[{"external_id":{"pmid":["37632747"]},"file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":4879455,"file_name":"2023_CellPress_Nardin.pdf","success":1,"date_updated":"2023-09-15T07:12:46Z","checksum":"ca77a304fb813c292550b8604b0fb41d","date_created":"2023-09-15T07:12:46Z","file_id":"14337"}],"title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","publication":"Cell Reports","project":[{"call_identifier":"FP7","grant_number":"607616","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","name":"Inter-and intracellular signalling in schizophrenia"}],"citation":{"apa":"Nardin, M., Käfer, K., Stella, F., &#38; Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>","ista":"Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015.","mla":"Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>, vol. 42, no. 9, 113015, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>.","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).","ama":"Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. 2023;42(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>","chicago":"Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>.","ieee":"M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” <i>Cell Reports</i>, vol. 42, no. 9. Elsevier, 2023."},"has_accepted_license":"1","issue":"9","scopus_import":"1","ec_funded":1,"abstract":[{"text":"The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations.","lang":"eng"}],"oa_version":"Published Version","publication_status":"published","day":"26","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2023-09-15T07:14:12Z","status":"public","quality_controlled":"1","publication_identifier":{"eissn":["2211-1247"]},"month":"09","volume":42,"article_type":"original","pmid":1,"acknowledgement":"We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616).","department":[{"_id":"JoCs"}],"date_created":"2023-09-10T22:01:11Z","article_number":"113015","intvolume":"        42","ddc":["570"],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-09-15T07:12:46Z","oa":1,"_id":"14314","author":[{"orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","first_name":"Michele","full_name":"Nardin, Michele"},{"last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola","first_name":"Karola"},{"orcid":"0000-0001-9439-3148","last_name":"Stella","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","full_name":"Stella, Federico","first_name":"Federico"},{"last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"}],"date_published":"2023-09-26T00:00:00Z","publisher":"Elsevier","year":"2023","language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2023.113015","type":"journal_article"},{"intvolume":"        12","file_date_updated":"2023-09-15T06:59:10Z","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"department":[{"_id":"MaHe"}],"acknowledgement":"We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.","pmid":1,"date_created":"2023-09-10T22:01:11Z","article_number":"RP89066","article_type":"original","volume":12,"publication_identifier":{"eissn":["2050-084X"]},"quality_controlled":"1","month":"09","type":"journal_article","year":"2023","publisher":"eLife Sciences Publications","doi":"10.7554/eLife.89066","language":[{"iso":"eng"}],"date_published":"2023-09-04T00:00:00Z","_id":"14315","oa":1,"author":[{"last_name":"Cho","first_name":"Ukrae H.","full_name":"Cho, Ukrae H."},{"full_name":"Hetzer, Martin W","first_name":"Martin W","orcid":"0000-0002-2111-992X","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"has_accepted_license":"1","scopus_import":"1","citation":{"ieee":"U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2023.","chicago":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>. eLife Sciences Publications, 2023. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>.","ama":"Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>eLife</i>. 2023;12. doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>","apa":"Cho, U. H., &#38; Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>","ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","short":"U.H. Cho, M. Hetzer, ELife 12 (2023).","mla":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>."},"file":[{"file_size":3703097,"file_name":"2023_eLife_Cho.pdf","success":1,"date_updated":"2023-09-15T06:59:10Z","checksum":"db24bf3d595507387b48d3799c33e289","date_created":"2023-09-15T06:59:10Z","file_id":"14336","creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","external_id":{"pmid":["37665327"]},"publication":"eLife","status":"public","date_updated":"2023-09-15T07:07:10Z","abstract":[{"text":"During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"04","oa_version":"Published Version","publication_status":"published"},{"author":[{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"first_name":"Kaito","full_name":"Aoshima, Kaito","last_name":"Aoshima"},{"last_name":"Shimamura","first_name":"Hiroki","full_name":"Shimamura, Hiroki"},{"orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","first_name":"Daria E"},{"last_name":"Toshima","full_name":"Toshima, Junko Y.","first_name":"Junko Y."},{"last_name":"Toshima","first_name":"Jiro","full_name":"Toshima, Jiro"}],"_id":"14316","oa":1,"date_published":"2023-09-01T00:00:00Z","doi":"10.1242/jcs.261448","language":[{"iso":"eng"}],"year":"2023","publisher":"The Company of Biologists","type":"journal_article","month":"09","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"quality_controlled":"1","volume":136,"article_type":"original","article_number":"jcs261448","date_created":"2023-09-10T22:01:12Z","department":[{"_id":"DaSi"}],"pmid":1,"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       136","day":"01","oa_version":"Preprint","publication_status":"published","abstract":[{"lang":"eng","text":"Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway."}],"date_updated":"2023-09-20T09:14:15Z","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.03.27.534325"}],"publication":"Journal of Cell Science","title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","external_id":{"pmid":["37539494"]},"citation":{"ieee":"M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” <i>Journal of Cell Science</i>, vol. 136, no. 17. The Company of Biologists, 2023.","chicago":"Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>.","ama":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. 2023;136(17). doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>","mla":"Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>.","short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","apa":"Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &#38; Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>","ista":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448."},"scopus_import":"1","issue":"17"},{"status":"public","date_updated":"2025-07-14T09:09:56Z","day":"17","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","page":"86-112","oa_version":"Published Version","abstract":[{"text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples.","lang":"eng"}],"ec_funded":1,"scopus_import":"1","has_accepted_license":"1","alternative_title":["LNCS"],"citation":{"ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:86-112. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>","mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>.","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in <i>International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 86–112.","chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 13966:86–112. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>."},"project":[{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"publication":"International Conference on Computer Aided Verification","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"date_updated":"2023-09-20T08:46:43Z","file_id":"14349","date_created":"2023-09-20T08:46:43Z","checksum":"f143c8eedf609f20f2aad2eeb496d53f","file_size":531745,"file_name":"2023_LNCS_Akshay.pdf"}],"title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","type":"conference","doi":"10.1007/978-3-031-37709-9_5","language":[{"iso":"eng"}],"year":"2023","publisher":"Springer Nature","date_published":"2023-07-17T00:00:00Z","author":[{"last_name":"Akshay","full_name":"Akshay, S.","first_name":"S."},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"orcid":"0000-0002-1712-2165","last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias","first_name":"Tobias"},{"last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","first_name":"Dorde"}],"_id":"14317","oa":1,"conference":{"name":"CAV: Computer Aided Verification","end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France"},"file_date_updated":"2023-09-20T08:46:43Z","ddc":["000"],"article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"     13966","date_created":"2023-09-10T22:01:12Z","acknowledgement":"This work was supported in part by the ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","department":[{"_id":"KrCh"}],"volume":13966,"month":"07","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031377082"]},"quality_controlled":"1"},{"article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"file_date_updated":"2023-09-20T08:24:47Z","conference":{"end_date":"2023-07-22","start_date":"2023-07-17","name":"CAV: Computer Aided Verification","location":"Paris, France"},"intvolume":"     13966","date_created":"2023-09-10T22:01:12Z","department":[{"_id":"KrCh"}],"acknowledgement":"We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.","volume":13966,"month":"07","quality_controlled":"1","publication_identifier":{"isbn":["9783031377082"],"issn":["0302-9743"],"eissn":["1611-3349"]},"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-37709-9_2","publisher":"Springer Nature","year":"2023","date_published":"2023-07-17T00:00:00Z","author":[{"full_name":"Sun, Yican","first_name":"Yican","last_name":"Sun"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar"}],"oa":1,"_id":"14318","scopus_import":"1","alternative_title":["LNCS"],"has_accepted_license":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"citation":{"apa":"Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In <i>Computer Aided Verification</i> (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>","short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39.","mla":"Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” <i>Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>.","ista":"Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39.","ama":"Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: <i>Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:16-39. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>","chicago":"Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In <i>Computer Aided Verification</i>, 13966:16–39. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>.","ieee":"Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in <i>Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 16–39."},"publication":"Computer Aided Verification","related_material":{"link":[{"url":"https://github.com/boyvolcano/PRR","relation":"software"}]},"title":"Automated tail bound analysis for probabilistic recurrence relations","file":[{"creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2023_LNCS_Sun.pdf","file_size":624647,"file_id":"14348","date_created":"2023-09-20T08:24:47Z","checksum":"42917e086f8c7699f3bccf84f74fe000","date_updated":"2023-09-20T08:24:47Z","success":1}],"status":"public","date_updated":"2025-07-14T09:09:57Z","page":"16-39","publication_status":"published","oa_version":"Published Version","day":"17","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"abstract":[{"lang":"eng","text":"Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice."}]},{"date_created":"2023-09-10T22:01:12Z","article_number":"P3.10","department":[{"_id":"MaKw"}],"acknowledgement":"Anastos has received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Sk lodowska-Curie grant agreement No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft (DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).","file_date_updated":"2023-09-15T08:02:09Z","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","intvolume":"        30","month":"07","publication_identifier":{"eissn":["1077-8926"]},"quality_controlled":"1","volume":30,"article_type":"original","doi":"10.37236/11714","language":[{"iso":"eng"}],"year":"2023","publisher":"Electronic Journal of Combinatorics","type":"journal_article","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos","full_name":"Anastos, Michael","first_name":"Michael"},{"full_name":"Fabian, David","first_name":"David","last_name":"Fabian"},{"last_name":"Müyesser","full_name":"Müyesser, Alp","first_name":"Alp"},{"last_name":"Szabó","first_name":"Tibor","full_name":"Szabó, Tibor"}],"_id":"14319","oa":1,"date_published":"2023-07-28T00:00:00Z","arxiv":1,"citation":{"apa":"Anastos, M., Fabian, D., Müyesser, A., &#38; Szabó, T. (2023). Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>","mla":"Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3, P3.10, Electronic Journal of Combinatorics, 2023, doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>.","short":"M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023).","ista":"Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 30(3), P3.10.","ama":"Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. 2023;30(3). doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>","chicago":"Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2023. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>.","ieee":"M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets,” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3. Electronic Journal of Combinatorics, 2023."},"project":[{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"scopus_import":"1","issue":"3","has_accepted_license":"1","publication":"Electronic Journal of Combinatorics","file":[{"date_created":"2023-09-15T08:02:09Z","checksum":"52c46c8cb329f9aaee9ade01525f317b","file_id":"14338","date_updated":"2023-09-15T08:02:09Z","success":1,"file_name":"2023_elecJournCombinatorics_Anastos.pdf","file_size":247917,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"dernst"}],"title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","external_id":{"arxiv":["2212.03100"]},"date_updated":"2023-09-15T08:12:30Z","status":"public","license":"https://creativecommons.org/licenses/by-nd/4.0/","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"day":"28","oa_version":"Published Version","publication_status":"published","abstract":[{"lang":"eng","text":"We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We\r\nalso make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities."}],"ec_funded":1},{"quality_controlled":"1","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"09","volume":108,"article_type":"original","acknowledgement":"A.F.Y. acknowledges primary support from the Department of Energy under award DE-SC0020043, and additional support from the Gordon and Betty Moore Foundation under award GBMF9471 for group operations.","department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"date_created":"2023-09-12T07:12:12Z","article_number":"125411","intvolume":"       108","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa":1,"_id":"14320","author":[{"orcid":"0000-0002-5198-7445","last_name":"Henderson","id":"13C09E74-18D9-11E9-8878-32CFE5697425","first_name":"Paul M","full_name":"Henderson, Paul M"},{"full_name":"Ghazaryan, Areg","first_name":"Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander A.","full_name":"Zibrov, Alexander A.","last_name":"Zibrov"},{"full_name":"Young, Andrea F.","first_name":"Andrea F.","last_name":"Young"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"date_published":"2023-09-15T00:00:00Z","publisher":"American Physical Society","year":"2023","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.108.125411","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.06310","open_access":"1"}],"external_id":{"arxiv":["2210.06310"]},"title":"Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene","publication":"Physical Review B","arxiv":1,"citation":{"ieee":"P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn, “Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene,” <i>Physical Review B</i>, vol. 108, no. 12. American Physical Society, 2023.","chicago":"Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young, and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>.","ama":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. 2023;108(12). doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>","ista":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 108(12), 125411.","apa":"Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., &#38; Serbyn, M. (2023). Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>","short":"P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (2023).","mla":"Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>."},"issue":"12","scopus_import":"1","abstract":[{"lang":"eng","text":"The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance."}],"oa_version":"Preprint","publication_status":"published","day":"15","date_updated":"2023-09-20T09:38:24Z","status":"public"},{"quality_controlled":"1","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"month":"09","article_type":"original","volume":159,"pmid":1,"department":[{"_id":"MiLe"}],"acknowledgement":"We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot.","article_number":"104103","date_created":"2023-09-13T09:25:09Z","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"intvolume":"       159","article_processing_charge":"Yes (in subscription journal)","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-09-13T09:34:20Z","oa":1,"_id":"14321","author":[{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","last_name":"Al Hyder","full_name":"Al Hyder, Ragheed","first_name":"Ragheed"},{"id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","orcid":"0000-0001-6110-2359","first_name":"Alberto","full_name":"Cappellaro, Alberto"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"},{"full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}],"date_published":"2023-09-11T00:00:00Z","publisher":"AIP Publishing","year":"2023","language":[{"iso":"eng"}],"doi":"10.1063/5.0165806","type":"journal_article","external_id":{"arxiv":["2306.17592"],"pmid":["37694742"]},"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"acappell","date_created":"2023-09-13T09:34:20Z","file_id":"14322","checksum":"507ab65ab29e2c987c94cabad7c5370b","date_updated":"2023-09-13T09:34:20Z","success":1,"file_name":"104103_1_5.0165806.pdf","file_size":5749653}],"title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","publication":"The Journal of Chemical Physics","project":[{"name":"Non-equilibrium Field Theory of Molecular Rotations","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338","grant_number":"101062862"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770"}],"arxiv":1,"citation":{"ama":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. 2023;159(10). doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>","apa":"Al Hyder, R., Cappellaro, A., Lemeshko, M., &#38; Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>","ista":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103.","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023).","mla":"Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>.","ieee":"R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10. AIP Publishing, 2023.","chicago":"Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>."},"has_accepted_license":"1","issue":"10","scopus_import":"1","ec_funded":1,"abstract":[{"text":"We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.","lang":"eng"}],"oa_version":"Published Version","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"11","date_updated":"2023-09-20T09:48:12Z","status":"public"},{"publication_status":"published","oa_version":"Published Version","page":"151","day":"13","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube."}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"status":"public","date_updated":"2024-03-07T15:02:59Z","related_material":{"record":[{"id":"7883","status":"public","relation":"part_of_dissertation"}]},"file":[{"embargo":"2025-03-13","creator":"kkuzmicz","relation":"main_file","content_type":"application/pdf","access_level":"closed","file_size":10147911,"file_name":"PhDThesis_KK_final_pdfA.pdf","embargo_to":"open_access","date_updated":"2023-09-13T10:08:25Z","checksum":"bd83596869c814b24aeff7077d031c0e","date_created":"2023-09-13T09:52:52Z","file_id":"14324"},{"creator":"kkuzmicz","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":103980668,"file_name":"thesis_KK_final_corrections_092023.docx","date_updated":"2023-09-13T09:53:29Z","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","date_created":"2023-09-13T09:53:29Z","file_id":"14325"}],"title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","project":[{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","apa":"Kuzmicz-Kowalska, K. (2023). <i>Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>","mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023.","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>."},"date_published":"2023-09-13T00:00:00Z","author":[{"full_name":"Kuzmicz-Kowalska, Katarzyna","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","last_name":"Kuzmicz-Kowalska"}],"_id":"14323","type":"dissertation","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14323","publisher":"Institute of Science and Technology Austria","year":"2023","supervisor":[{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna"}],"month":"09","publication_identifier":{"issn":["2663 - 337X"]},"ddc":["570"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","file_date_updated":"2023-09-13T10:08:25Z","date_created":"2023-09-13T10:07:18Z","department":[{"_id":"GradSch"},{"_id":"AnKi"}]},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2307.09552","open_access":"1"}],"month":"07","external_id":{"arxiv":["2307.09552"]},"title":"Self-compatibility: Evaluating causal discovery without ground truth","publication":"arXiv","department":[{"_id":"FrLo"}],"citation":{"ama":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2307.09552\">10.48550/arXiv.2307.09552</a>","mla":"Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” <i>ArXiv</i>, 2307.09552, doi:<a href=\"https://doi.org/10.48550/arXiv.2307.09552\">10.48550/arXiv.2307.09552</a>.","apa":"Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., &#38; Janzing, D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2307.09552\">https://doi.org/10.48550/arXiv.2307.09552</a>","ista":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. arXiv, 2307.09552.","short":"P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv (n.d.).","ieee":"P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing, “Self-compatibility: Evaluating causal discovery without ground truth,” <i>arXiv</i>. .","chicago":"Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri, Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2307.09552\">https://doi.org/10.48550/arXiv.2307.09552</a>."},"arxiv":1,"article_number":"2307.09552","date_created":"2023-09-13T12:44:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","extern":"1","oa":1,"_id":"14333","author":[{"last_name":"Faller","first_name":"Philipp M.","full_name":"Faller, Philipp M."},{"last_name":"Vankadara","first_name":"Leena Chennuru","full_name":"Vankadara, Leena Chennuru"},{"first_name":"Atalanti A.","full_name":"Mastakouri, Atalanti A.","last_name":"Mastakouri"},{"first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"full_name":"Janzing, Dominik","first_name":"Dominik","last_name":"Janzing"}],"abstract":[{"text":"As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly only evaluated on simulated data. This is concerning, given that\r\nsimulations reflect common preconceptions about generating processes regarding\r\nnoise distributions, model classes, and more. In this work, we propose a novel\r\nmethod for falsifying the output of a causal discovery algorithm in the absence\r\nof ground truth. Our key insight is that while statistical learning seeks\r\nstability across subsets of data points, causal learning should seek stability\r\nacross subsets of variables. Motivated by this insight, our method relies on a\r\nnotion of compatibility between causal graphs learned on different subsets of\r\nvariables. We prove that detecting incompatibilities can falsify wrongly\r\ninferred causal relations due to violation of assumptions or errors from finite\r\nsample effects. Although passing such compatibility tests is only a necessary\r\ncriterion for good performance, we argue that it provides strong evidence for\r\nthe causal models whenever compatibility entails strong implications for the\r\njoint distribution. We also demonstrate experimentally that detection of\r\nincompatibilities can aid in causal model selection.","lang":"eng"}],"date_published":"2023-07-18T00:00:00Z","publication_status":"submitted","oa_version":"Preprint","day":"18","date_updated":"2023-09-13T12:47:53Z","year":"2023","language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2307.09552","type":"preprint","status":"public"},{"project":[{"call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"citation":{"ieee":"P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models,” <i>SciPost Physics</i>, vol. 15, no. 3. SciPost Foundation, 2023.","chicago":"Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” <i>SciPost Physics</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">https://doi.org/10.21468/scipostphys.15.3.093</a>.","ama":"Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. <i>SciPost Physics</i>. 2023;15(3). doi:<a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">10.21468/scipostphys.15.3.093</a>","short":"P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).","mla":"Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” <i>SciPost Physics</i>, vol. 15, no. 3, 093, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">10.21468/scipostphys.15.3.093</a>.","ista":"Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093.","apa":"Brighi, P., Ljubotina, M., &#38; Serbyn, M. (2023). Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">https://doi.org/10.21468/scipostphys.15.3.093</a>"},"arxiv":1,"issue":"3","has_accepted_license":"1","publication":"SciPost Physics","external_id":{"arxiv":["2210.15607"]},"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"12750"}]},"title":"Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models","file":[{"file_size":4866506,"file_name":"2023_SciPostPhysics_Brighi.pdf","date_updated":"2023-09-20T10:46:10Z","success":1,"checksum":"4cef6a8021f6b6c47ab2f2f2b1387ac2","file_id":"14350","date_created":"2023-09-20T10:46:10Z","creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access"}],"date_updated":"2023-09-20T10:46:29Z","status":"public","oa_version":"Published Version","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"13","ec_funded":1,"abstract":[{"lang":"eng","text":"Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies."}],"date_created":"2023-09-14T13:08:23Z","article_number":"093","acknowledgement":"We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry Abanin for useful\r\ndiscussions.The authors acknowledge support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger International\r\nInstitute for Mathematics and Physics (ESI).","department":[{"_id":"MaSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","ddc":["530"],"file_date_updated":"2023-09-20T10:46:10Z","keyword":["General Physics and Astronomy"],"intvolume":"        15","month":"09","quality_controlled":"1","publication_identifier":{"issn":["2542-4653"]},"volume":15,"article_type":"original","language":[{"iso":"eng"}],"doi":"10.21468/scipostphys.15.3.093","publisher":"SciPost Foundation","year":"2023","type":"journal_article","author":[{"first_name":"Pietro","full_name":"Brighi, Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","orcid":"0000-0002-7969-2729"},{"first_name":"Marko","full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"}],"oa":1,"_id":"14334","date_published":"2023-09-13T00:00:00Z"},{"oa_version":"Published Version","publication_status":"published","page":"1500-1513","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux."}],"date_updated":"2023-12-13T12:23:49Z","status":"public","publication":"Nature Plants","external_id":{"pmid":["37666965"],"isi":["001069238800014"]},"title":"Antigravitropic PIN polarization maintains non-vertical growth in lateral roots","file":[{"file_size":9647103,"file_name":"2023_NaturePlants_Roychoudhry.pdf","date_updated":"2023-09-20T10:51:31Z","success":1,"checksum":"3d6d5d5abb937c14a5f6f0afba3b8624","file_id":"14351","date_created":"2023-09-20T10:51:31Z","creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access"}],"citation":{"ieee":"S. Roychoudhry <i>et al.</i>, “Antigravitropic PIN polarization maintains non-vertical growth in lateral roots,” <i>Nature Plants</i>, vol. 9. Springer Nature, pp. 1500–1513, 2023.","chicago":"Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan, Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” <i>Nature Plants</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41477-023-01478-x\">https://doi.org/10.1038/s41477-023-01478-x</a>.","ama":"Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. <i>Nature Plants</i>. 2023;9:1500-1513. doi:<a href=\"https://doi.org/10.1038/s41477-023-01478-x\">10.1038/s41477-023-01478-x</a>","ista":"Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 9, 1500–1513.","mla":"Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” <i>Nature Plants</i>, vol. 9, Springer Nature, 2023, pp. 1500–13, doi:<a href=\"https://doi.org/10.1038/s41477-023-01478-x\">10.1038/s41477-023-01478-x</a>.","short":"S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar, M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml, S. Kepinski, Nature Plants 9 (2023) 1500–1513.","apa":"Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar, G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-023-01478-x\">https://doi.org/10.1038/s41477-023-01478-x</a>"},"has_accepted_license":"1","author":[{"last_name":"Roychoudhry","first_name":"S","full_name":"Roychoudhry, S"},{"first_name":"K","full_name":"Sageman-Furnas, K","last_name":"Sageman-Furnas"},{"last_name":"Wolverton","full_name":"Wolverton, C","first_name":"C"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","full_name":"Grones, Peter","first_name":"Peter"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","first_name":"Shutang"},{"full_name":"Molnar, Gergely","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar"},{"full_name":"De Angelis, M","first_name":"M","last_name":"De Angelis"},{"first_name":"HL","full_name":"Goodman, HL","last_name":"Goodman"},{"first_name":"N","full_name":"Capstaff, N","last_name":"Capstaff"},{"first_name":"Lloyd","full_name":"JPB, Lloyd","last_name":"JPB"},{"first_name":"J","full_name":"Mullen, J","last_name":"Mullen"},{"last_name":"Hangarter","full_name":"Hangarter, R","first_name":"R"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"last_name":"Kepinski","full_name":"Kepinski, S","first_name":"S"}],"oa":1,"_id":"14339","date_published":"2023-09-01T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1038/s41477-023-01478-x","publisher":"Springer Nature","year":"2023","type":"journal_article","month":"09","quality_controlled":"1","publication_identifier":{"issn":["2055-0278"]},"isi":1,"article_type":"original","volume":9,"date_created":"2023-09-15T09:56:01Z","pmid":1,"acknowledgement":"We thank D. Weijers, C. Schwechheimer and R. Offringa for generous sharing of published and unpublished materials and P. Masson for advice on the use of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1 and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust (RPG-2018-137 to S.K.).","department":[{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","ddc":["580"],"file_date_updated":"2023-09-20T10:51:31Z","intvolume":"         9"},{"external_id":{"pmid":["37673988"]},"related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://www.ista.ac.at/en/news/pumping-like-the-heart/"}]},"title":"Turbulence suppression by cardiac-cycle-inspired driving of pipe flow","publication":"Nature","issue":"7977","scopus_import":"1","project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960"},{"_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","call_identifier":"FWF","grant_number":"I04188"}],"citation":{"short":"D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.","mla":"Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” <i>Nature</i>, vol. 621, no. 7977, Springer Nature, 2023, pp. 71–74, doi:<a href=\"https://doi.org/10.1038/s41586-023-06399-5\">10.1038/s41586-023-06399-5</a>.","ista":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74.","apa":"Scarselli, D., Lopez Alonso, J. M., Varshney, A., &#38; Hof, B. (2023). Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06399-5\">https://doi.org/10.1038/s41586-023-06399-5</a>","ama":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. <i>Nature</i>. 2023;621(7977):71-74. doi:<a href=\"https://doi.org/10.1038/s41586-023-06399-5\">10.1038/s41586-023-06399-5</a>","chicago":"Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06399-5\">https://doi.org/10.1038/s41586-023-06399-5</a>.","ieee":"D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression by cardiac-cycle-inspired driving of pipe flow,” <i>Nature</i>, vol. 621, no. 7977. Springer Nature, pp. 71–74, 2023."},"abstract":[{"lang":"eng","text":"Flows through pipes and channels are, in practice, almost always turbulent, and the multiscale eddying motion is responsible for a major part of the encountered friction losses and pumping costs1. Conversely, for pulsatile flows, in particular for aortic blood flow, turbulence levels remain low despite relatively large peak velocities. For aortic blood flow, high turbulence levels are intolerable as they would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile mode that incorporates all the key features of the cardiac waveform. At Reynolds numbers comparable to those of aortic blood flow, turbulence is largely inhibited, whereas at much higher speeds, the turbulent drag is reduced by more than 25%. This specific operation mode is more efficient when compared with steady driving, which is the present situation for virtually all fluid transport processes ranging from heating circuits to water, gas and oil pipelines."}],"page":"71-74","oa_version":"None","publication_status":"published","day":"07","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"status":"public","date_updated":"2023-09-20T12:10:22Z","volume":621,"article_type":"original","quality_controlled":"1","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"09","intvolume":"       621","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"department":[{"_id":"BjHo"}],"acknowledgement":"We acknowledge the assistance of the Miba machine shop and the team of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.","date_created":"2023-09-17T22:01:09Z","date_published":"2023-09-07T00:00:00Z","_id":"14341","author":[{"first_name":"Davide","full_name":"Scarselli, Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","orcid":"0000-0001-5227-4271"},{"last_name":"Lopez Alonso","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","first_name":"Jose M","full_name":"Lopez Alonso, Jose M"},{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul","first_name":"Atul"},{"first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"type":"journal_article","publisher":"Springer Nature","year":"2023","language":[{"iso":"eng"}],"doi":"10.1038/s41586-023-06399-5"},{"file":[{"creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":1486715,"file_name":"2023_ApplPhysLetter_Lorenc.pdf","date_updated":"2023-09-20T11:36:16Z","success":1,"file_id":"14353","date_created":"2023-09-20T11:36:16Z","checksum":"89a1b604d58b209fec66c6b6f919ac98"}],"title":"Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam","external_id":{"arxiv":["2306.09043"]},"publication":"Applied Physics Letters","arxiv":1,"citation":{"ista":"Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104.","apa":"Lorenc, D., &#38; Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. <i>Applied Physics Letters</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0161713\">https://doi.org/10.1063/5.0161713</a>","short":"D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).","mla":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” <i>Applied Physics Letters</i>, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0161713\">10.1063/5.0161713</a>.","ama":"Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. <i>Applied Physics Letters</i>. 2023;123(9). doi:<a href=\"https://doi.org/10.1063/5.0161713\">10.1063/5.0161713</a>","chicago":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” <i>Applied Physics Letters</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0161713\">https://doi.org/10.1063/5.0161713</a>.","ieee":"D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam,” <i>Applied Physics Letters</i>, vol. 123, no. 9. AIP Publishing, 2023."},"has_accepted_license":"1","scopus_import":"1","issue":"9","abstract":[{"lang":"eng","text":"We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared frequency range that avoids using sophisticated infrared detectors. Our approach is based on using a near-infrared probe beam which interacts with a mid-IR beam via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring XPM-induced spectral modifications in the probe beam and comparing the experimental data with simulation results, we extract the value for the non-degenerate Kerr index. Finally, in order to obtain the value of degenerate mid-IR Kerr index, we use the well-established two-band formalism of Sheik-Bahae et al., which is shown to become particularly simple in the limit of low frequencies. The proposed technique is complementary to the conventional techniques, such as z-scan, and has the advantage of not requiring any mid-infrared detectors."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"28","publication_status":"published","oa_version":"Published Version","date_updated":"2023-09-20T11:50:06Z","status":"public","publication_identifier":{"issn":["0003-6951"]},"quality_controlled":"1","month":"08","article_type":"original","volume":123,"department":[{"_id":"ZhAl"}],"acknowledgement":"The work was supported by IST Austria. The authors would like to gratefully acknowledge the help and assistance of Professor John M. Dudley.","date_created":"2023-09-17T22:01:09Z","article_number":"091104","intvolume":"       123","file_date_updated":"2023-09-20T11:36:16Z","article_processing_charge":"Yes (in subscription journal)","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14342","oa":1,"author":[{"last_name":"Lorenc","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","full_name":"Lorenc, Dusan"},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek"}],"date_published":"2023-08-28T00:00:00Z","year":"2023","publisher":"AIP Publishing","doi":"10.1063/5.0161713","language":[{"iso":"eng"}],"type":"journal_article"},{"acknowledgement":"G.C. and L.E. gratefully acknowledge many discussions with Dominik Schröder at the preliminary stage of this project, especially his essential contribution to identify the correct generalisation of traceless observables to the deformed Wigner ensembles.\r\nL.E. and J.H. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331.","department":[{"_id":"LaEr"},{"_id":"GradSch"}],"date_created":"2023-09-17T22:01:09Z","article_number":"e74","intvolume":"        11","file_date_updated":"2023-09-20T11:09:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","ddc":["510"],"publication_identifier":{"eissn":["2050-5094"]},"quality_controlled":"1","month":"08","article_type":"original","volume":11,"isi":1,"year":"2023","publisher":"Cambridge University Press","doi":"10.1017/fms.2023.70","language":[{"iso":"eng"}],"type":"journal_article","_id":"14343","oa":1,"author":[{"orcid":"0000-0002-4901-7992","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","first_name":"Giorgio"},{"first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös"},{"orcid":"0000-0003-1106-327X","last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","full_name":"Henheik, Sven Joscha","first_name":"Sven Joscha"},{"last_name":"Kolupaiev","id":"149b70d4-896a-11ed-bdf8-8c63fd44ca61","full_name":"Kolupaiev, Oleksii","first_name":"Oleksii"}],"date_published":"2023-08-23T00:00:00Z","arxiv":1,"citation":{"ieee":"G. Cipolloni, L. Erdös, S. J. Henheik, and O. Kolupaiev, “Gaussian fluctuations in the equipartition principle for Wigner matrices,” <i>Forum of Mathematics, Sigma</i>, vol. 11. Cambridge University Press, 2023.","chicago":"Cipolloni, Giorgio, László Erdös, Sven Joscha Henheik, and Oleksii Kolupaiev. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.1017/fms.2023.70\">https://doi.org/10.1017/fms.2023.70</a>.","ama":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. Gaussian fluctuations in the equipartition principle for Wigner matrices. <i>Forum of Mathematics, Sigma</i>. 2023;11. doi:<a href=\"https://doi.org/10.1017/fms.2023.70\">10.1017/fms.2023.70</a>","apa":"Cipolloni, G., Erdös, L., Henheik, S. J., &#38; Kolupaiev, O. (2023). Gaussian fluctuations in the equipartition principle for Wigner matrices. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2023.70\">https://doi.org/10.1017/fms.2023.70</a>","mla":"Cipolloni, Giorgio, et al. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” <i>Forum of Mathematics, Sigma</i>, vol. 11, e74, Cambridge University Press, 2023, doi:<a href=\"https://doi.org/10.1017/fms.2023.70\">10.1017/fms.2023.70</a>.","short":"G. Cipolloni, L. Erdös, S.J. Henheik, O. Kolupaiev, Forum of Mathematics, Sigma 11 (2023).","ista":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. 2023. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 11, e74."},"project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","grant_number":"101020331"}],"has_accepted_license":"1","scopus_import":"1","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2023-09-20T11:09:35Z","success":1,"date_created":"2023-09-20T11:09:35Z","checksum":"eb747420e6a88a7796fa934151957676","file_id":"14352","file_size":852652,"file_name":"2023_ForumMathematics_Cipolloni.pdf"}],"title":"Gaussian fluctuations in the equipartition principle for Wigner matrices","external_id":{"arxiv":["2301.05181"],"isi":["001051980200001"]},"publication":"Forum of Mathematics, Sigma","date_updated":"2023-12-13T12:24:23Z","status":"public","abstract":[{"text":"The total energy of an eigenstate in a composite quantum system tends to be distributed equally among its constituents. We identify the quantum fluctuation around this equipartition principle in the simplest disordered quantum system consisting of linear combinations of Wigner matrices. As our main ingredient, we prove the Eigenstate Thermalisation Hypothesis and Gaussian fluctuation for general quadratic forms of the bulk eigenvectors of Wigner matrices with an arbitrary deformation.","lang":"eng"}],"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"23","oa_version":"Published Version","publication_status":"published"},{"doi":"10.1137/1.9781611977554.ch88","language":[{"iso":"eng"}],"year":"2023","publisher":"Society for Industrial and Applied Mathematics","type":"conference","author":[{"full_name":"Anastos, Michael","first_name":"Michael","last_name":"Anastos","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb"}],"_id":"14344","oa":1,"date_published":"2023-01-01T00:00:00Z","date_created":"2023-09-17T22:01:10Z","department":[{"_id":"MaKw"}],"conference":{"location":"Florence, Italy","name":"SODA: Symposium on Discrete Algorithms","end_date":"2023-01-25","start_date":"2023-01-22"},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      2023","month":"01","publication_identifier":{"isbn":["9781611977554"]},"quality_controlled":"1","volume":2023,"date_updated":"2023-09-25T09:13:41Z","status":"public","day":"01","page":"2286-2323","oa_version":"Preprint","publication_status":"published","abstract":[{"lang":"eng","text":"We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in two different settings. In the first one, G is given to us in the form of randomly ordered adjacency lists while in the second one, we are given the adjacency matrix of G. In each of the two settings we derive a deterministic algorithm that w.h.p. either finds a Hamilton cycle or returns a certificate that such a cycle does not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and  respectively, each being best possible in its own setting."}],"citation":{"chicago":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2023:2286–2323. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">https://doi.org/10.1137/1.9781611977554.ch88</a>.","ieee":"M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high probability,” in <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Florence, Italy, 2023, vol. 2023, pp. 2286–2323.","mla":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2023, Society for Industrial and Applied Mathematics, 2023, pp. 2286–323, doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">10.1137/1.9781611977554.ch88</a>.","ista":"Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.","short":"M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323.","apa":"Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem with high probability. In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">https://doi.org/10.1137/1.9781611977554.ch88</a>","ama":"Anastos M. Fast algorithms for solving the Hamilton cycle problem with high probability. In: <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">10.1137/1.9781611977554.ch88</a>"},"arxiv":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2111.14759"}],"publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","title":"Fast algorithms for solving the Hamilton cycle problem with high probability","external_id":{"arxiv":["2111.14759"]}},{"date_created":"2023-09-17T22:01:10Z","department":[{"_id":"HeEd"}],"acknowledgement":"Work by all authors but A. Garber is 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. Work by A. Garber is partially supported by the Alexander von Humboldt Foundation.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","month":"09","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"quality_controlled":"1","isi":1,"article_type":"original","doi":"10.1007/s00454-023-00566-1","language":[{"iso":"eng"}],"year":"2023","publisher":"Springer Nature","type":"journal_article","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"first_name":"Alexey","full_name":"Garber, Alexey","last_name":"Garber"},{"full_name":"Ghafari, Mohadese","first_name":"Mohadese","last_name":"Ghafari"},{"full_name":"Heiss, Teresa","first_name":"Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","last_name":"Heiss","orcid":"0000-0002-1780-2689"},{"first_name":"Morteza","full_name":"Saghafian, Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"_id":"14345","oa":1,"date_published":"2023-09-07T00:00:00Z","citation":{"ama":"Edelsbrunner H, Garber A, Ghafari M, Heiss T, Saghafian M. On angles in higher order Brillouin tessellations and related tilings in the plane. <i>Discrete and Computational Geometry</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s00454-023-00566-1\">10.1007/s00454-023-00566-1</a>","mla":"Edelsbrunner, Herbert, et al. “On Angles in Higher Order Brillouin Tessellations and Related Tilings in the Plane.” <i>Discrete and Computational Geometry</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00454-023-00566-1\">10.1007/s00454-023-00566-1</a>.","apa":"Edelsbrunner, H., Garber, A., Ghafari, M., Heiss, T., &#38; Saghafian, M. (2023). On angles in higher order Brillouin tessellations and related tilings in the plane. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-023-00566-1\">https://doi.org/10.1007/s00454-023-00566-1</a>","ista":"Edelsbrunner H, Garber A, Ghafari M, Heiss T, Saghafian M. 2023. On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry.","short":"H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, M. Saghafian, Discrete and Computational Geometry (2023).","ieee":"H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, and M. Saghafian, “On angles in higher order Brillouin tessellations and related tilings in the plane,” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023.","chicago":"Edelsbrunner, Herbert, Alexey Garber, Mohadese Ghafari, Teresa Heiss, and Morteza Saghafian. “On Angles in Higher Order Brillouin Tessellations and Related Tilings in the Plane.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-023-00566-1\">https://doi.org/10.1007/s00454-023-00566-1</a>."},"arxiv":1,"project":[{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-023-00566-1"}],"publication":"Discrete and Computational Geometry","title":"On angles in higher order Brillouin tessellations and related tilings in the plane","external_id":{"arxiv":["2204.01076"],"isi":["001060727600004"]},"date_updated":"2023-12-13T12:25:06Z","status":"public","day":"07","publication_status":"epub_ahead","oa_version":"Published Version","abstract":[{"lang":"eng","text":"For a locally finite set in R2, the order-k Brillouin tessellations form an infinite sequence of convex face-to-face tilings of the plane. If the set is coarsely dense and generic, then the corresponding infinite sequences of minimum and maximum angles are both monotonic in k. As an example, a stationary Poisson point process in R2  is locally finite, coarsely dense, and generic with probability one. For such a set, the distributions of angles in the Voronoi tessellations, Delaunay mosaics, and Brillouin tessellations are independent of the order and can be derived from the formula for angles in order-1 Delaunay mosaics given by Miles (Math. Biosci. 6, 85–127 (1970))."}],"ec_funded":1},{"publication_status":"published","oa_version":"Published Version","day":"13","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment."}],"status":"public","date_updated":"2023-12-21T14:30:01Z","publication":"Nature Communications","related_material":{"record":[{"status":"public","id":"14697","relation":"dissertation_contains"}]},"external_id":{"pmid":["37704612"],"isi":["001087583700008"]},"title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","file":[{"file_id":"14365","checksum":"ad670e3b3c64fc585675948370f6b149","date_created":"2023-09-25T08:22:58Z","success":1,"date_updated":"2023-09-25T08:22:58Z","file_name":"2023_NatureComm_Sitarska.pdf","file_size":2725421,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"dernst"}],"scopus_import":"1","has_accepted_license":"1","citation":{"chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>.","ieee":"E. Sitarska <i>et al.</i>, “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>","mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>, vol. 14, 5644, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>.","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644.","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>"},"date_published":"2023-09-13T00:00:00Z","author":[{"last_name":"Sitarska","full_name":"Sitarska, Ewa","first_name":"Ewa"},{"full_name":"Almeida, Silvia Dias","first_name":"Silvia Dias","last_name":"Almeida"},{"last_name":"Beckwith","full_name":"Beckwith, Marianne Sandvold","first_name":"Marianne Sandvold"},{"full_name":"Stopp, Julian A","first_name":"Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Czuchnowski","full_name":"Czuchnowski, Jakub","first_name":"Jakub"},{"last_name":"Siggel","first_name":"Marc","full_name":"Siggel, Marc"},{"last_name":"Roessner","full_name":"Roessner, Rita","first_name":"Rita"},{"first_name":"Aline","full_name":"Tschanz, Aline","last_name":"Tschanz"},{"first_name":"Christer","full_name":"Ejsing, Christer","last_name":"Ejsing"},{"last_name":"Schwab","full_name":"Schwab, Yannick","first_name":"Yannick"},{"first_name":"Jan","full_name":"Kosinski, Jan","last_name":"Kosinski"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K"},{"first_name":"Anna","full_name":"Kreshuk, Anna","last_name":"Kreshuk"},{"last_name":"Erzberger","first_name":"Anna","full_name":"Erzberger, Anna"},{"last_name":"Diz-Muñoz","first_name":"Alba","full_name":"Diz-Muñoz, Alba"}],"oa":1,"_id":"14360","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-41173-1","publisher":"Springer Nature","year":"2023","isi":1,"article_type":"original","volume":14,"month":"09","quality_controlled":"1","publication_identifier":{"eissn":["2041-1723"]},"ddc":["570"],"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-09-25T08:22:58Z","intvolume":"        14","date_created":"2023-09-24T22:01:10Z","article_number":"5644","pmid":1,"acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","department":[{"_id":"MiSi"}]},{"date_published":"2023-09-13T00:00:00Z","author":[{"orcid":"0000-0003-4844-6311","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Riedl, Michael"},{"first_name":"Isabelle D","full_name":"Mayer, Isabelle D","id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","last_name":"Mayer"},{"last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"_id":"14361","oa":1,"type":"journal_article","doi":"10.1038/s41467-023-41432-1","language":[{"iso":"eng"}],"year":"2023","publisher":"Springer Nature","isi":1,"article_type":"original","volume":14,"month":"09","publication_identifier":{"eissn":["2041-1723"]},"quality_controlled":"1","file_date_updated":"2023-09-25T08:32:37Z","article_processing_charge":"Yes","ddc":["530","570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        14","article_number":"5633","date_created":"2023-09-24T22:01:10Z","acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"13","oa_version":"Published Version","publication_status":"published","abstract":[{"text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives.","lang":"eng"}],"ec_funded":1,"status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"date_updated":"2023-12-13T12:29:41Z","publication":"Nature Communications","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"dernst","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","file_id":"14366","date_created":"2023-09-25T08:32:37Z","date_updated":"2023-09-25T08:32:37Z","success":1,"file_name":"2023_NatureComm_Riedl.pdf","file_size":2317272}],"title":"Synchronization in collectively moving inanimate and living active matter","external_id":{"pmid":["37704595"],"isi":["001087583700030"]},"scopus_import":"1","has_accepted_license":"1","citation":{"ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>, vol. 14, 5633, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>.","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., &#38; Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633.","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>."},"project":[{"call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","call_identifier":"H2020","grant_number":"724373"}]},{"status":"public","date_updated":"2024-01-30T13:22:04Z","abstract":[{"lang":"eng","text":"Motivated by recent applications to entropy theory in dynamical systems, we generalise notions introduced by Matthews and define weakly weighted and componentwise weakly weighted (generalised) quasi-metrics. We then systematise and extend to full generality the correspondences between these objects and other structures arising in theoretical computer science and dynamics. In particular, we study the correspondences with weak partial metrics and, if the underlying space is a semilattice, with invariant (generalised) quasi-metrics satisfying the descending path condition, and with strictly monotone semi(-co-)valuations.\r\nWe conclude discussing, for endomorphisms of generalised quasi-metric semilattices, a generalisation of both the known intrinsic semilattice entropy and the semigroup entropy."}],"oa_version":"Preprint","publication_status":"published","day":"25","scopus_import":"1","citation":{"ieee":"I. Castellano, A. Giordano Bruno, and N. Zava, “Weakly weighted generalised quasi-metric spaces and semilattices,” <i>Theoretical Computer Science</i>, vol. 977. Elsevier, 2023.","chicago":"Castellano, Ilaria, Anna Giordano Bruno, and Nicolò Zava. “Weakly Weighted Generalised Quasi-Metric Spaces and Semilattices.” <i>Theoretical Computer Science</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">https://doi.org/10.1016/j.tcs.2023.114129</a>.","ama":"Castellano I, Giordano Bruno A, Zava N. Weakly weighted generalised quasi-metric spaces and semilattices. <i>Theoretical Computer Science</i>. 2023;977. doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">10.1016/j.tcs.2023.114129</a>","mla":"Castellano, Ilaria, et al. “Weakly Weighted Generalised Quasi-Metric Spaces and Semilattices.” <i>Theoretical Computer Science</i>, vol. 977, 114129, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">10.1016/j.tcs.2023.114129</a>.","ista":"Castellano I, Giordano Bruno A, Zava N. 2023. Weakly weighted generalised quasi-metric spaces and semilattices. Theoretical Computer Science. 977, 114129.","short":"I. Castellano, A. Giordano Bruno, N. Zava, Theoretical Computer Science 977 (2023).","apa":"Castellano, I., Giordano Bruno, A., &#38; Zava, N. (2023). Weakly weighted generalised quasi-metric spaces and semilattices. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">https://doi.org/10.1016/j.tcs.2023.114129</a>"},"arxiv":1,"external_id":{"arxiv":["2212.08424"],"isi":["001076934000001"]},"title":"Weakly weighted generalised quasi-metric spaces and semilattices","publication":"Theoretical Computer Science","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.08424 "}],"type":"journal_article","publisher":"Elsevier","year":"2023","language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2023.114129","date_published":"2023-10-25T00:00:00Z","oa":1,"_id":"14362","author":[{"full_name":"Castellano, Ilaria","first_name":"Ilaria","last_name":"Castellano"},{"first_name":"Anna","full_name":"Giordano Bruno, Anna","last_name":"Giordano Bruno"},{"full_name":"Zava, Nicolò","first_name":"Nicolò","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","last_name":"Zava","orcid":"0000-0001-8686-1888"}],"intvolume":"       977","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"HeEd"}],"article_number":"114129","date_created":"2023-09-24T22:01:11Z","article_type":"original","volume":977,"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0304-3975"]},"month":"10"}]