[{"publication":"Physical Review E","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"status":"public","abstract":[{"text":"A floating Leidenfrost droplet exhibits curvature inversion of its underside, due to the balance of vapor pressure and surface tension. Using interferometric imaging, we find different behavior for a levitated hydrogel sphere. Curvature inversion is observed briefly just after deposition, but quickly gives way to a steady state with no inversion. We show the essential role of vaporization in shaping the underbelly of the hydrogel, where changes due to direct mass loss are more significant than the balance of vapor pressure and elastic forces.","lang":"eng"}],"month":"05","ddc":["530"],"article_number":"L053502","publisher":"American Physical Society","file_date_updated":"2026-06-16T11:21:53Z","article_type":"letter_note","volume":113,"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","OA_type":"hybrid","PlanS_conform":"1","date_created":"2026-06-10T07:36:41Z","oa":1,"type":"journal_article","oa_version":"Published Version","_id":"21982","department":[{"_id":"ScWa"},{"_id":"GradSch"}],"intvolume":"       113","arxiv":1,"OA_place":"publisher","corr_author":"1","author":[{"id":"b6798902-eea0-11ea-9cbc-a8e14286c631","last_name":"Diaz Melian","first_name":"Vicente L","full_name":"Diaz Melian, Vicente L"},{"last_name":"Lenton","id":"a550210f-223c-11ec-8182-e2d45e817efb","first_name":"Isaac C","orcid":"0000-0002-5010-6984","full_name":"Lenton, Isaac C"},{"full_name":"Binysh, Jack","first_name":"Jack","last_name":"Binysh"},{"full_name":"Souslov, Anton","first_name":"Anton","last_name":"Souslov"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R"}],"publication_status":"published","citation":{"chicago":"Diaz Melian, Vicente L, Isaac C Lenton, Jack Binysh, Anton Souslov, and Scott R Waitukaitis. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel Sphere.” <i>Physical Review E</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/m7gr-2t6j\">https://doi.org/10.1103/m7gr-2t6j</a>.","short":"V.L. Diaz Melian, I.C. Lenton, J. Binysh, A. Souslov, S.R. Waitukaitis, Physical Review E 113 (2026).","ista":"Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. 2026. Geometry of the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E. 113(5), L053502.","mla":"Diaz Melian, Vicente L., et al. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel Sphere.” <i>Physical Review E</i>, vol. 113, no. 5, L053502, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/m7gr-2t6j\">10.1103/m7gr-2t6j</a>.","ama":"Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. Geometry of the vapor layer under a Leidenfrost hydrogel sphere. <i>Physical Review E</i>. 2026;113(5). doi:<a href=\"https://doi.org/10.1103/m7gr-2t6j\">10.1103/m7gr-2t6j</a>","apa":"Diaz Melian, V. L., Lenton, I. C., Binysh, J., Souslov, A., &#38; Waitukaitis, S. R. (2026). Geometry of the vapor layer under a Leidenfrost hydrogel sphere. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/m7gr-2t6j\">https://doi.org/10.1103/m7gr-2t6j</a>","ieee":"V. L. Diaz Melian, I. C. Lenton, J. Binysh, A. Souslov, and S. R. Waitukaitis, “Geometry of the vapor layer under a Leidenfrost hydrogel sphere,” <i>Physical Review E</i>, vol. 113, no. 5. American Physical Society, 2026."},"title":"Geometry of the vapor layer under a Leidenfrost hydrogel sphere","doi":"10.1103/m7gr-2t6j","day":"14","year":"2026","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","creator":"dernst","date_created":"2026-06-16T11:21:53Z","success":1,"file_id":"22014","relation":"main_file","date_updated":"2026-06-16T11:21:53Z","checksum":"902cc8d177c8d3ae9cfe07c30375c9a9","file_name":"2026_PhysicalReviewE_DiazMelian.pdf","content_type":"application/pdf","file_size":3173197}],"external_id":{"arxiv":["2507.04982"]},"date_updated":"2026-06-16T11:24:18Z","date_published":"2026-05-14T00:00:00Z","issue":"5","acknowledgement":"This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop and the Scientific Computing Facility. J.B. acknowledges funding from the European Union's Horizon research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101106500.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"scopus_import":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","abstract":[{"lang":"eng","text":"We introduce JODIE, a genetic joint modeling approach that estimates how DNA loci influence human traits by partitioning genetic effects into four components: direct effects (from a child’s alleles), indirect maternal and paternal effects (from parents’ alleles), and parent-of-origin (PofO) effects (dependent on parental transmission of alleles), while uniquely accounting for assortative mating. We analyze 30,000 child-mother-father trios from the Estonian Biobank and the Norwegian Mother, Father, and Child Cohort, focusing on height, body mass index, and childhood educational test scores. We find direct effects to be the largest contributor to trait variation, but combined, indirect parental and PofO effects are similarly substantial. We support our results by within-family genome-wide association testing and identify 276 independently associated DNA regions with a complex interplay between direct, indirect, and PofO effects. By joint modeling, we show that direct, indirect, and PofO effects collectively shape human phenotypic variation across loci genome-wide."}],"month":"06","article_number":"101277","publisher":"Elsevier","article_type":"original","article_processing_charge":"Yes","quality_controlled":"1","OA_type":"gold","oa":1,"date_created":"2026-06-10T07:39:08Z","publication":"Cell Genomics","DOAJ_listed":"1","publication_identifier":{"eissn":["2666-979X"]},"doi":"10.1016/j.xgen.2026.101277","pmid":1,"year":"2026","day":"09","external_id":{"pmid":["40909755"]},"date_updated":"2026-06-19T07:00:47Z","date_published":"2026-06-09T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.xgen.2026.101277"}],"acknowledgement":"We thank Zoltan Kutalik, Peter Visscher, and members of the Robinson group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria.\r\nThe Norwegian Mother, Father, and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. We are grateful to all the participating families in Norway who take part in this on-going cohort study. We thank the Norwegian Institute of Public Health (NIPH) for generating high-quality genomic data. The research is part of the HARVEST collaboration, supported by the Research Council of Norway (#229624). We also thank the NORMENT Center for providing genotype data, funded by the Research Council of Norway (#223273), South East Norway Health Authorities, and Stiftelsen Kristian Gerhard Jebsen, and in collaboration with deCODE Genetics. We further thank the Center for Diabetes Research, the University of Bergen for providing genotype data funded by the ERC AdG project SELECTionPREDISPOSED, Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation, the Research Council of Norway, the Novo Nordisk Foundation, the University of Bergen, and the Western Norway Health Authorities. The MoBa work was performed on the TSD (Tjeneste for Sensitive Data) facilities, owned by the University of Oslo, operated and developed by the TSD service group at the University of Oslo, IT Department (USIT, tsd-drift@usit.uio.no). E.Y. is supported by the European Union (grant numbers 101045526 and 101073237) and the Research Council of Norway (grant numbers 336078, 288083, and 331640).\r\nWe would like to acknowledge the participants and investigators of the Generation Scotland Cohort study. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and methylation typing of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” [STRADL] ref. 104036/Z/14/Z).\r\nWe would like to thank and acknowledge the participants and investigators of the Estonian Biobank (EstBB) study. The research was conducted using the Estonian Center of Genomics/Roadmap II funded by the Estonian Research Council (project number TT17).\r\nNorwegian analyses were performed on resources provided by Sigma2 - the National Infrastructure for High-Performance Computing and Data Storage in Norway. Estonian Data analysis was carried out in the High-Performance Computing Center cloud provided by University of Tartu. Analysis of the Generation Scotland data and the summary statistics obtained from the other analyses was conducted at IST Austria and is supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa_version":"Published Version","_id":"21987","department":[{"_id":"MaRo"}],"project":[{"name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181"}],"OA_place":"publisher","corr_author":"1","author":[{"first_name":"Ilse","last_name":"Krätschmer","id":"30d4014e-7753-11eb-b44b-db6d61112e73","full_name":"Krätschmer, Ilse","orcid":"0000-0002-5636-9259"},{"last_name":"Hegemann","first_name":"Laura","full_name":"Hegemann, Laura"},{"last_name":"Hofmeister","first_name":"Robin J.","full_name":"Hofmeister, Robin J."},{"first_name":"Elizabeth C.","last_name":"Corfield","full_name":"Corfield, Elizabeth C."},{"last_name":"Mahmoudi","first_name":"Mahdi","full_name":"Mahmoudi, Mahdi"},{"first_name":"Olivier","last_name":"Delaneau","full_name":"Delaneau, Olivier"},{"last_name":"Andreassen","first_name":"Ole A.","full_name":"Andreassen, Ole A."},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"last_name":"Hayward","first_name":"Caroline","full_name":"Hayward, Caroline"},{"full_name":"Marioni, Riccardo E.","last_name":"Marioni","first_name":"Riccardo E."},{"full_name":"Ystrom, Eivind","last_name":"Ystrom","first_name":"Eivind"},{"last_name":"Havdahl","first_name":"Alexandra","full_name":"Havdahl, Alexandra"},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"}],"citation":{"ama":"Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>","ieee":"I. Krätschmer <i>et al.</i>, “Separating direct, indirect, and parent-of-origin genetic effects in the human population,” <i>Cell Genomics</i>. Elsevier.","apa":"Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi, M., Delaneau, O., … Robinson, M. R. (n.d.). Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>","mla":"Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>, 101277, Elsevier, doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>.","short":"I. Krätschmer, L. Hegemann, R.J. Hofmeister, E.C. Corfield, M. Mahmoudi, O. Delaneau, O.A. Andreassen, A. Campbell, C. Hayward, R.E. Marioni, E. Ystrom, A. Havdahl, M.R. Robinson, Cell Genomics (n.d.).","chicago":"Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield, Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>. Elsevier, n.d. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>.","ista":"Krätschmer I, Hegemann L, Hofmeister RJ, Corfield EC, Mahmoudi M, Delaneau O, Andreassen OA, Campbell A, Hayward C, Marioni RE, Ystrom E, Havdahl A, Robinson MR. Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics., 101277."},"publication_status":"inpress","title":"Separating direct, indirect, and parent-of-origin genetic effects in the human population"},{"oa_version":"Published Version","type":"journal_article","intvolume":"        18","department":[{"_id":"CaMu"},{"_id":"BjHo"},{"_id":"GradSch"}],"_id":"21013","title":"Convective self‐aggregation in diurnally oscillating sea surface temperature and solar forcing experiments","project":[{"grant_number":"805041","call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"OA_place":"publisher","corr_author":"1","publication_status":"published","citation":{"ama":"GOSWAMI BB, Lu Z, Muller CJ. Convective self‐aggregation in diurnally oscillating sea surface temperature and solar forcing experiments. <i>Journal of Advances in Modeling Earth Systems</i>. 2026;18(1). doi:<a href=\"https://doi.org/10.1029/2024ms004576\">10.1029/2024ms004576</a>","ieee":"B. B. GOSWAMI, Z. Lu, and C. J. Muller, “Convective self‐aggregation in diurnally oscillating sea surface temperature and solar forcing experiments,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 18, no. 1. Wiley, 2026.","apa":"GOSWAMI, B. B., Lu, Z., &#38; Muller, C. J. (2026). Convective self‐aggregation in diurnally oscillating sea surface temperature and solar forcing experiments. <i>Journal of Advances in Modeling Earth Systems</i>. Wiley. <a href=\"https://doi.org/10.1029/2024ms004576\">https://doi.org/10.1029/2024ms004576</a>","short":"B.B. GOSWAMI, Z. Lu, C.J. Muller, Journal of Advances in Modeling Earth Systems 18 (2026).","chicago":"GOSWAMI, BIDYUT B, Ziyin Lu, and Caroline J Muller. “Convective Self‐aggregation in Diurnally Oscillating Sea Surface Temperature and Solar Forcing Experiments.” <i>Journal of Advances in Modeling Earth Systems</i>. Wiley, 2026. <a href=\"https://doi.org/10.1029/2024ms004576\">https://doi.org/10.1029/2024ms004576</a>.","ista":"GOSWAMI BB, Lu Z, Muller CJ. 2026. Convective self‐aggregation in diurnally oscillating sea surface temperature and solar forcing experiments. Journal of Advances in Modeling Earth Systems. 18(1), e2024MS004576.","mla":"GOSWAMI, BIDYUT B., et al. “Convective Self‐aggregation in Diurnally Oscillating Sea Surface Temperature and Solar Forcing Experiments.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 18, no. 1, e2024MS004576, Wiley, 2026, doi:<a href=\"https://doi.org/10.1029/2024ms004576\">10.1029/2024ms004576</a>."},"author":[{"last_name":"GOSWAMI","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"BIDYUT B","full_name":"GOSWAMI, BIDYUT B","orcid":"0000-0001-8602-3083"},{"orcid":"0009-0008-5320-7730","full_name":"Lu, Ziyin","first_name":"Ziyin","id":"a6e549c6-8972-11ed-ae7b-a336d97ac043","last_name":"Lu"},{"full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller"}],"day":"12","year":"2026","doi":"10.1029/2024ms004576","date_published":"2026-01-12T00:00:00Z","date_updated":"2026-01-21T08:41:19Z","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","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"file":[{"success":1,"file_id":"21027","access_level":"open_access","date_created":"2026-01-21T08:39:01Z","creator":"dernst","content_type":"application/pdf","checksum":"6ea369e3b46bea58efab4f38b6c671a7","file_name":"2026_JAMES_Goswami.pdf","file_size":19509786,"relation":"main_file","date_updated":"2026-01-21T08:39:01Z"}],"acknowledgement":"The authors gratefully acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We are grateful to three anonymous reviewer(s) for their insightful suggestions that have improved the quality of our manuscript. Open Access funding provided by Institute of Science and Technology Austria/KEMÖ.","language":[{"iso":"eng"}],"issue":"1","scopus_import":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"}],"ec_funded":1,"publication":"Journal of Advances in Modeling Earth Systems","DOAJ_listed":"1","publication_identifier":{"eissn":["1942-2466"]},"month":"01","status":"public","abstract":[{"lang":"eng","text":"We have addressed convective self‐aggregation (CSA) in steady and oscillating sea surface temperature (SST) and solar radiation (SOLIN) cloud‐resolving model simulations in a non‐rotating radiative‐convective equilibrium (RCE) framework. Our experiment designs are motivated by land‐ocean heterogeneity of atmospheric convection. The steady and oscillating forcings are idealizations of ocean and land conditions, respectively, based on their differences in heat capacities. In both kinds of simulations, the diurnal mean SST and SOLIN are the same, and both SST and SOLIN are only varied in time (i.e., they are spatially homogeneous at any given time). We find that diurnally oscillating forcing accelerates CSA. Stronger long‐wave cooling in dry regions at night and during the warm SST phase (late afternoon) both allow the long‐wave feedback, known to favor aggregation, to intensify compared to steady forcing simulations. In addition to the long‐wave, reduced short‐wave warming in dry regions (during the day) further enhances radiative cooling there compared to moist regions. Overall, the radiative cooling is enhanced in dry regions compared to neighboring moist convective regions. A dry subsidence is driven by this net radiative (short‐wave plus long‐wave) cooling, consistent with earlier work on CSA. Stronger radiative cooling allows stronger subsidence which allows low‐level circulation to more efficiently transport moisture and energy up‐gradient, driving convection to aggregate faster. We also note a sensitivity of our experimental setup to initial conditions, more so at warmer SST. This stochastic behavior might be critical in reconciling the differences of opinion regarding the response of convection aggregation to oscillating SST forcing."}],"publisher":"Wiley","file_date_updated":"2026-01-21T08:39:01Z","article_type":"original","article_number":"e2024MS004576","ddc":["550"],"quality_controlled":"1","PlanS_conform":"1","oa":1,"OA_type":"gold","date_created":"2026-01-20T10:08:54Z","article_processing_charge":"Yes","volume":18},{"_id":"21015","intvolume":"        22","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"type":"journal_article","oa_version":"Published Version","publication_status":"published","author":[{"last_name":"Mishra","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","first_name":"Nikhil","full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788"},{"first_name":"Yuting I","id":"ee7a5ca8-8b71-11ed-b662-b3341c05b7eb","last_name":"Li","full_name":"Li, Yuting I"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"citation":{"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>.","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>.","short":"N. Mishra, Y.I. Li, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 22 (2026) 139–150.","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>","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>","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."},"corr_author":"1","OA_place":"publisher","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413"},{"_id":"917c023a-16d5-11f0-9cad-eb5cafc52090","name":"Cytoplasmic self-organization into cell-like compartments as a common guiding principle in early animal development"}],"title":"Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo","external_id":{"oaworkid":["W7118187193"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"creator":"dernst","date_created":"2026-01-21T08:21:11Z","access_level":"open_access","file_id":"21026","success":1,"date_updated":"2026-01-21T08:21:11Z","relation":"main_file","file_size":7335694,"file_name":"2026_NaturePhysics_Mishra.pdf","checksum":"0ab7ac2fbcb61a364dba57152db64ed7","content_type":"application/pdf"}],"date_published":"2026-01-05T00:00:00Z","date_updated":"2026-04-28T12:55:30Z","doi":"10.1038/s41567-025-03122-1","year":"2026","day":"05","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","related_material":{"link":[{"url":"https://ista.ac.at/en/news/geometry-shapes-life/","relation":"research_data","description":"News on ISTA website"}]},"language":[{"iso":"eng"}],"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).","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"],"issnl":[" 1745-2473"]},"publication":"Nature Physics","ec_funded":1,"page":"139-150","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."}],"status":"public","month":"01","volume":22,"article_processing_charge":"Yes (via OA deal)","oa":1,"date_created":"2026-01-20T10:12:19Z","PlanS_conform":"1","OA_type":"hybrid","quality_controlled":"1","ddc":["570"],"article_type":"original","file_date_updated":"2026-01-21T08:21:11Z","publisher":"Springer Nature","oaworkid":1},{"ec_funded":1,"month":"3","status":"public","license":"https://creativecommons.org/licenses/by-sa/4.0/","publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-03-24T07:21:43Z","date_created":"2026-02-04T16:38:02Z","oa":1,"article_processing_charge":"No","oa_version":"Published Version","type":"research_data","department":[{"_id":"GradSch"},{"_id":"CaHe"},{"_id":"EdHa"}],"_id":"21137","contributor":[{"last_name":"Keta","first_name":"Yann-Edwin","contributor_type":"researcher"},{"contributor_type":"supervisor","first_name":"Silke ","last_name":"Henkes"},{"orcid":"0000-0002-0912-4566","contributor_type":"supervisor","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"contributor_type":"supervisor","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"title":"Data associated with Keratins coordinate tissue spreading ","OA_place":"repository","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"8f060199-16d5-11f0-9cad-f3253b266c46","name":"Keratins in epithelial tissue spreading","grant_number":"PAT 5044023"},{"grant_number":"W1250-B20","call_identifier":"FWF","_id":"252C3B08-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems"}],"corr_author":"1","citation":{"mla":"Naik, Suyash. <i>Data Associated with Keratins Coordinate Tissue Spreading </i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>.","ista":"Naik S. 2026. Data associated with Keratins coordinate tissue spreading , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>.","chicago":"Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading .” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">https://doi.org/10.15479/AT-ISTA-21137</a>.","short":"S. Naik, (2026).","ieee":"S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute of Science and Technology Austria, 2026.","apa":"Naik, S. (2026). Data associated with Keratins coordinate tissue spreading . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">https://doi.org/10.15479/AT-ISTA-21137</a>","ama":"Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>"},"author":[{"full_name":"Naik, Suyash","orcid":"0000-0001-8421-5508","last_name":"Naik","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","first_name":"Suyash"}],"day":"24","year":"2026","doi":"10.15479/AT-ISTA-21137","date_updated":"2026-06-10T09:44:10Z","date_published":"2026-03-24T00:00:00Z","file":[{"content_type":"application/zip","file_name":"cells-main.zip","checksum":"5d1fda7e410f24c311fcf6bcf725698f","file_size":725916,"relation":"main_file","date_updated":"2026-03-16T11:51:10Z","description":"Python3 library written in C++20 to integrate vertex models. Please read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed instructions for installation and usage of the code in this repository. ","file_id":"21461","access_level":"open_access","date_created":"2026-03-16T11:51:10Z","creator":"snaik","title":"Cell git repository"},{"checksum":"ee350c8eaed99f3ca348c47c8b190d3c","file_name":"DevBranchDataRepo.zip","content_type":"application/x-zip-compressed","file_size":282168895,"relation":"main_file","date_updated":"2026-03-18T14:52:02Z","success":1,"file_id":"21464","access_level":"open_access","creator":"snaik","date_created":"2026-03-18T14:52:02Z"},{"file_id":"21466","success":1,"date_created":"2026-03-18T15:01:32Z","creator":"snaik","access_level":"open_access","file_size":2231,"content_type":"text/markdown","file_name":"ReadMe.md","checksum":"1ecaf2c1a2ce8ff9c75a128cc02d0b8f","date_updated":"2026-03-18T15:01:32Z","relation":"main_file"},{"creator":"snaik","date_created":"2026-03-18T15:12:57Z","access_level":"open_access","file_id":"21467","success":1,"date_updated":"2026-03-18T15:12:57Z","relation":"main_file","file_size":1951210,"file_name":"PaperSchematics.svg","checksum":"da9a4687e5144b61a64ca341f922046a","content_type":"image/svg+xml"},{"file_id":"21468","success":1,"creator":"snaik","date_created":"2026-03-21T03:37:43Z","access_level":"open_access","file_size":1897,"file_name":"maxwell_sketch.tex","checksum":"9ac1054b16c212c6f34d402dce2c80e0","content_type":"application/octet-stream","date_updated":"2026-03-21T03:37:43Z","relation":"main_file"},{"relation":"main_file","date_updated":"2026-03-24T07:21:43Z","file_name":"DataRepo.zip","checksum":"7c9ecf78e2593b3830d96fa94baa08df","content_type":"application/x-zip-compressed","file_size":749368723,"access_level":"open_access","creator":"snaik","date_created":"2026-03-24T07:21:43Z","success":1,"file_id":"21495"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"acknowledgement":"We thank all members of the Heisenberg, Henkes, and Hannezo groups for their support. We are also grateful to the Imaging and Optics, Scientific Computing, Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their technical assistance and support. Numerical simulations were performed using the computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020 research and innovation programme (grant agreement No. 665385). This work was supported by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to C.-P.H.","has_accepted_license":"1","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"LifeSc"}]},{"language":[{"iso":"eng"}],"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).","issue":"8106","has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/colliding-dust-and-the-sparks-of-creation/"}]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"year":"2026","day":"18","pmid":1,"doi":"10.1038/s41586-025-10088-w","date_published":"2026-03-18T00:00:00Z","date_updated":"2026-04-28T12:06:01Z","file":[{"relation":"main_file","date_updated":"2026-03-24T06:57:08Z","file_name":"2026_Nature_Grosjean.pdf","checksum":"dafef9ed575b44be4263e948a47ae056","content_type":"application/pdf","file_size":12245694,"access_level":"open_access","creator":"dernst","date_created":"2026-03-24T06:57:08Z","success":1,"file_id":"21494"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["41851325"]},"title":"Adventitious carbon breaks symmetry in oxide contact electrification","publication_status":"published","citation":{"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>","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>","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.","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>.","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>.","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."},"author":[{"full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","first_name":"Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","last_name":"Grosjean"},{"full_name":"Ostermann, Markus","first_name":"Markus","last_name":"Ostermann"},{"first_name":"Markus","last_name":"Sauer","full_name":"Sauer, Markus"},{"last_name":"Hahn","first_name":"Michael","full_name":"Hahn, Michael"},{"last_name":"Pichler","first_name":"Christian M.","full_name":"Pichler, Christian M."},{"first_name":"Florian","last_name":"Fahrnberger","full_name":"Fahrnberger, Florian"},{"orcid":"0000-0003-0463-5794","full_name":"Pertl, Felix","first_name":"Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","last_name":"Pertl"},{"first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel"},{"first_name":"Mason M.","last_name":"Link","full_name":"Link, Mason M."},{"full_name":"Kim, Seong H.","first_name":"Seong H.","last_name":"Kim"},{"full_name":"Schrader, Devin L.","last_name":"Schrader","first_name":"Devin L."},{"full_name":"Blanco, Adriana","first_name":"Adriana","last_name":"Blanco"},{"full_name":"Gracia, Francisco","last_name":"Gracia","first_name":"Francisco"},{"full_name":"Mujica, Nicolás","first_name":"Nicolás","last_name":"Mujica"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","corr_author":"1","project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","grant_number":"949120"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"oa_version":"Published Version","type":"journal_article","intvolume":"       651","department":[{"_id":"ScWa"},{"_id":"GradSch"},{"_id":"LifeSc"}],"_id":"21485","article_type":"original","file_date_updated":"2026-03-24T06:57:08Z","publisher":"Springer Nature","ddc":["540"],"PlanS_conform":"1","OA_type":"hybrid","oa":1,"date_created":"2026-03-23T15:04:00Z","quality_controlled":"1","volume":651,"article_processing_charge":"Yes (via OA deal)","month":"03","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."}],"status":"public","page":"626-631","ec_funded":1,"publication":"Nature","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]}},{"acknowledgement":"We thank all members of the Loose lab at ISTA for helpful discussions; M. Kojic for critical reading of the manuscript; A. Herrero (Sevilla University) for sharing her extensive BACTH plasmid library and other plasmids, as well as cyanobacterial strains; T. Dagan and F. Nies (both Kiel University) for sharing cyanobacterial strains and plasmids and for valuable discussions; N. Sapay and A. Michon for providing the Amphipaseek code, which enabled us to perform our large-scale amphipathic helix screen of cyanobacterial CorR proteins; V.-V. Hodirnau for support in cryo-ET data collection; and J. Hansen for advice about cryo-EM data processing.\r\nThis work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF), the Scientific Computing (SciComp), the Electron Microscopy Facility (EMF), and the Lab Support Facility (LSF). This work was funded by the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant 101034413 to B.L.S.); the European Research Council (ERC) of the European Union (grant ActinID 101076260 to F.K.M.S.); the Swiss National Science Foundation (starting grant TMSGI3_226208 to G.L.W.); and the Jean-Jacques et Letitia Lopez-Loreta Foundation (G.L.W.).","language":[{"iso":"eng"}],"issue":"6795","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"pmid":1,"year":"2026","day":"16","doi":"10.1126/science.aea6343","date_updated":"2026-04-28T13:29:05Z","date_published":"2026-04-16T00:00:00Z","external_id":{"pmid":["41990175"]},"title":"Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape","corr_author":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"_id":"bd980d18-d553-11ed-ba76-ceaa645c97eb","name":"A molecular atlas of Actin filament IDentities in the cell motility machinery","grant_number":"101076260"}],"citation":{"ama":"Springstein BL, Javoor M, Megrian D, et al. Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. <i>Science</i>. 2026;392(6795). doi:<a href=\"https://doi.org/10.1126/science.aea6343\">10.1126/science.aea6343</a>","ieee":"B. L. Springstein <i>et al.</i>, “Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape,” <i>Science</i>, vol. 392, no. 6795. AAAS, 2026.","apa":"Springstein, B. L., Javoor, M., Megrian, D., Hajdu, R., Hanke, D. M., Zens, B., … Loose, M. (2026). Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aea6343\">https://doi.org/10.1126/science.aea6343</a>","chicago":"Springstein, Benjamin L, Manjunath Javoor, Daniela Megrian, Roman Hajdu, Dustin M. Hanke, Bettina Zens, Gregor L. Weiss, Florian KM Schur, and Martin Loose. “Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cell Shape.” <i>Science</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/science.aea6343\">https://doi.org/10.1126/science.aea6343</a>.","short":"B.L. Springstein, M. Javoor, D. Megrian, R. Hajdu, D.M. Hanke, B. Zens, G.L. Weiss, F.K. Schur, M. Loose, Science 392 (2026).","ista":"Springstein BL, Javoor M, Megrian D, Hajdu R, Hanke DM, Zens B, Weiss GL, Schur FK, Loose M. 2026. Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. Science. 392(6795), eaea6343.","mla":"Springstein, Benjamin L., et al. “Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cell Shape.” <i>Science</i>, vol. 392, no. 6795, eaea6343, AAAS, 2026, doi:<a href=\"https://doi.org/10.1126/science.aea6343\">10.1126/science.aea6343</a>."},"author":[{"orcid":"0000-0002-3461-5391","full_name":"Springstein, Benjamin L","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","last_name":"Springstein","first_name":"Benjamin L"},{"last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","first_name":"Manjunath","full_name":"Javoor, Manjunath","orcid":"0000-0003-2311-2112"},{"last_name":"Megrian","first_name":"Daniela","full_name":"Megrian, Daniela"},{"full_name":"Hajdu, Roman","last_name":"Hajdu","id":"ffab949d-133f-11ed-8f02-94de21ace503","first_name":"Roman"},{"first_name":"Dustin M.","last_name":"Hanke","full_name":"Hanke, Dustin M."},{"full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina"},{"last_name":"Weiss","first_name":"Gregor L.","full_name":"Weiss, Gregor L."},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian Km","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian Km"},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"publication_status":"published","oa_version":"None","type":"journal_article","department":[{"_id":"MaLo"},{"_id":"FlSc"},{"_id":"GradSch"},{"_id":"EM-Fac"}],"intvolume":"       392","_id":"21762","publisher":"AAAS","article_type":"original","article_number":"eaea6343","quality_controlled":"1","OA_type":"closed access","date_created":"2026-04-26T22:01:46Z","volume":392,"article_processing_charge":"No","month":"04","status":"public","abstract":[{"text":"Bacteria, like eukaryotes, use conserved cytoskeletal systems for intracellular organization. The plasmid-encoded ParMRC system forms actin-like filaments that segregate low–copy number plasmids. In multicellular cyanobacteria such as Anabaena sp., we found that a chromosomally encoded ParMR system has evolved into a cytoskeletal system named CorMR with a function in cell shape control rather than DNA segregation. Live-cell imaging, in vitro reconstitution, and cryo–electron microscopy revealed that CorM formed dynamically unstable, antiparallel double-stranded filaments that were recruited to the membrane by CorR through an amphipathic helix conserved in multicellular cyanobacteria. CorMR filaments were regulated by MinC, which excluded them from the poles and division plane. Comparative genomics indicated that the repurposing of ParMR and Min systems coevolved with cyanobacterial multicellularity, highlighting the evolutionary plasticity of cytoskeletal systems in bacteria.","lang":"eng"}],"ec_funded":1,"publication":"Science","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]}},{"page":"237","month":"05","status":"public","abstract":[{"text":"As neural-network-based models grow both in size and popularity, interest has grown in making the models smaller and more efficient to train. To that end, many methods have been proposed to prune models by reducing their number of nonzero parameters. Additionally, parameter-efficient fine-tuning, in which a much smaller number of parameters than the total contained in the model is updated during training, has become very popular, especially in the space of Large Language Models. At the same time, the increasingly routine deployment of machine learning in real-world applications has spurred a drive to make them more trustworthy - in the sense of, among other things, being unbiased, interpretable, and editable. In this thesis, we examine the interplay between efficiency and trustworthiness.\r\n\r\nFirst, we analyze the effects of model pruning on bias in computer vision models, demonstrating that increased sparsity leads to greater bias, largely as a function of increased model uncertainty in marginal cases. Based on this observation, we propose several bias mitigation techniques. Then, we demonstrate that example-specific model pruning can improve model interpretation methods while improving pruning efficiency to make example-specific model pruning feasible in real time. Then, we investigate the effectiveness of parameter-efficient and data-efficient model personalization via fine-tuning, demonstrating that it is highly feasible with very small computational and data resources. Finally, we consider efficiency in editing model knowledge using a custom synthetic data framework, demonstrating that parameter-efficient, low-rank fine-tuning frequently outperforms full-rank fine-tuning, and, additionally, that restricting which model blocks are fine-tuned frequently improves results. Together, the results in this thesis provide new insights and techniques for combining trustworthiness and efficiency during neural network inference and training.\r\n\r\n-----------------“In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of [name of university or educational entity]’s products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.”","lang":"eng"}],"oa":1,"date_created":"2026-05-11T08:43:22Z","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-05-13T13:10:48Z","ddc":["000"],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","date_published":"2026-05-11T00:00:00Z","date_updated":"2026-05-19T11:20:28Z","file":[{"file_size":28479571,"checksum":"2e148dad920e3f9b7c32796e0ba2e5f7","file_name":"EIofinova_thesis_FinalVersion.zip","content_type":"application/zip","date_updated":"2026-05-11T08:36:01Z","relation":"source_file","file_id":"21856","creator":"eiofinov","date_created":"2026-05-11T08:36:01Z","access_level":"closed"},{"file_id":"21877","success":1,"creator":"eiofinov","date_created":"2026-05-13T13:10:48Z","access_level":"open_access","file_size":18137757,"checksum":"b10c2933f386f532b2dbf28b19c5525c","file_name":"2026_Iofinova_Eugenia_Thesis.pdf","content_type":"application/pdf","date_updated":"2026-05-13T13:10:48Z","relation":"main_file"}],"day":"11","year":"2026","doi":"10.15479/AT-ISTA-21854","related_material":{"record":[{"status":"public","id":"14771","relation":"part_of_dissertation"},{"status":"public","id":"18121","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"21858","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"21859"},{"id":"21857","relation":"part_of_dissertation","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"acknowledgement":"The research in this Ph.D. was funded in whole\r\nor in part by the Austrian Science Fund (FWF) W1260-N35 (Vienna Graduate School for\r\nComputational Optimization). For open access purposes the author has applied a CC BY\r\npublic copyright license to any author accepted manuscript version arising from this submission\r\nwherever possible. Additionally, I am grateful to Alois Schlögl, Waleed Khalid, and the rest of\r\nthe ISTA Scientific Computing team for building and maintaining the infrastructure I used\r\nto run experiments. I’m also deeply grateful to the Alistarh group’s administrative assistant,\r\nChristine Francois, who always deals with our nonsense with common sense and a smile.\r\n","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"}],"_id":"21854","oa_version":"Published Version","type":"dissertation","title":"On the utility and effects of efficiency in artificial neural networks","project":[{"grant_number":"W1260-N35","name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"}],"corr_author":"1","OA_place":"publisher","author":[{"id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","last_name":"Iofinova","first_name":"Eugenia B","orcid":"0000-0002-7778-3221","full_name":"Iofinova, Eugenia B"}],"publication_status":"published","citation":{"chicago":"Iofinova, Eugenia B. “On the Utility and Effects of Efficiency in Artificial Neural Networks.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21854\">https://doi.org/10.15479/AT-ISTA-21854</a>.","short":"E.B. Iofinova, On the Utility and Effects of Efficiency in Artificial Neural Networks, Institute of Science and Technology Austria, 2026.","ista":"Iofinova EB. 2026. On the utility and effects of efficiency in artificial neural networks. Institute of Science and Technology Austria.","mla":"Iofinova, Eugenia B. <i>On the Utility and Effects of Efficiency in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21854\">10.15479/AT-ISTA-21854</a>.","ama":"Iofinova EB. On the utility and effects of efficiency in artificial neural networks. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21854\">10.15479/AT-ISTA-21854</a>","ieee":"E. B. Iofinova, “On the utility and effects of efficiency in artificial neural networks,” Institute of Science and Technology Austria, 2026.","apa":"Iofinova, E. B. (2026). <i>On the utility and effects of efficiency in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21854\">https://doi.org/10.15479/AT-ISTA-21854</a>"}},{"article_processing_charge":"No","OA_type":"green","date_created":"2026-05-11T08:58:07Z","oa":1,"abstract":[{"lang":"eng","text":"As artificial neural networks, and specifically large language models, have improved rapidly in capabilities and quality, they have increasingly been deployed in real-world applications, from customer service to Google search, despite the fact that they frequently make factually incorrect or undesirable statements. This trend has inspired practical and academic interest in model editing, that is, in adjusting the weights of the model to modify its likely outputs for queries relating to a specific fact or set of facts. This may be done either to amend a fact or set of facts, for instance, to fix a frequent error in the training data, or to suppress a fact or set of facts entirely, for instance, in case of dangerous knowledge. Multiple methods have been proposed to do such edits. However, at the same time, it has been shown that such model editing can be brittle and incomplete. Moreover the effectiveness of any model editing method necessarily depends on the data on which the model is trained, and, therefore, a good understanding of the interaction of the training data distribution and the way it is stored in the network is necessary and helpful to reliably perform model editing. However, working with large language models trained on real-world data does not allow us to understand this relationship or fully measure the effects of model editing. We therefore propose Behemoth, a fully synthetic data generation framework. To demonstrate the practical insights from the framework, we explore model editing in the context of simple tabular data, demonstrating surprising findings that, in some cases, echo real-world results, for instance, that in some cases restricting the update rank results in a more effective update."}],"status":"public","month":"01","publication":"arXiv","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2601.23153"}],"language":[{"iso":"eng"}],"acknowledgement":"EI thanks Weiwei Yang, Janardhan Kulkani, and Kate Lytvynets for their advice and support in\r\ndeveloping an earlier version of the Behemoth library. This research was supported by the Scientific\r\nService Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).\r\nEI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35.\r\n","acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"21854","relation":"dissertation_contains"}]},"doi":"10.48550/arXiv.2601.23153","day":"30","year":"2026","external_id":{"arxiv":["2601.23153"]},"date_updated":"2026-05-19T11:20:27Z","date_published":"2026-01-30T00:00:00Z","arxiv":1,"author":[{"id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","last_name":"Iofinova","first_name":"Eugenia B","full_name":"Iofinova, Eugenia B","orcid":"0000-0002-7778-3221"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"draft","citation":{"ama":"Iofinova EB, Alistarh D-A. Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2601.23153\">10.48550/arXiv.2601.23153</a>","ieee":"E. B. Iofinova and D.-A. Alistarh, “Behemoth: Benchmarking unlearning in LLMs using fully synthetic data,” <i>arXiv</i>. .","apa":"Iofinova, E. B., &#38; Alistarh, D.-A. (n.d.). Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2601.23153\">https://doi.org/10.48550/arXiv.2601.23153</a>","mla":"Iofinova, Eugenia B., and Dan-Adrian Alistarh. “Behemoth: Benchmarking Unlearning in LLMs Using Fully Synthetic Data.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2601.23153\">10.48550/arXiv.2601.23153</a>.","short":"E.B. Iofinova, D.-A. Alistarh, ArXiv (n.d.).","chicago":"Iofinova, Eugenia B, and Dan-Adrian Alistarh. “Behemoth: Benchmarking Unlearning in LLMs Using Fully Synthetic Data.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2601.23153\">https://doi.org/10.48550/arXiv.2601.23153</a>.","ista":"Iofinova EB, Alistarh D-A. Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2601.23153\">10.48550/arXiv.2601.23153</a>."},"project":[{"grant_number":"W1260-N35","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","name":"Vienna Graduate School on Computational Optimization"}],"OA_place":"repository","corr_author":"1","title":"Behemoth: Benchmarking unlearning in LLMs using fully synthetic data","type":"preprint","oa_version":"Preprint","_id":"21859","department":[{"_id":"GradSch"},{"_id":"DaAl"}]},{"title":"How epistasis and purifying selection shape genetic diversity","publication_status":"published","author":[{"orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","first_name":"Kseniia","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"}],"citation":{"mla":"Khudiakova, Kseniia. <i>How Epistasis and Purifying Selection Shape Genetic Diversity</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21918\">10.15479/AT-ISTA-21918</a>.","ista":"Khudiakova K. 2026. How epistasis and purifying selection shape genetic diversity. Institute of Science and Technology Austria.","chicago":"Khudiakova, Kseniia. “How Epistasis and Purifying Selection Shape Genetic Diversity.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21918\">https://doi.org/10.15479/AT-ISTA-21918</a>.","short":"K. Khudiakova, How Epistasis and Purifying Selection Shape Genetic Diversity, Institute of Science and Technology Austria, 2026.","ieee":"K. Khudiakova, “How epistasis and purifying selection shape genetic diversity,” Institute of Science and Technology Austria, 2026.","apa":"Khudiakova, K. (2026). <i>How epistasis and purifying selection shape genetic diversity</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21918\">https://doi.org/10.15479/AT-ISTA-21918</a>","ama":"Khudiakova K. How epistasis and purifying selection shape genetic diversity. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21918\">10.15479/AT-ISTA-21918</a>"},"OA_place":"publisher","project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117"},{"grant_number":"26293","name":"The impact of deleterious mutations on small populations","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"corr_author":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"_id":"21918","oa_version":"Published Version","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"11447","status":"public"},{"relation":"part_of_dissertation","id":"12513","status":"deleted"},{"status":"public","relation":"part_of_dissertation","id":"21967"},{"id":"21968","relation":"part_of_dissertation","status":"public"}]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"At different stages of my PhD, my work was supported by several grants: the\r\nDOC fellowship of the Austrian Academy of Sciences (26293, awarded to me),\r\nthe FWF-SFB grant (PT1032F06504 n. F65, awarded to Jan Maas), and the ERC\r\ngrant (PR1032ERC01 n. 716117, awarded to Jan Maas). I also appreciate the help\r\nfrom the Scientific Computing unit for their advice on the cluster usage.","alternative_title":["ISTA Thesis"],"date_updated":"2026-06-12T12:43:35Z","date_published":"2026-06-07T00:00:00Z","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","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"file":[{"file_size":20549813,"content_type":"application/x-zip-compressed","checksum":"0cff64ae74f0f9f2d7011700c82f700a","file_name":"thesis.zip","date_updated":"2026-06-09T08:40:48Z","relation":"source_file","file_id":"21965","date_created":"2026-06-09T08:34:38Z","creator":"kkhudiak","access_level":"closed"},{"file_size":9387029,"content_type":"application/pdf","checksum":"547ae42de37cc86894af283f1664dbc8","file_name":"2026_Khudiakova_Ksenia_Thesis.pdf","embargo":"2027-06-10","embargo_to":"open_access","date_updated":"2026-06-11T12:14:53Z","relation":"main_file","file_id":"21969","date_created":"2026-06-09T12:28:51Z","creator":"kkhudiak","access_level":"closed"}],"year":"2026","day":"07","doi":"10.15479/AT-ISTA-21918","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"degree_awarded":"PhD","date_created":"2026-05-27T06:26:08Z","article_processing_charge":"No","file_date_updated":"2026-06-11T12:14:53Z","publisher":"Institute of Science and Technology Austria","ddc":["576"],"page":"89","month":"06","status":"public"},{"publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"publication":"Molecular Cell","dataavailabilitystatement":"This study did not generate new unique reagents. Strains and plasmids generated in this study are available from the lead contact without restrictions.\r\n• Source data are provided within this paper. The cryo-EM map is deposited in the Electron Microscopy Data Bank under accession number EMD-53848. The model is deposited in the Protein Data Bank under accession number 9R91. The structural data are publicly available as of the date of publication. Raw images of spot assays, SDS-PAGE and BN-PAGE gels with Coomassie staining and immunoblot images are available at Mendeley Data (https://doi.org/10.17632/v2g3p9n985.1).\r\n• This paper does not report original code.\r\n• Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","researchdata_availability":"yes","license":"https://creativecommons.org/licenses/by-nc/4.0/","month":"06","abstract":[{"text":"How the twin-arginine translocase (Tat) system transports fully folded substrate proteins across cellular membranes without disrupting membrane integrity has been a fundamental question in cell biology for decades. The Tat system, found in prokaryotes and plant organelles, recognizes a cargo signal peptide via a conserved twin-arginine motif. The multi-subunit Tat complex facilitates the proton-motive-force-dependent translocation process, yet its overall architecture has remained unknown. Here, we present the cryo-electron microscopy (cryo-EM) structure of the Escherichia coli (E. coli) trimeric TatB₃C₃ complex with bound substrate SufI, assembled in vivo. The complex adopts an unusual, wide-open, bowl-shaped architecture with a polar inner cavity. Unexpectedly, the cargo is engaged in a dual-contact mode: while the signal peptide binds inside one TatBC unit, the folded domain docks tightly onto an adjacent unit, possibly performing a proofreading function. This structure provides a mechanistic framework for substrate engagement and suggests the direct involvement of the entire Tat complex in substrate translocation.","lang":"eng"}],"status":"public","OA_type":"hybrid","oa":1,"date_created":"2026-06-28T22:01:35Z","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","publisher":"Elsevier","ddc":["570"],"das_tickbox":"1","department":[{"_id":"LeSa"}],"_id":"22148","oa_version":"Published Version","type":"journal_article","title":"Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo","publication_status":"inpress","citation":{"mla":"Zhao, Ziyu, and Leonid A. Sazanov. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo.” <i>Molecular Cell</i>, Elsevier, doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">10.1016/j.molcel.2026.05.026</a>.","short":"Z. Zhao, L.A. Sazanov, Molecular Cell (n.d.).","chicago":"Zhao, Ziyu, and Leonid A Sazanov. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo.” <i>Molecular Cell</i>. Elsevier, n.d. <a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">https://doi.org/10.1016/j.molcel.2026.05.026</a>.","ista":"Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. Molecular Cell.","ama":"Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. <i>Molecular Cell</i>. doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">10.1016/j.molcel.2026.05.026</a>","apa":"Zhao, Z., &#38; Sazanov, L. A. (n.d.). Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">https://doi.org/10.1016/j.molcel.2026.05.026</a>","ieee":"Z. Zhao and L. A. Sazanov, “Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo,” <i>Molecular Cell</i>. Elsevier."},"author":[{"full_name":"Zhao, Ziyu","last_name":"Zhao","id":"a63fe682-9f3a-11ee-bf8c-cfdf919b9850","first_name":"Ziyu"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"OA_place":"publisher","corr_author":"1","date_updated":"2026-06-29T12:55:19Z","date_published":"2026-06-22T00:00:00Z","external_id":{"biorxivid":["10.1101/2025.09.16.676506"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","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)"},"day":"22","year":"2026","biorxivid":1,"doi":"10.1016/j.molcel.2026.05.026","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"research_data","id":"22189","status":"for_moderation"}]},"scopus_import":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"supplementarymaterial":"yes","language":[{"iso":"eng"}],"acknowledgement":"We thank IST Austria for providing the funding. We thank IST Austria EM facility for the use of Titan Krios TEM. Data processing was performed using IST high-performance computer cluster. We thank Dr. R. Roemhild and Professor C. Guet (ISTA) for help in constructing Tat deletion strains and Dr. A. Charnagalov (ISTA) for technical help.","main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2026.05.026","open_access":"1"}]},{"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).","language":[{"iso":"eng"}],"scopus_import":"1","related_material":{"record":[{"status":"public","id":"21442","relation":"research_data"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","supplementarymaterial":"yes","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"pmid":1,"year":"2026","day":"23","doi":"10.1038/s41467-026-71914-x","date_updated":"2026-07-01T06:47:49Z","date_published":"2026-06-23T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2026_NatureComm_VargasBarroso.pdf","checksum":"d0b0093493926985b4c268662ff4d556","content_type":"application/pdf","file_size":18304997,"relation":"main_file","date_updated":"2026-07-01T06:46:06Z","success":1,"file_id":"22231","access_level":"open_access","creator":"dernst","date_created":"2026-07-01T06:46:06Z"}],"external_id":{"pmid":["42014695"]},"title":"Developmental emergence of sparse and structured synaptic connectivity in the hippocampal CA3 memory circuit","corr_author":"1","OA_place":"publisher","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692"},{"grant_number":"101199096","_id":"e62b56fe-ab3c-11f0-94c7-d181dd352b3b","name":"Synaptic mechanisms of engram storage and retrieval in CA3 hippocampal microcircuits"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"},{"grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"grant_number":"PAT 4178023","_id":"8d9195e9-16d5-11f0-9cad-d075be887a1e","name":"Synaptic networks of human brain"},{"name":"Reglas de Conectividad funcional en el hipocampo","_id":"26366136-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Vargas Barroso","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","first_name":"Victor M","full_name":"Vargas Barroso, Victor M"},{"first_name":"Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake"},{"id":"739d26c9-52e8-11ee-8d72-f14d3893b4ce","last_name":"Navas Olivé","first_name":"Andrea C","full_name":"Navas Olivé, Andrea C","orcid":"0000-0002-9280-8597"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"citation":{"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>.","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.","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>.","short":"V.M. Vargas Barroso, J. Watson, A.C. Navas Olivé, A. Schlögl, P.M. Jonas, Nature Communications 17 (2026).","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.","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>","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>"},"publication_status":"published","oa_version":"Published Version","type":"journal_article","das_tickbox":"1","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"intvolume":"        17","_id":"22229","publisher":"Springer Nature","article_type":"original","file_date_updated":"2026-07-01T06:46:06Z","ddc":["570"],"article_number":"5540","quality_controlled":"1","oa":1,"OA_type":"gold","date_created":"2026-06-30T13:05:52Z","PlanS_conform":"1","volume":17,"article_processing_charge":"Yes","month":"06","status":"public","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>"}],"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","ec_funded":1,"publication":"Nature Communications","DOAJ_listed":"1","publication_identifier":{"eissn":["2041-1723"]}},{"month":"07","abstract":[{"lang":"eng","text":"The appearance of simulated natural phenomena heavily depends on the way surfaces are textured. However, applying texture maps to dynamic deformable surfaces presents a significant challenge, due to ever-shifting differences in length scales involved. When these surfaces move and advect the texture along with them, their final appearance degrades as deformed regions dramatically distort their texture map. Modifications to the texture directly at the pixel level in response to the deformation may introduce ghosting artifacts and look unnatural. In the real world, the appearance of surface details on a deforming material changes through the interplay of physical processes such as rupturing, exposure of internal structure, or wrinkling. Motivated by these behaviors, in this work we explore how physical principles can guide the texturing methods based on the measure of surface deformation.\r\nWe present two novel wave-based procedural texturing algorithms which reproduce common physical properties like advection and self-similarity, enabling the plausible animation of deforming objects with extreme texture map distortions. Our algorithms are fully procedural, require no actual physics simulation, and store no state or history of deformation besides the input UV map, making them highly parallelizable on the GPU and efficient enough for real-time applications. We show the versatility of the method by animating physical phenomena with extreme deformations such as flowing lava, stretching putty and outpouring sludge."}],"status":"public","researchdata_availability":"no","article_type":"original","file_date_updated":"2026-05-29T13:19:37Z","publisher":"Association for Computing Machinery","article_number":"154","ddc":["006"],"OA_type":"gold","date_created":"2026-05-29T13:25:16Z","oa":1,"quality_controlled":"1","volume":45,"article_processing_charge":"Yes","publication":"ACM Transactions on Graphics","conference":{"location":"Los Angeles, CA, United States","end_date":"2026-07-23","start_date":"2026-07-19","name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques"},"publication_identifier":{"issn":["0730-0301"]},"day":"01","year":"2026","doi":"10.1145/3811353","date_published":"2026-07-01T00:00:00Z","date_updated":"2026-07-06T10:30:34Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":77337231,"content_type":"video/mp4","file_name":"tog454-article154-supplemental.mp4","checksum":"ea165bf731ddd3045f83878dcb833672","date_updated":"2026-05-29T13:19:33Z","relation":"main_file","file_id":"21924","success":1,"date_created":"2026-05-29T13:19:33Z","creator":"akalinov","access_level":"open_access"},{"file_id":"21925","success":1,"date_created":"2026-05-29T13:19:37Z","creator":"akalinov","access_level":"open_access","file_size":226633977,"content_type":"video/mp4","file_name":"tog454-article154-video.mp4","checksum":"6274cfb15ea5ba7324b74afc7b0d9629","date_updated":"2026-05-29T13:19:37Z","relation":"main_file"},{"content_type":"application/pdf","file_name":"tog454-article154-supplemental.pdf","checksum":"9d41b322a7876be9a3311017b9973183","file_size":6793867,"relation":"main_file","date_updated":"2026-05-29T13:19:33Z","success":1,"file_id":"21926","access_level":"open_access","date_created":"2026-05-29T13:19:33Z","creator":"akalinov"},{"date_created":"2026-05-29T13:19:36Z","creator":"akalinov","access_level":"open_access","file_id":"21927","success":1,"date_updated":"2026-05-29T13:19:36Z","relation":"main_file","file_size":84173392,"content_type":"application/pdf","checksum":"51bc60d2de867fbfa570652dec7993b4","file_name":"tog454-article154-main-1.pdf"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback. We also thank Jonathan Gagnon for their help with running the Lapped Textures codes and SideFX for the Houdini Education software licenses.\r\nImages in Fig. 2 by Kisoulou and Vultured on Unsplash, Michal Jarmoluk and Public Domain Pictures from Pixabay and Hawai‘i Volcanoes NPS on flickr. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing and was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","keyword":["Procedural animation"],"scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"supplementarymaterial":"yes","oa_version":"Published Version","type":"journal_article","intvolume":"        45","das_tickbox":"0","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"_id":"21923","title":"Physics-inspired procedural texturing of extremely deformable surfaces","author":[{"first_name":"Aleksei","last_name":"Kalinov","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","full_name":"Kalinov, Aleksei","orcid":"0000-0003-2189-3904"},{"full_name":"Ly, Mickaël","last_name":"Ly","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","first_name":"Mickaël"},{"first_name":"Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"citation":{"mla":"Kalinov, Aleksei, et al. “Physics-Inspired Procedural Texturing of Extremely Deformable Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 45, no. 4, 154, Association for Computing Machinery, 2026, doi:<a href=\"https://doi.org/10.1145/3811353\">10.1145/3811353</a>.","chicago":"Kalinov, Aleksei, Mickaël Ly, Christian Hafner, and Chris Wojtan. “Physics-Inspired Procedural Texturing of Extremely Deformable Surfaces.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2026. <a href=\"https://doi.org/10.1145/3811353\">https://doi.org/10.1145/3811353</a>.","short":"A. Kalinov, M. Ly, C. Hafner, C. Wojtan, ACM Transactions on Graphics 45 (2026).","ista":"Kalinov A, Ly M, Hafner C, Wojtan C. 2026. Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. 45(4), 154.","ama":"Kalinov A, Ly M, Hafner C, Wojtan C. Physics-inspired procedural texturing of extremely deformable surfaces. <i>ACM Transactions on Graphics</i>. 2026;45(4). doi:<a href=\"https://doi.org/10.1145/3811353\">10.1145/3811353</a>","ieee":"A. Kalinov, M. Ly, C. Hafner, and C. Wojtan, “Physics-inspired procedural texturing of extremely deformable surfaces,” <i>ACM Transactions on Graphics</i>, vol. 45, no. 4. Association for Computing Machinery, 2026.","apa":"Kalinov, A., Ly, M., Hafner, C., &#38; Wojtan, C. (2026). Physics-inspired procedural texturing of extremely deformable surfaces. <i>ACM Transactions on Graphics</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3811353\">https://doi.org/10.1145/3811353</a>"},"publication_status":"published","OA_place":"publisher","corr_author":"1","project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}]},{"page":"110","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","month":"03","status":"public","date_created":"2026-03-11T08:30:49Z","article_processing_charge":"No","file_date_updated":"2026-03-13T11:19:21Z","publisher":"Institute of Science and Technology Austria","ddc":["539","570"],"publication_identifier":{"isbn":["978-3-99078-076-3"],"issn":["2663-337X"]},"degree_awarded":"PhD","date_updated":"2026-07-06T12:38:16Z","date_published":"2026-03-11T00:00:00Z","file":[{"file_size":14662770,"content_type":"application/pdf","checksum":"47ce6a48a0c63f28eca6e64c9ffd2c84","embargo":"2026-09-11","embargo_to":"open_access","file_name":"2026_Dunajova_Zuzana_Thesis_pdfA.pdf","date_updated":"2026-03-12T20:38:52Z","relation":"main_file","file_id":"21446","date_created":"2026-03-12T20:38:52Z","creator":"zdunajov","access_level":"closed"},{"file_name":"Thesis-Dunajova_source_file.docx","checksum":"5dec5afdffd47c2b0b162d0fe1bed925","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":32961408,"relation":"source_file","date_updated":"2026-03-13T11:19:21Z","file_id":"21447","access_level":"closed","creator":"zdunajov","date_created":"2026-03-12T20:40:18Z"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"day":"11","year":"2026","doi":"10.15479/AT-ISTA-21423","has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"13314","relation":"part_of_dissertation"},{"status":"public","id":"13116","relation":"research_data"},{"id":"21439","relation":"research_data","status":"public"},{"status":"public","id":"21427","relation":"part_of_dissertation"}]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"Finally, I gratefully acknowledge funding from the DOC Fellowship of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360.","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"EdHa"}],"supervisor":[{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"_id":"21423","oa_version":"Published Version","type":"dissertation","title":"Geometry-driven self-organization of migrating cells and chiral filaments","author":[{"full_name":"Dunajova, Zuzana","last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"}],"citation":{"ama":"Dunajova Z. Geometry-driven self-organization of migrating cells and chiral filaments. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21423\">10.15479/AT-ISTA-21423</a>","apa":"Dunajova, Z. (2026). <i>Geometry-driven self-organization of migrating cells and chiral filaments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21423\">https://doi.org/10.15479/AT-ISTA-21423</a>","ieee":"Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral filaments,” Institute of Science and Technology Austria, 2026.","mla":"Dunajova, Zuzana. <i>Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21423\">10.15479/AT-ISTA-21423</a>.","short":"Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments, Institute of Science and Technology Austria, 2026.","chicago":"Dunajova, Zuzana. “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21423\">https://doi.org/10.15479/AT-ISTA-21423</a>.","ista":"Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria."},"publication_status":"published","corr_author":"1","OA_place":"repository","project":[{"name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360"}]},{"day":"12","year":"2026","doi":"10.15479/AT-ISTA-21439","date_updated":"2026-07-06T12:38:16Z","date_published":"2026-03-12T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"file":[{"file_name":"Supplementary_movies_Thesis_Dunajova.zip","checksum":"47809a9a31b748b16e21e92d11ddc87f","content_type":"application/zip","file_size":154465214,"relation":"main_file","date_updated":"2026-03-11T20:41:28Z","success":1,"file_id":"21440","access_level":"open_access","creator":"zdunajov","date_created":"2026-03-11T20:41:28Z"},{"file_size":2289,"checksum":"a64a174bc6abf0a5e77631e4fd121f1f","file_name":"readme.txt","content_type":"text/plain","date_updated":"2026-03-11T20:52:39Z","relation":"main_file","file_id":"21441","success":1,"creator":"zdunajov","date_created":"2026-03-11T20:52:39Z","access_level":"open_access"}],"related_material":{"record":[{"status":"public","id":"13314","relation":"used_in_publication"},{"status":"public","id":"21423","relation":"used_in_publication"},{"status":"public","id":"21427","relation":"used_in_publication"}]},"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"oa_version":"Published Version","type":"research_data","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"_id":"21439","contributor":[{"orcid":"0000-0003-1671-393X","contributor_type":"researcher","first_name":"Saren","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","first_name":"Philipp","contributor_type":"researcher","orcid":"0000-0001-9198-2182 "}],"title":"Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”","corr_author":"1","project":[{"name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360"}],"OA_place":"repository","author":[{"first_name":"Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","last_name":"Dunajova","full_name":"Dunajova, Zuzana"}],"citation":{"ista":"Dunajova Z. 2026. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21439\">10.15479/AT-ISTA-21439</a>.","chicago":"Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21439\">https://doi.org/10.15479/AT-ISTA-21439</a>.","short":"Z. Dunajova, (2026).","mla":"Dunajova, Zuzana. <i>Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.”</i> Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21439\">10.15479/AT-ISTA-21439</a>.","apa":"Dunajova, Z. (2026). Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21439\">https://doi.org/10.15479/AT-ISTA-21439</a>","ieee":"Z. Dunajova, “Supplementary movies to PhD thesis ‘Geometry-driven self-organization of migrating cells and chiral filaments.’” Institute of Science and Technology Austria, 2026.","ama":"Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21439\">10.15479/AT-ISTA-21439</a>"},"month":"03","status":"public","abstract":[{"lang":"eng","text":"These files contain supplementary movies accompanying the PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” by Zuzana Dunajova (2026). The videos provide additional visual material supporting the experiments and results described in the thesis."}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-03-11T20:52:39Z","ddc":["570"],"oa":1,"date_created":"2026-03-11T21:05:20Z","OA_type":"free access","article_processing_charge":"No"},{"date_published":"2026-01-28T00:00:00Z","date_updated":"2026-07-08T09:17:41Z","file":[{"success":1,"file_id":"21226","access_level":"open_access","creator":"dernst","date_created":"2026-02-16T09:26:02Z","file_name":"2026_RoyalSocPubProceedingsB_Barata.pdf","checksum":"d76afebca0a6f112df0146ae2d929f36","content_type":"application/pdf","file_size":2230841,"relation":"main_file","date_updated":"2026-02-16T09:26:02Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["41592777"]},"pmid":1,"year":"2026","day":"28","doi":"10.1098/rspb.2025.2471","scopus_import":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"acknowledgement":"This work was partly funded by an Austrian Science Foundation FWF ESPRIT fellowship (10.55776/ESP6331524) to C.B. We would like to thank the Vicoso group for their invaluable input and discussions throughout this work. We thank Filip Ruzicka for his insightful comments on the manuscript. All computational resources were provided by the Scientific Computing Unit at ISTA. This research was also supported through resources provided by the Imaging & Optics Facility (IOF) at ISTA.","language":[{"iso":"eng"}],"issue":"2063","intvolume":"       293","department":[{"_id":"BeVi"}],"das_tickbox":"1","_id":"21161","oa_version":"Published Version","type":"journal_article","title":"Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster","OA_place":"publisher","corr_author":"1","project":[{"grant_number":"ESP 6331524","name":"Does genetic drift set a limit on the adaptive evolution of sex-biased expression?","_id":"90ef7108-16d5-11f0-9cad-e6e116913473"}],"author":[{"orcid":"0000-0003-1945-2245","full_name":"De Castro Barbosa Rodrigues Barata, Carolina","first_name":"Carolina","id":"20565186-803f-11ed-ab7e-96a4ff7694ef","last_name":"De Castro Barbosa Rodrigues Barata"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","citation":{"ama":"de Castro Barbosa Rodrigues Barata C, Vicoso B. Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. <i>Proceedings of the Royal Society B Biological Sciences</i>. 2026;293(2063). doi:<a href=\"https://doi.org/10.1098/rspb.2025.2471\">10.1098/rspb.2025.2471</a>","ieee":"C. de Castro Barbosa Rodrigues Barata and B. Vicoso, “Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster,” <i>Proceedings of the Royal Society B Biological Sciences</i>, vol. 293, no. 2063. Royal Society of London, 2026.","apa":"de Castro Barbosa Rodrigues Barata, C., &#38; Vicoso, B. (2026). Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. <i>Proceedings of the Royal Society B Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rspb.2025.2471\">https://doi.org/10.1098/rspb.2025.2471</a>","mla":"de Castro Barbosa Rodrigues Barata, Carolina, and Beatriz Vicoso. “Single-Nucleus Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.” <i>Proceedings of the Royal Society B Biological Sciences</i>, vol. 293, no. 2063, 20252471, Royal Society of London, 2026, doi:<a href=\"https://doi.org/10.1098/rspb.2025.2471\">10.1098/rspb.2025.2471</a>.","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, and Beatriz Vicoso. “Single-Nucleus Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.” <i>Proceedings of the Royal Society B Biological Sciences</i>. Royal Society of London, 2026. <a href=\"https://doi.org/10.1098/rspb.2025.2471\">https://doi.org/10.1098/rspb.2025.2471</a>.","short":"C. de Castro Barbosa Rodrigues Barata, B. Vicoso, Proceedings of the Royal Society B Biological Sciences 293 (2026).","ista":"de Castro Barbosa Rodrigues Barata C, Vicoso B. 2026. Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. Proceedings of the Royal Society B Biological Sciences. 293(2063), 20252471."},"month":"01","status":"public","abstract":[{"text":"In many species, sex-biased expression is widespread and thought to contribute to sexual dimorphism. While bulk RNA-sequencing has been instrumental in identifying strongly sex-biased genes, it lacks resolution to assess variation across cell-types and tissue compartments. Using single-nucleus expression data from the Fly Cell Atlas, we investigate sex differences in adult Drosophila melanogaster. We find that differences in cell-type composition between the sexes are not a major source of sex-bias, as for the vast majority of genes, the degree of sex-bias is similar regardless of whether sex differences in cell-type composition are controlled for or not. Our analysis confirms a deficit of X-linked male-biased genes in the body’s somatic tissues that is widespread across cell-types. We also find the excess of X-linked female-biased genes to be associated with nervous system cells in the head but with epithelial cells in the body’s somatic tissues, showing that single-nucleus data crucially resolves sex-bias at the cell-type level. We investigate dosage compensation (DC) across 15 tissues and 17 cell-types. We observe that it varies throughout the body. Surprisingly, we observe a lack of DC in a cluster of main cells within the male accessory glands. This result highlights the importance of understanding context-dependent DC.","lang":"eng"}],"quality_controlled":"1","oa":1,"PlanS_conform":"1","OA_type":"hybrid","date_created":"2026-02-08T23:02:49Z","volume":293,"article_processing_charge":"Yes (via OA deal)","publisher":"Royal Society of London","article_type":"original","file_date_updated":"2026-02-16T09:26:02Z","article_number":"20252471","ddc":["570"],"publication_identifier":{"eissn":["1471-2954"]},"publication":"Proceedings of the Royal Society B Biological Sciences"},{"ddc":["570"],"article_type":"original","publisher":"Springer Nature","article_processing_charge":"Yes","OA_type":"gold","date_created":"2026-07-14T07:27:59Z","oa":1,"PlanS_conform":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters the nucleus, where it transcribes protein-coding genes. Although transcription by Pol II is intensively studied, how this central multi-subunit enzyme is made and the role of dedicated assembly factors remains unclear. Here, we report the integrative structural analysis of a native human Pol II from the cytoplasm captured near the end of biogenesis. The complex contains Gdown1 and three biogenesis factors – RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the complex reveals how Gdown1 and RPAP2 associate with Pol II and prevent the premature association of transcription factors. Further biochemical and cryo-EM analysis reveals how RPAP2 tethers GPN1–GPN3 to the complex and how the assembly of the RPAP2–GPN1–GPN3 complex is controlled by GTP hydrolysis. The combined results uncover a network of interactions that chaperone cytoplasmic Pol II to prevent aberrant interactions, reveal a molecular switch regulating biogenesis factor association, and suggest a general mechanism for the action of GPN-loop GTPase family of enzymes."}],"status":"public","month":"07","researchdata_availability":"yes","dataavailabilitystatement":"The\r\nc ryo EM maps generated in this study were deposited to the EM Data Bank under the\r\naccession codes: EMD 55583 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55583\r\n(Pol II Gdown1 RPAP2 composite map), EMD 55578\r\n[https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55578 Pol II Gdown1 RPAP2 Pol II core\r\nmap EMD 55579 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55579 Pol II\r\nGdown1 RPAP2 Pol II stalk map EMD 55580\r\n[https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55580 Pol II Gdown1 RPAP2 RPAP2\r\nmap EMD 55581 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55 581 Pol II\r\nGdown1 RPAP2 Gdown1 N terminus map EMD 55582\r\n[https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55582 Pol II Gdown1 RPAP2 Gdown1\r\nC terminus map and EMD 55585 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD\r\n55585 RPAP2 GPN1 GPN3 map Model coordi nates were deposited to the PDBe under\r\nthe accession codes: 9T5H [http://doi.org/10.2210/pdb 9T5H / (Pol II Gdown1\r\nRPAP2 complex structure) and 9T5J [http://doi.org/10.2210/pdb 9T5H / (GPN1\r\nGPN3 RPAP2 structure). Immunoprecipitation mass spectrometry and crosslinking mass\r\nspectrometry proteomics data have been deposited to the ProteomeXchange Consortium\r\nvia the PRIDE partner repository with the dataset identifiers PXD071638\r\n[http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD 071638 and\r\nP XD070852\r\n[http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD 070852\r\nAlphaFold3 structure predictions have been deposited to the Zenodo repository\r\nhttps://doi.org/10.5281/zenodo.20687910 P reviously published model coordinates\r\nwere utilized and are available at the PDB under the accession codes 8QEP\r\n[http://doi.org/10.2210/pdb 8QEP / 9BZ 0 [http://doi.org/10.2210/pdb 9BZ 0 /\r\nand 7B7U [http://doi.org/10.2210/pdb 7B7U / Source Data are provided with this\r\npaper.","publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"DOAJ_listed":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41467-026-75416-8","open_access":"1"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank A. Salmazo for assistance with Pol II purification. We thank staff at the Vienna BioCenter Core Facilities (VBCF) Proteomics facility for immunoprecipitation-mass spectrometry analysis, and J.A. Stopp for assistance with IP-MS data visualization. This research was further supported by the Scientific Service Units (SSUs) of ISTA through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF). F.H. was funded by the Endowed Professorship of the Lower Austria Research Funding Agency (GFF NÖ) and by the Austrian Research Promotion Agency (FFG) through the COIN Establishment Grant n.o. 45624401.","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}],"supplementarymaterial":"yes","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","biorxivid":1,"doi":"10.1038/s41467-026-75416-8","day":"13","year":"2026","external_id":{"biorxivid":["10.64898/2025.12.10.692585"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2026-07-13T00:00:00Z","date_updated":"2026-07-16T11:29:31Z","publication_status":"epub_ahead","citation":{"ama":"Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. Structure of cytoplasmic RNA polymerase II. <i>Nature Communications</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41467-026-75416-8\">10.1038/s41467-026-75416-8</a>","ieee":"A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, and C. Bernecky, “Structure of cytoplasmic RNA polymerase II,” <i>Nature Communications</i>. Springer Nature, 2026.","apa":"Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., &#38; Bernecky, C. (2026). Structure of cytoplasmic RNA polymerase II. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-75416-8\">https://doi.org/10.1038/s41467-026-75416-8</a>","chicago":"Hlavata, Annamaria, Benjamin Neuditschko, Ulla Schellhaas, Clemens Plaschka, Franz Herzog, and Carrie Bernecky. “Structure of Cytoplasmic RNA Polymerase II.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-75416-8\">https://doi.org/10.1038/s41467-026-75416-8</a>.","short":"A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, C. Bernecky, Nature Communications (2026).","ista":"Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. 2026. Structure of cytoplasmic RNA polymerase II. Nature Communications.","mla":"Hlavata, Annamaria, et al. “Structure of Cytoplasmic RNA Polymerase II.” <i>Nature Communications</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-75416-8\">10.1038/s41467-026-75416-8</a>."},"author":[{"full_name":"Hlavata, Annamaria","first_name":"Annamaria","last_name":"Hlavata","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin","last_name":"Neuditschko","full_name":"Neuditschko, Benjamin"},{"full_name":"Schellhaas, Ulla","last_name":"Schellhaas","first_name":"Ulla"},{"full_name":"Plaschka, Clemens","first_name":"Clemens","last_name":"Plaschka"},{"first_name":"Franz","last_name":"Herzog","full_name":"Herzog, Franz"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A"}],"OA_place":"publisher","corr_author":"1","title":"Structure of cytoplasmic RNA polymerase II","type":"journal_article","oa_version":"Published Version","_id":"22333","das_tickbox":"1","department":[{"_id":"CaBe"}]},{"title":"Data heterogeneity and personalization in federated learning","citation":{"chicago":"Scott, Jonathan A. “Data Heterogeneity and Personalization in Federated Learning.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21198\">https://doi.org/10.15479/AT-ISTA-21198</a>.","short":"J.A. Scott, Data Heterogeneity and Personalization in Federated Learning, Institute of Science and Technology Austria, 2026.","ista":"Scott JA. 2026. Data heterogeneity and personalization in federated learning. Institute of Science and Technology Austria.","mla":"Scott, Jonathan A. <i>Data Heterogeneity and Personalization in Federated Learning</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21198\">10.15479/AT-ISTA-21198</a>.","ama":"Scott JA. Data heterogeneity and personalization in federated learning. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21198\">10.15479/AT-ISTA-21198</a>","ieee":"J. A. Scott, “Data heterogeneity and personalization in federated learning,” Institute of Science and Technology Austria, 2026.","apa":"Scott, J. A. (2026). <i>Data heterogeneity and personalization in federated learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21198\">https://doi.org/10.15479/AT-ISTA-21198</a>"},"author":[{"first_name":"Jonathan A","id":"e499926b-f6e0-11ea-865d-9c63db0031e8","last_name":"Scott","full_name":"Scott, Jonathan A"}],"publication_status":"published","OA_place":"publisher","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"supervisor":[{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"_id":"21198","oa_version":"Published Version","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"20819","status":"public"},{"id":"17411","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"18120","relation":"part_of_dissertation"},{"id":"21207","relation":"part_of_dissertation","status":"public"}]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"This research was funded in part by the Austrian Science Fund (FWF)\r\n[10.55776/COE12]. Furthermore, the candidate acknowledges the support from the Scientific\r\nService Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","alternative_title":["ISTA Thesis"],"date_published":"2026-02-09T00:00:00Z","date_updated":"2026-07-22T06:34:27Z","file":[{"relation":"source_file","date_updated":"2026-02-17T11:46:22Z","checksum":"121c1d968bd86f3630aa7e81d5bbbcb0","file_name":"2026_Scott_Jonathan_Thesis_Source.zip","content_type":"application/zip","file_size":272379252,"access_level":"closed","creator":"jscott","date_created":"2026-02-17T11:46:22Z","file_id":"21298"},{"creator":"jscott","date_created":"2026-02-27T10:25:41Z","access_level":"open_access","file_id":"21366","success":1,"date_updated":"2026-02-27T10:25:41Z","relation":"main_file","file_size":15220298,"file_name":"2026_Jonathan_Scott_Thesis.pdf","checksum":"6e3e08ba474bbee8511cc8a839ab2077","content_type":"application/pdf"}],"year":"2026","day":"09","doi":"10.15479/AT-ISTA-21198","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","date_created":"2026-02-09T14:59:53Z","oa":1,"article_processing_charge":"No","file_date_updated":"2026-02-27T10:25:41Z","publisher":"Institute of Science and Technology Austria","ddc":["005"],"page":"158","month":"02","abstract":[{"lang":"eng","text":"In recent years there has been a massive increase in the amount of data generated in a\r\ndecentralized manner. Ever more powerful edge devices, such as smartphones, have become\r\nubiquitous in most societies on earth. Through text typed, photos taken and apps used,\r\nthese devices, which we refer to as clients, generate enormous amounts of high quality and\r\ncomplex data. Moreover, the nature of these devices means the data they generate is often\r\nsensitive and privacy concerns prevent it being gathered and stored in a central location. This\r\npresents a challenge to the modern machine learning paradigm that requires central access\r\nto large amounts of data. Federated learning (FL) has emerged as one of the answers to\r\nthis problem. Rather than bringing the data to the model, FL sends the model to the data.\r\nModel training takes place on device, with periodically synchronized updates, allowing data to\r\nremain locally stored. While this approach offers significant privacy advantages it comes with\r\nits own set of unique challenges. These include: data heterogeneity, the notion that different\r\ndevices generate data in distinct ways which can negatively impact training dynamics; systems\r\nheterogeneity, meaning that different devices may have differing hardware specifications; high\r\ncommunication costs, which are induced by the repeated transferring of models over the\r\nnetwork and low device computational power, which limits the use of larger models on device.\r\nIn this thesis we present a range of methods for federated learning. We focus primarily on\r\nthe challenge of data heterogeneity, though the methods presented are designed to be well\r\nadapted to the other challenges of a federated setting, such as the constraints of limited\r\ncompute and communication overhead. We first present a method for explicitly modeling client\r\ndata heterogeneity. The approach formulates clients as samples from a certain probability\r\ndistribution and infers the parameters of this distribution from the available training clients.\r\nThis learned distribution then represents the heterogeneity present among the clients and can\r\nbe sampled from in order to create new simulated clients that are similar to the real clients we\r\nhave observed so far. Following this we present two methods for directly dealing with data\r\nheterogeneity through personalization. Highly heterogeneous client data distributions can mean\r\nthat learning a single global model becomes suboptimal, and some form of personalization of\r\nmodels to each individual client is required. Our approaches are based around hypernetworks,\r\nwhich we use to generate personalized model parameters without the need for additional\r\ntraining or finetuning. In the first approach we focus on generating full parameterizations of\r\nclient models using learned embeddings of client data and labels, with a hypernetwork located\r\non the central server. In the second approach we address the more challenging scenario where\r\nwe want to generate a personalized model for a client without any label information. The\r\nhypernetwork is trained to generate a low dimensional representation of a client’s personalized\r\nmodel parameters, allowing it to be transferred to and run on the client devices. In our final\r\npresented method, we change our focus and rather than aim to directly address the challenge\r\nof data heterogeneity, we instead ensure we are unaffected by it. This is done in the context\r\nof k-means clustering and we present a method for federated clustering with a focus on added\r\nprivacy guarantees."}],"status":"public"},{"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"status":"public","abstract":[{"lang":"eng","text":"This thesis examines how geometry and topology intersect in the representation, transformation, and analysis of complex shapes. It considers how continuous manifolds relate to their discrete analogues, how topological structures evolve in persistence vineyards, and how tools from topological data analysis can illuminate problems in mathematical physics. Central to this exploration is the question of how structure, both geometric and topological, persists or changes under approximation, sampling, or deformation. The work develops new approaches to skeletal and grid-based representations of surfaces, reveals the full expressive capacity of persistence vineyards, and applies topological methods to the longstanding problem of equilibria in electrostatic fields. These threads braid together into a broader understanding of how topology and geometry inform one another across theory, computation, and application."}],"month":"01","page":"122","ddc":["514","516"],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-01-30T11:40:09Z","article_processing_charge":"No","date_created":"2026-01-20T21:38:40Z","oa":1,"type":"dissertation","oa_version":"Published Version","_id":"21021","department":[{"_id":"GradSch"},{"_id":"HeEd"},{"_id":"UlWa"}],"supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"OA_place":"publisher","corr_author":"1","publication_status":"published","citation":{"apa":"Fillmore, C. D. (2026). <i>Braiding geometry and topology to study shapes and data</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21021\">https://doi.org/10.15479/AT-ISTA-21021</a>","ieee":"C. D. Fillmore, “Braiding geometry and topology to study shapes and data,” Institute of Science and Technology Austria, 2026.","ama":"Fillmore CD. Braiding geometry and topology to study shapes and data. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21021\">10.15479/AT-ISTA-21021</a>","mla":"Fillmore, Christopher D. <i>Braiding Geometry and Topology to Study Shapes and Data</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21021\">10.15479/AT-ISTA-21021</a>.","ista":"Fillmore CD. 2026. Braiding geometry and topology to study shapes and data. Institute of Science and Technology Austria.","chicago":"Fillmore, Christopher D. “Braiding Geometry and Topology to Study Shapes and Data.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21021\">https://doi.org/10.15479/AT-ISTA-21021</a>.","short":"C.D. Fillmore, Braiding Geometry and Topology to Study Shapes and Data, Institute of Science and Technology Austria, 2026."},"author":[{"full_name":"Fillmore, Christopher D","last_name":"Fillmore","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","first_name":"Christopher D"}],"title":"Braiding geometry and topology to study shapes and data","doi":"10.15479/AT-ISTA-21021","year":"2026","day":"21","file":[{"file_size":55954297,"content_type":"application/pdf","checksum":"4c0889130095c31d4e5088c5b8dfd607","file_name":"2025_Fillmore_Christopher_Thesis.pdf","date_updated":"2026-01-30T11:40:09Z","relation":"main_file","file_id":"21046","date_created":"2026-01-26T19:44:46Z","creator":"cfillmor","access_level":"open_access"},{"date_created":"2026-01-26T19:46:20Z","creator":"cfillmor","access_level":"closed","file_id":"21047","date_updated":"2026-01-26T19:46:20Z","relation":"source_file","file_size":166080788,"content_type":"application/x-zip-compressed","checksum":"d69afb71d82ab98f856886126ee7303a","file_name":"Thesis.zip"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2026-01-21T00:00:00Z","date_updated":"2026-07-22T06:33:54Z","alternative_title":["ISTA Thesis"],"acknowledgement":"The research presented in this thesis was funded by the DFG Collaborative Research\r\nCenter TRR 109, ‘Discretization in Geometry and Dynamics’.\r\n","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"20260","status":"public"},{"id":"21051","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"21050","status":"public"}]},"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"text":"Uncovering the genetic architecture of complex traits and pinpointing causal molecular drivers require the ability to distinguish true signals from noise within massive, high-dimensional omics datasets. To extract meaningful biological insights from these datasets, such as identifying causal genetic variants and proteins, scalable and accurate inference methods are essential. To this end, this thesis develops novel Bayesian inference frameworks based on Vector Approximate Message Passing and demonstrates their effectiveness in the modeling of disease onset times and quantitative physical and clinical measures.\r\n\r\nFirst, we introduce gVAMP, a Bayesian framework tailored for Genome-Wide Association Studies that enables the joint modeling of quantitative complex traits across millions of genetic variants. gVAMP demonstrates superior accuracy in variable selection and out-of-sample polygenic risk prediction compared to state-of-the-art approaches. We model human height using 17 million whole-genome sequence variants from the UK Biobank, incorporating a vast number of rare variants and revealing novel associations. gVAMP achieves a prediction accuracy of approximately 46% for human height, representing the highest reported performance for this trait to date. \r\n\r\nSecond, we present vampW, a Bayesian framework for survival analysis applied to proteomic data. By effectively handling right-censoring and complex protein dependencies within the UK Biobank Pharma Proteomics Project dataset, vampW identifies 219 protein associations across 24 disease outcomes, the majority of which are not among the top marginal discoveries. We further adjust protein levels for exponential age effects, yielding 1,308 associations and highlighting the sensitivity of the analysis to the chosen age-correction methodology. Finally, vampW improves upon the variable selection capabilities of the commonly used (penalized) variants of the Cox proportional hazards model and delivers state-of-the-art out-of-sample prediction of disease onset times.\r\n\r\nCollectively, these methods provide powerful tools for dissecting the genetic architecture of complex traits and the proteomic drivers of disease onset. Furthermore, by delivering accurate polygenic risk scores and precise predictions of onset times, this work advances the capabilities of personalized medicine and clinical risk stratification.","lang":"eng"}],"status":"public","month":"07","page":"169","ddc":["576","610","006"],"file_date_updated":"2026-07-13T14:56:41Z","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","oa":1,"date_created":"2026-07-10T13:27:20Z","type":"dissertation","oa_version":"Published Version","_id":"22258","doi_confirm":"1","department":[{"_id":"GradSch"},{"_id":"MaRo"},{"_id":"MaMo"}],"das_tickbox":"1","supervisor":[{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli"}],"author":[{"full_name":"Depope, Al","first_name":"Al","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830","last_name":"Depope"}],"citation":{"mla":"Depope, Al. <i>From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22258\">10.15479/AT-ISTA-22258</a>.","ista":"Depope A. 2026. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. Institute of Science and Technology Austria.","short":"A. Depope, From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics, Institute of Science and Technology Austria, 2026.","chicago":"Depope, Al. “From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22258\">https://doi.org/10.15479/AT-ISTA-22258</a>.","ieee":"A. Depope, “From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics,” Institute of Science and Technology Austria, 2026.","apa":"Depope, A. (2026). <i>From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22258\">https://doi.org/10.15479/AT-ISTA-22258</a>","ama":"Depope A. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22258\">10.15479/AT-ISTA-22258</a>"},"publication_status":"published","OA_place":"publisher","corr_author":"1","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"grant_number":"101161364","_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits"},{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"title":"From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics","doi":"10.15479/AT-ISTA-22258","day":"11","year":"2026","file":[{"file_size":25109878,"content_type":"application/pdf","file_name":"2026_Depope_Al_Thesis.pdf","checksum":"9ab386790515628d957a194f30a7ccb4","date_updated":"2026-07-13T14:52:19Z","relation":"main_file","file_id":"22316","date_created":"2026-07-13T14:52:19Z","creator":"adepope","access_level":"open_access"},{"file_size":1203199939,"checksum":"8ed8fb63f76a695d5b6fec35343f4b90","file_name":"2026_Depope_Al_Thesis.zip","content_type":"application/zip","date_updated":"2026-07-13T14:56:41Z","relation":"source_file","file_id":"22317","creator":"adepope","date_created":"2026-07-13T14:56:41Z","access_level":"closed"}],"date_published":"2026-07-11T00:00:00Z","date_updated":"2026-07-23T05:33:50Z","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"acknowledgement":"This work was supported in part by the Swiss National Science Foundation through the\r\nEccellenza Grant \"Improving estimation and prediction of common complex disease risk\"\r\n(grant number PCEGP3_181181); the European Research Council through the grant\r\n\"Inference in High Dimensions: Light-speed Algorithms and Information Limits\" (grant\r\nnumber 101161364); and the Fondation Jean-Jacques et Felicia Lopez-Loreta through the\r\nPrix Lopez-Loretta 2019.\r\n","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"id":"21488","relation":"part_of_dissertation","status":"public"}]},"keyword":["Approximate Message Passing","GWAS","Genomics","Proteomics","Survival modeling"]}]