[{"article_type":"original","publisher":"Springer Nature","language":[{"iso":"eng"}],"doi":"10.1007/s00208-024-02812-0","date_published":"2024-10-01T00:00:00Z","file":[{"success":1,"relation":"main_file","creator":"dernst","date_created":"2025-01-09T08:23:36Z","file_size":661557,"content_type":"application/pdf","date_updated":"2025-01-09T08:23:36Z","file_name":"2024_MathAnnalen_Agresti.pdf","checksum":"d55cac8bddea09a97f06612825c4f229","access_level":"open_access","file_id":"18790"}],"oa":1,"quality_controlled":"1","year":"2024","page":"2727-2766","external_id":{"arxiv":["2306.11081"],"pmid":["39351582"],"isi":["001172711400002"]},"_id":"15098","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"pmid":1,"scopus_import":"1","month":"10","arxiv":1,"type":"journal_article","volume":390,"publication_status":"published","citation":{"ista":"Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. 390, 2727–2766.","mla":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” <i>Mathematische Annalen</i>, vol. 390, Springer Nature, 2024, pp. 2727–66, doi:<a href=\"https://doi.org/10.1007/s00208-024-02812-0\">10.1007/s00208-024-02812-0</a>.","chicago":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” <i>Mathematische Annalen</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00208-024-02812-0\">https://doi.org/10.1007/s00208-024-02812-0</a>.","short":"A. Agresti, E. Luongo, Mathematische Annalen 390 (2024) 2727–2766.","ama":"Agresti A, Luongo E. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. <i>Mathematische Annalen</i>. 2024;390:2727-2766. doi:<a href=\"https://doi.org/10.1007/s00208-024-02812-0\">10.1007/s00208-024-02812-0</a>","apa":"Agresti, A., &#38; Luongo, E. (2024). Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. <i>Mathematische Annalen</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00208-024-02812-0\">https://doi.org/10.1007/s00208-024-02812-0</a>","ieee":"A. Agresti and E. Luongo, “Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions,” <i>Mathematische Annalen</i>, vol. 390. Springer Nature, pp. 2727–2766, 2024."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","article_processing_charge":"Yes (via OA deal)","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).","date_created":"2024-03-10T23:00:54Z","file_date_updated":"2025-01-09T08:23:36Z","status":"public","publication":"Mathematische Annalen","publication_identifier":{"eissn":["1432-1807"],"issn":["0025-5831"]},"ec_funded":1,"department":[{"_id":"JuFi"}],"project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"OA_type":"hybrid","has_accepted_license":"1","isi":1,"ddc":["510"],"day":"01","title":"Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions","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","date_updated":"2025-09-04T12:19:59Z","intvolume":"       390","author":[{"last_name":"Agresti","full_name":"Agresti, Antonio","first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962"},{"first_name":"Eliseo","last_name":"Luongo","full_name":"Luongo, Eliseo"}],"license":"https://creativecommons.org/licenses/by/4.0/"},{"scopus_import":"1","month":"04","pmid":1,"_id":"15099","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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. 40(4), 337–351.","mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” <i>Trends in Genetics</i>, vol. 40, no. 4, Elsevier, 2024, pp. 337–51, doi:<a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">10.1016/j.tig.2024.01.002</a>.","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.” <i>Trends in Genetics</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">https://doi.org/10.1016/j.tig.2024.01.002</a>.","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics 40 (2024) 337–351.","apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., &#38; Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">https://doi.org/10.1016/j.tig.2024.01.002</a>","ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. <i>Trends in Genetics</i>. 2024;40(4):337-351. doi:<a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">10.1016/j.tig.2024.01.002</a>","ieee":"K. Johannesson <i>et al.</i>, “Diverse pathways to speciation revealed by marine snails,” <i>Trends in Genetics</i>, vol. 40, no. 4. Elsevier, pp. 337–351, 2024."},"publication_status":"published","type":"journal_article","volume":40,"oa":1,"file":[{"file_id":"17313","access_level":"open_access","checksum":"3077ea808c4cdc24d02dc58aced7eb35","file_name":"2024_TrendsGenetics_Johannesson.pdf","date_updated":"2024-07-22T12:05:58Z","content_type":"application/pdf","file_size":2288340,"date_created":"2024-07-22T12:05:58Z","creator":"dernst","relation":"main_file","success":1}],"issue":"4","publisher":"Elsevier","doi":"10.1016/j.tig.2024.01.002","date_published":"2024-04-01T00:00:00Z","language":[{"iso":"eng"}],"article_type":"review","external_id":{"pmid":["38395682"],"isi":["001224671300001"]},"page":"337-351","year":"2024","quality_controlled":"1","title":"Diverse pathways to speciation revealed by marine snails","day":"01","ddc":["570"],"has_accepted_license":"1","isi":1,"department":[{"_id":"NiBa"}],"author":[{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"}],"intvolume":"        40","date_updated":"2025-09-04T12:18:08Z","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"status":"public","file_date_updated":"2024-07-22T12:05:58Z","date_created":"2024-03-10T23:00:54Z","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.","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1362-4555"],"issn":["0168-9525"]},"publication":"Trends in Genetics"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","orcid":"0009-0001-5009-4987","last_name":"Hübner","full_name":"Hübner, Valentin"},{"first_name":"Maria","full_name":"Kleshnina, Maria","last_name":"Kleshnina"}],"corr_author":"1","type":"research_data_reference","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."}],"citation":{"ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.","ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.10639167\">10.5281/ZENODO.10639167</a>","apa":"Hübner, V., &#38; Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.10639167\">https://doi.org/10.5281/ZENODO.10639167</a>","ista":"Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.10639167\">10.5281/ZENODO.10639167</a>.","mla":"Hübner, Valentin, and Maria Kleshnina. <i>Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.”</i> Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.10639167\">10.5281/ZENODO.10639167</a>.","chicago":"Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.10639167\">https://doi.org/10.5281/ZENODO.10639167</a>.","short":"V. Hübner, M. Kleshnina, (2024)."},"date_updated":"2025-09-04T12:14:54Z","oa_version":"Published Version","month":"02","day":"09","ddc":["000"],"title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","department":[{"_id":"KrCh"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"15108","has_accepted_license":"1","related_material":{"record":[{"relation":"used_in_publication","id":"15083","status":"public"}]},"year":"2024","date_published":"2024-02-09T00:00:00Z","publisher":"Zenodo","doi":"10.5281/ZENODO.10639167","status":"public","oa":1,"main_file_link":[{"url":"https://10.5281/zenodo.10639167","open_access":"1"}],"date_created":"2024-03-12T13:02:58Z","article_processing_charge":"No"},{"year":"2024","quality_controlled":"1","external_id":{"isi":["001203872000001"]},"article_type":"original","date_published":"2024-06-05T00:00:00Z","publisher":"Elsevier","language":[{"iso":"eng"}],"doi":"10.1016/j.ces.2024.119959","oa":1,"volume":291,"type":"journal_article","citation":{"apa":"Yao, Z., Liu, X., Bunting, R., &#38; Wang, J. (2024). Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. <i>Chemical Engineering Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ces.2024.119959\">https://doi.org/10.1016/j.ces.2024.119959</a>","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. <i>Chemical Engineering Science</i>. 2024;291. doi:<a href=\"https://doi.org/10.1016/j.ces.2024.119959\">10.1016/j.ces.2024.119959</a>","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,” <i>Chemical Engineering Science</i>, vol. 291. Elsevier, 2024.","mla":"Yao, Zihao, et al. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” <i>Chemical Engineering Science</i>, vol. 291, 119959, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.ces.2024.119959\">10.1016/j.ces.2024.119959</a>.","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.” <i>Chemical Engineering Science</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.ces.2024.119959\">https://doi.org/10.1016/j.ces.2024.119959</a>.","short":"Z. Yao, X. Liu, R. Bunting, J. Wang, Chemical Engineering Science 291 (2024)."},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"15114","scopus_import":"1","month":"06","publication":"Chemical Engineering Science","publication_identifier":{"issn":["0009-2509"]},"article_processing_charge":"No","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).","status":"public","date_created":"2024-03-17T23:00:57Z","main_file_link":[{"url":"https://doi.org/10.1016/j.ces.2024.119959","open_access":"1"}],"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."}],"intvolume":"       291","date_updated":"2025-09-04T13:02:40Z","oa_version":"None","article_number":"119959","author":[{"first_name":"Zihao","full_name":"Yao, Zihao","last_name":"Yao"},{"full_name":"Liu, Xu","last_name":"Liu","first_name":"Xu"},{"orcid":"0000-0001-6928-074X","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","first_name":"Rhys","full_name":"Bunting, Rhys","last_name":"Bunting"},{"last_name":"Wang","full_name":"Wang, Jianguo","first_name":"Jianguo"}],"department":[{"_id":"MaIb"}],"OA_type":"free access","isi":1,"day":"05","title":"Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","citation":{"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).","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.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2313162121\">https://doi.org/10.1073/pnas.2313162121</a>.","ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, 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. 121(11), e2313162121.","mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11, e2313162121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2313162121\">10.1073/pnas.2313162121</a>.","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. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2313162121\">https://doi.org/10.1073/pnas.2313162121</a>","ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(11). doi:<a href=\"https://doi.org/10.1073/pnas.2313162121\">10.1073/pnas.2313162121</a>","ieee":"G. Giubertoni <i>et al.</i>, “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11. National Academy of Sciences, 2024."},"volume":121,"type":"journal_article","pmid":1,"scopus_import":"1","month":"03","_id":"15116","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"external_id":{"pmid":["38451946"],"isi":["001206387400001"]},"quality_controlled":"1","year":"2024","file":[{"date_created":"2024-03-19T10:22:42Z","relation":"main_file","creator":"dernst","success":1,"file_id":"15125","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","access_level":"open_access","file_name":"2024_PNAS_Giubertoni.pdf","date_updated":"2024-03-19T10:22:42Z","content_type":"application/pdf","file_size":12952586}],"oa":1,"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","date_published":"2024-03-12T00:00:00Z","doi":"10.1073/pnas.2313162121","issue":"11","article_type":"original","author":[{"first_name":"Giulia","last_name":"Giubertoni","full_name":"Giubertoni, Giulia"},{"first_name":"Liru","last_name":"Feng","full_name":"Feng, Liru"},{"full_name":"Klein, Kevin","last_name":"Klein","first_name":"Kevin"},{"first_name":"Guido","last_name":"Giannetti","full_name":"Giannetti, Guido"},{"first_name":"Luco","last_name":"Rutten","full_name":"Rutten, Luco"},{"first_name":"Yeji","last_name":"Choi","full_name":"Choi, Yeji"},{"first_name":"Anouk","last_name":"Van Der Net","full_name":"Van Der Net, Anouk"},{"first_name":"Gerard","last_name":"Castro-Linares","full_name":"Castro-Linares, Gerard"},{"first_name":"Federico","full_name":"Caporaletti, Federico","last_name":"Caporaletti"},{"first_name":"Dimitra","full_name":"Micha, Dimitra","last_name":"Micha"},{"first_name":"Johannes","full_name":"Hunger, Johannes","last_name":"Hunger"},{"last_name":"Deblais","full_name":"Deblais, Antoine","first_name":"Antoine"},{"full_name":"Bonn, Daniel","last_name":"Bonn","first_name":"Daniel"},{"first_name":"Nico","full_name":"Sommerdijk, Nico","last_name":"Sommerdijk"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela"},{"first_name":"Ioana M.","last_name":"Ilie","full_name":"Ilie, Ioana M."},{"last_name":"Koenderink","full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H."},{"first_name":"Sander","full_name":"Woutersen, Sander","last_name":"Woutersen"}],"oa_version":"Published Version","article_number":"e2313162121","intvolume":"       121","date_updated":"2025-09-04T13:03:56Z","abstract":[{"lang":"eng","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."}],"title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","ddc":["550"],"day":"12","has_accepted_license":"1","isi":1,"department":[{"_id":"AnSa"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"15126"}]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_created":"2024-03-17T23:00:57Z","file_date_updated":"2024-03-19T10:22:42Z","status":"public","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.","article_processing_charge":"Yes (in subscription journal)"},{"date_created":"2024-03-17T23:00:57Z","status":"public","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.","article_processing_charge":"No","ec_funded":1,"publication_identifier":{"eissn":["1095-9203"]},"publication":"Science","title":"Structure, biophysics, and circuit function of a \"giant\" cortical presynaptic terminal","day":"08","isi":1,"department":[{"_id":"PeJo"}],"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"}],"author":[{"orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","full_name":"Vandael, David H","last_name":"Vandael"},{"full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"oa_version":"None","date_updated":"2025-09-04T13:04:34Z","intvolume":"       383","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."}],"publisher":"AAAS","date_published":"2024-03-08T00:00:00Z","doi":"10.1126/science.adg6757","language":[{"iso":"eng"}],"issue":"6687","article_type":"review","external_id":{"isi":["001216996700015"],"pmid":["38452088"]},"page":"eadg6757","quality_controlled":"1","year":"2024","pmid":1,"scopus_import":"1","month":"03","_id":"15117","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","citation":{"ieee":"D. H. Vandael and P. M. Jonas, “Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal,” <i>Science</i>, vol. 383, no. 6687. AAAS, p. eadg6757, 2024.","ama":"Vandael DH, Jonas PM. Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. <i>Science</i>. 2024;383(6687):eadg6757. doi:<a href=\"https://doi.org/10.1126/science.adg6757\">10.1126/science.adg6757</a>","apa":"Vandael, D. H., &#38; Jonas, P. M. (2024). Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adg6757\">https://doi.org/10.1126/science.adg6757</a>","chicago":"Vandael, David H, and Peter M Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” <i>Science</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/science.adg6757\">https://doi.org/10.1126/science.adg6757</a>.","mla":"Vandael, David H., and Peter M. Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” <i>Science</i>, vol. 383, no. 6687, AAAS, 2024, p. eadg6757, doi:<a href=\"https://doi.org/10.1126/science.adg6757\">10.1126/science.adg6757</a>.","ista":"Vandael DH, Jonas PM. 2024. Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal. Science. 383(6687), eadg6757.","short":"D.H. Vandael, P.M. Jonas, Science 383 (2024) eadg6757."},"corr_author":"1","volume":383,"type":"journal_article"},{"title":"Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division","day":"04","isi":1,"project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division"}],"department":[{"_id":"MaLo"}],"author":[{"full_name":"Nußbaum, Phillip","last_name":"Nußbaum","first_name":"Phillip"},{"last_name":"Kureisaite-Ciziene","full_name":"Kureisaite-Ciziene, Danguole","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"},{"full_name":"Kojic, Marko","last_name":"Kojic","orcid":"0000-0001-7244-8128","first_name":"Marko","id":"73e7ecd4-dc85-11ea-9058-88a16394b160"},{"first_name":"Najwa","full_name":"Taib, Najwa","last_name":"Taib"},{"last_name":"Yeates","full_name":"Yeates, Anna","first_name":"Anna"},{"last_name":"Tourte","full_name":"Tourte, Maxime","first_name":"Maxime"},{"last_name":"Gribaldo","full_name":"Gribaldo, Simonetta","first_name":"Simonetta"},{"last_name":"Loose","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724"},{"first_name":"Jan","last_name":"Löwe","full_name":"Löwe, Jan"},{"first_name":"Sonja Verena","full_name":"Albers, Sonja Verena","last_name":"Albers"}],"intvolume":"         9","date_updated":"2026-04-07T12:27:57Z","oa_version":"None","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"}],"status":"public","date_created":"2024-03-17T23:00:58Z","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.","article_processing_charge":"No","publication_identifier":{"eissn":["2058-5276"]},"acknowledged_ssus":[{"_id":"LifeSc"}],"publication":"Nature Microbiology","related_material":{"record":[{"relation":"dissertation_contains","id":"20741","status":"public"}]},"month":"03","scopus_import":"1","pmid":1,"_id":"15118","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. <i>Nature Microbiology</i>. 2024;9(3):698-711. doi:<a href=\"https://doi.org/10.1038/s41564-024-01600-5\">10.1038/s41564-024-01600-5</a>","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. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-024-01600-5\">https://doi.org/10.1038/s41564-024-01600-5</a>","ieee":"P. Nußbaum <i>et al.</i>, “Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division,” <i>Nature Microbiology</i>, vol. 9, no. 3. Springer Nature, pp. 698–711, 2024.","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.” <i>Nature Microbiology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41564-024-01600-5\">https://doi.org/10.1038/s41564-024-01600-5</a>.","mla":"Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” <i>Nature Microbiology</i>, vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:<a href=\"https://doi.org/10.1038/s41564-024-01600-5\">10.1038/s41564-024-01600-5</a>.","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.","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."},"publication_status":"published","type":"journal_article","volume":9,"issue":"3","doi":"10.1038/s41564-024-01600-5","date_published":"2024-03-04T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Springer Nature","article_type":"original","external_id":{"pmid":["38443575"],"isi":["001183270800021"]},"page":"698-711","year":"2024","quality_controlled":"1"},{"external_id":{"arxiv":["2106.01274"]},"page":"413-430","quality_controlled":"1","year":"2024","oa":1,"doi":"10.1214/22-AIHP1333","publisher":"Institute of Mathematical Statistics","date_published":"2024-02-01T00:00:00Z","language":[{"iso":"eng"}],"issue":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","citation":{"apa":"Agresti, A., &#38; Veraar, M. (2024). Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. <i>Annales de l’institut Henri Poincare Probability and Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/22-AIHP1333\">https://doi.org/10.1214/22-AIHP1333</a>","ama":"Agresti A, Veraar M. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. <i>Annales de l’institut Henri Poincare Probability and Statistics</i>. 2024;60(1):413-430. doi:<a href=\"https://doi.org/10.1214/22-AIHP1333\">10.1214/22-AIHP1333</a>","ieee":"A. Agresti and M. Veraar, “Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions,” <i>Annales de l’institut Henri Poincare Probability and Statistics</i>, 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.” <i>Annales de l’institut Henri Poincare Probability and Statistics</i>. Institute of Mathematical Statistics, 2024. <a href=\"https://doi.org/10.1214/22-AIHP1333\">https://doi.org/10.1214/22-AIHP1333</a>.","mla":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” <i>Annales de l’institut Henri Poincare Probability and Statistics</i>, vol. 60, no. 1, Institute of Mathematical Statistics, 2024, pp. 413–30, doi:<a href=\"https://doi.org/10.1214/22-AIHP1333\">10.1214/22-AIHP1333</a>.","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.","short":"A. Agresti, M. Veraar, Annales de l’institut Henri Poincare Probability and Statistics 60 (2024) 413–430."},"corr_author":"1","volume":60,"type":"journal_article","arxiv":1,"month":"02","scopus_import":"1","_id":"15119","publication_identifier":{"issn":["0246-0203"]},"publication":"Annales de l'institut Henri Poincare Probability and Statistics","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.01274","open_access":"1"}],"date_created":"2024-03-17T23:00:58Z","status":"public","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.","article_processing_charge":"No","author":[{"full_name":"Agresti, Antonio","last_name":"Agresti","orcid":"0000-0002-9573-2962","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"oa_version":"Preprint","date_updated":"2024-10-09T21:08:30Z","intvolume":"        60","abstract":[{"lang":"eng","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."}],"title":"Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions","day":"01","department":[{"_id":"JuFi"}]},{"article_type":"original","issue":"1","date_published":"2024-03-01T00:00:00Z","language":[{"iso":"eng"}],"publisher":"American Physical Society","doi":"10.1103/PhysRevResearch.6.013223","oa":1,"file":[{"file_id":"15123","access_level":"open_access","checksum":"274c9f1b15b3547a10a03f39e4ccc582","file_name":"2024_PhysicalReviewResearch_Sack.pdf","date_updated":"2024-03-19T07:16:38Z","content_type":"application/pdf","file_size":2777593,"date_created":"2024-03-19T07:16:38Z","relation":"main_file","creator":"dernst","success":1}],"year":"2024","quality_controlled":"1","external_id":{"arxiv":["2307.14427"]},"_id":"15122","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"month":"03","scopus_import":"1","arxiv":1,"corr_author":"1","volume":6,"type":"journal_article","citation":{"ieee":"S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation,” <i>Physical Review Research</i>, vol. 6, no. 1. American Physical Society, 2024.","apa":"Sack, S., &#38; Egger, D. J. (2024). Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.013223\">https://doi.org/10.1103/PhysRevResearch.6.013223</a>","ama":"Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. <i>Physical Review Research</i>. 2024;6(1). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.013223\">10.1103/PhysRevResearch.6.013223</a>","chicago":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.013223\">https://doi.org/10.1103/PhysRevResearch.6.013223</a>.","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.","mla":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” <i>Physical Review Research</i>, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.013223\">10.1103/PhysRevResearch.6.013223</a>.","short":"S. Sack, D.J. Egger, Physical Review Research 6 (2024)."},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","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.","status":"public","file_date_updated":"2024-03-19T07:16:38Z","date_created":"2024-03-17T23:00:59Z","publication":"Physical Review Research","publication_identifier":{"eissn":["2643-1564"]},"DOAJ_listed":"1","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"IMB PhD Nomination Fellowship - Stefan Sack"}],"department":[{"_id":"MaSe"}],"has_accepted_license":"1","day":"01","ddc":["530"],"title":"Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation","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"}],"intvolume":"         6","date_updated":"2025-05-14T09:32:15Z","article_number":"013223","oa_version":"Published Version","author":[{"last_name":"Sack","full_name":"Sack, Stefan","first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508"},{"first_name":"Daniel J.","last_name":"Egger","full_name":"Egger, Daniel J."}]},{"article_processing_charge":"No","extern":"1","doi":"10.21942/UVA.24829896","date_published":"2024-02-14T00:00:00Z","publisher":"Figshare","main_file_link":[{"open_access":"1","url":"https://doi.org/10.21942/UVA.24829896"}],"date_created":"2024-03-19T10:47:16Z","oa":1,"status":"public","related_material":{"record":[{"id":"15116","relation":"used_in_publication","status":"public"}]},"year":"2024","has_accepted_license":"1","_id":"15126","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ddc":["550"],"day":"14","month":"02","title":"Dataset Collagen Self Assembly in H2O and D2O","type":"research_data_reference","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\"."}],"oa_version":"Published Version","date_updated":"2025-09-04T13:03:56Z","citation":{"ieee":"G. Giubertoni and S. Woutersen, “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024.","ama":"Giubertoni G, Woutersen S. Dataset Collagen Self Assembly in H2O and D2O. 2024. doi:<a href=\"https://doi.org/10.21942/UVA.24829896\">10.21942/UVA.24829896</a>","apa":"Giubertoni, G., &#38; Woutersen, S. (2024). Dataset Collagen Self Assembly in H2O and D2O. Figshare. <a href=\"https://doi.org/10.21942/UVA.24829896\">https://doi.org/10.21942/UVA.24829896</a>","short":"G. Giubertoni, S. Woutersen, (2024).","chicago":"Giubertoni, G., and S. Woutersen. “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024. <a href=\"https://doi.org/10.21942/UVA.24829896\">https://doi.org/10.21942/UVA.24829896</a>.","mla":"Giubertoni, G., and S. Woutersen. <i>Dataset Collagen Self Assembly in H2O and D2O</i>. Figshare, 2024, doi:<a href=\"https://doi.org/10.21942/UVA.24829896\">10.21942/UVA.24829896</a>.","ista":"Giubertoni G, Woutersen S. 2024. Dataset Collagen Self Assembly in H2O and D2O, Figshare, <a href=\"https://doi.org/10.21942/UVA.24829896\">10.21942/UVA.24829896</a>."},"author":[{"full_name":"Giubertoni, G.","last_name":"Giubertoni","first_name":"G."},{"full_name":"Woutersen, S.","last_name":"Woutersen","first_name":"S."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Rockefeller University Press","doi":"10.1083/jcb.202309125","language":[{"iso":"eng"}],"date_published":"2024-03-20T00:00:00Z","issue":"6","file":[{"checksum":"90d1984a93660735e506c2a304bc3f73","access_level":"open_access","file_name":"2024_JCB_Zens.pdf","file_id":"15188","file_size":11907016,"date_updated":"2024-03-25T12:52:04Z","content_type":"application/pdf","date_created":"2024-03-25T12:52:04Z","success":1,"creator":"dernst","relation":"main_file"}],"oa":1,"article_type":"original","external_id":{"isi":["001264190100001"],"pmid":["38506714"]},"quality_controlled":"1","year":"2024","pmid":1,"month":"03","scopus_import":"1","_id":"15146","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":223,"type":"journal_article","corr_author":"1","publication_status":"published","citation":{"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. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. 2024;223(6). doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>","ieee":"B. Zens <i>et al.</i>, “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” <i>Journal of Cell Biology</i>, vol. 223, no. 6. Rockefeller University Press, 2024.","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.","mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>.","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.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2024. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>.","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)."},"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).","date_created":"2024-03-21T06:45:51Z","file_date_updated":"2024-03-25T12:52:04Z","status":"public","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"ec_funded":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"publication":"Journal of Cell Biology","ddc":["570"],"day":"20","title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435"},{"call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","_id":"2615199A-B435-11E9-9278-68D0E5697425","grant_number":"21317"},{"name":"CryoMinflux-guided in-situ visual proteomics and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01"}],"isi":1,"has_accepted_license":"1","author":[{"full_name":"Zens, Bettina","last_name":"Zens","orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina"},{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Fäßler, Florian","last_name":"Fäßler"},{"full_name":"Hansen, Jesse","last_name":"Hansen","orcid":"0000-0001-7967-2085","first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","orcid":"0000-0002-3616-8580","last_name":"Datler","full_name":"Datler, Julia"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","orcid":"0000-0003-3904-947X","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin"},{"last_name":"Zheden","full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0002-9438-4783"},{"first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","last_name":"Alanko","full_name":"Alanko, Jonna H"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt"},{"last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"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"}],"article_number":"e202309125","oa_version":"Published Version","intvolume":"       223","date_updated":"2025-09-04T13:17:16Z"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":347,"corr_author":"1","type":"journal_article","citation":{"ieee":"R. Campbell, F. Hörsch, and B. Moore, “Decompositions into two linear forests of bounded lengths,” <i>Discrete Mathematics</i>, vol. 347, no. 6. Elsevier, 2024.","apa":"Campbell, R., Hörsch, F., &#38; Moore, B. (2024). Decompositions into two linear forests of bounded lengths. <i>Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disc.2024.113962\">https://doi.org/10.1016/j.disc.2024.113962</a>","ama":"Campbell R, Hörsch F, Moore B. Decompositions into two linear forests of bounded lengths. <i>Discrete Mathematics</i>. 2024;347(6). doi:<a href=\"https://doi.org/10.1016/j.disc.2024.113962\">10.1016/j.disc.2024.113962</a>","ista":"Campbell R, Hörsch F, Moore B. 2024. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 347(6), 113962.","chicago":"Campbell, Rutger, Florian Hörsch, and Benjamin Moore. “Decompositions into Two Linear Forests of Bounded Lengths.” <i>Discrete Mathematics</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.disc.2024.113962\">https://doi.org/10.1016/j.disc.2024.113962</a>.","mla":"Campbell, Rutger, et al. “Decompositions into Two Linear Forests of Bounded Lengths.” <i>Discrete Mathematics</i>, vol. 347, no. 6, 113962, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.disc.2024.113962\">10.1016/j.disc.2024.113962</a>.","short":"R. Campbell, F. Hörsch, B. Moore, Discrete Mathematics 347 (2024)."},"publication_status":"published","month":"06","scopus_import":"1","arxiv":1,"_id":"15163","external_id":{"isi":["001226893800001"],"arxiv":["2301.11615"]},"year":"2024","quality_controlled":"1","issue":"6","date_published":"2024-06-01T00:00:00Z","publisher":"Elsevier","doi":"10.1016/j.disc.2024.113962","language":[{"iso":"eng"}],"oa":1,"article_type":"original","author":[{"first_name":"Rutger","last_name":"Campbell","full_name":"Campbell, 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"}],"abstract":[{"lang":"eng","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."}],"intvolume":"       347","date_updated":"2025-09-04T13:10:26Z","article_number":"113962","oa_version":"Preprint","day":"01","title":"Decompositions into two linear forests of bounded lengths","department":[{"_id":"MaKw"}],"isi":1,"publication_identifier":{"issn":["0012-365X"]},"publication":"Discrete Mathematics","acknowledgement":"We wish to thank Dániel Marx and András Sebő for making us aware of the results in [8] and some clarifications on them.","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.11615"}],"date_created":"2024-03-24T23:00:58Z","article_processing_charge":"No"},{"type":"journal_article","volume":126,"citation":{"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,” <i>Medical Engineering and Physics</i>, vol. 126. Elsevier, 2024.","apa":"Silva-Henao, J. D., Schober, S., Pahr, D. H., &#38; Reisinger, A. G. (2024). Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. <i>Medical Engineering and Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">https://doi.org/10.1016/j.medengphy.2024.104143</a>","ama":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. <i>Medical Engineering and Physics</i>. 2024;126. doi:<a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">10.1016/j.medengphy.2024.104143</a>","short":"J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering and Physics 126 (2024).","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.” <i>Medical Engineering and Physics</i>, vol. 126, 104143, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">10.1016/j.medengphy.2024.104143</a>.","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.” <i>Medical Engineering and Physics</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">https://doi.org/10.1016/j.medengphy.2024.104143</a>."},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"15164","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"month":"04","scopus_import":"1","pmid":1,"year":"2024","quality_controlled":"1","external_id":{"pmid":["38621845"],"isi":["001219145400001"]},"article_type":"original","date_published":"2024-04-01T00:00:00Z","publisher":"Elsevier","language":[{"iso":"eng"}],"doi":"10.1016/j.medengphy.2024.104143","oa":1,"file":[{"success":1,"relation":"main_file","creator":"dernst","date_created":"2024-03-25T08:29:52Z","file_size":10039402,"date_updated":"2024-03-25T08:29:52Z","content_type":"application/pdf","checksum":"974acbf2731e7382dcf5920ac762e551","access_level":"open_access","file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf","file_id":"15177"}],"abstract":[{"lang":"eng","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."}],"date_updated":"2025-09-04T13:11:03Z","intvolume":"       126","article_number":"104143","oa_version":"Published Version","author":[{"first_name":"Juan D.","full_name":"Silva-Henao, Juan D.","last_name":"Silva-Henao"},{"last_name":"Schober","full_name":"Schober, Sophie","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie"},{"first_name":"Dieter H.","last_name":"Pahr","full_name":"Pahr, Dieter H."},{"first_name":"Andreas G.","last_name":"Reisinger","full_name":"Reisinger, Andreas G."}],"department":[{"_id":"PreCl"}],"has_accepted_license":"1","isi":1,"day":"01","ddc":["610"],"title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading","publication":"Medical Engineering and Physics","publication_identifier":{"eissn":["1873-4030"],"issn":["1350-4533"]},"article_processing_charge":"Yes (in subscription journal)","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.","file_date_updated":"2024-03-25T08:29:52Z","status":"public","date_created":"2024-03-24T23:00:58Z"},{"DOAJ_listed":"1","ec_funded":1,"publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]},"publication":"Geophysical Research Letters","file_date_updated":"2024-03-25T08:36:00Z","status":"public","date_created":"2024-03-24T23:00:58Z","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).","article_processing_charge":"Yes","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"last_name":"Goswami","full_name":"Goswami, Bidyut B","first_name":"Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","orcid":"0000-0001-8602-3083"}],"date_updated":"2025-09-04T13:11:41Z","intvolume":"        51","article_number":"e2023GL106569","oa_version":"Published Version","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"}],"title":"A pre-monsoon signal of false alarms of Indian monsoon droughts","day":"16","ddc":["550"],"has_accepted_license":"1","isi":1,"OA_type":"gold","project":[{"grant_number":"805041","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate"}],"department":[{"_id":"CaMu"}],"external_id":{"isi":["001181635700001"]},"year":"2024","quality_controlled":"1","oa":1,"file":[{"date_updated":"2024-03-25T08:36:00Z","content_type":"application/pdf","file_size":2887134,"file_id":"15178","access_level":"open_access","checksum":"243bd966aca968ec7d9e474af8639f8d","file_name":"2024_GeophysResLetters_Goswami.pdf","relation":"main_file","creator":"dernst","success":1,"date_created":"2024-03-25T08:36:00Z"}],"issue":"5","APC_amount":"1470 EUR","language":[{"iso":"eng"}],"publisher":"Wiley","doi":"10.1029/2023GL106569","date_published":"2024-03-16T00:00:00Z","article_type":"original","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"GOSWAMI BB. 2024. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 51(5), e2023GL106569.","mla":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” <i>Geophysical Research Letters</i>, vol. 51, no. 5, e2023GL106569, Wiley, 2024, doi:<a href=\"https://doi.org/10.1029/2023GL106569\">10.1029/2023GL106569</a>.","chicago":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” <i>Geophysical Research Letters</i>. Wiley, 2024. <a href=\"https://doi.org/10.1029/2023GL106569\">https://doi.org/10.1029/2023GL106569</a>.","short":"B.B. GOSWAMI, Geophysical Research Letters 51 (2024).","ieee":"B. B. GOSWAMI, “A pre-monsoon signal of false alarms of Indian monsoon droughts,” <i>Geophysical Research Letters</i>, vol. 51, no. 5. Wiley, 2024.","apa":"GOSWAMI, B. B. (2024). A pre-monsoon signal of false alarms of Indian monsoon droughts. <i>Geophysical Research Letters</i>. Wiley. <a href=\"https://doi.org/10.1029/2023GL106569\">https://doi.org/10.1029/2023GL106569</a>","ama":"GOSWAMI BB. A pre-monsoon signal of false alarms of Indian monsoon droughts. <i>Geophysical Research Letters</i>. 2024;51(5). doi:<a href=\"https://doi.org/10.1029/2023GL106569\">10.1029/2023GL106569</a>"},"publication_status":"published","corr_author":"1","volume":51,"type":"journal_article","scopus_import":"1","month":"03","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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"},"_id":"15165"},{"article_processing_charge":"No","date_created":"2024-03-24T23:00:58Z","status":"public","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","publication":"Science","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"isi":1,"department":[{"_id":"MaIb"}],"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"title":"Electron highways are cooler","day":"14","oa_version":"None","date_updated":"2025-09-04T13:12:19Z","intvolume":"       383","abstract":[{"lang":"eng","text":"Reducing defects boosts room-temperature performance of a thermoelectric device"}],"author":[{"first_name":"Navita","id":"6ebe278d-ba0b-11ee-8184-f34cdc671de4","orcid":"0000-0001-7408-8197","last_name":"Navita","full_name":"Navita, Navita"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez"}],"article_type":"letter_note","language":[{"iso":"eng"}],"date_published":"2024-03-14T00:00:00Z","publisher":"American Association for the Advancement of Science","doi":"10.1126/science.ado4077","issue":"6688","quality_controlled":"1","year":"2024","external_id":{"isi":["001273082800019"],"pmid":["38484066"]},"page":"1184","_id":"15166","pmid":1,"scopus_import":"1","month":"03","publication_status":"published","citation":{"ieee":"N. Jakhar and M. Ibáñez, “Electron highways are cooler,” <i>Science</i>, vol. 383, no. 6688. American Association for the Advancement of Science, p. 1184, 2024.","ama":"Jakhar N, Ibáñez M. Electron highways are cooler. <i>Science</i>. 2024;383(6688):1184. doi:<a href=\"https://doi.org/10.1126/science.ado4077\">10.1126/science.ado4077</a>","apa":"Jakhar, N., &#38; Ibáñez, M. (2024). Electron highways are cooler. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.ado4077\">https://doi.org/10.1126/science.ado4077</a>","short":"N. Jakhar, M. Ibáñez, Science 383 (2024) 1184.","chicago":"Jakhar, Navita, and Maria Ibáñez. “Electron Highways Are Cooler.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.ado4077\">https://doi.org/10.1126/science.ado4077</a>.","mla":"Jakhar, Navita, and Maria Ibáñez. “Electron Highways Are Cooler.” <i>Science</i>, vol. 383, no. 6688, American Association for the Advancement of Science, 2024, p. 1184, doi:<a href=\"https://doi.org/10.1126/science.ado4077\">10.1126/science.ado4077</a>.","ista":"Jakhar N, Ibáñez M. 2024. Electron highways are cooler. Science. 383(6688), 1184."},"corr_author":"1","volume":383,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"article_type":"original","oa":1,"date_published":"2024-03-19T00:00:00Z","publisher":"American Physical Society","doi":"10.1103/PhysRevA.109.033315","language":[{"iso":"eng"}],"issue":"3","quality_controlled":"1","year":"2024","external_id":{"arxiv":["2311.14536"],"isi":["001198511300017"]},"_id":"15167","arxiv":1,"scopus_import":"1","month":"03","publication_status":"published","citation":{"ieee":"R. Al Hyder, F. Chevy, and X. Leyronas, “Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy,” <i>Physical Review A</i>, vol. 109, no. 3. American Physical Society, 2024.","ama":"Al Hyder R, Chevy F, Leyronas X. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. <i>Physical Review A</i>. 2024;109(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.109.033315\">10.1103/PhysRevA.109.033315</a>","apa":"Al Hyder, R., Chevy, F., &#38; Leyronas, X. (2024). Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.109.033315\">https://doi.org/10.1103/PhysRevA.109.033315</a>","short":"R. Al Hyder, F. Chevy, X. Leyronas, Physical Review A 109 (2024).","mla":"Al Hyder, Ragheed, et al. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” <i>Physical Review A</i>, vol. 109, no. 3, 033315, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevA.109.033315\">10.1103/PhysRevA.109.033315</a>.","chicago":"Al Hyder, Ragheed, F. Chevy, and X. Leyronas. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” <i>Physical Review A</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevA.109.033315\">https://doi.org/10.1103/PhysRevA.109.033315</a>.","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."},"volume":109,"corr_author":"1","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","date_created":"2024-03-24T23:00:59Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2311.14536"}],"status":"public","acknowledgement":"We thank Félix Werner and Kris Van Houcke for interesting discussions.","publication":"Physical Review A","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"isi":1,"department":[{"_id":"MiLe"}],"title":"Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy","day":"19","article_number":"033315","oa_version":"Preprint","intvolume":"       109","date_updated":"2025-09-04T13:07:33Z","abstract":[{"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.","lang":"eng"}],"author":[{"full_name":"Al Hyder, Ragheed","last_name":"Al Hyder","id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed"},{"first_name":"F.","last_name":"Chevy","full_name":"Chevy, F."},{"first_name":"X.","last_name":"Leyronas","full_name":"Leyronas, X."}]},{"project":[{"name":"Algorithms for Embeddings and Homotopy Theory","grant_number":"P31312","call_identifier":"FWF","_id":"26611F5C-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"department":[{"_id":"UlWa"}],"isi":1,"has_accepted_license":"1","day":"01","alternative_title":["LIPIcs"],"ddc":["510"],"title":"Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs","abstract":[{"text":"A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its vertices with colours 1, … , k such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO k-colouring with a fixed number of colours is NP-complete (and in the special case of graphs, LO colouring coincides with the usual graph colouring). 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).","lang":"eng"}],"intvolume":"       289","date_updated":"2026-04-07T12:36:50Z","article_number":"34","oa_version":"Published Version","author":[{"id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","last_name":"Filakovský","full_name":"Filakovský, Marek"},{"first_name":"Tamio Vesa","full_name":"Nakajima, Tamio Vesa","last_name":"Nakajima"},{"last_name":"Opršal","full_name":"Opršal, Jakub","first_name":"Jakub","id":"ec596741-c539-11ec-b829-c79322a91242","orcid":"0000-0003-1245-3456"},{"first_name":"Gianluca","id":"0433290C-AF8F-11E9-A4C7-F729E6697425","full_name":"Tasinato, Gianluca","last_name":"Tasinato"},{"orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","last_name":"Wagner"}],"article_processing_charge":"No","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).","status":"public","file_date_updated":"2024-03-25T07:44:30Z","date_created":"2024-03-24T23:00:59Z","publication":"41st International Symposium on Theoretical Aspects of Computer Science","related_material":{"record":[{"id":"20339","relation":"dissertation_contains","status":"public"}]},"publication_identifier":{"isbn":["9783959773119"],"eissn":["1868-8969"]},"conference":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","end_date":"2024-03-14","location":"Clermont-Ferrand, France","start_date":"2024-03-12"},"ec_funded":1,"_id":"15168","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"month":"03","scopus_import":"1","arxiv":1,"type":"conference","corr_author":"1","volume":289,"citation":{"mla":"Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” <i>41st International Symposium on Theoretical Aspects of Computer Science</i>, vol. 289, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.STACS.2024.34\">10.4230/LIPIcs.STACS.2024.34</a>.","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.","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 <i>41st International Symposium on Theoretical Aspects of Computer Science</i>, Vol. 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.STACS.2024.34\">https://doi.org/10.4230/LIPIcs.STACS.2024.34</a>.","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.","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 <i>41st International Symposium on Theoretical Aspects of Computer Science</i>, Clermont-Ferrand, France, 2024, vol. 289.","apa":"Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., &#38; Wagner, U. (2024). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In <i>41st International Symposium on Theoretical Aspects of Computer Science</i> (Vol. 289). Clermont-Ferrand, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.STACS.2024.34\">https://doi.org/10.4230/LIPIcs.STACS.2024.34</a>","ama":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In: <i>41st International Symposium on Theoretical Aspects of Computer Science</i>. Vol 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.STACS.2024.34\">10.4230/LIPIcs.STACS.2024.34</a>"},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2024-03-01T00:00:00Z","doi":"10.4230/LIPIcs.STACS.2024.34","language":[{"iso":"eng"}],"oa":1,"file":[{"success":1,"creator":"dernst","relation":"main_file","date_created":"2024-03-25T07:44:30Z","file_size":927290,"content_type":"application/pdf","date_updated":"2024-03-25T07:44:30Z","file_name":"2024_LIPICs_Filakovsky.pdf","access_level":"open_access","checksum":"0524d4189fd1ed08989546511343edf3","file_id":"15175"}],"year":"2024","quality_controlled":"1","external_id":{"arxiv":["2312.12981"],"isi":["001300393400034"]}},{"author":[{"last_name":"Chintaluri","full_name":"Chintaluri, Chaitanya","first_name":"Chaitanya","id":"E4EDB536-3485-11EA-98D2-20AF3DDC885E"},{"full_name":"Bejtka, Marta","last_name":"Bejtka","first_name":"Marta"},{"last_name":"Sredniawa","full_name":"Sredniawa, Wladyslaw","first_name":"Wladyslaw"},{"full_name":"Czerwinski, Michal","last_name":"Czerwinski","first_name":"Michal"},{"first_name":"Jakub M.","full_name":"Dzik, Jakub M.","last_name":"Dzik"},{"full_name":"Jedrzejewska-Szmek, Joanna","last_name":"Jedrzejewska-Szmek","first_name":"Joanna"},{"first_name":"Daniel K.","last_name":"Wojciki","full_name":"Wojciki, Daniel K."}],"oa_version":"Published Version","article_number":"e1011941","date_updated":"2025-09-04T13:08:54Z","intvolume":"        20","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."}],"title":"kCSD-python, reliable current source density estimation with quality control","ddc":["000","570"],"day":"14","has_accepted_license":"1","isi":1,"OA_type":"gold","department":[{"_id":"TiVo"}],"DOAJ_listed":"1","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"related_material":{"link":[{"relation":"software","url":"https://github.com/Neuroinflab/kCSD-python"}]},"publication":"PLoS Computational Biology","date_created":"2024-03-24T23:00:59Z","status":"public","file_date_updated":"2025-06-25T05:47:36Z","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). ","article_processing_charge":"Yes","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","citation":{"ieee":"C. Chintaluri <i>et al.</i>, “kCSD-python, reliable current source density estimation with quality control,” <i>PLoS Computational Biology</i>, vol. 20, no. 3. Public Library of Science, 2024.","ama":"Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source density estimation with quality control. <i>PLoS Computational Biology</i>. 2024;20(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">10.1371/journal.pcbi.1011941</a>","apa":"Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek, J., &#38; Wojciki, D. K. (2024). kCSD-python, reliable current source density estimation with quality control. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">https://doi.org/10.1371/journal.pcbi.1011941</a>","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.” <i>PLoS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">https://doi.org/10.1371/journal.pcbi.1011941</a>.","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.” <i>PLoS Computational Biology</i>, vol. 20, no. 3, e1011941, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">10.1371/journal.pcbi.1011941</a>.","short":"C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek, D.K. Wojciki, PLoS Computational Biology 20 (2024)."},"type":"journal_article","volume":20,"corr_author":"1","pmid":1,"scopus_import":"1","month":"03","_id":"15169","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"external_id":{"isi":["001190689800001"],"pmid":["38484020"]},"quality_controlled":"1","year":"2024","file":[{"file_size":2540277,"content_type":"application/pdf","date_updated":"2025-06-25T05:47:36Z","file_name":"2024_PLoSCompBio_Chintaluri.pdf","checksum":"c09718d0d09614642d877d0716ce32e8","access_level":"open_access","file_id":"19897","success":1,"creator":"dernst","relation":"main_file","date_created":"2025-06-25T05:47:36Z"}],"oa":1,"doi":"10.1371/journal.pcbi.1011941","publisher":"Public Library of Science","language":[{"iso":"eng"}],"date_published":"2024-03-14T00:00:00Z","issue":"3","article_type":"original"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":964,"type":"journal_article","citation":{"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 &#62; 5. Astrophysical Journal. 964, 39.","mla":"Greene, Jenny E., et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z &#62; 5.” <i>Astrophysical Journal</i>, vol. 964, 39, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/1538-4357/ad1e5f\">10.3847/1538-4357/ad1e5f</a>.","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 &#62; 5.” <i>Astrophysical Journal</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/1538-4357/ad1e5f\">https://doi.org/10.3847/1538-4357/ad1e5f</a>.","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).","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 &#62; 5. <i>Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ad1e5f\">https://doi.org/10.3847/1538-4357/ad1e5f</a>","ama":"Greene JE, Labbe I, Goulding AD, et al. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z &#62; 5. <i>Astrophysical Journal</i>. 2024;964. doi:<a href=\"https://doi.org/10.3847/1538-4357/ad1e5f\">10.3847/1538-4357/ad1e5f</a>","ieee":"J. E. Greene <i>et al.</i>, “UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z &#62; 5,” <i>Astrophysical Journal</i>, vol. 964. IOP Publishing, 2024."},"publication_status":"published","scopus_import":"1","month":"03","arxiv":1,"_id":"15170","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"external_id":{"isi":["001184746500001"],"arxiv":["2309.05714"]},"year":"2024","quality_controlled":"1","publisher":"IOP Publishing","doi":"10.3847/1538-4357/ad1e5f","language":[{"iso":"eng"}],"date_published":"2024-03-01T00:00:00Z","oa":1,"file":[{"file_size":2700137,"date_updated":"2024-03-25T08:02:43Z","content_type":"application/pdf","checksum":"389a880e176799d5c062ea7cb82d08c9","access_level":"open_access","file_name":"2024_AstrophysicalJourn_Greene.pdf","file_id":"15176","success":1,"relation":"main_file","creator":"dernst","date_created":"2024-03-25T08:02:43Z"}],"article_type":"original","author":[{"full_name":"Greene, Jenny E.","last_name":"Greene","first_name":"Jenny E."},{"full_name":"Labbe, Ivo","last_name":"Labbe","first_name":"Ivo"},{"first_name":"Andy D.","last_name":"Goulding","full_name":"Goulding, Andy D."},{"last_name":"Furtak","full_name":"Furtak, Lukas J.","first_name":"Lukas J."},{"full_name":"Chemerynska, Iryna","last_name":"Chemerynska","first_name":"Iryna"},{"full_name":"Kokorev, Vasily","last_name":"Kokorev","first_name":"Vasily"},{"first_name":"Pratika","full_name":"Dayal, Pratika","last_name":"Dayal"},{"last_name":"Volonteri","full_name":"Volonteri, Marta","first_name":"Marta"},{"first_name":"Christina C.","full_name":"Williams, Christina C.","last_name":"Williams"},{"full_name":"Wang, Bingjie","last_name":"Wang","first_name":"Bingjie"},{"first_name":"David J.","last_name":"Setton","full_name":"Setton, David J."},{"first_name":"Adam J.","full_name":"Burgasser, Adam J.","last_name":"Burgasser"},{"first_name":"Rachel","last_name":"Bezanson","full_name":"Bezanson, Rachel"},{"first_name":"Hakim","full_name":"Atek, Hakim","last_name":"Atek"},{"first_name":"Gabriel","full_name":"Brammer, Gabriel","last_name":"Brammer"},{"last_name":"Cutler","full_name":"Cutler, Sam E.","first_name":"Sam E."},{"first_name":"Robert","last_name":"Feldmann","full_name":"Feldmann, Robert"},{"full_name":"Fujimoto, Seiji","last_name":"Fujimoto","first_name":"Seiji"},{"full_name":"Glazebrook, Karl","last_name":"Glazebrook","first_name":"Karl"},{"first_name":"Anna","last_name":"De Graaff","full_name":"De Graaff, Anna"},{"full_name":"Khullar, Gourav","last_name":"Khullar","first_name":"Gourav"},{"full_name":"Leja, Joel","last_name":"Leja","first_name":"Joel"},{"full_name":"Marchesini, Danilo","last_name":"Marchesini","first_name":"Danilo"},{"last_name":"Maseda","full_name":"Maseda, Michael V.","first_name":"Michael V."},{"orcid":"0000-0003-2871-127X","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee"},{"first_name":"Tim B.","last_name":"Miller","full_name":"Miller, Tim B."},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"first_name":"Themiya","full_name":"Nanayakkara, Themiya","last_name":"Nanayakkara"},{"first_name":"Pascal A.","full_name":"Oesch, Pascal A.","last_name":"Oesch"},{"last_name":"Pan","full_name":"Pan, Richard","first_name":"Richard"},{"first_name":"Casey","last_name":"Papovich","full_name":"Papovich, Casey"},{"first_name":"Sedona H.","full_name":"Price, Sedona H.","last_name":"Price"},{"first_name":"Pieter","last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter"},{"last_name":"Weaver","full_name":"Weaver, John R.","first_name":"John R."},{"first_name":"Katherine E.","full_name":"Whitaker, Katherine E.","last_name":"Whitaker"},{"first_name":"Adi","full_name":"Zitrin, Adi","last_name":"Zitrin"}],"abstract":[{"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.","lang":"eng"}],"date_updated":"2025-09-04T13:09:41Z","intvolume":"       964","oa_version":"Published Version","article_number":"39","day":"01","ddc":["550"],"title":"UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5","department":[{"_id":"JoMa"}],"isi":1,"has_accepted_license":"1","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"DOAJ_listed":"1","publication":"Astrophysical Journal","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.","status":"public","file_date_updated":"2024-03-25T08:02:43Z","date_created":"2024-03-24T23:00:59Z","article_processing_charge":"Yes"},{"publication":"Nature Neuroscience","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"ec_funded":1,"article_processing_charge":"Yes (via OA deal)","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.","file_date_updated":"2025-06-25T08:45:32Z","status":"public","date_created":"2024-03-24T23:01:00Z","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."}],"intvolume":"        27","date_updated":"2025-09-04T13:06:06Z","oa_version":"Published Version","author":[{"full_name":"Agnes, Everton J.","last_name":"Agnes","first_name":"Everton J."},{"full_name":"Vogels, Tim P","last_name":"Vogels","orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"department":[{"_id":"TiVo"}],"has_accepted_license":"1","OA_type":"hybrid","isi":1,"day":"01","ddc":["570"],"title":"Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks","year":"2024","quality_controlled":"1","page":"964-974","external_id":{"isi":["001190081400001"],"pmid":["38509348 "]},"article_type":"original","publisher":"Springer Nature","language":[{"iso":"eng"}],"date_published":"2024-05-01T00:00:00Z","doi":"10.1038/s41593-024-01597-4","oa":1,"file":[{"date_created":"2025-06-25T08:45:32Z","relation":"main_file","creator":"dernst","success":1,"file_id":"19902","file_name":"2025_NatureNeuroscience_Agnes.pdf","access_level":"open_access","checksum":"dfca68a24749575b912b3a78a7de4516","content_type":"application/pdf","date_updated":"2025-06-25T08:45:32Z","file_size":10508018}],"volume":27,"type":"journal_article","citation":{"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.” <i>Nature Neuroscience</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41593-024-01597-4\">https://doi.org/10.1038/s41593-024-01597-4</a>.","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. 27, 964–974.","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.” <i>Nature Neuroscience</i>, vol. 27, Springer Nature, 2024, pp. 964–74, doi:<a href=\"https://doi.org/10.1038/s41593-024-01597-4\">10.1038/s41593-024-01597-4</a>.","short":"E.J. Agnes, T.P. Vogels, Nature Neuroscience 27 (2024) 964–974.","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,” <i>Nature Neuroscience</i>, vol. 27. Springer Nature, pp. 964–974, 2024.","ama":"Agnes EJ, Vogels TP. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. <i>Nature Neuroscience</i>. 2024;27:964-974. doi:<a href=\"https://doi.org/10.1038/s41593-024-01597-4\">10.1038/s41593-024-01597-4</a>","apa":"Agnes, E. J., &#38; Vogels, T. P. (2024). Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-024-01597-4\">https://doi.org/10.1038/s41593-024-01597-4</a>"},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"15171","month":"05","scopus_import":"1","pmid":1}]