[{"citation":{"short":"G.N. Hibshman, J.P.K. Bravo, M.M. Hooper, T.L. Dangerfield, H. Zhang, I.J. Finkelstein, K.A. Johnson, D.W. Taylor, Nature Communications 15 (2024).","chicago":"Hibshman, Grace N., Jack Peter Kelly Bravo, Matthew M. Hooper, Tyler L. Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David W. Taylor. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47830-3\">https://doi.org/10.1038/s41467-024-47830-3</a>.","ista":"Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW. 2024. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nature Communications. 15, 3663.","ama":"Hibshman GN, Bravo JPK, Hooper MM, et al. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47830-3\">10.1038/s41467-024-47830-3</a>","apa":"Hibshman, G. N., Bravo, J. P. K., Hooper, M. M., Dangerfield, T. L., Zhang, H., Finkelstein, I. J., … Taylor, D. W. (2024). Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47830-3\">https://doi.org/10.1038/s41467-024-47830-3</a>","ieee":"G. N. Hibshman <i>et al.</i>, “Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","mla":"Hibshman, Grace N., et al. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” <i>Nature Communications</i>, vol. 15, 3663, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47830-3\">10.1038/s41467-024-47830-3</a>."},"date_published":"2024-04-30T00:00:00Z","year":"2024","status":"public","extern":"1","publication_status":"published","language":[{"iso":"eng"}],"external_id":{"pmid":["38688943"]},"quality_controlled":"1","author":[{"full_name":"Hibshman, Grace N.","first_name":"Grace N.","last_name":"Hibshman"},{"last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly","first_name":"Jack Peter Kelly"},{"full_name":"Hooper, Matthew M.","first_name":"Matthew M.","last_name":"Hooper"},{"last_name":"Dangerfield","first_name":"Tyler L.","full_name":"Dangerfield, Tyler L."},{"full_name":"Zhang, Hongshan","first_name":"Hongshan","last_name":"Zhang"},{"full_name":"Finkelstein, Ilya J.","first_name":"Ilya J.","last_name":"Finkelstein"},{"full_name":"Johnson, Kenneth A.","first_name":"Kenneth A.","last_name":"Johnson"},{"last_name":"Taylor","full_name":"Taylor, David W.","first_name":"David W."}],"intvolume":"        15","publisher":"Springer Nature","abstract":[{"text":"CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for <jats:italic>Streptococcus pyogenes</jats:italic> Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing.","lang":"eng"}],"oa":1,"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-14T12:34:26Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-024-47830-3"}],"title":"Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9","publication":"Nature Communications","date_created":"2024-06-04T06:42:07Z","_id":"17113","volume":15,"day":"30","doi":"10.1038/s41467-024-47830-3","publication_identifier":{"issn":["2041-1723"]},"article_number":"3663","article_type":"original","article_processing_charge":"Yes","scopus_import":"1","type":"journal_article","month":"04","oa_version":"Published Version"},{"month":"04","type":"journal_article","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"Yes","article_type":"original","article_number":"3324","day":"18","doi":"10.1038/s41467-024-47506-y","publication_identifier":{"issn":["2041-1723"]},"volume":15,"_id":"17114","publication":"Nature Communications","title":"RNA targeting and cleavage by the type III-Dv CRISPR effector complex","date_created":"2024-06-04T06:43:02Z","pmid":1,"date_updated":"2024-06-04T07:05:26Z","main_file_link":[{"url":"https://doi.org/10.1038/s41467-024-47506-y","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction<jats:sup>1–5</jats:sup>. Target RNA cleavage at regular intervals is characteristic of type III effector complexes<jats:sup>6–8</jats:sup>. Here, we determine the structures of the <jats:italic>Synechocystis</jats:italic> type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors<jats:sup>9,10</jats:sup>, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2′-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes.","lang":"eng"}],"oa":1,"publisher":"Springer Nature","author":[{"first_name":"Evan A.","full_name":"Schwartz, Evan A.","last_name":"Schwartz"},{"first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","last_name":"Bravo"},{"last_name":"Ahsan","full_name":"Ahsan, Mohd","first_name":"Mohd"},{"last_name":"Macias","first_name":"Luis A.","full_name":"Macias, Luis A."},{"full_name":"McCafferty, Caitlyn L.","first_name":"Caitlyn L.","last_name":"McCafferty"},{"first_name":"Tyler L.","full_name":"Dangerfield, Tyler L.","last_name":"Dangerfield"},{"full_name":"Walker, Jada N.","first_name":"Jada N.","last_name":"Walker"},{"last_name":"Brodbelt","first_name":"Jennifer S.","full_name":"Brodbelt, Jennifer S."},{"first_name":"Giulia","full_name":"Palermo, Giulia","last_name":"Palermo"},{"last_name":"Fineran","full_name":"Fineran, Peter C.","first_name":"Peter C."},{"last_name":"Fagerlund","first_name":"Robert D.","full_name":"Fagerlund, Robert D."},{"last_name":"Taylor","full_name":"Taylor, David W.","first_name":"David W."}],"intvolume":"        15","language":[{"iso":"eng"}],"external_id":{"pmid":["38637512"]},"quality_controlled":"1","citation":{"short":"E.A. Schwartz, J.P.K. Bravo, M. Ahsan, L.A. Macias, C.L. McCafferty, T.L. Dangerfield, J.N. Walker, J.S. Brodbelt, G. Palermo, P.C. Fineran, R.D. Fagerlund, D.W. Taylor, Nature Communications 15 (2024).","chicago":"Schwartz, Evan A., Jack Peter Kelly Bravo, Mohd Ahsan, Luis A. Macias, Caitlyn L. McCafferty, Tyler L. Dangerfield, Jada N. Walker, et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR Effector Complex.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47506-y\">https://doi.org/10.1038/s41467-024-47506-y</a>.","ista":"Schwartz EA, Bravo JPK, Ahsan M, Macias LA, McCafferty CL, Dangerfield TL, Walker JN, Brodbelt JS, Palermo G, Fineran PC, Fagerlund RD, Taylor DW. 2024. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature Communications. 15, 3324.","ieee":"E. A. Schwartz <i>et al.</i>, “RNA targeting and cleavage by the type III-Dv CRISPR effector complex,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ama":"Schwartz EA, Bravo JPK, Ahsan M, et al. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47506-y\">10.1038/s41467-024-47506-y</a>","apa":"Schwartz, E. A., Bravo, J. P. K., Ahsan, M., Macias, L. A., McCafferty, C. L., Dangerfield, T. L., … Taylor, D. W. (2024). RNA targeting and cleavage by the type III-Dv CRISPR effector complex. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47506-y\">https://doi.org/10.1038/s41467-024-47506-y</a>","mla":"Schwartz, Evan A., et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR Effector Complex.” <i>Nature Communications</i>, vol. 15, 3324, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47506-y\">10.1038/s41467-024-47506-y</a>."},"status":"public","extern":"1","publication_status":"published","year":"2024","date_published":"2024-04-18T00:00:00Z"},{"scopus_import":"1","ddc":["570"],"department":[{"_id":"PeJo"}],"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","type":"journal_article","month":"05","publication_identifier":{"eissn":["1471-244X"]},"day":"29","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1186/s12888-024-05849-2","_id":"17122","volume":24,"article_type":"original","article_number":"401","oa":1,"abstract":[{"text":"Background: Motor alterations and lowered physical activity are common in affective disorders. Previous research has indicated a link between depressive symptoms and declining muscle strength primarily focusing on the elderly but not younger individuals. Thus, we aimed to evaluate the relationship between mood and muscle strength in a sample of N = 73 young to middle-aged hospitalized patients (18–49 years, mean age 30.7 years) diagnosed with major depressive, bipolar and schizoaffective disorder, with a focus on moderating effects of psychopharmacotherapy. The study was carried out as a prospective observational study at a German psychiatric university hospital between September 2021 and March 2022.\r\nMethods: Employing a standardized strength circuit consisting of computerized strength training devices, we measured the maximal muscle strength (Fmax) using three repetitions maximum across four muscle regions (abdomen, arm, back, leg) at three time points (t1-t3) over four weeks accompanied by psychometric testing (MADRS, BPRS, YRMS) and blood lipid profiling in a clinical setting. For analysis of psychopharmacotherapy, medication was split into activating (AM) and inhibiting (IM) medication and dosages were normalized by the respective WHO defined daily dose.\r\nResults: While we observed a significant decrease of the MADRS score and increase of the relative total Fmax (rTFmax) in the first two weeks (t1-t2) but not later (both p < .001), we did not reveal a significant bivariate correlation between disease severity (MADRS) and muscle strength (rTFmax) at any of the timepoints. Individuals with longer disease history displayed reduced rTFmax (p = .048). IM was significantly associated with decreased rTFmax (p = .032). Regression models provide a more substantial effect of gender, age, and IM on muscle strength than the depressive episode itself (p < .001).\r\nConclusions: The results of the study indicate that disease severity and muscle strength are not associated in young to middle-aged inpatients with affective disorders using a strength circuit as observational measurement. Future research will be needed to differentiate the effect of medication, gender, and age on muscle strength and to develop interventions for prevention of muscle weakness, especially in younger patients with chronic affective illnesses.","lang":"eng"}],"file":[{"date_created":"2024-06-10T10:44:26Z","file_id":"17131","success":1,"date_updated":"2024-06-10T10:44:26Z","access_level":"open_access","checksum":"5df60d3c9388955c5b682ea34748d59d","relation":"main_file","content_type":"application/pdf","file_size":2320147,"file_name":"2024_BMCPsychiatry_Ramming.pdf","creator":"dernst"}],"publisher":"Springer Nature","date_created":"2024-06-09T22:01:01Z","acknowledgement":"This work was supported by the project ‘Fellows Ride’ of the Thomas Lurz und Dieter Schneider Stiftung and by the ‘Würzburger Bündnis gegen Depression’ (to S.K.-S).\r\nOpen Access funding enabled and organized by Projekt DEAL.","title":"The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study","publication":"BMC Psychiatry","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"date_updated":"2025-04-23T07:51:51Z","quality_controlled":"1","external_id":{"pmid":["38811916"]},"language":[{"iso":"eng"}],"year":"2024","date_published":"2024-05-29T00:00:00Z","publication_status":"published","status":"public","file_date_updated":"2024-06-10T10:44:26Z","citation":{"ieee":"H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, and S. Kittel-Schneider, “The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study,” <i>BMC Psychiatry</i>, vol. 24. Springer Nature, 2024.","apa":"Ramming, H., Theuerkauf, L., Hoos, O., Lichter, K., &#38; Kittel-Schneider, S. (2024). The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. <i>BMC Psychiatry</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12888-024-05849-2\">https://doi.org/10.1186/s12888-024-05849-2</a>","ama":"Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. <i>BMC Psychiatry</i>. 2024;24. doi:<a href=\"https://doi.org/10.1186/s12888-024-05849-2\">10.1186/s12888-024-05849-2</a>","ista":"Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. 2024. The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. BMC Psychiatry. 24, 401.","mla":"Ramming, Hannah, et al. “The Association between Maximal Muscle Strength, Disease Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective Disorders – a Prospective Pilot Study.” <i>BMC Psychiatry</i>, vol. 24, 401, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1186/s12888-024-05849-2\">10.1186/s12888-024-05849-2</a>.","short":"H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, S. Kittel-Schneider, BMC Psychiatry 24 (2024).","chicago":"Ramming, Hannah, Linda Theuerkauf, Olaf Hoos, Katharina Lichter, and Sarah Kittel-Schneider. “The Association between Maximal Muscle Strength, Disease Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective Disorders – a Prospective Pilot Study.” <i>BMC Psychiatry</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1186/s12888-024-05849-2\">https://doi.org/10.1186/s12888-024-05849-2</a>."},"has_accepted_license":"1","intvolume":"        24","author":[{"last_name":"Ramming","full_name":"Ramming, Hannah","first_name":"Hannah"},{"full_name":"Theuerkauf, Linda","first_name":"Linda","last_name":"Theuerkauf"},{"full_name":"Hoos, Olaf","first_name":"Olaf","last_name":"Hoos"},{"first_name":"Katharina","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","full_name":"Lichter, Katharina","orcid":"0000-0002-1485-0351","last_name":"Lichter"},{"last_name":"Kittel-Schneider","full_name":"Kittel-Schneider, Sarah","first_name":"Sarah"}]},{"oa_version":"Published Version","APC_amount":"2570,79 EUR","month":"06","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","isi":1,"ddc":["570"],"scopus_import":"1","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"article_number":"e2322326121","article_type":"original","volume":121,"project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"_id":"17123","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"doi":"10.1073/pnas.2322326121","day":"04","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"date_updated":"2025-09-08T07:51:01Z","acknowledgement":"We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns, Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 343-2022). This research was performed in part at the Aspen Center for Physics, which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon and Betty Moore Foundation Grant No. 2919.02.","date_created":"2024-06-09T22:01:02Z","related_material":{"link":[{"relation":"software","url":"https://github.com/dbrueckner/SelforgInformation"},{"relation":"press_release","description":"News on the ISTA website","url":"https://ista.ac.at/en/news/the-embryo-assembles-itself/"}]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"Information content and optimization of self-organized developmental systems","publisher":"National Academy of Sciences","oa":1,"abstract":[{"text":"A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction–diffusion models of self-organization. This paves a way toward a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and mechanical signaling processes.","lang":"eng"}],"file":[{"access_level":"open_access","date_updated":"2024-06-10T10:27:37Z","success":1,"file_id":"17130","date_created":"2024-06-10T10:27:37Z","creator":"dernst","file_name":"2024_PNAS_Brueckner.pdf","file_size":12329234,"relation":"main_file","content_type":"application/pdf","checksum":"59797a75db7beb3721ed7a4d14c241f9"}],"OA_place":"publisher","issue":"23","intvolume":"       121","author":[{"first_name":"David","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","last_name":"Brückner"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"has_accepted_license":"1","publication_status":"published","status":"public","date_published":"2024-06-04T00:00:00Z","year":"2024","OA_type":"hybrid","corr_author":"1","file_date_updated":"2024-06-10T10:27:37Z","citation":{"short":"D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","chicago":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>.","apa":"Brückner, D., &#38; Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>","ama":"Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(23). doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>","ieee":"D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23. National Academy of Sciences, 2024.","ista":"Brückner D, Tkačik G. 2024. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 121(23), e2322326121.","mla":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23, e2322326121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001244835000006"],"pmid":["38819997"]}},{"_id":"17124","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"volume":2024,"day":"01","tmp":{"short":"CC BY-NC-ND (3.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","image":"/images/cc_by_nc_nd.png"},"doi":"10.3791/66278","publication_identifier":{"issn":["1940-087X"]},"article_number":"e66278","article_type":"original","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"MaIb"}],"scopus_import":"1","ddc":["530"],"isi":1,"type":"journal_article","month":"05","oa_version":"Published Version","APC_amount":"4394,84 EUR","corr_author":"1","file_date_updated":"2025-02-17T15:08:55Z","OA_type":"hybrid","citation":{"short":"C. Fiedler, Y. Liu, M. Ibáñez, Journal of Visualized Experiments 2024 (2024).","chicago":"Fiedler, Christine, Yu Liu, and Maria Ibáñez. “Solution-Processed, Surface-Engineered, Polycrystalline CdSe-SnSe Exhibiting Low Thermal Conductivity.” <i>Journal of Visualized Experiments</i>. MyJove Corporation, 2024. <a href=\"https://doi.org/10.3791/66278\">https://doi.org/10.3791/66278</a>.","ista":"Fiedler C, Liu Y, Ibáñez M. 2024. Solution-processed, surface-engineered, polycrystalline CdSe-SnSe exhibiting low thermal conductivity. Journal of Visualized Experiments. 2024(207), e66278.","ieee":"C. Fiedler, Y. Liu, and M. Ibáñez, “Solution-processed, surface-engineered, polycrystalline CdSe-SnSe exhibiting low thermal conductivity,” <i>Journal of Visualized Experiments</i>, vol. 2024, no. 207. MyJove Corporation, 2024.","apa":"Fiedler, C., Liu, Y., &#38; Ibáñez, M. (2024). Solution-processed, surface-engineered, polycrystalline CdSe-SnSe exhibiting low thermal conductivity. <i>Journal of Visualized Experiments</i>. MyJove Corporation. <a href=\"https://doi.org/10.3791/66278\">https://doi.org/10.3791/66278</a>","ama":"Fiedler C, Liu Y, Ibáñez M. Solution-processed, surface-engineered, polycrystalline CdSe-SnSe exhibiting low thermal conductivity. <i>Journal of Visualized Experiments</i>. 2024;2024(207). doi:<a href=\"https://doi.org/10.3791/66278\">10.3791/66278</a>","mla":"Fiedler, Christine, et al. “Solution-Processed, Surface-Engineered, Polycrystalline CdSe-SnSe Exhibiting Low Thermal Conductivity.” <i>Journal of Visualized Experiments</i>, vol. 2024, no. 207, e66278, MyJove Corporation, 2024, doi:<a href=\"https://doi.org/10.3791/66278\">10.3791/66278</a>."},"year":"2024","date_published":"2024-05-01T00:00:00Z","status":"public","publication_status":"published","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"external_id":{"pmid":["38829127"],"isi":["001281657200005"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","full_name":"Fiedler, Christine","first_name":"Christine","last_name":"Fiedler"},{"last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","first_name":"Yu"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria"}],"intvolume":"      2024","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","issue":"207","has_accepted_license":"1","publisher":"MyJove Corporation","OA_place":"publisher","abstract":[{"lang":"eng","text":"In recent years, solution processes have gained considerable traction as a cost-effective and scalable method to produce high-performance thermoelectric materials. The process entails a series of critical steps: synthesis, purification, thermal treatments, and consolidation, each playing a pivotal role in determining performance, stability, and reproducibility. We have noticed a need for more comprehensive details for each of the described steps in most published works. Recognizing the significance of detailed synthetic protocols, we describe here the approach used to synthesize and characterize one of the highest-performing polycrystalline p-type SnSe. In particular, we report the synthesis of SnSe particles in water and the subsequent surface treatment with CdSe molecular complexes that yields CdSe-SnSe nanocomposites upon consolidation. Moreover, the surface treatment inhibits grain growth through Zenner pinning of secondary phase CdSe nanoparticles and enhances defect formation at different length scales. The enhanced complexity in the CdSe-SnSe nanocomposite microstructure with respect to SnSe promotes phonon scattering and thereby significantly reduces the thermal conductivity. Such surface engineering provides opportunities in solution processing for introducing and controlling defects, making it possible to optimize the transport properties and attain a high thermoelectric figure of merit."}],"file":[{"creator":"dernst","file_name":"2024_JoVE_Fiedler.pdf","file_size":1371995,"relation":"main_file","content_type":"application/pdf","checksum":"ddb41f1ce2333484ab5cd109ac2941c0","date_updated":"2025-02-17T15:08:55Z","access_level":"open_access","success":1,"date_created":"2025-02-17T15:08:55Z","file_id":"19047"}],"oa":1,"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-08T07:51:46Z","title":"Solution-processed, surface-engineered, polycrystalline CdSe-SnSe exhibiting low thermal conductivity","publication":"Journal of Visualized Experiments","date_created":"2024-06-09T22:01:02Z","acknowledgement":"The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF) and the Lab Support Facility (LSF). This work was financially supported by the Institute of Science and Technology Austria and the Werner Siemens Foundation."},{"article_type":"review","day":"30","doi":"10.1021/acsnano.3c10201","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"_id":"17125","volume":18,"type":"journal_article","month":"05","oa_version":"None","department":[{"_id":"MaIb"}],"page":"14791-14840","scopus_import":"1","isi":1,"article_processing_charge":"No","author":[{"last_name":"Bassani","first_name":"Carlos L.","full_name":"Bassani, Carlos L."},{"first_name":"Greg","full_name":"Van Anders, Greg","last_name":"Van Anders"},{"last_name":"Banin","first_name":"Uri","full_name":"Banin, Uri"},{"first_name":"Dmitry","full_name":"Baranov, Dmitry","last_name":"Baranov"},{"last_name":"Chen","full_name":"Chen, Qian","first_name":"Qian"},{"last_name":"Dijkstra","first_name":"Marjolein","full_name":"Dijkstra, Marjolein"},{"first_name":"Michael S.","full_name":"Dimitriyev, Michael S.","last_name":"Dimitriyev"},{"first_name":"Efi","full_name":"Efrati, Efi","last_name":"Efrati"},{"first_name":"Jordi","full_name":"Faraudo, Jordi","last_name":"Faraudo"},{"last_name":"Gang","full_name":"Gang, Oleg","first_name":"Oleg"},{"first_name":"Nicola","full_name":"Gaston, Nicola","last_name":"Gaston"},{"first_name":"Ramin","full_name":"Golestanian, Ramin","last_name":"Golestanian"},{"full_name":"Guerrero-Garcia, G. Ivan","first_name":"G. Ivan","last_name":"Guerrero-Garcia"},{"first_name":"Michael","full_name":"Gruenwald, Michael","last_name":"Gruenwald"},{"last_name":"Haji-Akbari","full_name":"Haji-Akbari, Amir","first_name":"Amir"},{"last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"last_name":"Karg","full_name":"Karg, Matthias","first_name":"Matthias"},{"first_name":"Tobias","full_name":"Kraus, Tobias","last_name":"Kraus"},{"full_name":"Lee, Byeongdu","first_name":"Byeongdu","last_name":"Lee"},{"last_name":"Van Lehn","first_name":"Reid C.","full_name":"Van Lehn, Reid C."},{"first_name":"Robert J.","full_name":"Macfarlane, Robert J.","last_name":"Macfarlane"},{"full_name":"Mognetti, Bortolo M.","first_name":"Bortolo M.","last_name":"Mognetti"},{"full_name":"Nikoubashman, Arash","first_name":"Arash","last_name":"Nikoubashman"},{"first_name":"Saeed","full_name":"Osat, Saeed","last_name":"Osat"},{"last_name":"Prezhdo","first_name":"Oleg V.","full_name":"Prezhdo, Oleg V."},{"last_name":"Rotskoff","first_name":"Grant M.","full_name":"Rotskoff, Grant M."},{"first_name":"Leonor","full_name":"Saiz, Leonor","last_name":"Saiz"},{"first_name":"An Chang","full_name":"Shi, An Chang","last_name":"Shi"},{"last_name":"Skrabalak","first_name":"Sara","full_name":"Skrabalak, Sara"},{"full_name":"Smalyukh, Ivan I.","first_name":"Ivan I.","last_name":"Smalyukh"},{"last_name":"Tagliazucchi","full_name":"Tagliazucchi, Mario","first_name":"Mario"},{"last_name":"Talapin","full_name":"Talapin, Dmitri V.","first_name":"Dmitri V."},{"first_name":"Alexei V.","full_name":"Tkachenko, Alexei V.","last_name":"Tkachenko"},{"full_name":"Tretiak, Sergei","first_name":"Sergei","last_name":"Tretiak"},{"last_name":"Vaknin","first_name":"David","full_name":"Vaknin, David"},{"first_name":"Asaph","full_name":"Widmer-Cooper, Asaph","last_name":"Widmer-Cooper"},{"first_name":"Gerard C.L.","full_name":"Wong, Gerard C.L.","last_name":"Wong"},{"last_name":"Ye","full_name":"Ye, Xingchen","first_name":"Xingchen"},{"first_name":"Shan","full_name":"Zhou, Shan","last_name":"Zhou"},{"first_name":"Eran","full_name":"Rabani, Eran","last_name":"Rabani"},{"full_name":"Engel, Michael","first_name":"Michael","last_name":"Engel"},{"last_name":"Travesset","first_name":"Alex","full_name":"Travesset, Alex"}],"intvolume":"        18","issue":"23","language":[{"iso":"eng"}],"external_id":{"isi":["001236199900001"],"pmid":["38814908"]},"quality_controlled":"1","OA_type":"closed access","citation":{"ieee":"C. L. Bassani <i>et al.</i>, “Nanocrystal assemblies: Current advances and open problems,” <i>ACS Nano</i>, vol. 18, no. 23. American Chemical Society, pp. 14791–14840, 2024.","apa":"Bassani, C. L., Van Anders, G., Banin, U., Baranov, D., Chen, Q., Dijkstra, M., … Travesset, A. (2024). Nanocrystal assemblies: Current advances and open problems. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.3c10201\">https://doi.org/10.1021/acsnano.3c10201</a>","ama":"Bassani CL, Van Anders G, Banin U, et al. Nanocrystal assemblies: Current advances and open problems. <i>ACS Nano</i>. 2024;18(23):14791-14840. doi:<a href=\"https://doi.org/10.1021/acsnano.3c10201\">10.1021/acsnano.3c10201</a>","ista":"Bassani CL, Van Anders G, Banin U, Baranov D, Chen Q, Dijkstra M, Dimitriyev MS, Efrati E, Faraudo J, Gang O, Gaston N, Golestanian R, Guerrero-Garcia GI, Gruenwald M, Haji-Akbari A, Ibáñez M, Karg M, Kraus T, Lee B, Van Lehn RC, Macfarlane RJ, Mognetti BM, Nikoubashman A, Osat S, Prezhdo OV, Rotskoff GM, Saiz L, Shi AC, Skrabalak S, Smalyukh II, Tagliazucchi M, Talapin DV, Tkachenko AV, Tretiak S, Vaknin D, Widmer-Cooper A, Wong GCL, Ye X, Zhou S, Rabani E, Engel M, Travesset A. 2024. Nanocrystal assemblies: Current advances and open problems. ACS Nano. 18(23), 14791–14840.","mla":"Bassani, Carlos L., et al. “Nanocrystal Assemblies: Current Advances and Open Problems.” <i>ACS Nano</i>, vol. 18, no. 23, American Chemical Society, 2024, pp. 14791–840, doi:<a href=\"https://doi.org/10.1021/acsnano.3c10201\">10.1021/acsnano.3c10201</a>.","short":"C.L. Bassani, G. Van Anders, U. Banin, D. Baranov, Q. Chen, M. Dijkstra, M.S. Dimitriyev, E. Efrati, J. Faraudo, O. Gang, N. Gaston, R. Golestanian, G.I. Guerrero-Garcia, M. Gruenwald, A. Haji-Akbari, M. Ibáñez, M. Karg, T. Kraus, B. Lee, R.C. Van Lehn, R.J. Macfarlane, B.M. Mognetti, A. Nikoubashman, S. Osat, O.V. Prezhdo, G.M. Rotskoff, L. Saiz, A.C. Shi, S. Skrabalak, I.I. Smalyukh, M. Tagliazucchi, D.V. Talapin, A.V. Tkachenko, S. Tretiak, D. Vaknin, A. Widmer-Cooper, G.C.L. Wong, X. Ye, S. Zhou, E. Rabani, M. Engel, A. Travesset, ACS Nano 18 (2024) 14791–14840.","chicago":"Bassani, Carlos L., Greg Van Anders, Uri Banin, Dmitry Baranov, Qian Chen, Marjolein Dijkstra, Michael S. Dimitriyev, et al. “Nanocrystal Assemblies: Current Advances and Open Problems.” <i>ACS Nano</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsnano.3c10201\">https://doi.org/10.1021/acsnano.3c10201</a>."},"year":"2024","date_published":"2024-05-30T00:00:00Z","status":"public","publication_status":"published","title":"Nanocrystal assemblies: Current advances and open problems","publication":"ACS Nano","date_created":"2024-06-09T22:01:02Z","acknowledgement":"This research was supported in part by the National Science Foundation under Grant No. NSF PHY-1748958 to the Kavli Institute for Theoretical Physics. The biophysics part of this paper was supported in part by the Gordon and Betty Moore Foundation Grant No. 2919.02. CLB acknowledges the sponsorship of the Alexander von Humboldt Foundation through the Humboldt Research Fellowship for postdoctoral researchers, and the support of the Emerging Talents Initiative (ETI) and the EAM Starting Grant (EAM-SG23-1) of the Competence Center Engineering of Advanced Materials of the Friedrich-Alexander-Universität Erlangen-Nürnberg. CLB and ME acknowledge the support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Project-ID 416229255-SFB 1411. The research of AT was supported by the U.S. Department of Energy (U.S. DOE), Office of Basic Energy Sciences, Division of Materials Sciences and Engineering. Iowa State University operates Ames National Laboratory for the U.S. DOE under Contract DE-AC02-07CH11358.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"date_updated":"2025-09-08T07:52:37Z","abstract":[{"text":"We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.","lang":"eng"}],"publisher":"American Chemical Society"},{"status":"public","publication_status":"published","year":"2024","date_published":"2024-05-08T00:00:00Z","alternative_title":["LNCS"],"citation":{"mla":"Tairi, Erkan, and Akin Ünal. “Lower Bounds for Lattice-Based Compact Functional Encryption.” <i>Advances in Cryptology – EUROCRYPT 2024</i>, vol. 14652, Springer Nature, 2024, pp. 249–79, doi:<a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">10.1007/978-3-031-58723-8_9</a>.","apa":"Tairi, E., &#38; Ünal, A. (2024). Lower bounds for lattice-based compact functional encryption. In <i>Advances in Cryptology – EUROCRYPT 2024</i> (Vol. 14652, pp. 249–279). Zurich, Switzerland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">https://doi.org/10.1007/978-3-031-58723-8_9</a>","ieee":"E. Tairi and A. Ünal, “Lower bounds for lattice-based compact functional encryption,” in <i>Advances in Cryptology – EUROCRYPT 2024</i>, Zurich, Switzerland, 2024, vol. 14652, pp. 249–279.","ama":"Tairi E, Ünal A. Lower bounds for lattice-based compact functional encryption. In: <i>Advances in Cryptology – EUROCRYPT 2024</i>. Vol 14652. Springer Nature; 2024:249-279. doi:<a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">10.1007/978-3-031-58723-8_9</a>","ista":"Tairi E, Ünal A. 2024. Lower bounds for lattice-based compact functional encryption. Advances in Cryptology – EUROCRYPT 2024. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 14652, 249–279.","chicago":"Tairi, Erkan, and Akin Ünal. “Lower Bounds for Lattice-Based Compact Functional Encryption.” In <i>Advances in Cryptology – EUROCRYPT 2024</i>, 14652:249–79. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">https://doi.org/10.1007/978-3-031-58723-8_9</a>.","short":"E. Tairi, A. Ünal, in:, Advances in Cryptology – EUROCRYPT 2024, Springer Nature, 2024, pp. 249–279."},"quality_controlled":"1","external_id":{"isi":["001278247600009"]},"language":[{"iso":"eng"}],"intvolume":"     14652","author":[{"last_name":"Tairi","full_name":"Tairi, Erkan","first_name":"Erkan"},{"full_name":"Ünal, Akin","orcid":"0000-0002-8929-0221","id":"f6b56fb6-dc63-11ee-9dbf-f6780863a85a","first_name":"Akin","last_name":"Ünal"}],"publisher":"Springer Nature","oa":1,"abstract":[{"text":"Functional encryption (FE) is a primitive where the holder of a master secret key can control which functions a user can evaluate on encrypted data. It is a powerful primitive that even implies indistinguishability obfuscation (iO), given sufficiently compact ciphertexts (Ananth-Jain, CRYPTO’15 and Bitansky-Vaikuntanathan, FOCS’15). However, despite being extensively studied, there are FE schemes, such as function-hiding inner-product FE (Bishop-Jain-Kowalczyk, AC’15, Abdalla-Catalano-Fiore-Gay-Ursu, CRYPTO’18) and compact quadratic FE (Baltico-Catalano-Fiore-Gay, Lin, CRYPTO’17), that can be only realized using pairings. This raises the question if there are some mathematical barriers that hinder us from realizing these FE schemes from other assumptions.\r\n\r\nIn this paper, we study the difficulty of constructing lattice-based compact FE. We generalize the impossibility results of Ünal (EC’20) for lattice-based function-hiding FE, and extend it to the case of compact FE. Concretely, we prove lower bounds for lattice-based compact FE schemes which meet some (natural) algebraic restrictions at encryption and decryption, and have ciphertexts of linear size and secret keys of minimal degree. We see our results as important indications of why it is hard to construct lattice-based FE schemes for new functionalities, and which mathematical barriers have to be overcome.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2023/719.pdf"}],"date_updated":"2025-09-08T07:48:18Z","acknowledgement":"We want to thank the anonymous reviewers of TCC and Eurocrypt for their very helpful comments and suggestions. This work has received funding from the Austrian Science Fund (FWF) and netidee SCIENCE via grant P31621-N38 (PROFET).","date_created":"2024-06-09T22:01:03Z","publication":"Advances in Cryptology – EUROCRYPT 2024","title":"Lower bounds for lattice-based compact functional encryption","volume":14652,"_id":"17126","conference":{"start_date":"2024-05-26","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","end_date":"2024-05-30","location":"Zurich, Switzerland"},"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031587221"],"eissn":["1611-3349"]},"day":"08","doi":"10.1007/978-3-031-58723-8_9","article_processing_charge":"No","isi":1,"scopus_import":"1","page":"249-279","department":[{"_id":"KrPi"}],"oa_version":"Submitted Version","month":"05","type":"conference"},{"file":[{"access_level":"open_access","date_updated":"2024-08-20T08:36:32Z","date_created":"2024-08-20T08:36:32Z","file_id":"17446","success":1,"creator":"vwang","file_name":"Paucity_phenomena_for_polynomial_products__Wang_Xu_ (7).pdf","file_size":331775,"content_type":"application/pdf","relation":"main_file","checksum":"ae386a4031856efac23c7cdcb53b559b"}],"abstract":[{"text":"Let  P(x)∈Z[x] be a polynomial with at least two distinct complex roots. We prove that the number of solutions  (x1,…,xk,y1,…,yk)∈[N]2k to the equation\r\n∏1≤i≤kP(xi)=∏1≤j≤kP(yj)≠0\r\n(for any  k≥1 ) is asymptotically  k!Nk  as  N→+∞. This solves a question first proposed and studied by Najnudel. The result can also be interpreted as saying that all even moments of random partial sums  1N√∑n≤Nf(P(n)) match standard complex Gaussian moments as  N→+∞\r\n , where  f is the Steinhaus random multiplicative function.","lang":"eng"}],"oa":1,"publisher":"London Mathematical Society","ec_funded":1,"publication":"Bulletin of the London Mathematical Society","title":"Paucity phenomena for polynomial products","acknowledgement":"We thank Oleksiy Klurman, Ilya Shkredov, and Igor Shparlinski for helpful comments on earlier versions of the paper, and thank Yotam Hendel for providing a reference for Lemma 2.1. We also thank the anonymous referee for their generous corrections and comments. The first author has received funding from the European Union's Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement Number: 101034413. The second author is partially supported by the Cuthbert C. Hurd Graduate Fellowship in the Mathematical Sciences, Stanford.","date_created":"2024-06-09T22:01:03Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-08T08:57:32Z","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.02908"}],"external_id":{"isi":["001235729900001"],"arxiv":["2211.02908"]},"language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2024-08-20T08:36:32Z","citation":{"ieee":"V. Wang and M. W. Xu, “Paucity phenomena for polynomial products,” <i>Bulletin of the London Mathematical Society</i>, vol. 56, no. 8. London Mathematical Society, pp. 2718–2726, 2024.","apa":"Wang, V., &#38; Xu, M. W. (2024). Paucity phenomena for polynomial products. <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/blms.13095\">https://doi.org/10.1112/blms.13095</a>","ama":"Wang V, Xu MW. Paucity phenomena for polynomial products. <i>Bulletin of the London Mathematical Society</i>. 2024;56(8):2718-2726. doi:<a href=\"https://doi.org/10.1112/blms.13095\">10.1112/blms.13095</a>","ista":"Wang V, Xu MW. 2024. Paucity phenomena for polynomial products. Bulletin of the London Mathematical Society. 56(8), 2718–2726.","mla":"Wang, Victor, and Max Wenqiang Xu. “Paucity Phenomena for Polynomial Products.” <i>Bulletin of the London Mathematical Society</i>, vol. 56, no. 8, London Mathematical Society, 2024, pp. 2718–26, doi:<a href=\"https://doi.org/10.1112/blms.13095\">10.1112/blms.13095</a>.","short":"V. Wang, M.W. Xu, Bulletin of the London Mathematical Society 56 (2024) 2718–2726.","chicago":"Wang, Victor, and Max Wenqiang Xu. “Paucity Phenomena for Polynomial Products.” <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society, 2024. <a href=\"https://doi.org/10.1112/blms.13095\">https://doi.org/10.1112/blms.13095</a>."},"publication_status":"published","status":"public","year":"2024","date_published":"2024-08-01T00:00:00Z","has_accepted_license":"1","author":[{"last_name":"Wang","first_name":"Victor","full_name":"Wang, Victor","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","orcid":"0000-0002-0704-7026"},{"full_name":"Xu, Max Wenqiang","first_name":"Max Wenqiang","last_name":"Xu"}],"issue":"8","intvolume":"        56","page":"2718-2726","department":[{"_id":"TiBr"}],"ddc":["512"],"isi":1,"scopus_import":"1","article_processing_charge":"No","month":"08","type":"journal_article","oa_version":"Submitted Version","doi":"10.1112/blms.13095","day":"01","publication_identifier":{"issn":["0024-6093"],"eissn":["1469-2120"]},"volume":56,"project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"_id":"17127","article_type":"original"},{"publisher":"Springer Nature","abstract":[{"text":"The onset of turbulence in pipe flow has defied detailed understanding ever since the first observations of the spatially heterogeneous nature of the transition. Recent theoretical studies and experiments in simpler, shear-driven flows suggest that the onset of turbulence is a directed-percolation non-equilibrium phase transition, but whether these findings are generic and also apply to open or pressure-driven flows is unknown. In pipe flow, the extremely long time scales near the transition make direct observations of critical behaviour virtually impossible. Here we find a technical solution to that limitation and show that the universality class of the transition is directed percolation, from which a jammed phase of puffs emerges above the critical point. Our method is to experimentally characterize all pairwise interactions between localized patches of turbulence puffs and use these interactions as input for renormalization group and computer simulations of minimal models that extrapolate to long length and time scales. The strong interactions in the jamming regime enable us to explicitly measure the turbulent fraction and confirm model predictions. Our work shows that directed-percolation scaling applies beyond simple closed shear flows and underscores how statistical mechanics can lead to profound, quantitative and predictive insights on turbulent flows and their phases.","lang":"eng"}],"date_updated":"2025-09-08T07:50:20Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We gratefully acknowledge the assistance of J. M. Lopez with DNSs at an early stage of this work. This work was partially supported by two grants from the Simons Foundation (grant nos. 662985 (N.G.) and 662960 (B.H.)) and by Ministry of Science and Technology, Taiwan (grant nos. MOST 109-2112-M-001-017-MY3 and MOST 111-2112-M-001-027-MY3 (H.-Y.S.)). Part of this work was performed using computing resources of CRIANN (Normandy, France).","date_created":"2024-06-09T22:01:03Z","publication":"Nature Physics","title":"Directed percolation and puff jamming near the transition to pipe turbulence","status":"public","publication_status":"published","date_published":"2024-08-01T00:00:00Z","year":"2024","corr_author":"1","citation":{"chicago":"Lemoult, Grégoire M, Mukund Vasudevan, Hong Yan Shih, Gaute Linga, Joachim Mathiesen, Nigel Goldenfeld, and Björn Hof. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02513-0\">https://doi.org/10.1038/s41567-024-02513-0</a>.","short":"G.M. Lemoult, M. Vasudevan, H.Y. Shih, G. Linga, J. Mathiesen, N. Goldenfeld, B. Hof, Nature Physics 20 (2024) 1339–1345.","mla":"Lemoult, Grégoire M., et al. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1339–45, doi:<a href=\"https://doi.org/10.1038/s41567-024-02513-0\">10.1038/s41567-024-02513-0</a>.","apa":"Lemoult, G. M., Vasudevan, M., Shih, H. Y., Linga, G., Mathiesen, J., Goldenfeld, N., &#38; Hof, B. (2024). Directed percolation and puff jamming near the transition to pipe turbulence. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02513-0\">https://doi.org/10.1038/s41567-024-02513-0</a>","ieee":"G. M. Lemoult <i>et al.</i>, “Directed percolation and puff jamming near the transition to pipe turbulence,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1339–1345, 2024.","ama":"Lemoult GM, Vasudevan M, Shih HY, et al. Directed percolation and puff jamming near the transition to pipe turbulence. <i>Nature Physics</i>. 2024;20:1339-1345. doi:<a href=\"https://doi.org/10.1038/s41567-024-02513-0\">10.1038/s41567-024-02513-0</a>","ista":"Lemoult GM, Vasudevan M, Shih HY, Linga G, Mathiesen J, Goldenfeld N, Hof B. 2024. Directed percolation and puff jamming near the transition to pipe turbulence. Nature Physics. 20, 1339–1345."},"quality_controlled":"1","external_id":{"isi":["001232300600001"]},"language":[{"iso":"eng"}],"intvolume":"        20","author":[{"id":"4787FE80-F248-11E8-B48F-1D18A9856A87","full_name":"Lemoult, Grégoire M","first_name":"Grégoire M","last_name":"Lemoult"},{"last_name":"Vasudevan","first_name":"Mukund","full_name":"Vasudevan, Mukund","id":"3C5A959A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shih, Hong Yan","first_name":"Hong Yan","last_name":"Shih"},{"last_name":"Linga","first_name":"Gaute","full_name":"Linga, Gaute"},{"last_name":"Mathiesen","full_name":"Mathiesen, Joachim","first_name":"Joachim"},{"last_name":"Goldenfeld","full_name":"Goldenfeld, Nigel","first_name":"Nigel"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","last_name":"Hof"}],"article_processing_charge":"No","isi":1,"scopus_import":"1","page":"1339-1345","department":[{"_id":"BjHo"}],"oa_version":"None","month":"08","type":"journal_article","volume":20,"_id":"17128","project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"day":"01","doi":"10.1038/s41567-024-02513-0","article_type":"original"},{"publication_status":"submitted","status":"public","_id":"17136","year":"2024","date_published":"2024-06-11T00:00:00Z","citation":{"short":"P. Arkhipov, ArXiv (n.d.).","chicago":"Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular Graphs: Experimental Results.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2406.07026\">https://doi.org/10.48550/arXiv.2406.07026</a>.","ieee":"P. Arkhipov, “Majority dynamics and internal partitions of random regular graphs: Experimental results,” <i>arXiv</i>. .","ama":"Arkhipov P. Majority dynamics and internal partitions of random regular graphs: Experimental results. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2406.07026\">10.48550/arXiv.2406.07026</a>","apa":"Arkhipov, P. (n.d.). Majority dynamics and internal partitions of random regular graphs: Experimental results. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2406.07026\">https://doi.org/10.48550/arXiv.2406.07026</a>","ista":"Arkhipov P. Majority dynamics and internal partitions of random regular graphs: Experimental results. arXiv, 2406.07026.","mla":"Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular Graphs: Experimental Results.” <i>ArXiv</i>, 2406.07026, doi:<a href=\"https://doi.org/10.48550/arXiv.2406.07026\">10.48550/arXiv.2406.07026</a>."},"external_id":{"arxiv":["2406.07026"]},"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2406.07026","day":"11","article_number":"2406.07026","author":[{"last_name":"Arkhipov","id":"b25f2ab2-1fed-11ee-8599-fe02d211784f","full_name":"Arkhipov, Pavel","first_name":"Pavel"}],"article_processing_charge":"No","oa":1,"department":[{"_id":"GradSch"}],"abstract":[{"text":"This paper focuses on Majority Dynamics in sparse graphs, in particular, as a\r\ntool to study internal cuts. It is known that, in Majority Dynamics on a finite\r\ngraph, each vertex eventually either comes to a fixed state, or oscillates with\r\nperiod two. The empirical evidence acquired by simulations suggests that for\r\nrandom odd-regular graphs, approximately half of the vertices end up\r\noscillating with high probability. We notice a local symmetry between\r\noscillating and non-oscillating vertices, that potentially can explain why the\r\nfraction of the oscillating vertices is concentrated around $\\frac{1}{2}$. In\r\nour simulations, we observe that the parts of random odd-regular graph under\r\nMajority Dynamics with high probability do not contain $\\lceil \\frac{d}{2}\r\n\\rceil$-cores at any timestep, and thus, one cannot use Majority Dynamics to\r\nprove that internal cuts exist in odd-regular graphs almost surely. However, we\r\nsuggest a modification of Majority Dynamics, that yields parts with desired\r\ncores with high probability.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2406.07026"}],"arxiv":1,"date_updated":"2024-06-17T10:45:32Z","acknowledgement":"I am grateful to Matthew Kwan for setting the problem, providing useful literature,\r\nfruitful discussions, text review, mentorship, general encouragement and support.","oa_version":"Preprint","date_created":"2024-06-12T07:01:52Z","month":"06","publication":"arXiv","type":"preprint","title":"Majority dynamics and internal partitions of random regular graphs: Experimental results"},{"publication_identifier":{"isbn":["9783200096455"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"13","doi":"10.25365/phaidra.463","_id":"17139","conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","end_date":"2024-06-13","location":"Grundlsee, Austria","start_date":"2024-06-10"},"oa_version":"Published Version","month":"06","type":"conference_abstract","ddc":["000"],"page":"46","department":[{"_id":"ScienComp"}],"article_processing_charge":"No","has_accepted_license":"1","author":[{"last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"first_name":"Waleed","id":"097c0562-3cf0-11ee-8fd3-e7a79c1e2fd1","full_name":"Khalid, Waleed","last_name":"Khalid"},{"last_name":"Elefante","full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"last_name":"Stadlbauer","first_name":"Stephan","full_name":"Stadlbauer, Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","language":[{"iso":"eng"}],"publication_status":"published","status":"public","date_published":"2024-06-13T00:00:00Z","year":"2024","citation":{"ieee":"A. Schlögl, W. Khalid, S. Elefante, and S. Stadlbauer, “How much memory per CPU core is requested?,” in <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, Grundlsee, Austria, 2024, p. 46.","ama":"Schlögl A, Khalid W, Elefante S, Stadlbauer S. How much memory per CPU core is requested? In: <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>. EuroCC Austria; 2024:46. doi:<a href=\"https://doi.org/10.25365/phaidra.463\">10.25365/phaidra.463</a>","apa":"Schlögl, A., Khalid, W., Elefante, S., &#38; Stadlbauer, S. (2024). How much memory per CPU core is requested? In <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i> (p. 46). Grundlsee, Austria: EuroCC Austria. <a href=\"https://doi.org/10.25365/phaidra.463\">https://doi.org/10.25365/phaidra.463</a>","ista":"Schlögl A, Khalid W, Elefante S, Stadlbauer S. 2024. How much memory per CPU core is requested? ASHPC24 - Austrian-Slovenian HPC Meeting 2024. ASHPC: Austrian-Slovenian HPC Meeting, 46.","mla":"Schlögl, Alois, et al. “How Much Memory per CPU Core Is Requested?” <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, EuroCC Austria, 2024, p. 46, doi:<a href=\"https://doi.org/10.25365/phaidra.463\">10.25365/phaidra.463</a>.","short":"A. Schlögl, W. Khalid, S. Elefante, S. Stadlbauer, in:, ASHPC24 - Austrian-Slovenian HPC Meeting 2024, EuroCC Austria, 2024, p. 46.","chicago":"Schlögl, Alois, Waleed Khalid, Stefano Elefante, and Stephan Stadlbauer. “How Much Memory per CPU Core Is Requested?” In <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, 46. EuroCC Austria, 2024. <a href=\"https://doi.org/10.25365/phaidra.463\">https://doi.org/10.25365/phaidra.463</a>."},"file_date_updated":"2024-06-17T09:36:51Z","date_created":"2024-06-14T09:06:36Z","publication":"ASHPC24 - Austrian-Slovenian HPC Meeting 2024","title":"How much memory per CPU core is requested?","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-06-17T09:40:37Z","oa":1,"file":[{"content_type":"application/pdf","relation":"main_file","checksum":"f7d3dded6df2dcdb4818904cf2e1c183","creator":"dernst","file_name":"2024_ASHPC_Schloegl.pdf","file_size":206746,"file_id":"17153","date_created":"2024-06-17T09:36:51Z","success":1,"date_updated":"2024-06-17T09:36:51Z","access_level":"open_access"}],"publisher":"EuroCC Austria"},{"publication_status":"published","status":"public","year":"2024","date_published":"2024-09-27T00:00:00Z","file_date_updated":"2025-01-02T10:26:22Z","citation":{"short":"Z. Zhang, H. Chen, S. Peng, H. Han, Journal of Experimental Botany 75 (2024).","chicago":"Zhang, Zilin, Huihuang Chen, Shuaiying Peng, and Huibin Han. “Slow and Rapid Auxin Responses in Arabidopsis.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jxb/erae246\">https://doi.org/10.1093/jxb/erae246</a>.","ista":"Zhang Z, Chen H, Peng S, Han H. 2024. Slow and rapid auxin responses in Arabidopsis. Journal of Experimental Botany. 75(18), erae246.","ieee":"Z. Zhang, H. Chen, S. Peng, and H. Han, “Slow and rapid auxin responses in Arabidopsis,” <i>Journal of Experimental Botany</i>, vol. 75, no. 18. Oxford University Press, 2024.","apa":"Zhang, Z., Chen, H., Peng, S., &#38; Han, H. (2024). Slow and rapid auxin responses in Arabidopsis. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erae246\">https://doi.org/10.1093/jxb/erae246</a>","ama":"Zhang Z, Chen H, Peng S, Han H. Slow and rapid auxin responses in Arabidopsis. <i>Journal of Experimental Botany</i>. 2024;75(18). doi:<a href=\"https://doi.org/10.1093/jxb/erae246\">10.1093/jxb/erae246</a>","mla":"Zhang, Zilin, et al. “Slow and Rapid Auxin Responses in Arabidopsis.” <i>Journal of Experimental Botany</i>, vol. 75, no. 18, erae246, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/jxb/erae246\">10.1093/jxb/erae246</a>."},"OA_type":"hybrid","quality_controlled":"1","external_id":{"isi":["001270051200001"],"pmid":["38794966"]},"language":[{"iso":"eng"}],"issue":"18","intvolume":"        75","author":[{"last_name":"Zhang","first_name":"Zilin","full_name":"Zhang, Zilin"},{"last_name":"Chen","full_name":"Chen, Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang"},{"full_name":"Peng, Shuaiying","first_name":"Shuaiying","last_name":"Peng"},{"first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han"}],"has_accepted_license":"1","publisher":"Oxford University Press","oa":1,"file":[{"success":1,"date_created":"2025-01-02T10:26:22Z","file_id":"18720","date_updated":"2025-01-02T10:26:22Z","access_level":"open_access","checksum":"91b9435ed0f6640809c7588df19abf2f","content_type":"application/pdf","relation":"main_file","file_name":"2024_JourExperimentalBotany_Zhang.pdf","file_size":763097,"creator":"dernst"}],"abstract":[{"lang":"eng","text":"The TIR1/AFB–Aux/IAA–ARF canonical auxin signaling pathway is widely accepted to (de)active transcriptional regulation, thus controlling auxin-associated developmental processes. However, the theme of a rapid auxin response has emerged since the 2018 Auxins and Cytokinin in Plant Development conference. To date, a few signaling components have been identified to mediate both slow and rapid auxin responses, which unveils the complexity of auxin signaling."}],"OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-08T07:57:50Z","pmid":1,"acknowledgement":"We thank other lab members for their critical comments on this manuscript. We also thank the editor and reviewers for their constructive comments to improve our manuscript. We apologize to authors whose important work we could not include due to space limitations.\r\nThis work is supported by funding from Jiangxi Agricultural University (9232308314) and the Science and Technology Department of Jiangxi Province (20223BCJ25037) to HBH, and the Science and Technology Department of Jiangxi Province (20202ACB215002) to SYP.","date_created":"2024-06-15T19:50:15Z","publication":"Journal of Experimental Botany","title":"Slow and rapid auxin responses in Arabidopsis","volume":75,"_id":"17141","publication_identifier":{"issn":["0022-0957"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"27","doi":"10.1093/jxb/erae246","article_number":"erae246","article_type":"original","article_processing_charge":"No","ddc":["580"],"isi":1,"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"oa_version":"Published Version","month":"09","type":"journal_article"},{"department":[{"_id":"RySh"},{"_id":"GaNo"},{"_id":"MaJö"}],"scopus_import":"1","ddc":["570"],"isi":1,"article_processing_charge":"Yes","type":"journal_article","month":"06","APC_amount":"6081,83 EUR","oa_version":"Published Version","DOAJ_listed":"1","day":"10","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1371/journal.pbio.3002668","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"_id":"17142","project":[{"grant_number":"756502","name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"volume":22,"article_type":"original","article_number":"e3002668","file":[{"file_size":4016568,"file_name":"2024_PloS_Burnett.pdf","creator":"dernst","checksum":"496e1aa4fd5b92b7e4087ecc2c964133","content_type":"application/pdf","relation":"main_file","date_updated":"2025-01-09T10:39:41Z","access_level":"open_access","date_created":"2025-01-09T10:39:41Z","file_id":"18805","success":1}],"OA_place":"publisher","abstract":[{"lang":"eng","text":"Despite the diverse genetic origins of autism spectrum disorders (ASDs), affected individuals share strikingly similar and correlated behavioural traits that include perceptual and sensory processing challenges. Notably, the severity of these sensory symptoms is often predictive of the expression of other autistic traits. However, the origin of these perceptual deficits remains largely elusive. Here, we show a recurrent impairment in visual threat perception that is similarly impaired in 3 independent mouse models of ASD with different molecular aetiologies. Interestingly, this deficit is associated with reduced avoidance of threatening environments—a nonperceptual trait. Focusing on a common cause of ASDs, the Setd5 gene mutation, we define the molecular mechanism. We show that the perceptual impairment is caused by a potassium channel (Kv1)-mediated hypoexcitability in a subcortical node essential for the initiation of escape responses, the dorsal periaqueductal grey (dPAG). Targeted pharmacological Kv1 blockade rescued both perceptual and place avoidance deficits, causally linking seemingly unrelated trait deficits to the dPAG. Furthermore, we show that different molecular mechanisms converge on similar behavioural phenotypes by demonstrating that the autism models Cul3 and Ptchd1, despite having similar behavioural phenotypes, differ in their functional and molecular alteration. Our findings reveal a link between rapid perception controlled by subcortical pathways and appropriate learned interactions with the environment and define a nondevelopmental source of such deficits in ASD."}],"oa":1,"publisher":"Public Library of Science","ec_funded":1,"title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","related_material":{"record":[{"id":"15385","relation":"research_data","status":"public"}],"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.11130587"}]},"publication":"PLoS Biology","date_created":"2024-06-16T22:01:05Z","acknowledgement":"This work was supported by a European Research Council Starting Grant 756502 (MJ). ","date_updated":"2025-09-08T07:57:11Z","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"external_id":{"isi":["001246176800003"],"pmid":["38857283"]},"quality_controlled":"1","OA_type":"gold","corr_author":"1","file_date_updated":"2025-01-09T10:39:41Z","citation":{"short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, PLoS Biology 22 (2024).","chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” <i>PLoS Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>.","ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. PLoS Biology. 22, e3002668.","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. <i>PLoS Biology</i>. 2024;22. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice,” <i>PLoS Biology</i>, vol. 22. Public Library of Science, 2024.","mla":"Burnett, Laura, et al. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” <i>PLoS Biology</i>, vol. 22, e3002668, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>."},"date_published":"2024-06-10T00:00:00Z","year":"2024","publication_status":"published","status":"public","has_accepted_license":"1","author":[{"last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura","first_name":"Laura"},{"first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"},{"last_name":"Symonova","orcid":"0000-0003-2012-9947","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga"},{"last_name":"Masson","first_name":"Tomas","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","orcid":"0000-0002-2634-6283","full_name":"Masson, Tomas"},{"last_name":"Vega Zuniga","full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A"},{"last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto"},{"last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"},{"last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"intvolume":"        22"},{"month":"06","type":"conference","oa_version":"Published Version","department":[{"_id":"HeEd"}],"ddc":["510"],"scopus_import":"1","article_processing_charge":"No","article_number":"69","doi":"10.4230/LIPIcs.SoCG.2024.69","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"01","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773164"]},"conference":{"location":"Athens, Greece","end_date":"2024-06-14","name":"SoCG: Symposium on Computational Geometry"},"volume":293,"_id":"17144","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Mathematics, Computer Science","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Learning and triangulating manifolds via collapses","grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"publication":"40th International Symposium on Computational Geometry","title":"The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms","acknowledgement":"This research has been supported by the European Research Council (ERC), grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant No. I 02979-N35.\r\nSupported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) grant No. M-3073, and the welcome package from IDEX of the Université Cô d'Azur.\r\nWe are greatly indebted to Fred Chazal for sharing his insights. We further thank Erin Chambers, Christopher Fillmore, and Elizabeth Stephenson for early discussions and all members of the Edelsbrunner group (Institute of Science and Technology Austria) and the Datashape team (Inria) for the atmosphere in which this research was conducted.","date_created":"2024-06-16T22:01:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-15T07:16:58Z","arxiv":1,"file":[{"checksum":"b40ff456c19294adb5d9613fcfd751c6","content_type":"application/pdf","relation":"main_file","file_name":"2024_LIPICS_Kourimska.pdf","file_size":1612558,"creator":"dernst","date_created":"2024-06-17T08:33:40Z","file_id":"17150","success":1,"access_level":"open_access","date_updated":"2024-06-17T08:33:40Z"}],"abstract":[{"text":"We prove that the medial axis of closed sets is Hausdorff stable in the following sense: Let 𝒮 ⊆ ℝ^d be a fixed closed set that contains a bounding sphere. That is, the bounding sphere is part of the set 𝒮. Consider the space of C^{1,1} diffeomorphisms of ℝ^d to itself, which keep the bounding sphere invariant. The map from this space of diffeomorphisms (endowed with a Banach norm) to the space of closed subsets of ℝ^d (endowed with the Hausdorff distance), mapping a diffeomorphism F to the closure of the medial axis of F(𝒮), is Lipschitz. This extends a previous stability result of Chazal and Soufflet on the stability of the medial axis of C² manifolds under C² ambient diffeomorphisms.","lang":"eng"}],"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ec_funded":1,"has_accepted_license":"1","author":[{"last_name":"Kourimska","first_name":"Hana","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","orcid":"0000-0001-7841-0091","full_name":"Kourimska, Hana"},{"first_name":"André","full_name":"Lieutier, André","last_name":"Lieutier"},{"first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"intvolume":"       293","external_id":{"arxiv":["2212.01118"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"chicago":"Kourimska, Hana, André Lieutier, and Mathijs Wintraecken. “The Medial Axis of Any Closed Bounded Set Is Lipschitz Stable with Respect to the Hausdorff Distance Under Ambient Diffeomorphisms.” In <i>40th International Symposium on Computational Geometry</i>, Vol. 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.69\">https://doi.org/10.4230/LIPIcs.SoCG.2024.69</a>.","short":"H. Kourimska, A. Lieutier, M. Wintraecken, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Kourimska, Hana, et al. “The Medial Axis of Any Closed Bounded Set Is Lipschitz Stable with Respect to the Hausdorff Distance Under Ambient Diffeomorphisms.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, 69, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.69\">10.4230/LIPIcs.SoCG.2024.69</a>.","ama":"Kourimska H, Lieutier A, Wintraecken M. The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.69\">10.4230/LIPIcs.SoCG.2024.69</a>","apa":"Kourimska, H., Lieutier, A., &#38; Wintraecken, M. (2024). The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.69\">https://doi.org/10.4230/LIPIcs.SoCG.2024.69</a>","ieee":"H. Kourimska, A. Lieutier, and M. Wintraecken, “The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293.","ista":"Kourimska H, Lieutier A, Wintraecken M. 2024. The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 69."},"file_date_updated":"2024-06-17T08:33:40Z","alternative_title":["LIPIcs"],"publication_status":"published","status":"public","date_published":"2024-06-01T00:00:00Z","year":"2024"},{"has_accepted_license":"1","intvolume":"       293","author":[{"last_name":"Rote","full_name":"Rote, Günter","first_name":"Günter"},{"last_name":"Rüber","first_name":"Moritz","full_name":"Rüber, Moritz"},{"first_name":"Morteza","full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","last_name":"Saghafian"}],"quality_controlled":"1","external_id":{"arxiv":["2402.15787"]},"language":[{"iso":"eng"}],"publication_status":"published","status":"public","date_published":"2024-06-01T00:00:00Z","year":"2024","alternative_title":["LIPIcs"],"citation":{"mla":"Rote, Günter, et al. “Grid Peeling of Parabolas.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, 76, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.76\">10.4230/LIPIcs.SoCG.2024.76</a>.","ama":"Rote G, Rüber M, Saghafian M. Grid peeling of parabolas. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.76\">10.4230/LIPIcs.SoCG.2024.76</a>","apa":"Rote, G., Rüber, M., &#38; Saghafian, M. (2024). Grid peeling of parabolas. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.76\">https://doi.org/10.4230/LIPIcs.SoCG.2024.76</a>","ieee":"G. Rote, M. Rüber, and M. Saghafian, “Grid peeling of parabolas,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293.","ista":"Rote G, Rüber M, Saghafian M. 2024. Grid peeling of parabolas. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 76.","chicago":"Rote, Günter, Moritz Rüber, and Morteza Saghafian. “Grid Peeling of Parabolas.” In <i>40th International Symposium on Computational Geometry</i>, Vol. 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.76\">https://doi.org/10.4230/LIPIcs.SoCG.2024.76</a>.","short":"G. Rote, M. Rüber, M. Saghafian, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024."},"file_date_updated":"2024-06-17T08:40:04Z","acknowledgement":"Part of this work was done while G.R. enjoyed the hospitality of the Institute of Science and Technology Austria (ISTA) as a visiting professor during his sabbatical in the winter semester 2022/23.","date_created":"2024-06-16T22:01:06Z","publication":"40th International Symposium on Computational Geometry","title":"Grid peeling of parabolas","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"date_updated":"2024-06-17T08:41:56Z","oa":1,"file":[{"checksum":"fbad1de06383a6b7e8a1cb3e8c7205ce","content_type":"application/pdf","relation":"main_file","file_name":"2024_LIPICS_Rote.pdf","file_size":1430896,"creator":"dernst","date_created":"2024-06-17T08:40:04Z","success":1,"file_id":"17151","access_level":"open_access","date_updated":"2024-06-17T08:40:04Z"}],"abstract":[{"lang":"eng","text":"Grid peeling is the process of repeatedly removing the convex hull vertices of the grid points that lie inside a given convex curve. It has been conjectured that, for a more and more refined grid, grid peeling converges to a continuous process, the affine curve-shortening flow, which deforms the curve based on the curvature. We prove this conjecture for one class of curves, parabolas with a vertical axis, and we determine the value of the constant factor in the formula that relates the two processes."}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_number":"76","publication_identifier":{"isbn":["9783959773164"],"issn":["1868-8969"]},"day":"01","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.4230/LIPIcs.SoCG.2024.76","volume":293,"_id":"17145","conference":{"location":"Athens, Greece","end_date":"2024-06-14","name":"SoCG: Symposium on Computational Geometry","start_date":"2024-06-11"},"oa_version":"Published Version","month":"06","type":"conference","ddc":["510"],"scopus_import":"1","department":[{"_id":"HeEd"}],"article_processing_charge":"No"},{"article_number":"53","publication_identifier":{"isbn":["9783959773164"],"issn":["1868-8969"]},"day":"01","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.4230/LIPIcs.SoCG.2024.53","_id":"17146","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"Mathematics, Computer Science"}],"volume":293,"conference":{"location":"Athens, Greece","name":"SoCG: Symposium on Computational Geometry","end_date":"2024-06-14","start_date":"2024-06-11"},"oa_version":"Published Version","type":"conference","month":"06","scopus_import":"1","ddc":["510"],"department":[{"_id":"HeEd"}],"article_processing_charge":"No","has_accepted_license":"1","intvolume":"       293","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner"},{"first_name":"János","full_name":"Pach, János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","last_name":"Pach"}],"quality_controlled":"1","external_id":{"arxiv":["2310.14801"]},"language":[{"iso":"eng"}],"year":"2024","date_published":"2024-06-01T00:00:00Z","status":"public","publication_status":"published","alternative_title":["LIPIcs"],"citation":{"chicago":"Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.” In <i>40th International Symposium on Computational Geometry</i>, Vol. 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.53\">https://doi.org/10.4230/LIPIcs.SoCG.2024.53</a>.","short":"H. Edelsbrunner, J. Pach, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, 53, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.53\">10.4230/LIPIcs.SoCG.2024.53</a>.","ista":"Edelsbrunner H, Pach J. 2024. Maximum Betti numbers of Čech complexes. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 53.","ieee":"H. Edelsbrunner and J. Pach, “Maximum Betti numbers of Čech complexes,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293.","ama":"Edelsbrunner H, Pach J. Maximum Betti numbers of Čech complexes. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.53\">10.4230/LIPIcs.SoCG.2024.53</a>","apa":"Edelsbrunner, H., &#38; Pach, J. (2024). Maximum Betti numbers of Čech complexes. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.53\">https://doi.org/10.4230/LIPIcs.SoCG.2024.53</a>"},"file_date_updated":"2024-06-17T08:46:33Z","date_created":"2024-06-16T22:01:06Z","acknowledgement":"The first author is supported by the European Research Council (ERC), grant no. 788183, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant no. {I 02979-N35.} The second author is supported by the European Research Council (ERC), grant \"GeoScape\" and by the Hungarian Science Foundation (NKFIH), grant K-131529. Both authors are supported by the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.\r\nThe authors thank Matt Kahle for communicating the question about extremal Čech complexes, Ben Schweinhart for early discussions on the linked circles construction in three dimensions, and Gábor Tardos for helpful remarks and suggestions.","title":"Maximum Betti numbers of Čech complexes","publication":"40th International Symposium on Computational Geometry","related_material":{"record":[{"relation":"later_version","id":"20657","status":"public"}]},"arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-12-01T15:19:20Z","oa":1,"abstract":[{"lang":"eng","text":"The Upper Bound Theorem for convex polytopes implies that the p-th Betti number of the Čech complex of any set of N points in ℝ^d and any radius satisfies β_p = O(N^m), with m = min{p+1, ⌈d/2⌉}. We construct sets in even and odd dimensions, which prove that this upper bound is asymptotically tight. For example, we describe a set of N = 2(n+1) points in ℝ³ and two radii such that the first Betti number of the Čech complex at one radius is (n+1)² - 1, and the second Betti number of the Čech complex at the other radius is n². In particular, there is an arrangement of n contruent balls in ℝ³ that enclose a quadratic number of voids, which answers a long-standing open question in computational geometry."}],"file":[{"success":1,"date_created":"2024-06-17T08:46:33Z","file_id":"17152","access_level":"open_access","date_updated":"2024-06-17T08:46:33Z","relation":"main_file","content_type":"application/pdf","checksum":"5442d44fb89d77477a87668d6e61aac9","creator":"dernst","file_name":"2024_LIPICS_Edelsbrunner.pdf","file_size":766562}],"ec_funded":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"day":"19","doi":"10.1109/ICASSP48485.2024.10447198","publication_identifier":{"issn":["1520-6149"],"isbn":["9798350344851"]},"conference":{"start_date":"2024-04-14","location":"Seoul, Korea","end_date":"2024-04-19","name":"ICASSP: International Conference on Acoustics, Speech and Signal Processing"},"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"_id":"17147","page":"13151-13155","department":[{"_id":"MaMo"},{"_id":"MaRo"}],"isi":1,"scopus_import":"1","article_processing_charge":"No","month":"04","type":"conference","oa_version":"Submitted Version","external_id":{"isi":["001396233806078"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"quality_controlled":"1","corr_author":"1","citation":{"mla":"Depope, Al, et al. “Inference of Genetic Effects via Approximate Message Passing.” <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, IEEE, 2024, pp. 13151–55, doi:<a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">10.1109/ICASSP48485.2024.10447198</a>.","ista":"Depope A, Mondelli M, Robinson MR. 2024. Inference of genetic effects via approximate message passing. 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing. ICASSP: International Conference on Acoustics, Speech and Signal Processing, 13151–13155.","apa":"Depope, A., Mondelli, M., &#38; Robinson, M. R. (2024). Inference of genetic effects via approximate message passing. In <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i> (pp. 13151–13155). Seoul, Korea: IEEE. <a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">https://doi.org/10.1109/ICASSP48485.2024.10447198</a>","ieee":"A. Depope, M. Mondelli, and M. R. Robinson, “Inference of genetic effects via approximate message passing,” in <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, Seoul, Korea, 2024, pp. 13151–13155.","ama":"Depope A, Mondelli M, Robinson MR. Inference of genetic effects via approximate message passing. In: <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>. IEEE; 2024:13151-13155. doi:<a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">10.1109/ICASSP48485.2024.10447198</a>","chicago":"Depope, Al, Marco Mondelli, and Matthew Richard Robinson. “Inference of Genetic Effects via Approximate Message Passing.” In <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, 13151–55. IEEE, 2024. <a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">https://doi.org/10.1109/ICASSP48485.2024.10447198</a>.","short":"A. Depope, M. Mondelli, M.R. Robinson, in:, 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing, IEEE, 2024, pp. 13151–13155."},"OA_type":"green","publication_status":"published","status":"public","year":"2024","date_published":"2024-04-19T00:00:00Z","author":[{"last_name":"Depope","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830","full_name":"Depope, Al","first_name":"Al"},{"first_name":"Marco","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","last_name":"Mondelli"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"}],"abstract":[{"lang":"eng","text":"Efficient utilization of large-scale biobank data is crucial for inferring the genetic basis of disease and predicting health outcomes from the DNA. Yet we lack efficient, accurate methods that scale to data where electronic health records are linked to whole genome sequence information. To address this issue, our paper develops a new algorithmic paradigm based on Approximate Message Passing (AMP), which is specifically tailored for genomic prediction and association testing. Our method yields comparable out-of-sample prediction accuracy to the state of the art on UK Biobank traits, whilst dramatically improving computational complexity, with a 8x-speed up in the run time. In addition, AMP theory provides a joint association testing framework, which outperforms the currently used REGENIE method, in roughly a third of the compute time. This first, truly large-scale application of the AMP framework lays the foundations for a far wider range of statistical analyses for hundreds of millions of variables measured on millions of people."}],"OA_place":"repository","oa":1,"publisher":"IEEE","publication":"2024 IEEE International Conference on Acoustics, Speech, and Signal Processing","title":"Inference of genetic effects via approximate message passing","acknowledgement":"This work was supported by a Lopez-Loreta Prize to MM, an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and core funding from ISTA. The authors thank Philip Schniter, Matthew Stephens and Pragya Sur for valuable suggestions on an early version of the work. The authors acknowledge the participants and investigators of the UK Biobank study. High-performance\r\ncomputing was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","date_created":"2024-06-16T22:01:07Z","date_updated":"2025-11-05T07:21:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://openreview.net/forum?id=aQYCDxfZV0","open_access":"1"}]},{"publication_identifier":{"eissn":["2699-0016"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.5194/mr-5-69-2024","day":"11","project":[{"name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches","grant_number":"26777","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0"}],"_id":"17161","volume":5,"article_type":"original","scopus_import":"1","ddc":["530"],"department":[{"_id":"PaSc"}],"page":"69-86","article_processing_charge":"Yes","oa_version":"Published Version","type":"journal_article","month":"06","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["40384772"]},"date_published":"2024-06-11T00:00:00Z","year":"2024","status":"public","publication_status":"published","citation":{"short":"K. Aebischer, L.M. Becker, P. Schanda, M. Ernst, Magnetic Resonance 5 (2024) 69–86.","chicago":"Aebischer, Kathrin, Lea Marie Becker, Paul Schanda, and Matthias Ernst. “Evaluating the Motional Timescales Contributing to Averaged Anisotropic Interactions in MAS Solid-State NMR.” <i>Magnetic Resonance</i>. Copernicus Publications, 2024. <a href=\"https://doi.org/10.5194/mr-5-69-2024\">https://doi.org/10.5194/mr-5-69-2024</a>.","ieee":"K. Aebischer, L. M. Becker, P. Schanda, and M. Ernst, “Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR,” <i>Magnetic Resonance</i>, vol. 5, no. 1. Copernicus Publications, pp. 69–86, 2024.","ama":"Aebischer K, Becker LM, Schanda P, Ernst M. Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR. <i>Magnetic Resonance</i>. 2024;5(1):69-86. doi:<a href=\"https://doi.org/10.5194/mr-5-69-2024\">10.5194/mr-5-69-2024</a>","apa":"Aebischer, K., Becker, L. M., Schanda, P., &#38; Ernst, M. (2024). Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR. <i>Magnetic Resonance</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/mr-5-69-2024\">https://doi.org/10.5194/mr-5-69-2024</a>","ista":"Aebischer K, Becker LM, Schanda P, Ernst M. 2024. Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR. Magnetic Resonance. 5(1), 69–86.","mla":"Aebischer, Kathrin, et al. “Evaluating the Motional Timescales Contributing to Averaged Anisotropic Interactions in MAS Solid-State NMR.” <i>Magnetic Resonance</i>, vol. 5, no. 1, Copernicus Publications, 2024, pp. 69–86, doi:<a href=\"https://doi.org/10.5194/mr-5-69-2024\">10.5194/mr-5-69-2024</a>."},"file_date_updated":"2024-06-27T06:42:55Z","has_accepted_license":"1","intvolume":"         5","issue":"1","author":[{"full_name":"Aebischer, Kathrin","first_name":"Kathrin","last_name":"Aebischer"},{"last_name":"Becker","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie"},{"first_name":"Paul","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"first_name":"Matthias","full_name":"Ernst, Matthias","last_name":"Ernst"}],"oa":1,"file":[{"success":1,"file_id":"17181","date_created":"2024-06-27T06:42:55Z","access_level":"open_access","date_updated":"2024-06-27T06:42:55Z","checksum":"d01074f6919387fcaf8c9ebed320ccae","content_type":"application/pdf","relation":"main_file","file_size":6736194,"file_name":"2024_MagneticResonance_Aebischer.pdf","creator":"dernst"}],"abstract":[{"lang":"eng","text":"Dynamic processes in molecules can occur on a wide range of timescales, and it is important to understand which timescales of motion contribute to different parameters used in dynamics measurements. For spin relaxation, this can easily be understood from the sampling frequencies of the spectral-density function by different relaxation-rate constants. In addition to data from relaxation measurements, determining dynamically averaged anisotropic interactions in magic-angle spinning (MAS) solid-state NMR allows for better quantification of the amplitude of molecular motion. For partially averaged anisotropic interactions, the relevant timescales of motion are not so clearly defined. Whether the averaging depends on the experimental methods (e.g., pulse sequences) or conditions (e.g., MAS frequency, magnitude of anisotropic interaction, radio-frequency field amplitudes) is not fully understood. To investigate these questions, we performed numerical simulations of dynamic systems based on the stochastic Liouville equation using several experiments for recoupling the dipolar coupling, chemical-shift anisotropy or quadrupolar coupling. As described in the literature, the transition between slow motion, where parameters characterizing the anisotropic interaction are not averaged, and fast motion, where the tensors are averaged leading to a scaled anisotropic quantity, occurs over a window of motional rate constants that depends mainly on the strength of the interaction. This transition region can span 2 orders of magnitude in exchange-rate constants (typically in the microsecond range) but depends only marginally on the employed recoupling scheme or sample spinning frequency. The transition region often coincides with a fast relaxation of coherences, making precise quantitative measurements difficult. Residual couplings in off-magic-angle experiments, however, average over longer timescales of motion. While in principle one may gain information on the timescales of motion from the transition area, extracting such information is hampered by low signal-to-noise ratio in experimental spectra due to fast relaxation that occurs in the same region."}],"publisher":"Copernicus Publications","date_created":"2024-06-23T22:01:02Z","acknowledgement":"We would like to thank Kay Saalwächter for pointing out important aspects of the intermediate regime during the open review process. Lea Marie Becker is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria.\r\nThis research has been supported by the Österreichischen Akademie der Wissenschaften (grant no. PR10660EAW01) and the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (grant nos. 200020_188988 and 200020_219375).","title":"Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR","publication":"Magnetic Resonance","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-11T13:26:12Z","pmid":1},{"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"short":"K. Chatterjee, A.K. Goharshady, T. Meggendorfer, D. Zikelic, Proceedings of the ACM on Programming Languages 8 (2024).","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Tobias Meggendorfer, and Dorde Zikelic. “Quantitative Bounds on Resource Usage of Probabilistic Programs.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3649824\">https://doi.org/10.1145/3649824</a>.","ista":"Chatterjee K, Goharshady AK, Meggendorfer T, Zikelic D. 2024. Quantitative bounds on resource usage of probabilistic programs. Proceedings of the ACM on Programming Languages. 8(OOPSLA1), 107.","ama":"Chatterjee K, Goharshady AK, Meggendorfer T, Zikelic D. Quantitative bounds on resource usage of probabilistic programs. <i>Proceedings of the ACM on Programming Languages</i>. 2024;8(OOPSLA1). doi:<a href=\"https://doi.org/10.1145/3649824\">10.1145/3649824</a>","apa":"Chatterjee, K., Goharshady, A. K., Meggendorfer, T., &#38; Zikelic, D. (2024). Quantitative bounds on resource usage of probabilistic programs. <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3649824\">https://doi.org/10.1145/3649824</a>","ieee":"K. Chatterjee, A. K. Goharshady, T. Meggendorfer, and D. Zikelic, “Quantitative bounds on resource usage of probabilistic programs,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 8, no. OOPSLA1. Association for Computing Machinery, 2024.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Bounds on Resource Usage of Probabilistic Programs.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 8, no. OOPSLA1, 107, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3649824\">10.1145/3649824</a>."},"file_date_updated":"2024-06-27T07:48:16Z","publication_status":"published","status":"public","date_published":"2024-04-29T00:00:00Z","year":"2024","has_accepted_license":"1","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","last_name":"Goharshady"},{"last_name":"Meggendorfer","first_name":"Tobias","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"last_name":"Zikelic","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699"}],"issue":"OOPSLA1","intvolume":"         8","file":[{"date_updated":"2024-06-27T07:48:16Z","access_level":"open_access","file_id":"17182","success":1,"date_created":"2024-06-27T07:48:16Z","creator":"dernst","file_size":413096,"file_name":"2024_ProcACMProgLanguage_Chatterjee.pdf","relation":"main_file","content_type":"application/pdf","checksum":"9243ded966f71df1572be5466019be5c"}],"abstract":[{"text":"Cost analysis, also known as resource usage analysis, is the task of finding bounds on the total cost of a program and is a well-studied problem in static analysis. In this work, we consider two classical quantitative problems in cost analysis for probabilistic programs. The first problem is to find a bound on the expected total cost of the program. This is a natural measure for the resource usage of the program and can also be directly applied to average-case runtime analysis. The second problem asks for a tail bound, i.e. ‍given a threshold t the goal is to find a probability bound p such that ℙ[total cost ≥ t] ≤ p. Intuitively, given a threshold t on the resource, the problem is to find the likelihood that the total cost exceeds this threshold.\r\nFirst, for expectation bounds, a major obstacle in previous works on cost analysis is that they can handle only non-negative costs or bounded variable updates. In contrast, we provide a new variant of the standard notion of cost martingales, that allows us to find expectation bounds for a class of programs with general positive or negative costs and no restriction on the variable updates. More specifically, our approach is applicable as long as there is a lower bound on the total cost incurred along every path.\r\nSecond, for tail bounds, all previous methods are limited to programs in which the expected total cost is finite. In contrast, we present a novel approach, based on a combination of our martingale-based method for expectation bounds with a quantitative safety analysis, to obtain a solution to the tail bound problem that is applicable even to programs with infinite expected cost. Specifically, this allows us to obtain runtime tail bounds for programs that do not terminate almost-surely.\r\nIn summary, we provide a novel combination of martingale-based cost analysis and quantitative safety analysis that is able to find expectation and tail cost bounds for probabilistic programs, without the restrictions of non-negative costs, bounded updates, or finiteness of the expected total cost. Finally, we provide experimental results showcasing that our approach can solve instances that were beyond the reach of previous methods.","lang":"eng"}],"oa":1,"publisher":"Association for Computing Machinery","ec_funded":1,"publication":"Proceedings of the ACM on Programming Languages","title":"Quantitative bounds on resource usage of probabilistic programs","acknowledgement":"This work was supported in part by the European Research Council (ERC) under Grant No. 863818\r\n(ForM-SMArt) and the Hong Kong Research Grants Council under ECS Project No. 26208122.","date_created":"2024-06-23T22:01:02Z","date_updated":"2025-04-14T07:52:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"29","doi":"10.1145/3649824","publication_identifier":{"eissn":["2475-1421"]},"volume":8,"_id":"17162","project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"article_type":"original","article_number":"107","department":[{"_id":"KrCh"}],"ddc":["000"],"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","month":"04","type":"journal_article","oa_version":"Published Version"},{"author":[{"first_name":"Dominique","full_name":"Attali, Dominique","last_name":"Attali"},{"full_name":"Kourimska, Hana","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","orcid":"0000-0001-7841-0091","first_name":"Hana","last_name":"Kourimska"},{"last_name":"Fillmore","first_name":"Christopher D","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","full_name":"Fillmore, Christopher D"},{"last_name":"Ghosh","first_name":"Ishika","full_name":"Ghosh, Ishika","id":"ee449b28-344d-11ef-a6d5-9ca430e9e9ff"},{"last_name":"Lieutier","full_name":"Lieutier, André","first_name":"André"},{"first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-208X","last_name":"Stephenson"},{"orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","first_name":"Mathijs","last_name":"Wintraecken"}],"intvolume":"       293","has_accepted_license":"1","alternative_title":["LIPIcs"],"citation":{"chicago":"Attali, Dominique, Hana Kourimska, Christopher D Fillmore, Ishika Ghosh, André Lieutier, Elizabeth R Stephenson, and Mathijs Wintraecken. “Tight Bounds for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.” In <i>40th International Symposium on Computational Geometry</i>, 293:11:1-11:19. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">https://doi.org/10.4230/LIPIcs.SoCG.2024.11</a>.","short":"D. Attali, H. Kourimska, C.D. Fillmore, I. Ghosh, A. Lieutier, E.R. Stephenson, M. Wintraecken, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19.","mla":"Attali, Dominique, et al. “Tight Bounds for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">10.4230/LIPIcs.SoCG.2024.11</a>.","ista":"Attali D, Kourimska H, Fillmore CD, Ghosh I, Lieutier A, Stephenson ER, Wintraecken M. 2024. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 11:1-11:19.","ama":"Attali D, Kourimska H, Fillmore CD, et al. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:11:1-11:19. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">10.4230/LIPIcs.SoCG.2024.11</a>","ieee":"D. Attali <i>et al.</i>, “Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293, p. 11:1-11:19.","apa":"Attali, D., Kourimska, H., Fillmore, C. D., Ghosh, I., Lieutier, A., Stephenson, E. R., &#38; Wintraecken, M. (2024). Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293, p. 11:1-11:19). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">https://doi.org/10.4230/LIPIcs.SoCG.2024.11</a>"},"file_date_updated":"2024-06-25T11:47:26Z","publication_status":"published","status":"public","date_published":"2024-06-06T00:00:00Z","year":"2024","language":[{"iso":"eng"}],"external_id":{"arxiv":["2206.10485"]},"quality_controlled":"1","date_updated":"2025-04-15T07:16:57Z","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"40th International Symposium on Computational Geometry","title":"Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds","acknowledgement":"This research has been supported by the European Research Council (ERC), grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant No. I 02979-N35.\r\nWintraecken, Mathijs: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) grant No. M-3073, and the welcome package from IDEX of the Université Côte d'Azur.","date_created":"2024-06-25T11:45:58Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ec_funded":1,"file":[{"file_size":20886142,"file_name":"LIPIcs.SoCG.2024.11.pdf","creator":"cfillmor","checksum":"6a2ddc8b51aa58f197a8b294750f1f8d","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2024-06-25T11:47:26Z","date_created":"2024-06-25T11:47:26Z","file_id":"17171","success":1}],"abstract":[{"text":"In this article we extend and strengthen the seminal work by Niyogi, Smale, and Weinberger on the learning of the homotopy type from a sample of an underlying space. In their work, Niyogi, Smale, and Weinberger studied samples of C² manifolds with positive reach embedded in ℝ^d. We extend their results in the following ways: - As the ambient space we consider both ℝ^d and Riemannian manifolds with lower bounded sectional curvature. - In both types of ambient spaces, we study sets of positive reach - a significantly more general setting than C² manifolds - as well as general manifolds of positive reach. - The sample P of a set (or a manifold) 𝒮 of positive reach may be noisy. We work with two one-sided Hausdorff distances - ε and δ - between P and 𝒮. We provide tight bounds in terms of ε and δ, that guarantee that there exists a parameter r such that the union of balls of radius r centred at the sample P deformation-retracts to 𝒮. We exhibit their tightness by an explicit construction. We carefully distinguish the roles of δ and ε. This is not only essential to achieve tight bounds, but also sensible in practical situations, since it allows one to adapt the bound according to sample density and the amount of noise present in the sample separately.","lang":"eng"}],"oa":1,"conference":{"start_date":"2024-06-11","name":"SoCG: Symposium on Computational Geometry","end_date":"2024-06-14","location":"Athens, Greece"},"volume":293,"_id":"17170","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","grant_number":"Z00342"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"},{"name":"Learning and triangulating manifolds via collapses","grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"day":"06","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.4230/LIPIcs.SoCG.2024.11","publication_identifier":{"isbn":["9783959773164"],"eissn":["1868-8969"]},"month":"06","type":"conference","oa_version":"Published Version","article_processing_charge":"No","page":"11:1-11:19","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"ddc":["516"],"scopus_import":"1"}]