[{"author":[{"last_name":"Garcia Castillo","first_name":"Diego Fernando","full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"}],"date_updated":"2026-10-21T08:18:21Z","status":"public","OA_place":"publisher","type":"dissertation","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"18498","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18491"}]},"abstract":[{"lang":"eng","text":"Rapid local adaptation to new environments is critical for species persistence, especially in introduced populations. The evolutionary success of these populations is fundamentally dictated by the organization of genetic variation—the genomic architecture—in the face of severe demographic constraints, such as the founder effects and genetic bottlenecks that frequently accompany colonization. A central question in evolutionary biology is whether rapid adaptation relies on major-effect loci, such as chromosomal inversions, or on many small-effect loci dispersed across the genome. Furthermore, the genomic architecture strongly influences the extent to which evolutionary outcomes are predictable. Using introduced populations of the marine snail, Littorina saxatilis, as a model, this thesis investigates how genetic variation and genomic structure drive adaptation following introduction. We employed a population genomics approach on experimentally and accidentally introduced populations to dissect the specific genomic features that underpin divergence in newly colonized environments.\r\n\r\nIn Chapter 2, we tested the predictability of local adaptation through an uncommon 30-year transplant experiment in nature. By distinguishing allele and chromosomal inversion frequency changes from neutral expectations, we found that evolutionary change was highly predictable at the macro-scale (phenotypes and chromosomal inversions), but less robust at the level of individual collinear loci. This result demonstrates that evolution can be predictable when a population possesses sufficient standing genetic variation (SGV), with chromosomal inversions acting as key integrated units that facilitate a rapid response to selection. Building on this, Chapter 3 applied whole-genome sequencing to three accidentally introduced populations (Venice, San Francisco, and Redwood City) to investigate their likely source and genomic patterns of divergence. We identified genomic regions of remarkable divergence potentially associated with local adaptation, and likely fuelled by SGV, while explicitly acknowledging the difficulty in disentangling selection signals from the genome-wide effects of demographic processes. Furthermore, we found that the divergence patterns relied extensively on the collinear genome in these introduced populations, and less clearly on the chromosomal inversions. This observation contrasts with local adaptation observed in the experimental system that relied on both collinear loci and highly selected chromosomal inversions, highlighting how demographic history and genomic architecture influence the detectable signature of local adaptation.\r\n\r\nA major limitation to conducting large-scale comparative evolutionary studies is the lack of data standardization, which prevents the integration of community knowledge and high-resolution environmental and genetic data. Chapter 4 addresses this by developing a community database for the Littorina system. This platform implements standardized protocols for the integration of diverse phenotypic and environmental data from multiple Littorina species. Likewise, the platform also centralizes the availability of associated genomic data through links to external repositories. This database represents a crucial tool to test complex, large-scale evolutionary hypotheses.\r\n\r\nCollectively, this thesis strongly reinforces the fundamental importance of SGV as the raw material for successful local adaptation, a conclusion supported by evidence in both experimental and accidental introductions. Furthermore, this work highlights the critical role of the genomic architecture—specifically chromosomal inversions—in driving the predictability and effectiveness of adaptive responses. Our findings underscore how the interplay between SGV and genomic architecture dictates the trajectory and detectability of evolution in colonizing populations, while simultaneously providing a necessary tool to advance comparative evolutionary genomics in emerging model organisms."}],"publisher":"Institute of Science and Technology Austria","month":"01","ddc":["576"],"date_published":"2026-01-16T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","citation":{"apa":"Garcia Castillo, D. F. (2026). <i>The genomic architecture of local adaptation in introduced populations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20991\">https://doi.org/10.15479/AT-ISTA-20991</a>","mla":"Garcia Castillo, Diego Fernando. <i>The Genomic Architecture of Local Adaptation in Introduced Populations</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20991\">10.15479/AT-ISTA-20991</a>.","chicago":"Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation in Introduced Populations.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-20991\">https://doi.org/10.15479/AT-ISTA-20991</a>.","short":"D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026.","ama":"Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20991\">10.15479/AT-ISTA-20991</a>","ieee":"D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced populations,” Institute of Science and Technology Austria, 2026.","ista":"Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria."},"oa_version":"Published Version","publication_status":"published","date_created":"2026-01-16T09:47:59Z","year":"2026","acknowledgement":"I acknowledge the funding agencies 1Norwegian Research Council RCN project 315287.\r\n2The FIASCO project \"Illuminating range shifts through evolutionary FIASCO: contrasting\r\nFaIling And Successful ColOnizations in replicated wild populations\", funded by the\r\nEuropean Union - Next Generation EU (Piano Nazionale di Ripresa e Resilienza - MUR\r\ncode: P202229JBC, CUP: C53D23007100001). 3Ecotypic formation in Littorina saxatilis\r\nin the Western Atlantic and comparisons across the North Atlantic. University of\r\nGothenburg Research Travel Grant, Tjarno Marine Laboratory, Sweden. $3023 (2018).\r\n4JIN project (Young Researchers, Spanish Ministry of Science, RTI2018-101274-J-I00)","file_date_updated":"2026-01-16T13:08:59Z","page":"199","day":"16","publication_identifier":{"isbn":["978-3-99078-077-0"],"issn":["2663-337X"]},"supervisor":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20991","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"20991","title":"The genomic architecture of local adaptation in introduced populations","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","file":[{"file_id":"20996","date_created":"2026-01-16T12:25:13Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dgarciac","checksum":"841f1bc073d667125729b2a017f8c37a","file_name":"2026_Garcia_Diego_Thesis.docx","file_size":22456421,"access_level":"closed","date_updated":"2026-01-16T12:25:13Z","relation":"source_file"},{"access_level":"open_access","relation":"main_file","date_updated":"2026-01-16T12:25:13Z","success":1,"date_created":"2026-01-16T12:25:13Z","file_id":"20997","content_type":"application/pdf","checksum":"a1f33d4f183ce7072eee42a6ccf5340b","creator":"dgarciac","file_size":9556719,"file_name":"2026_Garcia_Diego_Thesis.pdf"},{"date_updated":"2026-01-16T13:08:14Z","relation":"supplementary_material","access_level":"closed","description":"Source code of the PostgreSQL database, front-end and back-end of the LittorinaDB web application developed as a product of the 4th chapter of the thesis.","file_size":54491433,"file_name":"2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar","checksum":"98a80691067174c30fe53f38ce7344e6","creator":"dgarciac","content_type":"application/x-compressed","file_id":"20998","date_created":"2026-01-16T13:08:14Z"},{"file_name":"2026_DiegoGarcia_Thesis-Supplementary_Material.rar","file_size":7982811,"creator":"dgarciac","checksum":"99a3cab2fa36666b9a92eefc27d586da","content_type":"application/x-compressed","date_created":"2026-01-16T13:08:14Z","file_id":"20999","date_updated":"2026-01-16T13:08:14Z","relation":"supplementary_material","access_level":"open_access"},{"file_name":"README.txt","file_size":732,"creator":"dgarciac","checksum":"255fdf56b2932c46bf27c63aa6106a4f","content_type":"text/plain","date_created":"2026-01-16T13:08:59Z","file_id":"21000","relation":"supplementary_material","date_updated":"2026-01-16T13:08:59Z","access_level":"open_access"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"oa":1,"doi":"10.15479/AT-ISTA-20991","corr_author":"1"},{"date_updated":"2026-10-21T08:39:24Z","author":[{"last_name":"Pertl","first_name":"Felix","full_name":"Pertl, Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","orcid":"0000-0003-0463-5794"}],"type":"dissertation","OA_place":"publisher","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"20481"},{"status":"public","id":"12109","relation":"part_of_dissertation"},{"status":"public","id":"19278","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"17373"}]},"abstract":[{"text":"Contact electrification (CE) is a simple yet elusive phenomenon that occurs when two materials come into contact and separate, leaving behind net electrical charge. Despite its ubiquity, the microscopic origin of CE remains unclear. In this thesis, we investigate CE from three complementary perspectives: developing a quantitative method to measure charge at the nanoscale, exploring the dynamic behavior of charge on insulating surfaces, and uncovering the role of mechanical history in forming a triboelectric series.\r\n\r\nIn the first part, we establish a rigorous framework for converting qualitative Kelvin probe force microscopy (KPFM) voltage maps into quantitative charge density distributions. Using finite element method (FEM) simulations, we determine the point-spread function of the KPFM tip–sample geometry and demonstrate that the true surface charge can be reconstructed by numerical deconvolution. This procedure enables the recovery of both the magnitude and sign of charge density with high fidelity, resolving nanoscale features that are otherwise obscured. Applying the method to contact-charged SiO$_2$ surfaces, we show that existing analytical approximations, such as parallel plate or spherical models, can miscalculate charge magnitude by orders of magnitude. Our hybrid FEM/KPFM approach therefore provides a fast and general method to convert qualitative KPFM signals into quantitative charge data, enabling nanoscale charge mapping under realistic experimental conditions.\r\n\r\nIn the second part, we study the temporal stability of CE-induced charges and identify the key material factors that determine whether KPFM can capture meaningful charge patterns. Through time-resolved experiments combining a custom-built transfer system with both microscopic and macroscopic measurements, we demonstrate that only the best insulators, such as SiO$_2$, preserve CE charge long enough for stationary imaging. For less conductive polymers, such as PDMS, charge decays within the duration of a single KPFM scan due to bulk conduction. Using a simple capacitor-based model, we reproduce the observed decay dynamics and confirm that the transferred charge decays characteristic to the sample's bulk conductivity. Further, we always observe homogeneous charge transfer.\r\n\r\nIn the third part, we address the question: can we form a triboelectric series with identical materials? Using controlled repetitive contact experiments, we show that nominally identical materials can progressively order themselves into a triboelectric series, where surfaces with more contact history charge negatively relative to fresher ones. By constructing a minimal model based on this ``contact bias'', we replicate the evolution from random to ordered charging observed in experiments. Supporting surface analyses, including atomic force microscopy, reveal that repeated contact induces nanoscale morphological changes, suggesting a mechanism tightly coupled to mechanical strain. These results highlight the crucial role of surface history and nanoscale mechanics in dictating charge transfer, motivating further exploration of mechanisms such as mechanochemical bond cleavage and flexoelectric polarization.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","doi_confirm":"1","citation":{"short":"F. Pertl, Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging, Institute of Science and Technology Austria, 2026.","apa":"Pertl, F. (2026). <i>Experimental probing of nanoscale charge features and surface morphology changes during tribocharging</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22684\">https://doi.org/10.15479/AT-ISTA-22684</a>","chicago":"Pertl, Felix. “Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22684\">https://doi.org/10.15479/AT-ISTA-22684</a>.","mla":"Pertl, Felix. <i>Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22684\">10.15479/AT-ISTA-22684</a>.","ama":"Pertl F. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22684\">10.15479/AT-ISTA-22684</a>","ista":"Pertl F. 2026. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. Institute of Science and Technology Austria.","ieee":"F. Pertl, “Experimental probing of nanoscale charge features and surface morphology changes during tribocharging,” Institute of Science and Technology Austria, 2026."},"oa_version":"Published Version","month":"08","ddc":["530"],"publisher":"Institute of Science and Technology Austria","date_published":"2026-08-12T00:00:00Z","acknowledgement":"This project has received financing from the European Research Council grant agreement\r\nno. 949120 under the European Union’s Horizon 2020 research and innovation programme.\r\nThis research was supported by the Scientific Service Units of The Institute of Science\r\nand Technology Austria (ISTA) through resources provided by the Miba Machine Shop, the\r\nNanofabrication Facility, the Lab Support Facility, the Scientific Computing Facility and the\r\nElectron Microscopy Facility. We thank Florian Stumpf from Park Systems for useful discussions\r\nand support with scanning probe microscopy. We thank Joaquin Garcia-Suarez and Guillaume\r\nAnciaux for the suggestion to look into the roughness power spectral density. We thank\r\nIrina-Malina Strugaru for help with testing the device for Young’s modulus measurements.\r\n","file_date_updated":"2026-08-12T13:04:21Z","year":"2026","date_created":"2026-08-12T09:44:40Z","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ScWa"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22684","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-083-1"],"issn":["2663-337X"]},"day":"12","page":"107","supervisor":[{"orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R"}],"_id":"22684","title":"Experimental probing of nanoscale charge features and surface morphology changes during tribocharging","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ec_funded":1,"has_accepted_license":"1","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"corr_author":"1","file":[{"date_updated":"2026-08-12T13:04:21Z","relation":"source_file","access_level":"closed","file_name":"2026_Pertl_Felix_Thesis.zip","file_size":31192621,"creator":"fpertl","checksum":"0a4f5a941c40b921447e72291d72bc6f","content_type":"application/x-zip-compressed","date_created":"2026-08-12T13:04:21Z","file_id":"22690"},{"access_level":"open_access","date_updated":"2026-08-12T13:04:21Z","relation":"main_file","content_type":"application/pdf","date_created":"2026-08-12T13:04:21Z","file_id":"22691","file_name":"2026_Pertl_Felix_Thesis.pdf","file_size":27882509,"checksum":"ae60dcdb363222138886b2857643d4e3","creator":"fpertl"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.15479/AT-ISTA-22684","project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","call_identifier":"H2020"}],"oa":1},{"volume":31,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","das_tickbox":"1","external_id":{"isi":["001287455300001"]},"article_type":"original","corr_author":"1","oa":1,"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"doi":"10.1007/s00031-024-09873-0","mathsc":["14B05","14D23","14G20","16G20"],"researchdata_availability":"not applicable","file":[{"access_level":"open_access","relation":"main_file","date_updated":"2026-07-23T05:50:09Z","success":1,"date_created":"2026-07-23T05:50:09Z","file_id":"22385","content_type":"application/pdf","creator":"dernst","checksum":"8985b4154b730284d3412ddc9e55d965","file_name":"2026_TransformationGroups_Vernet.pdf","file_size":912029}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"fulldoi":"https://doi.org/10.1007/s00031-024-09873-0","supplementarymaterial":"no","department":[{"_id":"TaHa"}],"publication_identifier":{"issn":["1083-4362"],"eissn":["1531-586X"]},"page":"1047-1083","day":"01","title":"Rational singularities for moment maps of totally negative quivers","_id":"17437","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","citation":{"short":"T. Vernet, Transformation Groups 31 (2026) 1047–1083.","apa":"Vernet, T. (2026). Rational singularities for moment maps of totally negative quivers. <i>Transformation Groups</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00031-024-09873-0\">https://doi.org/10.1007/s00031-024-09873-0</a>","chicago":"Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” <i>Transformation Groups</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00031-024-09873-0\">https://doi.org/10.1007/s00031-024-09873-0</a>.","mla":"Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” <i>Transformation Groups</i>, vol. 31, Springer Nature, 2026, pp. 1047–83, doi:<a href=\"https://doi.org/10.1007/s00031-024-09873-0\">10.1007/s00031-024-09873-0</a>.","ama":"Vernet T. Rational singularities for moment maps of totally negative quivers. <i>Transformation Groups</i>. 2026;31:1047-1083. doi:<a href=\"https://doi.org/10.1007/s00031-024-09873-0\">10.1007/s00031-024-09873-0</a>","ieee":"T. Vernet, “Rational singularities for moment maps of totally negative quivers,” <i>Transformation Groups</i>, vol. 31. Springer Nature, pp. 1047–1083, 2026.","ista":"Vernet T. 2026. Rational singularities for moment maps of totally negative quivers. Transformation Groups. 31, 1047–1083."},"date_published":"2026-03-01T00:00:00Z","publisher":"Springer Nature","month":"03","ddc":["510"],"file_date_updated":"2026-07-23T05:50:09Z","intvolume":"        31","acknowledgement":"I would like to warmly thank Dimitri Wyss for his guidance and supervision and Nero Budur for helpful discussions and answering all my questions on his previous works. I would also like to thank Francesca Carocci, Ben Davison, Lucien Hennecart and Olivier Schiffmann for helpful remarks and discussions during the writing of this paper. Finally, I would like to thank the anonymous referees for their careful reading and suggesting improvements in the exposition.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). This work was supported by the Swiss National Science Foundation [No. 196960]. This project has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","isi":1,"publication_status":"published","year":"2026","publication":"Transformation Groups","date_created":"2024-08-18T22:01:04Z","OA_type":"hybrid","dataavailabilitystatement":"Not applicable.","scopus_import":"1","date_updated":"2026-10-21T10:55:21Z","author":[{"full_name":"Vernet, Tanguy","id":"19f1e3bf-c59a-11ee-a1af-ed269948817b","last_name":"Vernet","first_name":"Tanguy"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We prove that the zero-fiber of the moment map of a totally negative quiver has rational singularities. Our proof consists in generalizing dimension bounds on jet spaces of this fiber, which were introduced by Budur. We also transfer the rational singularities property to other moduli spaces of objects in 2-Calabi-Yau categories, based on recent work of Davison. This has interesting arithmetic applications on quiver moment maps and moduli spaces of objects in 2-Calabi-Yau categories. First, we generalize results of Wyss on the asymptotic behaviour of counts of jets of quiver moment maps over finite fields. Moreover, we interpret the limit of counts of jets on a given moduli space as its p-adic volume under a canonical measure analogous to the measure built by Carocci, Orecchia and Wyss on certain moduli spaces of coherent sheaves."}],"OA_place":"publisher","type":"journal_article","quality_controlled":"1","status":"public","PlanS_conform":"1"},{"arxiv":1,"day":"04","publication_identifier":{"issn":["1942-3454"],"eissn":["1942-3462"]},"department":[{"_id":"UlWa"}],"supplementarymaterial":"no","fulldoi":"https://doi.org/10.1145/3779121","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"22247","title":"Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs","article_type":"original","external_id":{"arxiv":["2312.12981"]},"das_tickbox":"0","article_processing_charge":"Yes","volume":18,"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"access_level":"open_access","relation":"main_file","date_updated":"2026-07-06T09:03:02Z","success":1,"file_id":"22252","date_created":"2026-07-06T09:03:02Z","content_type":"application/pdf","checksum":"0399ab94085878fc810084845eabd627","creator":"dernst","file_size":941518,"file_name":"2026_TransactionsGraphics_Filakovsky.pdf"}],"researchdata_availability":"no","keyword":["Constraint satisfaction problem","hypergraph colouring","promise problem","topological methods"],"project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory","call_identifier":"FWF"},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"oa":1,"doi":"10.1145/3779121","issue":"2","corr_author":"1","author":[{"full_name":"Filakovský, Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","last_name":"Filakovský","first_name":"Marek"},{"last_name":"Nakajima","first_name":"Tamio Vesa","full_name":"Nakajima, Tamio Vesa"},{"last_name":"Opršal","first_name":"Jakub","full_name":"Opršal, Jakub","id":"ec596741-c539-11ec-b829-c79322a91242","orcid":"0000-0003-1245-3456"},{"first_name":"Gianluca","last_name":"Tasinato","id":"0433290C-AF8F-11E9-A4C7-F729E6697425","full_name":"Tasinato, Gianluca"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568"}],"date_updated":"2026-10-21T13:23:55Z","scopus_import":"1","OA_type":"gold","PlanS_conform":"1","status":"public","quality_controlled":"1","type":"journal_article","OA_place":"publisher","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"15168"}]},"abstract":[{"text":"A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its vertices with colours 1, …, k such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO k-colouring with a fixed number of colours is NP-complete (and in the special case of graphs, LO colouring coincides with the usual graph colouring).\r\nHere, we investigate the complexity of approximating the “linearly ordered chromatic number” of a hypergraph. We prove that the following promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable. We prove this result by a combination of algebraic, topological, and combinatorial methods, building on and extending a topological approach for studying approximate graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023).","lang":"eng"}],"language":[{"iso":"eng"}],"ddc":["500"],"month":"05","publisher":"Association for Computing Machinery","date_published":"2026-05-04T00:00:00Z","oa_version":"Published Version","citation":{"ista":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. 2026. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. ACM Transactions on Computation Theory. 18(2), 10.","ieee":"M. Filakovský, T. V. Nakajima, J. Opršal, G. Tasinato, and U. Wagner, “Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs,” <i>ACM Transactions on Computation Theory</i>, vol. 18, no. 2. Association for Computing Machinery, 2026.","ama":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. <i>ACM Transactions on Computation Theory</i>. 2026;18(2). doi:<a href=\"https://doi.org/10.1145/3779121\">10.1145/3779121</a>","short":"M. Filakovský, T.V. Nakajima, J. Opršal, G. Tasinato, U. Wagner, ACM Transactions on Computation Theory 18 (2026).","chicago":"Filakovský, Marek, Tamio Vesa Nakajima, Jakub Opršal, Gianluca Tasinato, and Uli Wagner. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” <i>ACM Transactions on Computation Theory</i>. Association for Computing Machinery, 2026. <a href=\"https://doi.org/10.1145/3779121\">https://doi.org/10.1145/3779121</a>.","mla":"Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” <i>ACM Transactions on Computation Theory</i>, vol. 18, no. 2, 10, Association for Computing Machinery, 2026, doi:<a href=\"https://doi.org/10.1145/3779121\">10.1145/3779121</a>.","apa":"Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., &#38; Wagner, U. (2026). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. <i>ACM Transactions on Computation Theory</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3779121\">https://doi.org/10.1145/3779121</a>"},"publication":"ACM Transactions on Computation Theory","date_created":"2026-07-05T22:01:37Z","year":"2026","publication_status":"published","acknowledgement":"This research was supported by the Charles University project PRIMUS/21/SCI/014, by the Ministry of Education, Youth\r\nand Sports of the Czech Republic under the project MSCAfellow5_MUNI (CZ.02.01.01/00/22_010/0003229), and by the\r\nAustrian Science Fund (FWF project P31312-N35). This research was funded by UKRI EP/X024431/1 and by a Clarendon\r\nFund Scholarship. This project has received funding from the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant Agreement No 101034413.\r\n","article_number":"10","intvolume":"        18","file_date_updated":"2026-07-06T09:03:02Z"},{"year":"2026","date_created":"2025-06-22T22:02:07Z","publication":"Discrete & Computational Geometry","publication_status":"published","file_date_updated":"2026-07-23T11:14:05Z","acknowledgement":"Work by BA was supported by NSF grants CCF 15-40656 and CCF 20-08551, and by grant 2014/170 from the US-Israel Binational Science Foundation. Part of this research was conducted while BA was visiting ISTA in the summers of 2022 and 2023. The visit of BA to ISTA in the summer of 2022 was supported by an ISTA Visiting Professorship. Research of BA also partially supported by ERC grant no. 882971, “GeoScape,” and by the Erdős Center. Work by AB was supported by Australian Research Council grant DP220102212. Work by IR was supported by a Tandon School of Engineering Fellowship and by NSF Grant CCF-20-08551. BA and AB would like to thank William Steiger for insightful initial discussions of the problems addressed in this work. Open Access funding enabled and organized by CAUL and its Member Institutions.","isi":1,"intvolume":"        75","date_published":"2026-06-01T00:00:00Z","month":"06","ddc":["500"],"publisher":"Springer Nature","oa_version":"Published Version","citation":{"ieee":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning points in 3D, and efficiently too,” <i>Discrete &#38; Computational Geometry</i>, vol. 75. Springer Nature, pp. 1331–1355, 2026.","ista":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. 2026. Eight-partitioning points in 3D, and efficiently too. Discrete &#38; Computational Geometry. 75, 1331–1355.","ama":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points in 3D, and efficiently too. <i>Discrete &#38; Computational Geometry</i>. 2026;75:1331-1355. doi:<a href=\"https://doi.org/10.1007/s00454-025-00739-0\">10.1007/s00454-025-00739-0</a>","short":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, U. Wagner, Discrete &#38; Computational Geometry 75 (2026) 1331–1355.","mla":"Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>Discrete &#38; Computational Geometry</i>, vol. 75, Springer Nature, 2026, pp. 1331–55, doi:<a href=\"https://doi.org/10.1007/s00454-025-00739-0\">10.1007/s00454-025-00739-0</a>.","chicago":"Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00454-025-00739-0\">https://doi.org/10.1007/s00454-025-00739-0</a>.","apa":"Aronov, B., Basit, A., Ramesh, I., Tasinato, G., &#38; Wagner, U. (2026). Eight-partitioning points in 3D, and efficiently too. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-025-00739-0\">https://doi.org/10.1007/s00454-025-00739-0</a>"},"PlanS_conform":"1","quality_controlled":"1","status":"public","abstract":[{"text":"An eight-partition of a finite set of points (respectively, of a continuous mass distribution) in R^3\r\n consists of three planes that divide the space into 8 octants, such that each open octant contains at most 1/8 of the points (respectively, of the mass). In 1966, Hadwiger showed that any mass distribution in R^3 admits an eight-partition; moreover, one can prescribe the normal direction of one of the three planes. The analogous result for finite point sets follows by a standard limit argument. We prove the following variant of this result: any mass distribution (or point set) in R^3 admits an eight-partition for which the intersection of two of the planes is a line with a prescribed direction. Moreover, we present an efficient algorithm for calculating an eight-partition of a set of n points in R^3 (with prescribed normal direction of one of the planes) in time O(n^7/3). A preliminary version of this work appeared in SoCG’24 (Aronov et al., 40th International Symposium on Computational Geometry, 2024).","lang":"eng"}],"related_material":{"record":[{"id":"20339","relation":"dissertation_contains","status":"public"},{"relation":"earlier_version","id":"18917","status":"public"}],"link":[{"url":"https://doi.org/10.1007/s00454-025-00759-w","relation":"erratum"}]},"language":[{"iso":"eng"}],"type":"journal_article","OA_place":"publisher","author":[{"full_name":"Aronov, Boris","first_name":"Boris","last_name":"Aronov"},{"full_name":"Basit, Abdul","first_name":"Abdul","last_name":"Basit"},{"last_name":"Ramesh","first_name":"Indu","full_name":"Ramesh, Indu"},{"last_name":"Tasinato","first_name":"Gianluca","full_name":"Tasinato, Gianluca","id":"0433290C-AF8F-11E9-A4C7-F729E6697425"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"date_updated":"2026-10-21T13:38:17Z","scopus_import":"1","OA_type":"hybrid","doi":"10.1007/s00454-025-00739-0","oa":1,"file":[{"access_level":"open_access","date_updated":"2026-07-23T11:14:05Z","relation":"main_file","success":1,"date_created":"2026-07-23T11:14:05Z","file_id":"22395","content_type":"application/pdf","creator":"dernst","checksum":"a32774a0d14f46cafbd77bfb9d9ac4b6","file_name":"2026_DiscreteCompGeom_Aronov.pdf","file_size":525281}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"researchdata_availability":"no","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2403.02627"],"isi":["001506904300001"]},"article_type":"original","das_tickbox":"0","volume":75,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Eight-partitioning points in 3D, and efficiently too","_id":"19860","page":"1331-1355","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"arxiv":1,"day":"01","supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1007/s00454-025-00739-0","department":[{"_id":"UlWa"}]},{"oa_version":"Accepted Version","citation":{"ama":"Kulich I, Vladimirtsev D, Randuch M, et al. Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. <i>Science</i>. 2026;392(6795):296-300. doi:<a href=\"https://doi.org/10.1126/science.adu8197\">10.1126/science.adu8197</a>","ieee":"I. Kulich <i>et al.</i>, “Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation,” <i>Science</i>, vol. 392, no. 6795. AAAS, pp. 296–300, 2026.","ista":"Kulich I, Vladimirtsev D, Randuch M, Gao S, Citterico M, Konrad KR, Nagel G, Wrzaczek M, Cascaro L, Vinet P, Durand P, Asnacios A, Verma L, Bennett MJ, Pandey BK, Friml J. 2026. Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. Science. 392(6795), 296–300.","apa":"Kulich, I., Vladimirtsev, D., Randuch, M., Gao, S., Citterico, M., Konrad, K. R., … Friml, J. (2026). Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adu8197\">https://doi.org/10.1126/science.adu8197</a>","mla":"Kulich, Ivan, et al. “Calcium-Triggered Apoplastic ROS Bursts Balance Gravity and Mechanical Signals for Soil Navigation.” <i>Science</i>, vol. 392, no. 6795, AAAS, 2026, pp. 296–300, doi:<a href=\"https://doi.org/10.1126/science.adu8197\">10.1126/science.adu8197</a>.","chicago":"Kulich, Ivan, Dmitrii Vladimirtsev, Marek Randuch, Shiqiang Gao, Matteo Citterico, Kai R. Konrad, Georg Nagel, et al. “Calcium-Triggered Apoplastic ROS Bursts Balance Gravity and Mechanical Signals for Soil Navigation.” <i>Science</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/science.adu8197\">https://doi.org/10.1126/science.adu8197</a>.","short":"I. Kulich, D. Vladimirtsev, M. Randuch, S. Gao, M. Citterico, K.R. Konrad, G. Nagel, M. Wrzaczek, L. Cascaro, P. Vinet, P. Durand, A. Asnacios, L. Verma, M.J. Bennett, B.K. Pandey, J. Friml, Science 392 (2026) 296–300."},"month":"04","ddc":["580"],"publisher":"AAAS","pmid":1,"date_published":"2026-04-16T00:00:00Z","acknowledgement":"We gratefully acknowledge the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) (both of ISTA) and the Hounsfield CT Facility (University of Nottingham) for support with imaging and the Growth Facility (IPMB) for plant cultivation. We thank M. Fendrych and his team for help with the microfluidics upgrades and J. Atkinson at the University of Nottingham MakerSpace for 3D printing of Arabidopsis mini-soil columns.\r\nThis project received funding from the European Research Council (ERC; 101142681 CYNIPS) and the Austrian Science Fund (FWF; P 37051-B). I.K. was cofunded by the European Union, Horizon Europe, project MOLIPEC, ID 101087030 and CSF project 25-16449S. L.V. and B.K.P. acknowledge funding from UK Research and Innovation (UKRI) Frontiers Research (EP/Y036697/1). M.J.B. acknowledges funding from ERC SYNERGY (grant 101118769 HYDROSENSING). The study was partially supported by the Université Paris Cité, Idex ANR-18-IDEX-0001, funded by the French Government through its “Investments for the Future” program and also by the projects “Mecha-Nuc” ANR-20-CE13-0025-03 and “scEm-bryoMech” ANR-21-CE13-0046. P.D. acknowledges support by Human Frontier Science Program Organization grant 2022-RG107. P.V. acknowledges support provided by “Programme blanc” of the Graduate School BIOSPHERA, Université Paris-Saclay. Phytohormonal analysis was performed using the service laboratory funded by Toward Next GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of the European Regional Development Fund (ERDF) program Johannes Amos Comenius. This research was funded in whole or in part by the Austrian Science Fund (P 37051-B) and UK Research and Innovation (EP/Y036697/1), cOAlition S organizations, and by the European Research Council (101142681 CYNIPS, 101118769 HYDROSENSING); as required, the author will make the Author Accepted Manuscript (AAM) version available under a CC BY public copyright license.","intvolume":"       392","file_date_updated":"2026-05-07T05:54:43Z","date_created":"2026-04-26T22:01:47Z","publication":"Science","year":"2026","publication_status":"published","date_updated":"2026-10-22T09:15:44Z","scopus_import":"1","OA_type":"green","author":[{"full_name":"Kulich, Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","last_name":"Kulich","first_name":"Ivan"},{"id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","full_name":"Vladimirtsev, Dmitrii","first_name":"Dmitrii","last_name":"Vladimirtsev"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek","first_name":"Marek","last_name":"Randuch"},{"last_name":"Gao","first_name":"Shiqiang","full_name":"Gao, Shiqiang"},{"full_name":"Citterico, Matteo","last_name":"Citterico","first_name":"Matteo"},{"last_name":"Konrad","first_name":"Kai R.","full_name":"Konrad, Kai R."},{"last_name":"Nagel","first_name":"Georg","full_name":"Nagel, Georg"},{"last_name":"Wrzaczek","first_name":"Michael","full_name":"Wrzaczek, Michael"},{"full_name":"Cascaro, Léa","first_name":"Léa","last_name":"Cascaro"},{"last_name":"Vinet","first_name":"Pauline","full_name":"Vinet, Pauline"},{"full_name":"Durand, Pauline","first_name":"Pauline","last_name":"Durand"},{"first_name":"Atef","last_name":"Asnacios","full_name":"Asnacios, Atef"},{"first_name":"Lokesh","last_name":"Verma","full_name":"Verma, Lokesh"},{"first_name":"Malcolm J.","last_name":"Bennett","full_name":"Bennett, Malcolm J."},{"full_name":"Pandey, Bipin K.","last_name":"Pandey","first_name":"Bipin K."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"type":"journal_article","OA_place":"repository","abstract":[{"lang":"eng","text":"Reactive oxygen species (ROS) have been implicated in multiple signaling processes in plants, but the underlying mechanisms and roles remain enigmatic. In this study, we developed a method of live imaging of apoplastic ROS at the root surface. Distinct signals, including auxin, extracellular adenosine triphosphate, and rapid alkalinization factor 1 peptide, induce cytosolic calcium transients and apoplastic ROS bursts. Genetic and optogenetic manipulations of Arabidopsis identified calcium transients as necessary and sufficient for ROS bursts through activation of reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidases RBOHC and RBOHF. Apoplastic ROS bursts are not required, but they do limit gravity-induced root bending. Root bending is sensed by the stretch-activated calcium channel MCA1, leading to NADPH oxidase activation. The resulting ROS production stiffens cell walls to facilitate soil penetration. Apoplastic ROS thus provides a means to balance tissue flexibility and stiffness to navigate soil."}],"related_material":{"record":[{"id":"23145","relation":"dissertation_contains","status":"public"}]},"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","has_accepted_license":"1","volume":392,"article_type":"original","external_id":{"pmid":["41990180"]},"article_processing_charge":"No","issue":"6795","corr_author":"1","file":[{"content_type":"application/pdf","file_id":"21832","date_created":"2026-05-07T05:54:43Z","file_name":"2026_Science_Kulich_accepted.pdf","file_size":6150733,"creator":"dernst","checksum":"eb5b29247832ecdc53c8146da0509bbe","access_level":"open_access","success":1,"date_updated":"2026-05-07T05:54:43Z","relation":"main_file"}],"doi":"10.1126/science.adu8197","oa":1,"project":[{"_id":"8f347782-16d5-11f0-9cad-8c19706ee739","name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681"},{"grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"department":[{"_id":"JiFr"},{"_id":"GradSch"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"fulldoi":"https://doi.org/10.1126/science.adu8197","day":"16","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"page":"296-300","_id":"21763","title":"Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","OA_place":"publisher","type":"dissertation","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"12291","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"21763","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"23175"},{"status":"public","id":"23174","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"20656","status":"public"}]},"author":[{"last_name":"Randuch","first_name":"Marek","full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"}],"date_updated":"2026-10-22T09:15:44Z","publication_status":"published","date_created":"2026-10-16T17:14:40Z","year":"2026","acknowledgement":"European Research Council (101142681 CYNIPS), Cyclic nucleotides as second messengers \r\nin plants, DOI: https://doi.org/10.3030/101142681 \r\nAustrian Science Fund (P 37051-B), Guanylate cyclase activity of TIR1/AFBs auxin receptors, \r\nDOI: https://doi.org/10.55776/P37051 ","file_date_updated":"2026-10-20T11:48:37Z","publisher":"Institute of Science and Technology Austria","ddc":["580"],"month":"10","date_published":"2026-10-18T00:00:00Z","license":"https://creativecommons.org/licenses/by-sa/4.0/","doi_confirm":"1","citation":{"ama":"Randuch M. Fast growth responses in plants: Growth regulation and phospho-proteomic . 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-23145\">10.15479/AT-ISTA-23145</a>","ista":"Randuch M. 2026. Fast growth responses in plants: Growth regulation and phospho-proteomic . Institute of Science and Technology Austria.","ieee":"M. Randuch, “Fast growth responses in plants: Growth regulation and phospho-proteomic ,” Institute of Science and Technology Austria, 2026.","short":"M. Randuch, Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic , Institute of Science and Technology Austria, 2026.","apa":"Randuch, M. (2026). <i>Fast growth responses in plants: Growth regulation and phospho-proteomic </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-23145\">https://doi.org/10.15479/AT-ISTA-23145</a>","mla":"Randuch, Marek. <i>Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic </i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-23145\">10.15479/AT-ISTA-23145</a>.","chicago":"Randuch, Marek. “Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic .” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-23145\">https://doi.org/10.15479/AT-ISTA-23145</a>."},"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"23145","title":"Fast growth responses in plants: Growth regulation and phospho-proteomic ","page":"289","publication_identifier":{"issn":["2663-337X"]},"day":"18","supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-23145","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"},{"_id":"Bio"}],"degree_awarded":"PhD","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"file":[{"file_name":"2026_Marek_Randuch_Thesis.docx","file_size":89544771,"creator":"mranduch","checksum":"4ace20ba4f1bb0f8dcc3f8eb45eb68fa","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2026-10-20T09:17:28Z","file_id":"23176","date_updated":"2026-10-20T11:48:37Z","relation":"source_file","access_level":"closed"},{"creator":"mranduch","checksum":"fc630c7e8d795e7f13000cbb428424b3","file_name":"2026_Marek_Randuch_Thesis.pdf","file_size":28321059,"date_created":"2026-10-20T09:17:20Z","file_id":"23177","content_type":"application/pdf","relation":"main_file","date_updated":"2026-10-20T11:48:37Z","embargo_to":"open_access","embargo":"2027-10-20","access_level":"closed"}],"project":[{"name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"},{"name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"}],"doi":"10.15479/AT-ISTA-23145","corr_author":"1","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","has_accepted_license":"1"},{"status":"public","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"23145","relation":"dissertation_contains"}]},"abstract":[{"text":"Plants must continually balance growth with arrest, especially under stress. Auxin signaling acts as a central regulatory hub in this process, yet the mechanisms that dynamically tune early auxin signalling in real time remain unknown. Here, we used the light-gated, Ca2+-permeable Channelrhodopsin 2 variant XXM2.0 to optogenetically impose defined Ca2+ signatures on Arabidopsis root cells. Repetitive light activation triggered cytosolic Ca2+ signals that in turn suppressed auxin-induced membrane depolarization and Ca2+ transients. Moreover, prolonged optogenetic Ca2+ stimulation affects auxin-responsive transcriptional reprogramming. As phenotypic output, reversible inhibition of root growth by suppressing cell division and elongation was observed. We further identify a candidate CaM7–CNGC14 module that likely mediates Ca2+-dependent gating of early auxin signalling. Our study thus introduces a synthetic biology approach to decompose calcium–auxin crosstalk in plant cells, and demonstrates that optogenetically imposed cytosolic Ca2+ signals act as dynamic regulators of auxin susceptibility in roots.","lang":"eng"}],"OA_place":"repository","type":"preprint","author":[{"full_name":"Song, Huifang","last_name":"Song","first_name":"Huifang"},{"first_name":"Angel","last_name":"Baudon","full_name":"Baudon, Angel"},{"first_name":"Matthias","last_name":"Freund","full_name":"Freund, Matthias"},{"full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","first_name":"Marek"},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"full_name":"Ondřej, Novák","first_name":"Novák","last_name":"Ondřej"},{"full_name":"He, Zhaohui","first_name":"Zhaohui","last_name":"He"},{"full_name":"Kaufmann, Kerstin","first_name":"Kerstin","last_name":"Kaufmann"},{"full_name":"Li, Nan","last_name":"Li","first_name":"Nan"},{"full_name":"Gilliham, Matthew","last_name":"Gilliham","first_name":"Matthew"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rainer","last_name":"Hedrich","full_name":"Hedrich, Rainer"},{"full_name":"Huang, Shouguang","first_name":"Shouguang","last_name":"Huang"}],"OA_type":"green","date_updated":"2026-10-22T09:15:44Z","publication_status":"draft","publication":"bioRxiv","date_created":"2026-10-19T11:51:47Z","year":"2026","acknowledgement":"We would like to thank Dirk Becker (University of Wuerzburg) for his help in making the optogenetic constructs and for his comments on the manuscript. We also appreciate Rob Roelfsema (University of Wuerzburg) for his feedback on the manuscript. We sincerely thank the anonymous reviewers for the thoughtful and inspiring suggestions that helped broaden the discussion and identify important future research directions. Funding\r\nNational Key R&D Program of China, 2025YFA0923400 (RH)\r\n\r\nNational Natural Science Foundation of China (NSFC), W2531024 (RH); 32271501(NL)\r\n\r\nNSFC-Excellent Young Scientists Fund Program (overseas) (SH)\r\n\r\nNSFC-RFIS, ZB2025101410702 (RH)\r\n\r\nGuangdong Pearl River Talents Program, 2023ZT10N033\r\n\r\nChina Scholarship Council no. 202306510063 (HS)\r\n\r\nThe European Research Council grant 101142681 CYNIPS (JF)\r\n\r\nAustrian Science Fund grant FWF; P 37051-B (JF)\r\n\r\nGerman Research Foundation grant CRC 1644 (512328399; 512328399) (KK, ZH)\r\n\r\nERC Synergy project STARMORPH, reg. no. 101166880 (AP, ON)","date_published":"2026-08-26T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"08","oa_version":"Preprint","citation":{"ama":"Song H, Baudon A, Freund M, et al. Ca2+ signature gates early auxin signaling in Arabidopsis roots. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.10.04.680446\">10.1101/2025.10.04.680446</a>","ista":"Song H, Baudon A, Freund M, Randuch M, Pěnčík A, Ondřej N, He Z, Kaufmann K, Li N, Gilliham M, Friml J, Hedrich R, Huang S. Ca2+ signature gates early auxin signaling in Arabidopsis roots. bioRxiv, <a href=\"https://doi.org/10.1101/2025.10.04.680446\">10.1101/2025.10.04.680446</a>.","ieee":"H. Song <i>et al.</i>, “Ca2+ signature gates early auxin signaling in Arabidopsis roots,” <i>bioRxiv</i>. .","apa":"Song, H., Baudon, A., Freund, M., Randuch, M., Pěnčík, A., Ondřej, N., … Huang, S. (n.d.). Ca2+ signature gates early auxin signaling in Arabidopsis roots. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.10.04.680446\">https://doi.org/10.1101/2025.10.04.680446</a>","mla":"Song, Huifang, et al. “Ca2+ Signature Gates Early Auxin Signaling in Arabidopsis Roots.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.10.04.680446\">10.1101/2025.10.04.680446</a>.","chicago":"Song, Huifang, Angel Baudon, Matthias Freund, Marek Randuch, Aleš Pěnčík, Novák Ondřej, Zhaohui He, et al. “Ca2+ Signature Gates Early Auxin Signaling in Arabidopsis Roots.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.10.04.680446\">https://doi.org/10.1101/2025.10.04.680446</a>.","short":"H. Song, A. Baudon, M. Freund, M. Randuch, A. Pěnčík, N. Ondřej, Z. He, K. Kaufmann, N. Li, M. Gilliham, J. Friml, R. Hedrich, S. Huang, BioRxiv (n.d.)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Ca2+ signature gates early auxin signaling in Arabidopsis roots","biorxivid":1,"_id":"23175","day":"26","fulldoi":"https://doi.org/10.1101/2025.10.04.680446","department":[{"_id":"JiFr"}],"oa":1,"doi":"10.1101/2025.10.04.680446","project":[{"grant_number":"101142681","name":"Cyclic nucleotides as second messengers in plants","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"corr_author":"1","article_processing_charge":"No","external_id":{"biorxivid":["10.1101/2025.10.04.680446"]},"main_file_link":[{"url":"https://doi.org/10.1101/2025.10.04.680446","open_access":"1"}]},{"article_processing_charge":"No","alternative_title":["Technical Digest Series"],"corr_author":"1","conference":{"name":"CLEO: Fundamental Science","location":"Long Beach, CA, United States","start_date":"2026-05-02","end_date":"2026-05-06"},"doi":"10.1364/CLEO_FS.2026.FTU1B.4","fulldoi":"https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4","department":[{"_id":"ChRo"}],"publication_identifier":{"isbn":["9781957171586"]},"day":"15","title":"Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators","_id":"23197","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mamian, Karen, et al. “Collective Optonuclear Cavity Quantum Electrodynamics in 229Th Nanophotonic Resonators.” <i>CLEO Fundamental Science Proceedings</i>, FTU1B.4, Optica Publishing Group, 2026, doi:<a href=\"https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4\">10.1364/CLEO_FS.2026.FTU1B.4</a>.","chicago":"Mamian, Karen, Jan De Haan, Toby Bi, Swadheen Dubey, Georgy A. Kazakov, Kjeld Beeks, Christoph Marquardt, et al. “Collective Optonuclear Cavity Quantum Electrodynamics in 229Th Nanophotonic Resonators.” In <i>CLEO Fundamental Science Proceedings</i>. Optica Publishing Group, 2026. <a href=\"https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4\">https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4</a>.","apa":"Mamian, K., De Haan, J., Bi, T., Dubey, S., Kazakov, G. A., Beeks, K., … Roques-Carmes, C. (2026). Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators. In <i>CLEO Fundamental Science Proceedings</i>. Long Beach, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4\">https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4</a>","short":"K. Mamian, J. De Haan, T. Bi, S. Dubey, G.A. Kazakov, K. Beeks, C. Marquardt, S. Kraemer, L.M.C. Pereira, P. Del’Haye, K. Van Gasse, T. Schumm, C. Roques-Carmes, in:, CLEO Fundamental Science Proceedings, Optica Publishing Group, 2026.","ista":"Mamian K, De Haan J, Bi T, Dubey S, Kazakov GA, Beeks K, Marquardt C, Kraemer S, Pereira LMC, Del’Haye P, Van Gasse K, Schumm T, Roques-Carmes C. 2026. Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators. CLEO Fundamental Science Proceedings. CLEO: Fundamental Science, Technical Digest Series, , FTU1B.4.","ieee":"K. Mamian <i>et al.</i>, “Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators,” in <i>CLEO Fundamental Science Proceedings</i>, Long Beach, CA, United States, 2026.","ama":"Mamian K, De Haan J, Bi T, et al. Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators. In: <i>CLEO Fundamental Science Proceedings</i>. Optica Publishing Group; 2026. doi:<a href=\"https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4\">10.1364/CLEO_FS.2026.FTU1B.4</a>"},"oa_version":"None","date_published":"2026-05-15T00:00:00Z","month":"05","publisher":"Optica Publishing Group","article_number":"FTU1B.4","publication":"CLEO Fundamental Science Proceedings","year":"2026","date_created":"2026-10-25T23:02:24Z","publication_status":"published","date_updated":"2026-10-27T10:53:59Z","OA_type":"closed access","scopus_import":"1","author":[{"id":"d21e88e4-b0a3-11f1-8f28-b033c1af3b5a","full_name":"Mamian, Karen","first_name":"Karen","last_name":"Mamian"},{"last_name":"De Haan","first_name":"Jan","full_name":"De Haan, Jan"},{"first_name":"Toby","last_name":"Bi","full_name":"Bi, Toby"},{"last_name":"Dubey","first_name":"Swadheen","full_name":"Dubey, Swadheen"},{"last_name":"Kazakov","first_name":"Georgy A.","full_name":"Kazakov, Georgy A."},{"full_name":"Beeks, Kjeld","last_name":"Beeks","first_name":"Kjeld"},{"first_name":"Christoph","last_name":"Marquardt","full_name":"Marquardt, Christoph"},{"first_name":"Sandro","last_name":"Kraemer","full_name":"Kraemer, Sandro"},{"full_name":"Pereira, Lino M.C.","last_name":"Pereira","first_name":"Lino M.C."},{"last_name":"Del’Haye","first_name":"Pascal","full_name":"Del’Haye, Pascal"},{"full_name":"Van Gasse, Kasper","last_name":"Van Gasse","first_name":"Kasper"},{"full_name":"Schumm, Thorsten","last_name":"Schumm","first_name":"Thorsten"},{"first_name":"Charles","last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles"}],"abstract":[{"text":"We develop a quantum theory of light-matter interactions in 229Th nanophotonic resonators pumped via the optonuclear quadrupolar effect, predicting detectable photon fluxes with realistic platforms and revealing how collective dynamics shape the future nuclear clock performance.","lang":"eng"}],"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","status":"public"},{"publication_status":"epub_ahead","date_created":"2026-06-10T07:37:12Z","publication":"Current Opinion in Genetics & Development","year":"2026","intvolume":"        99","acknowledgement":"We thank Nick Barton and Noa Ottilie Borst for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA).\r\nThis study was supported by the European Molecular Biology Laboratory (J.C.); the European Molecular Biology Laboratory Interdisciplinary Postdoc Programme (EIPOD) under the Marie Skłodowska-Curie Actions cofund (S.H.A.).","article_number":"102483","date_published":"2026-05-09T00:00:00Z","publisher":"Elsevier","month":"05","ddc":["570"],"citation":{"short":"E. Mascolo, R.E. Körei, S. Herrera-Álvarez, C.C. Guet, J. Crocker, G. Tkačik, Current Opinion in Genetics &#38; Development 99 (2026).","chicago":"Mascolo, Elia, Reka E Körei, Santiago Herrera-Álvarez, Calin C Guet, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.gde.2026.102483\">https://doi.org/10.1016/j.gde.2026.102483</a>.","mla":"Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 99, 102483, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102483\">10.1016/j.gde.2026.102483</a>.","apa":"Mascolo, E., Körei, R. E., Herrera-Álvarez, S., Guet, C. C., Crocker, J., &#38; Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2026.102483\">https://doi.org/10.1016/j.gde.2026.102483</a>","ieee":"E. Mascolo, R. E. Körei, S. Herrera-Álvarez, C. C. Guet, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 99. Elsevier, 2026.","ista":"Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics &#38; Development. 99, 102483.","ama":"Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. <i>Current Opinion in Genetics &#38; Development</i>. 2026;99. doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102483\">10.1016/j.gde.2026.102483</a>"},"oa_version":"Published Version","quality_controlled":"1","status":"public","PlanS_conform":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype–phenotype map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the first of a two-part series, we briefly review the pertinent modeling and simulation efforts for a unique system that enables close, quantitative, and mechanistic links between biophysics, as well as systems, synthetic, and evolutionary biology."}],"OA_place":"publisher","type":"journal_article","author":[{"id":"776a6ed0-a053-11f0-8635-80b95e0e0d53","full_name":"Mascolo, Elia","first_name":"Elia","last_name":"Mascolo","orcid":"0000-0003-2977-7844"},{"id":"50FDE43E-AA30-11E9-A72B-8A12E6697425","full_name":"Körei, Reka E","first_name":"Reka E","last_name":"Körei"},{"first_name":"Santiago","last_name":"Herrera-Álvarez","full_name":"Herrera-Álvarez, Santiago"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"full_name":"Crocker, Justin","last_name":"Crocker","first_name":"Justin"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"OA_type":"hybrid","scopus_import":"1","date_updated":"2026-10-27T13:12:27Z","oa":1,"doi":"10.1016/j.gde.2026.102483","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"corr_author":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","external_id":{"arxiv":["2601.19681"]},"volume":99,"has_accepted_license":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.gde.2026.102483","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps","_id":"21983","arxiv":1,"publication_identifier":{"issn":["0959-437X"],"eissn":["1879-0380"]},"day":"09","fulldoi":"https://doi.org/10.1016/j.gde.2026.102483","department":[{"_id":"GradSch"},{"_id":"CaGu"},{"_id":"GaTk"}]},{"acknowledgement":"We thank Michael J. Axtell for generously sharing ago4-4 ago6-2, ago6-2 ago9-1 double and ago4-4 ago6-2 ago9-1 triple mutants. We thank the John Innes Centre Bioimaging Facility and ISTA Imaging and Optics Facility for their assistance with the confocal microscopy, and the ISTA Scientific Computing Facility for high performance computing resources. This work was funded by a Marie Curie Postdoctoral Fellowship (101153710; C.Y.), a European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 (ISTA Bridge Fellowship) (S.X.), a DFG grant (FOR 5235 CSCS; A.S.), a European Research Council (ERC) Starting Grant (804981; X.F) and an ERC Consolidator Grant (101126201; C.Y. and XF).","article_number":"10758","intvolume":"        17","file_date_updated":"2026-10-28T08:41:06Z","publication":"Nature Communications","date_created":"2026-10-27T10:38:56Z","year":"2026","publication_status":"published","oa_version":"Published Version","citation":{"ama":"Long J, Yang C, Xu S, et al. Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. <i>Nature Communications</i>. 2026;17. doi:<a href=\"https://doi.org/10.1038/s41467-026-77326-1\">10.1038/s41467-026-77326-1</a>","ieee":"J. Long <i>et al.</i>, “Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline,” <i>Nature Communications</i>, vol. 17. Springer Nature, 2026.","ista":"Long J, Yang C, Xu S, De Jaeger-Braet JG, She W, Ono S, Walker J, de Souza Vieira Y, Schnittger A, Feng X. 2026. Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. Nature Communications. 17, 10758.","apa":"Long, J., Yang, C., Xu, S., De Jaeger-Braet, J. G., She, W., Ono, S., … Feng, X. (2026). Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-77326-1\">https://doi.org/10.1038/s41467-026-77326-1</a>","chicago":"Long, Jincheng, Chao Yang, Shujuan Xu, Joke G De Jaeger-Braet, Wenjing She, Seijiro Ono, James Walker, Ygor de Souza Vieira, Arp Schnittger, and Xiaoqi Feng. “Multiple Argonaute Complexes Orchestrate Epigenetic Silencing in the Arabidopsis Germline.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-77326-1\">https://doi.org/10.1038/s41467-026-77326-1</a>.","mla":"Long, Jincheng, et al. “Multiple Argonaute Complexes Orchestrate Epigenetic Silencing in the Arabidopsis Germline.” <i>Nature Communications</i>, vol. 17, 10758, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-77326-1\">10.1038/s41467-026-77326-1</a>.","short":"J. Long, C. Yang, S. Xu, J.G. De Jaeger-Braet, W. She, S. Ono, J. Walker, Y. de Souza Vieira, A. Schnittger, X. Feng, Nature Communications 17 (2026)."},"month":"10","ddc":["580"],"publisher":"Springer Nature","pmid":1,"date_published":"2026-10-14T00:00:00Z","type":"journal_article","OA_place":"publisher","abstract":[{"lang":"eng","text":"Small RNAs (sRNAs) are widespread across diverse flowering plant species and play important roles regulating reproduction and environmental responses. However, how sRNAs exert their function is largely unknown, likely due to their typical origin in non-genic regions, the lack of distinct gene targets, and the sparse characterization of their associated Argonaute (AGO) effector proteins. Here we show that Arabidopsis male reproductive sRNAs associate with AGO4, 5, 6 and 9, all of which are enriched in meiocytes along with RNA Polymerase V (Pol V). This enables these sRNAs to methylate loci with imperfect sequence homology. AGO4, AGO6 and AGO9 predominantly load 24-nucleotide (nt) Pol IV-derived sRNAs and mediate DNA methylation in meiocytes in a dosage-dependent manner. Despite closer homology to microRNA-associated AGO1 and AGO10, AGO5 primarily binds CLSY3- and Pol IV-derived 21-24 nt sRNAs. Transcriptomic and methylomic analyses of meiocytes from single and compound ago mutants demonstrate distinct yet complementary roles of AGO4/6/9 and AGO5 in regulating protein-coding genes and silencing transposons in the germline. These molecular disruptions are accompanied by significant meiotic defects. Together, our findings reveal how AGO4/6/9-mediated DNA methylation and AGO5, likely acting through post-transcriptional gene silencing, work together to promote male germline development."}],"language":[{"iso":"eng"}],"PlanS_conform":"1","status":"public","quality_controlled":"1","date_updated":"2026-10-28T08:43:20Z","scopus_import":"1","OA_type":"gold","dataavailabilitystatement":"Illumina sequencing data (RIP-seq, BS-seq, and RNA-seq) generated in this study have been deposited in the NCBI BioProject and are accessible under accession number PRJNA1192978. Published BS-seq data of Arabidopsis meiocyte used in this study for Fig. 4a are available in the NCBI GEO database under accession code GSE161625. All custom codes are available via the request to the corresponding author.","author":[{"full_name":"Long, Jincheng","first_name":"Jincheng","last_name":"Long"},{"full_name":"Yang, Chao","id":"082e3e6e-8069-11ed-8390-c8cce7b1aaca","last_name":"Yang","first_name":"Chao"},{"first_name":"Shujuan","last_name":"Xu","id":"9724dd9d-f591-11ee-bd51-e97ed0652286","full_name":"Xu, Shujuan"},{"full_name":"De Jaeger-Braet, Joke G","id":"26bd38d3-c59a-11ee-a1af-d7a988cafcc5","last_name":"De Jaeger-Braet","first_name":"Joke G"},{"last_name":"She","first_name":"Wenjing","full_name":"She, Wenjing"},{"full_name":"Ono, Seijiro","last_name":"Ono","first_name":"Seijiro"},{"first_name":"James","last_name":"Walker","full_name":"Walker, James"},{"id":"af019b77-d2a9-11f1-9e65-c47a5932b764","full_name":"de Souza Vieira, Ygor","first_name":"Ygor","last_name":"de Souza Vieira"},{"first_name":"Arp","last_name":"Schnittger","full_name":"Schnittger, Arp"},{"orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi"}],"DOAJ_listed":"1","corr_author":"1","file":[{"checksum":"f24efcba89d880d48fef04b780923780","creator":"dernst","file_size":4220128,"file_name":"2026_NatureComm_Long.pdf","file_id":"23204","date_created":"2026-10-28T08:41:06Z","content_type":"application/pdf","date_updated":"2026-10-28T08:41:06Z","relation":"main_file","success":1,"access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"researchdata_availability":"yes","oa":1,"doi":"10.1038/s41467-026-77326-1","project":[{"_id":"8e917275-16d5-11f0-9cad-fee255fa62e0","grant_number":"101153710","name":"The moleculaR mEchAnismS Of dNa methylatIon reprogrammiNg in Arabidopsis sexual lineaGe"},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"call_identifier":"H2020","name":"Establishment, modulation and inheritance of sexual lineage specific DNA methylation in plants","grant_number":"804981","_id":"bdb51a6e-d553-11ed-ba76-c2025f3d5725"},{"grant_number":"101126201","name":"Mechanisms and biological functions of H3K27me3 reprogramming in plant microspores","_id":"7c012eb8-9f16-11ee-852c-dc2b6371d5a0"}],"has_accepted_license":"1","volume":17,"article_type":"original","external_id":{"pmid":["42869904"]},"das_tickbox":"1","article_processing_charge":"Yes","_id":"23198","title":"Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"XiFe"}],"supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1038/s41467-026-77326-1","day":"14","publication_identifier":{"eissn":["2041-1723"]}},{"DOAJ_listed":"1","author":[{"last_name":"Stephenson","first_name":"Mabel G.","full_name":"Stephenson, Mabel G."},{"first_name":"John","last_name":"Chisholm","full_name":"Chisholm, John"},{"first_name":"A.","last_name":"Saldana-Lopez","full_name":"Saldana-Lopez, A."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X"},{"full_name":"Henry, Alaina","first_name":"Alaina","last_name":"Henry"},{"last_name":"Naidu","first_name":"Rohan P.","full_name":"Naidu, Rohan P."},{"last_name":"Flury","first_name":"Sophia R.","full_name":"Flury, Sophia R."},{"full_name":"Hutchison, Taylor A.","last_name":"Hutchison","first_name":"Taylor A."},{"last_name":"Finkelstein","first_name":"Steven L.","full_name":"Finkelstein, Steven L."},{"last_name":"Guseva","first_name":"Natalia G.","full_name":"Guseva, Natalia G."},{"full_name":"Izotov, Yuri I.","first_name":"Yuri I.","last_name":"Izotov"},{"last_name":"Marques-Chaves","first_name":"Rui","full_name":"Marques-Chaves, Rui"},{"last_name":"Oesch","first_name":"Pascal A.","full_name":"Oesch, Pascal A."},{"first_name":"Naveen A.","last_name":"Reddy","full_name":"Reddy, Naveen A."},{"last_name":"Schaerer","first_name":"Daniel","full_name":"Schaerer, Daniel"}],"date_updated":"2026-10-28T08:05:42Z","scopus_import":"1","OA_type":"gold","PlanS_conform":"1","quality_controlled":"1","status":"public","abstract":[{"text":"We investigate the low-ionization electron density in the interstellar medium (ISM) of galaxies across 0 < z < 8,\r\nderived with the [O II] λλ3727, 3730 and [S II] λλ6718, 6733 doublets, using both deep JWST/NIRCam/grism\r\nand NIRSpec/MSA spectroscopy. Along with ancillary density samples from the literature at 0 < z < 6, we\r\nassemble three samples containing a total of 703 galaxies spanning 3.7 < z < 7.8 at 〈z〉 ∼ 5.6; 691 galaxies in the\r\nluminosity-complete NIRCam/grism programs CONGRESS and FRESCO at 〈z〉 ∼ 4.3 and ∼5.3, respectively;\r\nand 12 galaxies with high-resolution NIRSpec/MSA spectra from the GO 1871 and GLASS programs. We find\r\nmedian electron densities of ne[S II] = + 463 203 cm 281 3\r\nfor CONGRESS, ne[S II] = + 301 206 cm 388 3\r\nfor FRESCO, and\r\nne[O II] = + 202 102 cm 145 3\r\nfor the NIRSpec/MSA sample. The median low-ionization ne increases from z = 0 to 4,\r\nin agreement with previous studies and those using JWST observations. However, beyond z ∼ 4 median ne begins\r\nto deviate from a monotonically increasing evolution with z. We find a positive, but shallow, correlation between\r\nO32 (a proxy for the ionization parameter) and ne, while also confirming a positive correlation between O32 and z.\r\nWe suggest that these trends are possibly due to an evolving ISM gas density and ionization structure, and\r\npropose a toy model where the gas clumping evolves with z to explain the observed density and ionization\r\nvariations.","lang":"eng"}],"language":[{"iso":"eng"}],"type":"journal_article","OA_place":"publisher","date_published":"2026-10-15T00:00:00Z","month":"10","ddc":["520"],"publisher":"IOP Publishing","oa_version":"Published Version","citation":{"apa":"Stephenson, M. G., Chisholm, J., Saldana-Lopez, A., Matthee, J. J., Henry, A., Naidu, R. P., … Schaerer, D. (2026). The evolution of low-ionization electron densities in galaxies across cosmic epochs. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ae9eb7\">https://doi.org/10.3847/1538-4357/ae9eb7</a>","chicago":"Stephenson, Mabel G., John Chisholm, A. Saldana-Lopez, Jorryt J Matthee, Alaina Henry, Rohan P. Naidu, Sophia R. Flury, et al. “The Evolution of Low-Ionization Electron Densities in Galaxies across Cosmic Epochs.” <i>The Astrophysical Journal</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.3847/1538-4357/ae9eb7\">https://doi.org/10.3847/1538-4357/ae9eb7</a>.","mla":"Stephenson, Mabel G., et al. “The Evolution of Low-Ionization Electron Densities in Galaxies across Cosmic Epochs.” <i>The Astrophysical Journal</i>, vol. 1010, no. 2, 184, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.3847/1538-4357/ae9eb7\">10.3847/1538-4357/ae9eb7</a>.","short":"M.G. Stephenson, J. Chisholm, A. Saldana-Lopez, J.J. Matthee, A. Henry, R.P. Naidu, S.R. Flury, T.A. Hutchison, S.L. Finkelstein, N.G. Guseva, Y.I. Izotov, R. Marques-Chaves, P.A. Oesch, N.A. Reddy, D. Schaerer, The Astrophysical Journal 1010 (2026).","ama":"Stephenson MG, Chisholm J, Saldana-Lopez A, et al. The evolution of low-ionization electron densities in galaxies across cosmic epochs. <i>The Astrophysical Journal</i>. 2026;1010(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ae9eb7\">10.3847/1538-4357/ae9eb7</a>","ista":"Stephenson MG, Chisholm J, Saldana-Lopez A, Matthee JJ, Henry A, Naidu RP, Flury SR, Hutchison TA, Finkelstein SL, Guseva NG, Izotov YI, Marques-Chaves R, Oesch PA, Reddy NA, Schaerer D. 2026. The evolution of low-ionization electron densities in galaxies across cosmic epochs. The Astrophysical Journal. 1010(2), 184.","ieee":"M. G. Stephenson <i>et al.</i>, “The evolution of low-ionization electron densities in galaxies across cosmic epochs,” <i>The Astrophysical Journal</i>, vol. 1010, no. 2. IOP Publishing, 2026."},"publication":"The Astrophysical Journal","year":"2026","date_created":"2026-10-27T10:40:40Z","publication_status":"published","file_date_updated":"2026-10-28T08:02:57Z","acknowledgement":"We are grateful for the support for programs GO 1871, GO 1895, and GO 3577 provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127. This work is based in part on observations made with the NASA/ESA/CSA JWST. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with programs GO 1324, GO 1871, GO 1895 and GO 3577. The specific observations analyzed can be accessed via DOI: 10.17909/01dt-fm17.\r\n\r\nA.S.L. acknowledges support from Knut and Alice Wallenberg Foundation. T.A.H. acknowledges support from an appointment to the NASA Postdoctoral Program at the NASA Goddard Space, administered by Oak Ridge Associated Universities under contract with NASA, as well as the University of Maryland Baltimore County and the Center for Space Sciences and Technology. N.G.G. and Y.I.I. and acknowledge support from the joint Ukrainian-Swiss project No. 224866. This work has received funding from the Swiss State Secretariat for Education, Research, and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant DNRF140.\r\n\r\nFacility: JWST (NIRCam - , NIRSpec).\r\n\r\nSoftware: numpy (v.1.24.3; C. R. Harris et al. 2020), scipy (v.1.13.1; P. Virtanen et al. 2020), astropy (Astropy Collaboration et al. 2013, 2018, 2022), pyneb (v.1.1.24; V. Luridiana et al. 2013, 2015; C. Morisset et al. 2020), msaexp (v.0.8.4; G. B. Brammer 2022), msafit (A. de Graaff et al. 2024), grizli (G. Brammer 2018), EAZY (G. B. Brammer et al. 2008), BAGPIPES (A. C. Carnall et al. 2018), Prospector (B. D. Johnson et al. 2019, 2021), pysersic (I. Pasha & T. B. Miller 2023), GALFIT (C. Y. Peng et al. 2002, 2010), kendall (S. R. Flury et al. 2022; S. R. Flury 2023).","article_number":"184","intvolume":"      1010","arxiv":1,"publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"day":"15","fulldoi":"https://doi.org/10.3847/1538-4357/ae9eb7","department":[{"_id":"JoMa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The evolution of low-ionization electron densities in galaxies across cosmic epochs","_id":"23200","article_processing_charge":"Yes","external_id":{"arxiv":["2608.23846"]},"article_type":"original","das_tickbox":"0","has_accepted_license":"1","volume":1010,"doi":"10.3847/1538-4357/ae9eb7","oa":1,"file":[{"content_type":"application/pdf","file_id":"23202","date_created":"2026-10-28T08:02:57Z","file_name":"2026_AstrophysicalJour_Stephenson.pdf","file_size":4194012,"creator":"dernst","checksum":"6968c85ac6ccc997a30dab818dc04e42","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2026-10-28T08:02:57Z"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"issue":"2"},{"quality_controlled":"1","status":"public","PlanS_conform":"1","OA_place":"publisher","type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"text":"The physics governing the morphology of radio-loud active galactic nucleus (AGN) jets is not fully understood. We investigate how magnetization, flickering jet power and the interplay between them affects the morphology of radio galaxies. We present a grid of relativistic magnetohydrodynamic simulations using the pluto code covering constant and variable jets with two levels of magnetization. We find that the constant high-magnetization jets can lead to highly asymmetrical cocoon morphologies, while the variable high-magnetization jet can exhibit a broken morphology, caused by a discontinuous jet beam. Our work highlights the importance of magnetization and variability on the stability and resulting morphology of radio-loud AGN jets, suggesting both are significant factors in addition to jet power or environment. Furthermore, we show that the interaction between magnetization and variability can lead to the development of localized kink instabilities along the jet beam. Finally, we discuss the effects of hydrodynamic mixing in low-magnetization jets and the role of viewing-angle dependence in comparisons between our simulations and observed sources. To facilitate this comparison we present a library of simulated radio images at different times in the simulations and from various viewing angles, which highlight a diverse set of complex morphologies.","lang":"eng"}],"author":[{"last_name":"Elley","first_name":"Emma L","full_name":"Elley, Emma L"},{"full_name":"Matthews, James H","first_name":"James H","last_name":"Matthews"},{"orcid":"0009-0006-0716-0965","first_name":"Henry William","last_name":"Whitehead","id":"b5363ed7-0345-11f1-8029-eef7ff5d6bfc","full_name":"Whitehead, Henry William"},{"full_name":"Cooper, Alex J","last_name":"Cooper","first_name":"Alex J"}],"DOAJ_listed":"1","OA_type":"gold","scopus_import":"1","dataavailabilitystatement":"The data underlying this article are available from the authors on reasonable request. Furthermore, the data for the simulated radio images from various angles as discussed in Section 2.3 are publicly available as FITS files from https://doi.org/10.5281/zenodo.20140021.","date_updated":"2026-10-28T08:19:37Z","publication_status":"published","publication":"Monthly Notices of the Royal Astronomical Society","date_created":"2026-10-27T10:39:59Z","year":"2026","intvolume":"       552","acknowledgement":"JHM and ELE acknowledge funding from a Royal Society University Research Fellowship (URF\\R1\\221062). AJC acknowledges support from the Oxford Hintze Centre for Astrophysical Surveys, which is funded through generous support from the Hintze Family Charitable Foundation. HW acknowledges funding by the Science and Technology Facilities Council Grant Number ST/W000903/1 and the ISTA-Fellow programme. The authors acknowledge the use of resources provided by the Isambard 3 Tier-2 HPC Facility. Isambard 3 is hosted by the University of Bristol and operated by the GW4 Alliance (https://gw4.ac.uk) and is funded by UK Research and Innovation and the Engineering and Physical Sciences Research Council (EP/X039137/1). The authors would like to acknowledge the use of the University of Oxford Advanced Research Computing (ARC) facility in carrying out this work (https://doi.org/10.5281/zenodo.22558). We are grateful for the use of the following software packages: pluto (A. Mignone et al. 2007) and matplotlib (J. D. Hunter 2007). We are grateful to Dipanjan Mukherjee, Imogen Whittam, Matt Jarvis, Judith Croston and Fraser Cowie for useful discussions. The authors wish to thank the anonymous referee for their helpful and constructive comments which have improved the quality of this manuscript.","article_number":"stag1798","file_date_updated":"2026-10-28T08:19:16Z","publisher":"Oxford University Press","ddc":["520"],"month":"11","date_published":"2026-11-01T00:00:00Z","oa_version":"Published Version","citation":{"short":"E.L. Elley, J.H. Matthews, H.W. Whitehead, A.J. Cooper, Monthly Notices of the Royal Astronomical Society 552 (2026).","chicago":"Elley, Emma L, James H Matthews, Henry William Whitehead, and Alex J Cooper. “The Impact of Flickering Variability and Magnetization on the Dynamics, Stability, and Morphology of Radio-Loud AGN Jets.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/mnras/stag1798\">https://doi.org/10.1093/mnras/stag1798</a>.","mla":"Elley, Emma L., et al. “The Impact of Flickering Variability and Magnetization on the Dynamics, Stability, and Morphology of Radio-Loud AGN Jets.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 552, no. 4, stag1798, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/mnras/stag1798\">10.1093/mnras/stag1798</a>.","apa":"Elley, E. L., Matthews, J. H., Whitehead, H. W., &#38; Cooper, A. J. (2026). The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stag1798\">https://doi.org/10.1093/mnras/stag1798</a>","ista":"Elley EL, Matthews JH, Whitehead HW, Cooper AJ. 2026. The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets. Monthly Notices of the Royal Astronomical Society. 552(4), stag1798.","ieee":"E. L. Elley, J. H. Matthews, H. W. Whitehead, and A. J. Cooper, “The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 552, no. 4. Oxford University Press, 2026.","ama":"Elley EL, Matthews JH, Whitehead HW, Cooper AJ. The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets. <i>Monthly Notices of the Royal Astronomical Society</i>. 2026;552(4). doi:<a href=\"https://doi.org/10.1093/mnras/stag1798\">10.1093/mnras/stag1798</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"23199","title":"The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets","day":"01","arxiv":1,"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"department":[{"_id":"ZoHa"}],"fulldoi":"https://doi.org/10.1093/mnras/stag1798","supplementarymaterial":"yes","researchdata_availability":"upon request","file":[{"date_created":"2026-10-28T08:19:16Z","file_id":"23203","content_type":"application/pdf","checksum":"57e15f531d22d18eaeca96d58b2ab911","creator":"dernst","file_size":8344810,"file_name":"2026_MonthNoticesRAS_Elley.pdf","access_level":"open_access","relation":"main_file","date_updated":"2026-10-28T08:19:16Z","success":1}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.1093/mnras/stag1798","oa":1,"issue":"4","das_tickbox":"1","external_id":{"arxiv":["2605.13469"]},"article_type":"original","article_processing_charge":"Yes","volume":552,"has_accepted_license":"1"},{"month":"05","publisher":"Optica Publishing Group","article_processing_charge":"No","date_published":"2026-05-15T00:00:00Z","alternative_title":["Technical Digest Series"],"citation":{"ista":"Mor PA, Kroo AR, Valdez CG, Šimić M, Karnieli A, Cavicchioli G, Sun Z, Grimaldi V, Fan S, Solgaard O, Miller DAB, Roques-Carmes C. 2026. Variational processing of partially coherent light in a photonic integrated circuit. CLEO Science and Innovations Proceedings. CLEO: Conference on Lasers and Electro-Optics, Technical Digest Series, , STU2F.1.","ieee":"P. A. Mor <i>et al.</i>, “Variational processing of partially coherent light in a photonic integrated circuit,” in <i>CLEO Science and Innovations Proceedings</i>, Long Beach, CA, United States, 2026.","ama":"Mor PA, Kroo AR, Valdez CG, et al. Variational processing of partially coherent light in a photonic integrated circuit. In: <i>CLEO Science and Innovations Proceedings</i>. Optica Publishing Group; 2026. doi:<a href=\"https://doi.org/10.1364/CLEO_SI.2026.STU2F.1\">10.1364/CLEO_SI.2026.STU2F.1</a>","short":"P.A. Mor, A.R. Kroo, C.G. Valdez, M. Šimić, A. Karnieli, G. Cavicchioli, Z. Sun, V. Grimaldi, S. Fan, O. Solgaard, D.A.B. Miller, C. Roques-Carmes, in:, CLEO Science and Innovations Proceedings, Optica Publishing Group, 2026.","chicago":"Mor, Paul Alexis, Annie R. Kroo, Carson G. Valdez, Marko Šimić, Aviv Karnieli, Gabriele Cavicchioli, Zhanghao Sun, et al. “Variational Processing of Partially Coherent Light in a Photonic Integrated Circuit.” In <i>CLEO Science and Innovations Proceedings</i>. Optica Publishing Group, 2026. <a href=\"https://doi.org/10.1364/CLEO_SI.2026.STU2F.1\">https://doi.org/10.1364/CLEO_SI.2026.STU2F.1</a>.","mla":"Mor, Paul Alexis, et al. “Variational Processing of Partially Coherent Light in a Photonic Integrated Circuit.” <i>CLEO Science and Innovations Proceedings</i>, STU2F.1, Optica Publishing Group, 2026, doi:<a href=\"https://doi.org/10.1364/CLEO_SI.2026.STU2F.1\">10.1364/CLEO_SI.2026.STU2F.1</a>.","apa":"Mor, P. A., Kroo, A. R., Valdez, C. G., Šimić, M., Karnieli, A., Cavicchioli, G., … Roques-Carmes, C. (2026). Variational processing of partially coherent light in a photonic integrated circuit. In <i>CLEO Science and Innovations Proceedings</i>. Long Beach, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/CLEO_SI.2026.STU2F.1\">https://doi.org/10.1364/CLEO_SI.2026.STU2F.1</a>"},"oa_version":"None","publication":"CLEO Science and Innovations Proceedings","year":"2026","date_created":"2026-10-25T23:02:24Z","doi":"10.1364/CLEO_SI.2026.STU2F.1","publication_status":"published","article_number":"STU2F.1","conference":{"start_date":"2026-05-02","location":"Long Beach, CA, United States","name":"CLEO: Conference on Lasers and Electro-Optics","end_date":"2026-05-06"},"publication_identifier":{"isbn":["9781957171586"]},"day":"15","author":[{"first_name":"Paul Alexis","last_name":"Mor","full_name":"Mor, Paul Alexis"},{"last_name":"Kroo","first_name":"Annie R.","full_name":"Kroo, Annie R."},{"last_name":"Valdez","first_name":"Carson G.","full_name":"Valdez, Carson G."},{"last_name":"Šimić","first_name":"Marko","full_name":"Šimić, Marko"},{"full_name":"Karnieli, Aviv","last_name":"Karnieli","first_name":"Aviv"},{"first_name":"Gabriele","last_name":"Cavicchioli","full_name":"Cavicchioli, Gabriele"},{"full_name":"Sun, Zhanghao","last_name":"Sun","first_name":"Zhanghao"},{"last_name":"Grimaldi","first_name":"Vittorio","full_name":"Grimaldi, Vittorio"},{"first_name":"Shanhui","last_name":"Fan","full_name":"Fan, Shanhui"},{"full_name":"Solgaard, Olav","first_name":"Olav","last_name":"Solgaard"},{"first_name":"David A.B.","last_name":"Miller","full_name":"Miller, David A.B."},{"first_name":"Charles","last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles"}],"department":[{"_id":"ChRo"}],"date_updated":"2026-10-28T07:57:55Z","fulldoi":"https://doi.org/10.1364/CLEO_SI.2026.STU2F.1","scopus_import":"1","OA_type":"closed access","status":"public","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","_id":"23196","abstract":[{"text":"We introduce an experimental realization of the measurement, processing, and generation of partially coherent light on a photonic chip. This device relies on self-configuring networks optimized sequentially to learn the coherency matrix of input light.","lang":"eng"}],"title":"Variational processing of partially coherent light in a photonic integrated circuit","language":[{"iso":"eng"}]},{"_id":"18706","title":"Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"supplementarymaterial":"no","fulldoi":"https://doi.org/10.1017/s0956792524000810","publication_identifier":{"eissn":["1469-4425"],"issn":["0956-7925"]},"page":"614-642","day":"01","issue":"3","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"checksum":"d038f4d00cbfbde2672c17138eab21c9","creator":"dernst","file_size":612317,"file_name":"2026_EuropJourAppliedMath_Portinale.pdf","date_created":"2026-07-23T05:55:03Z","file_id":"22386","content_type":"application/pdf","date_updated":"2026-07-23T05:55:03Z","relation":"main_file","success":1,"access_level":"open_access"}],"researchdata_availability":"no","keyword":["optimal transport","discrete-to-continuum","homogenisation","linear growth","gamma-convergence"],"doi":"10.1017/s0956792524000810","oa":1,"project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"has_accepted_license":"1","volume":37,"external_id":{"isi":["001381435800001"]},"article_type":"original","das_tickbox":"0","article_processing_charge":"Yes","type":"journal_article","OA_place":"publisher","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20563"}]},"abstract":[{"text":"We prove discrete-to-continuum convergence for dynamical optimal transport on  Zd\r\n -periodic graphs with cost functional having linear growth at infinity. This result provides an answer to a problem left open by Gladbach, Kopfer, Maas, and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the convergence behaviour of discrete boundary-value dynamical transport problems is proved under the stronger assumption of superlinear growth. Our result extends the known literature to some important classes of examples, such as scaling limits of  1 -Wasserstein transport problems. Similarly to what happens in the quadratic case, the geometry of the graph plays a crucial role in the structure of the limit cost function, as we discuss in the final part of this work, which includes some visual representations.","lang":"eng"}],"language":[{"iso":"eng"}],"PlanS_conform":"1","quality_controlled":"1","status":"public","date_updated":"2026-11-10T23:31:08Z","scopus_import":"1","OA_type":"gold","author":[{"first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo"},{"id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","full_name":"Quattrocchi, Filippo","first_name":"Filippo","last_name":"Quattrocchi","orcid":"0009-0000-9773-1931"}],"DOAJ_listed":"1","acknowledgement":"L.P. gratefully acknowledges fundings from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – GZ 2047/1, Projekt-ID 390685813. F.Q. gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.","isi":1,"intvolume":"        37","file_date_updated":"2026-07-23T05:55:03Z","date_created":"2024-12-23T11:03:59Z","year":"2026","publication":"European Journal of Applied Mathematics","publication_status":"published","citation":{"ama":"Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>. 2026;37(3):614-642. doi:<a href=\"https://doi.org/10.1017/s0956792524000810\">10.1017/s0956792524000810</a>","ieee":"L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs,” <i>European Journal of Applied Mathematics</i>, vol. 37, no. 3. Cambridge University Press, pp. 614–642, 2026.","ista":"Portinale L, Quattrocchi F. 2026. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. 37(3), 614–642.","short":"L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics 37 (2026) 614–642.","apa":"Portinale, L., &#38; Quattrocchi, F. (2026). Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0956792524000810\">https://doi.org/10.1017/s0956792524000810</a>","mla":"Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal of Applied Mathematics</i>, vol. 37, no. 3, Cambridge University Press, 2026, pp. 614–42, doi:<a href=\"https://doi.org/10.1017/s0956792524000810\">10.1017/s0956792524000810</a>.","chicago":"Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal of Applied Mathematics</i>. Cambridge University Press, 2026. <a href=\"https://doi.org/10.1017/s0956792524000810\">https://doi.org/10.1017/s0956792524000810</a>."},"oa_version":"Published Version","ddc":["500"],"month":"06","publisher":"Cambridge University Press","date_published":"2026-06-01T00:00:00Z"},{"author":[{"id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana","first_name":"Zuzana","last_name":"Dunajova"}],"date_updated":"2026-10-16T08:12:11Z","status":"public","related_material":{"record":[{"id":"13314","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"research_data","id":"13116"},{"status":"public","id":"21439","relation":"research_data"},{"id":"21427","relation":"part_of_dissertation","status":"public"}]},"abstract":[{"lang":"eng","text":"Biological systems, such as cytoskeletal filaments and multicellular collectives, exhibit rich \r\nself-organization driven by their intrinsic activity and physical constraints. Across scales, \r\ngeometry plays a central role: the shape of active units and the structure of their environment \r\nstrongly influence how order emerges in these far-from-equilibrium systems. In this thesis, \r\nwe combine minimal active-matter models with bottom-up in vitro experiments to identify \r\nthe principles by which geometry and activity shape collective behavior in biological matter. \r\nAt the subcellular scale, we investigate how the physical properties of chiral FtsZ filaments \r\ngovern their large-scale organization. Using a mesoscopic model validated by reconstituted \r\nfilament assays, we show that filament shape, intrinsic curvature, and flexibility, together with \r\nactivity-driven straightening, determine whether filaments form chiral rings, polar bands, or \r\nnematic-like states. Our model shows that small changes in filament mechanics produce large \r\nshifts in collective structures, revealing how the geometry of individual filaments amplifies \r\nthrough activity to control patterns relevant for bacterial cytokinesis. \r\nAt the cellular scale, we examine how geometry of the external environment influences \r\ncollective cancer cell migration. Experiments in controlled microfabricated obstacle \r\nenvironments demonstrate that geometric disorder alone can induce a transition from \r\ncollective to single-cell invasion. A minimal model of active particles in disordered geometries \r\nreproduces these effects, demonstrating that cell dissemination results both from local \r\ngeometrical constraints and a global integration of spatial disorder over time. Surprisingly, \r\nthis transition is accompanied by a change in the universality class of interface dynamics, \r\nrevealing that cell-environment interactions can shift the collective behavior of an invasive \r\nfront purely through mechanics.  \r\nIn the last system, we study how cell-intrinsic geometry and chirality affect collective motion \r\nin confined and unconfined settings. Using a minimal model inspired by in vitro experiments, \r\nwe analyze motile cells that exhibit persistent rotation due to intrinsic left-right asymmetry. \r\nIn circular confinement, this simplified chiral model reproduces several experimentally \r\nobserved features within specific parameter regimes. At high densities in unconfined \r\nenvironments, however, intrinsic chirality becomes masked even before the onset of the \r\njamming transition. These results show that single-cell geometric asymmetry does not \r\nnecessarily translate into large-scale chiral flows, offering new insight into how forces and \r\nsymmetries shape collective motion in dense cellular systems. \r\nOverall, this work uncovers how geometric constraints – embedded in the intrinsic \r\narchitecture of an active filament or encoded in the complexity of a microenvironment \r\ncouple to active forces to generate different classes of complex behaviors. "}],"language":[{"iso":"eng"}],"type":"dissertation","OA_place":"repository","date_published":"2026-03-11T00:00:00Z","month":"03","ddc":["539","570"],"publisher":"Institute of Science and Technology Austria","citation":{"ieee":"Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral filaments,” Institute of Science and Technology Austria, 2026.","ista":"Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria.","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>","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>.","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>.","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>","short":"Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments, Institute of Science and Technology Austria, 2026."},"oa_version":"Published Version","doi_confirm":"1","date_created":"2026-03-11T08:30:49Z","year":"2026","publication_status":"published","file_date_updated":"2026-09-11T22:30:02Z","acknowledgement":"Finally, I gratefully acknowledge funding from the DOC Fellowship of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360.","supervisor":[{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561"}],"day":"11","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-076-3"]},"page":"110","fulldoi":"https://doi.org/10.15479/AT-ISTA-21423","acknowledged_ssus":[{"_id":"ScienComp"}],"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Geometry-driven self-organization of migrating cells and chiral filaments","_id":"21423","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","has_accepted_license":"1","doi":"10.15479/AT-ISTA-21423","oa":1,"project":[{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360","name":"Motile active matter models of migrating cells and chiral filaments"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"file":[{"access_level":"open_access","embargo":"2026-09-11","relation":"main_file","date_updated":"2026-09-11T22:30:02Z","content_type":"application/pdf","date_created":"2026-03-12T20:38:52Z","file_id":"21446","file_size":14662770,"file_name":"2026_Dunajova_Zuzana_Thesis_pdfA.pdf","checksum":"47ce6a48a0c63f28eca6e64c9ffd2c84","creator":"zdunajov"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2026-03-12T20:40:18Z","file_id":"21447","file_size":32961408,"file_name":"Thesis-Dunajova_source_file.docx","checksum":"5dec5afdffd47c2b0b162d0fe1bed925","creator":"zdunajov","access_level":"closed","embargo_to":"open_access","relation":"source_file","date_updated":"2026-09-11T22:30:02Z"}],"corr_author":"1"},{"file_date_updated":"2026-03-11T20:52:39Z","contributor":[{"orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Tasciyan","first_name":"Saren"},{"orcid":"0000-0001-9198-2182 ","first_name":"Philipp","last_name":"Radler","contributor_type":"researcher","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2026-03-11T21:05:20Z","year":"2026","citation":{"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>.","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>","short":"Z. Dunajova, (2026).","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>.","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. 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The videos provide additional visual material supporting the experiments and results described in the thesis."}],"related_material":{"record":[{"status":"public","id":"13314","relation":"used_in_publication"},{"status":"public","id":"21427","relation":"used_in_publication"},{"relation":"used_in_publication","id":"21423","status":"public"}]},"OA_place":"repository","type":"research_data","status":"public","OA_type":"free access","date_updated":"2026-11-10T23:31:12Z","author":[{"first_name":"Zuzana","last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana"}],"corr_author":"1","doi":"10.15479/AT-ISTA-21439","oa":1,"project":[{"name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"file":[{"content_type":"application/zip","date_created":"2026-03-11T20:41:28Z","file_id":"21440","file_name":"Supplementary_movies_Thesis_Dunajova.zip","file_size":154465214,"checksum":"47809a9a31b748b16e21e92d11ddc87f","creator":"zdunajov","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2026-03-11T20:41:28Z"},{"file_name":"readme.txt","file_size":2289,"creator":"zdunajov","checksum":"a64a174bc6abf0a5e77631e4fd121f1f","content_type":"text/plain","file_id":"21441","date_created":"2026-03-11T20:52:39Z","success":1,"relation":"main_file","date_updated":"2026-03-11T20:52:39Z","access_level":"open_access"}],"has_accepted_license":"1","article_processing_charge":"No","title":"Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”","_id":"21439","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","fulldoi":"https://doi.org/10.15479/AT-ISTA-21439","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"department":[{"_id":"GradSch"},{"_id":"EdHa"}],"day":"12"},{"keyword":["Time-Space Lower Bounds","Blockchains"],"doi":"10.4230/LIPIcs.ITC.2025.4","oa":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","file_id":"22118","date_created":"2026-06-22T08:54:32Z","file_name":"2025_LIPIcs_Pietrzak.pdf","file_size":772046,"creator":"dernst","checksum":"3f791b03df26853342855a9d9581cb58","access_level":"open_access","success":1,"date_updated":"2026-06-22T08:54:32Z","relation":"main_file"}],"corr_author":"1","cryptoeprintid":1,"conference":{"name":"ITC: Information Theoretic Cryptography","start_date":"2025-08-16","location":"Santa Barbara, CA, United States","end_date":"2025-08-17"},"alternative_title":["LIPIcs"],"article_processing_charge":"Yes","external_id":{"cryptoeprintid":["2025/723"]},"das_tickbox":"0","volume":343,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Time-space tradeoffs of truncation with preprocessing","_id":"22007","publication_identifier":{"isbn":["9783959773850"],"eissn":["1868-8969"]},"day":"08","fulldoi":"https://doi.org/10.4230/LIPIcs.ITC.2025.4","department":[{"_id":"KrPi"}],"date_created":"2026-06-14T22:01:45Z","publication":"6th Conference on Information-Theoretic Cryptography","year":"2025","publication_status":"published","file_date_updated":"2026-06-22T08:54:32Z","article_number":"4:1-4:10","intvolume":"       343","date_published":"2025-09-08T00:00:00Z","ddc":["000"],"month":"09","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","citation":{"ama":"Pietrzak KZ, Wang P. Time-space tradeoffs of truncation with preprocessing. In: <i>6th Conference on Information-Theoretic Cryptography</i>. Vol 343. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2025. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITC.2025.4\">10.4230/LIPIcs.ITC.2025.4</a>","ista":"Pietrzak KZ, Wang P. 2025. Time-space tradeoffs of truncation with preprocessing. 6th Conference on Information-Theoretic Cryptography. ITC: Information Theoretic Cryptography, LIPIcs, vol. 343, 4:1-4:10.","ieee":"K. Z. Pietrzak and P. Wang, “Time-space tradeoffs of truncation with preprocessing,” in <i>6th Conference on Information-Theoretic Cryptography</i>, Santa Barbara, CA, United States, 2025, vol. 343.","short":"K.Z. Pietrzak, P. Wang, in:, 6th Conference on Information-Theoretic Cryptography, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025.","apa":"Pietrzak, K. Z., &#38; Wang, P. (2025). Time-space tradeoffs of truncation with preprocessing. In <i>6th Conference on Information-Theoretic Cryptography</i> (Vol. 343). Santa Barbara, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ITC.2025.4\">https://doi.org/10.4230/LIPIcs.ITC.2025.4</a>","chicago":"Pietrzak, Krzysztof Z, and Pengxiang Wang. “Time-Space Tradeoffs of Truncation with Preprocessing.” In <i>6th Conference on Information-Theoretic Cryptography</i>, Vol. 343. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025. <a href=\"https://doi.org/10.4230/LIPIcs.ITC.2025.4\">https://doi.org/10.4230/LIPIcs.ITC.2025.4</a>.","mla":"Pietrzak, Krzysztof Z., and Pengxiang Wang. “Time-Space Tradeoffs of Truncation with Preprocessing.” <i>6th Conference on Information-Theoretic Cryptography</i>, vol. 343, 4:1-4:10, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITC.2025.4\">10.4230/LIPIcs.ITC.2025.4</a>."},"oa_version":"Published Version","status":"public","quality_controlled":"1","abstract":[{"text":"Truncation of cryptographic outputs is a technique that was recently introduced in Baldimtsi et al. [Foteini Baldimtsi et al., 2022]. The general idea is to try out many inputs to some cryptographic algorithm until the output (e.g. a public-key or some hash value) falls into some sparse set and thus can be compressed: by trying out an expected 2^k different inputs one will find an output that starts with k zeros.\r\nUsing such truncation one can for example save substantial gas fees on Blockchains where storing values is very expensive. While [Foteini Baldimtsi et al., 2022] show that truncation preserves the security of the underlying primitive, they only consider a setting without preprocessing. In this work we show that lower bounds on the time-space tradeoff for inverting random functions and permutations also hold with truncation, except for parameters ranges where the bound fails to hold for \"trivial\" reasons.\r\nConcretely, it’s known that any algorithm that inverts a random function or permutation with range N making T queries and using S bits of auxiliary input must satisfy S⋅ T ≥ Nlog N. This lower bound no longer holds in the truncated setting where one must only invert a challenge from a range of size N/2^k, as now one can simply save the replies to all N/2^k challenges, which requires S = log N⋅ N /2^k bits and allows to invert with T = 1 query.\r\nWe show that with truncation, whenever S is somewhat smaller than the log N⋅ N /2^k bits required to store the entire truncated function table, the known S⋅ T ≥ Nlog N lower bound applies.","lang":"eng"}],"language":[{"iso":"eng"}],"type":"conference","OA_place":"publisher","author":[{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"full_name":"Wang, Pengxiang","first_name":"Pengxiang","last_name":"Wang"}],"date_updated":"2026-06-22T08:57:41Z","OA_type":"gold","scopus_import":"1"},{"volume":267,"has_accepted_license":"1","external_id":{"arxiv":["2410.14649"]},"alternative_title":["PMLR"],"article_processing_charge":"No","conference":{"end_date":"2025-07-19","name":"ICML: International Conference on Machine Learning","location":"Vancouver, Canada","start_date":"2025-07-13"},"corr_author":"1","file":[{"creator":"dernst","checksum":"1d744fbaeb199b08e8b6f48bc0dd047e","file_name":"2025_ICML_Sieberling.pdf","file_size":908379,"date_created":"2025-12-16T12:32:40Z","file_id":"20828","content_type":"application/pdf","date_updated":"2025-12-16T12:32:40Z","relation":"main_file","success":1,"access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa":1,"department":[{"_id":"DaAl"}],"arxiv":1,"page":"55556-55590","day":"01","publication_identifier":{"eissn":["2640-3498"]},"_id":"20820","title":"EvoPress: Accurate dynamic model compression via evolutionary search","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sieberling O, Kuznedelev D, Kurtic E, Alistarh D-A. 2025. EvoPress: Accurate dynamic model compression via evolutionary search. 42nd International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 267, 55556–55590.","ieee":"O. Sieberling, D. Kuznedelev, E. Kurtic, and D.-A. Alistarh, “EvoPress: Accurate dynamic model compression via evolutionary search,” in <i>42nd International Conference on Machine Learning</i>, Vancouver, Canada, 2025, vol. 267, pp. 55556–55590.","ama":"Sieberling O, Kuznedelev D, Kurtic E, Alistarh D-A. EvoPress: Accurate dynamic model compression via evolutionary search. In: <i>42nd International Conference on Machine Learning</i>. Vol 267. ML Research Press; 2025:55556-55590.","short":"O. Sieberling, D. Kuznedelev, E. Kurtic, D.-A. Alistarh, in:, 42nd International Conference on Machine Learning, ML Research Press, 2025, pp. 55556–55590.","chicago":"Sieberling, Oliver, Denis Kuznedelev, Eldar Kurtic, and Dan-Adrian Alistarh. “EvoPress: Accurate Dynamic Model Compression via Evolutionary Search.” In <i>42nd International Conference on Machine Learning</i>, 267:55556–90. ML Research Press, 2025.","mla":"Sieberling, Oliver, et al. “EvoPress: Accurate Dynamic Model Compression via Evolutionary Search.” <i>42nd International Conference on Machine Learning</i>, vol. 267, ML Research Press, 2025, pp. 55556–90.","apa":"Sieberling, O., Kuznedelev, D., Kurtic, E., &#38; Alistarh, D.-A. (2025). EvoPress: Accurate dynamic model compression via evolutionary search. In <i>42nd International Conference on Machine Learning</i> (Vol. 267, pp. 55556–55590). Vancouver, Canada: ML Research Press."},"oa_version":"Published Version","month":"05","ddc":["000"],"publisher":"ML Research Press","date_published":"2025-05-01T00:00:00Z","intvolume":"       267","file_date_updated":"2025-12-16T12:32:40Z","year":"2025","date_created":"2025-12-14T23:02:05Z","publication":"42nd International Conference on Machine Learning","publication_status":"published","date_updated":"2025-12-16T12:34:32Z","OA_type":"gold","scopus_import":"1","author":[{"first_name":"Oliver","last_name":"Sieberling","full_name":"Sieberling, Oliver"},{"first_name":"Denis","last_name":"Kuznedelev","full_name":"Kuznedelev, Denis"},{"first_name":"Eldar","last_name":"Kurtic","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","full_name":"Kurtic, Eldar"},{"last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"type":"conference","OA_place":"publisher","abstract":[{"text":"The high computational costs of large language models (LLMs) have led to a flurry of research on LLM compression, via methods such as quantization, sparsification, or structured pruning. A new frontier in this area is given by dynamic, non-uniform compression methods, which adjust the compression levels (e.g., sparsity) per-block or even per-layer in order to minimize accuracy loss, while guaranteeing a global compression threshold. Yet, current methods rely on estimating the \"importance\" of a given layer, implicitly assuming that layers contribute independently to the overall compression error. We begin from the motivating observation that this independence assumption does not generally hold for LLM compression: pruning a model further may even significantly recover performance. To address this, we propose EvoPress, a novel evolutionary framework for dynamic LLM compression. By formulating dynamic compression as a general optimization problem, EvoPress identifies optimal compression profiles in a highly efficient manner, and generalizes across diverse models and compression techniques. Via EvoPress, we achieve state-of-the-art performance for dynamic compression of Llama, Mistral, and Phi models, setting new benchmarks for structural pruning (block/layer dropping), unstructured sparsity, and quantization with dynamic bitwidths.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1"},{"article_processing_charge":"No","alternative_title":["PMLR"],"external_id":{"arxiv":["2505.14371"]},"volume":267,"has_accepted_license":"1","oa":1,"project":[{"_id":"8e35c14b-16d5-11f0-9cad-a3fc35339161","grant_number":"101158077","name":"FastML: Efficient and Cost-Effective Distributed Machine Learning"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"checksum":"a7edf0e4304171a3e035842b3aab1704","creator":"dernst","file_size":756213,"file_name":"2025_ICML_Nguyen.pdf","date_created":"2025-12-16T12:45:41Z","file_id":"20830","content_type":"application/pdf","date_updated":"2025-12-16T12:45:41Z","relation":"main_file","success":1,"access_level":"open_access"}],"conference":{"name":"ICML: International Conference on Machine Learning","location":"Vancouver, Canada","start_date":"2025-07-13","end_date":"2025-07-19"},"arxiv":1,"page":"46026-46072","day":"01","publication_identifier":{"eissn":["2640-3498"]},"department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Layer-wise quantization for quantized optimistic dual averaging","_id":"20821","date_published":"2025-05-01T00:00:00Z","publisher":"ML Research Press","month":"05","ddc":["000"],"oa_version":"Published Version","citation":{"apa":"Nguyen, A. D., Markov, I., Wu, F. Z., Ramezani-Kebrya, A., Antonakopoulos, K., Alistarh, D.-A., &#38; Cevher, V. (2025). Layer-wise quantization for quantized optimistic dual averaging. In <i>42nd International Conference on Machine Learning</i> (Vol. 267, pp. 46026–46072). Vancouver, Canada: ML Research Press.","chicago":"Nguyen, Anh Duc, Ilia Markov, Frank Zhengqing Wu, Ali Ramezani-Kebrya, Kimon Antonakopoulos, Dan-Adrian Alistarh, and Volkan Cevher. “Layer-Wise Quantization for Quantized Optimistic Dual Averaging.” In <i>42nd International Conference on Machine Learning</i>, 267:46026–72. ML Research Press, 2025.","mla":"Nguyen, Anh Duc, et al. “Layer-Wise Quantization for Quantized Optimistic Dual Averaging.” <i>42nd International Conference on Machine Learning</i>, vol. 267, ML Research Press, 2025, pp. 46026–72.","short":"A.D. Nguyen, I. Markov, F.Z. Wu, A. Ramezani-Kebrya, K. Antonakopoulos, D.-A. Alistarh, V. Cevher, in:, 42nd International Conference on Machine Learning, ML Research Press, 2025, pp. 46026–46072.","ama":"Nguyen AD, Markov I, Wu FZ, et al. Layer-wise quantization for quantized optimistic dual averaging. In: <i>42nd International Conference on Machine Learning</i>. Vol 267. ML Research Press; 2025:46026-46072.","ista":"Nguyen AD, Markov I, Wu FZ, Ramezani-Kebrya A, Antonakopoulos K, Alistarh D-A, Cevher V. 2025. Layer-wise quantization for quantized optimistic dual averaging. 42nd International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 267, 46026–46072.","ieee":"A. D. Nguyen <i>et al.</i>, “Layer-wise quantization for quantized optimistic dual averaging,” in <i>42nd International Conference on Machine Learning</i>, Vancouver, Canada, 2025, vol. 267, pp. 46026–46072."},"publication_status":"published","date_created":"2025-12-14T23:02:06Z","publication":"42nd International Conference on Machine Learning","year":"2025","file_date_updated":"2025-12-16T12:45:41Z","intvolume":"       267","acknowledgement":"This work was supported by Hasler Foundation Program: Hasler Responsible AI (project number 21043). The research was also sponsored by the Army Research Office and was accomplished under Grant Number W911NF-24-1-0048. This work was further funded by the Swiss National Science Foundation (SNSF) under grant number 200021_205011. We also acknowledge project A11 of the Swiss National Supercomputing Centre (CSCS) for providing computing resources. Dan Alistarh and Ilia Markov were supported in part through the ERC Proofof-Concept grant FastML (Grant Agreement 101158077). Ali Ramezani-Kebrya was supported by the Research Council of Norway through FRIPRO Grant under project number 356103, its Centres of Excellence scheme, Integreat - Norwegian Centre for knowledge-driven machine learning under\r\nproject number 332645 - and its Centre for Research-based Innovation funding scheme (Visual Intelligence under grant no. 309439).","author":[{"full_name":"Nguyen, Anh Duc","first_name":"Anh Duc","last_name":"Nguyen"},{"id":"D0CF4148-C985-11E9-8066-0BDEE5697425","full_name":"Markov, Ilia","first_name":"Ilia","last_name":"Markov"},{"last_name":"Wu","first_name":"Frank Zhengqing","full_name":"Wu, Frank Zhengqing"},{"full_name":"Ramezani-Kebrya, Ali","first_name":"Ali","last_name":"Ramezani-Kebrya"},{"first_name":"Kimon","last_name":"Antonakopoulos","full_name":"Antonakopoulos, Kimon"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"last_name":"Cevher","first_name":"Volkan","full_name":"Cevher, Volkan"}],"OA_type":"gold","scopus_import":"1","date_updated":"2025-12-16T12:46:54Z","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Modern deep neural networks exhibit heterogeneity across numerous layers of various types such as residuals, multi-head attention, etc., due to varying structures (dimensions, activation functions, etc.), distinct representation characteristics, which impact predictions. We develop a general layer-wise quantization framework with tight variance and code-length bounds, adapting to the heterogeneities over the course of training. We then apply a new layer-wise quantization technique within distributed variational inequalities (VIs), proposing a novel Quantized Optimistic Dual Averaging (QODA) algorithm with adaptive learning rates, which achieves competitive convergence rates for monotone VIs. We empirically show that QODA achieves up to a 150% speedup over the baselines in end-to-end training time for training Wasserstein GAN on 12+GPUs."}],"OA_place":"publisher","type":"conference"}]