[{"author":[{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea","first_name":"Andrea"},{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","last_name":"Khudiakova","first_name":"Kseniia","full_name":"Khudiakova, Kseniia"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"language":[{"iso":"eng"}],"month":"02","type":"journal_article","article_processing_charge":"Yes (via OA deal)","publication":"Evolution Letters","scopus_import":"1","ddc":["570"],"volume":7,"file_date_updated":"2023-08-16T11:43:33Z","date_created":"2023-02-06T13:59:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","project":[{"call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"715257","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated."}],"pmid":1,"_id":"12521","acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","oa":1,"external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"date_updated":"2023-08-16T11:44:32Z","status":"public","intvolume":"         7","has_accepted_license":"1","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","publication_identifier":{"issn":["2056-3744"]},"issue":"1","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"qrac004","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"day":"01","doi":"10.1093/evlett/qrac004","year":"2023","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"file":[{"creator":"dernst","date_created":"2023-08-16T11:43:33Z","success":1,"file_id":"14068","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":2592189,"checksum":"a240a041cb9b9b7c8ba93a4706674a3f","file_name":"2023_EvLetters_Mrnjavac.pdf","date_updated":"2023-08-16T11:43:33Z"}],"oa_version":"Published Version","date_published":"2023-02-01T00:00:00Z","article_type":"original","citation":{"ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” <i>Evolution Letters</i>, vol. 7, no. 1. Oxford University Press, 2023.","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. 2023;7(1). doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., &#38; Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>."},"publication_status":"published","quality_controlled":"1"},{"date_created":"2023-02-09T07:45:05Z","page":"46","file_date_updated":"2024-02-09T23:30:03Z","ddc":["570"],"article_processing_charge":"No","type":"dissertation","month":"02","author":[{"id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","full_name":"Kirillova, Kseniia","first_name":"Kseniia","last_name":"Kirillova"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Master's Thesis"],"_id":"12531","abstract":[{"text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","degree_awarded":"MS","year":"2023","doi":"10.15479/at:ista:12531","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"day":"08","publication_identifier":{"issn":["2791-4585"]},"title":"Panoramic functional gradients across the mouse retina","has_accepted_license":"1","status":"public","date_updated":"2024-02-09T23:30:04Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","supervisor":[{"first_name":"Maximilian A","full_name":"Jösch, Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publication_status":"published","citation":{"ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","mla":"Kirillova, Kseniia. <i>Panoramic Functional Gradients across the Mouse Retina</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>.","apa":"Kirillova, K. (2023). <i>Panoramic functional gradients across the mouse retina</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>"},"date_published":"2023-02-08T00:00:00Z","file":[{"access_level":"open_access","relation":"main_file","checksum":"57d8da3a6c749eb1556b7435fe266a5f","file_size":8369317,"embargo":"2024-02-08","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","date_updated":"2024-02-09T23:30:03Z","creator":"cchlebak","date_created":"2023-02-09T08:03:32Z","file_id":"12532","content_type":"application/pdf"},{"date_updated":"2024-02-09T23:30:03Z","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","embargo_to":"open_access","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","file_size":11204408,"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_id":"12535","date_created":"2023-02-10T09:32:06Z","creator":"cchlebak"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"MaJö"}]},{"date_created":"2023-02-10T09:02:26Z","file_date_updated":"2023-02-13T10:38:10Z","volume":5,"ddc":["530"],"publication":"Physical Review Research","article_processing_charge":"No","scopus_import":"1","type":"journal_article","author":[{"last_name":"Ghazaryan","first_name":"Areg","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359","last_name":"Cappellaro","full_name":"Cappellaro, Alberto","first_name":"Alberto"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"},{"last_name":"Volosniev","full_name":"Volosniev, Artem","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"01","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).","_id":"12534","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"}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"}],"publisher":"American Physical Society","year":"2023","publication_identifier":{"issn":["2643-1564"]},"title":"Dissipative dynamics of an impurity with spin-orbit coupling","issue":"1","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1103/physrevresearch.5.013029","day":"20","article_number":"013029","date_updated":"2023-02-20T07:02:00Z","intvolume":"         5","status":"public","oa":1,"quality_controlled":"1","citation":{"short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","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>.","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.","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.","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>","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>."},"publication_status":"published","article_type":"original","date_published":"2023-01-20T00:00:00Z","department":[{"_id":"MiLe"}],"file":[{"creator":"dernst","date_created":"2023-02-13T10:38:10Z","success":1,"content_type":"application/pdf","file_id":"12546","checksum":"6068b62874c0099628a108bb9c5c6bd2","file_size":865150,"relation":"main_file","access_level":"open_access","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","date_updated":"2023-02-13T10:38:10Z"}],"oa_version":"Published Version"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","abstract":[{"lang":"eng","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."}],"_id":"12542","language":[{"iso":"eng"}],"month":"02","author":[{"full_name":"Villalba Requena, Ana","first_name":"Ana","last_name":"Villalba Requena","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"type":"journal_article","article_processing_charge":"No","publication":"Neuron","scopus_import":"1","volume":111,"page":"291-293","date_created":"2023-02-12T23:00:58Z","department":[{"_id":"SiHi"}],"oa_version":"None","date_published":"2023-02-01T00:00:00Z","article_type":"letter_note","publication_status":"published","citation":{"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>.","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>","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>","ista":"Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293.","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>.","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."},"quality_controlled":"1","external_id":{"isi":["000994473300001"]},"date_updated":"2023-08-01T13:10:27Z","status":"public","intvolume":"       111","title":"Going back in time with TEMPO","issue":"3","publication_identifier":{"eissn":["1097-4199"]},"isi":1,"day":"01","doi":"10.1016/j.neuron.2023.01.006","year":"2023"},{"scopus_import":"1","publication":"Nature Ecology and Evolution","article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"month":"03","author":[{"id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock","full_name":"Stock, Miriam","first_name":"Miriam"},{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","first_name":"Barbara","full_name":"Milutinovic, Barbara","last_name":"Milutinovic"},{"last_name":"Hönigsberger","first_name":"Michaela","full_name":"Hönigsberger, Michaela","id":"953894f3-25bd-11ec-8556-f70a9d38ef60"},{"last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"id":"39523C54-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer"},{"first_name":"Niklas","full_name":"Kampleitner, Niklas","last_name":"Kampleitner","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671"},{"full_name":"Schmitt, Thomas","first_name":"Thomas","last_name":"Schmitt"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"date_created":"2023-02-12T23:00:59Z","page":"450-460","related_material":{"link":[{"url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/","description":"News on ISTA website","relation":"press_release"}]},"file_date_updated":"2023-08-16T11:54:59Z","volume":7,"ddc":["570"],"ec_funded":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"project":[{"grant_number":"771402","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"}],"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","_id":"12543","pmid":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"}],"intvolume":"         7","status":"public","date_updated":"2023-08-16T11:55:48Z","external_id":{"isi":["000924572800001"],"pmid":["36732670"]},"oa":1,"year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1038/s41559-023-01981-6","day":"01","isi":1,"title":"Pathogen evasion of social immunity","has_accepted_license":"1","publication_identifier":{"eissn":["2397-334X"]},"article_type":"original","date_published":"2023-03-01T00:00:00Z","file":[{"checksum":"8244f4650a0e7aeea488d1bcd4a31702","file_size":1600499,"relation":"main_file","access_level":"open_access","file_name":"2023_NatureEcoEvo_Stock.pdf","date_updated":"2023-08-16T11:54:59Z","creator":"dernst","success":1,"date_created":"2023-08-16T11:54:59Z","content_type":"application/pdf","file_id":"14069"}],"oa_version":"Published Version","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"quality_controlled":"1","publication_status":"published","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>","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>","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>.","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.","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>.","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.","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."}},{"abstract":[{"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.","lang":"eng"}],"pmid":1,"_id":"12544","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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Chemical Society","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"ddc":["510","540"],"volume":63,"file_date_updated":"2023-08-16T12:21:13Z","page":"973-985","date_created":"2023-02-12T23:00:59Z","month":"02","language":[{"iso":"eng"}],"author":[{"last_name":"Koehl","first_name":"Patrice","full_name":"Koehl, Patrice"},{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy","first_name":"Arseniy"},{"last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","article_processing_charge":"No","publication":"Journal of Chemical Information and Modeling","scopus_import":"1","citation":{"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>.","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>","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>.","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985.","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."},"publication_status":"published","quality_controlled":"1","department":[{"_id":"HeEd"}],"file":[{"file_name":"2023_JCIM_Koehl.pdf","access_level":"open_access","relation":"main_file","file_size":8069223,"checksum":"7d20562269edff1e31b9d6019d4983b0","date_updated":"2023-08-16T12:21:13Z","creator":"dernst","file_id":"14070","content_type":"application/pdf","date_created":"2023-08-16T12:21:13Z","success":1}],"oa_version":"Published Version","date_published":"2023-02-13T00:00:00Z","article_type":"original","title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","has_accepted_license":"1","issue":"3","publication_identifier":{"issn":["1549-9596"],"eissn":["1549-960X"]},"isi":1,"doi":"10.1021/acs.jcim.2c01346","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"13","year":"2023","oa":1,"external_id":{"pmid":["36638318"],"isi":["000920370700001"]},"date_updated":"2023-08-16T12:22:07Z","status":"public","intvolume":"        63"},{"article_type":"original","date_published":"2023-01-24T00:00:00Z","department":[{"_id":"GradSch"}],"oa_version":"Preprint","quality_controlled":"1","arxiv":1,"citation":{"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>.","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>","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.","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>.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","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."},"publication_status":"published","date_updated":"2023-08-01T13:09:45Z","intvolume":"       107","status":"public","oa":1,"external_id":{"isi":["000963909800006"],"arxiv":["2301.01856"]},"year":"2023","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","issue":"1","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"day":"24","article_number":"014608","doi":"10.1103/PhysRevE.107.014608","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01856"}],"publisher":"American Physical Society","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.","_id":"12545","abstract":[{"lang":"eng","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."}],"publication":"Physical Review E","article_processing_charge":"No","scopus_import":"1","type":"journal_article","author":[{"id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","last_name":"Rojas Vega","first_name":"Mauricio Nicolas","full_name":"Rojas Vega, Mauricio Nicolas"},{"last_name":"De Castro","full_name":"De Castro, Pablo","first_name":"Pablo"},{"last_name":"Soto","full_name":"Soto, Rodrigo","first_name":"Rodrigo"}],"language":[{"iso":"eng"}],"month":"01","date_created":"2023-02-12T23:00:59Z","volume":107},{"date_created":"2023-02-14T07:56:21Z","file_date_updated":"2023-02-14T07:58:26Z","ddc":["600"],"publication":"2022 IEEE International Conference on Data Mining Workshops","article_processing_charge":"No","type":"conference","language":[{"iso":"eng"}],"month":"02","author":[{"last_name":"Forghani","full_name":"Forghani, Mohammad","first_name":"Mohammad"},{"last_name":"Claramunt","full_name":"Claramunt, Christophe","first_name":"Christophe"},{"first_name":"Farid","full_name":"Karimipour, Farid","last_name":"Karimipour","orcid":"0000-0001-6746-4174","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425"},{"full_name":"Heiler, Georg","first_name":"Georg","last_name":"Heiler"}],"conference":{"location":"Orlando, FL, United States","name":"ICDMW: Conference on Data Mining Workshops","start_date":"2022-11-28","end_date":"2022-12-01"},"_id":"12548","abstract":[{"text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Institute of Electrical and Electronics Engineers","year":"2023","title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","has_accepted_license":"1","publication_identifier":{"eisbn":["9798350346091"],"eissn":["2375-9259"]},"day":"08","article_number":"00093","doi":"10.1109/icdmw58026.2022.00093","isi":1,"date_updated":"2023-08-01T13:15:48Z","status":"public","oa":1,"external_id":{"isi":["000971492200145"]},"quality_controlled":"1","publication_status":"published","citation":{"apa":"Forghani, M., Claramunt, C., Karimipour, F., &#38; Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In <i>2022 IEEE International Conference on Data Mining Workshops</i>. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">https://doi.org/10.1109/icdmw58026.2022.00093</a>","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: <i>2022 IEEE International Conference on Data Mining Workshops</i>. Institute of Electrical and Electronics Engineers; 2023. doi:<a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">10.1109/icdmw58026.2022.00093</a>","chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In <i>2022 IEEE International Conference on Data Mining Workshops</i>. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">https://doi.org/10.1109/icdmw58026.2022.00093</a>.","ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in <i>2022 IEEE International Conference on Data Mining Workshops</i>, Orlando, FL, United States, 2023.","mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” <i>2022 IEEE International Conference on Data Mining Workshops</i>, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:<a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">10.1109/icdmw58026.2022.00093</a>.","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023.","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093."},"date_published":"2023-02-08T00:00:00Z","department":[{"_id":"HeEd"}],"oa_version":"Submitted Version","file":[{"creator":"fkarimip","success":1,"date_created":"2023-02-14T07:58:26Z","file_id":"12549","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c253bee25e6dfe484f96662daa119cb6","file_size":1183339,"file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","date_updated":"2023-02-14T07:58:26Z"}]},{"citation":{"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>.","short":"D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512.","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.","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.","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>","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>","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>."},"publication_status":"published","quality_controlled":"1","department":[{"_id":"SiHi"}],"oa_version":"None","date_published":"2023-03-01T00:00:00Z","article_type":"original","title":"Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons","publication_identifier":{"eissn":["1522-1598"],"issn":["0022-3077"]},"issue":"3","isi":1,"doi":"10.1152/jn.00172.2022","keyword":["Physiology","General Neuroscience"],"day":"01","year":"2023","external_id":{"pmid":["36695533"],"isi":["000957721600001"]},"date_updated":"2023-09-05T12:13:34Z","status":"public","intvolume":"       129","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"}],"pmid":1,"_id":"12562","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.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"American Physiological Society","volume":129,"page":"501-512","date_created":"2023-02-15T14:46:14Z","month":"03","author":[{"last_name":"Ladle","full_name":"Ladle, David R.","first_name":"David R."},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","publication":"Journal of Neurophysiology"},{"arxiv":1,"quality_controlled":"1","publication_status":"published","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 &#38; Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/20m1378223\">https://doi.org/10.1137/20m1378223</a>.","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 &#38; Applied Mathematics. <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>","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.","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 &#38; 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 &#38; Applied Mathematics, 2023, pp. 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."},"date_published":"2023-01-01T00:00:00Z","article_type":"original","oa_version":"Preprint","department":[{"_id":"UlWa"}],"year":"2023","isi":1,"day":"01","keyword":["General Mathematics","General Computer Science"],"doi":"10.1137/20m1378223","issue":"1","title":"Topology and adjunction in promise constraint satisfaction","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"status":"public","intvolume":"        52","date_updated":"2023-08-01T13:11:30Z","external_id":{"arxiv":["2003.11351"],"isi":["000955000000001"]},"oa":1,"_id":"12563","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. ","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."}],"ec_funded":1,"publisher":"Society for Industrial & Applied Mathematics","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2003.11351"}],"project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2023-02-16T07:03:52Z","page":"38-79","volume":52,"scopus_import":"1","article_processing_charge":"No","publication":"SIAM Journal on Computing","language":[{"iso":"eng"}],"month":"01","author":[{"last_name":"Krokhin","full_name":"Krokhin, Andrei","first_name":"Andrei"},{"id":"ec596741-c539-11ec-b829-c79322a91242","orcid":"0000-0003-1245-3456","last_name":"Opršal","first_name":"Jakub","full_name":"Opršal, Jakub"},{"last_name":"Wrochna","full_name":"Wrochna, Marcin","first_name":"Marcin"},{"last_name":"Živný","first_name":"Stanislav","full_name":"Živný, Stanislav"}],"type":"journal_article"},{"external_id":{"isi":["000934262700001"]},"oa":1,"intvolume":"       948","status":"public","date_updated":"2023-08-01T13:17:20Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"28","article_number":"113733","doi":"10.1016/j.tcs.2023.113733","isi":1,"has_accepted_license":"1","issue":"2","publication_identifier":{"issn":["0304-3975"]},"title":"Wait-free approximate agreement on graphs","year":"2023","oa_version":"Published Version","file":[{"creator":"dernst","date_created":"2023-02-20T07:30:20Z","success":1,"file_id":"12570","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":602333,"checksum":"b27c5290f2f1500c403494364ee39c9f","file_name":"2023_TheoreticalCompScience_Alistarh.pdf","date_updated":"2023-02-20T07:30:20Z"}],"department":[{"_id":"DaAl"}],"article_type":"original","date_published":"2023-02-28T00:00:00Z","citation":{"ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","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>.","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023).","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.","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>.","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>","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>"},"publication_status":"published","quality_controlled":"1","type":"journal_article","month":"02","author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"last_name":"Ellen","full_name":"Ellen, Faith","first_name":"Faith"},{"orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","first_name":"Joel","last_name":"Rybicki"}],"language":[{"iso":"eng"}],"scopus_import":"1","publication":"Theoretical Computer Science","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2023-02-20T07:30:20Z","volume":948,"ddc":["000"],"date_created":"2023-02-19T23:00:55Z","project":[{"call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"},{"name":"Coordination in constrained and natural distributed systems","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"840605"}],"publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ec_funded":1,"abstract":[{"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.","lang":"eng"}],"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.","_id":"12566"},{"external_id":{"isi":["000930324700001"]},"oa":1,"status":"public","intvolume":"        24","date_updated":"2023-08-01T13:16:36Z","isi":1,"day":"21","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"2128","doi":"10.3390/ijms24032128","issue":"3","publication_identifier":{"eissn":["1422-0067"]},"title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","has_accepted_license":"1","year":"2023","file":[{"creator":"dernst","content_type":"application/pdf","file_id":"12569","date_created":"2023-02-20T07:09:27Z","success":1,"file_name":"2023_IJMS_Mrestani.pdf","checksum":"69a35dcd3e0249f902ab881b06ee2e58","file_size":2823025,"access_level":"open_access","relation":"main_file","date_updated":"2023-02-20T07:09:27Z"}],"oa_version":"Published Version","department":[{"_id":"PeJo"}],"date_published":"2023-01-21T00:00:00Z","article_type":"original","citation":{"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>.","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>","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.","short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (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>.","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."},"publication_status":"published","quality_controlled":"1","language":[{"iso":"eng"}],"author":[{"last_name":"Mrestani","first_name":"Achmed","full_name":"Mrestani, Achmed"},{"last_name":"Lichter","full_name":"Lichter, Katharina","first_name":"Katharina","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d"},{"full_name":"Sirén, Anna Leena","first_name":"Anna Leena","last_name":"Sirén"},{"last_name":"Heckmann","first_name":"Manfred","full_name":"Heckmann, Manfred"},{"last_name":"Paul","first_name":"Mila M.","full_name":"Paul, Mila M."},{"last_name":"Pauli","first_name":"Martin","full_name":"Pauli, Martin"}],"month":"01","type":"journal_article","scopus_import":"1","article_processing_charge":"No","publication":"International Journal of Molecular Sciences","volume":24,"ddc":["570"],"file_date_updated":"2023-02-20T07:09:27Z","date_created":"2023-02-19T23:00:56Z","publisher":"MDPI","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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."}],"_id":"12567","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."},{"date_updated":"2023-05-08T10:52:49Z","extern":"1","status":"public","intvolume":"        24","oa":1,"external_id":{"pmid":["36639687"]},"year":"2023","title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","publication_identifier":{"issn":["1474-760X"]},"doi":"10.1186/s13059-022-02844-2","article_number":"7","day":"13","date_published":"2023-01-13T00:00:00Z","article_type":"original","department":[{"_id":"XiFe"}],"oa_version":"Published Version","quality_controlled":"1","citation":{"ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. <i>Genome Biology</i>. 2023;24. doi:<a href=\"https://doi.org/10.1186/s13059-022-02844-2\">10.1186/s13059-022-02844-2</a>","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-022-02844-2\">https://doi.org/10.1186/s13059-022-02844-2</a>","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” <i>Genome Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13059-022-02844-2\">https://doi.org/10.1186/s13059-022-02844-2</a>.","ieee":"L. Zhao <i>et al.</i>, “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” <i>Genome Biology</i>, vol. 24. Springer Nature, 2023.","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” <i>Genome Biology</i>, vol. 24, 7, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13059-022-02844-2\">10.1186/s13059-022-02844-2</a>.","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7."},"publication_status":"published","article_processing_charge":"No","publication":"Genome Biology","scopus_import":"1","month":"01","author":[{"last_name":"Zhao","first_name":"Long","full_name":"Zhao, Long"},{"last_name":"Yang","full_name":"Yang, Yiman","first_name":"Yiman"},{"last_name":"Chen","first_name":"Jinchao","full_name":"Chen, Jinchao"},{"first_name":"Xuelei","full_name":"Lin, Xuelei","last_name":"Lin"},{"full_name":"Zhang, Hao","first_name":"Hao","last_name":"Zhang"},{"first_name":"Hao","full_name":"Wang, Hao","last_name":"Wang"},{"last_name":"Wang","first_name":"Hongzhe","full_name":"Wang, Hongzhe"},{"first_name":"Xiaomin","full_name":"Bie, Xiaomin","last_name":"Bie"},{"last_name":"Jiang","full_name":"Jiang, Jiafu","first_name":"Jiafu"},{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng"},{"last_name":"Fu","first_name":"Xiangdong","full_name":"Fu, Xiangdong"},{"last_name":"Zhang","full_name":"Zhang, Xiansheng","first_name":"Xiansheng"},{"last_name":"Du","full_name":"Du, Zhuo","first_name":"Zhuo"},{"first_name":"Jun","full_name":"Xiao, Jun","last_name":"Xiao"}],"language":[{"iso":"eng"}],"type":"journal_article","date_created":"2023-02-23T09:13:49Z","volume":24,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"pmid":1,"_id":"12668","abstract":[{"text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.","lang":"eng"}]},{"_id":"12669","pmid":1,"abstract":[{"lang":"eng","text":"The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/plcell/koac346"}],"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-02-23T09:14:59Z","volume":35,"scopus_import":"1","publication":"The Plant Cell","article_processing_charge":"No","type":"journal_article","month":"06","author":[{"last_name":"Manavella","full_name":"Manavella, Pablo A","first_name":"Pablo A"},{"full_name":"Godoy Herz, Micaela A","first_name":"Micaela A","last_name":"Godoy Herz"},{"full_name":"Kornblihtt, Alberto R","first_name":"Alberto R","last_name":"Kornblihtt"},{"full_name":"Sorenson, Reed","first_name":"Reed","last_name":"Sorenson"},{"last_name":"Sieburth","full_name":"Sieburth, Leslie E","first_name":"Leslie E"},{"first_name":"Kentaro","full_name":"Nakaminami, Kentaro","last_name":"Nakaminami"},{"last_name":"Seki","full_name":"Seki, Motoaki","first_name":"Motoaki"},{"full_name":"Ding, Yiliang","first_name":"Yiliang","last_name":"Ding"},{"full_name":"Sun, Qianwen","first_name":"Qianwen","last_name":"Sun"},{"last_name":"Kang","first_name":"Hunseung","full_name":"Kang, Hunseung"},{"first_name":"Federico D","full_name":"Ariel, Federico D","last_name":"Ariel"},{"last_name":"Crespi","full_name":"Crespi, Martin","first_name":"Martin"},{"full_name":"Giudicatti, Axel J","first_name":"Axel J","last_name":"Giudicatti"},{"last_name":"Cai","full_name":"Cai, Qiang","first_name":"Qiang"},{"full_name":"Jin, Hailing","first_name":"Hailing","last_name":"Jin"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"full_name":"Qi, Yijun","first_name":"Yijun","last_name":"Qi"},{"first_name":"Craig S","full_name":"Pikaard, Craig S","last_name":"Pikaard"}],"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"apa":"Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth, L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling open questions in plant RNA biology. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac346\">https://doi.org/10.1093/plcell/koac346</a>","ama":"Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling open questions in plant RNA biology. <i>The Plant Cell</i>. 2023;35(6). doi:<a href=\"https://doi.org/10.1093/plcell/koac346\">10.1093/plcell/koac346</a>","chicago":"Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson, Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” <i>The Plant Cell</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/plcell/koac346\">https://doi.org/10.1093/plcell/koac346</a>.","ieee":"P. A. Manavella <i>et al.</i>, “Beyond transcription: compelling open questions in plant RNA biology,” <i>The Plant Cell</i>, vol. 35, no. 6. Oxford University Press, 2023.","short":"P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth, K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J. Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).","mla":"Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” <i>The Plant Cell</i>, vol. 35, no. 6, koac346, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/plcell/koac346\">10.1093/plcell/koac346</a>.","ista":"Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 35(6), koac346."},"publication_status":"published","article_type":"original","date_published":"2023-06-01T00:00:00Z","oa_version":"Published Version","department":[{"_id":"XiFe"}],"year":"2023","day":"01","article_number":"koac346","doi":"10.1093/plcell/koac346","keyword":["Cell Biology","Plant Science"],"title":"Beyond transcription: compelling open questions in plant RNA biology","issue":"6","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"intvolume":"        35","status":"public","extern":"1","date_updated":"2023-10-04T09:48:43Z","external_id":{"pmid":["36477566"]},"oa":1},{"year":"2023","title":"Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons","issue":"3","publication_identifier":{"eissn":["2211-1247"]},"has_accepted_license":"1","isi":1,"day":"28","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"112132","doi":"10.1016/j.celrep.2023.112132","date_updated":"2023-11-02T12:23:45Z","status":"public","intvolume":"        42","oa":1,"external_id":{"isi":["000944921600001"]},"quality_controlled":"1","citation":{"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.","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).","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>.","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.","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>","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>."},"publication_status":"published","date_published":"2023-03-28T00:00:00Z","article_type":"original","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"oa_version":"Published Version","file":[{"file_name":"2023_CellReports_Lyons.pdf","relation":"main_file","access_level":"open_access","checksum":"6cbc44fdb18bf18834c9e2a5b9c67123","file_size":8401261,"date_updated":"2023-05-11T10:41:42Z","creator":"kschuh","file_id":"12941","content_type":"application/pdf","date_created":"2023-05-11T10:41:42Z","success":1}],"date_created":"2023-02-23T09:17:44Z","volume":42,"ddc":["580"],"file_date_updated":"2023-05-11T10:41:42Z","article_processing_charge":"Yes","publication":"Cell Reports","scopus_import":"1","month":"03","author":[{"full_name":"Lyons, David B.","first_name":"David B.","last_name":"Lyons"},{"full_name":"Briffa, Amy","first_name":"Amy","last_name":"Briffa"},{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"last_name":"Choi","full_name":"Choi, Jaemyung","first_name":"Jaemyung"},{"first_name":"Elizabeth","full_name":"Hollwey, Elizabeth","last_name":"Hollwey","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"full_name":"Colicchio, Jack","first_name":"Jack","last_name":"Colicchio"},{"first_name":"Ian","full_name":"Anderson, Ian","last_name":"Anderson"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng"},{"last_name":"Howard","full_name":"Howard, Martin","first_name":"Martin"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"language":[{"iso":"eng"}],"type":"journal_article","_id":"12672","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.","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"}],"ec_funded":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","project":[{"grant_number":"725746","call_identifier":"H2020","_id":"62935a00-2b32-11ec-9570-eff30fa39068","name":"Quantitative analysis of DNA methylation maintenance with chromatin"}]},{"abstract":[{"text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein--protein interactions. By studying a pair of structurally homologous cross-β amyloid fibrils, HET-s and HELLF, with a specific isotope-labeling approach and magic-angle-spinning (MAS) NMR, we have characterized the dynamic behavior of Phe and Tyr aromatic rings to show that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips, on a variety of time scales from ns to µs. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from a NMR structural ensemble of such amyloid cross-β architecture.","lang":"eng"}],"pmid":1,"acknowledgement":"We thank AlbertA. Smith (Leipzig)for insightful discussions. This work was supported by funding from the European Research Council (StG-2012-311318 to P.S.) and used the platforms of the Grenoble Instruct-ERIC center (ISBG;UMS 3518 CNRS-CEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology(PSB) and facilities and expertiseof the Biophysical and Structural Chemistry platform (BPCS) at IECB,CNRSUAR3033,INSERMUS001 and Bordeaux University.","_id":"12675","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","file_date_updated":"2023-08-16T12:33:31Z","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/dancing-styles-of-atoms/"}],"record":[{"status":"public","id":"14861","relation":"other"},{"status":"public","id":"12497","relation":"research_data"}]},"ddc":["540"],"volume":62,"date_created":"2023-02-24T10:45:01Z","type":"journal_article","language":[{"iso":"eng"}],"author":[{"full_name":"Becker, Lea Marie","first_name":"Lea Marie","last_name":"Becker","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"first_name":"Mélanie","full_name":"Berbon, Mélanie","last_name":"Berbon"},{"last_name":"Vallet","full_name":"Vallet, Alicia","first_name":"Alicia"},{"full_name":"Grelard, Axelle","first_name":"Axelle","last_name":"Grelard"},{"last_name":"Morvan","full_name":"Morvan, Estelle","first_name":"Estelle"},{"first_name":"Benjamin","full_name":"Bardiaux, Benjamin","last_name":"Bardiaux"},{"last_name":"Lichtenecker","first_name":"Roman","full_name":"Lichtenecker, Roman"},{"full_name":"Ernst, Matthias","first_name":"Matthias","last_name":"Ernst"},{"full_name":"Loquet, Antoine","first_name":"Antoine","last_name":"Loquet"},{"last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"month":"05","publication":"Angewandte Chemie International Edition","article_processing_charge":"Yes (via OA deal)","publication_status":"published","citation":{"short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie International Edition 62 (2023).","mla":"Becker, Lea Marie, et al. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 19, e202219314, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/anie.202219314\">10.1002/anie.202219314</a>.","ieee":"L. M. Becker <i>et al.</i>, “The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues,” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 19. Wiley, 2023.","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 62(19), e202219314.","ama":"Becker LM, Berbon M, Vallet A, et al. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. <i>Angewandte Chemie International Edition</i>. 2023;62(19). doi:<a href=\"https://doi.org/10.1002/anie.202219314\">10.1002/anie.202219314</a>","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202219314\">https://doi.org/10.1002/anie.202219314</a>","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” <i>Angewandte Chemie International Edition</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/anie.202219314\">https://doi.org/10.1002/anie.202219314</a>."},"quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"file":[{"file_id":"14072","content_type":"application/pdf","success":1,"date_created":"2023-08-16T12:33:31Z","creator":"dernst","date_updated":"2023-08-16T12:33:31Z","file_name":"2023_AngewChemInt_Becker.pdf","access_level":"open_access","relation":"main_file","file_size":1422445,"checksum":"7dd083ed8850faa55c34e411ed390de9"}],"oa_version":"Published Version","article_type":"original","date_published":"2023-05-01T00:00:00Z","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"title":"The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues","issue":"19","has_accepted_license":"1","article_number":"e202219314","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"doi":"10.1002/anie.202219314","keyword":["General Chemistry","Catalysis"],"day":"01","isi":1,"year":"2023","oa":1,"external_id":{"pmid":["36738230"],"isi":["000956919900001"]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","date_updated":"2024-02-21T12:14:06Z","intvolume":"        62","status":"public"},{"doi":"10.1137/1.9781611977554.ch173","day":"01","title":"Faster algorithm for turn-based stochastic games with bounded treewidth","publication_identifier":{"isbn":["9781611977554"]},"year":"2023","oa":1,"status":"public","date_updated":"2025-07-14T09:09:50Z","publication_status":"published","citation":{"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.","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.","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>.","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>.","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>","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>"},"quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_published":"2023-02-01T00:00:00Z","date_created":"2023-02-24T12:20:47Z","page":"4590-4605","type":"conference","conference":{"end_date":"2023-01-25","start_date":"2023-01-22","location":"Florence, Italy","name":"SODA: Symposium on Discrete Algorithms"},"month":"02","language":[{"iso":"eng"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","first_name":"Tobias","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer"},{"last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","orcid":"0000-0002-1419-3267","last_name":"Svoboda","full_name":"Svoboda, Jakub","first_name":"Jakub"}],"publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","_id":"12676","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611977554.ch173"}],"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"publisher":"Society for Industrial and Applied Mathematics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1},{"publication_status":"published","citation":{"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>","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>","ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.","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).","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>."},"quality_controlled":"1","department":[{"_id":"SiHi"}],"oa_version":"Published Version","file":[{"creator":"dernst","success":1,"date_created":"2023-08-16T12:29:06Z","content_type":"application/pdf","file_id":"14071","checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","file_size":1787894,"access_level":"open_access","relation":"main_file","file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf","date_updated":"2023-08-16T12:29:06Z"}],"article_type":"review","date_published":"2023-04-01T00:00:00Z","has_accepted_license":"1","publication_identifier":{"issn":["0959-4388"]},"title":"Principles of neural stem cell lineage progression: Insights from developing cerebral cortex","issue":"4","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1016/j.conb.2023.102695","day":"01","keyword":["General Neuroscience"],"article_number":"102695","isi":1,"year":"2023","oa":1,"external_id":{"pmid":["36842274"],"isi":["000953497700001"]},"date_updated":"2023-08-16T12:30:25Z","intvolume":"        79","status":"public","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"}],"pmid":1,"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.","_id":"12679","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"publisher":"Elsevier","ec_funded":1,"file_date_updated":"2023-08-16T12:29:06Z","ddc":["570"],"volume":79,"date_created":"2023-02-26T12:24:21Z","type":"journal_article","language":[{"iso":"eng"}],"author":[{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"month":"04","publication":"Current Opinion in Neurobiology","article_processing_charge":"Yes (via OA deal)","scopus_import":"1"},{"arxiv":1,"quality_controlled":"1","citation":{"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>.","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>","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>","ista":"Ivanov G, Köse S. 2023. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. 346(6), 113363.","short":"G. Ivanov, S. Köse, Discrete Mathematics 346 (2023).","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>.","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."},"publication_status":"published","date_published":"2023-06-01T00:00:00Z","article_type":"letter_note","department":[{"_id":"UlWa"},{"_id":"GradSch"}],"oa_version":"Preprint","year":"2023","publication_identifier":{"issn":["0012-365X"]},"issue":"6","title":"Erdős-Ko-Rado and Hilton-Milner theorems for two-forms","article_number":"113363","day":"01","doi":"10.1016/j.disc.2023.113363","date_updated":"2023-10-04T11:54:57Z","status":"public","intvolume":"       346","oa":1,"external_id":{"arxiv":["2201.10892"]},"_id":"12680","abstract":[{"lang":"eng","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2201.10892","open_access":"1"}],"date_created":"2023-02-26T23:01:00Z","volume":346,"related_material":{"record":[{"id":"13331","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","publication":"Discrete Mathematics","scopus_import":"1","language":[{"iso":"eng"}],"author":[{"last_name":"Ivanov","first_name":"Grigory","full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"last_name":"Köse","full_name":"Köse, Seyda","first_name":"Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb"}],"month":"06","type":"journal_article"},{"page":"675-705","date_created":"2023-02-26T23:01:01Z","file_date_updated":"2023-02-27T09:23:02Z","ddc":["530"],"volume":55,"publication":"Annual Review of Fluid Mechanics","article_processing_charge":"No","scopus_import":"1","type":"journal_article","month":"01","author":[{"full_name":"Dubief, Yves","first_name":"Yves","last_name":"Dubief"},{"full_name":"Terrapon, Vincent E.","first_name":"Vincent E.","last_name":"Terrapon"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn"}],"language":[{"iso":"eng"}],"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).","_id":"12681","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Annual Reviews","year":"2023","issue":"1","title":"Elasto-inertial turbulence","has_accepted_license":"1","publication_identifier":{"issn":["0066-4189"],"eissn":["1545-4479"]},"doi":"10.1146/annurev-fluid-032822-025933","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"19","isi":1,"date_updated":"2023-08-01T13:19:47Z","intvolume":"        55","status":"public","oa":1,"external_id":{"isi":["000915418100026"]},"quality_controlled":"1","citation":{"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>.","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.","ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705.","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>","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>","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>."},"publication_status":"published","article_type":"original","date_published":"2023-01-19T00:00:00Z","department":[{"_id":"BjHo"}],"oa_version":"Published Version","file":[{"date_updated":"2023-02-27T09:23:02Z","relation":"main_file","access_level":"open_access","file_size":4036706,"checksum":"2666aa3af2a25252d35eb8681d3edff7","file_name":"2023_AnnReviewFluidMech_Dubief.pdf","date_created":"2023-02-27T09:23:02Z","success":1,"file_id":"12690","content_type":"application/pdf","creator":"dernst"}]}]