[{"type":"journal_article","article_type":"original","status":"public","_id":"14796","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"date_updated":"2024-03-05T09:35:25Z","scopus_import":"1","intvolume":" 383","month":"01","abstract":[{"text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.","lang":"eng"}],"oa_version":"None","pmid":1,"issue":"6678","volume":383,"related_material":{"record":[{"id":"14812","status":"public","relation":"research_data"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","description":"News on ISTA Website"}]},"publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"external_id":{"pmid":["38175895"]},"article_processing_charge":"No","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Zuzanna B.","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B."},{"first_name":"Martin D.","last_name":"Garlovsky","full_name":"Garlovsky, Martin D."},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","last_name":"Pal","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469"},{"first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria","last_name":"Shipilina"},{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","last_name":"Garcia Castillo","full_name":"Garcia Castillo, Diego Fernando"},{"last_name":"Lifchitz","full_name":"Lifchitz, Hila","first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac"},{"full_name":"Le Moan, Alan","last_name":"Le Moan","first_name":"Alan"},{"first_name":"Erica","last_name":"Leder","full_name":"Leder, Erica"},{"last_name":"Reeve","full_name":"Reeve, James","first_name":"James"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"title":"The genetic basis of a recent transition to live-bearing in marine snails","citation":{"ieee":"S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982","ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982.","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","quality_controlled":"1","acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","page":"114-119","date_created":"2024-01-14T23:00:56Z","date_published":"2024-01-05T00:00:00Z","doi":"10.1126/science.adi2982","year":"2024","publication":"Science","day":"05"},{"date_published":"2024-02-23T00:00:00Z","doi":"10.15479/at:ista:15020","date_created":"2024-02-23T14:02:04Z","page":"158","day":"23","has_accepted_license":"1","year":"2024","publisher":"Institute of Science and Technology Austria","oa":1,"title":"Genetic information and biological optimization","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Hledik, Michal","last_name":"Hledik"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020"},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7553"},{"id":"12081","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"7606","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"file_id":"15021","checksum":"b2d3da47c98d481577a4baf68944fe41","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-02-23T13:50:53Z","file_name":"hledik thesis pdfa 2b.pdf","date_updated":"2024-02-23T13:50:53Z","file_size":7102089,"creator":"mhledik"},{"creator":"mhledik","date_updated":"2024-02-23T14:20:16Z","file_size":14014790,"date_created":"2024-02-23T13:50:54Z","file_name":"hledik thesis source.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","file_id":"15022","checksum":"eda9b9430da2610fee7ce1c1419a479a"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"file_date_updated":"2024-02-23T14:20:16Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"ddc":["576","519"],"supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"date_updated":"2024-03-06T14:22:52Z","status":"public","keyword":["Theoretical biology","Optimality","Evolution","Information"],"type":"dissertation","_id":"15020"},{"author":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"article_processing_charge":"No","title":"Eva Benkova","citation":{"ista":"Benková E. 2024. Eva Benkova, Elsevier,p.","chicago":"Benková, Eva. Eva Benkova. Current Biology. Vol. 34. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.039.","short":"E. Benková, Eva Benkova, Elsevier, 2024.","ieee":"E. Benková, Eva Benkova, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","ama":"Benková E. Eva Benkova. Vol 34. Elsevier; 2024:R3-R5. doi:10.1016/j.cub.2023.11.039","apa":"Benková, E. (2024). Eva Benkova. Current Biology (Vol. 34, pp. R3–R5). Elsevier. https://doi.org/10.1016/j.cub.2023.11.039","mla":"Benková, Eva. “Eva Benkova.” Current Biology, vol. 34, no. 1, Elsevier, 2024, pp. R3–5, doi:10.1016/j.cub.2023.11.039."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"R3-R5","doi":"10.1016/j.cub.2023.11.039","date_published":"2024-01-08T00:00:00Z","date_created":"2024-01-21T23:00:56Z","year":"2024","day":"08","publication":"Current Biology","quality_controlled":"1","publisher":"Elsevier","oa":1,"department":[{"_id":"EvBe"}],"date_updated":"2024-03-12T12:19:12Z","type":"other_academic_publication","status":"public","_id":"14842","issue":"1","volume":34,"publication_identifier":{"eissn":["1879-0445"]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2023.11.039","open_access":"1"}],"month":"01","intvolume":" 34","abstract":[{"lang":"eng","text":"Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability."}],"oa_version":"Published Version"},{"type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"15084","file_date_updated":"2024-03-12T13:42:42Z","department":[{"_id":"RySh"},{"_id":"PeJo"}],"date_updated":"2024-03-12T13:44:18Z","ddc":["570"],"month":"02","intvolume":" 121","abstract":[{"lang":"eng","text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"oa_version":"Published Version","pmid":1,"issue":"8","volume":121,"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/","description":"News on ISTA Website"}],"record":[{"relation":"research_data","status":"public","id":"13173"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","file_id":"15110","success":1,"creator":"dernst","date_updated":"2024-03-12T13:42:42Z","file_size":13648221,"date_created":"2024-03-12T13:42:42Z","file_name":"2024_PNAS_Koppensteiner.pdf"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_number":"e2301449121","author":[{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner"},{"last_name":"Bhandari","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Önal","orcid":"0000-0002-2771-2011","full_name":"Önal, Hüseyin C","first_name":"Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","first_name":"Carolina","full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane"},{"first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","last_name":"Le Monnier"},{"first_name":"Utsa","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2","full_name":"Roy, Utsa","last_name":"Roy"},{"first_name":"Yukihiro","full_name":"Nakamura, Yukihiro","last_name":"Nakamura"},{"last_name":"Sadakata","full_name":"Sadakata, Tetsushi","first_name":"Tetsushi"},{"first_name":"Makoto","last_name":"Sanbo","full_name":"Sanbo, Makoto"},{"first_name":"Masumi","full_name":"Hirabayashi, Masumi","last_name":"Hirabayashi"},{"first_name":"JeongSeop","full_name":"Rhee, JeongSeop","last_name":"Rhee"},{"full_name":"Brose, Nils","last_name":"Brose","first_name":"Nils"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38346189"]},"title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","citation":{"apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 2024;121(8). doi:10.1073/pnas.2301449121","ieee":"P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences, vol. 121, no. 8. Proceedings of the National Academy of Sciences, 2024.","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences 121 (2024).","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences, vol. 121, no. 8, e2301449121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121.","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 121(8), e2301449121.","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","date_published":"2024-02-20T00:00:00Z","doi":"10.1073/pnas.2301449121","date_created":"2024-03-05T09:23:55Z","has_accepted_license":"1","year":"2024","day":"20","publication":"Proceedings of the National Academy of Sciences"},{"article_number":"e2315558121","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 121(10), e2315558121.","chicago":"Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121.","short":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of the National Academy of Sciences 121 (2024).","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” Proceedings of the National Academy of Sciences, vol. 121, no. 10. Proceedings of the National Academy of Sciences, 2024.","ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 2024;121(10). doi:10.1073/pnas.2315558121","apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2315558121","mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences, vol. 121, no. 10, e2315558121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2315558121."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","first_name":"Valentin","last_name":"Hübner","full_name":"Hübner, Valentin"},{"last_name":"Staab","full_name":"Staab, Manuel","first_name":"Manuel"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kleshnina, Maria","last_name":"Kleshnina","first_name":"Maria"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38408249"]},"title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010) (to M.K.).","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2024","day":"05","publication":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.2315558121","date_published":"2024-03-05T00:00:00Z","date_created":"2024-03-05T09:18:49Z","_id":"15083","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","date_updated":"2024-03-12T13:29:25Z","ddc":["000"],"file_date_updated":"2024-03-12T13:12:22Z","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation."}],"pmid":1,"oa_version":"Published Version","month":"03","intvolume":" 121","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","file":[{"file_name":"2024_PNAS_Huebner.pdf","date_created":"2024-03-12T13:12:22Z","creator":"dernst","file_size":2203220,"date_updated":"2024-03-12T13:12:22Z","success":1,"checksum":"068520e3efd4d008bb9177e8aedb7d22","file_id":"15109","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"10","volume":121,"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/","description":"News on ISTA Website"}],"record":[{"status":"public","id":"15108","relation":"research_data"}]},"ec_funded":1},{"day":"09","has_accepted_license":"1","year":"2024","date_published":"2024-02-09T00:00:00Z","doi":"10.5281/ZENODO.10639167","related_material":{"record":[{"status":"public","id":"15083","relation":"used_in_publication"}]},"date_created":"2024-03-12T13:02:58Z","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","abstract":[{"lang":"eng","text":"in the research article \"Efficiency and resilience of cooperation in asymmetric social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for the case of two and three players, both described below."}],"month":"02","publisher":"Zenodo","oa":1,"main_file_link":[{"url":"https://10.5281/zenodo.10639167","open_access":"1"}],"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167.","ista":"Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167.","mla":"Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167.","ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167","apa":"Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167","short":"V. Hübner, M. Kleshnina, (2024).","ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024."},"date_updated":"2024-03-12T13:29:26Z","title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","department":[{"_id":"KrCh"}],"author":[{"last_name":"Hübner","full_name":"Hübner, Valentin","first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910"},{"first_name":"Maria","last_name":"Kleshnina","full_name":"Kleshnina, Maria"}],"article_processing_charge":"No","_id":"15108","status":"public","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"date_updated":"2024-03-13T09:01:20Z","ddc":["550"],"department":[{"_id":"CaMu"}],"file_date_updated":"2024-03-13T08:59:21Z","_id":"15097","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1991-9603"],"issn":["1991-959X"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"270d2340402729b0532f7072ea914cae","file_id":"15111","success":1,"creator":"dernst","date_updated":"2024-03-13T08:59:21Z","file_size":13364601,"date_created":"2024-03-13T08:59:21Z","file_name":"2024_GeoscientificModelDev_Schmidt.pdf"}],"language":[{"iso":"eng"}],"issue":"4","volume":17,"abstract":[{"text":"Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 17","citation":{"ista":"Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584.","chicago":"Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang, Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development. European Geosciences Union, 2024. https://doi.org/10.5194/gmd-17-1563-2024.","apa":"Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta, D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. European Geosciences Union. https://doi.org/10.5194/gmd-17-1563-2024","ama":"Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 2024;17(4):1563-1584. doi:10.5194/gmd-17-1563-2024","short":"H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta, P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams, B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584.","ieee":"H. Schmidt et al., “Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model,” Geoscientific Model Development, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584, 2024.","mla":"Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development, vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:10.5194/gmd-17-1563-2024."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Hauke","full_name":"Schmidt, Hauke","last_name":"Schmidt"},{"full_name":"Rast, Sebastian","last_name":"Rast","first_name":"Sebastian"},{"first_name":"Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","full_name":"Bao, Jiawei","last_name":"Bao"},{"last_name":"Cassim","full_name":"Cassim, Amrit","first_name":"Amrit"},{"last_name":"Fang","full_name":"Fang, Shih Wei","first_name":"Shih Wei"},{"full_name":"Jimenez-De La Cuesta, Diego","last_name":"Jimenez-De La Cuesta","first_name":"Diego"},{"first_name":"Paul","full_name":"Keil, Paul","last_name":"Keil"},{"last_name":"Kluft","full_name":"Kluft, Lukas","first_name":"Lukas"},{"last_name":"Kroll","full_name":"Kroll, Clarissa","first_name":"Clarissa"},{"full_name":"Lang, Theresa","last_name":"Lang","first_name":"Theresa"},{"first_name":"Ulrike","last_name":"Niemeier","full_name":"Niemeier, Ulrike"},{"first_name":"Andrea","last_name":"Schneidereit","full_name":"Schneidereit, Andrea"},{"last_name":"Williams","full_name":"Williams, Andrew I.L.","first_name":"Andrew I.L."},{"full_name":"Stevens, Bjorn","last_name":"Stevens","first_name":"Bjorn"}],"article_processing_charge":"Yes (via OA deal)","title":"Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model","has_accepted_license":"1","year":"2024","day":"22","publication":"Geoscientific Model Development","page":"1563-1584","date_published":"2024-02-22T00:00:00Z","doi":"10.5194/gmd-17-1563-2024","date_created":"2024-03-10T23:00:53Z","acknowledgement":"The authors wish to thank Ann Kristin Naumann and three anonymous reviewers for very helpful comments on an earlier version of this paper. We are grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding running the simulations. We thank Luis Kornblueh for providing an external vertical grid generator and resolving the memory requirements for the very fine vertical grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial support from the SOCTOC project within the framework of the ROMIC program, funded by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe article processing charges for this open-access publication were covered by the Max Planck Society.","quality_controlled":"1","publisher":"European Geosciences Union","oa":1},{"day":"26","publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics","has_accepted_license":"1","year":"2024","doi":"10.1017/prm.2024.7","date_published":"2024-02-26T00:00:00Z","date_created":"2023-01-16T11:45:22Z","acknowledgement":"Silverman, and Paul Voutier for the comments on the earlier version of this paper. The first author acknowledges the support by Dioscuri programme initiated by the Max Planck Society, jointly managed with the National Science Centre (Poland), and mutually funded by the Polish Ministry of Science and Higher Education and the German Federal Ministry of Education and Research. The second author has been supported by MIUR (Italy) through PRIN 2017 ‘Geometric, algebraic and analytic methods in arithmetic’ and has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/prm.2024.7.","ista":"Naskręcki B, Verzobio M. 2024. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics., 2203.02015.","mla":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics, 2203.02015, Cambridge University Press, 2024, doi:10.1017/prm.2024.7.","ama":"Naskręcki B, Verzobio M. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. 2024. doi:10.1017/prm.2024.7","apa":"Naskręcki, B., & Verzobio, M. (2024). Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press. https://doi.org/10.1017/prm.2024.7","ieee":"B. Naskręcki and M. Verzobio, “Common valuations of division polynomials,” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024.","short":"B. Naskręcki, M. Verzobio, Proceedings of the Royal Society of Edinburgh Section A: Mathematics (2024)."},"title":"Common valuations of division polynomials","author":[{"last_name":"Naskręcki","full_name":"Naskręcki, Bartosz","first_name":"Bartosz"},{"id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","first_name":"Matteo","last_name":"Verzobio","full_name":"Verzobio, Matteo","orcid":"0000-0002-0854-0306"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2203.02015"]},"article_number":"2203.02015","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1473-7124"],"issn":["0308-2105"]},"publication_status":"epub_ahead","ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields.","lang":"eng"}],"month":"02","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/prm.2024.7"}],"ddc":["510"],"date_updated":"2024-03-13T11:55:21Z","department":[{"_id":"TiBr"}],"_id":"12311","status":"public","keyword":["Elliptic curves","Néron models","division polynomials","height functions","discrete valuation rings"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"department":[{"_id":"NiBa"}],"date_updated":"2024-03-13T12:08:57Z","ddc":["570"],"type":"journal_article","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"15099","publication_identifier":{"eissn":["1362-4555"],"issn":["0168-9525"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.tig.2024.01.002"}],"month":"02","abstract":[{"lang":"eng","text":"Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems."}],"oa_version":"Published Version","pmid":1,"author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Le Moan, Alan","last_name":"Le Moan","first_name":"Alan"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"}],"external_id":{"pmid":["38395682"]},"article_processing_charge":"Yes (in subscription journal)","title":"Diverse pathways to speciation revealed by marine snails","citation":{"ieee":"K. Johannesson et al., “Diverse pathways to speciation revealed by marine snails,” Trends in Genetics. Cell Press, 2024.","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics (2024).","ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 2024. doi:10.1016/j.tig.2024.01.002","apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. Trends in Genetics. Cell Press. https://doi.org/10.1016/j.tig.2024.01.002","mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics, Cell Press, 2024, doi:10.1016/j.tig.2024.01.002.","ista":"Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics.","chicago":"Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics. Cell Press, 2024. https://doi.org/10.1016/j.tig.2024.01.002."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-02-22T00:00:00Z","doi":"10.1016/j.tig.2024.01.002","date_created":"2024-03-10T23:00:54Z","has_accepted_license":"1","year":"2024","day":"22","publication":"Trends in Genetics","quality_controlled":"1","publisher":"Cell Press","oa":1,"acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft."},{"publication_identifier":{"issn":["0025-5831"],"eissn":["1432-1807"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00208-024-02812-0"}],"month":"02","date_updated":"2024-03-13T12:20:23Z","department":[{"_id":"JuFi"}],"_id":"15098","article_type":"original","type":"journal_article","status":"public","year":"2024","day":"27","publication":"Mathematische Annalen","date_published":"2024-02-27T00:00:00Z","doi":"10.1007/s00208-024-02812-0","date_created":"2024-03-10T23:00:54Z","acknowledgement":"The authors thank Professor Franco Flandoli for useful discussions and valuable insight into the subject. In particular, A.A. would like to thank professor Franco Flandoli for hosting and financially contributing to his research visit at Scuola Normale di Pisa in January 2023, where this work started. E.L. would like to express sincere gratitude to Professor Marco Fuhrman for igniting his interest in this particular field of research. E.L. want to thank Professor Matthias Hieber and Dr. Martin Saal for useful discussions. Finally, the authors thank the anonymous referee for helpful comments which improved the paper from its initial version.Open access funding provided by Scuola Normale Superiore within the CRUI-CARE Agreement. A. Agresti has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"citation":{"chicago":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen. Springer Nature, 2024. https://doi.org/10.1007/s00208-024-02812-0.","ista":"Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen.","mla":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen, Springer Nature, 2024, doi:10.1007/s00208-024-02812-0.","apa":"Agresti, A., & Luongo, E. (2024). Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-024-02812-0","ama":"Agresti A, Luongo E. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. 2024. doi:10.1007/s00208-024-02812-0","short":"A. Agresti, E. Luongo, Mathematische Annalen (2024).","ieee":"A. Agresti and E. Luongo, “Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions,” Mathematische Annalen. Springer Nature, 2024."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962","last_name":"Agresti"},{"full_name":"Luongo, Eliseo","last_name":"Luongo","first_name":"Eliseo"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2306.11081"]},"title":"Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions","project":[{"grant_number":"948819","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, n.d. https://doi.org/10.1016/j.neuron.2023.12.002.","ista":"Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron.","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron, Elsevier, doi:10.1016/j.neuron.2023.12.002.","short":"J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron (n.d.).","ieee":"J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” Neuron. Elsevier.","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. doi:10.1016/j.neuron.2023.12.002","apa":"Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., & Jonas, P. M. (n.d.). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002"},"title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","author":[{"id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing","last_name":"Chen","full_name":"Chen, JingJing"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong"},{"first_name":"Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Arai","full_name":"Arai, Itaru"},{"full_name":"Kim, Olena","last_name":"Kim","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"external_id":{"pmid":["38215739"]},"article_processing_charge":"No","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"day":"11","publication":"Neuron","year":"2024","doi":"10.1016/j.neuron.2023.12.002","date_published":"2024-01-11T00:00:00Z","date_created":"2024-01-21T23:00:56Z","acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","quality_controlled":"1","publisher":"Elsevier","date_updated":"2024-03-14T13:14:18Z","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"_id":"14843","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"publication_status":"inpress","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"15101"}],"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/","relation":"press_release"}]},"ec_funded":1,"pmid":1,"oa_version":"None","abstract":[{"text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"month":"01","scopus_import":"1"},{"month":"03","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"related_material":{"record":[{"id":"14843","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"checksum":"db4947474ffa271e66c254b6fe876a55","file_id":"15104","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"Thesis_Jingjing CHEN.docx","date_created":"2024-03-11T14:10:58Z","file_size":11271363,"date_updated":"2024-03-12T07:12:17Z","creator":"jchen"},{"file_name":"Thesis_Jingjing CHEN_merged.pdf","date_created":"2024-03-11T14:11:06Z","file_size":16627311,"date_updated":"2024-03-11T14:11:06Z","creator":"jchen","embargo":"2024-04-01","checksum":"a5eeae8b5702cd540f5d03469bc33dde","file_id":"15105","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"15101","department":[{"_id":"GradSch"},{"_id":"PeJo"}],"file_date_updated":"2024-03-12T07:12:17Z","ddc":["570"],"supervisor":[{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-14T13:14:19Z","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:15101","date_published":"2024-03-11T00:00:00Z","date_created":"2024-03-11T10:09:54Z","page":"84","day":"11","has_accepted_license":"1","year":"2024","project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits"},{"grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","author":[{"id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing","full_name":"Chen, JingJing","last_name":"Chen"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","mla":"Chen, JingJing. Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101","apa":"Chen, J. (2024). Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101"}},{"month":"03","intvolume":" 6","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Quantum computers are increasing in size and quality but are still very noisy. Error mitigation extends the size of the quantum circuits that noisy devices can meaningfully execute. However, state-of-the-art error mitigation methods are hard to implement and the limited qubit connectivity in superconducting qubit devices restricts most applications to the hardware's native topology. Here we show a quantum approximate optimization algorithm (QAOA) on nonplanar random regular graphs with up to 40 nodes enabled by a machine learning-based error mitigation. We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful parameter optimization for the largest graph which requires running quantum circuits with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and not only expectation values, in quantum approximate optimization. These results are a step towards executing quantum approximate optimization at a scale that is not classically simulable. Reaching such system sizes is key to properly understanding the true potential of heuristic algorithms like QAOA.","lang":"eng"}],"volume":6,"issue":"1","file":[{"success":1,"checksum":"274c9f1b15b3547a10a03f39e4ccc582","file_id":"15123","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2024_PhysicalReviewResearch_Sack.pdf","date_created":"2024-03-19T07:16:38Z","file_size":2777593,"date_updated":"2024-03-19T07:16:38Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"15122","department":[{"_id":"MaSe"}],"file_date_updated":"2024-03-19T07:16:38Z","ddc":["530"],"date_updated":"2024-03-19T07:24:03Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"S.H.S. acknowledges support from the IBM Ph.D. fellowship 2022 in quantum computing. The authors also thank M. Serbyn, R. Kueng, R. A. Medina, and S. Woerner for fruitful discussions.","date_published":"2024-03-01T00:00:00Z","doi":"10.1103/PhysRevResearch.6.013223","date_created":"2024-03-17T23:00:59Z","day":"01","publication":"Physical Review Research","has_accepted_license":"1","year":"2024","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices"}],"article_number":"013223","title":"Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation","author":[{"first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan"},{"first_name":"Daniel J.","full_name":"Egger, Daniel J.","last_name":"Egger"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2307.14427"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Sack, S., & Egger, D. J. (2024). Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013223","ama":"Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 2024;6(1). doi:10.1103/PhysRevResearch.6.013223","short":"S. Sack, D.J. Egger, Physical Review Research 6 (2024).","ieee":"S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","mla":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013223.","ista":"Sack S, Egger DJ. 2024. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 6(1), 013223.","chicago":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013223."}},{"day":"04","publication":"Nature Microbiology","year":"2024","doi":"10.1038/s41564-024-01600-5","date_published":"2024-03-04T00:00:00Z","date_created":"2024-03-17T23:00:58Z","page":"698-711","acknowledgement":"We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673; RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and support. We thank Scientific Computing at the MRC LMB for their support. We thank L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support Facility for help with the SEC coupled with multi-angle light scattering experiments. We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C. and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and the computational and storage services (Maestro cluster) provided by the IT department at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF) Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.","publisher":"Springer Nature","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"P. Nußbaum et al., “Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division,” Nature Microbiology, vol. 9, no. 3. Springer Nature, pp. 698–711, 2024.","short":"P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic, N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature Microbiology 9 (2024) 698–711.","apa":"Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic, M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-024-01600-5","ama":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 2024;9(3):698-711. doi:10.1038/s41564-024-01600-5","mla":"Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology, vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:10.1038/s41564-024-01600-5.","ista":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 9(3), 698–711.","chicago":"Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology. Springer Nature, 2024. https://doi.org/10.1038/s41564-024-01600-5."},"title":"Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division","author":[{"full_name":"Nußbaum, Phillip","last_name":"Nußbaum","first_name":"Phillip"},{"full_name":"Kureisaite-Ciziene, Danguole","last_name":"Kureisaite-Ciziene","first_name":"Danguole"},{"full_name":"Bellini, Dom","last_name":"Bellini","first_name":"Dom"},{"first_name":"Chris","last_name":"Van Der Does","full_name":"Van Der Does, Chris"},{"id":"73e7ecd4-dc85-11ea-9058-88a16394b160","first_name":"Marko","full_name":"Kojic, Marko","last_name":"Kojic"},{"first_name":"Najwa","full_name":"Taib, Najwa","last_name":"Taib"},{"first_name":"Anna","full_name":"Yeates, Anna","last_name":"Yeates"},{"first_name":"Maxime","full_name":"Tourte, Maxime","last_name":"Tourte"},{"last_name":"Gribaldo","full_name":"Gribaldo, Simonetta","first_name":"Simonetta"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"},{"full_name":"Löwe, Jan","last_name":"Löwe","first_name":"Jan"},{"last_name":"Albers","full_name":"Albers, Sonja Verena","first_name":"Sonja Verena"}],"article_processing_charge":"No","external_id":{"pmid":["38443575"]},"project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2058-5276"]},"publication_status":"published","issue":"3","volume":9,"pmid":1,"oa_version":"None","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"text":"Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea.","lang":"eng"}],"month":"03","intvolume":" 9","scopus_import":"1","date_updated":"2024-03-19T07:30:53Z","department":[{"_id":"MaLo"}],"_id":"15118","status":"public","type":"journal_article","article_type":"original"},{"title":"Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions","article_processing_charge":"No","external_id":{"arxiv":["2106.01274"]},"author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio","last_name":"Agresti","orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio"},{"last_name":"Veraar","full_name":"Veraar, Mark","first_name":"Mark"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1, Institute of Mathematical Statistics, 2024, pp. 413–30, doi:10.1214/22-AIHP1333.","apa":"Agresti, A., & Veraar, M. (2024). Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AIHP1333","ama":"Agresti A, Veraar M. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 2024;60(1):413-430. doi:10.1214/22-AIHP1333","short":"A. Agresti, M. Veraar, Annales de l’institut Henri Poincare Probability and Statistics 60 (2024) 413–430.","ieee":"A. Agresti and M. Veraar, “Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions,” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1. Institute of Mathematical Statistics, pp. 413–430, 2024.","chicago":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/22-AIHP1333.","ista":"Agresti A, Veraar M. 2024. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 60(1), 413–430."},"date_created":"2024-03-17T23:00:58Z","doi":"10.1214/22-AIHP1333","date_published":"2024-02-01T00:00:00Z","page":"413-430","publication":"Annales de l'institut Henri Poincare Probability and Statistics","day":"01","year":"2024","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","acknowledgement":"The first author has been partially supported by the Nachwuchsring – Network for the promotion of young scientists – at TU Kaiserslautern. The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO). The authors thank the anonymous referees and Max Sauerbrey for careful reading and helpful suggestions.","department":[{"_id":"JuFi"}],"date_updated":"2024-03-19T08:14:17Z","status":"public","type":"journal_article","article_type":"original","_id":"15119","issue":"1","volume":60,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0246-0203"]},"intvolume":" 60","month":"02","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.01274","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"In this paper we consider an SPDE where the leading term is a second order operator with periodic boundary conditions, coefficients which are measurable in (t,ω) , and Hölder continuous in space. Assuming stochastic parabolicity conditions, we prove Lp((0,T)×Ω,tκdt;Hσ,q(Td)) -estimates. The main novelty is that we do not require p=q . Moreover, we allow arbitrary σ∈R and weights in time. Such mixed regularity estimates play a crucial role in applications to nonlinear SPDEs which is clear from our previous work. To prove our main results we develop a general perturbation theory for SPDEs. Moreover, we prove a new result on pointwise multiplication in spaces with fractional smoothness.","lang":"eng"}]},{"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","file":[{"file_name":"2024_PNAS_Habig.pdf","date_created":"2024-03-19T09:02:57Z","creator":"dernst","file_size":5750361,"date_updated":"2024-03-19T09:02:57Z","success":1,"checksum":"f5e871db617b682edc71fcd08670dc81","file_id":"15124","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":121,"issue":"11","ec_funded":1,"abstract":[{"text":"Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"03","intvolume":" 121","date_updated":"2024-03-19T09:07:20Z","ddc":["570"],"department":[{"_id":"SyCr"}],"file_date_updated":"2024-03-19T09:02:57Z","_id":"14478","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","has_accepted_license":"1","year":"2024","day":"12","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2024-03-12T00:00:00Z","doi":"10.1073/pnas.2316284121","date_created":"2023-10-31T13:30:00Z","acknowledgement":"We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V. Meyling for the fungal strains. We further thank Chengshu Wang for providing the short sequencing reads for M. guizhouense ARESF977 he used for his published genome assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the manuscript. Fig. 1A was created with BioRender.com. This study received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German Research Foundation (DFG grant HA9263/1-1) to M.H.","quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","oa":1,"citation":{"short":"M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ieee":"M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer, “Frequent horizontal chromosome transfer between asexual fungal insect pathogens,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","ama":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2316284121","apa":"Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., & Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2316284121","mla":"Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2316284121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2316284121.","ista":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2316284121.","chicago":"Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2316284121."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Michael","full_name":"Habig, Michael","last_name":"Habig"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","full_name":"Grasse, Anna V","last_name":"Grasse"},{"first_name":"Judith","last_name":"Müller","full_name":"Müller, Judith"},{"first_name":"Eva H.","full_name":"Stukenbrock, Eva H.","last_name":"Stukenbrock"},{"id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","first_name":"Hanna","full_name":"Leitner, Hanna","last_name":"Leitner"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38442176"]},"title":"Frequent horizontal chromosome transfer between asexual fungal insect pathogens","article_number":"e2316284121","project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}]},{"abstract":[{"lang":"eng","text":"Given a fixed finite metric space (V,μ), the {\\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.\r\n"}],"oa_version":"Preprint","scopus_import":"1","month":"03","publication_identifier":{"issn":["0025-5610"],"eissn":["1436-4646"]},"publication_status":"epub_ahead","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"e7e83065f7bc18b9c188bf93b5ca5db6","file_id":"10046","file_size":603672,"date_updated":"2021-09-27T10:54:51Z","creator":"mdvorak","file_name":"Generalized-0-Ext.pdf","date_created":"2021-09-27T10:54:51Z"}],"language":[{"iso":"eng"}],"_id":"10045","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["minimum 0-extension problem","metric labeling problem","discrete metric spaces","metric extensions","computational complexity","valued constraint satisfaction problems","discrete convex analysis","L-convex functions"],"date_updated":"2024-03-19T08:20:31Z","ddc":["004"],"department":[{"_id":"GradSch"},{"_id":"VlKo"}],"file_date_updated":"2021-09-27T10:54:51Z","acknowledgement":"We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions. Open access funding provided by Institute of Science and Technology (IST Austria).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"has_accepted_license":"1","year":"2024","day":"07","publication":"Mathematical Programming","date_published":"2024-03-07T00:00:00Z","doi":"10.1007/s10107-024-02064-5","date_created":"2021-09-27T10:48:23Z","article_number":"2109.10203","citation":{"mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming, 2109.10203, Springer Nature, 2024, doi:10.1007/s10107-024-02064-5.","ieee":"M. Dvorak and V. Kolmogorov, “Generalized minimum 0-extension problem and discrete convexity,” Mathematical Programming. Springer Nature, 2024.","short":"M. Dvorak, V. Kolmogorov, Mathematical Programming (2024).","apa":"Dvorak, M., & Kolmogorov, V. (2024). Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02064-5","ama":"Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 2024. doi:10.1007/s10107-024-02064-5","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02064-5.","ista":"Dvorak M, Kolmogorov V. 2024. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming., 2109.10203."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","first_name":"Martin","last_name":"Dvorak","full_name":"Dvorak, Martin","orcid":"0000-0001-5293-214X"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"external_id":{"arxiv":["2109.10203"]},"article_processing_charge":"Yes (via OA deal)","title":"Generalized minimum 0-extension problem and discrete convexity"},{"type":"journal_article","article_type":"original","status":"public","_id":"15121","department":[{"_id":"MoHe"}],"date_updated":"2024-03-19T08:32:32Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.09217"}],"month":"03","abstract":[{"lang":"eng","text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time 0(mE-1), beating the running time of the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1-E)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is 0(mE-1), where m is the sum of the number of initially existing and inserted edges."}],"oa_version":"Preprint","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"13236"}]},"ec_funded":1,"publication_identifier":{"issn":["0025-5610"],"eissn":["1436-4646"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"author":[{"first_name":"Da Wei","last_name":"Zheng","full_name":"Zheng, Da Wei"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"external_id":{"arxiv":["2301.09217"]},"article_processing_charge":"No","title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","citation":{"mla":"Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming, Springer Nature, 2024, doi:10.1007/s10107-024-02066-3.","ieee":"D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” Mathematical Programming. Springer Nature, 2024.","short":"D.W. Zheng, M.H. Henzinger, Mathematical Programming (2024).","ama":"Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. 2024. doi:10.1007/s10107-024-02066-3","apa":"Zheng, D. W., & Henzinger, M. H. (2024). Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02066-3","chicago":"Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02066-3.","ista":"Zheng DW, Henzinger MH. 2024. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"The first author thanks Chandra Chekuri for useful discussions about this paper. This work was done in part at the University of Vienna. 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. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","doi":"10.1007/s10107-024-02066-3","date_published":"2024-03-06T00:00:00Z","date_created":"2024-03-17T23:00:58Z","year":"2024","day":"06","publication":"Mathematical Programming"},{"title":"Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling","author":[{"first_name":"Zihao","full_name":"Yao, Zihao","last_name":"Yao"},{"full_name":"Liu, Xu","last_name":"Liu","first_name":"Xu"},{"first_name":"Rhys","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","last_name":"Bunting","orcid":"0000-0001-6928-074X","full_name":"Bunting, Rhys"},{"first_name":"Jianguo","full_name":"Wang, Jianguo","last_name":"Wang"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Yao Z, Liu X, Bunting R, Wang J. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 2024;291. doi:10.1016/j.ces.2024.119959","apa":"Yao, Z., Liu, X., Bunting, R., & Wang, J. (2024). Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. Elsevier. https://doi.org/10.1016/j.ces.2024.119959","ieee":"Z. Yao, X. Liu, R. Bunting, and J. Wang, “Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling,” Chemical Engineering Science, vol. 291. Elsevier, 2024.","short":"Z. Yao, X. Liu, R. Bunting, J. Wang, Chemical Engineering Science 291 (2024).","mla":"Yao, Zihao, et al. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science, vol. 291, 119959, Elsevier, 2024, doi:10.1016/j.ces.2024.119959.","ista":"Yao Z, Liu X, Bunting R, Wang J. 2024. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 291, 119959.","chicago":"Yao, Zihao, Xu Liu, Rhys Bunting, and Jianguo Wang. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science. Elsevier, 2024. https://doi.org/10.1016/j.ces.2024.119959."},"article_number":"119959","date_published":"2024-03-04T00:00:00Z","doi":"10.1016/j.ces.2024.119959","date_created":"2024-03-17T23:00:57Z","day":"04","publication":"Chemical Engineering Science","year":"2024","quality_controlled":"1","publisher":"Elsevier","acknowledgement":"The authors acknowledge the financial support from the National Key Research and Development Project of China (2021YFA1500900, 2022YFE0113800), the National Natural Science Foundation of China (22141001, U21A20298), Zhejiang Innovation Team (2017R5203).","department":[{"_id":"MaIb"}],"date_updated":"2024-03-19T08:47:42Z","status":"public","article_type":"original","type":"journal_article","_id":"15114","volume":291,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0009-2509"]},"publication_status":"epub_ahead","month":"03","intvolume":" 291","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"As a key liquid organic hydrogen carrier, investigating the decomposition of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms and key intermediates involved in the dehydrogenation process of formic acid remain a great topic of debate due to ambiguous adsorbate interactions. In this research, we develop an advanced microkinetic model based on first-principles calculations, accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage effects in formic acid dehydrogenation. Our findings unequivocally demonstrate that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental results, the selectivity of H2 in the decomposition of formic acid on the Pd (1 1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic analysis aligns perfectly with experimental values at a temperature of 373 K."}]},{"scopus_import":"1","intvolume":" 121","month":"03","abstract":[{"text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":121,"related_material":{"record":[{"status":"public","id":"15126","relation":"research_data"}]},"issue":"11","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"15125","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","success":1,"creator":"dernst","date_updated":"2024-03-19T10:22:42Z","file_size":12952586,"date_created":"2024-03-19T10:22:42Z","file_name":"2024_PNAS_Giubertoni.pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"15116","file_date_updated":"2024-03-19T10:22:42Z","department":[{"_id":"AnSa"}],"date_updated":"2024-03-19T11:41:32Z","ddc":["550"],"oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress.","date_created":"2024-03-17T23:00:57Z","date_published":"2024-03-12T00:00:00Z","doi":"10.1073/pnas.2313162121","year":"2024","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"12","article_number":"e2313162121","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38451946"]},"author":[{"full_name":"Giubertoni, Giulia","last_name":"Giubertoni","first_name":"Giulia"},{"first_name":"Liru","full_name":"Feng, Liru","last_name":"Feng"},{"first_name":"Kevin","full_name":"Klein, Kevin","last_name":"Klein"},{"last_name":"Giannetti","full_name":"Giannetti, Guido","first_name":"Guido"},{"first_name":"Luco","full_name":"Rutten, Luco","last_name":"Rutten"},{"full_name":"Choi, Yeji","last_name":"Choi","first_name":"Yeji"},{"last_name":"Van Der Net","full_name":"Van Der Net, Anouk","first_name":"Anouk"},{"last_name":"Castro-Linares","full_name":"Castro-Linares, Gerard","first_name":"Gerard"},{"first_name":"Federico","last_name":"Caporaletti","full_name":"Caporaletti, Federico"},{"first_name":"Dimitra","last_name":"Micha","full_name":"Micha, Dimitra"},{"full_name":"Hunger, Johannes","last_name":"Hunger","first_name":"Johannes"},{"first_name":"Antoine","last_name":"Deblais","full_name":"Deblais, Antoine"},{"last_name":"Bonn","full_name":"Bonn, Daniel","first_name":"Daniel"},{"last_name":"Sommerdijk","full_name":"Sommerdijk, Nico","first_name":"Nico"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"full_name":"Ilie, Ioana M.","last_name":"Ilie","first_name":"Ioana M."},{"last_name":"Koenderink","full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H."},{"first_name":"Sander","last_name":"Woutersen","full_name":"Woutersen, Sander"}],"title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","citation":{"chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America. 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Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2313162121","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2313162121","ieee":"G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This zip file contains data, and analysis for the paper \"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration\"."}],"month":"02","publisher":"Figshare","oa":1,"main_file_link":[{"url":"https://doi.org/10.21942/UVA.24829896","open_access":"1"}],"day":"14","has_accepted_license":"1","year":"2024","related_material":{"record":[{"status":"public","id":"15116","relation":"used_in_publication"}]},"date_published":"2024-02-14T00:00:00Z","doi":"10.21942/UVA.24829896","date_created":"2024-03-19T10:47:16Z","_id":"15126","status":"public","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["550"],"citation":{"chicago":"Giubertoni, G., and S. Woutersen. “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024. https://doi.org/10.21942/UVA.24829896.","ista":"Giubertoni G, Woutersen S. 2024. Dataset Collagen Self Assembly in H2O and D2O, Figshare, 10.21942/UVA.24829896.","mla":"Giubertoni, G., and S. Woutersen. Dataset Collagen Self Assembly in H2O and D2O. Figshare, 2024, doi:10.21942/UVA.24829896.","apa":"Giubertoni, G., & Woutersen, S. (2024). Dataset Collagen Self Assembly in H2O and D2O. Figshare. https://doi.org/10.21942/UVA.24829896","ama":"Giubertoni G, Woutersen S. Dataset Collagen Self Assembly in H2O and D2O. 2024. doi:10.21942/UVA.24829896","ieee":"G. Giubertoni and S. Woutersen, “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024.","short":"G. Giubertoni, S. Woutersen, (2024)."},"date_updated":"2024-03-19T11:41:33Z","title":"Dataset Collagen Self Assembly in H2O and D2O","author":[{"last_name":"Giubertoni","full_name":"Giubertoni, G.","first_name":"G."},{"last_name":"Woutersen","full_name":"Woutersen, S.","first_name":"S."}],"article_processing_charge":"No"},{"project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"}],"citation":{"ista":"Vandael DH, Jonas PM. 2024. Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal. Science. 383(6687), eadg6757.","chicago":"Vandael, David H, and Peter M Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science. AAAS, 2024. https://doi.org/10.1126/science.adg6757.","ama":"Vandael DH, Jonas PM. Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. 2024;383(6687):eadg6757. doi:10.1126/science.adg6757","apa":"Vandael, D. H., & Jonas, P. M. (2024). Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. AAAS. https://doi.org/10.1126/science.adg6757","ieee":"D. H. Vandael and P. M. Jonas, “Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal,” Science, vol. 383, no. 6687. AAAS, p. eadg6757, 2024.","short":"D.H. Vandael, P.M. Jonas, Science 383 (2024) eadg6757.","mla":"Vandael, David H., and Peter M. Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science, vol. 383, no. 6687, AAAS, 2024, p. eadg6757, doi:10.1126/science.adg6757."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["38452088"]},"article_processing_charge":"No","author":[{"last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"title":"Structure, biophysics, and circuit function of a \"giant\" cortical presynaptic terminal","acknowledgement":"We thank previous students, postdocs, and collaborators, particularly J. Geiger, and (in alphabetical order) H. Alle, J. Bischofberger, C. Borges-Merjane, D. Engel, M. Frotscher, S. Hallermann, M. Heckmann, S. Jamrichova, O. Kim, L. Li, K. Lichter, P. Lin, J. Lübke, Y. Okamoto, C. Pawlu, C. Schmidt-Hieber, N. Spruston, and N. Vyleta for their outstanding experimental contributions. We also thank P. Castillo, J. Geiger, T. Sakaba, S. Siegert, T. Vogels, and J. Watson for critically reading the manuscript, E. Kralli-Beller for text editing, and J. Malikovic and L. Slomianka for useful discussions. We apologize that, due to space constraints, not all relevant papers could be cited.\r\nThis project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, AdG “GIANTSYN”) and the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein Award; P 36232-B, stand-alone grant), both to P.J.","publisher":"AAAS","quality_controlled":"1","year":"2024","publication":"Science","day":"08","page":"eadg6757","date_created":"2024-03-17T23:00:57Z","doi":"10.1126/science.adg6757","date_published":"2024-03-08T00:00:00Z","_id":"15117","type":"journal_article","article_type":"review","status":"public","date_updated":"2024-03-20T07:42:52Z","department":[{"_id":"PeJo"}],"abstract":[{"lang":"eng","text":"The hippocampal mossy fiber synapse, formed between axons of dentate gyrus granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the trisynaptic circuitry of the hippocampus. Because of its comparatively large size, this synapse is accessible to direct presynaptic recording, allowing a rigorous investigation of the biophysical mechanisms of synaptic transmission and plasticity. Furthermore, because of its placement in the very center of the hippocampal memory circuit, this synapse seems to be critically involved in several higher network functions, such as learning, memory, pattern separation, and pattern completion. Recent work based on new technologies in both nanoanatomy and nanophysiology, including presynaptic patch-clamp recording, paired recording, super-resolution light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy, has provided new insights into the structure, biophysics, and network function of this intriguing synapse. This brings us one step closer to answering a fundamental question in neuroscience: how basic synaptic properties shape higher network computations."}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 383","month":"03","publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"6687","volume":383},{"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2024-03-08T00:00:00Z","doi":"10.15479/at:ista:15094","date_created":"2024-03-08T15:28:10Z","page":"108","day":"08","has_accepted_license":"1","year":"2024","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"grant_number":"Z00342","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Discretization in Geometry and Dynamics","grant_number":"I4887"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"title":"Persistence and Morse theory for discrete geometric structures","author":[{"full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria."},"month":"03","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n"}],"related_material":{"record":[{"id":"11660","status":"public","relation":"part_of_dissertation"},{"id":"11658","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"13182","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"15090","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"15091"},{"status":"public","id":"15093","relation":"part_of_dissertation"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"checksum":"1e468bfa42a7dcf04d89f4dadc621c87","file_id":"15112","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-03-14T08:55:07Z","file_name":"Thesis Sebastiano.pdf","creator":"scultrer","date_updated":"2024-03-14T08:55:07Z","file_size":4106872},{"file_name":"Thesis (1).zip","date_created":"2024-03-14T08:56:24Z","creator":"scultrer","file_size":4746234,"date_updated":"2024-03-14T14:14:35Z","checksum":"bcbd213490f5a7e68855a092bbce93f1","file_id":"15113","relation":"source_file","access_level":"closed","content_type":"application/zip"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"15094","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"file_date_updated":"2024-03-14T14:14:35Z","ddc":["514","500","516"],"supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-20T09:36:57Z"},{"type":"conference","conference":{"name":"SODA: Symposium on Discrete Algorigthms","location":"Alexandria, VA, USA","end_date":"2024-01-10","start_date":"2024-01-07"},"status":"public","_id":"15093","department":[{"_id":"HeEd"},{"_id":"MoHe"}],"date_updated":"2024-03-20T09:36:56Z","main_file_link":[{"url":"https://arxiv.org/abs/2311.01115","open_access":"1"}],"month":"01","abstract":[{"lang":"eng","text":"We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right."}],"oa_version":"Preprint","related_material":{"record":[{"relation":"dissertation_contains","id":"15094","status":"public"}]},"ec_funded":1,"publication_identifier":{"eisbn":["9781611977912"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"grant_number":"Z00422","name":"Wittgenstein Award - Monika Henzinger","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"}],"author":[{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano","last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"full_name":"Ost, Lara","last_name":"Ost","first_name":"Lara"}],"external_id":{"arxiv":["2311.01115"]},"article_processing_charge":"No","title":"Dynamically maintaining the persistent homology of time series","editor":[{"first_name":"David P.","last_name":"Woodruff","full_name":"Woodruff, David P."}],"citation":{"ista":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. 2024. Dynamically maintaining the persistent homology of time series. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete Algorigthms, 243–295.","chicago":"Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika H Henzinger, and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.” In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11.","short":"S. Cultrera di Montesano, H. Edelsbrunner, M.H. Henzinger, L. Ost, in:, D.P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.","ieee":"S. Cultrera di Montesano, H. Edelsbrunner, M. H. Henzinger, and L. Ost, “Dynamically maintaining the persistent homology of time series,” in Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria, VA, USA, 2024, pp. 243–295.","ama":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. Dynamically maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11","apa":"Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M. H., & Ost, L. (2024). Dynamically maintaining the persistent homology of time series. In D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11","mla":"Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"acknowledgement":"The first and second authors are funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The third author received funding by the European Research Council under the European Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The fourth author is funded by the Vienna Graduate School on Computational Optimization, FWF project no. W1260-N35.","page":"243 - 295","doi":"10.1137/1.9781611977912.11","date_published":"2024-01-04T00:00:00Z","date_created":"2024-03-08T10:27:39Z","year":"2024","day":"04","publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)"},{"month":"02","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2212.03128"}],"oa_version":"Preprint","abstract":[{"text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided.","lang":"eng"}],"date_created":"2024-03-08T10:13:59Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"15094"}]},"date_published":"2024-02-07T00:00:00Z","language":[{"iso":"eng"}],"publication":"arXiv","day":"07","publication_status":"submitted","year":"2024","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"preprint","article_number":"2212.03128","_id":"15091","department":[{"_id":"HeEd"}],"title":"Chromatic alpha complexes","external_id":{"arxiv":["2212.03128"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano"},{"first_name":"Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov","full_name":"Draganov, Ondrej"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128.","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv.","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128."},"date_updated":"2024-03-20T09:36:56Z"},{"date_updated":"2024-03-25T07:04:05Z","department":[{"_id":"TiVo"}],"_id":"15171","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"The brain’s functionality is developed and maintained through synaptic plasticity. As synapses undergo plasticity, they also affect each other. The nature of such ‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses must be monitored simultaneously. To help understand the experimentally observed phenomena, we introduce a framework that formalizes synaptic co-dependency between different connection types. The resulting model explains how inhibition can gate excitatory plasticity while neighboring excitatory–excitatory interactions determine the strength of long-term potentiation. Furthermore, we show how the interplay between excitatory and inhibitory synapses can account for the quick rise and long-term stability of a variety of synaptic weight profiles, such as orientation tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks, co-dependent plasticity produces rich and stable motor cortex-like dynamics with high input sensitivity. Our results suggest an essential role for the neighborly synaptic interaction during learning, connecting micro-level physiology with network-wide phenomena."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41593-024-01597-4","open_access":"1"}],"month":"03","citation":{"ista":"Agnes EJ, Vogels TP. 2024. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience.","chicago":"Agnes, Everton J., and Tim P Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-024-01597-4.","apa":"Agnes, E. J., & Vogels, T. P. (2024). Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-024-01597-4","ama":"Agnes EJ, Vogels TP. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. 2024. doi:10.1038/s41593-024-01597-4","ieee":"E. J. Agnes and T. P. Vogels, “Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks,” Nature Neuroscience. Springer Nature, 2024.","short":"E.J. Agnes, T.P. Vogels, Nature Neuroscience (2024).","mla":"Agnes, Everton J., and Tim P. Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-024-01597-4."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Agnes","full_name":"Agnes, Everton J.","first_name":"Everton J."},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"}],"article_processing_charge":"Yes (via OA deal)","title":"Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks","project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020"}],"year":"2024","day":"20","publication":"Nature Neuroscience","doi":"10.1038/s41593-024-01597-4","date_published":"2024-03-20T00:00:00Z","date_created":"2024-03-24T23:01:00Z","acknowledgement":"We thank C. Currin, B. Podlaski and the members of the Vogels group for fruitful discussions. E.J.A. and T.P.V. were supported by a Research Project Grant from the Leverhulme Trust (RPG-2016-446; TPV), a Sir Henry Dale Fellowship from the Wellcome Trust and the Royal Society (WT100000; T.P.V.), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; T.P.V.) and a European Research Council Consolidator Grant (SYNAPSEEK, 819603; T.P.V.). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. Open access funding provided by University of Basel.","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"citation":{"ista":"Esposito AR, Mondelli M. Concentration without independence via information measures. IEEE Transactions on Information Theory.","chicago":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” IEEE Transactions on Information Theory. IEEE, n.d. https://doi.org/10.1109/TIT.2024.3367767.","apa":"Esposito, A. R., & Mondelli, M. (n.d.). Concentration without independence via information measures. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2024.3367767","ama":"Esposito AR, Mondelli M. Concentration without independence via information measures. IEEE Transactions on Information Theory. doi:10.1109/TIT.2024.3367767","ieee":"A. R. Esposito and M. Mondelli, “Concentration without independence via information measures,” IEEE Transactions on Information Theory. IEEE.","short":"A.R. Esposito, M. Mondelli, IEEE Transactions on Information Theory (n.d.).","mla":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” IEEE Transactions on Information Theory, IEEE, doi:10.1109/TIT.2024.3367767."},"date_updated":"2024-03-25T07:15:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"9583e921-e1ad-11ec-9862-cef099626dc9","first_name":"Amedeo Roberto","full_name":"Esposito, Amedeo Roberto","last_name":"Esposito"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"article_processing_charge":"No","external_id":{"arxiv":["2303.07245"]},"title":"Concentration without independence via information measures","department":[{"_id":"MaMo"}],"_id":"15172","type":"journal_article","article_type":"original","status":"public","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"publication_status":"inpress","year":"2024","day":"20","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Information Theory","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"14922"}]},"doi":"10.1109/TIT.2024.3367767","date_published":"2024-02-20T00:00:00Z","date_created":"2024-03-24T23:01:00Z","abstract":[{"text":"We propose a novel approach to concentration for non-independent random variables. The main idea is to “pretend” that the random variables are independent and pay a multiplicative price measuring how far they are from actually being independent. This price is encapsulated in the Hellinger integral between the joint and the product of the marginals, which is then upper bounded leveraging tensorisation properties. Our bounds represent a natural generalisation of concentration inequalities in the presence of dependence: we recover exactly the classical bounds (McDiarmid’s inequality) when the random variables are independent. Furthermore, in a “large deviations” regime, we obtain the same decay in the probability as for the independent case, even when the random variables display non-trivial dependencies. To show this, we consider a number of applications of interest. First, we provide a bound for Markov chains with finite state space. Then, we consider the Simple Symmetric Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting in which the stochastic process depends on its entire past. To conclude, we propose an application to Markov Chain Monte Carlo methods, where our approach leads to an improved lower bound on the minimum burn-in period required to reach a certain accuracy. In all of these settings, we provide a regime of parameters in which our bound fares better than what the state of the art can provide.","lang":"eng"}],"oa_version":"None","scopus_import":"1","publisher":"IEEE","quality_controlled":"1","month":"02"},{"oa":1,"quality_controlled":"1","publisher":"IOP Publishing","acknowledgement":"J.E.G. and A.D.G acknowledge support from NSF/AAG grant No. 1007094, and J.E.G. also acknowledges support from NSF/AAG grant No. 1007052. A.Z. acknowledges support by grant No. 2020750 from the United States-Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF), and by the Ministry of Science & Technology of Israel. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant No. 140. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. P.D. acknowledges support from the NWO grant 016.VIDI.189.162 (\"ODIN\") and from the European Commission's and University of Groningen's CO-FUND Rosalind Franklin program. K.G. and T.N. acknowledge support from Australian Research Council Laureate Fellowship FL180100060. H.A. and I.C. acknowledge support from CNES, focused on the JWST mission, and the Programme National Cosmology and Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, cofunded by CEA and CNES. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. The research of C.C.W. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation. B.W. acknowledges support from JWST-GO-02561.022-A. A.J.B. acknowledges funding support from NASA/ADAP grant 21-ADAP21-0187. Support for this work was provided by The Brinson Foundation through a Brinson Prize Fellowship grant. R.P.N. acknowledges support for this work provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. C.P. thanks Marsha and Ralph Schilling for the generous support of this research.","date_created":"2024-03-24T23:00:59Z","date_published":"2024-03-01T00:00:00Z","doi":"10.3847/1538-4357/ad1e5f","year":"2024","has_accepted_license":"1","publication":"Astrophysical Journal","day":"01","article_number":"39","external_id":{"arxiv":["2309.05714"]},"article_processing_charge":"Yes","author":[{"full_name":"Greene, Jenny E.","last_name":"Greene","first_name":"Jenny E."},{"first_name":"Ivo","full_name":"Labbe, Ivo","last_name":"Labbe"},{"first_name":"Andy D.","full_name":"Goulding, Andy D.","last_name":"Goulding"},{"first_name":"Lukas J.","full_name":"Furtak, Lukas J.","last_name":"Furtak"},{"last_name":"Chemerynska","full_name":"Chemerynska, Iryna","first_name":"Iryna"},{"last_name":"Kokorev","full_name":"Kokorev, Vasily","first_name":"Vasily"},{"first_name":"Pratika","last_name":"Dayal","full_name":"Dayal, Pratika"},{"first_name":"Marta","full_name":"Volonteri, Marta","last_name":"Volonteri"},{"first_name":"Christina C.","last_name":"Williams","full_name":"Williams, Christina C."},{"first_name":"Bingjie","full_name":"Wang, Bingjie","last_name":"Wang"},{"last_name":"Setton","full_name":"Setton, David J.","first_name":"David J."},{"last_name":"Burgasser","full_name":"Burgasser, Adam J.","first_name":"Adam J."},{"full_name":"Bezanson, Rachel","last_name":"Bezanson","first_name":"Rachel"},{"first_name":"Hakim","last_name":"Atek","full_name":"Atek, Hakim"},{"full_name":"Brammer, Gabriel","last_name":"Brammer","first_name":"Gabriel"},{"last_name":"Cutler","full_name":"Cutler, Sam E.","first_name":"Sam E."},{"last_name":"Feldmann","full_name":"Feldmann, Robert","first_name":"Robert"},{"first_name":"Seiji","full_name":"Fujimoto, Seiji","last_name":"Fujimoto"},{"full_name":"Glazebrook, Karl","last_name":"Glazebrook","first_name":"Karl"},{"first_name":"Anna","full_name":"De Graaff, Anna","last_name":"De Graaff"},{"first_name":"Gourav","last_name":"Khullar","full_name":"Khullar, Gourav"},{"last_name":"Leja","full_name":"Leja, Joel","first_name":"Joel"},{"first_name":"Danilo","full_name":"Marchesini, Danilo","last_name":"Marchesini"},{"full_name":"Maseda, Michael V.","last_name":"Maseda","first_name":"Michael V."},{"orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"last_name":"Miller","full_name":"Miller, Tim B.","first_name":"Tim B."},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"last_name":"Nanayakkara","full_name":"Nanayakkara, Themiya","first_name":"Themiya"},{"last_name":"Oesch","full_name":"Oesch, Pascal A.","first_name":"Pascal A."},{"last_name":"Pan","full_name":"Pan, Richard","first_name":"Richard"},{"last_name":"Papovich","full_name":"Papovich, Casey","first_name":"Casey"},{"full_name":"Price, Sedona H.","last_name":"Price","first_name":"Sedona H."},{"last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter","first_name":"Pieter"},{"last_name":"Weaver","full_name":"Weaver, John R.","first_name":"John R."},{"first_name":"Katherine E.","last_name":"Whitaker","full_name":"Whitaker, Katherine E."},{"first_name":"Adi","full_name":"Zitrin, Adi","last_name":"Zitrin"}],"title":"UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5","citation":{"short":"J.E. Greene, I. Labbe, A.D. Goulding, L.J. Furtak, I. Chemerynska, V. Kokorev, P. Dayal, M. Volonteri, C.C. Williams, B. Wang, D.J. Setton, A.J. Burgasser, R. Bezanson, H. Atek, G. Brammer, S.E. Cutler, R. Feldmann, S. Fujimoto, K. Glazebrook, A. De Graaff, G. Khullar, J. Leja, D. Marchesini, M.V. Maseda, J.J. Matthee, T.B. Miller, R.P. Naidu, T. Nanayakkara, P.A. Oesch, R. Pan, C. Papovich, S.H. Price, P. Van Dokkum, J.R. Weaver, K.E. Whitaker, A. Zitrin, Astrophysical Journal 964 (2024).","ieee":"J. E. Greene et al., “UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5,” Astrophysical Journal, vol. 964. IOP Publishing, 2024.","apa":"Greene, J. E., Labbe, I., Goulding, A. D., Furtak, L. J., Chemerynska, I., Kokorev, V., … Zitrin, A. (2024). UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad1e5f","ama":"Greene JE, Labbe I, Goulding AD, et al. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. 2024;964. doi:10.3847/1538-4357/ad1e5f","mla":"Greene, Jenny E., et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal, vol. 964, 39, IOP Publishing, 2024, doi:10.3847/1538-4357/ad1e5f.","ista":"Greene JE, Labbe I, Goulding AD, Furtak LJ, Chemerynska I, Kokorev V, Dayal P, Volonteri M, Williams CC, Wang B, Setton DJ, Burgasser AJ, Bezanson R, Atek H, Brammer G, Cutler SE, Feldmann R, Fujimoto S, Glazebrook K, De Graaff A, Khullar G, Leja J, Marchesini D, Maseda MV, Matthee JJ, Miller TB, Naidu RP, Nanayakkara T, Oesch PA, Pan R, Papovich C, Price SH, Van Dokkum P, Weaver JR, Whitaker KE, Zitrin A. 2024. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. 964, 39.","chicago":"Greene, Jenny E., Ivo Labbe, Andy D. Goulding, Lukas J. Furtak, Iryna Chemerynska, Vasily Kokorev, Pratika Dayal, et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad1e5f."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 964","month":"03","abstract":[{"lang":"eng","text":"The James Webb Space Telescope is revealing a new population of dust-reddened broad-line active galactic nuclei (AGN) at redshifts z ≳ 5. Here we present deep NIRSpec/Prism spectroscopy from the Cycle 1 Treasury program Ultradeep NIRSpec and NIRCam ObserVations before the Epoch of Reionization (UNCOVER) of 15 AGN candidates selected to be compact, with red continua in the rest-frame optical but with blue slopes in the UV. From NIRCam photometry alone, they could have been dominated by dusty star formation or an AGN. Here we show that the majority of the compact red sources in UNCOVER are dust-reddened AGN: 60% show definitive evidence for broad-line Hα with a FWHM > 2000 km s −1, 20% of the current data are inconclusive, and 20% are brown dwarf stars. We propose an updated photometric criterion to select red z > 5 AGN that excludes brown dwarfs and is expected to yield >80% AGN. Remarkably, among all zphot > 5 galaxies with F277W – F444W > 1 in UNCOVER at least 33% are AGN regardless of compactness, climbing to at least 80% AGN for sources with F277W – F444W > 1.6. The confirmed AGN have black hole masses of 107–109M⊙. While their UV luminosities (−16 > MUV > −20 AB mag) are low compared to UV-selected AGN at these epochs, consistent with percent-level scattered AGN light or low levels of unobscured star formation, the inferred bolometric luminosities are typical of 107–109M⊙ black holes radiating at ∼10%–40% the Eddington limit. The number densities are surprisingly high at ∼10−5 Mpc−3 mag−1, 100 times more common than the faintest UV-selected quasars, while accounting for ∼1% of the UV-selected galaxies. While their UV faintness suggests they may not contribute strongly to reionization, their ubiquity poses challenges to models of black hole growth."}],"oa_version":"Published Version","volume":964,"publication_status":"published","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2024-03-25T08:02:43Z","file_size":2700137,"date_created":"2024-03-25T08:02:43Z","file_name":"2024_AstrophysicalJourn_Greene.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"15176","checksum":"389a880e176799d5c062ea7cb82d08c9","success":1}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"15170","department":[{"_id":"JoMa"}],"file_date_updated":"2024-03-25T08:02:43Z","date_updated":"2024-03-25T08:04:13Z","ddc":["550"]},{"project":[{"call_identifier":"FWF","_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory"},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"article_number":"34","title":"Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs","external_id":{"arxiv":["2312.12981"]},"article_processing_charge":"No","author":[{"full_name":"Filakovský, Marek","last_name":"Filakovský","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"},{"full_name":"Nakajima, Tamio Vesa","last_name":"Nakajima","first_name":"Tamio Vesa"},{"id":"ec596741-c539-11ec-b829-c79322a91242","first_name":"Jakub","last_name":"Opršal","orcid":"0000-0003-1245-3456","full_name":"Opršal, Jakub"},{"last_name":"Tasinato","full_name":"Tasinato, Gianluca","id":"0433290C-AF8F-11E9-A4C7-F729E6697425","first_name":"Gianluca"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Filakovský, Marek, Tamio Vesa Nakajima, Jakub Opršal, Gianluca Tasinato, and Uli Wagner. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” In 41st International Symposium on Theoretical Aspects of Computer Science, Vol. 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.STACS.2024.34.","ista":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. 2024. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. 41st International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 289, 34.","mla":"Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” 41st International Symposium on Theoretical Aspects of Computer Science, vol. 289, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.STACS.2024.34.","ieee":"M. Filakovský, T. V. Nakajima, J. Opršal, G. Tasinato, and U. Wagner, “Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs,” in 41st International Symposium on Theoretical Aspects of Computer Science, Clermont-Ferrand, France, 2024, vol. 289.","short":"M. Filakovský, T.V. Nakajima, J. Opršal, G. Tasinato, U. Wagner, in:, 41st International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ama":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In: 41st International Symposium on Theoretical Aspects of Computer Science. Vol 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.STACS.2024.34","apa":"Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., & Wagner, U. (2024). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In 41st International Symposium on Theoretical Aspects of Computer Science (Vol. 289). Clermont-Ferrand, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2024.34"},"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"Marek Filakovský: This research was supported by Charles University (project PRIMUS/\r\n21/SCI/014), the Austrian Science Fund (FWF project P31312-N35), and MSCAfellow5_MUNI\r\n(CZ.02.01.01/00/22_010/0003229). Tamio-Vesa Nakajima: This research was funded by UKRI EP/X024431/1 and by a Clarendon Fund Scholarship. All data is provided in full in the results section of this paper. Jakub Opršal: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Uli Wagner: This research was supported by the Austrian Science Fund (FWF project P31312-N35).","date_created":"2024-03-24T23:00:59Z","doi":"10.4230/LIPIcs.STACS.2024.34","date_published":"2024-03-01T00:00:00Z","publication":"41st International Symposium on Theoretical Aspects of Computer Science","day":"01","year":"2024","has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","end_date":"2024-03-14","location":"Clermont-Ferrand, France","start_date":"2024-03-12"},"type":"conference","_id":"15168","file_date_updated":"2024-03-25T07:44:30Z","department":[{"_id":"UlWa"}],"ddc":["510"],"date_updated":"2024-03-25T07:45:54Z","intvolume":" 289","month":"03","alternative_title":["LIPIcs"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its vertices with colours 1, … , k such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO k-colouring with a fixed number of colours is NP-complete (and in the special case of graphs, LO colouring coincides with the usual graph colouring). Here, we investigate the complexity of approximating the \"linearly ordered chromatic number\" of a hypergraph. We prove that the following promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable. We prove this result by a combination of algebraic, topological, and combinatorial methods, building on and extending a topological approach for studying approximate graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023)."}],"ec_funded":1,"volume":289,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"0524d4189fd1ed08989546511343edf3","file_id":"15175","success":1,"creator":"dernst","date_updated":"2024-03-25T07:44:30Z","file_size":927290,"date_created":"2024-03-25T07:44:30Z","file_name":"2024_LIPICs_Filakovsky.pdf"}],"publication_status":"published","publication_identifier":{"isbn":["9783959773119"],"eissn":["1868-8969"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Silva-Henao, Juan D., Sophie Schober, Dieter H. Pahr, and Andreas G. Reisinger. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics. Elsevier, 2024. https://doi.org/10.1016/j.medengphy.2024.104143.","ista":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. 2024. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 126, 104143.","mla":"Silva-Henao, Juan D., et al. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics, vol. 126, 104143, Elsevier, 2024, doi:10.1016/j.medengphy.2024.104143.","ama":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 2024;126. doi:10.1016/j.medengphy.2024.104143","apa":"Silva-Henao, J. D., Schober, S., Pahr, D. H., & Reisinger, A. G. (2024). Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. Elsevier. https://doi.org/10.1016/j.medengphy.2024.104143","short":"J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering and Physics 126 (2024).","ieee":"J. D. Silva-Henao, S. Schober, D. H. Pahr, and A. G. Reisinger, “Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading,” Medical Engineering and Physics, vol. 126. Elsevier, 2024."},"title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading","article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Juan D.","full_name":"Silva-Henao, Juan D.","last_name":"Silva-Henao"},{"full_name":"Schober, Sophie","last_name":"Schober","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie"},{"last_name":"Pahr","full_name":"Pahr, Dieter H.","first_name":"Dieter H."},{"full_name":"Reisinger, Andreas G.","last_name":"Reisinger","first_name":"Andreas G."}],"article_number":"104143","publication":"Medical Engineering and Physics","day":"01","year":"2024","has_accepted_license":"1","date_created":"2024-03-24T23:00:58Z","doi":"10.1016/j.medengphy.2024.104143","date_published":"2024-04-01T00:00:00Z","acknowledgement":"The authors declare no conflict of interest related to this study. This project was funded by the Gesellschaft fuer Forschungsfoerderung Niederoesterreich m.b.H. Life Science Call 2017 Grant No. LS17004 and Science call 2019 Dissertationen Grant No. SC19014. No ethical approval was required for this study.","oa":1,"quality_controlled":"1","publisher":"Elsevier","ddc":["610"],"date_updated":"2024-03-25T08:31:01Z","file_date_updated":"2024-03-25T08:29:52Z","department":[{"_id":"PreCl"}],"_id":"15164","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2024-03-25T08:29:52Z","file_size":10039402,"date_created":"2024-03-25T08:29:52Z","file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"974acbf2731e7382dcf5920ac762e551","file_id":"15177","success":1}],"publication_status":"published","publication_identifier":{"issn":["1350-4533"],"eissn":["1873-4030"]},"volume":126,"oa_version":"Published Version","abstract":[{"text":"Primary implant stability, which refers to the stability of the implant during the initial healing period is a crucial factor in determining the long-term success of the implant and lays the foundation for secondary implant stability achieved through osseointegration. Factors affecting primary stability include implant design, surgical technique, and patient-specific factors like bone quality and morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis locking screws under dynamic loads, which can lead to the formation of micro cracks and defects that slowly degrade the mechanical connection between the bone and screw, thus compromising the initial stability and secondary stability of the implant. Monotonic quasi-static loading used for testing the holding capacity of implanted screws is not well suited to capture this behavior since it cannot capture the progressive deterioration of peri‑implant bone at small displacements. In order to address this issue, this study aims to determine a critical point of loss of primary implant stability in osteosynthesis locking screws under cyclic overloading by investigating the evolution of damage, dissipated energy, and permanent deformation. A custom-made test setup was used to test implanted 2.5 mm locking screws under cyclic overloading test. For each loading cycle, maximum forces and displacement were recorded as well as initial and final cycle displacements and used to calculate damage and energy dissipation evolution. The results of this study demonstrate that for axial, shear, and mixed loading significant damage and energy dissipation can be observed at approximately 20 % of the failure force. Additionally, at this load level, permanent deformations on the screw-bone interface were found to be in the range of 50 to 150 mm which promotes osseointegration and secondary implant stability. This research can assist surgeons in making informed preoperative decisions by providing a better understanding of the critical point of loss of primary implant stability, thus improving the long-term success of the implant and overall patient satisfaction.","lang":"eng"}],"intvolume":" 126","month":"04","scopus_import":"1"},{"acknowledgement":"The Python implementation of kCSD was started by Grzegorz Parka during Google Summer of Code project through the International Neuroinformatics Coordinating Facility. Jan Mąka implemented the first Python version of skCSD class. This work was supported by the Polish National Science Centre (2013/08/W/NZ4/00691 to DKW; 2015/17/B/ST7/04123 to DKW). ","quality_controlled":"1","publisher":"Public Library of Science","publication":"PLoS Computational Biology","day":"14","year":"2024","date_created":"2024-03-24T23:00:59Z","date_published":"2024-03-14T00:00:00Z","doi":"10.1371/journal.pcbi.1011941","article_number":"e1011941","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chintaluri, Chaitanya, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski, Jakub M. Dzik, Joanna Jedrzejewska-Szmek, and Daniel K. Wojciki. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” PLoS Computational Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1011941.","ista":"Chintaluri C, Bejtka M, Sredniawa W, Czerwinski M, Dzik JM, Jedrzejewska-Szmek J, Wojciki DK. 2024. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 20(3), e1011941.","mla":"Chintaluri, Chaitanya, et al. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” PLoS Computational Biology, vol. 20, no. 3, e1011941, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1011941.","apa":"Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek, J., & Wojciki, D. K. (2024). kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011941","ama":"Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 2024;20(3). doi:10.1371/journal.pcbi.1011941","short":"C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek, D.K. Wojciki, PLoS Computational Biology 20 (2024).","ieee":"C. Chintaluri et al., “kCSD-python, reliable current source density estimation with quality control,” PLoS Computational Biology, vol. 20, no. 3. Public Library of Science, 2024."},"title":"kCSD-python, reliable current source density estimation with quality control","article_processing_charge":"Yes","author":[{"first_name":"Chaitanya","id":"E4EDB536-3485-11EA-98D2-20AF3DDC885E","last_name":"Chintaluri","full_name":"Chintaluri, Chaitanya"},{"first_name":"Marta","last_name":"Bejtka","full_name":"Bejtka, Marta"},{"first_name":"Wladyslaw","full_name":"Sredniawa, Wladyslaw","last_name":"Sredniawa"},{"first_name":"Michal","last_name":"Czerwinski","full_name":"Czerwinski, Michal"},{"last_name":"Dzik","full_name":"Dzik, Jakub M.","first_name":"Jakub M."},{"first_name":"Joanna","full_name":"Jedrzejewska-Szmek, Joanna","last_name":"Jedrzejewska-Szmek"},{"first_name":"Daniel K.","full_name":"Wojciki, Daniel K.","last_name":"Wojciki"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Interpretation of extracellular recordings can be challenging due to the long range of electric field. This challenge can be mitigated by estimating the current source density (CSD). Here we introduce kCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method and related tools to facilitate CSD analysis of experimental data and the interpretation of results. We show how to counter the limitations imposed by noise and assumptions in the method itself. kCSD-python allows CSD estimation for an arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter Notebook tutorial which illustrates a typical analytical workflow and main functionalities useful in validating analysis results."}],"intvolume":" 20","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"issue":"3","volume":20,"related_material":{"link":[{"url":"https://github.com/Neuroinflab/kCSD-python","relation":"software"}]},"_id":"15169","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-03-25T07:54:23Z","department":[{"_id":"TiVo"}]},{"doi":"10.1103/PhysRevA.109.033315","date_published":"2024-03-19T00:00:00Z","date_created":"2024-03-24T23:00:59Z","day":"19","publication":"Physical Review A","year":"2024","publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"We thank Félix Werner and Kris Van Houcke for interesting discussions.","title":"Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy","author":[{"first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","full_name":"Al Hyder, Ragheed","last_name":"Al Hyder"},{"first_name":"F.","full_name":"Chevy, F.","last_name":"Chevy"},{"first_name":"X.","full_name":"Leyronas, X.","last_name":"Leyronas"}],"article_processing_charge":"No","external_id":{"arxiv":["2311.14536"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Al Hyder R, Chevy F, Leyronas X. 2024. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. 109(3), 033315.","chicago":"Al Hyder, Ragheed, F. Chevy, and X. Leyronas. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” Physical Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.033315.","ieee":"R. Al Hyder, F. Chevy, and X. Leyronas, “Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy,” Physical Review A, vol. 109, no. 3. American Physical Society, 2024.","short":"R. Al Hyder, F. Chevy, X. Leyronas, Physical Review A 109 (2024).","ama":"Al Hyder R, Chevy F, Leyronas X. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. 2024;109(3). doi:10.1103/PhysRevA.109.033315","apa":"Al Hyder, R., Chevy, F., & Leyronas, X. (2024). Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.109.033315","mla":"Al Hyder, Ragheed, et al. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” Physical Review A, vol. 109, no. 3, 033315, American Physical Society, 2024, doi:10.1103/PhysRevA.109.033315."},"article_number":"033315","volume":109,"issue":"3","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"publication_status":"published","month":"03","intvolume":" 109","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2311.14536"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We perform a diagrammatic analysis of the energy of a mobile impurity immersed in a strongly interacting two-component Fermi gas to second order in the impurity-bath interaction. These corrections demonstrate divergent behavior in the limit of large impurity momentum. We show the fundamental processes responsible for these logarithmically divergent terms. We study the problem in the general case without any assumptions regarding the fermion-fermion interactions in the bath. We show that the divergent term can be summed up to all orders in the Fermi-Fermi interaction and that the resulting expression is equivalent to the one obtained in the few-body calculation. Finally, we provide a perturbative calculation to the second order in the Fermi-Fermi interaction, and we show the diagrams responsible for these terms."}],"department":[{"_id":"MiLe"}],"date_updated":"2024-03-25T07:36:55Z","status":"public","type":"journal_article","article_type":"original","_id":"15167"},{"year":"2024","publication":"Discrete Mathematics","day":"19","date_created":"2024-03-24T23:00:58Z","doi":"10.1016/j.disc.2024.113962","date_published":"2024-03-19T00:00:00Z","acknowledgement":"We wish to thank Dániel Marx and András Sebő for making us aware of the results in [8] and some clarifications on them.","oa":1,"publisher":"Elsevier","quality_controlled":"1","citation":{"mla":"Campbell, Rutger, et al. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics, vol. 347, no. 6, 113962, Elsevier, 2024, doi:10.1016/j.disc.2024.113962.","ama":"Campbell R, Hörsch F, Moore B. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 2024;347(6). doi:10.1016/j.disc.2024.113962","apa":"Campbell, R., Hörsch, F., & Moore, B. (2024). Decompositions into two linear forests of bounded lengths. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2024.113962","ieee":"R. Campbell, F. Hörsch, and B. Moore, “Decompositions into two linear forests of bounded lengths,” Discrete Mathematics, vol. 347, no. 6. Elsevier, 2024.","short":"R. Campbell, F. Hörsch, B. Moore, Discrete Mathematics 347 (2024).","chicago":"Campbell, Rutger, Florian Hörsch, and Benjamin Moore. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics. Elsevier, 2024. https://doi.org/10.1016/j.disc.2024.113962.","ista":"Campbell R, Hörsch F, Moore B. 2024. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 347(6), 113962."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2301.11615"]},"article_processing_charge":"No","author":[{"full_name":"Campbell, Rutger","last_name":"Campbell","first_name":"Rutger"},{"last_name":"Hörsch","full_name":"Hörsch, Florian","first_name":"Florian"},{"id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","first_name":"Benjamin","full_name":"Moore, Benjamin","last_name":"Moore"}],"title":"Decompositions into two linear forests of bounded lengths","article_number":"113962","publication_status":"epub_ahead","publication_identifier":{"issn":["0012-365X"]},"language":[{"iso":"eng"}],"issue":"6","volume":347,"abstract":[{"text":"For some k∈Z≥0∪{∞}, we call a linear forest k-bounded if each of its components has at most k edges. We will say a (k,ℓ)-bounded linear forest decomposition of a graph G is a partition of E(G) into the edge sets of two linear forests Fk,Fℓ where Fk is k-bounded and Fℓ is ℓ-bounded. We show that the problem of deciding whether a given graph has such a decomposition is NP-complete if both k and ℓ are at least 2, NP-complete if k≥9 and ℓ=1, and is in P for (k,ℓ)=(2,1). Before this, the only known NP-complete cases were the (2,2) and (3,3) cases. Our hardness result answers a question of Bermond et al. from 1984. We also show that planar graphs of girth at least nine decompose into a linear forest and a matching, which in particular is stronger than 3-edge-colouring such graphs.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.11615","open_access":"1"}],"scopus_import":"1","intvolume":" 347","month":"03","date_updated":"2024-03-25T08:09:43Z","department":[{"_id":"MaKw"}],"_id":"15163","article_type":"original","type":"journal_article","status":"public"},{"citation":{"chicago":"Matthee, Jorryt J, Rohan P. Naidu, Gabriel Brammer, John Chisholm, Anna-Christina Eilers, Andy Goulding, Jenny Greene, et al. “Little Red Dots: An Abundant Population of Faint Active Galactic Nuclei at z ∼ 5 Revealed by the EIGER and FRESCO JWST Surveys.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad2345.","ista":"Matthee JJ, Naidu RP, Brammer G, Chisholm J, Eilers A-C, Goulding A, Greene J, Kashino D, Labbe I, Lilly SJ, Mackenzie R, Oesch PA, Weibel A, Wuyts S, Xiao M, Bordoloi R, Bouwens R, van Dokkum P, Illingworth G, Kramarenko I, Maseda MV, Mason C, Meyer RA, Nelson EJ, Reddy NA, Shivaei I, Simcoe RA, Yue M. 2024. Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. 963(2), 129.","mla":"Matthee, Jorryt J., et al. “Little Red Dots: An Abundant Population of Faint Active Galactic Nuclei at z ∼ 5 Revealed by the EIGER and FRESCO JWST Surveys.” The Astrophysical Journal, vol. 963, no. 2, 129, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad2345.","ieee":"J. J. Matthee et al., “Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys,” The Astrophysical Journal, vol. 963, no. 2. American Astronomical Society, 2024.","short":"J.J. Matthee, R.P. Naidu, G. Brammer, J. Chisholm, A.-C. Eilers, A. Goulding, J. Greene, D. Kashino, I. Labbe, S.J. Lilly, R. Mackenzie, P.A. Oesch, A. Weibel, S. Wuyts, M. Xiao, R. Bordoloi, R. Bouwens, P. van Dokkum, G. Illingworth, I. Kramarenko, M.V. Maseda, C. Mason, R.A. Meyer, E.J. Nelson, N.A. Reddy, I. Shivaei, R.A. Simcoe, M. Yue, The Astrophysical Journal 963 (2024).","apa":"Matthee, J. J., Naidu, R. P., Brammer, G., Chisholm, J., Eilers, A.-C., Goulding, A., … Yue, M. (2024). Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad2345","ama":"Matthee JJ, Naidu RP, Brammer G, et al. Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. 2024;963(2). doi:10.3847/1538-4357/ad2345"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","author":[{"last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"first_name":"Gabriel","last_name":"Brammer","full_name":"Brammer, Gabriel"},{"full_name":"Chisholm, John","last_name":"Chisholm","first_name":"John"},{"first_name":"Anna-Christina","full_name":"Eilers, Anna-Christina","last_name":"Eilers"},{"last_name":"Goulding","full_name":"Goulding, Andy","first_name":"Andy"},{"full_name":"Greene, Jenny","last_name":"Greene","first_name":"Jenny"},{"first_name":"Daichi","full_name":"Kashino, Daichi","last_name":"Kashino"},{"first_name":"Ivo","last_name":"Labbe","full_name":"Labbe, Ivo"},{"first_name":"Simon J.","full_name":"Lilly, Simon J.","last_name":"Lilly"},{"last_name":"Mackenzie","full_name":"Mackenzie, Ruari","first_name":"Ruari"},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"first_name":"Andrea","last_name":"Weibel","full_name":"Weibel, Andrea"},{"full_name":"Wuyts, Stijn","last_name":"Wuyts","first_name":"Stijn"},{"last_name":"Xiao","full_name":"Xiao, Mengyuan","first_name":"Mengyuan"},{"first_name":"Rongmon","last_name":"Bordoloi","full_name":"Bordoloi, Rongmon"},{"first_name":"Rychard","full_name":"Bouwens, Rychard","last_name":"Bouwens"},{"full_name":"van Dokkum, Pieter","last_name":"van Dokkum","first_name":"Pieter"},{"full_name":"Illingworth, Garth","last_name":"Illingworth","first_name":"Garth"},{"last_name":"Kramarenko","full_name":"Kramarenko, Ivan","first_name":"Ivan"},{"first_name":"Michael V.","full_name":"Maseda, Michael V.","last_name":"Maseda"},{"first_name":"Charlotte","last_name":"Mason","full_name":"Mason, Charlotte"},{"last_name":"Meyer","full_name":"Meyer, Romain A.","first_name":"Romain A."},{"first_name":"Erica J.","full_name":"Nelson, Erica J.","last_name":"Nelson"},{"first_name":"Naveen A.","full_name":"Reddy, Naveen A.","last_name":"Reddy"},{"first_name":"Irene","full_name":"Shivaei, Irene","last_name":"Shivaei"},{"first_name":"Robert A.","full_name":"Simcoe, Robert A.","last_name":"Simcoe"},{"first_name":"Minghao","full_name":"Yue, Minghao","last_name":"Yue"}],"title":"Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys","article_number":"129","project":[{"grant_number":"101076224","name":"Young galaxies as tracers and agents of cosmic reionization","_id":"bd9b2118-d553-11ed-ba76-db24564edfea"}],"year":"2024","has_accepted_license":"1","publication":"The Astrophysical Journal","day":"07","date_created":"2024-03-25T08:54:47Z","date_published":"2024-03-07T00:00:00Z","doi":"10.3847/1538-4357/ad2345","acknowledgement":"We thank the anonymous referee for constructive comments that helped improve the manuscript. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with program Nos. 1243 and 1895. The specific observations analyzed can be accessed via doi:10.17909/4xx0-zj76. Funded by the European Union (ERC, AGENTS, 101076224). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work for R.P.N. was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. Support for this work for G.I. was provided by NASA through grant JWST-GO-01895 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract No. MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant No. 140.\r\nFacility: JWST - James Webb Space Telescope, HST - Hubble Space Telescope satellite\r\nSoftware: Python, matplotlib (Hunter 2007), numpy (Harris et al. 2020), scipy (Virtanen et al. 2020), Astropy (Astropy Collaboration et al. 2013, 2018), Imfit (Erwin 2015).","oa":1,"quality_controlled":"1","publisher":"American Astronomical Society","date_updated":"2024-03-25T09:37:27Z","ddc":["550"],"file_date_updated":"2024-03-25T09:31:58Z","department":[{"_id":"JoMa"}],"_id":"15180","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","publication_status":"published","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"language":[{"iso":"eng"}],"file":[{"checksum":"dc7af4694f9f94a551417ab49fa43edf","file_id":"15184","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-03-25T09:31:58Z","file_name":"2024_AstrophysicalJourn_Matthee.pdf","date_updated":"2024-03-25T09:31:58Z","file_size":6047536,"creator":"dernst"}],"volume":963,"issue":"2","abstract":[{"lang":"eng","text":"Characterizing the prevalence and properties of faint active galactic nuclei (AGNs) in the early Universe is key for understanding the formation of supermassive black holes (SMBHs) and determining their role in cosmic reionization. We perform a spectroscopic search for broad Hα emitters at z ≈ 4–6 using deep JWST/NIRCam imaging and wide field slitless spectroscopy from the EIGER and FRESCO surveys. We identify 20 Hα lines at z = 4.2–5.5 that have broad components with line widths from ∼1200–3700 km s−1, contributing ∼30%–90% of the total line flux. We interpret these broad components as being powered by accretion onto SMBHs with implied masses ∼107–8M⊙. In the UV luminosity range MUV,AGN+host = −21 to −18, we measure number densities of ≈10−5 cMpc−3. This is an order of magnitude higher than expected from extrapolating quasar UV luminosity functions (LFs). Yet, such AGN are found in only <1% of star-forming galaxies at z ∼ 5. The number density discrepancy is much lower when compared to the broad Hα LF. The SMBH mass function agrees with large cosmological simulations. In two objects, we detect complex Hα profiles that we tentatively interpret as caused by absorption signatures from dense gas fueling SMBH growth and outflows. We may be witnessing early AGN feedback that will clear dust-free pathways through which more massive blue quasars are seen. We uncover a strong correlation between reddening and the fraction of total galaxy luminosity arising from faint AGN. This implies that early SMBH growth is highly obscured and that faint AGN are only minor contributors to cosmic reionization."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 963","month":"03"},{"publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"a19c43b260ea0bbaf895a29712e3153c","file_id":"15185","creator":"dernst","file_size":1499302,"date_updated":"2024-03-25T09:42:10Z","file_name":"2024_ScienceAdv_Palkina.pdf","date_created":"2024-03-25T09:42:10Z"}],"language":[{"iso":"eng"}],"issue":"10","volume":10,"abstract":[{"text":"The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 10","date_updated":"2024-03-25T09:44:53Z","ddc":["580"],"file_date_updated":"2024-03-25T09:42:10Z","department":[{"_id":"FyKo"}],"_id":"15179","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","year":"2024","day":"01","publication":"Science Advances","date_published":"2024-03-01T00:00:00Z","doi":"10.1126/sciadv.adk1992","date_created":"2024-03-25T08:54:33Z","acknowledgement":"We thank Milaboratory (milaboratory.com) for the access to computing and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance with experiments.\r\nThis study was partially funded by Light Bio and Planta. The Synthetic biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/. Plant transformations were funded by RFBR and MOST, project number 21-54-52004. Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/. Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal de Investigación (cofinanced by the European Regional Development Fund).","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"citation":{"mla":"Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances, vol. 10, no. 10, adk1992, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1992.","ama":"Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained luminescence. Science Advances. 2024;10(10). doi:10.1126/sciadv.adk1992","apa":"Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1992","short":"K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina, L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez, V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk, A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N. Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob, D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024).","ieee":"K. A. Palkina et al., “A hybrid pathway for self-sustained luminescence,” Science Advances, vol. 10, no. 10. American Association for the Advancement of Science, 2024.","chicago":"Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I. Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez, et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1992.","ista":"Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Kseniia A.","full_name":"Palkina, Kseniia A.","last_name":"Palkina"},{"full_name":"Karataeva, Tatiana A.","last_name":"Karataeva","first_name":"Tatiana A."},{"first_name":"Maxim M.","full_name":"Perfilov, Maxim M.","last_name":"Perfilov"},{"first_name":"Liliia I.","last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia I."},{"first_name":"Nadezhda M.","last_name":"Markina","full_name":"Markina, Nadezhda M."},{"last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa"},{"first_name":"Elena","last_name":"Garcia-Perez","full_name":"Garcia-Perez, Elena"},{"full_name":"Vazquez-Vilar, Marta","last_name":"Vazquez-Vilar","first_name":"Marta"},{"first_name":"Marta","last_name":"Rodriguez-Rodriguez","full_name":"Rodriguez-Rodriguez, Marta"},{"first_name":"Victor","last_name":"Vazquez-Vilriales","full_name":"Vazquez-Vilriales, Victor"},{"first_name":"Ekaterina S.","last_name":"Shakhova","full_name":"Shakhova, Ekaterina S."},{"last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana"},{"full_name":"Belozerova, Olga A.","last_name":"Belozerova","first_name":"Olga A."},{"full_name":"Kovalchuk, Sergey I.","last_name":"Kovalchuk","first_name":"Sergey I."},{"first_name":"Anna","last_name":"Alekberova","full_name":"Alekberova, Anna"},{"last_name":"Malyshevskaia","full_name":"Malyshevskaia, Alena K.","first_name":"Alena K."},{"first_name":"Evgenia N.","last_name":"Bugaeva","full_name":"Bugaeva, Evgenia N."},{"last_name":"Guglya","full_name":"Guglya, Elena B.","first_name":"Elena B."},{"full_name":"Balakireva, Anastasia","last_name":"Balakireva","first_name":"Anastasia"},{"full_name":"Sytov, Nikita","last_name":"Sytov","first_name":"Nikita"},{"full_name":"Bezlikhotnova, Anastasia","last_name":"Bezlikhotnova","first_name":"Anastasia"},{"first_name":"Daria I.","full_name":"Boldyreva, Daria I.","last_name":"Boldyreva"},{"first_name":"Vladislav V.","full_name":"Babenko, Vladislav V.","last_name":"Babenko"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"last_name":"Choob","full_name":"Choob, Vladimir V.","first_name":"Vladimir V."},{"full_name":"Orzaez, Diego","last_name":"Orzaez","first_name":"Diego"},{"first_name":"Ilia V.","full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"first_name":"Karen S.","full_name":"Sarkisyan, Karen S.","last_name":"Sarkisyan"}],"article_processing_charge":"Yes","title":"A hybrid pathway for self-sustained luminescence","article_number":"adk1992"},{"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","keyword":["General Earth and Planetary Sciences","Geophysics"],"status":"public","_id":"15186","file_date_updated":"2024-03-25T11:28:25Z","department":[{"_id":"CaMu"}],"date_updated":"2024-03-25T11:32:06Z","ddc":["550"],"intvolume":" 51","month":"03","abstract":[{"lang":"eng","text":"The elimination of rain evaporation in the planetary boundary layer (PBL) has been found to lead to convective self‐aggregation (CSA) even without radiative feedback, but the precise mechanisms underlying this phenomenon remain unclear. We conducted cloud‐resolving simulations with two domain sizes and progressively reduced rain evaporation in the PBL. Surprisingly, CSA only occurred when rain evaporation was almost completely removed. The additional convective heating resulting from the reduction of evaporative cooling in the moist patch was found to be the trigger, thereafter a dry subsidence intrusion into the PBL in the dry patch takes over and sets CSA in motion. Temperature and moisture anomalies oppose each other in their buoyancy effects, hence explaining the need for almost total rain evaporation removal. We also found radiative cooling and not cold pools to be the leading cause for the comparative ease of CSA to take place in the larger domain."}],"oa_version":"Published Version","ec_funded":1,"volume":51,"issue":"6","publication_status":"published","publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2024-03-25T11:28:25Z","file_name":"2024_GeophysResLetters_Hwong.pdf","creator":"dernst","date_updated":"2024-03-25T11:28:25Z","file_size":1280108,"file_id":"15187","checksum":"eacb011091a503b9e7b748fef639ba4c","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate"}],"article_number":" e2023GL106523","article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Hwong","full_name":"Hwong, Yi-Ling","orcid":"0000-0001-9281-3479","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller"}],"title":"The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation","citation":{"ista":"Hwong Y-L, Muller CJ. 2024. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 51(6), e2023GL106523.","chicago":"Hwong, Yi-Ling, and Caroline J Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical Research Letters. American Geophysical Union, 2024. https://doi.org/10.1029/2023gl106523.","ama":"Hwong Y-L, Muller CJ. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 2024;51(6). doi:10.1029/2023gl106523","apa":"Hwong, Y.-L., & Muller, C. J. (2024). The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl106523","ieee":"Y.-L. Hwong and C. J. Muller, “The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation,” Geophysical Research Letters, vol. 51, no. 6. American Geophysical Union, 2024.","short":"Y.-L. Hwong, C.J. Muller, Geophysical Research Letters 51 (2024).","mla":"Hwong, Yi-Ling, and Caroline J. Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical Research Letters, vol. 51, no. 6, e2023GL106523, American Geophysical Union, 2024, doi:10.1029/2023gl106523."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"American Geophysical Union","quality_controlled":"1","acknowledgement":"YLH is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant 101034413. CM gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant 805041). The authors warmly thank Steven Sherwood, Jiawei Bao, Bidyut Goswami, and Martin Janssens for stimulating and helpful discussions. They also thank Christopher Holloway and an anonymous reviewer for providing helpful feedback that greatly improved this manuscript.\r\n","date_created":"2024-03-25T10:27:30Z","doi":"10.1029/2023gl106523","date_published":"2024-03-19T00:00:00Z","year":"2024","has_accepted_license":"1","publication":"Geophysical Research Letters","day":"19"},{"article_number":"013257","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Becker, A., Georgios Koutentakis, and P. Schmelcher. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013257.","ista":"Becker A, Koutentakis G, Schmelcher P. 2024. Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 6(1), 013257.","mla":"Becker, A., et al. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research, vol. 6, no. 1, 013257, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013257.","ieee":"A. Becker, G. Koutentakis, and P. Schmelcher, “Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","short":"A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 6 (2024).","ama":"Becker A, Koutentakis G, Schmelcher P. Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013257","apa":"Becker, A., Koutentakis, G., & Schmelcher, P. (2024). Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013257"},"title":"Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions","external_id":{"arxiv":["2310.17995"]},"article_processing_charge":"Yes","author":[{"full_name":"Becker, A.","last_name":"Becker","first_name":"A."},{"last_name":"Koutentakis","full_name":"Koutentakis, Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","first_name":"Georgios"},{"first_name":"P.","last_name":"Schmelcher","full_name":"Schmelcher, P."}],"acknowledgement":"This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project ID 390715994.\r\nG.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","publication":"Physical Review Research","day":"01","year":"2024","has_accepted_license":"1","date_created":"2024-03-25T08:57:07Z","date_published":"2024-03-01T00:00:00Z","doi":"10.1103/physrevresearch.6.013257","_id":"15181","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["530"],"date_updated":"2024-03-25T09:27:37Z","department":[{"_id":"MiLe"}],"file_date_updated":"2024-03-25T09:24:55Z","oa_version":"Published Version","abstract":[{"text":"We demonstrate the failure of the adiabatic Born-Oppenheimer approximation to describe the ground state of a quantum impurity within an ultracold Fermi gas despite substantial mass differences between the bath and impurity species. Increasing repulsion leads to the appearance of nonadiabatic couplings between the fast bath and slow impurity degrees of freedom, which reduce the parity symmetry of the latter according to the pseudo Jahn-Teller effect. The presence of this mechanism is associated to a conical intersection involving the impurity position and the inverse of the interaction strength, which acts as a synthetic dimension. We elucidate the presence of these effects via a detailed ground-state analysis involving the comparison of ab initio fully correlated simulations with effective models. Our study suggests ultracold atomic ensembles as potent emulators of complex molecular phenomena.","lang":"eng"}],"intvolume":" 6","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2024_PhysicalReviewResearch_Becker.pdf","date_created":"2024-03-25T09:24:55Z","creator":"dernst","file_size":2207067,"date_updated":"2024-03-25T09:24:55Z","success":1,"file_id":"15183","checksum":"4e0e58d1f58386fb016284c84db2a300","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"ec_funded":1,"volume":6,"issue":"1"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/aenm.202400408"}],"scopus_import":"1","month":"03","abstract":[{"text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"oa_version":"Published Version","publication_status":"epub_ahead","publication_identifier":{"eissn":["1614-6840"],"issn":["1614-6832"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"15182","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"date_updated":"2024-03-25T09:21:05Z","oa":1,"publisher":"Wiley","quality_controlled":"1","acknowledgement":"This work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the Technical University of Vienna is acknowledged for EBSD sample preparation and analysis. R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2021 SGR 01061.","date_created":"2024-03-25T08:57:40Z","doi":"10.1002/aenm.202400408","date_published":"2024-03-13T00:00:00Z","year":"2024","publication":"Advanced Energy Materials","day":"13","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"article_number":"2400408","article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias","first_name":"Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425"},{"full_name":"Milillo, Francesco","last_name":"Milillo","id":"38b830db-ea88-11ee-bf9b-929beaf79054","first_name":"Francesco"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano","last_name":"Calcabrini"},{"full_name":"Fiedler, Christine","last_name":"Fiedler","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","first_name":"Christine"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona","full_name":"Horta, Sharona","last_name":"Horta"},{"id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel","last_name":"Balazs","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel"},{"first_name":"Marissa J.","full_name":"Strumolo, Marissa J.","last_name":"Strumolo"},{"first_name":"Roger","full_name":"Hasler, Roger","last_name":"Hasler"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"full_name":"Tkadletz, Michael","last_name":"Tkadletz","first_name":"Michael"},{"first_name":"Richard L.","full_name":"Brutchey, Richard L.","last_name":"Brutchey"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"}],"title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","citation":{"ista":"Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials., 2400408.","chicago":"Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler, Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials. Wiley, 2024. https://doi.org/10.1002/aenm.202400408.","apa":"Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs, D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. Wiley. https://doi.org/10.1002/aenm.202400408","ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 2024. doi:10.1002/aenm.202400408","ieee":"T. Kleinhanns et al., “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” Advanced Energy Materials. Wiley, 2024.","short":"T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs, M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced Energy Materials (2024).","mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials, 2400408, Wiley, 2024, doi:10.1002/aenm.202400408."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"issue":"5","volume":51,"ec_funded":1,"publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2024-03-25T08:36:00Z","file_size":2887134,"date_created":"2024-03-25T08:36:00Z","file_name":"2024_GeophysResLetters_Goswami.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"15178","checksum":"243bd966aca968ec7d9e474af8639f8d","success":1}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 51","abstract":[{"text":"Current knowledge suggests a drought Indian monsoon (perhaps a severe one) when the El Nino Southern Oscillation and Pacific Decadal Oscillation each exhibit positive phases (a joint positive phase). For the monsoons, which are exceptions in this regard, we found northeast India often gets excess pre-monsoon rainfall. Further investigation reveals that this excess pre-monsoon rainfall is produced by the interaction of the large-scale circulation associated with the joint phase with the mountains in northeast India. We posit that a warmer troposphere, a consequence of excess rainfall over northeast India, drives a stronger monsoon circulation and enhances monsoon rainfall over central India. Hence, we argue that pre-monsoon rainfall over northeast India can be used for seasonal monsoon rainfall prediction over central India. Most importantly, its predictive value is at its peak when the Pacific Ocean exhibits a joint positive phase and the threat of extreme drought monsoon looms over India.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"CaMu"}],"file_date_updated":"2024-03-25T08:36:00Z","date_updated":"2024-03-25T10:00:57Z","ddc":["550"],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"15165","date_published":"2024-03-16T00:00:00Z","doi":"10.1029/2023GL106569","date_created":"2024-03-24T23:00:58Z","has_accepted_license":"1","year":"2024","day":"16","publication":"Geophysical Research Letters","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"The author gratefully acknowledges ISTA for supporting this research through funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Project CLUSTER, grant agreement No. 805041).","author":[{"last_name":"Goswami","orcid":"0000-0001-8602-3083","full_name":"Goswami, Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"Bidyut B"}],"article_processing_charge":"Yes","title":"A pre-monsoon signal of false alarms of Indian monsoon droughts","citation":{"ista":"GOSWAMI BB. 2024. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 51(5), e2023GL106569.","chicago":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” Geophysical Research Letters. Wiley, 2024. https://doi.org/10.1029/2023GL106569.","apa":"GOSWAMI, B. B. (2024). A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. Wiley. https://doi.org/10.1029/2023GL106569","ama":"GOSWAMI BB. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 2024;51(5). doi:10.1029/2023GL106569","short":"B.B. GOSWAMI, Geophysical Research Letters 51 (2024).","ieee":"B. B. GOSWAMI, “A pre-monsoon signal of false alarms of Indian monsoon droughts,” Geophysical Research Letters, vol. 51, no. 5. Wiley, 2024.","mla":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” Geophysical Research Letters, vol. 51, no. 5, e2023GL106569, Wiley, 2024, doi:10.1029/2023GL106569."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate"}],"article_number":"e2023GL106569"},{"scopus_import":"1","month":"03","intvolume":" 383","abstract":[{"text":"Reducing defects boosts room-temperature performance of a thermoelectric device","lang":"eng"}],"oa_version":"None","issue":"6688","volume":383,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"letter_note","type":"journal_article","status":"public","_id":"15166","department":[{"_id":"MaIb"}],"date_updated":"2024-03-25T10:31:20Z","publisher":"American Association for the Advancement of Science","quality_controlled":"1","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","page":"1184","doi":"10.1126/science.ado4077","date_published":"2024-03-14T00:00:00Z","date_created":"2024-03-24T23:00:58Z","year":"2024","day":"14","publication":"Science","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"author":[{"full_name":"Navita, Navita","last_name":"Navita","id":"6ebe278d-ba0b-11ee-8184-f34cdc671de4","first_name":"Navita"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"}],"article_processing_charge":"No","title":"Electron highways are cooler","citation":{"chicago":"Jakhar, Navita, and Maria Ibáñez. “Electron Highways Are Cooler.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.ado4077.","ista":"Jakhar N, Ibáñez M. 2024. Electron highways are cooler. Science. 383(6688), 1184.","mla":"Jakhar, Navita, and Maria Ibáñez. “Electron Highways Are Cooler.” Science, vol. 383, no. 6688, American Association for the Advancement of Science, 2024, p. 1184, doi:10.1126/science.ado4077.","apa":"Jakhar, N., & Ibáñez, M. (2024). Electron highways are cooler. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.ado4077","ama":"Jakhar N, Ibáñez M. Electron highways are cooler. Science. 2024;383(6688):1184. doi:10.1126/science.ado4077","short":"N. Jakhar, M. Ibáñez, Science 383 (2024) 1184.","ieee":"N. Jakhar and M. Ibáñez, “Electron highways are cooler,” Science, vol. 383, no. 6688. American Association for the Advancement of Science, p. 1184, 2024."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2024-03-25T13:03:57Z","ddc":["570"],"department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"file_date_updated":"2024-03-25T12:52:04Z","_id":"15146","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"15188","checksum":"90d1984a93660735e506c2a304bc3f73","creator":"dernst","file_size":11907016,"date_updated":"2024-03-25T12:52:04Z","file_name":"2024_JCB_Zens.pdf","date_created":"2024-03-25T12:52:04Z"}],"ec_funded":1,"volume":223,"issue":"6","abstract":[{"text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 223","month":"03","citation":{"ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 2024;223(6). doi:10.1083/jcb.202309125","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202309125","ieee":"B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” Journal of Cell Biology, vol. 223, no. 6. Rockefeller University Press, 2024.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller University Press, 2024. https://doi.org/10.1083/jcb.202309125."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["38506714"]},"author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","last_name":"Zens","full_name":"Zens, Bettina"},{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","last_name":"Hansen","full_name":"Hansen, Jesse"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"last_name":"Datler","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa","last_name":"Zheden"},{"orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","last_name":"Alanko","first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","article_number":"e202309125","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","grant_number":"E435","_id":"7bd318a1-9f16-11ee-852c-cc9217763180"},{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"_id":"2615199A-B435-11E9-9278-68D0E5697425","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","grant_number":"21317"},{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ visual proteomics and structure determination"}],"year":"2024","has_accepted_license":"1","publication":"Journal of Cell Biology","day":"20","date_created":"2024-03-21T06:45:51Z","doi":"10.1083/jcb.202309125","date_published":"2024-03-20T00:00:00Z","acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","oa":1,"publisher":"Rockefeller University Press","quality_controlled":"1"},{"department":[{"_id":"RoSe"}],"date_updated":"2024-03-28T10:54:02Z","status":"public","article_type":"original","type":"journal_article","_id":"14931","ec_funded":1,"volume":286,"issue":"7","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0022-1236"],"eissn":["1096--0783"]},"intvolume":" 286","month":"01","main_file_link":[{"url":"https://doi.org/10.1016/j.jfa.2024.110320","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15].","lang":"eng"}],"title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2301.04894"]},"author":[{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320.","ista":"Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.","ama":"Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 2024;286(7). doi:10.1016/j.jfa.2024.110320","apa":"Lauritsen, A. B., & Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110320","short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).","ieee":"A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” Journal of Functional Analysis, vol. 286, no. 7. Elsevier, 2024."},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"article_number":"110320","date_created":"2024-02-04T23:00:53Z","date_published":"2024-01-24T00:00:00Z","doi":"10.1016/j.jfa.2024.110320","publication":"Journal of Functional Analysis","day":"24","year":"2024","oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged."},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"183-205","doi":"10.1007/978-1-0716-2887-4_12","date_published":"2023-01-19T00:00:00Z","date_created":"2023-01-29T23:00:58Z","has_accepted_license":"1","year":"2023","day":"19","publication":"Cell Migration in Three Dimensions","author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele","first_name":"Colinda L.G.J."}],"article_processing_charge":"No","external_id":{"pmid":["36653709"]},"title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","editor":[{"first_name":"Coert","last_name":"Margadant","full_name":"Margadant, Coert"}],"citation":{"apa":"Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature. https://doi.org/10.1007/978-1-0716-2887-4_12","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","month":"01","intvolume":" 2608","abstract":[{"text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":2608,"publication_identifier":{"isbn":["9781071628867"],"eissn":["1940-6029"],"eisbn":["9781071628874"]},"publication_status":"published","file":[{"date_created":"2023-02-03T10:56:39Z","file_name":"2023_MIMB_Hannezo.pdf","creator":"dernst","date_updated":"2023-02-03T10:56:39Z","file_size":826598,"file_id":"12500","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"type":"book_chapter","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","series_title":"MIMB","_id":"12428","file_date_updated":"2023-02-03T10:56:39Z","department":[{"_id":"EdHa"}],"date_updated":"2023-02-03T10:58:56Z","ddc":["570"]},{"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12546","checksum":"6068b62874c0099628a108bb9c5c6bd2","success":1,"date_updated":"2023-02-13T10:38:10Z","file_size":865150,"creator":"dernst","date_created":"2023-02-13T10:38:10Z","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf"}],"language":[{"iso":"eng"}],"issue":"1","volume":5,"ec_funded":1,"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"}],"oa_version":"Published Version","scopus_import":"1","month":"01","intvolume":" 5","date_updated":"2023-02-20T07:02:00Z","ddc":["530"],"department":[{"_id":"MiLe"}],"file_date_updated":"2023-02-13T10:38:10Z","_id":"12534","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","year":"2023","day":"20","publication":"Physical Review Research","date_published":"2023-01-20T00:00:00Z","doi":"10.1103/physrevresearch.5.013029","date_created":"2023-02-10T09:02:26Z","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).","publisher":"American Physical Society","quality_controlled":"1","oa":1,"citation":{"ama":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 2023;5(1). doi:10.1103/physrevresearch.5.013029","apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.5.013029","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” Physical Review Research, vol. 5, no. 1. American Physical Society, 2023.","mla":"Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research, vol. 5, no. 1, 013029, American Physical Society, 2023, doi:10.1103/physrevresearch.5.013029.","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.","chicago":"Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/physrevresearch.5.013029."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev"}],"article_processing_charge":"No","title":"Dissipative dynamics of an impurity with spin-orbit coupling","article_number":"013029","project":[{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"volume":55,"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","file_id":"12688","success":1,"date_updated":"2023-02-27T07:46:45Z","file_size":21484855,"creator":"dernst","date_created":"2023-02-27T07:46:45Z","file_name":"2023_NatureGenetics_Zeller.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"02","intvolume":" 55","abstract":[{"lang":"eng","text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages."}],"oa_version":"Published Version","file_date_updated":"2023-02-27T07:46:45Z","department":[{"_id":"ScienComp"}],"date_updated":"2023-02-27T07:48:24Z","ddc":["570","000"],"type":"journal_article","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Genetics"],"_id":"12158","page":"333-345","date_published":"2023-02-01T00:00:00Z","doi":"10.1038/s41588-022-01260-3","date_created":"2023-01-12T12:09:09Z","has_accepted_license":"1","year":"2023","day":"01","publication":"Nature Genetics","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","author":[{"first_name":"Peter","full_name":"Zeller, Peter","last_name":"Zeller"},{"first_name":"Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b","last_name":"Yeung","full_name":"Yeung, Jake","orcid":"0000-0003-1732-1559"},{"first_name":"Helena","full_name":"Viñas Gaza, Helena","last_name":"Viñas Gaza"},{"first_name":"Buys Anton","full_name":"de Barbanson, Buys Anton","last_name":"de Barbanson"},{"last_name":"Bhardwaj","full_name":"Bhardwaj, Vivek","first_name":"Vivek"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"first_name":"Reinier","last_name":"van der Linden","full_name":"van der Linden, Reinier"},{"first_name":"Alexander","last_name":"van Oudenaarden","full_name":"van Oudenaarden, Alexander"}],"article_processing_charge":"No","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","citation":{"mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature, 2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345. doi:10.1038/s41588-022-01260-3","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-022-01260-3","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"last_name":"Saona Urmeneta","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda","full_name":"Svoboda, Jakub"}],"article_processing_charge":"No","title":"Faster algorithm for turn-based stochastic games with bounded treewidth","citation":{"mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:10.1137/1.9781611977554.ch173.","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.","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, pp. 4590–4605.","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch173.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","page":"4590-4605","date_published":"2023-02-01T00:00:00Z","doi":"10.1137/1.9781611977554.ch173","date_created":"2023-02-24T12:20:47Z","year":"2023","day":"01","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","type":"conference","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2023-01-22","end_date":"2023-01-25","location":"Florence, Italy"},"status":"public","_id":"12676","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_updated":"2023-02-27T09:01:16Z","main_file_link":[{"url":"https://doi.org/10.1137/1.9781611977554.ch173","open_access":"1"}],"month":"02","abstract":[{"lang":"eng","text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth."}],"oa_version":"Published Version","ec_funded":1,"publication_identifier":{"isbn":["9781611977554"]},"publication_status":"published","language":[{"iso":"eng"}]},{"year":"2023","day":"01","publication":"DNA Manipulation and Analysis","page":"33-44","doi":"10.1007/978-1-0716-3004-4_3","date_published":"2023-03-01T00:00:00Z","date_created":"2023-03-12T23:01:02Z","quality_controlled":"1","publisher":"Springer Nature","citation":{"mla":"Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.” DNA Manipulation and Analysis, edited by Garry Scarlett, vol. 2633, Springer Nature, 2023, pp. 33–44, doi:10.1007/978-1-0716-3004-4_3.","ieee":"S. Arroyo-Urea, J. Watson, and J. García-Nafría, “Molecular Cloning Using In Vivo DNA Assembly,” in DNA Manipulation and Analysis, vol. 2633, G. Scarlett, Ed. New York, NY, United States: Springer Nature, 2023, pp. 33–44.","short":"S. Arroyo-Urea, J. Watson, J. García-Nafría, in:, G. Scarlett (Ed.), DNA Manipulation and Analysis, Springer Nature, New York, NY, United States, 2023, pp. 33–44.","ama":"Arroyo-Urea S, Watson J, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. In: Scarlett G, ed. DNA Manipulation and Analysis. Vol 2633. MIMB. New York, NY, United States: Springer Nature; 2023:33-44. doi:10.1007/978-1-0716-3004-4_3","apa":"Arroyo-Urea, S., Watson, J., & García-Nafría, J. (2023). Molecular Cloning Using In Vivo DNA Assembly. In G. Scarlett (Ed.), DNA Manipulation and Analysis (Vol. 2633, pp. 33–44). New York, NY, United States: Springer Nature. https://doi.org/10.1007/978-1-0716-3004-4_3","chicago":"Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular Cloning Using In Vivo DNA Assembly.” In DNA Manipulation and Analysis, edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3004-4_3.","ista":"Arroyo-Urea S, Watson J, García-Nafría J. 2023.Molecular Cloning Using In Vivo DNA Assembly. In: DNA Manipulation and Analysis. Methods in Molecular Biology, vol. 2633, 33–44."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Sandra","last_name":"Arroyo-Urea","full_name":"Arroyo-Urea, Sandra"},{"last_name":"Watson","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"García-Nafría, Javier","last_name":"García-Nafría","first_name":"Javier"}],"article_processing_charge":"No","external_id":{"pmid":["36853454"]},"editor":[{"first_name":"Garry","last_name":"Scarlett","full_name":"Scarlett, Garry"}],"title":"Molecular Cloning Using In Vivo DNA Assembly","publication_identifier":{"eisbn":["978-1-0716-3004-4"],"eissn":["1940-6029"],"isbn":["978-1-0716-3003-7"],"issn":["1064-3745"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":2633,"abstract":[{"text":"Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"month":"03","place":"New York, NY, United States","intvolume":" 2633","date_updated":"2023-03-16T08:34:24Z","department":[{"_id":"PeJo"}],"_id":"12720","series_title":"MIMB","type":"book_chapter","status":"public"},{"date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577481","date_created":"2023-03-19T23:00:58Z","page":"107-118","day":"25","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9798400700156"]},"publication_status":"published","year":"2023","month":"02","quality_controlled":"1","scopus_import":"1","publisher":"Association for Computing Machinery","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04986"}],"oa_version":"Preprint","abstract":[{"text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations.","lang":"eng"}],"department":[{"_id":"DaAl"}],"title":"Fast and scalable channels in Kotlin Coroutines","author":[{"first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","last_name":"Koval"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"first_name":"Roman","full_name":"Elizarov, Roman","last_name":"Elizarov"}],"article_processing_charge":"No","external_id":{"arxiv":["2211.04986"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 107–118.","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable Channels in Kotlin Coroutines.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 107–18. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577481.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–118.","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Montreal, QC, Canada, 2023, pp. 107–118.","ama":"Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2023:107-118. doi:10.1145/3572848.3577481","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577481","mla":"Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–18, doi:10.1145/3572848.3577481."},"date_updated":"2023-03-20T07:29:28Z","status":"public","type":"conference","conference":{"end_date":"2023-03-01","location":"Montreal, QC, Canada","start_date":"2023-02-25","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"_id":"12735"},{"page":"438-440","date_created":"2023-03-19T23:00:58Z","date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577512","publication_status":"published","year":"2023","publication_identifier":{"isbn":["9798400700156"]},"language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","day":"25","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","month":"02","abstract":[{"lang":"eng","text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al."}],"acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Aksenov","full_name":"Aksenov, Vitaly","first_name":"Vitaly"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","full_name":"Brown, Trevor A","last_name":"Brown"},{"last_name":"Fedorov","full_name":"Fedorov, Alexander","first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"last_name":"Kokorin","full_name":"Kokorin, Ilya","first_name":"Ilya"}],"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"title":"Unexpected scaling in path copying trees","date_updated":"2023-03-20T07:57:27Z","citation":{"chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577512.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"start_date":"2023-02-25","end_date":"2023-03-01","location":"Montreal, QB, Canada","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"type":"conference_poster","status":"public","_id":"12736"},{"file_date_updated":"2023-03-27T06:37:22Z","department":[{"_id":"MoHe"}],"date_updated":"2023-03-27T06:46:27Z","ddc":["000"],"conference":{"end_date":"2023-03-09","location":"Hamburg, Germany","start_date":"2023-03-07","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","_id":"12760","volume":254,"publication_status":"published","publication_identifier":{"isbn":["9783959772662"],"issn":["1868-8969"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-03-27T06:37:22Z","file_size":872706,"creator":"dernst","date_created":"2023-03-27T06:37:22Z","file_name":"2023_LIPICS_HenzingerM.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12769","checksum":"22141ab8bc55188e2dfff665e5daecbd","success":1}],"scopus_import":"1","alternative_title":["LIPIcs"],"intvolume":" 254","month":"03","abstract":[{"text":"Dynamic programming (DP) is one of the fundamental paradigms in algorithm design. However,\r\nmany DP algorithms have to fill in large DP tables, represented by two-dimensional arrays, which causes at least quadratic running times and space usages. This has led to the development of improved algorithms for special cases when the DPs satisfy additional properties like, e.g., the Monge property or total monotonicity.\r\nIn this paper, we consider a new condition which assumes (among some other technical assumptions) that the rows of the DP table are monotone. Under this assumption, we introduce\r\na novel data structure for computing (1 + ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting, and with polylogarithmic update times when the DP entries change\r\ndynamically. To the best of our knowledge, our new condition is incomparable to previous conditions and is the first which allows to derive dynamic algorithms based on existing DPs. Instead of using two-dimensional arrays to store the DP tables, we store the rows of the DP tables using monotone piecewise constant functions. This allows us to store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits, and to perform operations, such as (min, +)-convolution or rounding, on these functions in polylogarithmic time.\r\nWe further present several applications of our data structure. For bicriteria versions of k-balanced graph partitioning and simultaneous source location, we obtain the first dynamic algorithms with subpolynomial update times, as well as the first static algorithms using only near-linear time and space. Additionally, we obtain the currently fastest algorithm for fully dynamic knapsack.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","external_id":{"arxiv":["2301.01744"]},"author":[{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Neumann, Stefan","last_name":"Neumann","first_name":"Stefan"},{"first_name":"Harald","last_name":"Räcke","full_name":"Räcke, Harald"},{"last_name":"Schmid","full_name":"Schmid, Stefan","first_name":"Stefan"}],"title":"Dynamic maintenance of monotone dynamic programs and applications","citation":{"apa":"Henzinger, M. H., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In 40th International Symposium on Theoretical Aspects of Computer Science (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36","ama":"Henzinger MH, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: 40th International Symposium on Theoretical Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36","short":"M.H. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"M. H. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in 40th International Symposium on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.","mla":"Henzinger, Monika H., et al. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” 40th International Symposium on Theoretical Aspects of Computer Science, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.STACS.2023.36.","ista":"Henzinger MH, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36.","chicago":"Henzinger, Monika H, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In 40th International Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"36","date_created":"2023-03-26T22:01:07Z","date_published":"2023-03-01T00:00:00Z","doi":"10.4230/LIPIcs.STACS.2023.36","year":"2023","has_accepted_license":"1","publication":"40th International Symposium on Theoretical Aspects of Computer Science","day":"01","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science Fund (FWF) project I 5025-N (DELTA), 2020-2024."}]