[{"page":"1-20","volume":13298,"type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11707","year":"2022","status":"public","oa":1,"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 840605. This work was supported in part by the Academy of Finland, Grants 314888 and 333837. The authors would also like to thank David Harris, Neven Villani, and the anonymous reviewers for their very helpful comments and feedback on previous versions of this work.","external_id":{"isi":["000876977400001"],"arxiv":["2102.08703"]},"citation":{"apa":"Balliu, A., Hirvonen, J., Melnyk, D., Olivetti, D., Rybicki, J., &#38; Suomela, J. (2022). Local mending. In M. Parter (Ed.), <i>International Colloquium on Structural Information and Communication Complexity</i> (Vol. 13298, pp. 1–20). Paderborn, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>","ieee":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, and J. Suomela, “Local mending,” in <i>International Colloquium on Structural Information and Communication Complexity</i>, Paderborn, Germany, 2022, vol. 13298, pp. 1–20.","chicago":"Balliu, Alkida, Juho Hirvonen, Darya Melnyk, Dennis Olivetti, Joel Rybicki, and Jukka Suomela. “Local Mending.” In <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, 13298:1–20. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>.","ista":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. 2022. Local mending. International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication ComplexityLNCS vol. 13298, 1–20.","short":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, J. Suomela, in:, M. Parter (Ed.), International Colloquium on Structural Information and Communication Complexity, Springer Nature, 2022, pp. 1–20.","mla":"Balliu, Alkida, et al. “Local Mending.” <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, vol. 13298, Springer Nature, 2022, pp. 1–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>.","ama":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. Local mending. In: Parter M, ed. <i>International Colloquium on Structural Information and Communication Complexity</i>. Vol 13298. LNCS. Springer Nature; 2022:1-20. doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>"},"publication_identifier":{"isbn":["9783031099922"],"issn":["0302-9743"],"eissn":["1611-3349"]},"title":"Local mending","department":[{"_id":"DaAl"}],"publication":"International Colloquium on Structural Information and Communication Complexity","publisher":"Springer Nature","oa_version":"Preprint","ec_funded":1,"date_created":"2022-07-31T22:01:49Z","arxiv":1,"abstract":[{"lang":"eng","text":"In this work we introduce the graph-theoretic notion of mendability: for each locally checkable graph problem we can define its mending radius, which captures the idea of how far one needs to modify a partial solution in order to “patch a hole.” We explore how mendability is connected to the existence of efficient algorithms, especially in distributed, parallel, and fault-tolerant settings. It is easy to see that O(1)-mendable problems are also solvable in O(log∗n) rounds in the LOCAL model of distributed computing. One of the surprises is that in paths and cycles, a converse also holds in the following sense: if a problem Π can be solved in O(log∗n), there is always a restriction Π′⊆Π that is still efficiently solvable but that is also O(1)-mendable. We also explore the structure of the landscape of mendability. For example, we show that in trees, the mending radius of any locally checkable problem is O(1), Θ(logn), or Θ(n), while in general graphs the structure is much more diverse."}],"series_title":"LNCS","intvolume":"     13298","main_file_link":[{"url":"https://arxiv.org/abs/2102.08703","open_access":"1"}],"publication_status":"published","day":"25","project":[{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","name":"Coordination in constrained and natural distributed systems","grant_number":"840605","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"isi":1,"month":"06","conference":{"location":"Paderborn, Germany","start_date":"2022-06-27","name":"SIROCCO: Structural Information and Communication Complexity","end_date":"2022-06-29"},"editor":[{"last_name":"Parter","first_name":"Merav","full_name":"Parter, Merav"}],"date_published":"2022-06-25T00:00:00Z","author":[{"first_name":"Alkida","last_name":"Balliu","full_name":"Balliu, Alkida"},{"first_name":"Juho","last_name":"Hirvonen","full_name":"Hirvonen, Juho"},{"full_name":"Melnyk, Darya","last_name":"Melnyk","first_name":"Darya"},{"full_name":"Olivetti, Dennis","first_name":"Dennis","last_name":"Olivetti"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki","first_name":"Joel"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"}],"date_updated":"2023-08-03T12:16:29Z","doi":"10.1007/978-3-031-09993-9_1","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1"},{"month":"07","citation":{"ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>","mla":"Budanur, Nazmi B. <i>Burakbudanur/Autoacc-Public</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>.","ista":"Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>.","short":"N.B. Budanur, (2022).","chicago":"Budanur, Nazmi B. “Burakbudanur/Autoacc-Public.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>.","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","apa":"Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>"},"ddc":["000"],"day":"06","status":"public","oa":1,"has_accepted_license":"1","year":"2022","_id":"11711","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.6802720","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"lang":"eng","text":"Codes and data for reproducing the results of N. B. Budanur and B. Hof \"An autonomous compartmental model for accelerating epidemics\""}],"article_processing_charge":"No","doi":"10.5281/ZENODO.6802720","date_updated":"2023-08-03T12:24:21Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11704"}]},"date_published":"2022-07-06T00:00:00Z","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","first_name":"Nazmi B"}],"date_created":"2022-08-01T08:06:33Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa_version":"Published Version","publisher":"Zenodo","title":"burakbudanur/autoacc-public","department":[{"_id":"BjHo"}]},{"publication_status":"published","file":[{"checksum":"008156e5340e9789f0f6d82bde4d347a","file_name":"2022_BMCResearchNotes_Nikolic.pdf","file_size":1545310,"date_updated":"2022-08-01T09:24:42Z","file_id":"11714","date_created":"2022-08-01T09:24:42Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"}],"intvolume":"        15","license":"https://creativecommons.org/licenses/by/4.0/","project":[{"_id":"26956E74-B435-11E9-9278-68D0E5697425","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","grant_number":"V00738","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"month":"05","day":"13","ddc":["570"],"pmid":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"173","file_date_updated":"2022-08-01T09:24:42Z","quality_controlled":"1","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"date_updated":"2022-08-01T09:27:40Z","related_material":{"link":[{"url":"https://doi.org/10.1186/s13104-022-06152-7","relation":"erratum"}]},"doi":"10.1186/s13104-022-06061-9","article_processing_charge":"No","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","last_name":"Nikolic","orcid":"0000-0001-9068-6090","first_name":"Nela"},{"last_name":"Sauert","first_name":"Martina","full_name":"Sauert, Martina"},{"last_name":"Albanese","first_name":"Tanino G.","full_name":"Albanese, Tanino G."},{"first_name":"Isabella","last_name":"Moll","full_name":"Moll, Isabella"}],"date_published":"2022-05-13T00:00:00Z","year":"2022","has_accepted_license":"1","_id":"11713","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":15,"publication_identifier":{"issn":["1756-0500"]},"citation":{"ama":"Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. 2022;15. doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","ista":"Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. BMC Research Notes. 15, 173.","mla":"Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>, vol. 15, 173, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>.","ieee":"N. Nikolic, M. Sauert, T. G. Albanese, and I. Moll, “Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli,” <i>BMC Research Notes</i>, vol. 15. Springer Nature, 2022.","chicago":"Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>.","apa":"Nikolic, N., Sauert, M., Albanese, T. G., &#38; Moll, I. (2022). Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>"},"external_id":{"pmid":["35562780"]},"article_type":"letter_note","acknowledgement":"We acknowledge the Max Perutz Labs FACS Facility together with Thomas Sauer. NN is grateful to Călin C. Guet for his support.\r\nThis work was funded by the Elise Richter grant V738 of the Austrian Science Fund (FWF), and the FWF Lise Meitner grant M1697, to NN; and by the FWF grant P22249, FWF Special Research Program RNA-REG F43 (subproject F4316), and FWF doctoral program RNA Biology (W1207), to IM. Open access funding provided by the Austrian Science Fund.","oa":1,"status":"public","oa_version":"Published Version","date_created":"2022-08-01T09:04:27Z","publisher":"Springer Nature","department":[{"_id":"CaGu"}],"title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","publication":"BMC Research Notes","abstract":[{"text":"Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes.","lang":"eng"}]},{"abstract":[{"text":"We study rigidity of rational maps that come from Newton's root finding method for polynomials of arbitrary degrees. We establish dynamical rigidity of these maps: each point in the Julia set of a Newton map is either rigid (i.e. its orbit can be distinguished in combinatorial terms from all other orbits), or the orbit of this point eventually lands in the filled-in Julia set of a polynomial-like restriction of the original map. As a corollary, we show that the Julia sets of Newton maps in many non-trivial cases are locally connected; in particular, every cubic Newton map without Siegel points has locally connected Julia set.\r\nIn the parameter space of Newton maps of arbitrary degree we obtain the following rigidity result: any two combinatorially equivalent Newton maps are quasiconformally conjugate in a neighborhood of their Julia sets provided that they either non-renormalizable, or they are both renormalizable “in the same way”.\r\nOur main tool is a generalized renormalization concept called “complex box mappings” for which we extend a dynamical rigidity result by Kozlovski and van Strien so as to include irrationally indifferent and renormalizable situations.","lang":"eng"}],"ec_funded":1,"date_created":"2022-08-01T17:08:16Z","oa_version":"Published Version","publication":"Advances in Mathematics","department":[{"_id":"VaKa"}],"title":"Rigidity of Newton dynamics","publisher":"Elsevier","citation":{"short":"K. Drach, D. Schleicher, Advances in Mathematics 408 (2022).","mla":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>, vol. 408, no. Part A, 108591, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>.","ista":"Drach K, Schleicher D. 2022. Rigidity of Newton dynamics. Advances in Mathematics. 408(Part A), 108591.","ama":"Drach K, Schleicher D. Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. 2022;408(Part A). doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>","apa":"Drach, K., &#38; Schleicher, D. (2022). Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>","chicago":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>.","ieee":"K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” <i>Advances in Mathematics</i>, vol. 408, no. Part A. Elsevier, 2022."},"publication_identifier":{"issn":["0001-8708"]},"status":"public","acknowledgement":"We are grateful to a number of colleagues for helpful and inspiring discussions during the time when we worked on this project, in particular Dima Dudko, Misha Hlushchanka, John Hubbard, Misha Lyubich, Oleg Kozlovski, and Sebastian van Strien. Finally, we would like to thank our dynamics research group for numerous helpful and enjoyable discussions: Konstantin Bogdanov, Roman Chernov, Russell Lodge, Steffen Maaß, David Pfrang, Bernhard Reinke, Sergey Shemyakov, and Maik Sowinski. We gratefully acknowledge support by the Advanced Grant “HOLOGRAM” (#695 621) of the European Research Council (ERC), as well as hospitality of Cornell University in the spring of 2018 while much of this work was prepared. The first-named author also acknowledges the support of the ERC Advanced Grant “SPERIG” (#885 707).","oa":1,"issue":"Part A","article_type":"original","external_id":{"isi":["000860924200005"]},"_id":"11717","year":"2022","has_accepted_license":"1","volume":408,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","keyword":["General Mathematics"],"scopus_import":"1","quality_controlled":"1","date_published":"2022-10-29T00:00:00Z","author":[{"orcid":"0000-0002-9156-8616","last_name":"Drach","first_name":"Kostiantyn","id":"fe8209e2-906f-11eb-847d-950f8fc09115","full_name":"Drach, Kostiantyn"},{"last_name":"Schleicher","first_name":"Dierk","full_name":"Schleicher, Dierk"}],"article_processing_charge":"Yes (via OA deal)","date_updated":"2023-08-03T12:36:07Z","doi":"10.1016/j.aim.2022.108591","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-02-02T07:39:09Z","article_number":"108591","isi":1,"month":"10","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"885707","name":"Spectral rigidity and integrability for billiards and geodesic flows","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}],"ddc":["510"],"day":"29","intvolume":"       408","file":[{"content_type":"application/pdf","success":1,"date_created":"2023-02-02T07:39:09Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_size":2164036,"file_name":"2022_AdvancesMathematics_Drach.pdf","checksum":"2710e6f5820f8c20a676ddcbb30f0e8d","file_id":"12474","date_updated":"2023-02-02T07:39:09Z"}],"publication_status":"published"},{"ddc":["580"],"day":"25","pmid":1,"month":"07","isi":1,"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file":[{"date_updated":"2022-08-08T07:42:09Z","file_id":"11747","file_size":2506262,"file_name":"2022_PNAS_Li.pdf","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2022-08-08T07:42:09Z"}],"publication_status":"published","intvolume":"       119","article_processing_charge":"No","doi":"10.1073/pnas.2121058119","date_updated":"2024-10-29T10:12:30Z","date_published":"2022-07-25T00:00:00Z","author":[{"last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"last_name":"Chen","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang"},{"full_name":"Alotaibi, Saqer S.","last_name":"Alotaibi","first_name":"Saqer S."},{"full_name":"Pěnčík, Aleš","last_name":"Pěnčík","first_name":"Aleš"},{"first_name":"Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"quality_controlled":"1","keyword":["Multidisciplinary"],"scopus_import":"1","article_number":"e2121058119","file_date_updated":"2022-08-08T07:42:09Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"issue":"31","external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"article_type":"original","status":"public","acknowledgement":"We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”","oa":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"citation":{"ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>","mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 31, e2121058119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>.","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. 119(31), e2121058119.","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences 119 (2022).","chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>.","ieee":"L. Li <i>et al.</i>, “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &#38; Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":119,"has_accepted_license":"1","year":"2022","_id":"11723","abstract":[{"lang":"eng","text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term."}],"publisher":"Proceedings of the National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","date_created":"2022-08-04T20:06:49Z","oa_version":"Published Version"},{"publication_identifier":{"eissn":["1572-9613"],"issn":["0022-4715"]},"citation":{"ama":"Henheik SJ, Lauritsen AB. The BCS energy gap at high density. <i>Journal of Statistical Physics</i>. 2022;189. doi:<a href=\"https://doi.org/10.1007/s10955-022-02965-9\">10.1007/s10955-022-02965-9</a>","short":"S.J. Henheik, A.B. Lauritsen, Journal of Statistical Physics 189 (2022).","mla":"Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at High Density.” <i>Journal of Statistical Physics</i>, vol. 189, 5, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10955-022-02965-9\">10.1007/s10955-022-02965-9</a>.","ista":"Henheik SJ, Lauritsen AB. 2022. The BCS energy gap at high density. Journal of Statistical Physics. 189, 5.","chicago":"Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “The BCS Energy Gap at High Density.” <i>Journal of Statistical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10955-022-02965-9\">https://doi.org/10.1007/s10955-022-02965-9</a>.","ieee":"S. J. Henheik and A. B. Lauritsen, “The BCS energy gap at high density,” <i>Journal of Statistical Physics</i>, vol. 189. Springer Nature, 2022.","apa":"Henheik, S. J., &#38; Lauritsen, A. B. (2022). The BCS energy gap at high density. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-022-02965-9\">https://doi.org/10.1007/s10955-022-02965-9</a>"},"article_type":"original","external_id":{"isi":["000833007200002"]},"acknowledgement":"We are grateful to Robert Seiringer for helpful discussions and many valuable comments\r\non an earlier version of the manuscript. J.H. acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond’ No. 101020331. Open access funding provided by Institute of Science and Technology (IST Austria)","oa":1,"status":"public","has_accepted_license":"1","year":"2022","_id":"11732","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":189,"abstract":[{"lang":"eng","text":"We study the BCS energy gap Ξ in the high–density limit and derive an asymptotic formula, which strongly depends on the strength of the interaction potential V on the Fermi surface. In combination with the recent result by one of us (Math. Phys. Anal. Geom. 25, 3, 2022) on the critical temperature Tc at high densities, we prove the universality of the ratio of the energy gap and the critical temperature."}],"oa_version":"Published Version","date_created":"2022-08-05T11:36:56Z","ec_funded":1,"publisher":"Springer Nature","title":"The BCS energy gap at high density","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"publication":"Journal of Statistical Physics","language":[{"iso":"eng"}],"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","call_identifier":"H2020"}],"isi":1,"month":"07","day":"29","ddc":["530"],"publication_status":"published","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2022-08-08T07:36:34Z","success":1,"date_updated":"2022-08-08T07:36:34Z","file_id":"11746","file_size":419563,"checksum":"b398c4dbf65f71d417981d6e366427e9","file_name":"2022_JourStatisticalPhysics_Henheik.pdf"}],"intvolume":"       189","quality_controlled":"1","scopus_import":"1","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"doi":"10.1007/s10955-022-02965-9","date_updated":"2023-09-05T14:57:49Z","article_processing_charge":"Yes (via OA deal)","author":[{"id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","full_name":"Henheik, Sven Joscha","last_name":"Henheik","orcid":"0000-0003-1106-327X","first_name":"Sven Joscha"},{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard"}],"date_published":"2022-07-29T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"5","file_date_updated":"2022-08-08T07:36:34Z"},{"abstract":[{"lang":"eng","text":"Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h2SNP. We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies."}],"oa_version":"Published Version","date_created":"2022-08-07T22:01:56Z","publisher":"Proceedings of the National Academy of Sciences","title":"Improving GWAS discovery and genomic prediction accuracy in biobank data","department":[{"_id":"MaRo"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_identifier":{"eissn":["1091-6490"]},"citation":{"apa":"Orliac, E. J., Trejo Banos, D., Ojavee, S. E., Läll, K., Mägi, R., Visscher, P. M., &#38; Robinson, M. R. (2022). Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>","chicago":"Orliac, Etienne J., Daniel Trejo Banos, Sven E. Ojavee, Kristi Läll, Reedik Mägi, Peter M. Visscher, and Matthew Richard Robinson. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>.","ieee":"E. J. Orliac <i>et al.</i>, “Improving GWAS discovery and genomic prediction accuracy in biobank data,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","short":"E.J. Orliac, D. Trejo Banos, S.E. Ojavee, K. Läll, R. Mägi, P.M. Visscher, M.R. Robinson, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ista":"Orliac EJ, Trejo Banos D, Ojavee SE, Läll K, Mägi R, Visscher PM, Robinson MR. 2022. Improving GWAS discovery and genomic prediction accuracy in biobank data. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121279119.","mla":"Orliac, Etienne J., et al. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121279119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>.","ama":"Orliac EJ, Trejo Banos D, Ojavee SE, et al. Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>"},"article_type":"original","external_id":{"isi":["000881496900003"]},"issue":"31","status":"public","oa":1,"acknowledgement":"This project was funded by Swiss National Science Foundation Eccellenza Grant PCEGP3-181181(toM.R.R.) and by core funding from the Institute of Science and Technology Austria. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). K.L. and R.M. were supported by the Estonian Research Council Grant PRG687. Estonian Biobank computations were performed in the High-Performance Computing Centre, University of Tartu.","has_accepted_license":"1","year":"2022","_id":"11733","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":119,"quality_controlled":"1","scopus_import":"1","date_updated":"2023-08-03T12:40:38Z","doi":"10.1073/pnas.2121279119","related_material":{"record":[{"relation":"research_data","status":"public","id":"13064"}]},"article_processing_charge":"No","author":[{"full_name":"Orliac, Etienne J.","last_name":"Orliac","first_name":"Etienne J."},{"full_name":"Trejo Banos, Daniel","first_name":"Daniel","last_name":"Trejo Banos"},{"first_name":"Sven E.","last_name":"Ojavee","full_name":"Ojavee, Sven E."},{"full_name":"Läll, Kristi","last_name":"Läll","first_name":"Kristi"},{"first_name":"Reedik","last_name":"Mägi","full_name":"Mägi, Reedik"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard"}],"date_published":"2022-07-29T00:00:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"article_number":"e2121279119","file_date_updated":"2022-08-08T07:31:19Z","language":[{"iso":"eng"}],"isi":1,"month":"07","day":"29","ddc":["570"],"publication_status":"published","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2022-08-08T07:31:19Z","file_id":"11745","date_updated":"2022-08-08T07:31:19Z","file_size":1001164,"file_name":"2022_PNAS_Orliac.pdf","checksum":"b5d2024e19fbad6f85a5e384e44d0f3b"}],"intvolume":"       119"},{"has_accepted_license":"1","year":"2022","_id":"11734","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":119,"publication_identifier":{"eissn":["1091-6490"]},"citation":{"apa":"Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., … Benková, E. (2022). Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>","chicago":"Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>.","ieee":"R. Abualia <i>et al.</i>, “Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","short":"R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry, A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2122460119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>.","ista":"Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2122460119.","ama":"Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>"},"issue":"31","article_type":"original","external_id":{"isi":["000881496900007"],"pmid":["35878040"]},"acknowledgement":"We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari, Marc¸al Gallem\u0003ı, Kaori Tabata, Andrej Hurn\u0003y, and Sascha Waidmann for sharing materials; and Marina Borges Osorio for critical reading of the manuscript. Work in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science Facilities of the Institute of Science\r\nand Technology Austria. We give sincere thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses. This work was funded by the Czech Science Foundation (Project No. 19-00973S).","oa":1,"status":"public","date_created":"2022-08-07T22:01:57Z","oa_version":"Published Version","publisher":"Proceedings of the National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences of the United States of America","department":[{"_id":"EvBe"}],"title":"Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses","abstract":[{"text":"Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.","lang":"eng"}],"file":[{"file_name":"2022_PNAS_Abualia.pdf","checksum":"6e97dedc281247fc3fe238a209f14af0","file_size":3092330,"date_updated":"2022-08-08T07:09:58Z","file_id":"11744","success":1,"date_created":"2022-08-08T07:09:58Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file"}],"publication_status":"published","intvolume":"       119","month":"07","isi":1,"project":[{"grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"ddc":["570"],"day":"25","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"article_number":"e2122460119","file_date_updated":"2022-08-08T07:09:58Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","date_updated":"2023-08-03T12:39:29Z","doi":"10.1073/pnas.2122460119","author":[{"orcid":"0000-0002-9357-9415","last_name":"Abualia","first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed"},{"full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Bouguyon, Eleonore","first_name":"Eleonore","last_name":"Bouguyon"},{"first_name":"Kevin","orcid":"0000-0002-1215-4264","last_name":"Domanegg","full_name":"Domanegg, Kevin","id":"a24c7829-16e8-11ed-8527-c4d36ffb7539"},{"full_name":"Krapp, Anne","last_name":"Krapp","first_name":"Anne"},{"last_name":"Nacry","first_name":"Philip","full_name":"Nacry, Philip"},{"full_name":"Gojon, Alain","first_name":"Alain","last_name":"Gojon"},{"full_name":"Lacombe, Benoit","last_name":"Lacombe","first_name":"Benoit"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"date_published":"2022-07-25T00:00:00Z"},{"date_created":"2022-08-07T22:01:57Z","ec_funded":1,"oa_version":"Submitted Version","publisher":"Association for Computing Machinery","publication":"ACM Transactions on Graphics","title":"Computational design of high-level interlocking puzzles","department":[{"_id":"BeBi"}],"abstract":[{"text":"Interlocking puzzles are intriguing geometric games where the puzzle pieces are held together based on their geometric arrangement, preventing the puzzle from falling apart. High-level-of-difficulty, or simply high-level, interlocking puzzles are a subclass of interlocking puzzles that require multiple moves to take out the first subassembly from the puzzle. Solving a high-level interlocking puzzle is a challenging task since one has to explore many different configurations of the puzzle pieces until reaching a configuration where the first subassembly can be taken out. Designing a high-level interlocking puzzle with a user-specified level of difficulty is even harder since the puzzle pieces have to be interlocking in all the configurations before the first subassembly is taken out.\r\n\r\nIn this paper, we present a computational approach to design high-level interlocking puzzles. The core idea is to represent all possible configurations of an interlocking puzzle as well as transitions among these configurations using a rooted, undirected graph called a disassembly graph and leverage this graph to find a disassembly plan that requires a minimal number of moves to take out the first subassembly from the puzzle. At the design stage, our algorithm iteratively constructs the geometry of each puzzle piece to expand the disassembly graph incrementally, aiming to achieve a user-specified level of difficulty. We show that our approach allows efficient generation of high-level interlocking puzzles of various shape complexities, including new solutions not attainable by state-of-the-art approaches.","lang":"eng"}],"year":"2022","has_accepted_license":"1","_id":"11735","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":41,"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"citation":{"ama":"Chen R, Wang Z, Song P, Bickel B. Computational design of high-level interlocking puzzles. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530071\">10.1145/3528223.3530071</a>","short":"R. Chen, Z. Wang, P. Song, B. Bickel, ACM Transactions on Graphics 41 (2022).","ista":"Chen R, Wang Z, Song P, Bickel B. 2022. Computational design of high-level interlocking puzzles. ACM Transactions on Graphics. 41(4), 150.","mla":"Chen, Rulin, et al. “Computational Design of High-Level Interlocking Puzzles.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 150, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530071\">10.1145/3528223.3530071</a>.","ieee":"R. Chen, Z. Wang, P. Song, and B. Bickel, “Computational design of high-level interlocking puzzles,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","chicago":"Chen, Rulin, Ziqi Wang, Peng Song, and Bernd Bickel. “Computational Design of High-Level Interlocking Puzzles.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530071\">https://doi.org/10.1145/3528223.3530071</a>.","apa":"Chen, R., Wang, Z., Song, P., &#38; Bickel, B. (2022). Computational design of high-level interlocking puzzles. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530071\">https://doi.org/10.1145/3528223.3530071</a>"},"issue":"4","article_type":"original","external_id":{"isi":["000830989200018"]},"oa":1,"status":"public","acknowledgement":"We thank the reviewers for the valuable comments, David Gontier for sharing the source code of the baseline design approach, Christian Hafner for proofreading the paper, Keenan Crane for the 3D model of Cow, and Thingiverse for the 3D models of Moai and Owl. This work was supported by the SUTD Start-up Research Grant (Number: SRG ISTD 2019 148), the Swiss National Science Foundation (NCCR Digital Fabrication Agreement #51NF40-141853), and\r\nthe European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 715767 – MATERIALIZABLE).","article_number":"150","file_date_updated":"2022-08-28T07:56:19Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","date_updated":"2023-08-03T13:21:22Z","doi":"10.1145/3528223.3530071","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/unlocking-interlocking-riddles/"}]},"date_published":"2022-07-22T00:00:00Z","author":[{"full_name":"Chen, Rulin","last_name":"Chen","first_name":"Rulin"},{"first_name":"Ziqi","last_name":"Wang","full_name":"Wang, Ziqi"},{"full_name":"Song, Peng","first_name":"Peng","last_name":"Song"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"}],"file":[{"access_level":"open_access","creator":"bbickel","relation":"main_file","success":1,"date_created":"2022-08-28T07:56:19Z","content_type":"application/pdf","file_id":"11992","date_updated":"2022-08-28T07:56:19Z","file_name":"Chen-2022-High-LevelPuzzle_authorVersion.pdf","checksum":"0b51651be45b1b33f2072bd5d2686c69","file_size":16896871}],"publication_status":"published","intvolume":"        41","isi":1,"month":"07","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"ddc":["000"],"day":"22"},{"year":"2022","_id":"11736","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":41,"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"citation":{"apa":"Sperl, G., Sánchez-Banderas, R. M., Li, M., Wojtan, C., &#38; Otaduy, M. A. (2022). Estimation of yarn-level simulation models for production fabrics. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530167\">https://doi.org/10.1145/3528223.3530167</a>","chicago":"Sperl, Georg, Rosa M. Sánchez-Banderas, Manwen Li, Chris Wojtan, and Miguel A. Otaduy. “Estimation of Yarn-Level Simulation Models for Production Fabrics.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530167\">https://doi.org/10.1145/3528223.3530167</a>.","ieee":"G. Sperl, R. M. Sánchez-Banderas, M. Li, C. Wojtan, and M. A. Otaduy, “Estimation of yarn-level simulation models for production fabrics,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","mla":"Sperl, Georg, et al. “Estimation of Yarn-Level Simulation Models for Production Fabrics.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 65, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530167\">10.1145/3528223.3530167</a>.","short":"G. Sperl, R.M. Sánchez-Banderas, M. Li, C. Wojtan, M.A. Otaduy, ACM Transactions on Graphics 41 (2022).","ista":"Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. 2022. Estimation of yarn-level simulation models for production fabrics. ACM Transactions on Graphics. 41(4), 65.","ama":"Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. Estimation of yarn-level simulation models for production fabrics. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530167\">10.1145/3528223.3530167</a>"},"external_id":{"isi":["000830989200114"]},"article_type":"original","issue":"4","oa":1,"acknowledgement":"We wish to thank the anonymous reviewers for their helpful comments. To develop this project, we were helped by many people both at Under Armour (Clay Dean, Randall Harward, Kyle Blakely, Craig Simile, Michael Seiz, Brooke Malone, Brittainy McFarland, Emilie Phan, Lindsey Kern, Courtney Oswald, Haley Barkley, Bob Chin, Adam Bayer, Connie Kwok, Marielle Newman, Nick Pence, Allison Hicks, Allison White, Candace Rubenstein, Jeremy Stangland, Fred Fagergren, Michael Mazzoleni, Nathaniel Berry, Manuel Frank) and SEDDI (Gabriel Cirio, Alejandro Rodríguez, Sofía Dominguez, Alicia Nicas, Elena Garcés, Daniel Rodríguez, David Pascual, Manuel Godoy, Sergio Suja, Sergio Ruiz, Roberto Condori, Alberto Martín, Graham Sullivan). We also thank the members of the Visual Computing Group at IST Austria and the Multimodal Simulation Lab at URJC for their feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing, and it was funded in part by the European Research Council (ERC Consolidator Grant 772738 TouchDesign).","status":"public","oa_version":"Published Version","date_created":"2022-08-07T22:01:58Z","publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"title":"Estimation of yarn-level simulation models for production fabrics","publication":"ACM Transactions on Graphics","abstract":[{"lang":"eng","text":"This paper introduces a methodology for inverse-modeling of yarn-level mechanics of cloth, based on the mechanical response of fabrics in the real world. We compiled a database from physical tests of several different knitted fabrics used in the textile industry. These data span different types of complex knit patterns, yarn compositions, and fabric finishes, and the results demonstrate diverse physical properties like stiffness, nonlinearity, and anisotropy.\r\n\r\nWe then develop a system for approximating these mechanical responses with yarn-level cloth simulation. To do so, we introduce an efficient pipeline for converting between fabric-level data and yarn-level simulation, including a novel swatch-level approximation for speeding up computation, and some small-but-necessary extensions to yarn-level models used in computer graphics. The dataset used for this paper can be found at http://mslab.es/projects/YarnLevelFabrics."}],"publication_status":"published","intvolume":"        41","main_file_link":[{"url":"https://doi.org/10.1145/3528223.3530167","open_access":"1"}],"language":[{"iso":"eng"}],"isi":1,"month":"07","day":"22","acknowledged_ssus":[{"_id":"ScienComp"}],"article_number":"65","quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12358"}],"link":[{"url":"https://ista.ac.at/en/news/digital-yarn-real-socks/","description":"News on the ISTA website","relation":"press_release"}]},"date_updated":"2023-08-03T12:38:30Z","doi":"10.1145/3528223.3530167","article_processing_charge":"No","author":[{"first_name":"Georg","last_name":"Sperl","full_name":"Sperl, Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sánchez-Banderas","first_name":"Rosa M.","full_name":"Sánchez-Banderas, Rosa M."},{"full_name":"Li, Manwen","first_name":"Manwen","last_name":"Li"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J"},{"first_name":"Miguel A.","last_name":"Otaduy","full_name":"Otaduy, Miguel A."}],"date_published":"2022-07-22T00:00:00Z"},{"author":[{"orcid":"0000-0002-1648-0999","last_name":"Dziom","first_name":"Uladzislau","id":"6A9A37C2-8C5C-11E9-AE53-F2FDE5697425","full_name":"Dziom, Uladzislau"},{"full_name":"Shuvaev, A.","last_name":"Shuvaev","first_name":"A."},{"full_name":"Gospodarič, J.","first_name":"J.","last_name":"Gospodarič"},{"full_name":"Novik, E. G.","last_name":"Novik","first_name":"E. G."},{"full_name":"Dobretsova, A. A.","first_name":"A. A.","last_name":"Dobretsova"},{"last_name":"Mikhailov","first_name":"N. N.","full_name":"Mikhailov, N. N."},{"first_name":"Z. D.","last_name":"Kvon","full_name":"Kvon, Z. D."},{"first_name":"Zhanybek","last_name":"Alpichshev","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pimenov","first_name":"A.","full_name":"Pimenov, A."}],"date_published":"2022-07-15T00:00:00Z","article_processing_charge":"No","date_updated":"2023-08-03T12:38:57Z","doi":"10.1103/PhysRevB.106.045302","scopus_import":"1","quality_controlled":"1","file_date_updated":"2022-08-08T06:58:22Z","article_number":"045302","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["530"],"day":"15","isi":1,"month":"07","language":[{"iso":"eng"}],"intvolume":"       106","file":[{"date_created":"2022-08-08T06:58:22Z","success":1,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","checksum":"115aff9e0cde2f806cb26953d7262791","file_name":"2022_PhysRevB_Dziom.pdf","file_size":774455,"file_id":"11743","date_updated":"2022-08-08T06:58:22Z"}],"publication_status":"published","abstract":[{"text":"Spin-orbit coupling in thin HgTe quantum wells results in a relativistic-like electron band structure, making it a versatile solid state platform to observe and control nontrivial electrodynamic phenomena. Here we report an observation of universal terahertz (THz) transparency determined by fine-structure constant α≈1/137 in 6.5-nm-thick HgTe layer, close to the critical thickness separating phases with topologically different electronic band structure. Using THz spectroscopy in a magnetic field we obtain direct evidence of asymmetric spin splitting of the Dirac cone. This particle-hole asymmetry facilitates optical control of edge spin currents in the quantum wells.","lang":"eng"}],"publication":"Physical Review B","department":[{"_id":"ZhAl"}],"title":"Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells","publisher":"American Physical Society","date_created":"2022-08-07T22:01:58Z","oa_version":"Published Version","status":"public","oa":1,"acknowledgement":"This work was supported by the Austrian Science Funds (W 1243, I 3456-N27, I 5539-N).","issue":"4","article_type":"original","external_id":{"isi":["000834349200010"]},"citation":{"ama":"Dziom U, Shuvaev A, Gospodarič J, et al. Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. <i>Physical Review B</i>. 2022;106(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">10.1103/PhysRevB.106.045302</a>","mla":"Dziom, Uladzislau, et al. “Universal Transparency and Asymmetric Spin Splitting near the Dirac Point in HgTe Quantum Wells.” <i>Physical Review B</i>, vol. 106, no. 4, 045302, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">10.1103/PhysRevB.106.045302</a>.","ista":"Dziom U, Shuvaev A, Gospodarič J, Novik EG, Dobretsova AA, Mikhailov NN, Kvon ZD, Alpichshev Z, Pimenov A. 2022. Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. Physical Review B. 106(4), 045302.","short":"U. Dziom, A. Shuvaev, J. Gospodarič, E.G. Novik, A.A. Dobretsova, N.N. Mikhailov, Z.D. Kvon, Z. Alpichshev, A. Pimenov, Physical Review B 106 (2022).","chicago":"Dziom, Uladzislau, A. Shuvaev, J. Gospodarič, E. G. Novik, A. A. Dobretsova, N. N. Mikhailov, Z. D. Kvon, Zhanybek Alpichshev, and A. Pimenov. “Universal Transparency and Asymmetric Spin Splitting near the Dirac Point in HgTe Quantum Wells.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">https://doi.org/10.1103/PhysRevB.106.045302</a>.","ieee":"U. Dziom <i>et al.</i>, “Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells,” <i>Physical Review B</i>, vol. 106, no. 4. American Physical Society, 2022.","apa":"Dziom, U., Shuvaev, A., Gospodarič, J., Novik, E. G., Dobretsova, A. A., Mikhailov, N. N., … Pimenov, A. (2022). Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">https://doi.org/10.1103/PhysRevB.106.045302</a>"},"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"volume":106,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"11737","has_accepted_license":"1","year":"2022"},{"title":"Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","department":[{"_id":"JaMa"}],"publication":"SIAM Journal on Mathematical Analysis","publisher":"Society for Industrial and Applied Mathematics","oa_version":"Preprint","date_created":"2022-08-07T22:01:59Z","ec_funded":1,"arxiv":1,"abstract":[{"text":"We consider finite-volume approximations of Fokker--Planck equations on bounded convex domains in $\\mathbb{R}^d$ and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker--Planck equation via the method of evolutionary $\\Gamma$-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalizing the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality.","lang":"eng"}],"page":"4297-4333","volume":54,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11739","year":"2022","oa":1,"acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme grant 716117 and by the AustrianScience Fund (FWF) through grants F65 and W1245.","status":"public","article_type":"original","external_id":{"isi":["000889274600001"],"arxiv":["2008.10962"]},"issue":"4","citation":{"ama":"Forkert DL, Maas J, Portinale L. Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(4):4297-4333. doi:<a href=\"https://doi.org/10.1137/21M1410968\">10.1137/21M1410968</a>","ista":"Forkert DL, Maas J, Portinale L. 2022. Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. SIAM Journal on Mathematical Analysis. 54(4), 4297–4333.","mla":"Forkert, Dominik L., et al. “Evolutionary $\\Gamma$-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 4, Society for Industrial and Applied Mathematics, 2022, pp. 4297–333, doi:<a href=\"https://doi.org/10.1137/21M1410968\">10.1137/21M1410968</a>.","short":"D.L. Forkert, J. Maas, L. Portinale, SIAM Journal on Mathematical Analysis 54 (2022) 4297–4333.","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 4. Society for Industrial and Applied Mathematics, pp. 4297–4333, 2022.","chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary $\\Gamma$-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1410968\">https://doi.org/10.1137/21M1410968</a>.","apa":"Forkert, D. L., Maas, J., &#38; Portinale, L. (2022). Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1410968\">https://doi.org/10.1137/21M1410968</a>"},"publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"date_published":"2022-07-18T00:00:00Z","author":[{"first_name":"Dominik L","last_name":"Forkert","full_name":"Forkert, Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan"},{"first_name":"Lorenzo","last_name":"Portinale","full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10022"}]},"doi":"10.1137/21M1410968","date_updated":"2023-08-03T12:37:21Z","article_processing_charge":"No","scopus_import":"1","keyword":["Fokker--Planck equation","gradient flow","evolutionary $\\Gamma$-convergence"],"quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2008.10962","open_access":"1"}],"intvolume":"        54","publication_status":"published","day":"18","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"_id":"260788DE-B435-11E9-9278-68D0E5697425","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"month":"07","isi":1},{"date_created":"2022-08-07T22:01:59Z","oa_version":"Published Version","publication":"Electronic Journal of Combinatorics","department":[{"_id":"MaKw"}],"title":"Phase transition in cohomology groups of non-uniform random simplicial complexes","publisher":"Electronic Journal of Combinatorics","abstract":[{"lang":"eng","text":"We consider a generalised model of a random simplicial complex, which arises from a random hypergraph. Our model is generated by taking the downward-closure of a non-uniform binomial random hypergraph, in which for each k, each set of k+1 vertices forms an edge with some probability pk independently. As a special case, this contains an extensively studied model of a (uniform) random simplicial complex, introduced by Meshulam and Wallach [Random Structures & Algorithms 34 (2009), no. 3, pp. 408–417].\r\nWe consider a higher-dimensional notion of connectedness on this new model according to the vanishing of cohomology groups over an arbitrary abelian group R. We prove that this notion of connectedness displays a phase transition and determine the threshold. We also prove a hitting time result for a natural process interpretation, in which simplices and their downward-closure are added one by one. In addition, we determine the asymptotic behaviour of cohomology groups inside the critical window around the time of the phase transition."}],"arxiv":1,"_id":"11740","year":"2022","has_accepted_license":"1","volume":29,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","citation":{"ama":"Cooley O, Del Giudice N, Kang M, Sprüssel P. Phase transition in cohomology groups of non-uniform random simplicial complexes. <i>Electronic Journal of Combinatorics</i>. 2022;29(3). doi:<a href=\"https://doi.org/10.37236/10607\">10.37236/10607</a>","ista":"Cooley O, Del Giudice N, Kang M, Sprüssel P. 2022. Phase transition in cohomology groups of non-uniform random simplicial complexes. Electronic Journal of Combinatorics. 29(3), P3.27.","short":"O. Cooley, N. Del Giudice, M. Kang, P. Sprüssel, Electronic Journal of Combinatorics 29 (2022).","mla":"Cooley, Oliver, et al. “Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.” <i>Electronic Journal of Combinatorics</i>, vol. 29, no. 3, P3.27, Electronic Journal of Combinatorics, 2022, doi:<a href=\"https://doi.org/10.37236/10607\">10.37236/10607</a>.","chicago":"Cooley, Oliver, Nicola Del Giudice, Mihyun Kang, and Philipp Sprüssel. “Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2022. <a href=\"https://doi.org/10.37236/10607\">https://doi.org/10.37236/10607</a>.","ieee":"O. Cooley, N. Del Giudice, M. Kang, and P. Sprüssel, “Phase transition in cohomology groups of non-uniform random simplicial complexes,” <i>Electronic Journal of Combinatorics</i>, vol. 29, no. 3. Electronic Journal of Combinatorics, 2022.","apa":"Cooley, O., Del Giudice, N., Kang, M., &#38; Sprüssel, P. (2022). Phase transition in cohomology groups of non-uniform random simplicial complexes. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/10607\">https://doi.org/10.37236/10607</a>"},"publication_identifier":{"eissn":["1077-8926"]},"status":"public","acknowledgement":"Supported by Austrian Science Fund (FWF): I3747, W1230.","oa":1,"issue":"3","external_id":{"isi":["000836200300001"],"arxiv":["2005.07103"]},"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png"},"file_date_updated":"2022-08-08T06:28:52Z","article_number":"P3.27","scopus_import":"1","quality_controlled":"1","author":[{"last_name":"Cooley","first_name":"Oliver","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d","full_name":"Cooley, Oliver"},{"last_name":"Del Giudice","first_name":"Nicola","full_name":"Del Giudice, Nicola"},{"last_name":"Kang","first_name":"Mihyun","full_name":"Kang, Mihyun"},{"last_name":"Sprüssel","first_name":"Philipp","full_name":"Sprüssel, Philipp"}],"date_published":"2022-07-29T00:00:00Z","article_processing_charge":"No","date_updated":"2023-08-03T12:37:54Z","doi":"10.37236/10607","intvolume":"        29","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2022-08-08T06:28:52Z","success":1,"date_updated":"2022-08-08T06:28:52Z","file_id":"11742","file_size":1768663,"checksum":"057c676dcee70236aa234d4ce6138c69","file_name":"2022_ElecJournCombinatorics_Cooley.pdf"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by-nd/4.0/","month":"07","isi":1,"language":[{"iso":"eng"}],"ddc":["510"],"day":"29"},{"language":[{"iso":"eng"}],"project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"isi":1,"month":"09","day":"23","ddc":["000"],"intvolume":"     13498","publication_status":"published","file":[{"checksum":"05c7dcfbb9053a98f46441fb2eccb213","file_name":"2022_LNCS_RV_Henzinger.pdf","file_size":477110,"date_updated":"2023-01-20T07:34:50Z","file_id":"12317","date_created":"2023-01-20T07:34:50Z","success":1,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file"}],"scopus_import":"1","quality_controlled":"1","date_published":"2022-09-23T00:00:00Z","author":[{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicolas Adrien","last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","last_name":"Sarac","first_name":"Naci E"}],"alternative_title":["LNCS"],"date_updated":"2023-08-03T13:38:46Z","doi":"10.1007/978-3-031-17196-3_11","article_processing_charge":"Yes","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"conference":{"end_date":"2022-09-30","name":"RV: Runtime Verification","start_date":"2022-09-28","location":"Tbilisi, Georgia"},"file_date_updated":"2023-01-20T07:34:50Z","citation":{"ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Abstract monitors for quantitative specifications. In: <i>22nd International Conference on Runtime Verification</i>. Vol 13498. Springer Nature; 2022:200-220. doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2022. Abstract monitors for quantitative specifications. 22nd International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 13498, 200–220.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 22nd International Conference on Runtime Verification, Springer Nature, 2022, pp. 200–220.","mla":"Henzinger, Thomas A., et al. “Abstract Monitors for Quantitative Specifications.” <i>22nd International Conference on Runtime Verification</i>, vol. 13498, Springer Nature, 2022, pp. 200–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Abstract Monitors for Quantitative Specifications.” In <i>22nd International Conference on Runtime Verification</i>, 13498:200–220. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Abstract monitors for quantitative specifications,” in <i>22nd International Conference on Runtime Verification</i>, Tbilisi, Georgia, 2022, vol. 13498, pp. 200–220.","apa":"Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2022). Abstract monitors for quantitative specifications. In <i>22nd International Conference on Runtime Verification</i> (Vol. 13498, pp. 200–220). Tbilisi, Georgia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>"},"publication_identifier":{"issn":["0302-9743"]},"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","oa":1,"status":"public","external_id":{"isi":["000866539700011"]},"_id":"11775","has_accepted_license":"1","year":"2022","page":"200-220","volume":13498,"type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Quantitative monitoring can be universal and approximate: For every finite sequence of observations, the specification provides a value and the monitor outputs a best-effort approximation of it. The quality of the approximation may depend on the resources that are available to the monitor. By taking to the limit the sequences of specification values and monitor outputs, we obtain precision-resource trade-offs also for limit monitoring. This paper provides a formal framework for studying such trade-offs using an abstract interpretation for monitors: For each natural number n, the aggregate semantics of a monitor at time n is an equivalence relation over all sequences of at most n observations so that two equivalent sequences are indistinguishable to the monitor and thus mapped to the same output. This abstract interpretation of quantitative monitors allows us to measure the number of equivalence classes (or “resource use”) that is necessary for a certain precision up to a certain time, or at any time. Our framework offers several insights. For example, we identify a family of specifications for which any resource-optimal exact limit monitor is independent of any error permitted over finite traces. Moreover, we present a specification for which any resource-optimal approximate limit monitor does not minimize its resource use at any time. "}],"oa_version":"Published Version","ec_funded":1,"date_created":"2022-08-08T17:09:09Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"title":"Abstract monitors for quantitative specifications","publication":"22nd International Conference on Runtime Verification","publisher":"Springer Nature"},{"ec_funded":1,"date_created":"2022-08-10T15:51:19Z","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"title":"High-dimensional expansion and crossing numbers of simplicial complexes","publisher":"Institute of Science and Technology","abstract":[{"lang":"eng","text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise."}],"_id":"11777","supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","first_name":"Uli"}],"has_accepted_license":"1","year":"2022","page":"170","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","citation":{"apa":"Wild, P. (2022). <i>High-dimensional expansion and crossing numbers of simplicial complexes</i>. Institute of Science and Technology. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>.","ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022.","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022.","mla":"Wild, Pascal. <i>High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes</i>. Institute of Science and Technology, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>.","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology.","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>"},"publication_identifier":{"isbn":["978-3-99078-021-3"],"issn":["2663-337X"]},"status":"public","oa":1,"file_date_updated":"2022-08-11T16:09:19Z","degree_awarded":"PhD","date_published":"2022-08-11T00:00:00Z","author":[{"last_name":"Wild","first_name":"Pascal","id":"4C20D868-F248-11E8-B48F-1D18A9856A87","full_name":"Wild, Pascal"}],"article_processing_charge":"No","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:11777","date_updated":"2023-06-22T09:56:36Z","file":[{"date_updated":"2022-08-10T15:34:04Z","file_id":"11780","file_size":16828,"file_name":"flags.py","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","relation":"supplementary_material","description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","access_level":"open_access","creator":"pwild","content_type":"text/x-python","date_created":"2022-08-10T15:34:04Z"},{"file_name":"lowerbound.cpp","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","file_size":12226,"file_id":"11781","date_updated":"2022-08-10T15:34:10Z","date_created":"2022-08-10T15:34:10Z","content_type":"text/x-c++src","access_level":"open_access","creator":"pwild","description":"Code for proof of Lemma 8.20 in Thesis","relation":"supplementary_material"},{"relation":"supplementary_material","description":"Code for proof of Proposition 7.9 in Thesis","creator":"pwild","access_level":"open_access","content_type":"text/x-python","date_created":"2022-08-10T15:34:17Z","file_id":"11782","date_updated":"2022-08-10T15:34:17Z","file_size":3240,"file_name":"upperbound.py","checksum":"4cf81455c49e5dec3b9b2e3980137eeb"},{"content_type":"application/pdf","date_created":"2022-08-11T16:08:33Z","relation":"main_file","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","access_level":"open_access","creator":"pwild","file_size":5086282,"file_name":"finalthesisPascalWildPDFA.pdf","checksum":"4e96575b10cbe4e0d0db2045b2847774","date_updated":"2022-08-11T16:08:33Z","file_id":"11809"},{"checksum":"92d94842a1fb6dca5808448137573b2e","file_name":"ThesisSubmission.zip","file_size":18150068,"date_updated":"2022-08-11T16:09:19Z","file_id":"11810","date_created":"2022-08-11T16:09:19Z","content_type":"application/zip","access_level":"closed","creator":"pwild","relation":"source_file"}],"publication_status":"published","month":"08","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"ddc":["500","516","514"],"day":"11"},{"isi":1,"month":"06","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"ddc":["530"],"day":"10","intvolume":"        63","file":[{"success":1,"date_created":"2022-08-11T07:03:02Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","file_name":"2022_JourMathPhysics_Bossmann.pdf","checksum":"d0d32c338c1896680174be88c70968fa","file_size":5957888,"date_updated":"2022-08-11T07:03:02Z","file_id":"11784"}],"publication_status":"published","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"scopus_import":"1","quality_controlled":"1","date_published":"2022-06-10T00:00:00Z","author":[{"full_name":"Bossmann, Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","orcid":"0000-0002-6854-1343","last_name":"Bossmann"}],"article_processing_charge":"Yes (via OA deal)","date_updated":"2023-08-03T12:46:28Z","doi":"10.1063/5.0089983","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-08-11T07:03:02Z","article_number":"061102","citation":{"ama":"Bossmann L. Low-energy spectrum and dynamics of the weakly interacting Bose gas. <i>Journal of Mathematical Physics</i>. 2022;63(6). doi:<a href=\"https://doi.org/10.1063/5.0089983\">10.1063/5.0089983</a>","mla":"Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting Bose Gas.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 6, 061102, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0089983\">10.1063/5.0089983</a>.","short":"L. Bossmann, Journal of Mathematical Physics 63 (2022).","ista":"Bossmann L. 2022. Low-energy spectrum and dynamics of the weakly interacting Bose gas. Journal of Mathematical Physics. 63(6), 061102.","chicago":"Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting Bose Gas.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0089983\">https://doi.org/10.1063/5.0089983</a>.","ieee":"L. Bossmann, “Low-energy spectrum and dynamics of the weakly interacting Bose gas,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 6. AIP Publishing, 2022.","apa":"Bossmann, L. (2022). Low-energy spectrum and dynamics of the weakly interacting Bose gas. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0089983\">https://doi.org/10.1063/5.0089983</a>"},"publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]},"status":"public","oa":1,"acknowledgement":"The author thanks Nataˇsa Pavlovic, Sören Petrat, Peter Pickl, Robert Seiringer, and Avy Soffer for the collaboration on Refs. 1, 2 and 21. Funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skℓodowska-Curie Grant Agreement\r\nNo. 754411 is gratefully acknowledged.","issue":"6","article_type":"original","external_id":{"isi":["000809648100002"],"arxiv":["2203.00730"]},"_id":"11783","year":"2022","has_accepted_license":"1","volume":63,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","abstract":[{"lang":"eng","text":"We consider a gas of N bosons with interactions in the mean-field scaling regime. We review the proof of an asymptotic expansion of its low-energy spectrum, eigenstates, and dynamics, which provides corrections to Bogoliubov theory to all orders in 1/ N. This is based on joint works with Petrat, Pickl, Seiringer, and Soffer. In addition, we derive a full asymptotic expansion of the ground state one-body reduced density matrix."}],"arxiv":1,"date_created":"2022-08-11T06:37:52Z","ec_funded":1,"oa_version":"Published Version","publication":"Journal of Mathematical Physics","title":"Low-energy spectrum and dynamics of the weakly interacting Bose gas","department":[{"_id":"RoSe"}],"publisher":"AIP Publishing"},{"month":"12","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"language":[{"iso":"eng"}],"ddc":["510"],"day":"01","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2020-05-04T10:33:42Z","date_updated":"2020-07-14T12:48:03Z","file_id":"7796","file_size":263926,"checksum":"f53e71fd03744075adcd0b8fc1b8423d","file_name":"2020_EuropMathematics_Akopyan.pdf"}],"publication_status":"published","intvolume":"         8","quality_controlled":"1","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","date_updated":"2024-02-22T15:58:42Z","doi":"10.1007/s40879-020-00405-0","date_published":"2022-12-01T00:00:00Z","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","first_name":"Arseniy"},{"full_name":"Karasev, Roman","first_name":"Roman","last_name":"Karasev"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:48:03Z","publication_identifier":{"eissn":["2199-6768"],"issn":["2199-675X"]},"citation":{"ama":"Akopyan A, Karasev R. When different norms lead to same billiard trajectories? <i>European Journal of Mathematics</i>. 2022;8(4):1309-1312. doi:<a href=\"https://doi.org/10.1007/s40879-020-00405-0\">10.1007/s40879-020-00405-0</a>","ista":"Akopyan A, Karasev R. 2022. When different norms lead to same billiard trajectories? European Journal of Mathematics. 8(4), 1309–1312.","short":"A. Akopyan, R. Karasev, European Journal of Mathematics 8 (2022) 1309–1312.","mla":"Akopyan, Arseniy, and Roman Karasev. “When Different Norms Lead to Same Billiard Trajectories?” <i>European Journal of Mathematics</i>, vol. 8, no. 4, Springer Nature, 2022, pp. 1309–12, doi:<a href=\"https://doi.org/10.1007/s40879-020-00405-0\">10.1007/s40879-020-00405-0</a>.","ieee":"A. Akopyan and R. Karasev, “When different norms lead to same billiard trajectories?,” <i>European Journal of Mathematics</i>, vol. 8, no. 4. Springer Nature, pp. 1309–1312, 2022.","chicago":"Akopyan, Arseniy, and Roman Karasev. “When Different Norms Lead to Same Billiard Trajectories?” <i>European Journal of Mathematics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40879-020-00405-0\">https://doi.org/10.1007/s40879-020-00405-0</a>.","apa":"Akopyan, A., &#38; Karasev, R. (2022). When different norms lead to same billiard trajectories? <i>European Journal of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40879-020-00405-0\">https://doi.org/10.1007/s40879-020-00405-0</a>"},"issue":"4","external_id":{"arxiv":["1912.12685"]},"article_type":"original","acknowledgement":"AA was supported by European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). RK was supported by the Federal professorship program Grant 1.456.2016/1.4 and the Russian Foundation for Basic Research Grants 18-01-00036 and 19-01-00169. Open access funding provided by Institute of Science and Technology (IST Austria). The authors thank Alexey Balitskiy, Milena Radnović, and Serge Tabachnikov for useful discussions.","status":"public","oa":1,"year":"2022","has_accepted_license":"1","_id":"7791","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":8,"page":"1309 - 1312","abstract":[{"lang":"eng","text":"Extending a result of Milena Radnovic and Serge Tabachnikov, we establish conditionsfor two different non-symmetric norms to define the same billiard reflection law."}],"arxiv":1,"ec_funded":1,"date_created":"2020-05-03T22:00:48Z","oa_version":"Published Version","publisher":"Springer Nature","publication":"European Journal of Mathematics","department":[{"_id":"HeEd"}],"title":"When different norms lead to same billiard trajectories?"},{"publisher":"Cold Spring Harbor Laboratory","publication":"bioRxiv","department":[{"_id":"TiVo"}],"title":"High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating","date_created":"2020-07-16T12:24:28Z","oa_version":"Preprint","article_processing_charge":"No","date_updated":"2024-03-06T12:03:59Z","doi":"10.1101/2020.01.08.898528","author":[{"full_name":"Podlaski, William F.","first_name":"William F.","orcid":"0000-0001-6619-7502","last_name":"Podlaski"},{"full_name":"Agnes, Everton J.","first_name":"Everton J.","last_name":"Agnes","orcid":"0000-0001-7184-7311"},{"first_name":"Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"date_published":"2022-12-21T00:00:00Z","abstract":[{"lang":"eng","text":"Context, such as behavioral state, is known to modulate memory formation and retrieval, but is usually ignored in associative memory models. Here, we propose several types of contextual modulation for associative memory networks that greatly increase their performance. In these networks, context inactivates specific neurons and connections, which modulates the effective connectivity of the network. Memories are stored only by the active components, thereby reducing interference from memories acquired in other contexts. Such networks exhibit several beneficial characteristics, including enhanced memory capacity, high robustness to noise, increased robustness to memory overloading, and better memory retention during continual learning. Furthermore, memories can be biased to have different relative strengths, or even gated on or off, according to contextual cues, providing a candidate model for cognitive control of memory and efficient memory search. An external context-encoding network can dynamically switch the memory network to a desired state, which we liken to experimentally observed contextual signals in prefrontal cortex and hippocampus. Overall, our work illustrates the benefits of organizing memory around context, and provides an important link between behavioral studies of memory and mechanistic details of neural circuits.</jats:p><jats:sec><jats:title>SIGNIFICANCE</jats:title><jats:p>Memory is context dependent — both encoding and recall vary in effectiveness and speed depending on factors like location and brain state during a task. We apply this idea to a simple computational model of associative memory through contextual gating of neurons and synaptic connections. Intriguingly, this results in several advantages, including vastly enhanced memory capacity, better robustness, and flexible memory gating. Our model helps to explain (i) how gating and inhibition contribute to memory processes, (ii) how memory access dynamically changes over time, and (iii) how context representations, such as those observed in hippocampus and prefrontal cortex, may interact with and control memory processes."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","year":"2022","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.01.08.898528 "}],"_id":"8125","day":"21","oa":1,"status":"public","month":"12","language":[{"iso":"eng"}],"locked":"1","citation":{"ama":"Podlaski WF, Agnes EJ, Vogels TP. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. <i>bioRxiv</i>. 2022. doi:<a href=\"https://doi.org/10.1101/2020.01.08.898528\">10.1101/2020.01.08.898528</a>","ista":"Podlaski WF, Agnes EJ, Vogels TP. 2022. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. bioRxiv, <a href=\"https://doi.org/10.1101/2020.01.08.898528\">10.1101/2020.01.08.898528</a>.","mla":"Podlaski, William F., et al. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2022, doi:<a href=\"https://doi.org/10.1101/2020.01.08.898528\">10.1101/2020.01.08.898528</a>.","short":"W.F. Podlaski, E.J. Agnes, T.P. Vogels, BioRxiv (2022).","ieee":"W. F. Podlaski, E. J. Agnes, and T. P. Vogels, “High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2022.","chicago":"Podlaski, William F., Everton J. Agnes, and Tim P Vogels. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2022. <a href=\"https://doi.org/10.1101/2020.01.08.898528\">https://doi.org/10.1101/2020.01.08.898528</a>.","apa":"Podlaski, W. F., Agnes, E. J., &#38; Vogels, T. P. (2022). High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.01.08.898528\">https://doi.org/10.1101/2020.01.08.898528</a>"}},{"file_date_updated":"2021-03-16T23:30:06Z","scopus_import":"1","quality_controlled":"1","date_published":"2022-01-01T00:00:00Z","author":[{"full_name":"Shehu, Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu"},{"first_name":"Olaniyi S.","last_name":"Iyiola","full_name":"Iyiola, Olaniyi S."}],"article_processing_charge":"No","date_updated":"2024-03-05T14:01:52Z","doi":"10.1080/00036811.2020.1736287","intvolume":"       101","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2020-10-12T10:42:54Z","embargo":"2021-03-15","file_id":"8648","date_updated":"2021-03-16T23:30:06Z","file_size":4282586,"checksum":"869efe8cb09505dfa6012f67d20db63d","file_name":"2020_ApplicAnalysis_Shehu.pdf"}],"publication_status":"published","isi":1,"month":"01","language":[{"iso":"eng"}],"project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"ddc":["510","515","518"],"day":"01","date_created":"2020-03-09T07:06:52Z","ec_funded":1,"oa_version":"Submitted Version","publication":"Applicable Analysis","title":"Weak convergence for variational inequalities with inertial-type method","department":[{"_id":"VlKo"}],"publisher":"Taylor & Francis","abstract":[{"text":"Weak convergence of inertial iterative method for solving variational inequalities is the focus of this paper. The cost function is assumed to be non-Lipschitz and monotone. We propose a projection-type method with inertial terms and give weak convergence analysis under appropriate conditions. Some test results are performed and compared with relevant methods in the literature to show the efficiency and advantages given by our proposed methods.","lang":"eng"}],"arxiv":1,"_id":"7577","year":"2022","has_accepted_license":"1","volume":101,"page":"192-216","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","citation":{"short":"Y. Shehu, O.S. Iyiola, Applicable Analysis 101 (2022) 192–216.","mla":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” <i>Applicable Analysis</i>, vol. 101, no. 1, Taylor &#38; Francis, 2022, pp. 192–216, doi:<a href=\"https://doi.org/10.1080/00036811.2020.1736287\">10.1080/00036811.2020.1736287</a>.","ista":"Shehu Y, Iyiola OS. 2022. Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. 101(1), 192–216.","ama":"Shehu Y, Iyiola OS. Weak convergence for variational inequalities with inertial-type method. <i>Applicable Analysis</i>. 2022;101(1):192-216. doi:<a href=\"https://doi.org/10.1080/00036811.2020.1736287\">10.1080/00036811.2020.1736287</a>","apa":"Shehu, Y., &#38; Iyiola, O. S. (2022). Weak convergence for variational inequalities with inertial-type method. <i>Applicable Analysis</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/00036811.2020.1736287\">https://doi.org/10.1080/00036811.2020.1736287</a>","ieee":"Y. Shehu and O. S. Iyiola, “Weak convergence for variational inequalities with inertial-type method,” <i>Applicable Analysis</i>, vol. 101, no. 1. Taylor &#38; Francis, pp. 192–216, 2022.","chicago":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” <i>Applicable Analysis</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/00036811.2020.1736287\">https://doi.org/10.1080/00036811.2020.1736287</a>."},"publication_identifier":{"eissn":["1563-504X"],"issn":["0003-6811"]},"acknowledgement":"The project of the first author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","oa":1,"status":"public","issue":"1","external_id":{"arxiv":["2101.08057"],"isi":["000518364100001"]},"article_type":"original"},{"file_date_updated":"2023-09-25T08:56:06Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.gim.2022.07.013","date_updated":"2023-09-25T08:57:07Z","article_processing_charge":"No","date_published":"2022-10-01T00:00:00Z","author":[{"first_name":"Elisa","last_name":"Cali","full_name":"Cali, Elisa"},{"full_name":"Lin, Sheng-Jia","first_name":"Sheng-Jia","last_name":"Lin"},{"full_name":"Rocca, Clarissa","first_name":"Clarissa","last_name":"Rocca"},{"first_name":"Yavuz","last_name":"Sahin","full_name":"Sahin, Yavuz"},{"first_name":"Aisha","last_name":"Al Shamsi","full_name":"Al Shamsi, Aisha"},{"full_name":"El Chehadeh, Salima","last_name":"El Chehadeh","first_name":"Salima"},{"first_name":"Myriam","last_name":"Chaabouni","full_name":"Chaabouni, Myriam"},{"first_name":"Kshitij","last_name":"Mankad","full_name":"Mankad, Kshitij"},{"first_name":"Evangelia","last_name":"Galanaki","full_name":"Galanaki, Evangelia"},{"full_name":"Efthymiou, Stephanie","last_name":"Efthymiou","first_name":"Stephanie"},{"full_name":"Sudhakar, Sniya","first_name":"Sniya","last_name":"Sudhakar"},{"full_name":"Athanasiou-Fragkouli, Alkyoni","first_name":"Alkyoni","last_name":"Athanasiou-Fragkouli"},{"first_name":"Tamer","last_name":"Celik","full_name":"Celik, Tamer"},{"last_name":"Narli","first_name":"Nejat","full_name":"Narli, Nejat"},{"full_name":"Bianca, Sebastiano","first_name":"Sebastiano","last_name":"Bianca"},{"first_name":"David","last_name":"Murphy","full_name":"Murphy, David"},{"first_name":"Francisco Martins De Carvalho","last_name":"Moreira","full_name":"Moreira, Francisco Martins De Carvalho"},{"full_name":"Accogli, Andrea","last_name":"Accogli","first_name":"Andrea"},{"full_name":"Petree, Cassidy","last_name":"Petree","first_name":"Cassidy"},{"id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","full_name":"Huang, Kevin","last_name":"Huang","orcid":"0000-0002-2512-7812","first_name":"Kevin"},{"full_name":"Monastiri, Kamel","first_name":"Kamel","last_name":"Monastiri"},{"first_name":"Masoud","last_name":"Edizadeh","full_name":"Edizadeh, Masoud"},{"last_name":"Nardello","first_name":"Rosaria","full_name":"Nardello, Rosaria"},{"first_name":"Marzia","last_name":"Ognibene","full_name":"Ognibene, Marzia"},{"last_name":"De Marco","first_name":"Patrizia","full_name":"De Marco, Patrizia"},{"last_name":"Ruggieri","first_name":"Martino","full_name":"Ruggieri, Martino"},{"last_name":"Zara","first_name":"Federico","full_name":"Zara, Federico"},{"full_name":"Striano, Pasquale","last_name":"Striano","first_name":"Pasquale"},{"full_name":"Sahin, Yavuz","last_name":"Sahin","first_name":"Yavuz"},{"last_name":"Al-Gazali","first_name":"Lihadh","full_name":"Al-Gazali, Lihadh"},{"last_name":"Warde","first_name":"Marie Therese Abi","full_name":"Warde, Marie Therese Abi"},{"last_name":"Gerard","first_name":"Benedicte","full_name":"Gerard, Benedicte"},{"full_name":"Zifarelli, Giovanni","last_name":"Zifarelli","first_name":"Giovanni"},{"last_name":"Beetz","first_name":"Christian","full_name":"Beetz, Christian"},{"last_name":"Fortuna","first_name":"Sara","full_name":"Fortuna, Sara"},{"full_name":"Soler, Miguel","first_name":"Miguel","last_name":"Soler"},{"full_name":"Valente, Enza Maria","first_name":"Enza Maria","last_name":"Valente"},{"full_name":"Varshney, Gaurav","first_name":"Gaurav","last_name":"Varshney"},{"first_name":"Reza","last_name":"Maroofian","full_name":"Maroofian, Reza"},{"last_name":"Salpietro","first_name":"Vincenzo","full_name":"Salpietro, Vincenzo"},{"full_name":"Houlden, Henry","last_name":"Houlden","first_name":"Henry"},{"last_name":"Grp","first_name":"SYNaPS Study","full_name":"Grp, SYNaPS Study"}],"quality_controlled":"1","scopus_import":"1","keyword":["Human mediator complex","MED11","MEDopathies"],"publication_status":"published","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2023-09-25T08:56:06Z","success":1,"date_updated":"2023-09-25T08:56:06Z","file_id":"14371","file_size":1434037,"checksum":"8117175a89129eb5022d81ffe7625f9f","file_name":"2022_GeneticsMedicine_Calin.pdf"}],"intvolume":"        24","day":"01","ddc":["570"],"language":[{"iso":"eng"}],"month":"10","publisher":"Elsevier","department":[{"_id":"GradSch"}],"title":"A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease","publication":"Genetics in Medicine","oa_version":"Published Version","date_created":"2023-09-20T20:57:18Z","extern":"1","abstract":[{"text":"Purpose: The mediator (MED) multisubunit-complex modulates the activity of the transcriptional machinery, and genetic defects in different MED subunits (17, 20, 27) have been implicated in neurologic diseases. In this study, we identified a recurrent homozygous variant in MED11 (c.325C>T; p.Arg109Ter) in 7 affected individuals from 5 unrelated families. Methods: To investigate the genetic cause of the disease, exome or genome sequencing were performed in 5 unrelated families identified via different research networks and Matchmaker Exchange. Deep clinical and brain imaging evaluations were performed by clinical pediatric neurologists and neuroradiologists. The functional effect of the candidate variant on both MED11 RNA and protein was assessed using reverse transcriptase polymerase chain reaction and western blotting using fibroblast cell lines derived from 1 affected individual and controls and through computational approaches. Knockouts in zebrafish were generated using clustered regularly interspaced short palindromic repeats/Cas9. Results: The disease was characterized by microcephaly, profound neurodevelopmental impairment, exaggerated startle response, myoclonic seizures, progressive widespread neurodegeneration, and premature death. Functional studies on patient-derived fibroblasts did not show a loss of protein function but rather disruption of the C-terminal of MED11, likely impairing binding to other MED subunits. A zebrafish knockout model recapitulates key clinical phenotypes. Conclusion: Loss of the C-terminal of MED subunit 11 may affect its binding efficiency to other MED subunits, thus implicating the MED-complex stability in brain development and neurodegeneration. (C) 2022 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics.","lang":"eng"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2194-2203","volume":24,"year":"2022","has_accepted_license":"1","_id":"14355","article_type":"original","issue":"10","status":"public","oa":1,"publication_identifier":{"issn":["1098-3600"]},"citation":{"short":"E. Cali, S.-J. Lin, C. Rocca, Y. Sahin, A. Al Shamsi, S. El Chehadeh, M. Chaabouni, K. Mankad, E. Galanaki, S. Efthymiou, S. Sudhakar, A. Athanasiou-Fragkouli, T. Celik, N. Narli, S. Bianca, D. Murphy, F.M.D.C. Moreira, A. Accogli, C. Petree, K. Huang, K. Monastiri, M. Edizadeh, R. Nardello, M. Ognibene, P. De Marco, M. Ruggieri, F. Zara, P. Striano, Y. Sahin, L. Al-Gazali, M.T.A. Warde, B. Gerard, G. Zifarelli, C. Beetz, S. Fortuna, M. Soler, E.M. Valente, G. Varshney, R. Maroofian, V. Salpietro, H. Houlden, Syn.S. Grp, Genetics in Medicine 24 (2022) 2194–2203.","mla":"Cali, Elisa, et al. “A Homozygous MED11 C-Terminal Variant Causes a Lethal Neurodegenerative Disease.” <i>Genetics in Medicine</i>, vol. 24, no. 10, Elsevier, 2022, pp. 2194–203, doi:<a href=\"https://doi.org/10.1016/j.gim.2022.07.013\">10.1016/j.gim.2022.07.013</a>.","ista":"Cali E, Lin S-J, Rocca C, Sahin Y, Al Shamsi A, El Chehadeh S, Chaabouni M, Mankad K, Galanaki E, Efthymiou S, Sudhakar S, Athanasiou-Fragkouli A, Celik T, Narli N, Bianca S, Murphy D, Moreira FMDC, Accogli A, Petree C, Huang K, Monastiri K, Edizadeh M, Nardello R, Ognibene M, De Marco P, Ruggieri M, Zara F, Striano P, Sahin Y, Al-Gazali L, Warde MTA, Gerard B, Zifarelli G, Beetz C, Fortuna S, Soler M, Valente EM, Varshney G, Maroofian R, Salpietro V, Houlden H, Grp SynS. 2022. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. 24(10), 2194–2203.","ama":"Cali E, Lin S-J, Rocca C, et al. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. <i>Genetics in Medicine</i>. 2022;24(10):2194-2203. doi:<a href=\"https://doi.org/10.1016/j.gim.2022.07.013\">10.1016/j.gim.2022.07.013</a>","apa":"Cali, E., Lin, S.-J., Rocca, C., Sahin, Y., Al Shamsi, A., El Chehadeh, S., … Grp, Syn. S. (2022). A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. <i>Genetics in Medicine</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gim.2022.07.013\">https://doi.org/10.1016/j.gim.2022.07.013</a>","chicago":"Cali, Elisa, Sheng-Jia Lin, Clarissa Rocca, Yavuz Sahin, Aisha Al Shamsi, Salima El Chehadeh, Myriam Chaabouni, et al. “A Homozygous MED11 C-Terminal Variant Causes a Lethal Neurodegenerative Disease.” <i>Genetics in Medicine</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.gim.2022.07.013\">https://doi.org/10.1016/j.gim.2022.07.013</a>.","ieee":"E. Cali <i>et al.</i>, “A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease,” <i>Genetics in Medicine</i>, vol. 24, no. 10. Elsevier, pp. 2194–2203, 2022."}}]