eb9"},{"last_name":"Das","full_name":"Das, Sambit","first_name":"Sambit"},{"last_name":"Gavini","full_name":"Gavini, Vikram","first_name":"Vikram"},{"first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"}],"issue":"18","type":"journal_article","status":"public","supplementarymaterial":"yes","article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-09-21T10:33:48Z","_id":"22967"},{"publisher":"Wiley","year":"2025","pmid":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"fulldoi":"https://doi.org/10.1002/ajb2.70129","citation":{"ista":"Fuster‐Calvo A, Jaworski CC, Ellis T, Baskett C. 2025. Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors. American Journal of Botany. 112(12), e70129.","ieee":"A. Fuster‐Calvo, C. C. Jaworski, T. Ellis, and C. Baskett, “Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors,” <i>American Journal of Botany</i>, vol. 112, no. 12. Wiley, 2025.","chicago":"Fuster‐Calvo, Alexandre, Coline C. Jaworski, Thomas Ellis, and Carina Baskett. “Reduced Fitness under Drought Stress in F1 Hybrids of Antirrhinum Majus Varieties with Divergent Flower Colors.” <i>American Journal of Botany</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/ajb2.70129\">https://doi.org/10.1002/ajb2.70129</a>.","ama":"Fuster‐Calvo A, Jaworski CC, Ellis T, Baskett C. Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors. <i>American Journal of Botany</i>. 2025;112(12). doi:<a href=\"https://doi.org/10.1002/ajb2.70129\">10.1002/ajb2.70129</a>","apa":"Fuster‐Calvo, A., Jaworski, C. C., Ellis, T., &#38; Baskett, C. (2025). Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors. <i>American Journal of Botany</i>. Wiley. <a href=\"https://doi.org/10.1002/ajb2.70129\">https://doi.org/10.1002/ajb2.70129</a>","mla":"Fuster‐Calvo, Alexandre, et al. “Reduced Fitness under Drought Stress in F1 Hybrids of Antirrhinum Majus Varieties with Divergent Flower Colors.” <i>American Journal of Botany</i>, vol. 112, no. 12, e70129, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/ajb2.70129\">10.1002/ajb2.70129</a>.","short":"A. Fuster‐Calvo, C.C. Jaworski, T. Ellis, C. Baskett, American Journal of Botany 112 (2025)."},"scopus_import":"1","oa_version":"None","language":[{"iso":"eng"}],"volume":112,"doi":"10.1002/ajb2.70129","department":[{"_id":"NiBa"}],"ec_funded":1,"article_number":"e70129","publication":"American Journal of Botany","publication_identifier":{"issn":["0002-9122"],"eissn":["1537-2197"]},"title":"Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors","publication_status":"published","external_id":{"pmid":["41327576 "]},"article_type":"original","author":[{"first_name":"Alexandre","full_name":"Fuster‐Calvo, Alexandre","last_name":"Fuster‐Calvo"},{"last_name":"Jaworski","full_name":"Jaworski, Coline C.","first_name":"Coline C."},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","last_name":"Ellis"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina"}],"issue":"12","type":"journal_article","status":"public","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-12-29T12:14:26Z","related_material":{"link":[{"relation":"software","url":"https://github.com/Alex-Fuster/hybrids_drought"}]},"_id":"20869","month":"12","date_updated":"2026-01-05T11:56:22Z","date_published":"2025-12-01T00:00:00Z","quality_controlled":"1","day":"01","abstract":[{"text":"Premise: What maintains trait divergence in the face of gene flow? Two varieties of wild snapdragon (Antirrhinum majus) characterized by divergent flower color hybridize in their native range. Selection on flower color genes is indicated by sharp clines, but the selective agents have not been demonstrated. Although previous work has focused on pollinators, pigmentation genes can also contribute to abiotic stress tolerance. We hypothesized that pigmentation in A. majus mediates stress tolerance, which could contribute to hybrid zone maintenance through parental niche divergence or hybrid maladaptation. Specifically, we tested whether morphotype mediates drought tolerance in an experiment comparing magenta-flowered var. pseudomajus, yellow-flowered var. striatum, and their pink-flowered hybrid cross.\r\nMethods: We experimentally compared drought tolerance of each morphotype from allopatric crosses within and between varieties using three greenhouse treatments. Control plants were watered as needed, while drought-treated plants were watered half as often, either from the transplant stage (“early” drought), or from flowering onset (“late” drought).\r\nResults: Parental morphotypes responded identically to drought in fitness and most phenotypic traits. However, hybrids had lower survival (14%) under late drought stress than parental morphotypes (70%). All hybrids that flowered in the late drought treatment died, compared to ~20% of flowering parental morphotypes.\r\nConclusions: Hybrid maladaptation to abiotic stress could potentially contribute to flower color divergence in the face of gene flow in A. majus. Further research should test the relevance of our results to field conditions and explicitly probe the role of flower color genes in drought tolerance.","lang":"eng"}],"acknowledgement":"Thank you to Doug Schemske and Nick Barton forcritically reviewing the manuscript, Beatriz Pablo Car-mona for assisting with data collection, Melinda Pickupand Eva Cereghetti for seedlings, and Louise Arathoon,Ksenia Khudiakova, Georg Rieckh, Daria Shiplina, andAnja Westram for help with experimental maintenance.We sincerely thank the Associate Editor Brenda Grewelland two anonymous reviewers for their thoughtfulcomments and suggestions, which substantially improved the clarity and quality of our manuscript. C.B. receivedfunding from the European Union's Horizon 2020 researchand innovation programme under the Marie Skłodowska‐Curie Grant Agreement No. 754411","intvolume":"       112","OA_type":"closed access"},{"type":"journal_article","author":[{"id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat","orcid":"0000-0001-8945-6992","full_name":"Artan, Murat","last_name":"Artan"},{"full_name":"Schön, Hanna","last_name":"Schön","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","first_name":"Hanna"},{"full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"}],"corr_author":"1","article_type":"original","_id":"20929","date_created":"2026-01-04T23:01:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","day":"11","oa":1,"date_published":"2025-12-11T00:00:00Z","date_updated":"2026-05-20T08:10:18Z","PlanS_conform":"1","month":"12","OA_type":"gold","intvolume":"        16","acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, and the Mass Spec Facility at the Max Perutz Labs, notably WeiQiang Chen and Markus Hartl, for invaluable discussions and comments on mass spec analyses of worm samples. All LC-MS/MS analyses were performed on instruments of the Vienna BioCenter Core Facilities (VBCF). Microscopy was supported by the Scientific Services Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF). We are grateful to Dr. Geraldine Seydoux (Johns Hopkins University) for worm strains and plasmids, and Dr. Seung-Jae V. Lee (KAIST) for RNAi clones. We are grateful to Ekaterina Lashmanova for designing the daf-16::TbID::mNG::3xFLAG knock-in construct and for her outstanding support in the lab. This work was supported by a Wellcome Investigator Award (209504/A/17/Z) to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).","file_date_updated":"2026-01-05T10:58:28Z","abstract":[{"lang":"eng","text":"Insulin/insulin-like growth factor signaling inhibits FOXO transcription factors to control development, homeostasis, and aging. Here, we use proximity labeling to identify proteins interacting with the C. elegans FOXO DAF-16. We show that in well-fed, unstressed animals harboring active insulin signaling, DAF-16 forms a complex with the PAR-1/MARK serine/threonine kinase, a key regulator of cell polarity. PAR-1 inhibits DAF-16 accumulation and promotes DAF-16 phosphorylation at S249, at a conserved motif that PAR-1/human MARK2 phosphorylates in vitro. DAF-2 insulin-like receptor signaling stimulates DAF-16 S249 phosphorylation, suggesting DAF-2 activates PAR-1. DAF-2 also promotes PAR-1 expression by inhibiting DAF-16. PAR-1 knockdown, or DAF-16 S249A, prolong lifespan, whereas phosphomimetic DAF-16 S249D suppresses the longevity of daf-2 mutants. At low insulin signaling, DAF-16 proximity labeling highlights transcription factors, chromatin regulators, and DNA repair proteins. One interactor, the zinc finger/homeobox protein ZFH-2/ZFHX3, forms a complex with DAF-16 and prolongs lifespan. Our work provides entry points for hypothesis-driven studies of FOXO function and longevity."}],"DOAJ_listed":"1","OA_place":"publisher","pmid":1,"acknowledged_ssus":[{"_id":"Bio"}],"year":"2025","publisher":"Springer Nature","volume":16,"language":[{"iso":"eng"}],"citation":{"short":"M. Artan, H. Schön, M. de Bono, Nature Communications 16 (2025).","mla":"Artan, Murat, et al. “Proximity Labeling of DAF-16 FOXO Highlights Aging Regulatory Proteins.” <i>Nature Communications</i>, vol. 16, 11355, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-66409-0\">10.1038/s41467-025-66409-0</a>.","apa":"Artan, M., Schön, H., &#38; de Bono, M. (2025). Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-66409-0\">https://doi.org/10.1038/s41467-025-66409-0</a>","chicago":"Artan, Murat, Hanna Schön, and Mario de Bono. “Proximity Labeling of DAF-16 FOXO Highlights Aging Regulatory Proteins.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-66409-0\">https://doi.org/10.1038/s41467-025-66409-0</a>.","ama":"Artan M, Schön H, de Bono M. Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-66409-0\">10.1038/s41467-025-66409-0</a>","ista":"Artan M, Schön H, de Bono M. 2025. Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins. Nature Communications. 16, 11355.","ieee":"M. Artan, H. Schön, and M. de Bono, “Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025."},"oa_version":"Published Version","scopus_import":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"}],"fulldoi":"https://doi.org/10.1038/s41467-025-66409-0","file":[{"success":1,"date_created":"2026-01-05T10:58:28Z","access_level":"open_access","file_id":"20941","content_type":"application/pdf","creator":"dernst","relation":"main_file","file_name":"2025_NatureComm_Artan.pdf","date_updated":"2026-01-05T10:58:28Z","file_size":1642352,"checksum":"748e2e003b878b85b6048d51621d6aae"}],"ec_funded":1,"department":[{"_id":"MaDe"}],"has_accepted_license":"1","doi":"10.1038/s41467-025-66409-0","APC_amount":"7068 EUR","ddc":["570"],"external_id":{"pmid":["41381452"]},"publication_status":"published","title":"Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins","publication_identifier":{"eissn":["2041-1723"]},"publication":"Nature Communications","article_number":"11355"},{"year":"2025","acknowledged_ssus":[{"_id":"Bio"}],"publisher":"Springer Nature","pmid":1,"citation":{"ama":"Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Garcia-Marques J, Lee T, eds. <i>Lineage Tracing</i>. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>","chicago":"Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” In <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>.","ista":"Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.","ieee":"G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM),” in <i>Lineage Tracing</i>, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.","mla":"Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>.","apa":"Cheung, G. T., Pauler, F., &#38; Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques &#38; T. Lee (Eds.), <i>Lineage Tracing</i> (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>","short":"G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.), Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151."},"scopus_import":"1","oa_version":"None","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1007/978-1-0716-4310-5_7","volume":2886,"language":[{"iso":"eng"}],"doi":"10.1007/978-1-0716-4310-5_7","ec_funded":1,"editor":[{"last_name":"Garcia-Marques","full_name":"Garcia-Marques, Jorge","first_name":"Jorge"},{"first_name":"Tzumin","full_name":"Lee, Tzumin","last_name":"Lee"}],"department":[{"_id":"SiHi"}],"publication_identifier":{"isbn":["9781071643099"],"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781071643105"]},"publication":"Lineage Tracing","external_id":{"pmid":["39745639"]},"place":"New York, NY","publication_status":"published","series_title":"MIMB","title":"Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)","author":[{"full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","last_name":"Cheung","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"page":"139-151","corr_author":"1","type":"book_chapter","article_processing_charge":"No","status":"public","_id":"18765","date_created":"2025-01-07T08:36:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-14T07:43:46Z","month":"01","day":"03","quality_controlled":"1","alternative_title":["Methods in Molecular Biology"],"date_published":"2025-01-03T00:00:00Z","acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. Experimental steps described were optimized with support provided by the Imaging & Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine (CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional funds: The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","intvolume":"      2886","abstract":[{"lang":"eng","text":"Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution."}],"OA_type":"closed access"},{"has_accepted_license":"1","ddc":["510"],"doi":"10.1007/s44007-025-00170-0","ec_funded":1,"department":[{"_id":"HeEd"}],"publication_identifier":{"eissn":["2730-9657"]},"publication":"La Matematica","title":"Burning or collapsing the medial axis is unstable","publication_status":"published","publisher":"Springer Nature","year":"2025","OA_place":"publisher","citation":{"chicago":"Chambers, Erin Wolf, Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs Wintraecken. “Burning or Collapsing the Medial Axis Is Unstable.” <i>La Matematica</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s44007-025-00170-0\">https://doi.org/10.1007/s44007-025-00170-0</a>.","ama":"Chambers EW, Fillmore CD, Stephenson ER, Wintraecken M. Burning or collapsing the medial axis is unstable. <i>La Matematica</i>. 2025;4:811-828. doi:<a href=\"https://doi.org/10.1007/s44007-025-00170-0\">10.1007/s44007-025-00170-0</a>","ieee":"E. W. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “Burning or collapsing the medial axis is unstable,” <i>La Matematica</i>, vol. 4. Springer Nature, pp. 811–828, 2025.","ista":"Chambers EW, Fillmore CD, Stephenson ER, Wintraecken M. 2025. Burning or collapsing the medial axis is unstable. La Matematica. 4, 811–828.","mla":"Chambers, Erin Wolf, et al. “Burning or Collapsing the Medial Axis Is Unstable.” <i>La Matematica</i>, vol. 4, Springer Nature, 2025, pp. 811–28, doi:<a href=\"https://doi.org/10.1007/s44007-025-00170-0\">10.1007/s44007-025-00170-0</a>.","apa":"Chambers, E. W., Fillmore, C. D., Stephenson, E. R., &#38; Wintraecken, M. (2025). Burning or collapsing the medial axis is unstable. <i>La Matematica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s44007-025-00170-0\">https://doi.org/10.1007/s44007-025-00170-0</a>","short":"E.W. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, La Matematica 4 (2025) 811–828."},"oa_version":"Published Version","scopus_import":"1","file":[{"access_level":"open_access","date_created":"2025-12-30T07:52:58Z","success":1,"file_name":"2025_LaMatematica_Chambers.pdf","date_updated":"2025-12-30T07:52:58Z","file_size":2678640,"checksum":"e2043259194bfcdf3d74c4da8a5a853f","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_id":"20885"}],"project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"}],"fulldoi":"https://doi.org/10.1007/s44007-025-00170-0","volume":4,"language":[{"iso":"eng"}],"date_updated":"2026-04-07T11:42:48Z","PlanS_conform":"1","month":"12","oa":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"01","date_published":"2025-12-01T00:00:00Z","file_date_updated":"2025-12-30T07:52:58Z","abstract":[{"lang":"eng","text":"The medial axis of a set consists of the points in the ambient space without a unique closest point in the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a skeleton topologically equivalent to the original set. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities, various prunings of the medial axis have been proposed in the computational geometry community. Here, we examine one type of pruning, called burning. Because of the good experimental results it was hoped that the burning method of simplifying the medial axis would be stable. In this work, we show a simple example that dashes such hopes. Based on Bing’s house with two rooms, we demonstrate an isotopy of a shape where the medial axis goes from collapsible to non-collapsible. More precisely, we consider the standard deformation retract from the closed ball to Bing’s house with two rooms, but stop just short of the point where Bing’s house becomes two dimensional. This way we obtain an isotopy from the 3-ball to a thickened version of Bing’s house. Under this isotopy, the medial axis goes from collapsible to non-collapsible. We stress that this isotopy can be made generic, in the sense of singularity theory, as developed by Arnol’d and Thom."}],"intvolume":"         4","acknowledgement":"We thank André Lieutier, David Letscher, Ellen Gasparovic, Kathryn Leonard, and Tao Ju for early discussions on this work. We also thank Lu Liu, Yajie Yan, and Tao Ju for sharing code to generate the examples. We further thank Abigail Thompson for discussion on the conjecture and James Damon for sharing his insight in singularity theory. We thank the reviewers for their detailed reviews, which helped to improve the exposition.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). Partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’ and the European Research Council (ERC), grant no. 788183, ‘Alpha Shape Theory Extended’. The first author was supported in part by the National Science Foundation through grants DBI-1759807, CCF-1907612, and CCF-2444309. The fourth author was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) M-3073, ANR grant StratMesh, ANR-24-CE48-1899, and the welcome package from IDEX of the Université Côte d’Azur, ANR-15-IDEX-01.","OA_type":"hybrid","author":[{"first_name":"Erin Wolf","last_name":"Chambers","full_name":"Chambers, Erin Wolf"},{"first_name":"Christopher D","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","full_name":"Fillmore, Christopher D","last_name":"Fillmore"},{"full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X","last_name":"Stephenson","first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220"}],"article_type":"original","page":"811-828","corr_author":"1","type":"journal_article","article_processing_charge":"Yes (via OA deal)","status":"public","related_material":{"record":[{"status":"public","id":"21021","relation":"dissertation_contains"}]},"_id":"20260","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-08-31T22:01:33Z"},{"publication_status":"published","title":"Cell-specific wiring routes information flow through hippocampal CA3","external_id":{"isi":["001544472300002"]},"publication":"Cell Reports","publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"article_number":"116080","department":[{"_id":"PeJo"}],"ec_funded":1,"doi":"10.1016/j.celrep.2025.116080","ddc":["570"],"has_accepted_license":"1","language":[{"iso":"eng"}],"volume":44,"fulldoi":"https://doi.org/10.1016/j.celrep.2025.116080","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Neuronal circuits in health and disease (Jonas)","grant_number":"COE16","_id":"0a6c8641-b036-11f1-bacf-e4eec62b5bb4"}],"file":[{"date_created":"2025-08-04T06:53:07Z","success":1,"access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"20106","content_type":"application/pdf","file_size":27695214,"checksum":"556ff9760661ecd23949d75031043b1f","file_name":"2025_CellReports_Watson.pdf","date_updated":"2025-08-04T06:53:07Z"}],"oa_version":"Published Version","citation":{"ieee":"J. Watson, V. M. Vargas Barroso, and P. M. Jonas, “Cell-specific wiring routes information flow through hippocampal CA3,” <i>Cell Reports</i>, vol. 44, no. 8. Elsevier, 2025.","ista":"Watson J, Vargas Barroso VM, Jonas PM. 2025. Cell-specific wiring routes information flow through hippocampal CA3. Cell Reports. 44(8), 116080.","chicago":"Watson, Jake, Victor M Vargas Barroso, and Peter M Jonas. “Cell-Specific Wiring Routes Information Flow through Hippocampal CA3.” <i>Cell Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">https://doi.org/10.1016/j.celrep.2025.116080</a>.","ama":"Watson J, Vargas Barroso VM, Jonas PM. Cell-specific wiring routes information flow through hippocampal CA3. <i>Cell Reports</i>. 2025;44(8). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">10.1016/j.celrep.2025.116080</a>","apa":"Watson, J., Vargas Barroso, V. M., &#38; Jonas, P. M. (2025). Cell-specific wiring routes information flow through hippocampal CA3. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">https://doi.org/10.1016/j.celrep.2025.116080</a>","mla":"Watson, Jake, et al. “Cell-Specific Wiring Routes Information Flow through Hippocampal CA3.” <i>Cell Reports</i>, vol. 44, no. 8, 116080, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">10.1016/j.celrep.2025.116080</a>.","short":"J. Watson, V.M. Vargas Barroso, P.M. Jonas, Cell Reports 44 (2025)."},"scopus_import":"1","OA_place":"publisher","DOAJ_listed":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"year":"2025","publisher":"Elsevier","OA_type":"gold","acknowledgement":"We thank Andrea Navas-Olive and Rebecca J. Morse-Mora for critically reading an earlier version of the manuscript. We also thank Florian Marr and Christina Altmutter for excellent technical assistance, Alois Schlögl for programming and data-handling assistance, Todor Asenov for technical support, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA. We are particularly grateful for assistance from the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, and Miba Machine Shop. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692 to P.J., Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W., and an ISTplus Fellowship through Marie Skłodowska-Curie grant agreement no. 754411 to V.V.-B.), the Austrian Science Fund (P 36232-B, PAT 4178023, and Cluster of Excellence 10.55776/COE16 to P.J.), and a CONACyT fellowship (289638 to V.V.-B.) and was supported by a non-stipendiary EMBO fellowship (ALTF 756–2020 to J.F.W.).","intvolume":"        44","file_date_updated":"2025-08-04T06:53:07Z","abstract":[{"text":"The hippocampus, critical for learning and memory, is dogmatically described as a trisynaptic circuit where dentate gyrus granule cells (GCs), CA3 pyramidal neurons (PNs), and CA1 PNs are serially connected. However, CA3 also forms an autoassociative network, and its PNs have diverse morphologies, intrinsic properties, and GC input levels. How PN subtypes compose this recurrent network is unknown. To determine the synaptic arrangement of identified CA3 PNs, we combine multicellular patch-clamp recording and post hoc morphological analysis in mouse hippocampal slices. PNs can be divided into distinct “superficial” and “deep” subclasses, the latter including previously reported “athorny” cells. Subclasses have distinct input-output transformations and asymmetric connectivity, which is more abundant from superficial to deep PNs, splitting CA3 locally into two parallel recurrent networks. Coincident spontaneous inhibition occurs frequently within but not between subclasses, implying subclass-specific inhibitory innervation. Our results suggest two separately controlled sublayers for parallel information processing in hippocampal CA3.","lang":"eng"}],"date_published":"2025-08-01T00:00:00Z","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"01","oa":1,"PlanS_conform":"1","month":"08","date_updated":"2026-09-16T06:58:59Z","date_created":"2025-08-03T22:01:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20099","status":"public","article_processing_charge":"Yes","isi":1,"type":"journal_article","issue":"8","article_type":"original","corr_author":"1","author":[{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","last_name":"Watson","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823"},{"full_name":"Vargas Barroso, Victor M","last_name":"Vargas Barroso","first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"}]},{"OA_place":"publisher","publisher":"Springer Nature","year":"2025","volume":15,"language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"mla":"Hübner, Valentin, et al. “Time-Dependent Strategies in Repeated Asymmetric Public Goods Games.” <i>Dynamic Games and Applications</i>, vol. 15, Springer Nature, 2025, pp. 1617–45, doi:<a href=\"https://doi.org/10.1007/s13235-025-00627-5\">10.1007/s13235-025-00627-5</a>.","apa":"Hübner, V., Hilbe, C., Staab, M., Kleshnina, M., &#38; Chatterjee, K. (2025). Time-dependent strategies in repeated asymmetric public goods games. <i>Dynamic Games and Applications</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s13235-025-00627-5\">https://doi.org/10.1007/s13235-025-00627-5</a>","short":"V. Hübner, C. Hilbe, M. Staab, M. Kleshnina, K. Chatterjee, Dynamic Games and Applications 15 (2025) 1617–1645.","ama":"Hübner V, Hilbe C, Staab M, Kleshnina M, Chatterjee K. Time-dependent strategies in repeated asymmetric public goods games. <i>Dynamic Games and Applications</i>. 2025;15:1617-1645. doi:<a href=\"https://doi.org/10.1007/s13235-025-00627-5\">10.1007/s13235-025-00627-5</a>","chicago":"Hübner, Valentin, Christian Hilbe, Manuel Staab, Maria Kleshnina, and Krishnendu Chatterjee. “Time-Dependent Strategies in Repeated Asymmetric Public Goods Games.” <i>Dynamic Games and Applications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s13235-025-00627-5\">https://doi.org/10.1007/s13235-025-00627-5</a>.","ieee":"V. Hübner, C. Hilbe, M. Staab, M. Kleshnina, and K. Chatterjee, “Time-dependent strategies in repeated asymmetric public goods games,” <i>Dynamic Games and Applications</i>, vol. 15. Springer Nature, pp. 1617–1645, 2025.","ista":"Hübner V, Hilbe C, Staab M, Kleshnina M, Chatterjee K. 2025. Time-dependent strategies in repeated asymmetric public goods games. Dynamic Games and Applications. 15, 1617–1645."},"scopus_import":"1","file":[{"file_size":1126178,"checksum":"de0a412cbb7d98bf5e6a551c26acbefa","file_name":"2025_DynGamesAppl_Huebner.pdf","date_updated":"2025-12-30T08:01:35Z","creator":"dernst","relation":"main_file","file_id":"20888","content_type":"application/pdf","access_level":"open_access","date_created":"2025-12-30T08:01:35Z","success":1}],"fulldoi":"https://doi.org/10.1007/s13235-025-00627-5","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"department":[{"_id":"KrCh"}],"has_accepted_license":"1","ddc":["000"],"doi":"10.1007/s13235-025-00627-5","external_id":{"isi":["001415587800001"]},"title":"Time-dependent strategies in repeated asymmetric public goods games","publication_status":"published","publication_identifier":{"eissn":["2153-0793"],"issn":["2153-0785"]},"publication":"Dynamic Games and Applications","type":"journal_article","isi":1,"author":[{"id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","first_name":"Valentin","full_name":"Hübner, Valentin","orcid":"0009-0001-5009-4987","last_name":"Hübner"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"first_name":"Manuel","last_name":"Staab","full_name":"Staab, Manuel"},{"full_name":"Kleshnina, Maria","orcid":"0000-0002-5518-8317","last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"corr_author":"1","article_type":"original","page":"1617-1645","related_material":{"record":[{"status":"public","id":"19903","relation":"dissertation_contains"}]},"_id":"19074","date_created":"2025-02-23T23:01:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","status":"public","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","day":"01","date_published":"2025-11-01T00:00:00Z","date_updated":"2026-09-16T06:58:23Z","month":"11","PlanS_conform":"1","OA_type":"hybrid","abstract":[{"lang":"eng","text":"The public goods game is among the most studied metaphors of cooperation in groups. In this game, individuals can use their endowments to make contributions towards a good that benefits everyone. Each individual, however, is tempted to free-ride on the contributions of others. Herein, we study repeated public goods games among asymmetric players. Previous work has explored to which extent asymmetry allows for full cooperation, such that players contribute their full endowment each round. However, by design that work focusses on equilibria where individuals make the same contribution each round. Instead, here we consider players whose contributions along the equilibrium path can change from one round to the next. We do so for three different models – one without any budget constraints, one with endowment constraints, and one in which individuals can save their current endowment to be used in subsequent rounds. In each case, we explore two key quantities: the welfare and the resource efficiency that can be achieved in equilibrium. Welfare corresponds to the sum of all players’ payoffs. Resource efficiency relates this welfare to the total contributions made by the players. Compared to constant contribution sequences, we find that time-dependent contributions can improve resource efficiency across all three models. Moreover, they can improve the players’ welfare in the model with savings."}],"file_date_updated":"2025-12-30T08:01:35Z","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010), and ARC SRIEAS Grant SR200100005 Securing Antarctica’s Environmental Future (to M.K.). Open access funding provided by Institute of Science and Technology (IST Austria).","intvolume":"        15"},{"article_processing_charge":"Yes (via OA deal)","status":"public","_id":"20324","related_material":{"record":[{"id":"18057","relation":"earlier_version","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-09-10T05:41:30Z","author":[{"first_name":"Soham","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","full_name":"Mukhopadhyay, Soham","orcid":"0000-0001-5263-5559","last_name":"Mukhopadhyay"},{"full_name":"Lancheros Naranjo, Diego A","last_name":"Lancheros Naranjo","id":"6c55e976-15b2-11ec-abd3-d790e8937fde","first_name":"Diego A"},{"first_name":"Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295","last_name":"Senior"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"}],"article_type":"original","corr_author":"1","isi":1,"type":"journal_article","intvolume":"        24","acknowledgement":"We gratefully acknowledge support from the Miba Machine Shop and the Nanofabrictation Facility at IST Austria. This work was supported by the Austrian FWF under Grant No. P33692-N (S.M., J.S., and A.P.H.), the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS Foundation research grant (A.P.H.).","file_date_updated":"2025-09-10T07:29:06Z","abstract":[{"text":"We report relaxation oscillations in a one-dimensional array of Josephson junctions, wherein the array dynamically switches between low-current and high-current states. The oscillations are current-voltage dual to those ordinarily observed in single junctions. The current-voltage dual circuit quantitatively accounts for temporal dynamics of the array, including the dependence on biasing conditions. Injection locking of the oscillations results in well-developed current plateaux. A thermal model explains the self-consistent reduction of the superconducting gap due to overheating of the array in the high-current state. Our work suggests that overheating determines the switching from the high-current state to the low-current state.","lang":"eng"}],"OA_type":"hybrid","date_updated":"2026-09-24T10:13:38Z","month":"07","PlanS_conform":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","day":"17","oa":1,"date_published":"2025-07-17T00:00:00Z","citation":{"short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, Physical Review Applied 24 (2025).","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson-Junction Array.” <i>Physical Review Applied</i>, vol. 24, 014035, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/qvls-7s3q\">10.1103/qvls-7s3q</a>.","apa":"Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., &#38; Higginbotham, A. P. (2025). Dual relaxation oscillations in a Josephson-junction array. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/qvls-7s3q\">https://doi.org/10.1103/qvls-7s3q</a>","ama":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson-junction array. <i>Physical Review Applied</i>. 2025;24. doi:<a href=\"https://doi.org/10.1103/qvls-7s3q\">10.1103/qvls-7s3q</a>","chicago":"Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson-Junction Array.” <i>Physical Review Applied</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/qvls-7s3q\">https://doi.org/10.1103/qvls-7s3q</a>.","ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. 2025. Dual relaxation oscillations in a Josephson-junction array. Physical Review Applied. 24, 014035.","ieee":"S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson-junction array,” <i>Physical Review Applied</i>, vol. 24. American Physical Society, 2025."},"scopus_import":"1","oa_version":"Published Version","fulldoi":"https://doi.org/10.1103/qvls-7s3q","project":[{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"file":[{"file_name":"2025_PhysReviewAppl_Mukhopadhyay.pdf","date_updated":"2025-09-10T07:29:06Z","checksum":"6cc3c9beeb7c0a88ee0a072c9a32b78b","file_size":1370466,"file_id":"20335","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","success":1,"date_created":"2025-09-10T07:29:06Z"}],"volume":24,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"year":"2025","publisher":"American Physical Society","OA_place":"publisher","publication":"Physical Review Applied","publication_identifier":{"issn":["2331-7019"]},"article_number":"014035","external_id":{"isi":["001537333100001"],"arxiv":["2408.07829 "]},"publication_status":"published","title":"Dual relaxation oscillations in a Josephson-junction array","has_accepted_license":"1","doi":"10.1103/qvls-7s3q","ddc":["530"],"ec_funded":1,"arxiv":1,"department":[{"_id":"GradSch"},{"_id":"AnHi"}]},{"oa":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"01","date_published":"2025-04-01T00:00:00Z","date_updated":"2026-10-01T11:19:12Z","PlanS_conform":"1","month":"04","OA_type":"hybrid","abstract":[{"lang":"eng","text":"Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens. "}],"file_date_updated":"2025-07-31T07:03:43Z","acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\nThis project has received funding from the European Research Council under the Horizon 2020 Framework Programme (grant agreement No 742985, J.F.). It has also received funding from the Horizon 2020 Framework Programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 (M.G.). S.T. has received funding as an ISTplus Fellow from the Horizon 2020 Framework Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from EMBO via a Long-Term Fellowship (grant number ALTF 679-2018). M.R.T. received funding from the Austrian Academy of Sciences with DOC fellowship no. 26137. The project has further received funding from the Austrian Science Fund, via grant DK W1232 (M.R.T., N.A.D., and J.G.D). W.J. received a postdoctoral fellowship from the Human Frontier Science Program (LT000557/2018). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","intvolume":"        37","isi":1,"type":"journal_article","issue":"4","author":[{"last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"last_name":"Truckenbrodt","full_name":"Truckenbrodt, Sven M","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Inumella, Syamala","orcid":"0009-0002-5890-120X","last_name":"Inumella","first_name":"Syamala","id":"F8660870-D756-11E9-98C5-34DFE5697425"},{"first_name":"Vitali","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","full_name":"Vistunou, Vitali","last_name":"Vistunou"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"last_name":"Tavakoli","orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","first_name":"Nathalie","last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie"},{"full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","last_name":"Vorlaufer","first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425"},{"orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke","last_name":"Jahr","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","full_name":"Randuch, Marek"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"article_type":"original","corr_author":"1","related_material":{"record":[{"relation":"research_data","id":"18837","status":"public"},{"id":"18689","relation":"earlier_version","status":"public"}]},"_id":"19003","date_created":"2025-02-05T06:52:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","status":"public","ec_funded":1,"department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"has_accepted_license":"1","ddc":["580"],"doi":"10.1093/plcell/koaf006","external_id":{"pmid":["39792900"],"isi":["001462763100001"]},"title":"Super-resolution expansion microscopy in plant roots","publication_status":"published","article_number":"koaf006","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"publication":"The Plant Cell","pmid":1,"OA_place":"publisher","publisher":"Oxford University Press","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"M-Shop"}],"year":"2025","volume":37,"language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","citation":{"mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>The Plant Cell</i>, vol. 37, no. 4, koaf006, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/plcell/koaf006\">10.1093/plcell/koaf006</a>.","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (2025). Super-resolution expansion microscopy in plant roots. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koaf006\">https://doi.org/10.1093/plcell/koaf006</a>","short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, The Plant Cell 37 (2025).","ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>The Plant Cell</i>. 2025;37(4). doi:<a href=\"https://doi.org/10.1093/plcell/koaf006\">10.1093/plcell/koaf006</a>","chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>The Plant Cell</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/plcell/koaf006\">https://doi.org/10.1093/plcell/koaf006</a>.","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>The Plant Cell</i>, vol. 37, no. 4. Oxford University Press, 2025.","ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. 2025. Super-resolution expansion microscopy in plant roots. The Plant Cell. 37(4), koaf006."},"file":[{"creator":"dernst","relation":"main_file","file_id":"20092","content_type":"application/pdf","date_updated":"2025-07-31T07:03:43Z","file_name":"2025_PlantCell_Gallei.pdf","file_size":53904111,"checksum":"9d3f8218ff37a29f29c48a7bbe831bd3","date_created":"2025-07-31T07:03:43Z","success":1,"access_level":"open_access"}],"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"269B5B22-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 679-2018","name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED"},{"grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets"}],"fulldoi":"https://doi.org/10.1093/plcell/koaf006"},{"language":[{"iso":"eng"}],"citation":{"apa":"Hübner, V. (2025). <i>Reciprocity and inequality in social dilemmas</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19903\">https://doi.org/10.15479/AT-ISTA-19903</a>","mla":"Hübner, Valentin. <i>Reciprocity and Inequality in Social Dilemmas</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19903\">10.15479/AT-ISTA-19903</a>.","short":"V. Hübner, Reciprocity and Inequality in Social Dilemmas, Institute of Science and Technology Austria, 2025.","ista":"Hübner V. 2025. Reciprocity and inequality in social dilemmas. Institute of Science and Technology Austria.","ieee":"V. Hübner, “Reciprocity and inequality in social dilemmas,” Institute of Science and Technology Austria, 2025.","chicago":"Hübner, Valentin. “Reciprocity and Inequality in Social Dilemmas.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19903\">https://doi.org/10.15479/AT-ISTA-19903</a>.","ama":"Hübner V. Reciprocity and inequality in social dilemmas. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19903\">10.15479/AT-ISTA-19903</a>"},"oa_version":"Published Version","fulldoi":"https://doi.org/10.15479/AT-ISTA-19903","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"COE12","_id":"4029cfc7-b034-11f1-9e55-88ab2ff3b6ee","name":"Bilateral Artificial Intelligence (Chatterjee)"}],"file":[{"access_level":"closed","date_created":"2025-06-25T13:38:07Z","file_size":6192760,"checksum":"794c02f8c82ca59ba6dda3bd7eed871a","file_name":"Thesis Valentin Hübner source.tar.xz","date_updated":"2025-06-25T13:38:07Z","file_id":"19905","content_type":"application/x-xz","creator":"vhuebner","relation":"source_file"},{"date_created":"2025-07-09T13:37:00Z","access_level":"open_access","relation":"main_file","creator":"vhuebner","content_type":"application/pdf","file_id":"19976","file_name":"Thesis Valentin Hübner.pdf","date_updated":"2025-07-09T13:37:00Z","checksum":"ac56063d81c81e40322b6ff5a8c4912e","file_size":4837864}],"OA_place":"publisher","doi_confirm":"1","year":"2025","publisher":"Institute of Science and Technology Austria","publication_status":"published","title":"Reciprocity and inequality in social dilemmas","supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"has_accepted_license":"1","degree_awarded":"PhD","doi":"10.15479/AT-ISTA-19903","ddc":["519"],"_id":"19903","related_material":{"record":[{"status":"public","id":"19843","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"19074"},{"status":"public","relation":"part_of_dissertation","id":"15083"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-06-25T13:50:10Z","article_processing_charge":"No","status":"public","type":"dissertation","author":[{"last_name":"Hübner","orcid":"0009-0001-5009-4987","full_name":"Hübner, Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","first_name":"Valentin"}],"corr_author":"1","page":"157","acknowledgement":"The research for this thesis was supported by the European Research Council\r\n(grant agreements No. 863818 and No. 850529), the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie grant agreement No. 754411),\r\nthe Austrian Science Fund (grant DOI 10.55776/COE12), the French Agence Nationale\r\nde la Recherche under the Programme d’investissements d’avenir (project reference 17-\r\nEURE-0010) and the Australian Government through the Australian Research Council\r\n(grant No. SR200100005, “Securing Antarctica’s Environmental Future”).","abstract":[{"text":"Cooperation, that is, one person paying a cost for another's benefit, is a fundamental principle without which no form of society could exist. The extent to which humans cooperate with each other is also an essential feature that differentiates them from other animals. Cooperation occurs even in the absence of altruistic motivations, when it is selfishly incentivised by the expectation of a future reward. For example, many economic interactions are well described that way. This kind of cooperation requires that people exhibit reciprocal behaviour that acts as a mechanism that rewards cooperation.\r\nWith game-theoretic models, it is possible to formally study potential such mechanisms and under what conditions they can exist. This thesis contributes to this effort by analysing recently introduced models of cooperation that advance on previous work by taking into account the potential for pre-existing inequality among cooperating individuals as well as the different forms that reciprocity can take.\r\nIndividuals may differ both intrinsically, in their abilities, as well as extrinsically, in the amount of resources they have available. Allowing for such differences in a model of cooperation helps to understand how inequality affects the potential for, and outcomes of, cooperation among unequals. In this thesis, it is shown that in the presence of intrinsic inequality, a similar unequal distribution of resources can increase the potential for cooperation. This effect is stronger the smaller the group is in which cooperation takes place. It is also shown that under particular assumptions, if the unequal members of a group vary the size of their contributions to a cooperative effort over time, they can thereby increase their efficiency and improve the collective outcome.\r\nCooperative behaviour in a two-person interaction can be rewarded either by direct reciprocation whenever the same two people interact again, or indirectly by a third party who observed the interaction. In the latter case of indirect reciprocity, individuals are proximally rewarded by a good reputation, which ultimately translates to being rewarded with cooperative behaviour by others. This mechanism can enable selfishly motivated cooperation even in circumstances where individuals are unlikely to meet again, akin to how money facilitates trade. While these two forms of reciprocity have mostly been studied in isolation, this thesis analyses both direct and indirect reciprocity in a general model in order to compare their relative effectiveness under different circumstances. The contribution of this thesis is an extension of previous work regarding a specific kind of interaction, whose parameters allow for convenient mathematical analysis, to the most general set of possible interactions.","lang":"eng"}],"file_date_updated":"2025-07-09T13:37:00Z","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"day":"25","oa":1,"date_published":"2025-06-25T00:00:00Z","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-15T10:10:25Z","month":"06"},{"article_processing_charge":"Yes (in subscription journal)","status":"public","_id":"14683","date_created":"2023-12-13T11:48:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207"},{"orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"article_type":"review","corr_author":"1","issue":"1","type":"journal_article","file_date_updated":"2024-07-16T11:50:03Z","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1"}],"intvolume":"         5","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","date_updated":"2025-04-15T08:23:06Z","month":"03","oa":1,"day":"15","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","date_published":"2024-03-15T00:00:00Z","citation":{"short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024).","apa":"Amberg, N., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>.","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2024. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024.","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>.","ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>"},"scopus_import":"1","oa_version":"Published Version","file":[{"checksum":"3f0ee62e04bf5a44b45b035662826e95","file_size":8871807,"file_name":"2024_STARProtoc_Amberg.pdf","date_updated":"2024-07-16T11:50:03Z","relation":"main_file","creator":"dernst","file_id":"17260","content_type":"application/pdf","access_level":"open_access","date_created":"2024-07-16T11:50:03Z","success":1}],"project":[{"call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T01031","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"fulldoi":"https://doi.org/10.1016/j.xpro.2023.102771","volume":5,"language":[{"iso":"eng"}],"publisher":"Elsevier","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"year":"2024","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"pmid":1,"article_number":"102771","publication":"STAR Protocols","publication_identifier":{"issn":["2666-1667"]},"external_id":{"pmid":["38070137"]},"title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","publication_status":"published","has_accepted_license":"1","ddc":["570"],"doi":"10.1016/j.xpro.2023.102771","ec_funded":1,"department":[{"_id":"SiHi"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-06-30T22:01:04Z","_id":"17187","status":"public","article_processing_charge":"Yes","type":"journal_article","issue":"3","article_type":"original","corr_author":"1","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","full_name":"Streicher, Carmen"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"OA_type":"gold","file_date_updated":"2025-01-09T12:12:40Z","abstract":[{"text":"The generation of diverse cell types during development is fundamental to brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks of lineage progression with precise spatial resolution in the brain.\r\nFor complete details on the use and execution of this protocol, please refer to\r\nCheung et al.1","lang":"eng"}],"acknowledgement":"We thank A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","intvolume":"         5","date_published":"2024-09-20T00:00:00Z","oa":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"20","month":"09","date_updated":"2025-12-30T10:54:11Z","language":[{"iso":"eng"}],"volume":5,"file":[{"file_name":"2024_STARProtoc_Cheung.pdf","date_updated":"2025-01-09T12:12:40Z","file_size":5186071,"checksum":"d8a8cdba82a394e731aa699ace1ae433","creator":"dernst","relation":"main_file","file_id":"18809","content_type":"application/pdf","access_level":"open_access","date_created":"2025-01-09T12:12:40Z","success":1}],"fulldoi":"https://doi.org/10.1016/j.xpro.2024.103157","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"scopus_import":"1","oa_version":"Published Version","citation":{"ama":"Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>","chicago":"Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>.","ieee":"G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","ista":"Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 5(3), 103157.","mla":"Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>, vol. 5, no. 3, 103157, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>.","apa":"Cheung, G. T., Streicher, C., &#38; Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>","short":"G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024)."},"pmid":1,"OA_place":"publisher","publisher":"Elsevier","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"year":"2024","title":"Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice","publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"pmid":["38935508"]},"article_number":"103157","publication":"STAR Protocols","publication_identifier":{"eissn":["2666-1667"]},"department":[{"_id":"SiHi"}],"ec_funded":1,"APC_amount":"804 EUR","ddc":["570"],"doi":"10.1016/j.xpro.2024.103157","has_accepted_license":"1"},{"external_id":{"isi":["001260942200003"]},"publication_status":"published","title":"Effect of ion irradiation on superconducting thin films","publication_identifier":{"eissn":["2166-532X"]},"publication":"APL Materials","article_number":"071101","ec_funded":1,"department":[{"_id":"AnHi"}],"has_accepted_license":"1","doi":"10.1063/5.0202851","ddc":["530"],"volume":12,"language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"short":"K. Kohopää, A. Ronzani, R.N. Jabdaraghi, A. Bera, M. Ribeiro, D. Hazra, J.L. Senior, M. Prunnila, J. Govenius, J.S. Lehtinen, A. Kemppinen, APL Materials 12 (2024).","mla":"Kohopää, Katja, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” <i>APL Materials</i>, vol. 12, no. 7, 071101, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0202851\">10.1063/5.0202851</a>.","apa":"Kohopää, K., Ronzani, A., Jabdaraghi, R. N., Bera, A., Ribeiro, M., Hazra, D., … Kemppinen, A. (2024). Effect of ion irradiation on superconducting thin films. <i>APL Materials</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0202851\">https://doi.org/10.1063/5.0202851</a>","chicago":"Kohopää, Katja, Alberto Ronzani, Robab Najafi Jabdaraghi, Arijit Bera, Mário Ribeiro, Dibyendu Hazra, Jorden L Senior, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” <i>APL Materials</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0202851\">https://doi.org/10.1063/5.0202851</a>.","ama":"Kohopää K, Ronzani A, Jabdaraghi RN, et al. Effect of ion irradiation on superconducting thin films. <i>APL Materials</i>. 2024;12(7). doi:<a href=\"https://doi.org/10.1063/5.0202851\">10.1063/5.0202851</a>","ista":"Kohopää K, Ronzani A, Jabdaraghi RN, Bera A, Ribeiro M, Hazra D, Senior JL, Prunnila M, Govenius J, Lehtinen JS, Kemppinen A. 2024. Effect of ion irradiation on superconducting thin films. APL Materials. 12(7), 071101.","ieee":"K. Kohopää <i>et al.</i>, “Effect of ion irradiation on superconducting thin films,” <i>APL Materials</i>, vol. 12, no. 7. AIP Publishing, 2024."},"scopus_import":"1","fulldoi":"https://doi.org/10.1063/5.0202851","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"file":[{"file_name":"2024_APLMaterial_Kohopaa.pdf","date_updated":"2024-07-16T06:30:30Z","checksum":"32a5cdf0ea9c937f806b6039f3219917","file_size":9408198,"file_id":"17244","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","success":1,"date_created":"2024-07-16T06:30:30Z"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"year":"2024","publisher":"AIP Publishing","acknowledgement":"We thank J. A. Sauls for useful discussions. For funding of our research project, we acknowledge the European Union’s Horizon 2020 Research and Innovation Program under Grant Agreement Nos. 862660/Quantum e-leaps, 899558/aCryComm, 766853/EFINED, and ECSEL programme 101007322/MatQu. This project has also received funding from Business Finland through Quantum Technologies Industrial (QuTI) Project No. 128291 and from Research Council of Finland through Grant Nos. 310909, 350220 and Finnish Quantum Flagship project 359284. This work was performed as part of the Research Council of Finland Centres of Excellence program (Project Nos. 336817, 336819, 352934, and 352935). We also acknowledge funding from an internal strategic innovation project of VTT related to the development of quantum computing technologies. This research was supported by the Scientific Service Units of IST Austria through resources provided by Electron Microscopy Facility. J. Senior acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. Ronzani acknowledges funding from Research Council of Finland (Research Fellowship Project No. 356542).","intvolume":"        12","file_date_updated":"2024-07-16T06:30:30Z","abstract":[{"text":"We demonstrate ion irradiation by argon or gallium as a wafer-scale post-processing method to increase disorder in superconducting thin films. We study several widely used superconductors, both single-elements and compounds. We show that ion irradiation increases normal-state resistivity in all our films, which is expected to enable tuning their superconducting properties, for example, toward a higher kinetic inductance. We observe an increase in superconducting transition temperature for Al and MoSi and a decrease for Nb, NbN, and TiN. In MoSi, ion irradiation also improves the mixing of the two materials. We demonstrate the fabrication of an amorphous and homogeneous film of MoSi with uniform thickness, which is promising, for example, for superconducting nanowire single-photon detectors.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","day":"01","oa":1,"date_published":"2024-07-01T00:00:00Z","date_updated":"2025-09-08T08:10:58Z","month":"07","_id":"17235","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-14T22:01:11Z","article_processing_charge":"Yes","status":"public","type":"journal_article","isi":1,"issue":"7","author":[{"full_name":"Kohopää, Katja","last_name":"Kohopää","first_name":"Katja"},{"first_name":"Alberto","last_name":"Ronzani","full_name":"Ronzani, Alberto"},{"full_name":"Jabdaraghi, Robab Najafi","last_name":"Jabdaraghi","first_name":"Robab Najafi"},{"first_name":"Arijit","full_name":"Bera, Arijit","last_name":"Bera"},{"full_name":"Ribeiro, Mário","last_name":"Ribeiro","first_name":"Mário"},{"last_name":"Hazra","full_name":"Hazra, Dibyendu","first_name":"Dibyendu"},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L","last_name":"Senior","full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295"},{"first_name":"Mika","full_name":"Prunnila, Mika","last_name":"Prunnila"},{"last_name":"Govenius","full_name":"Govenius, Joonas","first_name":"Joonas"},{"first_name":"Janne S.","last_name":"Lehtinen","full_name":"Lehtinen, Janne S."},{"first_name":"Antti","full_name":"Kemppinen, Antti","last_name":"Kemppinen"}],"article_type":"original"},{"acknowledgement":"For the beetle barcoding, we are very thankful to Brent Emerson’s laboratory at the Consejo Superior de Investigaciones Científicas (CSIC) at the Instituto de Productos Naturales y Agrobiología (IPNA) in La Laguna, Tenerife. Many thanks to numerous field assistants, especially Sandra Cuevas Gallego, Beatriz Pablo Carmona, Luís Santos Cid and Alex Fuster, for their assistance in data collection. Finally, we thank Jesús Muñoz, Virgilio Gómez-Rubio, and two anonymous reviewers for comments that greatly improved the quality of the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). CB received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. NB was funded by the FWF grant “Löwenmaul speciation” P 32166-B32.","intvolume":"        39","file_date_updated":"2024-09-11T07:14:03Z","abstract":[{"lang":"eng","text":"Context: Biotic resource exploitation is a critical determinant of species’ distributions. However, quantifying resource exploitation patterns through space and time can be difficult, complicating their incorporation in spatial ecology studies. Therefore, understanding the local drivers of spatial patterns of resource exploitation may contribute to better large-scale species distribution models.\r\nObjectives: We investigated (1) how the resource exploitation patterns of two trophic interactions (plant–insect) are explained by insect behaviour, resource aggregation, and potential insect-insect interactions. We also analyzed how (2) resource patch size and (3) resource accessibility in a heterogeneous landscape affected host exploitation patterns.\r\nMethods: We quantified nectar robbing by insects in the genus Bombus (bumblebees) and seed predation by Brachypterolus vestitus larvae (Antirrhinum beetle) on Antirrhinum majus L. (wild snapdragons) in the Pyrenees Mountains, Catalonia, Spain. We tested hypotheses about resource exploitation by integrating spatial analyses at multiple scales.\r\nResults: Both trophic interactions were aggregated, explained by the aggregation of their resource. At some scales, nectar robbing is more aggregated than the resource. Trophic interaction abundance is proportional to resource patch size, following the ideal free distribution model. Landscape features do not explain the locations exploited. Nectar robbing and seed predation occur together more often than expected.\r\nConclusions: Our findings suggest that multiple biotic and ecological spatial factors may simultaneously affect resource exploitation at a local scale. These findings should be considered when developing agricultural projects, management plans and conservation policies."}],"date_published":"2024-09-01T00:00:00Z","day":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","oa":1,"month":"09","date_updated":"2025-09-08T09:20:11Z","date_created":"2024-09-08T22:01:11Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17888","status":"public","article_processing_charge":"Yes (via OA deal)","issue":"9","type":"journal_article","isi":1,"corr_author":"1","article_type":"original","author":[{"id":"54359172-700c-11ef-a103-c1d91ceac6d6","first_name":"Guillem","full_name":"Pocull Belles, Guillem","last_name":"Pocull Belles"},{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"publication_status":"published","title":"Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects","external_id":{"isi":["001304011900001"]},"publication_identifier":{"eissn":["1572-9761"],"issn":["0921-2973"]},"publication":"Landscape Ecology","article_number":"172","department":[{"_id":"NiBa"}],"ec_funded":1,"doi":"10.1007/s10980-024-01899-9","ddc":["570"],"has_accepted_license":"1","language":[{"iso":"eng"}],"volume":39,"fulldoi":"https://doi.org/10.1007/s10980-024-01899-9","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"Snapdragon Speciation"}],"file":[{"file_name":"2024_LandscapeEcology_Pocull.pdf","date_updated":"2024-09-11T07:14:03Z","checksum":"2e1cbc320ec1b4447a5a8562a90bcbc3","file_size":1494987,"file_id":"18054","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","success":1,"date_created":"2024-09-11T07:14:03Z"}],"scopus_import":"1","oa_version":"Published Version","citation":{"apa":"Pocull Belles, G., Baskett, C., &#38; Barton, N. H. (2024). Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. <i>Landscape Ecology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10980-024-01899-9\">https://doi.org/10.1007/s10980-024-01899-9</a>","mla":"Pocull Belles, Guillem, et al. “Multiscale Spatial Analysis of Two Plant–Insect Interactions: Effects of Landscape, Resource Distribution, and Other Insects.” <i>Landscape Ecology</i>, vol. 39, no. 9, 172, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s10980-024-01899-9\">10.1007/s10980-024-01899-9</a>.","short":"G. Pocull Belles, C. Baskett, N.H. Barton, Landscape Ecology 39 (2024).","ieee":"G. Pocull Belles, C. Baskett, and N. H. Barton, “Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects,” <i>Landscape Ecology</i>, vol. 39, no. 9. Springer Nature, 2024.","ista":"Pocull Belles G, Baskett C, Barton NH. 2024. Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. Landscape Ecology. 39(9), 172.","ama":"Pocull Belles G, Baskett C, Barton NH. Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. <i>Landscape Ecology</i>. 2024;39(9). doi:<a href=\"https://doi.org/10.1007/s10980-024-01899-9\">10.1007/s10980-024-01899-9</a>","chicago":"Pocull Belles, Guillem, Carina Baskett, and Nicholas H Barton. “Multiscale Spatial Analysis of Two Plant–Insect Interactions: Effects of Landscape, Resource Distribution, and Other Insects.” <i>Landscape Ecology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s10980-024-01899-9\">https://doi.org/10.1007/s10980-024-01899-9</a>."},"year":"2024","publisher":"Springer Nature"},{"researchdata_availability":"no","acknowledgement":"This research has been supported by the European Research Council (ERC), grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant No. I 02979-N35.\r\nWintraecken, Mathijs: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) grant No. M-3073, and the welcome package from IDEX of the Université Côte d'Azur.","intvolume":"       293","file_date_updated":"2024-06-25T11:47:26Z","abstract":[{"text":"In this article we extend and strengthen the seminal work by Niyogi, Smale, and Weinberger on the learning of the homotopy type from a sample of an underlying space. In their work, Niyogi, Smale, and Weinberger studied samples of C² manifolds with positive reach embedded in ℝ^d. We extend their results in the following ways: - As the ambient space we consider both ℝ^d and Riemannian manifolds with lower bounded sectional curvature. - In both types of ambient spaces, we study sets of positive reach - a significantly more general setting than C² manifolds - as well as general manifolds of positive reach. - The sample P of a set (or a manifold) 𝒮 of positive reach may be noisy. We work with two one-sided Hausdorff distances - ε and δ - between P and 𝒮. We provide tight bounds in terms of ε and δ, that guarantee that there exists a parameter r such that the union of balls of radius r centred at the sample P deformation-retracts to 𝒮. We exhibit their tightness by an explicit construction. We carefully distinguish the roles of δ and ε. This is not only essential to achieve tight bounds, but also sensible in practical situations, since it allows one to adapt the bound according to sample density and the amount of noise present in the sample separately.","lang":"eng"}],"date_published":"2024-06-06T00:00:00Z","alternative_title":["LIPIcs"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","day":"06","oa":1,"month":"06","date_updated":"2026-10-02T11:23:43Z","date_created":"2024-06-25T11:45:58Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17170","status":"public","article_processing_charge":"No","supplementarymaterial":"no","type":"conference","conference":{"start_date":"2024-06-11","end_date":"2024-06-14","name":"SoCG: Symposium on Computational Geometry","location":"Athens, Greece"},"page":"11:1-11:19","author":[{"first_name":"Dominique","full_name":"Attali, Dominique","last_name":"Attali"},{"full_name":"Kourimska, Hana","orcid":"0000-0001-7841-0091","last_name":"Kourimska","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","first_name":"Hana"},{"id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","first_name":"Christopher D","last_name":"Fillmore","full_name":"Fillmore, Christopher D"},{"first_name":"Ishika","id":"ee449b28-344d-11ef-a6d5-9ca430e9e9ff","full_name":"Ghosh, Ishika","last_name":"Ghosh"},{"full_name":"Lieutier, André","last_name":"Lieutier","first_name":"André"},{"first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X","last_name":"Stephenson"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"publication_status":"published","das_tickbox":"0","title":"Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds","external_id":{"arxiv":["2206.10485"]},"publication":"40th International Symposium on Computational Geometry","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959773164"]},"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"arxiv":1,"ec_funded":1,"doi":"10.4230/LIPIcs.SoCG.2024.11","ddc":["516"],"has_accepted_license":"1","language":[{"iso":"eng"}],"volume":293,"fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2024.11","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"Mathematics, Computer Science","call_identifier":"FWF"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"}],"file":[{"access_level":"open_access","date_created":"2024-06-25T11:47:26Z","success":1,"date_updated":"2024-06-25T11:47:26Z","file_name":"LIPIcs.SoCG.2024.11.pdf","checksum":"6a2ddc8b51aa58f197a8b294750f1f8d","file_size":20886142,"creator":"cfillmor","relation":"main_file","content_type":"application/pdf","file_id":"17171"}],"citation":{"apa":"Attali, D., Kourimska, H., Fillmore, C. D., Ghosh, I., Lieutier, A., Stephenson, E. R., &#38; Wintraecken, M. (2024). Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293, p. 11:1-11:19). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">https://doi.org/10.4230/LIPIcs.SoCG.2024.11</a>","mla":"Attali, Dominique, et al. “Tight Bounds for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">10.4230/LIPIcs.SoCG.2024.11</a>.","short":"D. Attali, H. Kourimska, C.D. Fillmore, I. Ghosh, A. Lieutier, E.R. Stephenson, M. Wintraecken, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19.","ieee":"D. Attali <i>et al.</i>, “Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293, p. 11:1-11:19.","ista":"Attali D, Kourimska H, Fillmore CD, Ghosh I, Lieutier A, Stephenson ER, Wintraecken M. 2024. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 11:1-11:19.","ama":"Attali D, Kourimska H, Fillmore CD, et al. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:11:1-11:19. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">10.4230/LIPIcs.SoCG.2024.11</a>","chicago":"Attali, Dominique, Hana Kourimska, Christopher D Fillmore, Ishika Ghosh, André Lieutier, Elizabeth R Stephenson, and Mathijs Wintraecken. “Tight Bounds for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.” In <i>40th International Symposium on Computational Geometry</i>, 293:11:1-11:19. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">https://doi.org/10.4230/LIPIcs.SoCG.2024.11</a>."},"scopus_import":"1","oa_version":"Published Version","year":"2024","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"ec_funded":1,"doi":"10.1101/2024.02.21.581330","title":"Super-resolution expansion microscopy in plant roots","das_tickbox":"0","publication_status":"draft","publication":"bioRxiv","OA_place":"repository","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"year":"2024","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/2024.02.21.581330","open_access":"1"}],"fulldoi":"https://doi.org/10.1101/2024.02.21.581330","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED","_id":"269B5B22-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 679-2018"}],"citation":{"ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv, <a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>.","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>bioRxiv</i>. .","ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>","chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>.","short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>","mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>."},"oa_version":"Preprint","date_published":"2024-02-21T00:00:00Z","oa":1,"day":"21","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"month":"02","date_updated":"2026-10-02T11:27:43Z","researchdata_availability":"no","abstract":[{"text":"Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.","lang":"eng"}],"acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742985, J.F.). It has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D., J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","type":"preprint","corr_author":"1","author":[{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline"},{"id":"F8660870-D756-11E9-98C5-34DFE5697425","first_name":"Syamala","orcid":"0009-0002-5890-120X","full_name":"Inumella, Syamala","last_name":"Inumella"},{"last_name":"Vistunou","full_name":"Vistunou, Vitali","first_name":"Vitali","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"last_name":"Tavakoli","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","first_name":"Mojtaba"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","first_name":"Nathalie","last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie"},{"first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer","full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501"},{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke"},{"first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","full_name":"Randuch, Marek"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-12-19T12:28:00Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"19003"},{"id":"18681","relation":"dissertation_contains","status":"public"}]},"_id":"18689","status":"public","supplementarymaterial":"no","article_processing_charge":"No"}]