[{"status":"public","issue":"1","citation":{"mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” <i>Evolution: International Journal of Organic Evolution</i>, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:<a href=\"https://doi.org/10.1093/evolut/qpac004\">10.1093/evolut/qpac004</a>.","ieee":"D. I. Bolnick <i>et al.</i>, “A multivariate view of the speciation continuum,” <i>Evolution: International journal of organic evolution</i>, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. <i>Evolution: International journal of organic evolution</i>. 2023;77(1):318-328. doi:<a href=\"https://doi.org/10.1093/evolut/qpac004\">10.1093/evolut/qpac004</a>","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” <i>Evolution: International Journal of Organic Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolut/qpac004\">https://doi.org/10.1093/evolut/qpac004</a>.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. <i>Evolution: International Journal of Organic Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpac004\">https://doi.org/10.1093/evolut/qpac004</a>","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328."},"day":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/evolut/qpac004"}],"oa_version":"Published Version","external_id":{"pmid":["36622661"],"isi":["001021686300024"]},"volume":77,"ddc":["570"],"fulldoi":"https://doi.org/10.1093/evolut/qpac004","acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","intvolume":"        77","language":[{"iso":"eng"}],"abstract":[{"text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.","lang":"eng"}],"isi":1,"doi":"10.1093/evolut/qpac004","publication_identifier":{"eissn":["1558-5646"]},"department":[{"_id":"NiBa"}],"type":"journal_article","year":"2023","scopus_import":"1","pmid":1,"quality_controlled":"1","oa":1,"page":"318-328","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Oxford University Press","article_processing_charge":"No","date_updated":"2026-06-18T17:26:56Z","month":"01","date_created":"2023-02-05T23:00:59Z","article_type":"original","title":"A multivariate view of the speciation continuum","_id":"12514","publication":"Evolution: International journal of organic evolution","date_published":"2023-01-01T00:00:00Z","author":[{"full_name":"Bolnick, Daniel I.","last_name":"Bolnick","first_name":"Daniel I."},{"full_name":"Hund, Amanda K.","last_name":"Hund","first_name":"Amanda K."},{"first_name":"Patrik","last_name":"Nosil","full_name":"Nosil, Patrik"},{"first_name":"Foen","last_name":"Peng","full_name":"Peng, Foen"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"},{"full_name":"Subramanian, Swapna","first_name":"Swapna","last_name":"Subramanian"},{"first_name":"Jochen B.W.","last_name":"Wolf","full_name":"Wolf, Jochen B.W."},{"first_name":"Roman","last_name":"Yukilevich","full_name":"Yukilevich, Roman"}]},{"volume":16,"ddc":["570"],"fulldoi":"https://doi.org/10.3389/fnana.2022.1097467","intvolume":"        16","acknowledgement":"This work was partially supported by a grant from “Consello Social Universidade de Santiago de Compostela” 2022-PU004.We would like to show special gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia, Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación Galega de Caza for providing the red foxes used in this study.","language":[{"iso":"eng"}],"abstract":[{"text":"Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.","lang":"eng"}],"isi":1,"doi":"10.3389/fnana.2022.1097467","publication_identifier":{"eissn":["1662-5129"]},"has_accepted_license":"1","status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro, A. M., Larriva-Sahd, J. A., &#38; Sánchez-Quinteiro, P. (2023). The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. <i>Frontiers in Neuroanatomy</i>. Frontiers. <a href=\"https://doi.org/10.3389/fnana.2022.1097467\">https://doi.org/10.3389/fnana.2022.1097467</a>","ista":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467.","mla":"Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” <i>Frontiers in Neuroanatomy</i>, vol. 16, 1097467, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fnana.2022.1097467\">10.3389/fnana.2022.1097467</a>.","ieee":"I. Ortiz-Leal <i>et al.</i>, “The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway,” <i>Frontiers in Neuroanatomy</i>, vol. 16. Frontiers, 2023.","chicago":"Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” <i>Frontiers in Neuroanatomy</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fnana.2022.1097467\">https://doi.org/10.3389/fnana.2022.1097467</a>.","ama":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. <i>Frontiers in Neuroanatomy</i>. 2023;16. doi:<a href=\"https://doi.org/10.3389/fnana.2022.1097467\">10.3389/fnana.2022.1097467</a>","short":"I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023)."},"day":"10","oa_version":"Published Version","external_id":{"isi":["000919786900001"],"pmid":["36704406"]},"article_processing_charge":"No","month":"01","date_updated":"2023-08-16T11:37:52Z","date_created":"2023-02-05T23:01:00Z","article_type":"original","title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","_id":"12515","publication":"Frontiers in Neuroanatomy","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"49cd40f3bda6f267079427042e7d15e3","file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf","creator":"dernst","date_updated":"2023-02-06T07:56:14Z","success":1,"file_id":"12518","date_created":"2023-02-06T07:56:14Z","file_size":21943473}],"date_published":"2023-01-10T00:00:00Z","author":[{"last_name":"Ortiz-Leal","first_name":"Irene","full_name":"Ortiz-Leal, Irene"},{"full_name":"Torres, Mateo V.","last_name":"Torres","first_name":"Mateo V."},{"id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M","last_name":"Vargas Barroso","first_name":"Victor M"},{"full_name":"Fidalgo, Luis Eusebio","last_name":"Fidalgo","first_name":"Luis Eusebio"},{"full_name":"López-Beceiro, Ana María","first_name":"Ana María","last_name":"López-Beceiro"},{"full_name":"Larriva-Sahd, Jorge A.","last_name":"Larriva-Sahd","first_name":"Jorge A."},{"last_name":"Sánchez-Quinteiro","first_name":"Pablo","full_name":"Sánchez-Quinteiro, Pablo"}],"department":[{"_id":"PeJo"}],"type":"journal_article","scopus_import":"1","year":"2023","pmid":1,"oa":1,"quality_controlled":"1","article_number":"1097467","file_date_updated":"2023-02-06T07:56:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Frontiers"},{"article_processing_charge":"No","date_updated":"2025-04-14T07:48:54Z","month":"01","date_created":"2023-02-10T09:02:26Z","article_type":"original","title":"Dissipative dynamics of an impurity with spin-orbit coupling","_id":"12534","ec_funded":1,"publication":"Physical Review Research","file":[{"file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","creator":"dernst","relation":"main_file","checksum":"6068b62874c0099628a108bb9c5c6bd2","access_level":"open_access","content_type":"application/pdf","file_size":865150,"date_created":"2023-02-13T10:38:10Z","date_updated":"2023-02-13T10:38:10Z","file_id":"12546","success":1}],"author":[{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"last_name":"Cappellaro","orcid":"0000-0001-6110-2359","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","full_name":"Cappellaro, Alberto"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem"}],"date_published":"2023-01-20T00:00:00Z","department":[{"_id":"MiLe"}],"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"scopus_import":"1","type":"journal_article","year":"2023","corr_author":"1","article_number":"013029","oa":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-02-13T10:38:10Z","publisher":"American Physical Society","publication_status":"published","volume":5,"ddc":["530"],"fulldoi":"https://doi.org/10.1103/physrevresearch.5.013029","intvolume":"         5","acknowledgement":"We thank Rafael Barfknecht for help at the initial stages of this project; Fabian Brauneis for useful discussions; Miguel A. Garcia-March, Georgios Koutentakis, and Simeon Mistakidis\r\nfor comments on the paper. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","language":[{"iso":"eng"}],"abstract":[{"text":"Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics.","lang":"eng"}],"doi":"10.1103/physrevresearch.5.013029","publication_identifier":{"issn":["2643-1564"]},"has_accepted_license":"1","status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"1","citation":{"apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., &#38; Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.5.013029\">https://doi.org/10.1103/physrevresearch.5.013029</a>","ista":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. 2023. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 5(1), 013029.","mla":"Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” <i>Physical Review Research</i>, vol. 5, no. 1, 013029, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevresearch.5.013029\">10.1103/physrevresearch.5.013029</a>.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","ama":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of an impurity with spin-orbit coupling. <i>Physical Review Research</i>. 2023;5(1). doi:<a href=\"https://doi.org/10.1103/physrevresearch.5.013029\">10.1103/physrevresearch.5.013029</a>","chicago":"Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” <i>Physical Review Research</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevresearch.5.013029\">https://doi.org/10.1103/physrevresearch.5.013029</a>.","ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” <i>Physical Review Research</i>, vol. 5, no. 1. American Physical Society, 2023."},"day":"20","oa_version":"Published Version"},{"issue":"3","citation":{"ieee":"A. Villalba Requena and S. Hippenmeyer, “Going back in time with TEMPO,” <i>Neuron</i>, vol. 111, no. 3. Elsevier, pp. 291–293, 2023.","ama":"Villalba Requena A, Hippenmeyer S. Going back in time with TEMPO. <i>Neuron</i>. 2023;111(3):291-293. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.01.006\">10.1016/j.neuron.2023.01.006</a>","chicago":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” <i>Neuron</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.neuron.2023.01.006\">https://doi.org/10.1016/j.neuron.2023.01.006</a>.","short":"A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293.","mla":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” <i>Neuron</i>, vol. 111, no. 3, Elsevier, 2023, pp. 291–93, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.01.006\">10.1016/j.neuron.2023.01.006</a>.","ista":"Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293.","apa":"Villalba Requena, A., &#38; Hippenmeyer, S. (2023). Going back in time with TEMPO. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.01.006\">https://doi.org/10.1016/j.neuron.2023.01.006</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2023.01.006"}],"day":"01","external_id":{"pmid":["36731425"],"isi":["000994473300001"]},"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"isi":1,"abstract":[{"text":"In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo.","lang":"eng"}],"doi":"10.1016/j.neuron.2023.01.006","publication_identifier":{"eissn":["1097-4199"]},"volume":111,"ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.neuron.2023.01.006","intvolume":"       111","oa":1,"quality_controlled":"1","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"291-293","publisher":"Elsevier","publication_status":"published","department":[{"_id":"SiHi"}],"OA_type":"free access","type":"journal_article","year":"2023","scopus_import":"1","corr_author":"1","pmid":1,"_id":"12542","publication":"Neuron","author":[{"id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","full_name":"Villalba Requena, Ana","orcid":"0000-0002-5615-5277","last_name":"Villalba Requena","first_name":"Ana"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"}],"date_published":"2023-02-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-06-18T17:27:44Z","month":"02","date_created":"2023-02-12T23:00:58Z","article_type":"letter_note","title":"Going back in time with TEMPO"},{"acknowledged_ssus":[{"_id":"LifeSc"}],"ddc":["570"],"volume":7,"intvolume":"         7","acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.","fulldoi":"https://doi.org/10.1038/s41559-023-01981-6","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/","description":"News on ISTA website"}]},"isi":1,"abstract":[{"text":"Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2397-334X"]},"doi":"10.1038/s41559-023-01981-6","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","status":"public","citation":{"apa":"Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-023-01981-6\">https://doi.org/10.1038/s41559-023-01981-6</a>","ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460.","mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” <i>Nature Ecology and Evolution</i>, vol. 7, Springer Nature, 2023, pp. 450–60, doi:<a href=\"https://doi.org/10.1038/s41559-023-01981-6\">10.1038/s41559-023-01981-6</a>.","ieee":"M. Stock <i>et al.</i>, “Pathogen evasion of social immunity,” <i>Nature Ecology and Evolution</i>, vol. 7. Springer Nature, pp. 450–460, 2023.","short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41559-023-01981-6\">https://doi.org/10.1038/s41559-023-01981-6</a>.","ama":"Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. <i>Nature Ecology and Evolution</i>. 2023;7:450-460. doi:<a href=\"https://doi.org/10.1038/s41559-023-01981-6\">10.1038/s41559-023-01981-6</a>"},"external_id":{"isi":["000924572800001"],"pmid":["36732670"]},"oa_version":"Published Version","day":"01","date_updated":"2025-04-14T07:47:53Z","month":"03","article_processing_charge":"No","title":"Pathogen evasion of social immunity","article_type":"original","date_created":"2023-02-12T23:00:59Z","_id":"12543","ec_funded":1,"author":[{"first_name":"Miriam","last_name":"Stock","full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Milutinovic, Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic"},{"last_name":"Hönigsberger","first_name":"Michaela","id":"953894f3-25bd-11ec-8556-f70a9d38ef60","full_name":"Hönigsberger, Michaela"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V"},{"id":"39523C54-F248-11E8-B48F-1D18A9856A87","full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer","first_name":"Florian"},{"full_name":"Kampleitner, Niklas","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87","first_name":"Niklas","last_name":"Kampleitner"},{"first_name":"Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","last_name":"Schmitt","full_name":"Schmitt, Thomas"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"date_published":"2023-03-01T00:00:00Z","publication":"Nature Ecology and Evolution","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2023_NatureEcoEvo_Stock.pdf","creator":"dernst","checksum":"8244f4650a0e7aeea488d1bcd4a31702","relation":"main_file","date_updated":"2023-08-16T11:54:59Z","file_id":"14069","success":1,"date_created":"2023-08-16T11:54:59Z","file_size":1600499}],"year":"2023","scopus_import":"1","type":"journal_article","corr_author":"1","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"project":[{"name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402"},{"name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"pmid":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication_status":"published","page":"450-460","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-08-16T11:54:59Z"},{"language":[{"iso":"eng"}],"isi":1,"abstract":[{"lang":"eng","text":"Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol includes a sequential algorithm and a parallel algorithm. In the parallel version, we partition the atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented by a buffer zone to account for atoms whose ball representations may partially cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up compared to an independent serial implementation when using 32 processors. For instance, it takes 31 s to compute the geometric measures and derivatives of each atom in a viral capsid with more than 26 million atoms on 32 Intel processors running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant computations, which ultimately limit the impact of using multiple processors. AlphaMol is available as an OpenSource software."}],"doi":"10.1021/acs.jcim.2c01346","publication_identifier":{"issn":["1549-9596"],"eissn":["1549-960X"]},"volume":63,"ddc":["510","540"],"fulldoi":"https://doi.org/10.1021/acs.jcim.2c01346","acknowledgement":"P.K. acknowledges support from the University of California Multicampus Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant No.1760485). H.E. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access is funded by the Austrian Science Fund (FWF).","intvolume":"        63","issue":"3","citation":{"apa":"Koehl, P., Akopyan, A., &#38; Edelsbrunner, H. (2023). Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. <i>Journal of Chemical Information and Modeling</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jcim.2c01346\">https://doi.org/10.1021/acs.jcim.2c01346</a>","ista":"Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 63(3), 973–985.","mla":"Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” <i>Journal of Chemical Information and Modeling</i>, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85, doi:<a href=\"https://doi.org/10.1021/acs.jcim.2c01346\">10.1021/acs.jcim.2c01346</a>.","ieee":"P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives,” <i>Journal of Chemical Information and Modeling</i>, vol. 63, no. 3. American Chemical Society, pp. 973–985, 2023.","chicago":"Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” <i>Journal of Chemical Information and Modeling</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jcim.2c01346\">https://doi.org/10.1021/acs.jcim.2c01346</a>.","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985.","ama":"Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. <i>Journal of Chemical Information and Modeling</i>. 2023;63(3):973-985. doi:<a href=\"https://doi.org/10.1021/acs.jcim.2c01346\">10.1021/acs.jcim.2c01346</a>"},"day":"13","external_id":{"isi":["000920370700001"],"pmid":["36638318"]},"oa_version":"Published Version","has_accepted_license":"1","status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"12544","ec_funded":1,"publication":"Journal of Chemical Information and Modeling","file":[{"date_created":"2023-08-16T12:21:13Z","file_size":8069223,"file_id":"14070","success":1,"date_updated":"2023-08-16T12:21:13Z","file_name":"2023_JCIM_Koehl.pdf","creator":"dernst","relation":"main_file","checksum":"7d20562269edff1e31b9d6019d4983b0","access_level":"open_access","content_type":"application/pdf"}],"author":[{"first_name":"Patrice","last_name":"Koehl","full_name":"Koehl, Patrice"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","first_name":"Arseniy"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"}],"date_published":"2023-02-13T00:00:00Z","article_processing_charge":"No","month":"02","date_updated":"2025-04-15T07:16:52Z","date_created":"2023-02-12T23:00:59Z","article_type":"original","title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"973-985","file_date_updated":"2023-08-16T12:21:13Z","publisher":"American Chemical Society","publication_status":"published","department":[{"_id":"HeEd"}],"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"year":"2023","type":"journal_article","scopus_import":"1","corr_author":"1","pmid":1},{"_id":"12545","publication":"Physical Review E","author":[{"id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","full_name":"Rojas Vega, Mauricio Nicolas","last_name":"Rojas Vega","first_name":"Mauricio Nicolas"},{"full_name":"De Castro, Pablo","first_name":"Pablo","last_name":"De Castro"},{"last_name":"Soto","first_name":"Rodrigo","full_name":"Soto, Rodrigo"}],"date_published":"2023-01-24T00:00:00Z","article_processing_charge":"No","date_updated":"2025-03-06T14:01:47Z","month":"01","arxiv":1,"date_created":"2023-02-12T23:00:59Z","article_type":"original","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","quality_controlled":"1","oa":1,"article_number":"014608","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","publication_status":"published","department":[{"_id":"GradSch"}],"scopus_import":"1","type":"journal_article","year":"2023","pmid":1,"language":[{"iso":"eng"}],"isi":1,"abstract":[{"text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front.","lang":"eng"}],"doi":"10.1103/PhysRevE.107.014608","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"volume":107,"fulldoi":"https://doi.org/10.1103/PhysRevE.107.014608","intvolume":"       107","acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","issue":"1","citation":{"mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” <i>Physical Review E</i>, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">10.1103/PhysRevE.107.014608</a>.","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” <i>Physical Review E</i>, vol. 107, no. 1. American Physical Society, 2023.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. <i>Physical Review E</i>. 2023;107(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">10.1103/PhysRevE.107.014608</a>","chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">https://doi.org/10.1103/PhysRevE.107.014608</a>.","apa":"Rojas Vega, M. N., De Castro, P., &#38; Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">https://doi.org/10.1103/PhysRevE.107.014608</a>","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01856","open_access":"1"}],"day":"24","external_id":{"arxiv":["2301.01856"],"pmid":["36797971"],"isi":["000963909800006"]},"oa_version":"Preprint","status":"public"},{"quality_controlled":"1","page":"501-512","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","publisher":"American Physiological Society","department":[{"_id":"SiHi"}],"year":"2023","scopus_import":"1","type":"journal_article","pmid":1,"_id":"12562","publication":"Journal of Neurophysiology","date_published":"2023-03-01T00:00:00Z","author":[{"first_name":"David R.","last_name":"Ladle","full_name":"Ladle, David R."},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon"}],"article_processing_charge":"No","month":"03","date_updated":"2024-10-21T06:01:28Z","date_created":"2023-02-15T14:46:14Z","article_type":"original","title":"Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons","issue":"3","citation":{"ieee":"D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons,” <i>Journal of Neurophysiology</i>, vol. 129, no. 3. American Physiological Society, pp. 501–512, 2023.","chicago":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” <i>Journal of Neurophysiology</i>. American Physiological Society, 2023. <a href=\"https://doi.org/10.1152/jn.00172.2022\">https://doi.org/10.1152/jn.00172.2022</a>.","ama":"Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. <i>Journal of Neurophysiology</i>. 2023;129(3):501-512. doi:<a href=\"https://doi.org/10.1152/jn.00172.2022\">10.1152/jn.00172.2022</a>","short":"D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512.","mla":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” <i>Journal of Neurophysiology</i>, vol. 129, no. 3, American Physiological Society, 2023, pp. 501–12, doi:<a href=\"https://doi.org/10.1152/jn.00172.2022\">10.1152/jn.00172.2022</a>.","ista":"Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 129(3), 501–512.","apa":"Ladle, D. R., &#38; Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. <i>Journal of Neurophysiology</i>. American Physiological Society. <a href=\"https://doi.org/10.1152/jn.00172.2022\">https://doi.org/10.1152/jn.00172.2022</a>"},"day":"01","oa_version":"None","keyword":["Physiology","General Neuroscience"],"external_id":{"isi":["000957721600001"],"pmid":["36695533"]},"status":"public","language":[{"iso":"eng"}],"abstract":[{"text":"Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons.","lang":"eng"}],"isi":1,"doi":"10.1152/jn.00172.2022","publication_identifier":{"issn":["0022-3077"],"eissn":["1522-1598"]},"volume":129,"fulldoi":"https://doi.org/10.1152/jn.00172.2022","intvolume":"       129","acknowledgement":"The authors gratefully thank Dr. Silvia Arber, University of Basel and Friedrich Miescher Institute for Biomedical Research, for support and in whose lab the data were collected. For advice on statistical analysis, we thank Michael Bottomley from the Statistical Consulting Center, College of Science and Mathematics, Wright State University."},{"fulldoi":"https://doi.org/10.1137/20m1378223","acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","intvolume":"        52","volume":52,"doi":"10.1137/20m1378223","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"language":[{"iso":"eng"}],"isi":1,"abstract":[{"lang":"eng","text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems."}],"status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2003.11351","open_access":"1"}],"day":"01","keyword":["General Mathematics","General Computer Science"],"external_id":{"isi":["000955000000001"],"arxiv":["2003.11351"]},"oa_version":"Preprint","issue":"1","citation":{"chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/20m1378223\">https://doi.org/10.1137/20m1378223</a>.","ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. <i>SIAM Journal on Computing</i>. 2023;52(1):38-79. doi:<a href=\"https://doi.org/10.1137/20m1378223\">10.1137/20m1378223</a>","short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79.","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” <i>SIAM Journal on Computing</i>, vol. 52, no. 1. Society for Industrial and Applied Mathematics, pp. 38–79, 2023.","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” <i>SIAM Journal on Computing</i>, vol. 52, no. 1, Society for Industrial and Applied Mathematics, 2023, pp. 38–79, doi:<a href=\"https://doi.org/10.1137/20m1378223\">10.1137/20m1378223</a>.","ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79.","apa":"Krokhin, A., Opršal, J., Wrochna, M., &#38; Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20m1378223\">https://doi.org/10.1137/20m1378223</a>"},"arxiv":1,"date_created":"2023-02-16T07:03:52Z","title":"Topology and adjunction in promise constraint satisfaction","article_type":"original","article_processing_charge":"No","month":"01","date_updated":"2025-05-14T10:51:32Z","publication":"SIAM Journal on Computing","author":[{"last_name":"Krokhin","first_name":"Andrei","full_name":"Krokhin, Andrei"},{"first_name":"Jakub","last_name":"Opršal","orcid":"0000-0003-1245-3456","full_name":"Opršal, Jakub","id":"ec596741-c539-11ec-b829-c79322a91242"},{"full_name":"Wrochna, Marcin","last_name":"Wrochna","first_name":"Marcin"},{"last_name":"Živný","first_name":"Stanislav","full_name":"Živný, Stanislav"}],"date_published":"2023-01-01T00:00:00Z","_id":"12563","ec_funded":1,"department":[{"_id":"UlWa"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"year":"2023","scopus_import":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"38-79","publisher":"Society for Industrial and Applied Mathematics","publication_status":"published","quality_controlled":"1","oa":1},{"article_type":"original","title":"Wait-free approximate agreement on graphs","date_created":"2023-02-19T23:00:55Z","month":"02","date_updated":"2025-04-14T07:49:16Z","article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"full_name":"Ellen, Faith","last_name":"Ellen","first_name":"Faith"},{"full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki"}],"date_published":"2023-02-28T00:00:00Z","publication":"Theoretical Computer Science","file":[{"content_type":"application/pdf","access_level":"open_access","checksum":"b27c5290f2f1500c403494364ee39c9f","relation":"main_file","file_name":"2023_TheoreticalCompScience_Alistarh.pdf","creator":"dernst","date_updated":"2023-02-20T07:30:20Z","success":1,"file_id":"12570","file_size":602333,"date_created":"2023-02-20T07:30:20Z"}],"_id":"12566","ec_funded":1,"scopus_import":"1","year":"2023","type":"journal_article","corr_author":"1","department":[{"_id":"DaAl"}],"project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"},{"name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605"}],"publisher":"Elsevier","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2023-02-20T07:30:20Z","quality_controlled":"1","article_number":"113733","oa":1,"intvolume":"       948","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","fulldoi":"https://doi.org/10.1016/j.tcs.2023.113733","ddc":["000"],"volume":948,"publication_identifier":{"issn":["0304-3975"]},"doi":"10.1016/j.tcs.2023.113733","isi":1,"abstract":[{"lang":"eng","text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among  processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs."}],"language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","status":"public","external_id":{"isi":["000934262700001"]},"oa_version":"Published Version","day":"28","citation":{"ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","apa":"Alistarh, D.-A., Ellen, F., &#38; Rybicki, J. (2023). Wait-free approximate agreement on graphs. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">https://doi.org/10.1016/j.tcs.2023.113733</a>","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023).","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. <i>Theoretical Computer Science</i>. 2023;948(2). doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">10.1016/j.tcs.2023.113733</a>","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” <i>Theoretical Computer Science</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">https://doi.org/10.1016/j.tcs.2023.113733</a>.","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” <i>Theoretical Computer Science</i>, vol. 948, no. 2. Elsevier, 2023.","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” <i>Theoretical Computer Science</i>, vol. 948, no. 2, 113733, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">10.1016/j.tcs.2023.113733</a>."},"issue":"2"},{"oa":1,"quality_controlled":"1","article_number":"2128","file_date_updated":"2023-02-20T07:09:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"MDPI","department":[{"_id":"PeJo"}],"type":"journal_article","scopus_import":"1","year":"2023","pmid":1,"_id":"12567","file":[{"file_size":2823025,"date_created":"2023-02-20T07:09:27Z","date_updated":"2023-02-20T07:09:27Z","success":1,"file_id":"12569","relation":"main_file","checksum":"69a35dcd3e0249f902ab881b06ee2e58","file_name":"2023_IJMS_Mrestani.pdf","creator":"dernst","content_type":"application/pdf","access_level":"open_access"}],"publication":"International Journal of Molecular Sciences","date_published":"2023-01-21T00:00:00Z","author":[{"first_name":"Achmed","last_name":"Mrestani","full_name":"Mrestani, Achmed"},{"full_name":"Lichter, Katharina","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","first_name":"Katharina","orcid":"0000-0002-1485-0351","last_name":"Lichter"},{"first_name":"Anna Leena","last_name":"Sirén","full_name":"Sirén, Anna Leena"},{"last_name":"Heckmann","first_name":"Manfred","full_name":"Heckmann, Manfred"},{"first_name":"Mila M.","last_name":"Paul","full_name":"Paul, Mila M."},{"full_name":"Pauli, Martin","first_name":"Martin","last_name":"Pauli"}],"article_processing_charge":"No","month":"01","date_updated":"2025-04-23T08:48:27Z","date_created":"2023-02-19T23:00:56Z","article_type":"original","title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","issue":"3","citation":{"ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128.","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., &#38; Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms24032128\">https://doi.org/10.3390/ijms24032128</a>","ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. <i>International Journal of Molecular Sciences</i>. 2023;24(3). doi:<a href=\"https://doi.org/10.3390/ijms24032128\">10.3390/ijms24032128</a>","short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” <i>International Journal of Molecular Sciences</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/ijms24032128\">https://doi.org/10.3390/ijms24032128</a>.","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 3. MDPI, 2023.","mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 3, 2128, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/ijms24032128\">10.3390/ijms24032128</a>."},"day":"21","oa_version":"Published Version","external_id":{"isi":["000930324700001"],"pmid":["36768451"]},"has_accepted_license":"1","status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations."}],"isi":1,"doi":"10.3390/ijms24032128","publication_identifier":{"eissn":["1422-0067"]},"volume":24,"ddc":["570"],"fulldoi":"https://doi.org/10.3390/ijms24032128","acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","intvolume":"        24"},{"publisher":"Curran Associates","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-02-04T08:30:05Z","oa":1,"quality_controlled":"1","OA_place":"repository","year":"2023","type":"conference","corr_author":"1","OA_type":"green","department":[{"_id":"ChLa"}],"author":[{"last_name":"Scott","first_name":"Jonathan A","id":"e499926b-f6e0-11ea-865d-9c63db0031e8","full_name":"Scott, Jonathan A"},{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","last_name":"Yeo","orcid":"0009-0001-3676-4809","first_name":"Michelle X"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"date_published":"2023-11-27T00:00:00Z","publication":"Transactions in Machine Learning","file":[{"date_updated":"2025-02-04T08:30:05Z","success":1,"file_id":"18990","file_size":553717,"date_created":"2025-02-04T08:30:05Z","content_type":"application/pdf","access_level":"open_access","checksum":"aa322ad91cbd229f5cafe6733a119bd1","relation":"main_file","creator":"dernst","file_name":"2023_TMLR_Scott.pdf"}],"_id":"12660","title":"Cross-client label propagation for transductive and semi-supervised federated learning","arxiv":1,"date_created":"2023-02-20T08:21:50Z","date_updated":"2025-02-04T08:32:19Z","month":"11","article_processing_charge":"No","external_id":{"arxiv":["2210.06434"]},"oa_version":"Preprint","day":"27","citation":{"ista":"Scott JA, Yeo MX, Lampert C. 2023. Cross-client label propagation for transductive and semi-supervised federated learning. Transactions in Machine Learning. , TMLR, .","apa":"Scott, J. A., Yeo, M. X., &#38; Lampert, C. (2023). Cross-client label propagation for transductive and semi-supervised federated learning. In <i>Transactions in Machine Learning</i>. Curran Associates.","chicago":"Scott, Jonathan A, Michelle X Yeo, and Christoph Lampert. “Cross-Client Label Propagation for Transductive and Semi-Supervised Federated Learning.” In <i>Transactions in Machine Learning</i>. Curran Associates, 2023.","ama":"Scott JA, Yeo MX, Lampert C. Cross-client label propagation for transductive and semi-supervised federated learning. In: <i>Transactions in Machine Learning</i>. Curran Associates; 2023.","short":"J.A. Scott, M.X. Yeo, C. Lampert, in:, Transactions in Machine Learning, Curran Associates, 2023.","ieee":"J. A. Scott, M. X. Yeo, and C. Lampert, “Cross-client label propagation for transductive and semi-supervised federated learning,” in <i>Transactions in Machine Learning</i>, 2023.","mla":"Scott, Jonathan A., et al. “Cross-Client Label Propagation for Transductive and Semi-Supervised Federated Learning.” <i>Transactions in Machine Learning</i>, Curran Associates, 2023."},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","publication_identifier":{"issn":["2835-8856"]},"abstract":[{"lang":"eng","text":"We present Cross-Client Label Propagation(XCLP), a new method for transductive federated learning. XCLP estimates a data graph jointly from the data of multiple clients and computes labels for the unlabeled data by propagating label information across the graph. To avoid clients having to share their data with anyone, XCLP employs two cryptographically secure protocols: secure Hamming distance computation and secure summation. We demonstrate two distinct applications of XCLP within federated learning. In the first, we use it in a one-shot way to predict labels for unseen test points. In the second, we use it to repeatedly pseudo-label unlabeled training data in a federated semi-supervised setting. Experiments on both real federated and standard benchmark datasets show that in both applications XCLP achieves higher classification accuracy than alternative approaches."}],"language":[{"iso":"eng"}],"alternative_title":["TMLR"],"related_material":{"link":[{"url":"https://github.com/jonnyascott/xclp","relation":"software"}]},"ddc":["004"]},{"date_published":"2023-03-28T00:00:00Z","author":[{"last_name":"Lyons","first_name":"David B.","full_name":"Lyons, David B."},{"full_name":"Briffa, Amy","first_name":"Amy","last_name":"Briffa"},{"first_name":"Shengbo","last_name":"He","full_name":"He, Shengbo"},{"first_name":"Jaemyung","last_name":"Choi","full_name":"Choi, Jaemyung"},{"first_name":"Elizabeth","last_name":"Hollwey","full_name":"Hollwey, Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"full_name":"Colicchio, Jack","first_name":"Jack","last_name":"Colicchio"},{"first_name":"Ian","last_name":"Anderson","full_name":"Anderson, Ian"},{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234"},{"full_name":"Howard, Martin","first_name":"Martin","last_name":"Howard"},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"file":[{"date_created":"2023-05-11T10:41:42Z","file_size":8401261,"file_id":"12941","success":1,"date_updated":"2023-05-11T10:41:42Z","creator":"kschuh","file_name":"2023_CellReports_Lyons.pdf","checksum":"6cbc44fdb18bf18834c9e2a5b9c67123","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication":"Cell Reports","ec_funded":1,"_id":"12672","title":"Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons","article_type":"original","date_created":"2023-02-23T09:17:44Z","month":"03","date_updated":"2025-04-14T07:57:43Z","article_processing_charge":"Yes","publication_status":"published","publisher":"Elsevier","file_date_updated":"2023-05-11T10:41:42Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"article_number":"112132","quality_controlled":"1","corr_author":"1","year":"2023","type":"journal_article","scopus_import":"1","project":[{"call_identifier":"H2020","name":"Quantitative analysis of DNA methylation maintenance with chromatin","grant_number":"725746","_id":"62935a00-2b32-11ec-9570-eff30fa39068"}],"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publication_identifier":{"eissn":["2211-1247"]},"doi":"10.1016/j.celrep.2023.112132","abstract":[{"text":"Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.","lang":"eng"}],"isi":1,"language":[{"iso":"eng"}],"intvolume":"        42","acknowledgement":"The authors would like to thank Jasper Rine for advice and mentorship to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from the Helen Hay Whitney Foundation to D.B.L.","fulldoi":"https://doi.org/10.1016/j.celrep.2023.112132","ddc":["580"],"volume":42,"oa_version":"Published Version","external_id":{"isi":["000944921600001"]},"day":"28","citation":{"apa":"Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman, D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">https://doi.org/10.1016/j.celrep.2023.112132</a>","ista":"Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3), 112132.","mla":"Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” <i>Cell Reports</i>, vol. 42, no. 3, 112132, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">10.1016/j.celrep.2023.112132</a>.","ieee":"D. B. Lyons <i>et al.</i>, “Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons,” <i>Cell Reports</i>, vol. 42, no. 3. Elsevier, 2023.","ama":"Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. <i>Cell Reports</i>. 2023;42(3). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">10.1016/j.celrep.2023.112132</a>","chicago":"Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">https://doi.org/10.1016/j.celrep.2023.112132</a>.","short":"D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023)."},"issue":"3","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","status":"public"},{"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","fulldoi":"https://doi.org/10.1137/1.9781611977554.ch173","ddc":["000"],"publication_identifier":{"isbn":["9781611977554"]},"doi":"10.1137/1.9781611977554.ch173","abstract":[{"lang":"eng","text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth."}],"language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","day":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611977554.ch173"}],"citation":{"ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Florence, Italy, 2023, pp. 4590–4605.","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">10.1137/1.9781611977554.ch173</a>","short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605.","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 4590–4605. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">https://doi.org/10.1137/1.9781611977554.ch173</a>.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">10.1137/1.9781611977554.ch173</a>.","ista":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster algorithm for turn-based stochastic games with bounded treewidth. Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4590–4605.","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., &#38; Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">https://doi.org/10.1137/1.9781611977554.ch173</a>"},"title":"Faster algorithm for turn-based stochastic games with bounded treewidth","date_created":"2023-02-24T12:20:47Z","month":"02","date_updated":"2026-06-18T17:28:38Z","article_processing_charge":"No","date_published":"2023-02-01T00:00:00Z","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer"},{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","full_name":"Saona Urmeneta, Raimundo J","orcid":"0000-0001-5103-038X","last_name":"Saona Urmeneta","first_name":"Raimundo J"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda","first_name":"Jakub"}],"publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","conference":{"end_date":"2023-01-25","start_date":"2023-01-22","name":"SODA: Symposium on Discrete Algorithms","location":"Florence, Italy"},"ec_funded":1,"_id":"12676","corr_author":"1","year":"2023","type":"conference","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","page":"4590-4605","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa":1},{"day":"01","oa_version":"Published Version","keyword":["General Neuroscience"],"external_id":{"isi":["000953497700001"],"pmid":["36842274"]},"issue":"4","citation":{"mla":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” <i>Current Opinion in Neurobiology</i>, vol. 79, no. 4, 102695, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.conb.2023.102695\">10.1016/j.conb.2023.102695</a>.","ieee":"S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights from developing cerebral cortex,” <i>Current Opinion in Neurobiology</i>, vol. 79, no. 4. Elsevier, 2023.","short":"S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).","ama":"Hippenmeyer S. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. <i>Current Opinion in Neurobiology</i>. 2023;79(4). doi:<a href=\"https://doi.org/10.1016/j.conb.2023.102695\">10.1016/j.conb.2023.102695</a>","chicago":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.conb.2023.102695\">https://doi.org/10.1016/j.conb.2023.102695</a>.","apa":"Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2023.102695\">https://doi.org/10.1016/j.conb.2023.102695</a>","ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695."},"has_accepted_license":"1","status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.conb.2023.102695","publication_identifier":{"issn":["0959-4388"]},"language":[{"iso":"eng"}],"abstract":[{"text":"How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression.","lang":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1016/j.conb.2023.102695","intvolume":"        79","acknowledgement":"I wish to thank all current and past members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. I apologize to colleagues whose work I could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agree-ment no. 725780 LinPro) to SH.","volume":79,"ddc":["570"],"file_date_updated":"2023-08-16T12:29:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Elsevier","article_number":"102695","oa":1,"quality_controlled":"1","pmid":1,"project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"department":[{"_id":"SiHi"}],"corr_author":"1","scopus_import":"1","type":"journal_article","year":"2023","file":[{"success":1,"file_id":"14071","date_updated":"2023-08-16T12:29:06Z","file_size":1787894,"date_created":"2023-08-16T12:29:06Z","content_type":"application/pdf","access_level":"open_access","checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","relation":"main_file","file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf","creator":"dernst"}],"publication":"Current Opinion in Neurobiology","date_published":"2023-04-01T00:00:00Z","author":[{"first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"_id":"12679","date_created":"2023-02-26T12:24:21Z","article_type":"review","title":"Principles of neural stem cell lineage progression: Insights from developing cerebral cortex","article_processing_charge":"Yes (via OA deal)","date_updated":"2025-04-15T08:23:06Z","month":"04"},{"status":"public","issue":"6","citation":{"ieee":"G. Ivanov and S. Köse, “Erdős-Ko-Rado and Hilton-Milner theorems for two-forms,” <i>Discrete Mathematics</i>, vol. 346, no. 6. Elsevier, 2023.","ama":"Ivanov G, Köse S. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. <i>Discrete Mathematics</i>. 2023;346(6). doi:<a href=\"https://doi.org/10.1016/j.disc.2023.113363\">10.1016/j.disc.2023.113363</a>","short":"G. Ivanov, S. Köse, Discrete Mathematics 346 (2023).","chicago":"Ivanov, Grigory, and Seyda Köse. “Erdős-Ko-Rado and Hilton-Milner Theorems for Two-Forms.” <i>Discrete Mathematics</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.disc.2023.113363\">https://doi.org/10.1016/j.disc.2023.113363</a>.","mla":"Ivanov, Grigory, and Seyda Köse. “Erdős-Ko-Rado and Hilton-Milner Theorems for Two-Forms.” <i>Discrete Mathematics</i>, vol. 346, no. 6, 113363, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.disc.2023.113363\">10.1016/j.disc.2023.113363</a>.","ista":"Ivanov G, Köse S. 2023. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. 346(6), 113363.","apa":"Ivanov, G., &#38; Köse, S. (2023). Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. <i>Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disc.2023.113363\">https://doi.org/10.1016/j.disc.2023.113363</a>"},"day":"01","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2201.10892","open_access":"1"}],"oa_version":"Preprint","external_id":{"arxiv":["2201.10892"],"isi":["001189844500001"]},"volume":346,"related_material":{"record":[{"id":"13331","relation":"dissertation_contains","status":"public"}]},"fulldoi":"https://doi.org/10.1016/j.disc.2023.113363","intvolume":"       346","language":[{"iso":"eng"}],"abstract":[{"text":"The celebrated Erdős–Ko–Rado theorem about the maximal size of an intersecting family of r-element subsets of  was extended to the setting of exterior algebra in [5, Theorem 2.3] and in [6, Theorem 1.4]. However, the equality case has not been settled yet. In this short note, we show that the extension of the Erdős–Ko–Rado theorem and the characterization of the equality case therein, as well as those of the Hilton–Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms follow from a folklore puzzle about possible arrangements of an intersecting family of lines.","lang":"eng"}],"isi":1,"doi":"10.1016/j.disc.2023.113363","publication_identifier":{"issn":["0012-365X"]},"department":[{"_id":"UlWa"},{"_id":"GradSch"}],"corr_author":"1","scopus_import":"1","year":"2023","type":"journal_article","oa":1,"article_number":"113363","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","publisher":"Elsevier","article_processing_charge":"No","date_updated":"2026-04-07T13:29:28Z","month":"06","date_created":"2023-02-26T23:01:00Z","arxiv":1,"article_type":"letter_note","title":"Erdős-Ko-Rado and Hilton-Milner theorems for two-forms","_id":"12680","publication":"Discrete Mathematics","date_published":"2023-06-01T00:00:00Z","author":[{"first_name":"Grigory","orcid":"0000-0002-5021-3982","last_name":"Ivanov","full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"first_name":"Seyda","orcid":"0009-0008-0457-9730","last_name":"Köse","full_name":"Köse, Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb"}]},{"year":"2023","scopus_import":"1","type":"journal_article","department":[{"_id":"BjHo"}],"quality_controlled":"1","oa":1,"publication_status":"published","publisher":"Annual Reviews","file_date_updated":"2023-02-27T09:23:02Z","page":"675-705","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"01","date_updated":"2023-08-01T13:19:47Z","article_processing_charge":"No","article_type":"original","title":"Elasto-inertial turbulence","date_created":"2023-02-26T23:01:01Z","_id":"12681","date_published":"2023-01-19T00:00:00Z","author":[{"full_name":"Dubief, Yves","first_name":"Yves","last_name":"Dubief"},{"full_name":"Terrapon, Vincent E.","first_name":"Vincent E.","last_name":"Terrapon"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"file":[{"date_updated":"2023-02-27T09:23:02Z","success":1,"file_id":"12690","file_size":4036706,"date_created":"2023-02-27T09:23:02Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"2666aa3af2a25252d35eb8681d3edff7","creator":"dernst","file_name":"2023_AnnReviewFluidMech_Dubief.pdf"}],"publication":"Annual Review of Fluid Mechanics","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","citation":{"chicago":"Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” <i>Annual Review of Fluid Mechanics</i>. Annual Reviews, 2023. <a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">https://doi.org/10.1146/annurev-fluid-032822-025933</a>.","ama":"Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. <i>Annual Review of Fluid Mechanics</i>. 2023;55(1):675-705. doi:<a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">10.1146/annurev-fluid-032822-025933</a>","short":"Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705.","ieee":"Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” <i>Annual Review of Fluid Mechanics</i>, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.","mla":"Dubief, Yves, et al. “Elasto-Inertial Turbulence.” <i>Annual Review of Fluid Mechanics</i>, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:<a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">10.1146/annurev-fluid-032822-025933</a>.","ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705.","apa":"Dubief, Y., Terrapon, V. E., &#38; Hof, B. (2023). Elasto-inertial turbulence. <i>Annual Review of Fluid Mechanics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">https://doi.org/10.1146/annurev-fluid-032822-025933</a>"},"issue":"1","oa_version":"Published Version","external_id":{"isi":["000915418100026"]},"day":"19","ddc":["530"],"volume":55,"acknowledgement":"Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545).","intvolume":"        55","fulldoi":"https://doi.org/10.1146/annurev-fluid-032822-025933","abstract":[{"lang":"eng","text":"The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT."}],"isi":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0066-4189"],"eissn":["1545-4479"]},"doi":"10.1146/annurev-fluid-032822-025933"},{"day":"19","external_id":{"isi":["000915418100023"]},"oa_version":"Published Version","citation":{"apa":"Avila, M., Barkley, D., &#38; Hof, B. (2023). Transition to turbulence in pipe flow. <i>Annual Review of Fluid Mechanics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">https://doi.org/10.1146/annurev-fluid-120720-025957</a>","ista":"Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602.","mla":"Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” <i>Annual Review of Fluid Mechanics</i>, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:<a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">10.1146/annurev-fluid-120720-025957</a>.","ieee":"M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” <i>Annual Review of Fluid Mechanics</i>, vol. 55. Annual Reviews, pp. 575–602, 2023.","chicago":"Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” <i>Annual Review of Fluid Mechanics</i>. Annual Reviews, 2023. <a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">https://doi.org/10.1146/annurev-fluid-120720-025957</a>.","ama":"Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. <i>Annual Review of Fluid Mechanics</i>. 2023;55:575-602. doi:<a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">10.1146/annurev-fluid-120720-025957</a>","short":"M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602."},"status":"public","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1146/annurev-fluid-120720-025957","publication_identifier":{"issn":["0066-4189"]},"language":[{"iso":"eng"}],"isi":1,"abstract":[{"text":"Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed.","lang":"eng"}],"fulldoi":"https://doi.org/10.1146/annurev-fluid-120720-025957","intvolume":"        55","acknowledgement":"The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.).","volume":55,"ddc":["530"],"page":"575-602","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2023-02-27T09:35:52Z","publisher":"Annual Reviews","publication_status":"published","oa":1,"quality_controlled":"1","department":[{"_id":"BjHo"}],"project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"year":"2023","type":"journal_article","scopus_import":"1","publication":"Annual Review of Fluid Mechanics","file":[{"success":1,"file_id":"12691","date_updated":"2023-02-27T09:35:52Z","date_created":"2023-02-27T09:35:52Z","file_size":4769537,"content_type":"application/pdf","access_level":"open_access","checksum":"f99ef30f76cabc9e5e1946b380c16db4","relation":"main_file","creator":"dernst","file_name":"2023_AnnReviewFluidMech_Avila.pdf"}],"author":[{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"},{"first_name":"Dwight","last_name":"Barkley","full_name":"Barkley, Dwight"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"date_published":"2023-01-19T00:00:00Z","_id":"12682","date_created":"2023-02-26T23:01:01Z","title":"Transition to turbulence in pipe flow","article_type":"original","article_processing_charge":"No","date_updated":"2024-10-22T11:08:43Z","month":"01"},{"publication":"Electronic Communications in Probability","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2023_ElectCommProbability_Dubach.pdf","creator":"dernst","relation":"main_file","checksum":"a1c6f0a3e33688fd71309c86a9aad86e","file_id":"12692","success":1,"date_updated":"2023-02-27T09:43:27Z","date_created":"2023-02-27T09:43:27Z","file_size":479105}],"date_published":"2023-02-08T00:00:00Z","author":[{"full_name":"Dubach, Guillaume","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Guillaume","orcid":"0000-0001-6892-8137","last_name":"Dubach"},{"orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"}],"ec_funded":1,"_id":"12683","date_created":"2023-02-26T23:01:01Z","arxiv":1,"title":"Dynamics of a rank-one perturbation of a Hermitian matrix","article_type":"original","article_processing_charge":"No","month":"02","date_updated":"2025-04-14T07:44:00Z","file_date_updated":"2023-02-27T09:43:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1-13","publication_status":"published","publisher":"Institute of Mathematical Statistics","oa":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331"}],"department":[{"_id":"LaEr"}],"corr_author":"1","scopus_import":"1","type":"journal_article","year":"2023","doi":"10.1214/23-ECP516","publication_identifier":{"eissn":["1083-589X"]},"language":[{"iso":"eng"}],"abstract":[{"text":"We study the eigenvalue trajectories of a time dependent matrix Gt=H+itvv∗ for t≥0, where H is an N×N Hermitian random matrix and v is a unit vector. In particular, we establish that with high probability, an outlier can be distinguished at all times t>1+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines elements of Hermitian and non-Hermitian analysis, and illustrates some aspects of the intrinsic instability of (even weakly) non-Hermitian matrices.","lang":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1214/23-ECP516","acknowledgement":"G. Dubach gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. L. Erdős is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","intvolume":"        28","volume":28,"ddc":["510"],"day":"08","oa_version":"Published Version","external_id":{"isi":["000950650200005"],"arxiv":["2108.13694"]},"citation":{"apa":"Dubach, G., &#38; Erdös, L. (2023). Dynamics of a rank-one perturbation of a Hermitian matrix. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-ECP516\">https://doi.org/10.1214/23-ECP516</a>","ista":"Dubach G, Erdös L. 2023. Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. 28, 1–13.","mla":"Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” <i>Electronic Communications in Probability</i>, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–13, doi:<a href=\"https://doi.org/10.1214/23-ECP516\">10.1214/23-ECP516</a>.","short":"G. Dubach, L. Erdös, Electronic Communications in Probability 28 (2023) 1–13.","ama":"Dubach G, Erdös L. Dynamics of a rank-one perturbation of a Hermitian matrix. <i>Electronic Communications in Probability</i>. 2023;28:1-13. doi:<a href=\"https://doi.org/10.1214/23-ECP516\">10.1214/23-ECP516</a>","chicago":"Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/23-ECP516\">https://doi.org/10.1214/23-ECP516</a>.","ieee":"G. Dubach and L. Erdös, “Dynamics of a rank-one perturbation of a Hermitian matrix,” <i>Electronic Communications in Probability</i>, vol. 28. Institute of Mathematical Statistics, pp. 1–13, 2023."},"status":"public","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"oa":1,"citation":{"mla":"Cremer, Sylvia. <i>Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males </i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12693\">10.15479/AT:ISTA:12693</a>.","ama":"Cremer S. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12693\">10.15479/AT:ISTA:12693</a>","chicago":"Cremer, Sylvia. “Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males .” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12693\">https://doi.org/10.15479/AT:ISTA:12693</a>.","short":"S. Cremer, (2023).","ieee":"S. Cremer, “Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males .” Institute of Science and Technology Austria, 2023.","apa":"Cremer, S. (2023). Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12693\">https://doi.org/10.15479/AT:ISTA:12693</a>","ista":"Cremer S. 2023. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12693\">10.15479/AT:ISTA:12693</a>."},"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"28","file_date_updated":"2023-02-28T06:34:12Z","year":"2023","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"type":"research_data","corr_author":"1","status":"public","department":[{"_id":"SyCr"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"See Readme File for further information."}],"contributor":[{"id":"48204546-F248-11E8-B48F-1D18A9856A87","contributor_type":"data_collector","first_name":"Sina","last_name":"Metzler"},{"id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3","contributor_type":"data_collector","last_name":"Kirchner","first_name":"Jessica"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","contributor_type":"data_collector","first_name":"Anna V","last_name":"Grasse"}],"_id":"12693","author":[{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"date_published":"2023-02-28T00:00:00Z","file":[{"relation":"main_file","checksum":"c1565d655ca05601acfd84e0d12b8563","file_name":"Metzler_ReadMe.pdf","creator":"scremer","content_type":"application/pdf","access_level":"open_access","date_created":"2023-02-28T06:34:08Z","file_size":77070,"success":1,"file_id":"12694","date_updated":"2023-02-28T06:34:08Z"},{"relation":"main_file","checksum":"75c4c4948563d6261cb7548f80d909f1","file_name":"Metzler_RepositoryData.xlsx","creator":"scremer","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","access_level":"open_access","date_created":"2023-02-28T06:34:12Z","file_size":88001,"date_updated":"2023-02-28T06:34:12Z","success":1,"file_id":"12695"}],"doi":"10.15479/AT:ISTA:12693","date_updated":"2025-04-14T13:55:29Z","month":"02","ddc":["570"],"article_processing_charge":"No","title":"Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males ","fulldoi":"https://doi.org/10.15479/AT:ISTA:12693","date_created":"2023-02-28T06:38:37Z","related_material":{"record":[{"status":"public","id":"12696","relation":"used_in_publication"}]}}]