[{"ddc":["570"],"status":"public","corr_author":"1","month":"02","publication":"Genetics","issue":"2","intvolume":"       229","OA_type":"hybrid","language":[{"iso":"eng"}],"publisher":"Oxford University Press","abstract":[{"lang":"eng","text":"A major obstacle to predictive understanding of evolution stems from the complexity of biological systems, which prevents detailed characterization of key evolutionary properties. Here, we highlight some of the major sources of complexity that arise when relating molecular mechanisms to their evolutionary consequences and ask whether accounting for every mechanistic detail is important to accurately predict evolutionary outcomes. To do this, we developed a mechanistic model of a bacterial promoter regulated by 2 proteins, allowing us to connect any promoter genotype to 6 phenotypes that capture the dynamics of gene expression following an environmental switch. Accounting for the mechanisms that govern how this system works enabled us to provide an in-depth picture of how regulated bacterial promoters might evolve. More importantly, we used the model to explore which factors that contribute to the complexity of this system are essential for understanding its evolution, and which can be simplified without information loss. We found that several key evolutionary properties—the distribution of phenotypic and fitness effects of mutations, the evolutionary trajectories during selection for regulation—can be accurately captured without accounting for all, or even most, parameters of the system. Our findings point to the need for a mechanistic approach to studying evolution, as it enables tackling biological complexity and in doing so improves the ability to predict evolutionary outcomes."}],"has_accepted_license":"1","date_created":"2025-01-29T08:21:35Z","pmid":1,"article_number":"iyae191","date_published":"2025-02-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":1511688,"access_level":"open_access","content_type":"application/pdf","date_created":"2025-04-16T09:41:04Z","relation":"main_file","checksum":"f730e416795969449ef49d97b82ac494","creator":"dernst","file_name":"2025_Genetics_Grah.pdf","date_updated":"2025-04-16T09:41:04Z","success":1,"file_id":"19580"}],"year":"2025","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","oa":1,"type":"journal_article","isi":1,"oa_version":"Published Version","quality_controlled":"1","_id":"18936","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Grah, Rok, Calin C Guet, Gašper Tkačik, and Mato Lagator. “Linking Molecular Mechanisms to Their Evolutionary Consequences: A Primer.” <i>Genetics</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/genetics/iyae191\">https://doi.org/10.1093/genetics/iyae191</a>.","short":"R. Grah, C.C. Guet, G. Tkačik, M. Lagator, Genetics 229 (2025).","ieee":"R. Grah, C. C. Guet, G. Tkačik, and M. Lagator, “Linking molecular mechanisms to their evolutionary consequences: a primer,” <i>Genetics</i>, vol. 229, no. 2. Oxford University Press, 2025.","mla":"Grah, Rok, et al. “Linking Molecular Mechanisms to Their Evolutionary Consequences: A Primer.” <i>Genetics</i>, vol. 229, no. 2, iyae191, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/genetics/iyae191\">10.1093/genetics/iyae191</a>.","ista":"Grah R, Guet CC, Tkačik G, Lagator M. 2025. Linking molecular mechanisms to their evolutionary consequences: a primer. Genetics. 229(2), iyae191.","apa":"Grah, R., Guet, C. C., Tkačik, G., &#38; Lagator, M. (2025). Linking molecular mechanisms to their evolutionary consequences: a primer. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyae191\">https://doi.org/10.1093/genetics/iyae191</a>","ama":"Grah R, Guet CC, Tkačik G, Lagator M. Linking molecular mechanisms to their evolutionary consequences: a primer. <i>Genetics</i>. 2025;229(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyae191\">10.1093/genetics/iyae191</a>"},"doi":"10.1093/genetics/iyae191","volume":229,"scopus_import":"1","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_updated":"2025-05-19T14:08:02Z","title":"Linking molecular mechanisms to their evolutionary consequences: a primer","author":[{"full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","orcid":"0000-0003-2539-3560","first_name":"Rok"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"}],"external_id":{"isi":["001379194200001"],"pmid":["39601269"]},"license":"https://creativecommons.org/licenses/by/4.0/","OA_place":"publisher","file_date_updated":"2025-04-16T09:41:04Z","publication_identifier":{"eissn":["1943-2631"]},"acknowledgement":"The authors thank Nick Barton, Stepan Denisov, Claudia Igler, Srdjan Sarikas, Anna Staron, and the anonymous reviewers for useful comments and discussions that helped improve our work.\r\nFunding for this work was provided by the Wellcome Trust–Royal Society Sir Henry Dale Fellowship (216779/Z/19/Z) and the Royal Society Research Grant (RG\\R2\\232522) to M.L.","article_type":"original","day":"01"},{"quality_controlled":"1","oa_version":"None","_id":"18960","doi":"10.1101/cshperspect.a041653","citation":{"short":"D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17 (2025).","chicago":"Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2025. <a href=\"https://doi.org/10.1101/cshperspect.a041653\">https://doi.org/10.1101/cshperspect.a041653</a>.","apa":"Brückner, D., &#38; Hannezo, E. B. (2025). Tissue active matter: Integrating mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a041653\">https://doi.org/10.1101/cshperspect.a041653</a>","ama":"Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. 2025;17(4). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041653\">10.1101/cshperspect.a041653</a>","ista":"Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. 17(4), a041653.","ieee":"D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics and signaling into dynamical models,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.","mla":"Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press, 2025, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041653\">10.1101/cshperspect.a041653</a>."},"project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"},{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"volume":17,"department":[{"_id":"EdHa"}],"scopus_import":"1","date_updated":"2025-12-30T07:08:34Z","title":"Tissue active matter: Integrating mechanics and signaling into dynamical models","author":[{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","orcid":"0000-0001-7205-2975","first_name":"David"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B"}],"external_id":{"isi":["001456660400001"],"pmid":["38951023"]},"publication_identifier":{"issn":["1943-0264"]},"acknowledgement":"We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg for a critical reading of the manuscript and Claudia Flandoli for the artwork in the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from the European Research Council (ERC) under the European Union\\u2019s Horizon 2020 Research and Innovation Programme Grant Agreement no. 851288.","article_type":"original","day":"01","publication":"Cold Spring Harbor Perspectives in Biology","status":"public","month":"04","corr_author":"1","issue":"4","intvolume":"        17","OA_type":"closed access","language":[{"iso":"eng"}],"publisher":"Cold Spring Harbor Laboratory Press","date_created":"2025-01-29T13:33:47Z","abstract":[{"text":"The importance of physical forces in the morphogenesis, homeostatic function, and pathological dysfunction of multicellular tissues is being increasingly characterized, both theoretically and experimentally. Analogies between biological systems and inert materials such as foams, gels, and liquid crystals have provided striking insights into the core design principles underlying multicellular organization. However, these connections can seem surprising given that a key feature of multicellular systems is their ability to constantly consume energy, providing an active origin for the forces that they produce. Key emerging questions are, therefore, to understand whether and how this activity grants tissues novel properties that do not have counterparts in classical materials, as well as their consequences for biological function. Here, we review recent discoveries at the intersection of active matter and tissue biology, with an emphasis on how modeling and experiments can be combined to understand the dynamics of multicellular systems. These approaches suggest that a number of key biological tissue-scale phenomena, such as morphogenetic shape changes, collective migration, or fate decisions, share unifying design principles that can be described by physical models of tissue active matter.","lang":"eng"}],"pmid":1,"article_number":"a041653","date_published":"2025-04-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","article_processing_charge":"No","publication_status":"published","ec_funded":1,"isi":1,"type":"journal_article"},{"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"project":[{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342","name":"Mathematics, Computer Science"}],"doi":"10.15479/at:ista:18979","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"O. Draganov, Structures and Computations in Topological Data Analysis, Institute of Science and Technology Austria, 2025.","chicago":"Draganov, Ondrej. “Structures and Computations in Topological Data Analysis.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/at:ista:18979\">https://doi.org/10.15479/at:ista:18979</a>.","ama":"Draganov O. Structures and computations in topological data analysis. 2025. doi:<a href=\"https://doi.org/10.15479/at:ista:18979\">10.15479/at:ista:18979</a>","ista":"Draganov O. 2025. Structures and computations in topological data analysis. Institute of Science and Technology Austria.","apa":"Draganov, O. (2025). <i>Structures and computations in topological data analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18979\">https://doi.org/10.15479/at:ista:18979</a>","ieee":"O. Draganov, “Structures and computations in topological data analysis,” Institute of Science and Technology Austria, 2025.","mla":"Draganov, Ondrej. <i>Structures and Computations in Topological Data Analysis</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/at:ista:18979\">10.15479/at:ista:18979</a>."},"_id":"18979","oa_version":"Published Version","file_date_updated":"2025-02-04T16:22:07Z","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"15091","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18981","status":"public"}]},"acknowledgement":"The research presented in this thesis was funded with the Wittgenstein Prize,\r\nAustrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research\r\nCenter TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF),\r\ngrant no. I 02979-N35.\r\n","day":"03","OA_place":"publisher","author":[{"orcid":"0000-0003-0464-3823","last_name":"Draganov","first_name":"Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","full_name":"Draganov, Ondrej"}],"date_updated":"2026-04-07T11:47:30Z","title":"Structures and computations in topological data analysis","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Topological Data Analysis (TDA) is a discipline utilizing the mathematical field of topology to study data, most prominently collections of point sets. This thesis summarizes three projects related to computations in TDA.\r\n\r\nThe first one establishes a variant of TDA for chromatic point sets, where each point is given a color. For example, we are given positions of cells within a tumor microenvironment, and color the cancerous cells red, and the immune cells blue.\r\n\r\nThe aim is then to give a quantitative description of how the two or more sets of points spatially interact. Building on image, kernel and cokernel variants of persistent homology, we suggest six-packs of persistent diagrams as such a descriptor.\r\n\r\nWe describe a construction of a chromatic alpha complex, which enables  efficient computation of several variants of the six-packs. We give topological descriptions of natural subcomplexes of the chromatic alpha complex, and show that the radii of the simplices form a discrete Morse function. Finally, we provide an implementation of the presented chromatic TDA pipeline.\r\n\r\nThe second part aims to translate a powerful tool of sheaf theory to elementary terms using labeled matrices. The goal is to enable their use in computational settings. We show that derived categories of sheaves over finite posets have, up to isomorphism, unique objects---minimal injective resolutions---and give a concrete algorithm to compute them. We further describe simple algorithms to compute derived pushforwards and pullbacks for monotonic maps, and their proper variants for inclusions, and demonstrate their tractability by providing an implementation. Finally, we suggest a discrete definition of microsupport and show desirable properties inspired by discrete Morse theory.\r\n\r\nIn the last part, we present a collection of observations about collapses. We give a characterization of collapsibility in terms of unitriangular submatrices of the boundary matrix, a cotree-tree decomposition, and the optimal solution to a variant of the Procrustes problem. We establish relation between dual collapses and relative Morse theory and pose several open questions. Finally, focusing on complexes embedded in the three-dimensional Euclidean space, we describe a relation between the collapsibility and the triviality of a polygonal knot."}],"has_accepted_license":"1","date_created":"2025-01-31T17:04:40Z","publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"}],"language":[{"iso":"eng"}],"degree_awarded":"PhD","month":"02","status":"public","corr_author":"1","ddc":["514","004"],"page":"140","type":"dissertation","oa":1,"article_processing_charge":"No","year":"2025","keyword":["topological data analysis","chromatic point set","alpha complex","persistent homology","six pack","sheaf","microlocal discrete Morse","injective resolution","collapse","knot","discrete Morse theory"],"publication_status":"published","file":[{"file_size":11899491,"content_type":"application/zip","access_level":"closed","relation":"source_file","date_created":"2025-01-31T16:58:30Z","creator":"odragano","file_name":"Thesis.zip","checksum":"af6567e5d35e5eb330b8925ae37f1998","date_updated":"2025-01-31T16:58:30Z","file_id":"18983"},{"date_updated":"2025-02-04T16:22:07Z","file_id":"19000","file_size":8857514,"access_level":"open_access","content_type":"application/pdf","date_created":"2025-02-04T16:22:07Z","relation":"main_file","checksum":"c3fef68e35b9dc2020b2ca6006da6343","creator":"odragano","file_name":"Thesis.pdf"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2025-02-03T00:00:00Z"},{"arxiv":1,"DOAJ_listed":"1","day":"01","file_date_updated":"2025-12-30T07:24:34Z","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"acknowledgement":"We thank the participants of the 2023 Kavli Summer Program in Astrophysics, hosted by the Max Planck Institute for Astrophysics and funded by the Kavli Foundation. In particular, Holly Preece, Selma de Mink, and Stephen Justham for their feedback and comments on our work. ZX acknowledges support from the China Scholarship Council (CSC). ST acknowledges the funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 101034413. AAT acknowledges support from the Horizon Europe research and innovation programmes under the Marie Skłodowska-Curie grant agreement no. 101103134.","article_type":"original","external_id":{"arxiv":["2410.19695"],"isi":["001400731500001"]},"OA_place":"publisher","author":[{"last_name":"Xing","first_name":"Zepei","full_name":"Xing, Zepei"},{"full_name":"Torres Rodriguez, Santiago","id":"a8df4360-4328-11ee-8f1a-e502d0c83fc2","last_name":"Torres Rodriguez","orcid":"0000-0002-3150-8988","first_name":"Santiago"},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","full_name":"Götberg, Ylva Louise Linsdotter","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","last_name":"Götberg"},{"full_name":"Trani, Alessandro A.","first_name":"Alessandro A.","last_name":"Trani"},{"full_name":"Korol, Valeriya","last_name":"Korol","first_name":"Valeriya"},{"full_name":"Cuadra, Jorge","first_name":"Jorge","last_name":"Cuadra"}],"title":"Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries","date_updated":"2025-12-30T07:25:37Z","volume":537,"department":[{"_id":"YlGo"},{"_id":"LiBu"}],"scopus_import":"1","citation":{"ieee":"Z. Xing, S. Torres Rodriguez, Y. L. L. Götberg, A. A. Trani, V. Korol, and J. Cuadra, “Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 537, no. 1. Oxford University Press, pp. 285–292, 2025.","mla":"Xing, Zepei, et al. “Combining REBOUND and MESA: Dynamical Evolution of Planets Orbiting Interacting Binaries.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 537, no. 1, Oxford University Press, 2025, pp. 285–92, doi:<a href=\"https://doi.org/10.1093/mnras/stae2820\">10.1093/mnras/stae2820</a>.","apa":"Xing, Z., Torres Rodriguez, S., Götberg, Y. L. L., Trani, A. A., Korol, V., &#38; Cuadra, J. (2025). Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stae2820\">https://doi.org/10.1093/mnras/stae2820</a>","ista":"Xing Z, Torres Rodriguez S, Götberg YLL, Trani AA, Korol V, Cuadra J. 2025. Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries. Monthly Notices of the Royal Astronomical Society. 537(1), 285–292.","ama":"Xing Z, Torres Rodriguez S, Götberg YLL, Trani AA, Korol V, Cuadra J. Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries. <i>Monthly Notices of the Royal Astronomical Society</i>. 2025;537(1):285-292. doi:<a href=\"https://doi.org/10.1093/mnras/stae2820\">10.1093/mnras/stae2820</a>","chicago":"Xing, Zepei, Santiago Torres Rodriguez, Ylva Louise Linsdotter Götberg, Alessandro A. Trani, Valeriya Korol, and Jorge Cuadra. “Combining REBOUND and MESA: Dynamical Evolution of Planets Orbiting Interacting Binaries.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/mnras/stae2820\">https://doi.org/10.1093/mnras/stae2820</a>.","short":"Z. Xing, S. Torres Rodriguez, Y.L.L. Götberg, A.A. Trani, V. Korol, J. Cuadra, Monthly Notices of the Royal Astronomical Society 537 (2025) 285–292."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1093/mnras/stae2820","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"quality_controlled":"1","oa_version":"Published Version","_id":"18984","page":"285-292","oa":1,"ec_funded":1,"isi":1,"type":"journal_article","file":[{"date_created":"2025-12-30T07:24:34Z","relation":"main_file","creator":"dernst","checksum":"49fb4fe69f487d36169ccea60acbeccc","file_name":"2025_MonthlyNoticesRAS_Xing.pdf","file_size":2974244,"access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"20881","date_updated":"2025-12-30T07:24:34Z"}],"publication_status":"published","article_processing_charge":"Yes","year":"2025","date_published":"2025-02-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","has_accepted_license":"1","abstract":[{"text":"Although planets have been found orbiting binary systems, whether they can survive binary interactions is debated. While the tightest-orbit binaries should host the most dynamically stable and long-lived circumbinary planetary systems, they are also the systems that are expected to experience mass transfer, common envelope evolution, or stellar mergers. In this study, we explore the effect of stable non-conservative mass transfer on the dynamical evolution of circumbinary planets. We present a new script that seamlessly integrates binary evolution data from the 1D binary stellar evolution code MESA into the N-body simulation code REBOUND. This integration framework enables a comprehensive examination of the dynamical evolution of circumbinary planets orbiting mass-transferring binaries, while simultaneously accounting for the detailed stellar structure evolution. In addition, we introduce a recalibration method to mitigate numerical errors from updates of binary properties during the system's dynamical evolution. We construct a reference binary model in which a 2.21M⊙ star loses its hydrogen-rich envelope through non-conservative mass transfer to the 1.76M⊙ companion star, creating a 0.38M⊙ subdwarf. We find the tightest stable orbital separation for circumbinary planets to be ≃2.5 times the binary separation after mass transfer. Accounting for tides by using the interior stellar structure, we find that tidal effects become apparent after the rapid mass transfer phase and start to fade away during the latter stage of the slow mass transfer phase. Our research provides a new framework for exploring circumbinary planet dynamics in interacting binary systems.","lang":"eng"}],"date_created":"2025-02-02T23:01:53Z","intvolume":"       537","PlanS_conform":"1","OA_type":"gold","language":[{"iso":"eng"}],"issue":"1","month":"02","status":"public","ddc":["520"],"publication":"Monthly Notices of the Royal Astronomical Society"},{"language":[{"iso":"eng"}],"OA_type":"closed access","intvolume":"       387","abstract":[{"lang":"eng","text":"Persistent multiyear drought (MYD) events pose a growing threat to nature and humans in a changing climate. We identified and inventoried global MYDs by detecting spatiotemporally contiguous climatic anomalies, showing that MYDs have become drier, hotter, and led to increasingly diminished vegetation greenness. The global terrestrial land affected by MYDs has increased at a rate of 49,279 ± 14,771 square kilometers per year from 1980 to 2018. Temperate grasslands have exhibited the greatest declines in vegetation greenness during MYDs, whereas boreal and tropical forests have had comparably minor responses. With MYDs becoming more common, this global quantitative inventory of the occurrence, severity, trend, and impact of MYDs provides an important benchmark for facilitating more effective and collaborative preparedness toward mitigation of and adaptation to such extreme events."}],"date_created":"2025-02-02T23:01:54Z","pmid":1,"publisher":"AAAS","publication":"Science","status":"public","month":"01","issue":"6731","type":"journal_article","isi":1,"page":"278-284","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-01-17T00:00:00Z","article_processing_charge":"No","year":"2025","publication_status":"published","citation":{"chicago":"Chen, Liangzhi, Philipp Brun, Pascal Buri, Simone Fatichi, Arthur Gessler, Michael McCarthy, Francesca Pellicciotti, Benjamin Stocker, and Dirk Nikolaus Karger. “Global Increase in the Occurrence and Impact of Multiyear Droughts.” <i>Science</i>. AAAS, 2025. <a href=\"https://doi.org/10.1126/science.ado4245\">https://doi.org/10.1126/science.ado4245</a>.","short":"L. Chen, P. Brun, P. Buri, S. Fatichi, A. Gessler, M. McCarthy, F. Pellicciotti, B. Stocker, D.N. Karger, Science 387 (2025) 278–284.","mla":"Chen, Liangzhi, et al. “Global Increase in the Occurrence and Impact of Multiyear Droughts.” <i>Science</i>, vol. 387, no. 6731, AAAS, 2025, pp. 278–84, doi:<a href=\"https://doi.org/10.1126/science.ado4245\">10.1126/science.ado4245</a>.","ieee":"L. Chen <i>et al.</i>, “Global increase in the occurrence and impact of multiyear droughts,” <i>Science</i>, vol. 387, no. 6731. AAAS, pp. 278–284, 2025.","ista":"Chen L, Brun P, Buri P, Fatichi S, Gessler A, McCarthy M, Pellicciotti F, Stocker B, Karger DN. 2025. Global increase in the occurrence and impact of multiyear droughts. Science. 387(6731), 278–284.","apa":"Chen, L., Brun, P., Buri, P., Fatichi, S., Gessler, A., McCarthy, M., … Karger, D. N. (2025). Global increase in the occurrence and impact of multiyear droughts. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.ado4245\">https://doi.org/10.1126/science.ado4245</a>","ama":"Chen L, Brun P, Buri P, et al. Global increase in the occurrence and impact of multiyear droughts. <i>Science</i>. 2025;387(6731):278-284. doi:<a href=\"https://doi.org/10.1126/science.ado4245\">10.1126/science.ado4245</a>"},"doi":"10.1126/science.ado4245","scopus_import":"1","department":[{"_id":"FrPe"}],"volume":387,"_id":"18985","quality_controlled":"1","oa_version":"None","external_id":{"pmid":["39818908"],"isi":["001491931700027"]},"article_type":"original","publication_identifier":{"eissn":["1095-9203"]},"acknowledgement":"This study received support from the Extremes Research Program funded by the Swiss Federal Institute for Forest, Snow and Landscape Research (WSL) within the EMERGE project of the Extremes program.","day":"17","date_updated":"2025-09-30T10:24:34Z","title":"Global increase in the occurrence and impact of multiyear droughts","author":[{"first_name":"Liangzhi","last_name":"Chen","full_name":"Chen, Liangzhi"},{"last_name":"Brun","first_name":"Philipp","full_name":"Brun, Philipp"},{"id":"317987aa-9421-11ee-ac5a-b941b041abba","full_name":"Buri, Pascal","first_name":"Pascal","last_name":"Buri"},{"full_name":"Fatichi, Simone","first_name":"Simone","last_name":"Fatichi"},{"full_name":"Gessler, Arthur","first_name":"Arthur","last_name":"Gessler"},{"first_name":"Michael","last_name":"Mccarthy","full_name":"Mccarthy, Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f"},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","orcid":"0000-0002-5554-8087","first_name":"Francesca"},{"last_name":"Stocker","first_name":"Benjamin","full_name":"Stocker, Benjamin"},{"full_name":"Karger, Dirk Nikolaus","last_name":"Karger","first_name":"Dirk Nikolaus"}]},{"volume":7,"scopus_import":"1","department":[{"_id":"MaMo"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"J. Barbier, F. Camilli, Y. Xu, and M. Mondelli, “Information limits and Thouless-Anderson-Palmer equations for spiked matrix models with structured noise,” <i>Physical Review Research</i>, vol. 7. American Physical Society, 2025.","mla":"Barbier, Jean, et al. “Information Limits and Thouless-Anderson-Palmer Equations for Spiked Matrix Models with Structured Noise.” <i>Physical Review Research</i>, vol. 7, 013081, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.7.013081\">10.1103/PhysRevResearch.7.013081</a>.","apa":"Barbier, J., Camilli, F., Xu, Y., &#38; Mondelli, M. (2025). Information limits and Thouless-Anderson-Palmer equations for spiked matrix models with structured noise. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.7.013081\">https://doi.org/10.1103/PhysRevResearch.7.013081</a>","ista":"Barbier J, Camilli F, Xu Y, Mondelli M. 2025. Information limits and Thouless-Anderson-Palmer equations for spiked matrix models with structured noise. Physical Review Research. 7, 013081.","ama":"Barbier J, Camilli F, Xu Y, Mondelli M. Information limits and Thouless-Anderson-Palmer equations for spiked matrix models with structured noise. <i>Physical Review Research</i>. 2025;7. doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.7.013081\">10.1103/PhysRevResearch.7.013081</a>","chicago":"Barbier, Jean, Francesco Camilli, Yizhou Xu, and Marco Mondelli. “Information Limits and Thouless-Anderson-Palmer Equations for Spiked Matrix Models with Structured Noise.” <i>Physical Review Research</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevResearch.7.013081\">https://doi.org/10.1103/PhysRevResearch.7.013081</a>.","short":"J. Barbier, F. Camilli, Y. Xu, M. Mondelli, Physical Review Research 7 (2025)."},"doi":"10.1103/PhysRevResearch.7.013081","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"APC_amount":"3272,21 EUR","quality_controlled":"1","oa_version":"Published Version","_id":"18986","arxiv":1,"DOAJ_listed":"1","day":"22","acknowledgement":"J.B., F.C., and Y.X. were funded by the European Union (ERC, CHORAL, Project No. 101039794). Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. M.M. was supported by the 2019 Lopez-Loreta Prize. J.B. acknowledges discussions with TianQi Hou at the initial stage of the project, as well as with Antoine Bodin.","file_date_updated":"2025-02-03T08:27:59Z","publication_identifier":{"issn":["2643-1564"]},"article_type":"original","related_material":{"link":[{"url":"https://github.com/xu-yz19/spiked-matrix-models-with-structured-noise","relation":"software"}]},"external_id":{"arxiv":["2405.20993"]},"OA_place":"publisher","author":[{"full_name":"Barbier, Jean","last_name":"Barbier","first_name":"Jean"},{"full_name":"Camilli, Francesco","last_name":"Camilli","first_name":"Francesco"},{"first_name":"Yizhou","last_name":"Xu","full_name":"Xu, Yizhou"},{"first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"title":"Information limits and Thouless-Anderson-Palmer equations for spiked matrix models with structured noise","date_updated":"2026-05-06T12:57:36Z","publisher":"American Physical Society","has_accepted_license":"1","date_created":"2025-02-02T23:01:54Z","abstract":[{"text":"We consider a prototypical problem of Bayesian inference for a structured spiked model: a low-rank signal is corrupted by additive noise. While both information-theoretic and algorithmic limits are well understood when the noise is a Gaussian Wigner matrix, the more realistic case of structured noise still remains challenging. To capture the structure while maintaining mathematical tractability, a line of work has focused on rotationally invariant noise. However, existing studies either provide suboptimal algorithms or are limited to a special class of noise ensembles. In this paper, using tools from statistical physics (replica method) and random matrix theory (generalized spherical integrals) we establish the characterization of the information-theoretic limits for a noise matrix drawn from a general trace ensemble. Remarkably, our analysis unveils the asymptotic equivalence between the rotationally invariant model and a surrogate Gaussian one. Finally, we show how to saturate the predicted statistical limits using an efficient algorithm inspired by the theory of adaptive Thouless-Anderson-Palmer (TAP) equations.","lang":"eng"}],"intvolume":"         7","language":[{"iso":"eng"}],"OA_type":"gold","ddc":["530"],"status":"public","month":"01","publication":"Physical Review Research","oa":1,"type":"journal_article","file":[{"file_size":702543,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2025-02-03T08:27:59Z","creator":"dernst","file_name":"2025_PhysReviewResearch_Barbier.pdf","checksum":"52c5f72d80ffc928542469114fcdb62b","date_updated":"2025-02-03T08:27:59Z","success":1,"file_id":"18988"}],"publication_status":"published","year":"2025","article_processing_charge":"Yes","article_number":"013081","date_published":"2025-01-22T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"external_id":{"pmid":["39963288"]},"OA_place":"publisher","DOAJ_listed":"1","publication_identifier":{"eissn":["2632-1297"]},"acknowledgement":"We thank all individuals and relatives for consent to be part of the study. Families 1–4, 7, were collected as part of the SYNaPS Study Group collaboration funded by The Wellcome Trust and strategic award (Synaptopathies) funding (WT093205 MA and WT104033AIA), and research was conducted as part of the Queen Square Genomics group at the University College London, supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre. We are also grateful to Queen Square Genomics at the Institute of Neurology University College London, supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre, for the bioinformatics support. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission.\r\nThis study was funded by the Medical Research Council (MR/S01165X/1, MR/S005021/1, G0601943). The Medical Research Council (MR/S01165X/1, MR/S005021/1, MRC ICGNMD), Wellcome Trust 221951/Z/20/Z, Global Parkinson’s Genetics Program, Aligning Science Across Parkinson’s, The Michael J. Fox Foundation, The National Institute for Health Research University College London Hospitals Biomedical Research Centre, Rosetree Trust, Multiple System Atrophy Trust, Brain Research UK, Sparks Great Ormond Street Hospital Charity, Muscular Dystrophy, Muscular Dystrophy Association United States of America, and King Baudouin Foundation. H.T. was supported by the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 608473. M.S.A.-H. is funded by the Science and Technology Development Fund Academy of Science Research and Technology Egypt (Grant number: 33492, Ethical approval number: 20066). R.W.T. is funded by the Wellcome Centre for Mitochondrial Research (203105/Z/16/Z), the Mitochondrial Disease Patient Cohort (UK) (G0800674), the Medical Research Council International Centre for Genomic Medicine in Neuromuscular Disease (MR/S005021/1), the Medical Research Council (MR/W019027/1), the Lily Foundation, Mito Foundation, the Pathological Society, LifeArc, the UK National Institute for Health Research Biomedical Research Centre for Ageing and Age-related disease award to the Newcastle upon Tyne Foundation Hospitals NHS Trust and the UK NHS Highly Specialised Service for Rare Mitochondrial Disorders of Adults and Children. H.H. and R.K. are supported by Global Parkinson’s Genetic Program and The Michael J. Fox Foundation Grant ID: MJFF-022153.","article_type":"original","file_date_updated":"2025-08-05T11:54:23Z","day":"01","date_updated":"2025-08-05T11:55:15Z","title":"Biallelic NDUFA13 variants lead to a neurodevelopmental phenotype with gradual neurological impairment","author":[{"first_name":"Rauan","last_name":"Kaiyrzhanov","full_name":"Kaiyrzhanov, Rauan"},{"last_name":"Thompson","first_name":"Kyle","full_name":"Thompson, Kyle"},{"full_name":"Efthymiou, Stephanie","last_name":"Efthymiou","first_name":"Stephanie"},{"full_name":"Mukushev, Askhat","last_name":"Mukushev","first_name":"Askhat"},{"first_name":"Akbota","last_name":"Zharylkassyn","full_name":"Zharylkassyn, Akbota"},{"full_name":"Prasad, Chitra","first_name":"Chitra","last_name":"Prasad"},{"full_name":"Karimiani, Ehsan Ghayoor","last_name":"Karimiani","first_name":"Ehsan Ghayoor"},{"last_name":"Alvi","first_name":"Javeria Raza","full_name":"Alvi, Javeria Raza"},{"full_name":"Niyazov, Dmitriy","last_name":"Niyazov","first_name":"Dmitriy"},{"first_name":"Ahmad","last_name":"Alahmad","full_name":"Alahmad, Ahmad"},{"first_name":"Meisam","last_name":"Babaei","full_name":"Babaei, Meisam"},{"last_name":"Tajsharghi","first_name":"Homa","full_name":"Tajsharghi, Homa"},{"last_name":"Albash","first_name":"Buthaina","full_name":"Albash, Buthaina"},{"full_name":"Alaqeel, Ahmad","last_name":"Alaqeel","first_name":"Ahmad"},{"full_name":"Charif, Majida","first_name":"Majida","last_name":"Charif"},{"last_name":"Hashemi","first_name":"Narges","full_name":"Hashemi, Narges"},{"full_name":"Heidari, Morteza","first_name":"Morteza","last_name":"Heidari"},{"last_name":"Kalantar","first_name":"Seyed Mehdi","full_name":"Kalantar, Seyed Mehdi"},{"full_name":"Lenaers, Guy","first_name":"Guy","last_name":"Lenaers"},{"first_name":"Mohammad Yahya Vahidi","last_name":"Mehrjardi","full_name":"Mehrjardi, Mohammad Yahya Vahidi"},{"first_name":"Varunvenkat M.","last_name":"Srinivasan","full_name":"Srinivasan, Varunvenkat M."},{"full_name":"Gowda, Vykuntaraju K.","first_name":"Vykuntaraju K.","last_name":"Gowda"},{"full_name":"Mirabutalebi, Seyed Hamidreza","last_name":"Mirabutalebi","first_name":"Seyed Hamidreza"},{"full_name":"Carere, Deanna Alexis","last_name":"Carere","first_name":"Deanna Alexis"},{"first_name":"Mojtaba","last_name":"Movahedinia","full_name":"Movahedinia, Mojtaba"},{"full_name":"Murphy, David","last_name":"Murphy","first_name":"David"},{"first_name":"Robert","last_name":"Mcfarland","full_name":"Mcfarland, Robert"},{"full_name":"Abdel-Hamid, Mohamed S.","first_name":"Mohamed S.","last_name":"Abdel-Hamid"},{"last_name":"Elhossini","first_name":"Rasha M.","full_name":"Elhossini, Rasha M."},{"first_name":"Shahryar","last_name":"Alavi","full_name":"Alavi, Shahryar"},{"first_name":"Melanie","last_name":"Napier","full_name":"Napier, Melanie"},{"full_name":"Belanger-Quintana, Amaya","first_name":"Amaya","last_name":"Belanger-Quintana"},{"full_name":"Prasad, Asuri N.","first_name":"Asuri N.","last_name":"Prasad"},{"first_name":"Jessica","last_name":"Jakobczyk","full_name":"Jakobczyk, Jessica"},{"full_name":"Roubertie, Agathe","last_name":"Roubertie","first_name":"Agathe"},{"full_name":"Rupar, Tony","first_name":"Tony","last_name":"Rupar"},{"full_name":"Sultan, Tipu","last_name":"Sultan","first_name":"Tipu"},{"full_name":"Toosi, Mehran Beiraghi","first_name":"Mehran Beiraghi","last_name":"Toosi"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"},{"full_name":"Severino, Mariasavina","last_name":"Severino","first_name":"Mariasavina"},{"full_name":"Houlden, Henry","last_name":"Houlden","first_name":"Henry"},{"first_name":"Robert W.","last_name":"Taylor","full_name":"Taylor, Robert W."},{"full_name":"Maroofian, Reza","first_name":"Reza","last_name":"Maroofian"}],"doi":"10.1093/braincomms/fcae453","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"R. Kaiyrzhanov, K. Thompson, S. Efthymiou, A. Mukushev, A. Zharylkassyn, C. Prasad, E.G. Karimiani, J.R. Alvi, D. Niyazov, A. Alahmad, M. Babaei, H. Tajsharghi, B. Albash, A. Alaqeel, M. Charif, N. Hashemi, M. Heidari, S.M. Kalantar, G. Lenaers, M.Y.V. Mehrjardi, V.M. Srinivasan, V.K. Gowda, S.H. Mirabutalebi, D.A. Carere, M. Movahedinia, D. Murphy, R. Mcfarland, M.S. Abdel-Hamid, R.M. Elhossini, S. Alavi, M. Napier, A. Belanger-Quintana, A.N. Prasad, J. Jakobczyk, A. Roubertie, T. Rupar, T. Sultan, M.B. Toosi, L.A. Sazanov, M. Severino, H. Houlden, R.W. Taylor, R. Maroofian, Brain Communications 7 (2025).","chicago":"Kaiyrzhanov, Rauan, Kyle Thompson, Stephanie Efthymiou, Askhat Mukushev, Akbota Zharylkassyn, Chitra Prasad, Ehsan Ghayoor Karimiani, et al. “Biallelic NDUFA13 Variants Lead to a Neurodevelopmental Phenotype with Gradual Neurological Impairment.” <i>Brain Communications</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/braincomms/fcae453\">https://doi.org/10.1093/braincomms/fcae453</a>.","apa":"Kaiyrzhanov, R., Thompson, K., Efthymiou, S., Mukushev, A., Zharylkassyn, A., Prasad, C., … Maroofian, R. (2025). Biallelic NDUFA13 variants lead to a neurodevelopmental phenotype with gradual neurological impairment. <i>Brain Communications</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/braincomms/fcae453\">https://doi.org/10.1093/braincomms/fcae453</a>","ama":"Kaiyrzhanov R, Thompson K, Efthymiou S, et al. Biallelic NDUFA13 variants lead to a neurodevelopmental phenotype with gradual neurological impairment. <i>Brain Communications</i>. 2025;7(1). doi:<a href=\"https://doi.org/10.1093/braincomms/fcae453\">10.1093/braincomms/fcae453</a>","ista":"Kaiyrzhanov R, Thompson K, Efthymiou S, Mukushev A, Zharylkassyn A, Prasad C, Karimiani EG, Alvi JR, Niyazov D, Alahmad A, Babaei M, Tajsharghi H, Albash B, Alaqeel A, Charif M, Hashemi N, Heidari M, Kalantar SM, Lenaers G, Mehrjardi MYV, Srinivasan VM, Gowda VK, Mirabutalebi SH, Carere DA, Movahedinia M, Murphy D, Mcfarland R, Abdel-Hamid MS, Elhossini RM, Alavi S, Napier M, Belanger-Quintana A, Prasad AN, Jakobczyk J, Roubertie A, Rupar T, Sultan T, Toosi MB, Sazanov LA, Severino M, Houlden H, Taylor RW, Maroofian R. 2025. Biallelic NDUFA13 variants lead to a neurodevelopmental phenotype with gradual neurological impairment. Brain Communications. 7(1), fcae453.","mla":"Kaiyrzhanov, Rauan, et al. “Biallelic NDUFA13 Variants Lead to a Neurodevelopmental Phenotype with Gradual Neurological Impairment.” <i>Brain Communications</i>, vol. 7, no. 1, fcae453, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/braincomms/fcae453\">10.1093/braincomms/fcae453</a>.","ieee":"R. Kaiyrzhanov <i>et al.</i>, “Biallelic NDUFA13 variants lead to a neurodevelopmental phenotype with gradual neurological impairment,” <i>Brain Communications</i>, vol. 7, no. 1. Oxford University Press, 2025."},"volume":7,"scopus_import":"1","department":[{"_id":"LeSa"}],"quality_controlled":"1","oa_version":"Published Version","_id":"18987","oa":1,"type":"journal_article","article_number":"fcae453","date_published":"2025-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","file_name":"2025_BrainComm_Kaiyrzhanov.pdf","checksum":"bdf39b64d1c1d833a20b62836751fe44","relation":"main_file","date_created":"2025-08-05T11:54:23Z","content_type":"application/pdf","access_level":"open_access","file_size":1420646,"success":1,"file_id":"20126","date_updated":"2025-08-05T11:54:23Z"}],"year":"2025","article_processing_charge":"Yes","publication_status":"published","PlanS_conform":"1","intvolume":"         7","language":[{"iso":"eng"}],"OA_type":"gold","publisher":"Oxford University Press","abstract":[{"text":"Biallelic variants in NADH (nicotinamide adenine dinucleotide (NAD) + hydrogen (H))-ubiquinone oxidoreductase 1 alpha subcomplex 13 have been linked to mitochondrial complex I deficiency, nuclear type 28, based on three affected individuals from two families. With only two families reported, the clinical and molecular spectrum of NADH-ubiquinone oxidoreductase 1 alpha subcomplex 13–related diseases remains unclear. We report 10 additional affected individuals from nine independent families, identifying four missense variants (including recurrent c.170G > A) and three ultra-rare or novel predicted loss-of-function biallelic variants. Updated clinical–radiological data from previously reported families and a literature review compiling clinical features of all reported patients with isolated complex I deficiency caused by 43 genes encoding complex I subunits and assembly factors are also provided. Our cohort (mean age 7.8 ± 5.4 years; range 2.5–18) predominantly presented a moderate-to-severe neurodevelopmental syndrome with oculomotor abnormalities (84%), spasticity/hypertonia (83%), hypotonia (69%), cerebellar ataxia (66%), movement disorders (58%) and epilepsy (46%). Neuroimaging revealed bilateral symmetric T2 hyperintense substantia nigra lesions (91.6%) and optic nerve atrophy (66.6%). Protein modeling suggests missense variants destabilize a critical junction between the hydrophilic and membrane arms of complex I. Fibroblasts from two patients showed reduced complex I activity and compensatory complex IV activity increase. This study characterizes NADH-ubiquinone oxidoreductase 1 alpha subcomplex 13–related disease in 13 individuals, highlighting genotype–phenotype correlations.","lang":"eng"}],"has_accepted_license":"1","date_created":"2025-02-02T23:01:55Z","pmid":1,"month":"01","status":"public","ddc":["570"],"publication":"Brain Communications","issue":"1"},{"article_processing_charge":"No","year":"2025","keyword":["hippocampus","electrophysiology","behavior"],"file":[{"checksum":"04d761ed42e8879abffde04a560409ce","creator":"hchiossi","file_name":"Chiossi_etal_2025_PNAS_data.zip","relation":"main_file","date_created":"2025-02-04T10:16:52Z","content_type":"application/zip","access_level":"open_access","file_size":769383201,"file_id":"18992","success":1,"date_updated":"2025-02-04T10:16:52Z"},{"file_name":"readme.txt","checksum":"50602931dcd33e4f009ed46af11335f3","creator":"hchiossi","date_created":"2025-02-04T10:18:33Z","relation":"main_file","access_level":"open_access","content_type":"text/plain","file_size":3215,"file_id":"18993","success":1,"date_updated":"2025-02-04T10:18:33Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-02-04T00:00:00Z","type":"research_data","oa":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"}],"month":"02","ddc":["570"],"corr_author":"1","status":"public","has_accepted_license":"1","date_created":"2025-02-04T10:36:18Z","abstract":[{"lang":"eng","text":"Research data for the article \"Learning reshapes the hippocampal representation hierarchy\" from Chiossi et al. (PNAS, 2025). The data includes hippocampal CA1 unit activity and behaviour tracking of 5 Long Evans rats during the learning of an associative memory task. Detailed information can be found in the 'readme.txt' file."}],"publisher":"Institute of Science and Technology Austria","OA_type":"gold","author":[{"last_name":"Chiossi","orcid":"0009-0004-2973-278X","first_name":"Heloisa","full_name":"Chiossi, Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-05-06T13:12:00Z","title":"Research data for the publication \"Learning reshapes the hippocampal representation hierarchy\"","acknowledgement":"Thanks to Rebecca Morse for performing one of the experiments under H.S.C.C. supervision and Jago Wallenschus for technical support, especially with maze design.","related_material":{"record":[{"relation":"used_in_publication","id":"19453","status":"public"}]},"file_date_updated":"2025-02-04T10:18:33Z","day":"04","contributor":[{"contributor_type":"researcher","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","orcid":"0000-0001-8849-6570","first_name":"Michele"},{"contributor_type":"supervisor","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","OA_place":"repository","_id":"18991","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"citation":{"short":"H.S.C. Chiossi, (2025).","chicago":"Chiossi, Heloisa S. C. “Research Data for the Publication ‘Learning Reshapes the Hippocampal Representation Hierarchy.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:18991\">https://doi.org/10.15479/AT:ISTA:18991</a>.","ista":"Chiossi HSC. 2025. Research data for the publication ‘Learning reshapes the hippocampal representation hierarchy’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18991\">10.15479/AT:ISTA:18991</a>.","ama":"Chiossi HSC. Research data for the publication “Learning reshapes the hippocampal representation hierarchy.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18991\">10.15479/AT:ISTA:18991</a>","apa":"Chiossi, H. S. C. (2025). Research data for the publication “Learning reshapes the hippocampal representation hierarchy.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18991\">https://doi.org/10.15479/AT:ISTA:18991</a>","mla":"Chiossi, Heloisa S. C. <i>Research Data for the Publication “Learning Reshapes the Hippocampal Representation Hierarchy.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18991\">10.15479/AT:ISTA:18991</a>.","ieee":"H. S. C. Chiossi, “Research data for the publication ‘Learning reshapes the hippocampal representation hierarchy.’” Institute of Science and Technology Austria, 2025."},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.15479/AT:ISTA:18991"},{"scopus_import":"1","department":[{"_id":"MaKw"}],"volume":348,"citation":{"chicago":"Cortés, Pedro P., Pankaj Kumar, Benjamin Moore, Patrice Ossona de Mendez, and Daniel A. Quiroz. “Subchromatic Numbers of Powers of Graphs with Excluded Minors.” <i>Discrete Mathematics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.disc.2024.114377\">https://doi.org/10.1016/j.disc.2024.114377</a>.","short":"P.P. Cortés, P. Kumar, B. Moore, P. Ossona de Mendez, D.A. Quiroz, Discrete Mathematics 348 (2025).","mla":"Cortés, Pedro P., et al. “Subchromatic Numbers of Powers of Graphs with Excluded Minors.” <i>Discrete Mathematics</i>, vol. 348, no. 4, 114377, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.disc.2024.114377\">10.1016/j.disc.2024.114377</a>.","ieee":"P. P. Cortés, P. Kumar, B. Moore, P. Ossona de Mendez, and D. A. Quiroz, “Subchromatic numbers of powers of graphs with excluded minors,” <i>Discrete Mathematics</i>, vol. 348, no. 4. Elsevier, 2025.","ama":"Cortés PP, Kumar P, Moore B, Ossona de Mendez P, Quiroz DA. Subchromatic numbers of powers of graphs with excluded minors. <i>Discrete Mathematics</i>. 2025;348(4). doi:<a href=\"https://doi.org/10.1016/j.disc.2024.114377\">10.1016/j.disc.2024.114377</a>","apa":"Cortés, P. P., Kumar, P., Moore, B., Ossona de Mendez, P., &#38; Quiroz, D. A. (2025). Subchromatic numbers of powers of graphs with excluded minors. <i>Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disc.2024.114377\">https://doi.org/10.1016/j.disc.2024.114377</a>","ista":"Cortés PP, Kumar P, Moore B, Ossona de Mendez P, Quiroz DA. 2025. Subchromatic numbers of powers of graphs with excluded minors. Discrete Mathematics. 348(4), 114377."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.disc.2024.114377","_id":"19002","oa_version":"Published Version","quality_controlled":"1","day":"01","publication_identifier":{"issn":["0012-365X"]},"article_type":"original","acknowledgement":"We thank an anonymous referee for pointing out an error in an earlier version of Theorem 3.1. We also thank an anonymous referee for pointing out numerous typos in an earlier version of the paper.","file_date_updated":"2025-05-05T12:56:12Z","arxiv":1,"OA_place":"publisher","external_id":{"arxiv":["2306.02195"],"isi":["001401656900001"]},"author":[{"full_name":"Cortés, Pedro P.","last_name":"Cortés","first_name":"Pedro P."},{"first_name":"Pankaj","last_name":"Kumar","full_name":"Kumar, Pankaj"},{"full_name":"Moore, Benjamin","id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","first_name":"Benjamin","last_name":"Moore"},{"full_name":"Ossona de Mendez, Patrice","first_name":"Patrice","last_name":"Ossona de Mendez"},{"last_name":"Quiroz","first_name":"Daniel A.","full_name":"Quiroz, Daniel A."}],"title":"Subchromatic numbers of powers of graphs with excluded minors","date_updated":"2025-09-30T10:25:15Z","date_created":"2025-02-05T06:51:08Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"A k-subcolouring of a graph G is a function f : V (G) → {0,...,k − 1} such that the set of\r\nvertices coloured i induce a disjoint union of cliques. The subchromatic number, χsub(G),\r\nis the minimum k such that G admits a k-subcolouring. Nešetril, ˇ Ossona de Mendez,\r\nPilipczuk, and Zhu (2020), recently raised the problem of finding tight upper bounds for\r\nχsub(G2) when G is planar. We show that χsub(G2) ≤ 43 when G is planar, improving\r\ntheir bound of 135. We give even better bounds when the planar graph G has larger girth.\r\nMoreover, we show that χsub(G3) ≤ 95, improving the previous bound of 364. For these\r\nwe adapt some recent techniques of Almulhim and Kierstead (2022), while also extending\r\nthe decompositions of triangulated planar graphs of Van den Heuvel, Ossona de Mendez,\r\nQuiroz, Rabinovich and Siebertz (2017), to planar graphs of arbitrary girth. Note that these\r\ndecompositions are the precursors of the graph product structure theorem of planar graphs.\r\nWe give improved bounds for χsub(Gp) for all p ≥ 2, whenever G has bounded treewidth,\r\nbounded simple treewidth, bounded genus, or excludes a clique or biclique as a minor.\r\nFor this we introduce a family of parameters which form a gradation between the strong\r\nand the weak colouring numbers. We give upper bounds for these parameters for graphs\r\ncoming from such classes.\r\nFinally, we give a 2-approximation algorithm for the subchromatic number of graphs\r\nhaving a layering in which each layer has bounded cliquewidth and this layering is\r\ncomputable in polynomial time (like the class of all dth powers of planar graphs, for fixed\r\nd). This algorithm works even if the power p and the graph G is unknown."}],"publisher":"Elsevier","OA_type":"hybrid","language":[{"iso":"eng"}],"intvolume":"       348","issue":"4","corr_author":"1","status":"public","month":"04","ddc":["510"],"publication":"Discrete Mathematics","isi":1,"type":"journal_article","oa":1,"publication_status":"published","year":"2025","article_processing_charge":"Yes (via OA deal)","file":[{"date_updated":"2025-05-05T12:56:12Z","file_id":"19657","success":1,"access_level":"open_access","content_type":"application/pdf","file_size":850988,"checksum":"6723cbb02b6aea0d05f37d167da00c03","creator":"dernst","file_name":"2025_DiscreteMath_Cortes.pdf","date_created":"2025-05-05T12:56:12Z","relation":"main_file"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-04-01T00:00:00Z","article_number":"114377"},{"_id":"19003","oa_version":"Published Version","quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"269B5B22-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 679-2018","name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED"},{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, The Plant Cell 37 (2025).","chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>The Plant Cell</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/plcell/koaf006\">https://doi.org/10.1093/plcell/koaf006</a>.","ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>The Plant Cell</i>. 2025;37(4). doi:<a href=\"https://doi.org/10.1093/plcell/koaf006\">10.1093/plcell/koaf006</a>","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (2025). Super-resolution expansion microscopy in plant roots. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koaf006\">https://doi.org/10.1093/plcell/koaf006</a>","ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. 2025. Super-resolution expansion microscopy in plant roots. The Plant Cell. 37(4), koaf006.","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>The Plant Cell</i>, vol. 37, no. 4. Oxford University Press, 2025.","mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>The Plant Cell</i>, vol. 37, no. 4, koaf006, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/plcell/koaf006\">10.1093/plcell/koaf006</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1093/plcell/koaf006","scopus_import":"1","department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"volume":37,"title":"Super-resolution expansion microscopy in plant roots","date_updated":"2026-06-10T08:30:19Z","author":[{"first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M","first_name":"Sven M","last_name":"Truckenbrodt"},{"last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"orcid":"0009-0002-5890-120X","last_name":"Inumella","first_name":"Syamala","id":"F8660870-D756-11E9-98C5-34DFE5697425","full_name":"Inumella, Syamala"},{"last_name":"Vistunou","first_name":"Vitali","full_name":"Vistunou, Vitali","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81"},{"first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","first_name":"Mojtaba"},{"last_name":"Agudelo Duenas","first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jakob","orcid":"0009-0000-7590-3501","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425","full_name":"Vorlaufer, Jakob"},{"full_name":"Jahr, Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","orcid":"0000-0003-0201-2315","first_name":"Wiebke"},{"last_name":"Randuch","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","external_id":{"pmid":["39792900"],"isi":["001462763100001"]},"day":"01","acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\nThis project has received funding from the European Research Council under the Horizon 2020 Framework Programme (grant agreement No 742985, J.F.). It has also received funding from the Horizon 2020 Framework Programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 (M.G.). S.T. has received funding as an ISTplus Fellow from the Horizon 2020 Framework Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from EMBO via a Long-Term Fellowship (grant number ALTF 679-2018). M.R.T. received funding from the Austrian Academy of Sciences with DOC fellowship no. 26137. The project has further received funding from the Austrian Science Fund, via grant DK W1232 (M.R.T., N.A.D., and J.G.D). W.J. received a postdoctoral fellowship from the Human Frontier Science Program (LT000557/2018). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","article_type":"original","related_material":{"record":[{"relation":"earlier_version","id":"18689","status":"public"},{"status":"public","relation":"research_data","id":"18837"}]},"file_date_updated":"2025-07-31T07:03:43Z","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"publication":"The Plant Cell","ddc":["580"],"corr_author":"1","month":"04","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"M-Shop"}],"issue":"4","language":[{"iso":"eng"}],"OA_type":"hybrid","intvolume":"        37","PlanS_conform":"1","abstract":[{"text":"Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens. ","lang":"eng"}],"date_created":"2025-02-05T06:52:06Z","pmid":1,"has_accepted_license":"1","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"koaf006","date_published":"2025-04-01T00:00:00Z","publication_status":"published","year":"2025","article_processing_charge":"Yes (via OA deal)","file":[{"success":1,"file_id":"20092","date_updated":"2025-07-31T07:03:43Z","relation":"main_file","date_created":"2025-07-31T07:03:43Z","checksum":"9d3f8218ff37a29f29c48a7bbe831bd3","creator":"dernst","file_name":"2025_PlantCell_Gallei.pdf","file_size":53904111,"content_type":"application/pdf","access_level":"open_access"}],"ec_funded":1,"type":"journal_article","isi":1,"oa":1},{"type":"conference","oa":1,"article_processing_charge":"No","year":"2025","publication_status":"published","file":[{"file_id":"21048","success":1,"date_updated":"2026-01-27T12:43:25Z","checksum":"c4b5a4a644228c6d1b0283e1368bce9e","file_name":"4356_Unifying_Causal_Represent (1).pdf","creator":"flocatel","date_created":"2026-01-27T12:43:25Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":877014}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-01-22T00:00:00Z","has_accepted_license":"1","date_created":"2025-02-05T09:23:25Z","abstract":[{"text":"Causal representation learning aims at recovering latent causal variables from high-dimensional observations to solve causal downstream tasks, such as predicting the effect of new interventions or more robust classification. A plethora of methods have been developed, each tackling carefully crafted problem settings that lead to different types of identifiability. The folklore is that these different settings are important, as they are often linked to different rungs of Pearl's causal hierarchy, although not all neatly fit. Our main contribution is to show that many existing causal representation learning approaches methodologically align the representation to known data symmetries. Identification of the variables is guided by equivalence classes across different \"data pockets\" that are not necessarily causal. This result suggests important implications, allowing us to unify many existing approaches in a single method that can mix and match different assumptions, including non-causal ones, based on the invariances relevant to our application. It also significantly benefits applicability, which we demonstrate by improving treatment effect estimation on real-world high-dimensional ecological data. Overall, this paper clarifies the role of causality assumptions in the discovery of causal variables and shifts the focus to preserving data symmetries.","lang":"eng"}],"publisher":"ICLR","language":[{"iso":"eng"}],"OA_type":"gold","corr_author":"1","publication":"13th International Conference on Learning Representations","ddc":["000"],"month":"01","status":"public","file_date_updated":"2026-01-27T12:43:25Z","acknowledgement":"We thank Jiaqi Zhang, Francesco Montagna, David Lopez-Paz, Kartik Ahuja, Thomas Kipf, Sara\r\nMagliacane, Julius von Kügelgen, Kun Zhang, and Bernhard Schölkopf for extremely helpful discussion. Riccardo Cadei was supported by a Google Research Scholar Award to Francesco Locatello. We acknowledge the Third Bellairs Workshop on Causal Representation Learning held at the Bellairs Research Institute, February 9/16, 2024, and a debate on the difference between interventions and counterfactuals in disentanglement and CRL that took place during Dhanya Sridhar’s lecture, which motivated us to significantly broaden the scope of the paper. We thank Dhanya and all participants of the workshop.","day":"22","arxiv":1,"conference":{"end_date":"2025-04-28","name":"ICLR: International Conference on Learning Representations","location":"Singapore","start_date":"2025-04-24"},"OA_place":"publisher","external_id":{"arxiv":["2409.02772"]},"author":[{"first_name":"Dingling","last_name":"Yao","id":"d3e02e50-48a8-11ee-8f62-c108061797fa","full_name":"Yao, Dingling"},{"last_name":"Rancati","first_name":"Dario","id":"feb58f2e-72ef-11ef-b75a-8f0894539cd0","full_name":"Rancati, Dario"},{"last_name":"Cadei","first_name":"Riccardo","full_name":"Cadei, Riccardo","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b"},{"last_name":"Fumero","first_name":"Marco","full_name":"Fumero, Marco","id":"1c1593eb-393f-11ef-bb8e-ab4f1e979650"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"}],"date_updated":"2026-02-09T05:52:14Z","title":"Unifying causal representation learning with the invariance principle","scopus_import":"1","department":[{"_id":"FrLo"}],"citation":{"chicago":"Yao, Dingling, Dario Rancati, Riccardo Cadei, Marco Fumero, and Francesco Locatello. “Unifying Causal Representation Learning with the Invariance Principle.” In <i>13th International Conference on Learning Representations</i>. ICLR, 2025.","short":"D. Yao, D. Rancati, R. Cadei, M. Fumero, F. Locatello, in:, 13th International Conference on Learning Representations, ICLR, 2025.","ieee":"D. Yao, D. Rancati, R. Cadei, M. Fumero, and F. Locatello, “Unifying causal representation learning with the invariance principle,” in <i>13th International Conference on Learning Representations</i>, Singapore, 2025.","mla":"Yao, Dingling, et al. “Unifying Causal Representation Learning with the Invariance Principle.” <i>13th International Conference on Learning Representations</i>, ICLR, 2025.","ista":"Yao D, Rancati D, Cadei R, Fumero M, Locatello F. 2025. Unifying causal representation learning with the invariance principle. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ama":"Yao D, Rancati D, Cadei R, Fumero M, Locatello F. Unifying causal representation learning with the invariance principle. In: <i>13th International Conference on Learning Representations</i>. ICLR; 2025.","apa":"Yao, D., Rancati, D., Cadei, R., Fumero, M., &#38; Locatello, F. (2025). Unifying causal representation learning with the invariance principle. In <i>13th International Conference on Learning Representations</i>. Singapore: ICLR."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"19010","oa_version":"Published Version","quality_controlled":"1"},{"status":"public","publication":"Nature Physics","ddc":["530"],"corr_author":"1","month":"03","publisher":"Springer Nature","pmid":1,"abstract":[{"text":"False vacuum decay—the transition from a metastable quantum state to a true vacuum state—plays an important role in quantum field theory and non-equilibrium phenomena such as phase transitions and dynamical metastability. The non-perturbative nature of false vacuum decay and the limited experimental access to this process make it challenging to study, leaving several open questions regarding how true vacuum bubbles form, move and interact. Here we observe quantized bubble formation in real time, a key feature of false vacuum decay dynamics, using a quantum annealer with 5,564 superconducting flux qubits. We develop an effective model that captures both initial bubble creation and subsequent interactions, and remains accurate under dissipation. The annealer reveals coherent scaling laws in the driven many-body dynamics for more than 1,000 intrinsic qubit time units. This work provides a method for investigating false vacuum dynamics of large quantum systems in quantum annealers.","lang":"eng"}],"date_created":"2025-02-06T10:07:13Z","has_accepted_license":"1","intvolume":"        21","PlanS_conform":"1","OA_type":"hybrid","language":[{"iso":"eng"}],"file":[{"file_id":"20127","success":1,"date_updated":"2025-08-05T11:56:53Z","creator":"dernst","checksum":"b005ccf7448fee29c187cbc9b1944893","file_name":"2025_NaturePhysics_Vodeb.pdf","relation":"main_file","date_created":"2025-08-05T11:56:53Z","content_type":"application/pdf","access_level":"open_access","file_size":2252107}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","year":"2025","date_published":"2025-03-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"386-392","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","quality_controlled":"1","oa_version":"Published Version","_id":"19012","volume":21,"department":[{"_id":"MaSe"}],"scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41567-024-02765-w","citation":{"chicago":"Vodeb, Jaka, Jean-Yves Marc Desaules, Andrew Hallam, Andrea Rava, Gregor Humar, Dennis Willsch, Fengping Jin, Madita Willsch, Kristel Michielsen, and Zlatko Papić. “Stirring the False Vacuum via Interacting Quantized Bubbles on a 5,564-Qubit Quantum Annealer.” <i>Nature Physics</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41567-024-02765-w\">https://doi.org/10.1038/s41567-024-02765-w</a>.","short":"J. Vodeb, J.-Y.M. Desaules, A. Hallam, A. Rava, G. Humar, D. Willsch, F. Jin, M. Willsch, K. Michielsen, Z. Papić, Nature Physics 21 (2025) 386–392.","ieee":"J. Vodeb <i>et al.</i>, “Stirring the false vacuum via interacting quantized bubbles on a 5,564-qubit quantum annealer,” <i>Nature Physics</i>, vol. 21. Springer Nature, pp. 386–392, 2025.","mla":"Vodeb, Jaka, et al. “Stirring the False Vacuum via Interacting Quantized Bubbles on a 5,564-Qubit Quantum Annealer.” <i>Nature Physics</i>, vol. 21, Springer Nature, 2025, pp. 386–92, doi:<a href=\"https://doi.org/10.1038/s41567-024-02765-w\">10.1038/s41567-024-02765-w</a>.","apa":"Vodeb, J., Desaules, J.-Y. M., Hallam, A., Rava, A., Humar, G., Willsch, D., … Papić, Z. (2025). Stirring the false vacuum via interacting quantized bubbles on a 5,564-qubit quantum annealer. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02765-w\">https://doi.org/10.1038/s41567-024-02765-w</a>","ista":"Vodeb J, Desaules J-YM, Hallam A, Rava A, Humar G, Willsch D, Jin F, Willsch M, Michielsen K, Papić Z. 2025. Stirring the false vacuum via interacting quantized bubbles on a 5,564-qubit quantum annealer. Nature Physics. 21, 386–392.","ama":"Vodeb J, Desaules J-YM, Hallam A, et al. Stirring the false vacuum via interacting quantized bubbles on a 5,564-qubit quantum annealer. <i>Nature Physics</i>. 2025;21:386-392. doi:<a href=\"https://doi.org/10.1038/s41567-024-02765-w\">10.1038/s41567-024-02765-w</a>"},"project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"author":[{"first_name":"Jaka","last_name":"Vodeb","full_name":"Vodeb, Jaka"},{"full_name":"Desaules, Jean-Yves Marc","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","last_name":"Desaules","orcid":"0000-0002-3749-6375","first_name":"Jean-Yves Marc"},{"full_name":"Hallam, Andrew","first_name":"Andrew","last_name":"Hallam"},{"full_name":"Rava, Andrea","last_name":"Rava","first_name":"Andrea"},{"full_name":"Humar, Gregor","last_name":"Humar","first_name":"Gregor"},{"last_name":"Willsch","first_name":"Dennis","full_name":"Willsch, Dennis"},{"full_name":"Jin, Fengping","last_name":"Jin","first_name":"Fengping"},{"full_name":"Willsch, Madita","last_name":"Willsch","first_name":"Madita"},{"full_name":"Michielsen, Kristel","last_name":"Michielsen","first_name":"Kristel"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"title":"Stirring the false vacuum via interacting quantized bubbles on a 5,564-qubit quantum annealer","date_updated":"2025-09-30T10:29:15Z","arxiv":1,"day":"01","file_date_updated":"2025-08-05T11:56:53Z","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"article_type":"original","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/dancing-bubbles-model-a-cosmic-disaster/","description":"News on ISTA Website"}]},"acknowledgement":"J.V., D.W. and M.W. acknowledge support from the project Jülich UNified Infrastructure for Quantum computing (JUNIQ) that has received funding from the German Federal Ministry of Education and Research (BMBF) and the Ministry of Culture and Science of the State of North Rhine-Westphalia. A.R. acknowledges support from the project HPCQS (101018180) of the European High-Performance Computing Joint Undertaking (EuroHPC JU). J.-Y.D., A.H. and Z.P. acknowledge support from the Leverhulme Trust Research Leadership Award RL-2019-015 and EPSRC grant nos. EP/R513258/1 and EP/W026848/1. J.-Y.D. acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no.101034413. This research was supported in part by grant no. NSF PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP). Computational portions of this research work were carried out on ARC3 and ARC4, part of the high-performance computing facilities at the University of Leeds. G.H. acknowledges financial support from ARIS, P1-0040 Nonequilibrium Quantum System Dynamics. We gratefully acknowledge the Jülich Supercomputing Centre (https://www.fz-juelich.de/en/ias/jsc) for funding this project by providing computing time on the D-Wave Advantage System JUPSI through JUNIQ. We acknowledge helpful theoretical discussions with G. Lagnese and the quantum-simulation-related discussions with D-Wave’s experimental team, particularly A. MacDonald, G. Poulin-Lamarre, A. Daian and A. Berkley. We also thank V. Goliber and A. Mason for patiently organizing and mediating the corresponding meetings that enabled the discussions with D-Wave’s team. J.V., A.R., D.W., F.J., M.W. and K.M. gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC).","external_id":{"arxiv":["2406.14718"],"pmid":["40093970"],"isi":["001412684400001"]},"OA_place":"publisher"},{"date_created":"2025-02-09T23:01:50Z","pmid":1,"abstract":[{"lang":"eng","text":"When microplastics (MPs) enter water bodies, they undergo various transport processes, including sedimentation, which can be influenced by factors such as particle size, density, and interactions with other particles. Surface waters contain suspended natural particles (e.g., clay and silt), which may impact MP settling rates. Here, we investigated how the presence of suspended sediments (SS) influenced the deposition patterns and rates of MPs in turbid waters. We systematically analyzed the settling velocities of particles, including different MP sizes and SS concentrations, in a plexiglass column with a camera array. For each experimental variant, we collected data on thousands of individual MPs, strengthening the statistical analysis of the particles’ velocities. Simultaneous measurements of the SS flow and MPs trajectories revealed that the SS induced complex flow patterns, with MPs spending more time in downwelling flow regions, thereby accelerating MPs sedimentation. This effect was more pronounced when SS were aggregated. Additionally, we found that smaller MP fragments were more affected by the fluctuations than spheres or larger fragments. Collectively, our results provide valuable data for future MP fate models and help to understand the sedimentation processes of MPs in natural waters, which is crucial for assessing their environmental transport and impact."}],"publisher":"American Chemical Society","language":[{"iso":"eng"}],"OA_type":"closed access","intvolume":"        59","issue":"4","month":"01","publication":"Environmental Science and Technology","status":"public","page":"2257-2265","isi":1,"type":"journal_article","article_processing_charge":"No","year":"2025","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-01-27T00:00:00Z","department":[{"_id":"BjHo"}],"scopus_import":"1","volume":59,"citation":{"mla":"Parrella, Francesco, et al. “Microplastics Settling in Turbid Water: Impacts of Sediments-Induced Flow Patterns on Particle Deposition Rates.” <i>Environmental Science and Technology</i>, vol. 59, no. 4, American Chemical Society, 2025, pp. 2257–65, doi:<a href=\"https://doi.org/10.1021/acs.est.4c10551\">10.1021/acs.est.4c10551</a>.","ieee":"F. Parrella, S. Brizzolara, M. Holzner, and D. M. Mitrano, “Microplastics settling in turbid water: Impacts of sediments-induced flow patterns on particle deposition rates,” <i>Environmental Science and Technology</i>, vol. 59, no. 4. American Chemical Society, pp. 2257–2265, 2025.","ista":"Parrella F, Brizzolara S, Holzner M, Mitrano DM. 2025. Microplastics settling in turbid water: Impacts of sediments-induced flow patterns on particle deposition rates. Environmental Science and Technology. 59(4), 2257–2265.","ama":"Parrella F, Brizzolara S, Holzner M, Mitrano DM. Microplastics settling in turbid water: Impacts of sediments-induced flow patterns on particle deposition rates. <i>Environmental Science and Technology</i>. 2025;59(4):2257-2265. doi:<a href=\"https://doi.org/10.1021/acs.est.4c10551\">10.1021/acs.est.4c10551</a>","apa":"Parrella, F., Brizzolara, S., Holzner, M., &#38; Mitrano, D. M. (2025). Microplastics settling in turbid water: Impacts of sediments-induced flow patterns on particle deposition rates. <i>Environmental Science and Technology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.est.4c10551\">https://doi.org/10.1021/acs.est.4c10551</a>","chicago":"Parrella, Francesco, Stefano Brizzolara, Markus Holzner, and Denise M. Mitrano. “Microplastics Settling in Turbid Water: Impacts of Sediments-Induced Flow Patterns on Particle Deposition Rates.” <i>Environmental Science and Technology</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acs.est.4c10551\">https://doi.org/10.1021/acs.est.4c10551</a>.","short":"F. Parrella, S. Brizzolara, M. Holzner, D.M. Mitrano, Environmental Science and Technology 59 (2025) 2257–2265."},"doi":"10.1021/acs.est.4c10551","_id":"19015","oa_version":"None","quality_controlled":"1","acknowledgement":"F.P. and D.M.M. were funded through the Swiss National Science Foundation (grant number PCEFP2_186856).","article_type":"original","publication_identifier":{"issn":["0013-936X"],"eissn":["1520-5851"]},"day":"27","external_id":{"isi":["001406914100001"],"pmid":["39868426"]},"author":[{"first_name":"Francesco","last_name":"Parrella","full_name":"Parrella, Francesco"},{"last_name":"Brizzolara","first_name":"Stefano","full_name":"Brizzolara, Stefano","id":"4bbe33b8-c59a-11ee-a1af-fa33d1ac42c4"},{"last_name":"Holzner","first_name":"Markus","full_name":"Holzner, Markus"},{"full_name":"Mitrano, Denise M.","first_name":"Denise M.","last_name":"Mitrano"}],"date_updated":"2025-09-30T10:27:26Z","title":"Microplastics settling in turbid water: Impacts of sediments-induced flow patterns on particle deposition rates"},{"publication_status":"epub_ahead","article_processing_charge":"No","year":"2025","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-01-06T00:00:00Z","page":"1-43","type":"journal_article","isi":1,"oa":1,"status":"public","ddc":["500"],"month":"01","publication":"Canadian Journal of Mathematics","has_accepted_license":"1","abstract":[{"text":"Let f(r)(n;s,k) denote the maximum number of edges in an n-vertex r-uniform hypergraph containing no subgraph with k edges and at most s vertices. Brown, Erdős and Sós [New directions in the theory of graphs (Proc. Third Ann Arbor Conf., Univ. Michigan 1971), pp. 53--63, Academic Press 1973] conjectured that the limit limn→∞n−2f(3)(n;k+2,k) exists for all k. The value of the limit was previously determined for k=2 in the original paper of Brown, Erdős and Sós, for k=3 by Glock [Bull. Lond. Math. Soc. 51 (2019) 230--236] and for k=4 by Glock, Joos, Kim, Kühn, Lichev and Pikhurko [arXiv:2209.14177, accepted by Proc. Amer. Math. Soc.] while Delcourt and Postle [arXiv:2210.01105, accepted by Proc. Amer. Math. Soc.] proved the conjecture (without determining the limiting value).\r\nIn this paper, we determine the value of the limit in the Brown-Erdős-Sós Problem for k∈{5,6,7}. More generally, we obtain the value of limn→∞n−2f(r)(n;rk−2k+2,k) for all r≥3 and k∈{5,6,7}. In addition, by combining these new values with recent results of Bennett, Cushman and Dudek [arXiv:2309.00182] we obtain new asymptotic values for several generalised Ramsey numbers.","lang":"eng"}],"date_created":"2025-02-10T08:39:46Z","publisher":"Cambridge University Press","language":[{"iso":"eng"}],"OA_type":"hybrid","author":[{"last_name":"Glock","first_name":"Stefan","full_name":"Glock, Stefan"},{"full_name":"Kim, Jaehoon","last_name":"Kim","first_name":"Jaehoon"},{"first_name":"Lyuben","last_name":"Lichev","full_name":"Lichev, Lyuben","id":"9aa8388e-d003-11ee-8458-c4c1d7447977"},{"full_name":"Pikhurko, Oleg","last_name":"Pikhurko","first_name":"Oleg"},{"full_name":"Sun, Shumin","first_name":"Shumin","last_name":"Sun"}],"title":"On the (k + 2, k)-problem of Brown, Erdős, and Sós for k = 5,6,7","date_updated":"2025-09-30T10:28:07Z","day":"06","publication_identifier":{"issn":["0008-414X"],"eissn":["1496-4279"]},"article_type":"original","arxiv":1,"OA_place":"publisher","external_id":{"isi":["001416788600001"],"arxiv":["2403.04474"]},"_id":"19017","quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.4153/s0008414x25000021"}],"scopus_import":"1","department":[{"_id":"MaKw"}],"doi":"10.4153/s0008414x25000021","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Glock, Stefan, et al. “On the (k + 2, k)-Problem of Brown, Erdős, and Sós for k = 5,6,7.” <i>Canadian Journal of Mathematics</i>, Cambridge University Press, 2025, pp. 1–43, doi:<a href=\"https://doi.org/10.4153/s0008414x25000021\">10.4153/s0008414x25000021</a>.","ieee":"S. Glock, J. Kim, L. Lichev, O. Pikhurko, and S. Sun, “On the (k + 2, k)-problem of Brown, Erdős, and Sós for k = 5,6,7,” <i>Canadian Journal of Mathematics</i>. Cambridge University Press, pp. 1–43, 2025.","ama":"Glock S, Kim J, Lichev L, Pikhurko O, Sun S. On the (k + 2, k)-problem of Brown, Erdős, and Sós for k = 5,6,7. <i>Canadian Journal of Mathematics</i>. 2025:1-43. doi:<a href=\"https://doi.org/10.4153/s0008414x25000021\">10.4153/s0008414x25000021</a>","ista":"Glock S, Kim J, Lichev L, Pikhurko O, Sun S. 2025. On the (k + 2, k)-problem of Brown, Erdős, and Sós for k = 5,6,7. Canadian Journal of Mathematics., 1–43.","apa":"Glock, S., Kim, J., Lichev, L., Pikhurko, O., &#38; Sun, S. (2025). On the (k + 2, k)-problem of Brown, Erdős, and Sós for k = 5,6,7. <i>Canadian Journal of Mathematics</i>. Cambridge University Press. <a href=\"https://doi.org/10.4153/s0008414x25000021\">https://doi.org/10.4153/s0008414x25000021</a>","chicago":"Glock, Stefan, Jaehoon Kim, Lyuben Lichev, Oleg Pikhurko, and Shumin Sun. “On the (k + 2, k)-Problem of Brown, Erdős, and Sós for k = 5,6,7.” <i>Canadian Journal of Mathematics</i>. Cambridge University Press, 2025. <a href=\"https://doi.org/10.4153/s0008414x25000021\">https://doi.org/10.4153/s0008414x25000021</a>.","short":"S. Glock, J. Kim, L. Lichev, O. Pikhurko, S. Sun, Canadian Journal of Mathematics (2025) 1–43."}},{"author":[{"last_name":"Burova","first_name":"Sofiya","full_name":"Burova, Sofiya"},{"full_name":"Lichev, Lyuben","id":"9aa8388e-d003-11ee-8458-c4c1d7447977","first_name":"Lyuben","last_name":"Lichev"}],"date_updated":"2025-09-30T10:28:42Z","title":"The semi-random tree process","acknowledgement":"We are grateful to Dieter Mitsche for related discussions and to several anonymous referees for multiple useful comments.","article_type":"original","publication_identifier":{"issn":["0195-6698"]},"day":"01","arxiv":1,"OA_place":"repository","external_id":{"arxiv":["2204.07376 "],"isi":["001420659400001"]},"_id":"19018","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2204.07376"}],"quality_controlled":"1","oa_version":"Preprint","department":[{"_id":"MaKw"}],"scopus_import":"1","volume":126,"doi":"10.1016/j.ejc.2025.104120","citation":{"short":"S. Burova, L. Lichev, European Journal of Combinatorics 126 (2025).","chicago":"Burova, Sofiya, and Lyuben Lichev. “The Semi-Random Tree Process.” <i>European Journal of Combinatorics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.ejc.2025.104120\">https://doi.org/10.1016/j.ejc.2025.104120</a>.","ista":"Burova S, Lichev L. 2025. The semi-random tree process. European Journal of Combinatorics. 126, 104120.","ama":"Burova S, Lichev L. The semi-random tree process. <i>European Journal of Combinatorics</i>. 2025;126. doi:<a href=\"https://doi.org/10.1016/j.ejc.2025.104120\">10.1016/j.ejc.2025.104120</a>","apa":"Burova, S., &#38; Lichev, L. (2025). The semi-random tree process. <i>European Journal of Combinatorics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejc.2025.104120\">https://doi.org/10.1016/j.ejc.2025.104120</a>","ieee":"S. Burova and L. Lichev, “The semi-random tree process,” <i>European Journal of Combinatorics</i>, vol. 126. Elsevier, 2025.","mla":"Burova, Sofiya, and Lyuben Lichev. “The Semi-Random Tree Process.” <i>European Journal of Combinatorics</i>, vol. 126, 104120, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.ejc.2025.104120\">10.1016/j.ejc.2025.104120</a>."},"article_processing_charge":"No","year":"2025","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-05-01T00:00:00Z","article_number":"104120","type":"journal_article","isi":1,"oa":1,"month":"05","status":"public","publication":"European Journal of Combinatorics","date_created":"2025-02-10T09:00:53Z","abstract":[{"lang":"eng","text":"The online semi-random graph process is a one-player game which starts with the empty graph on n vertices. At every round, a player (called Builder) is presented with a vertex v chosen uniformly at random and independently from previous rounds, and constructs an edge of their choice that is incident to v. Inspired by recent advances on the semi-random graph process, we define a family of generalized online semi-random models.\r\nWe analyse a particular instance that shares similar features with the original semi-random graph process and determine the hitting times of the classical graph properties minimum degree k,k-connectivity, containment of a perfect matching, a Hamiltonian cycle and an \r\nH-factor for a fixed graph H possessing an additional tree-like property. Along the way, we derive a few consequences of the famous Aldous-Broder algorithm that may be of independent interest."}],"publisher":"Elsevier","OA_type":"green","language":[{"iso":"eng"}],"intvolume":"       126"},{"article_number":"14","date_published":"2025-01-25T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":1170930,"checksum":"c32511f2d09e6c164116793e784944b8","creator":"dernst","file_name":"2025_ClinicalEpigenetics_Bernabeu.pdf","date_created":"2025-02-17T08:44:23Z","relation":"main_file","date_updated":"2025-02-17T08:44:23Z","success":1,"file_id":"19030"}],"publication_status":"published","article_processing_charge":"Yes","year":"2025","oa":1,"type":"journal_article","isi":1,"ddc":["570"],"publication":"Clinical Epigenetics","month":"01","status":"public","intvolume":"        17","OA_type":"gold","language":[{"iso":"eng"}],"publisher":"Springer Nature","pmid":1,"date_created":"2025-02-16T23:02:33Z","abstract":[{"text":"Alcohol consumption is an important risk factor for multiple diseases. It is typically assessed via self-report, which is open to measurement error through recall bias. Instead, molecular data such as blood-based DNA methylation (DNAm) could be used to derive a more objective measure of alcohol consumption by incorporating information from cytosine-phosphate-guanine (CpG) sites known to be linked to the trait. Here, we explore the epigenetic architecture of self-reported weekly units of alcohol consumption in the Generation Scotland study. We first create a blood-based epigenetic score (EpiScore) of alcohol consumption using elastic net penalized linear regression. We explore the effect of pre-filtering for CpG features ahead of elastic net, as well as differential patterns by sex and by units consumed in the last week relative to an average week. The final EpiScore was trained on 16,717 individuals and tested in four external cohorts: the Lothian Birth Cohorts (LBC) of 1921 and 1936, the Sister Study, and the Avon Longitudinal Study of Parents and Children (total N across studies > 10,000). The maximum Pearson correlation between the EpiScore and self-reported alcohol consumption within cohort ranged from 0.41 to 0.53. In LBC1936, higher EpiScore levels had significant associations with poorer global brain imaging metrics, whereas self-reported alcohol consumption did not. Finally, we identified two novel CpG loci via a Bayesian penalized regression epigenome-wide association study of alcohol consumption. Together, these findings show how DNAm can objectively characterize patterns of alcohol consumption that associate with brain health, unlike self-reported estimates.","lang":"eng"}],"has_accepted_license":"1","title":"Blood-based epigenome-wide association study and prediction of alcohol consumption","date_updated":"2025-09-30T10:31:08Z","author":[{"first_name":"Elena","last_name":"Bernabeu","full_name":"Bernabeu, Elena"},{"last_name":"Chybowska","first_name":"Aleksandra D.","full_name":"Chybowska, Aleksandra D."},{"full_name":"Kresovich, Jacob K.","last_name":"Kresovich","first_name":"Jacob K."},{"full_name":"Suderman, Matthew","first_name":"Matthew","last_name":"Suderman"},{"full_name":"Mccartney, Daniel L.","first_name":"Daniel L.","last_name":"Mccartney"},{"first_name":"Robert F.","last_name":"Hillary","full_name":"Hillary, Robert F."},{"full_name":"Corley, Janie","last_name":"Corley","first_name":"Janie"},{"full_name":"Valdés-Hernández, Maria Del C.","first_name":"Maria Del C.","last_name":"Valdés-Hernández"},{"first_name":"Susana Muñoz","last_name":"Maniega","full_name":"Maniega, Susana Muñoz"},{"last_name":"Bastin","first_name":"Mark E.","full_name":"Bastin, Mark E."},{"full_name":"Wardlaw, Joanna M.","first_name":"Joanna M.","last_name":"Wardlaw"},{"first_name":"Zongli","last_name":"Xu","full_name":"Xu, Zongli"},{"full_name":"Sandler, Dale P.","last_name":"Sandler","first_name":"Dale P."},{"last_name":"Campbell","first_name":"Archie","full_name":"Campbell, Archie"},{"last_name":"Harris","first_name":"Sarah E.","full_name":"Harris, Sarah E."},{"full_name":"Mcintosh, Andrew M.","first_name":"Andrew M.","last_name":"Mcintosh"},{"last_name":"Taylor","first_name":"Jack A.","full_name":"Taylor, Jack A."},{"first_name":"Paul","last_name":"Yousefi","full_name":"Yousefi, Paul"},{"first_name":"Simon R.","last_name":"Cox","full_name":"Cox, Simon R."},{"full_name":"Evans, Kathryn L.","last_name":"Evans","first_name":"Kathryn L."},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","first_name":"Matthew Richard"},{"full_name":"Vallejos, Catalina A.","first_name":"Catalina A.","last_name":"Vallejos"},{"full_name":"Marioni, Riccardo E.","last_name":"Marioni","first_name":"Riccardo E."}],"external_id":{"pmid":["39863868"],"isi":["001406495600001"]},"OA_place":"publisher","DOAJ_listed":"1","day":"25","file_date_updated":"2025-02-17T08:44:23Z","article_type":"original","acknowledgement":"Generation Scotland: Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and DNA methylation profiling of the Generation Scotland samples were carried out by the Genetics Core Laboratory at the Edinburgh Clinical Research Facility, Edinburgh, Scotland, and were funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award STratifying Resilience and Depression Longitudinally (STRADL; Reference 104036/Z/14/Z) and 220857/Z/20/Z. The DNA methylation data assayed for Generation Scotland were partially funded by a 2018 NARSAD Young Investigator Grant from the Brain & Behavior Research Foundation (Ref: 27404; awardee: Dr David M Howard) and by a JMAS SIM fellowship from the Royal College of Physicians of Edinburgh (Awardee: Dr Heather C Whalley). Lothian Birth Cohorts: We thank the LBC1921 and LBC1936 participants and team members who contributed to these studies. The LBC1921 was supported by the UK’s Biotechnology and Biological Sciences Research Council (BBSRC), The Royal Society, and The Chief Scientist Office of the Scottish Government. The LBC1936 is supported by the BBSRC, and the Economic and Social Research Council [BB/W008793/1] (which supports S.E.H.), Age UK (Disconnected Mind project), the Milton Damerel Trust, the Medical Research Council (MR/M01311/1), and the University of Edinburgh. Methylation typing of LBC1936 was supported by the Centre for Cognitive Ageing and Cognitive Epidemiology (Pilot Fund award), Age UK, The Wellcome Trust Institutional Strategic Support Fund, The University of Edinburgh, and The University of Queensland. Genotyping was funded by the BBSRC (BB/F019394/1). S.R.C. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant Number 221890/Z/20/Z). ALSPAC: The UK Medical Research Council and Wellcome (Grant ref: 217065/Z/19/Z) and the University of Bristol provide core support for ALSPAC. This publication is the work of the authors and Matthew Suderman will serve as guarantors for the contents of this paper. A comprehensive list of grants funding is available on the ALSPAC website (http://www.bristol.ac.uk/alspac/external/documents/grant-acknowledgements.pdf). Funding for ALSPAC DNAm measurements was supported by the Wellcome (102215/2/13/2); the University of Bristol; the UK Economic and Social Research Council (ES/N000498/1); the UK Medical Research Council (MC_UU_12013/1, MC_UU_12013/2); and the John Templeton Foundation (60828). MS and PY work within the MRC Integrative Epidemiology Unit at the University of Bristol, which is supported by the Medical Research Council (MC_UU_00011/5). Sister Study: This research was supported by the Intramural Research Program of the National Institutes of Health (Z01-ES049033, Z01-ES049032, Z01-ES044005). A.D.C. was supported by a Medical Research Council PhD Studentship in Precision Medicine with funding from the Medical Research Council Doctoral Training Program and the University of Edinburgh College of Medicine and Veterinary Medicine. R.F.H is supported by an MRC IEU Fellowship. M.R.R. was funded by Swiss National Science Foundation Eccellenza Grant PCEGP3-181181 and by core funding from the Institute of Science and Technology Austria. E.B. and R.E.M. are supported by Alzheimer’s Society major project grant AS-PG-19b-010. This research was funded in whole, or in part, by the Wellcome Trust (104036/Z/14/Z, 220857/Z/20/Z, and 221890/Z/20/Z). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","publication_identifier":{"eissn":["1868-7083"],"issn":["1868-7075"]},"oa_version":"Published Version","quality_controlled":"1","_id":"19023","citation":{"short":"E. Bernabeu, A.D. Chybowska, J.K. Kresovich, M. Suderman, D.L. Mccartney, R.F. Hillary, J. Corley, M.D.C. Valdés-Hernández, S.M. Maniega, M.E. Bastin, J.M. Wardlaw, Z. Xu, D.P. Sandler, A. Campbell, S.E. Harris, A.M. Mcintosh, J.A. Taylor, P. Yousefi, S.R. Cox, K.L. Evans, M.R. Robinson, C.A. Vallejos, R.E. Marioni, Clinical Epigenetics 17 (2025).","chicago":"Bernabeu, Elena, Aleksandra D. Chybowska, Jacob K. Kresovich, Matthew Suderman, Daniel L. Mccartney, Robert F. Hillary, Janie Corley, et al. “Blood-Based Epigenome-Wide Association Study and Prediction of Alcohol Consumption.” <i>Clinical Epigenetics</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1186/s13148-025-01818-y\">https://doi.org/10.1186/s13148-025-01818-y</a>.","apa":"Bernabeu, E., Chybowska, A. D., Kresovich, J. K., Suderman, M., Mccartney, D. L., Hillary, R. F., … Marioni, R. E. (2025). Blood-based epigenome-wide association study and prediction of alcohol consumption. <i>Clinical Epigenetics</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13148-025-01818-y\">https://doi.org/10.1186/s13148-025-01818-y</a>","ista":"Bernabeu E, Chybowska AD, Kresovich JK, Suderman M, Mccartney DL, Hillary RF, Corley J, Valdés-Hernández MDC, Maniega SM, Bastin ME, Wardlaw JM, Xu Z, Sandler DP, Campbell A, Harris SE, Mcintosh AM, Taylor JA, Yousefi P, Cox SR, Evans KL, Robinson MR, Vallejos CA, Marioni RE. 2025. Blood-based epigenome-wide association study and prediction of alcohol consumption. Clinical Epigenetics. 17, 14.","ama":"Bernabeu E, Chybowska AD, Kresovich JK, et al. Blood-based epigenome-wide association study and prediction of alcohol consumption. <i>Clinical Epigenetics</i>. 2025;17. doi:<a href=\"https://doi.org/10.1186/s13148-025-01818-y\">10.1186/s13148-025-01818-y</a>","mla":"Bernabeu, Elena, et al. “Blood-Based Epigenome-Wide Association Study and Prediction of Alcohol Consumption.” <i>Clinical Epigenetics</i>, vol. 17, 14, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1186/s13148-025-01818-y\">10.1186/s13148-025-01818-y</a>.","ieee":"E. Bernabeu <i>et al.</i>, “Blood-based epigenome-wide association study and prediction of alcohol consumption,” <i>Clinical Epigenetics</i>, vol. 17. Springer Nature, 2025."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1186/s13148-025-01818-y","project":[{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk"}],"volume":17,"department":[{"_id":"MaRo"}],"scopus_import":"1"},{"page":"1135-1146","type":"journal_article","isi":1,"oa":1,"year":"2025","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","file":[{"date_updated":"2025-08-05T12:07:24Z","file_id":"20128","success":1,"access_level":"open_access","content_type":"application/pdf","file_size":4212615,"creator":"dernst","checksum":"a52b72a243a717d85c348f53898ad934","file_name":"2025_JourColloidScie_Scacchi.pdf","date_created":"2025-08-05T12:07:24Z","relation":"main_file"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-05-15T00:00:00Z","has_accepted_license":"1","date_created":"2025-02-16T23:02:33Z","abstract":[{"lang":"eng","text":"Aqueous two-phase systems (ATPSs), phase-separating solutions of water soluble but mutually immiscible molecular species, offer fascinating prospects for selective partitioning, purification, and extraction. Here, we formulate a general Brownian dynamics based coarse-grained simulation model for an ATPS of two water soluble but mutually immiscible polymer species. Including additional solute species into the model is straightforward, which enables capturing the assembly and partitioning response of, e.g., nanoparticles (NPs), additional macromolecular species, or impurities in the ATPS. We demonstrate that the simulation model captures satisfactorily the phase separation, partitioning, and interfacial properties of an actual ATPS using a model ATPS in which a polymer mixture of dextran and polyethylene glycol (PEG) phase separates, and magnetic NPs selectively partition into one of the two polymeric phases. Phase separation and NP partitioning are characterized both via the computational model and experimentally, under different conditions. The simulation model captures the trends observed in the experimental system and quantitatively links the partitioning behavior to the component species interactions. Finally, the simulation model reveals that the ATPS interface fluctuations in systems with magnetic NPs as a partitioned species can be controlled by the magnetic field at length scales much smaller than those probed experimentally to date."}],"pmid":1,"publisher":"Elsevier","OA_type":"hybrid","language":[{"iso":"eng"}],"PlanS_conform":"1","intvolume":"       686","ddc":["540"],"publication":"Journal of Colloid and Interface Science","month":"05","status":"public","file_date_updated":"2025-08-05T12:07:24Z","acknowledgement":"This work was supported by the Swiss National Science Foundation under the project no. P500PT_206916 (A.S.) and the Academy of Finland through its Centres of Excellence Programs (2022-2029, LIBER) under projects no. 346111 and 364205 (M.S.) and 346112 and 364206 (J.T.). MPH was supported by the National Science Foundation through the Princeton University (PCCM) Materials Research Science and Engineering Center DMR-2011750. A.S. warmly thanks Bob Evans for extensive scientific discussions and for his hospitality during the research visit in Bristol. Computational resources by CSC IT Centre for Finland, the Aalto Science-IT project, and RAMI – RawMatters Finland Infrastructure are also gratefully acknowledged.","related_material":{"record":[{"relation":"research_data","id":"19033","status":"public"}]},"publication_identifier":{"issnl":["0021-9797"],"issn":["0021-9797"],"eissn":["1095-7103"]},"article_type":"original","day":"15","arxiv":1,"OA_place":"publisher","external_id":{"arxiv":["2311.16906"],"pmid":["39933351"],"isi":["001426125300001"]},"author":[{"full_name":"Scacchi, Alberto","first_name":"Alberto","last_name":"Scacchi"},{"last_name":"Rigoni","first_name":"Carlo","full_name":"Rigoni, Carlo","id":"c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0"},{"first_name":"Mikko","last_name":"Haataja","full_name":"Haataja, Mikko"},{"last_name":"Timonen","first_name":"Jaakko V.I.","full_name":"Timonen, Jaakko V.I."},{"last_name":"Sammalkorpi","first_name":"Maria","full_name":"Sammalkorpi, Maria"}],"date_updated":"2025-09-30T10:31:45Z","title":"A coarse-grained model for aqueous two-phase systems: Application to ferrofluids","department":[{"_id":"RaKl"}],"scopus_import":"1","volume":686,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"A. Scacchi, C. Rigoni, M. Haataja, J.V.I. Timonen, M. Sammalkorpi, Journal of Colloid and Interface Science 686 (2025) 1135–1146.","chicago":"Scacchi, Alberto, Carlo Rigoni, Mikko Haataja, Jaakko V.I. Timonen, and Maria Sammalkorpi. “A Coarse-Grained Model for Aqueous Two-Phase Systems: Application to Ferrofluids.” <i>Journal of Colloid and Interface Science</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jcis.2025.01.256\">https://doi.org/10.1016/j.jcis.2025.01.256</a>.","ista":"Scacchi A, Rigoni C, Haataja M, Timonen JVI, Sammalkorpi M. 2025. A coarse-grained model for aqueous two-phase systems: Application to ferrofluids. Journal of Colloid and Interface Science. 686, 1135–1146.","apa":"Scacchi, A., Rigoni, C., Haataja, M., Timonen, J. V. I., &#38; Sammalkorpi, M. (2025). A coarse-grained model for aqueous two-phase systems: Application to ferrofluids. <i>Journal of Colloid and Interface Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcis.2025.01.256\">https://doi.org/10.1016/j.jcis.2025.01.256</a>","ama":"Scacchi A, Rigoni C, Haataja M, Timonen JVI, Sammalkorpi M. A coarse-grained model for aqueous two-phase systems: Application to ferrofluids. <i>Journal of Colloid and Interface Science</i>. 2025;686:1135-1146. doi:<a href=\"https://doi.org/10.1016/j.jcis.2025.01.256\">10.1016/j.jcis.2025.01.256</a>","ieee":"A. Scacchi, C. Rigoni, M. Haataja, J. V. I. Timonen, and M. Sammalkorpi, “A coarse-grained model for aqueous two-phase systems: Application to ferrofluids,” <i>Journal of Colloid and Interface Science</i>, vol. 686. Elsevier, pp. 1135–1146, 2025.","mla":"Scacchi, Alberto, et al. “A Coarse-Grained Model for Aqueous Two-Phase Systems: Application to Ferrofluids.” <i>Journal of Colloid and Interface Science</i>, vol. 686, Elsevier, 2025, pp. 1135–46, doi:<a href=\"https://doi.org/10.1016/j.jcis.2025.01.256\">10.1016/j.jcis.2025.01.256</a>."},"doi":"10.1016/j.jcis.2025.01.256","_id":"19024","quality_controlled":"1","oa_version":"Published Version"},{"publication":"Nano Letters","month":"02","corr_author":"1","status":"public","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"issue":"7","language":[{"iso":"eng"}],"OA_type":"green","intvolume":"        25","abstract":[{"lang":"eng","text":"The back-action damping of mechanical motion by electromagnetic radiation is typically overwhelmed by internal loss channels unless demanding experimental ingredients such as superconducting resonators, high-quality optical cavities, or large magnetic fields are employed. Here we demonstrate the first room temperature, cavity-free, all-electric device where back-action damping exceeds internal loss, enabled by a mechanically compliant parallel-plate capacitor with a nanoscale plate separation and an aspect ratio exceeding 1,000. The device has 4 orders of magnitude lower insertion loss than a comparable commercial quartz crystal and achieves a position imprecision rivaling optical interferometers. With the help of a back-action isolation scheme, we observe radiative cooling of mechanical motion by a remote cryogenic load. This work provides a technologically accessible route to high-precision sensing, transduction, and signal processing."}],"date_created":"2025-02-16T23:02:34Z","publisher":"American Chemical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-02-06T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2025","isi":1,"type":"journal_article","oa":1,"page":"2749-2755","_id":"19026","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2407.15314"}],"project":[{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition"},{"grant_number":"26088","name":"Surface Charge and Tunneling Multi-Mode Imaging","_id":"62843413-2b32-11ec-9570-c4ec6eabfae7"}],"doi":"10.1021/acs.nanolett.4c05796","citation":{"chicago":"Puglia, Denise, Rachel H Odessey, Peter Burns, Niklas Luhmann, Silvan Schmid, and Andrew P Higginbotham. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical Motion.” <i>Nano Letters</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acs.nanolett.4c05796\">https://doi.org/10.1021/acs.nanolett.4c05796</a>.","short":"D. Puglia, R.H. Odessey, P. Burns, N. Luhmann, S. Schmid, A.P. Higginbotham, Nano Letters 25 (2025) 2749–2755.","mla":"Puglia, Denise, et al. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical Motion.” <i>Nano Letters</i>, vol. 25, no. 7, American Chemical Society, 2025, pp. 2749–55, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.4c05796\">10.1021/acs.nanolett.4c05796</a>.","ieee":"D. Puglia, R. H. Odessey, P. Burns, N. Luhmann, S. Schmid, and A. P. Higginbotham, “Room temperature, cavity-free capacitive strong coupling to mechanical motion,” <i>Nano Letters</i>, vol. 25, no. 7. American Chemical Society, pp. 2749–2755, 2025.","ista":"Puglia D, Odessey RH, Burns P, Luhmann N, Schmid S, Higginbotham AP. 2025. Room temperature, cavity-free capacitive strong coupling to mechanical motion. Nano Letters. 25(7), 2749–2755.","ama":"Puglia D, Odessey RH, Burns P, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical motion. <i>Nano Letters</i>. 2025;25(7):2749-2755. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.4c05796\">10.1021/acs.nanolett.4c05796</a>","apa":"Puglia, D., Odessey, R. H., Burns, P., Luhmann, N., Schmid, S., &#38; Higginbotham, A. P. (2025). Room temperature, cavity-free capacitive strong coupling to mechanical motion. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.4c05796\">https://doi.org/10.1021/acs.nanolett.4c05796</a>"},"scopus_import":"1","department":[{"_id":"AnHi"}],"volume":25,"title":"Room temperature, cavity-free capacitive strong coupling to mechanical motion","date_updated":"2025-09-30T10:29:58Z","author":[{"id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise","orcid":"0000-0003-1144-2763","last_name":"Puglia","first_name":"Denise"},{"full_name":"Odessey, Rachel H","id":"9a7a5123-8972-11ed-ae7b-dd1f2af457bd","first_name":"Rachel H","last_name":"Odessey"},{"last_name":"Burns","first_name":"Peter","full_name":"Burns, Peter"},{"first_name":"Niklas","last_name":"Luhmann","full_name":"Luhmann, Niklas"},{"full_name":"Schmid, Silvan","first_name":"Silvan","last_name":"Schmid"},{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"repository","external_id":{"arxiv":["2407.15314"],"isi":["001415246000001"]},"day":"06","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"article_type":"original","related_material":{"record":[{"relation":"earlier_version","id":"18143","status":"public"}]},"acknowledgement":"We thank Carissa Kumar and Vibha Padmanabhan for assistance in comparing performance with devices across the literature. We thank Andrew Cleland for helpful comments on this work. We are grateful for support from the Miba Machine Shop and Nanofabrication facility at IST Austria. This work was supported by the Austrian FWF grant P33692–N and includes a recipient of a DOC Fellowship of the Austrian Academy of Sciences (DOC – No. 26088) at the Institute of Science and Technology, Austria.","arxiv":1},{"title":"Multilevel Monte Carlo methods for the Dean–Kawasaki equation from fluctuating hydrodynamics","date_updated":"2025-09-30T10:30:31Z","author":[{"full_name":"Cornalba, Federico","id":"2CEB641C-A400-11E9-A717-D712E6697425","first_name":"Federico","last_name":"Cornalba","orcid":"0000-0002-6269-5149"},{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L"}],"external_id":{"isi":["001447583400011"],"arxiv":["2311.08872"]},"OA_place":"publisher","arxiv":1,"day":"01","file_date_updated":"2025-02-17T08:32:23Z","article_type":"original","acknowledgement":"The work of the authors was supported by the Austrian Science Fund (FWF) projectF65.","publication_identifier":{"issn":["0036-1429"],"eissn":["1095-7170"]},"oa_version":"Published Version","quality_controlled":"1","_id":"19027","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Cornalba, Federico, and Julian L. Fischer. “Multilevel Monte Carlo Methods for the Dean–Kawasaki Equation from Fluctuating Hydrodynamics.” <i>SIAM Journal on Numerical Analysis</i>, vol. 63, no. 1, Society for Industrial and Applied Mathematics, 2025, pp. 262–87, doi:<a href=\"https://doi.org/10.1137/23M1617345\">10.1137/23M1617345</a>.","ieee":"F. Cornalba and J. L. Fischer, “Multilevel Monte Carlo methods for the Dean–Kawasaki equation from fluctuating hydrodynamics,” <i>SIAM Journal on Numerical Analysis</i>, vol. 63, no. 1. Society for Industrial and Applied Mathematics, pp. 262–287, 2025.","ista":"Cornalba F, Fischer JL. 2025. Multilevel Monte Carlo methods for the Dean–Kawasaki equation from fluctuating hydrodynamics. SIAM Journal on Numerical Analysis. 63(1), 262–287.","ama":"Cornalba F, Fischer JL. Multilevel Monte Carlo methods for the Dean–Kawasaki equation from fluctuating hydrodynamics. <i>SIAM Journal on Numerical Analysis</i>. 2025;63(1):262-287. doi:<a href=\"https://doi.org/10.1137/23M1617345\">10.1137/23M1617345</a>","apa":"Cornalba, F., &#38; Fischer, J. L. (2025). Multilevel Monte Carlo methods for the Dean–Kawasaki equation from fluctuating hydrodynamics. <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/23M1617345\">https://doi.org/10.1137/23M1617345</a>","chicago":"Cornalba, Federico, and Julian L Fischer. “Multilevel Monte Carlo Methods for the Dean–Kawasaki Equation from Fluctuating Hydrodynamics.” <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics, 2025. <a href=\"https://doi.org/10.1137/23M1617345\">https://doi.org/10.1137/23M1617345</a>.","short":"F. Cornalba, J.L. Fischer, SIAM Journal on Numerical Analysis 63 (2025) 262–287."},"doi":"10.1137/23M1617345","project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"volume":63,"department":[{"_id":"JuFi"}],"scopus_import":"1","date_published":"2025-02-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"date_created":"2025-02-17T08:32:23Z","relation":"main_file","creator":"dernst","file_name":"2025_SIAMNumerAnaly_Cornalba.pdf","checksum":"53505647e848ed50f7e0d00c369b14e7","file_size":2435019,"access_level":"open_access","content_type":"application/pdf","file_id":"19029","success":1,"date_updated":"2025-02-17T08:32:23Z"}],"publication_status":"published","year":"2025","article_processing_charge":"Yes (in subscription journal)","oa":1,"type":"journal_article","isi":1,"page":"262-287","status":"public","ddc":["510"],"month":"02","corr_author":"1","publication":"SIAM Journal on Numerical Analysis","issue":"1","intvolume":"        63","language":[{"iso":"eng"}],"OA_type":"hybrid","publisher":"Society for Industrial and Applied Mathematics","has_accepted_license":"1","date_created":"2025-02-16T23:02:34Z","abstract":[{"lang":"eng","text":"Stochastic PDEs of fluctuating hydrodynamics are a powerful tool for the description of fluctuations in many-particle systems. In this paper, we develop and analyze a multilevel Monte Carlo (MLMC) scheme for the Dean–Kawasaki equation, a pivotal representative of this class of SPDEs. We prove analytically and demonstrate numerically that our MLMC scheme provides a significant reduction in computational cost (with respect to a standard Monte Carlo method) in the simulation of the Dean–Kawasaki equation. Specifically, we link this reduction in cost to having a sufficiently large average particle density and show that sizeable cost reductions can be obtained even when we have solutions with regions of low density. Numerical simulations are provided in the two-dimensional case, confirming our theoretical predictions. Our results are formulated entirely in terms of the law of distributions rather than in terms of strong spatial norms: this crucially allows for MLMC speed-ups altogether despite the Dean–Kawasaki equation being highly singular."}]},{"author":[{"last_name":"Scacchi","first_name":"Alberto","full_name":"Scacchi, Alberto"}],"year":"2025","article_processing_charge":"No","title":"2025_SCACCHI_JCIS","date_published":"2025-02-05T00:00:00Z","date_updated":"2025-09-30T10:31:44Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05","acknowledgement":"This work was supported by the Swiss National Science Foundation under the project no. P500PT_206916 (A.S.) and the Academy of Finland through its Centres of Excellence Programs (2022-2029, LIBER) under projects no. 346111 and 364205 (M.S.) and 346112 and 364206 (J.T.). MPH was supported by the National Science Foundation through the Princeton University (PCCM) Materials Research Science and Engineering Center DMR-2011750. A.S. warmly thanks Bob Evans for extensive scientific discussions and for his hospitality during the research visit in Bristol. Computational resources by CSC IT Centre for Finland, the Aalto Science-IT project, and RAMI -- RawMatters Finland Infrastructure are also gratefully acknowledged.","related_material":{"record":[{"id":"19024","relation":"used_in_publication","status":"public"}]},"oa":1,"OA_place":"publisher","contributor":[{"last_name":"Rigoni","first_name":"Carlo","id":"c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0"},{"first_name":"Maria","last_name":"Sammalkorpi"},{"last_name":"Haataja","first_name":"Mikko"},{"last_name":"Timonen","first_name":"Jaakoo"}],"type":"research_data_reference","status":"public","month":"02","ddc":["530"],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1"}],"_id":"19033","publisher":"Fairdata","has_accepted_license":"1","date_created":"2025-02-17T09:00:36Z","abstract":[{"text":"This data set contains the simulation input files, scripts, and figures data belonging to the publication\r\n\r\nAlberto Scacchi, Carlo Rigoni, Mikko P. Haataja, Jakko V. I. Timonen, and Maria Sammalkorpi, \"A Coarse-grained Model for Aqueous Two-phase Systems: Application to Ferrofluids\", Journal of Colloids and Interface Science (2025). https://doi.org/10.1016/j.jcis.2025.01.256.","lang":"eng"}],"department":[{"_id":"RaKl"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Scacchi, Alberto. “2025_SCACCHI_JCIS.” Fairdata, 2025. <a href=\"https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1\">https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1</a>.","short":"A. Scacchi, (2025).","ieee":"A. Scacchi, “2025_SCACCHI_JCIS.” Fairdata, 2025.","mla":"Scacchi, Alberto. <i>2025_SCACCHI_JCIS</i>. Fairdata, 2025, doi:<a href=\"https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1\">10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1</a>.","ista":"Scacchi A. 2025. 2025_SCACCHI_JCIS, Fairdata, <a href=\"https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1\">10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1</a>.","apa":"Scacchi, A. (2025). 2025_SCACCHI_JCIS. Fairdata. <a href=\"https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1\">https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1</a>","ama":"Scacchi A. 2025_SCACCHI_JCIS. 2025. doi:<a href=\"https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1\">10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1</a>"},"doi":"10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1"}]