[{"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>","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>","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.","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.","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>.","short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39."},"file_date_updated":"2023-09-20T08:24:47Z","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer Nature","isi":1,"date_created":"2023-09-10T22:01:12Z","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.","fulldoi":"https://doi.org/10.1007/978-3-031-37709-9_2","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publication_status":"published","article_processing_charge":"Yes (in subscription journal)","day":"17","date_updated":"2025-09-09T12:55:28Z","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."}],"page":"16-39","title":"Automated tail bound analysis for probabilistic recurrence relations","publication":"Computer Aided Verification","author":[{"full_name":"Sun, Yican","last_name":"Sun","first_name":"Yican"},{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377082"],"issn":["0302-9743"]},"_id":"14318","year":"2023","conference":{"start_date":"2023-07-17","end_date":"2023-07-22","location":"Paris, France","name":"CAV: Computer Aided Verification"},"alternative_title":["LNCS"],"oa_version":"Published Version","intvolume":"     13966","date_published":"2023-07-17T00:00:00Z","type":"conference","external_id":{"isi":["001310805600002"]},"volume":13966,"language":[{"iso":"eng"}],"month":"07","ddc":["000"],"file":[{"content_type":"application/pdf","checksum":"42917e086f8c7699f3bccf84f74fe000","creator":"dernst","date_updated":"2023-09-20T08:24:47Z","file_name":"2023_LNCS_Sun.pdf","file_id":"14348","success":1,"access_level":"open_access","date_created":"2023-09-20T08:24:47Z","file_size":624647,"relation":"main_file"}],"quality_controlled":"1","scopus_import":"1","doi":"10.1007/978-3-031-37709-9_2","related_material":{"link":[{"url":"https://github.com/boyvolcano/PRR","relation":"software"}]},"has_accepted_license":"1","status":"public","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"department":[{"_id":"KrCh"}]},{"doi":"10.37236/11714","scopus_import":"1","has_accepted_license":"1","status":"public","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"department":[{"_id":"MaKw"}],"external_id":{"isi":["001042382200001"],"arxiv":["2212.03100"]},"volume":30,"language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":"        30","type":"journal_article","date_published":"2023-07-28T00:00:00Z","ddc":["510"],"file":[{"date_updated":"2023-09-15T08:02:09Z","file_name":"2023_elecJournCombinatorics_Anastos.pdf","content_type":"application/pdf","creator":"dernst","checksum":"52c46c8cb329f9aaee9ade01525f317b","file_size":247917,"relation":"main_file","access_level":"open_access","success":1,"file_id":"14338","date_created":"2023-09-15T08:02:09Z"}],"quality_controlled":"1","month":"07","arxiv":1,"date_updated":"2025-09-09T12:54:51Z","ec_funded":1,"publication_status":"published","day":"28","article_processing_charge":"Yes","publication_identifier":{"eissn":["1077-8926"]},"year":"2023","_id":"14319","abstract":[{"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.","lang":"eng"}],"author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","last_name":"Anastos","full_name":"Anastos, Michael"},{"last_name":"Fabian","full_name":"Fabian, David","first_name":"David"},{"first_name":"Alp","last_name":"Müyesser","full_name":"Müyesser, Alp"},{"full_name":"Szabó, Tibor","last_name":"Szabó","first_name":"Tibor"}],"title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","publication":"Electronic Journal of Combinatorics","license":"https://creativecommons.org/licenses/by-nd/4.0/","issue":"3","article_type":"original","citation":{"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.","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>","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>","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>.","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.","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>.","short":"M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023)."},"file_date_updated":"2023-09-15T08:02:09Z","article_number":"P3.10","oa":1,"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).","fulldoi":"https://doi.org/10.37236/11714","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Electronic Journal of Combinatorics","isi":1,"date_created":"2023-09-10T22:01:12Z"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.06310","open_access":"1"}],"quality_controlled":"1","month":"09","language":[{"iso":"eng"}],"volume":108,"external_id":{"arxiv":["2210.06310"]},"oa_version":"Preprint","type":"journal_article","date_published":"2023-09-15T00:00:00Z","intvolume":"       108","status":"public","department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"doi":"10.1103/physrevb.108.125411","scopus_import":"1","fulldoi":"https://doi.org/10.1103/physrevb.108.125411","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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-12T07:12:12Z","publisher":"American Physical Society","article_type":"original","issue":"12","citation":{"short":"P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (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>.","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.","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>","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>.","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>","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."},"oa":1,"article_number":"125411","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"_id":"14320","year":"2023","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."}],"author":[{"orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","first_name":"Paul M","full_name":"Henderson, Paul M","last_name":"Henderson"},{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"full_name":"Zibrov, Alexander A.","last_name":"Zibrov","first_name":"Alexander A."},{"full_name":"Young, Andrea F.","last_name":"Young","first_name":"Andrea F."},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"title":"Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene","publication":"Physical Review B","arxiv":1,"date_updated":"2023-09-20T09:38:24Z","day":"15","article_processing_charge":"No","publication_status":"published"},{"oa_version":"Published Version","type":"journal_article","date_published":"2023-09-11T00:00:00Z","intvolume":"       159","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"language":[{"iso":"eng"}],"volume":159,"external_id":{"arxiv":["2306.17592"],"isi":["001133333600011"],"pmid":["37694742"]},"month":"09","file":[{"date_updated":"2023-09-13T09:34:20Z","file_name":"104103_1_5.0165806.pdf","content_type":"application/pdf","checksum":"507ab65ab29e2c987c94cabad7c5370b","creator":"acappell","file_size":5749653,"relation":"main_file","success":1,"file_id":"14322","access_level":"open_access","date_created":"2023-09-13T09:34:20Z"}],"ddc":["530"],"quality_controlled":"1","scopus_import":"1","pmid":1,"doi":"10.1063/5.0165806","has_accepted_license":"1","status":"public","department":[{"_id":"MiLe"}],"project":[{"grant_number":"101062862","name":"Non-Equilibrium Field Theory of Molecular Rotations","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"corr_author":"1","file_date_updated":"2023-09-13T09:34:20Z","citation":{"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>.","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023).","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.","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>.","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>","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>","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."},"oa":1,"article_number":"104103","article_type":"original","issue":"10","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2023-09-13T09:25:09Z","isi":1,"publisher":"AIP Publishing","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.","fulldoi":"https://doi.org/10.1063/5.0165806","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"day":"11","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","arxiv":1,"date_updated":"2025-09-09T12:57:42Z","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"}],"title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","author":[{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed","full_name":"Al Hyder, Ragheed","last_name":"Al Hyder"},{"id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto","orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto","last_name":"Cappellaro"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"publication":"The Journal of Chemical Physics","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"_id":"14321","year":"2023"},{"extern":"1","day":"18","article_processing_charge":"No","publication_status":"submitted","date_updated":"2024-10-14T12:31:20Z","doi":"10.48550/arXiv.2307.09552","arxiv":1,"status":"public","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"}],"department":[{"_id":"FrLo"}],"title":"Self-compatibility: Evaluating causal discovery without ground truth","publication":"arXiv","author":[{"first_name":"Philipp M.","last_name":"Faller","full_name":"Faller, Philipp M."},{"first_name":"Leena Chennuru","last_name":"Vankadara","full_name":"Vankadara, Leena Chennuru"},{"first_name":"Atalanti A.","full_name":"Mastakouri, Atalanti A.","last_name":"Mastakouri"},{"full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"full_name":"Janzing, Dominik","last_name":"Janzing","first_name":"Dominik"}],"_id":"14333","year":"2023","citation":{"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>. .","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>","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>","ista":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. arXiv, 2307.09552.","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>.","short":"P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv (n.d.)."},"oa_version":"Preprint","oa":1,"date_published":"2023-07-18T00:00:00Z","type":"preprint","article_number":"2307.09552","language":[{"iso":"eng"}],"external_id":{"arxiv":["2307.09552"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-13T12:44:59Z","month":"07","fulldoi":"https://doi.org/10.48550/arXiv.2307.09552","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.09552"}]},{"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"12750"}]},"doi":"10.21468/scipostphys.15.3.093","scopus_import":"1","corr_author":"1","department":[{"_id":"MaSe"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020"}],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy"],"volume":15,"external_id":{"arxiv":["2210.15607"]},"type":"journal_article","date_published":"2023-09-13T00:00:00Z","intvolume":"        15","oa_version":"Published Version","quality_controlled":"1","file":[{"relation":"main_file","file_size":4866506,"date_created":"2023-09-20T10:46:10Z","success":1,"file_id":"14350","access_level":"open_access","file_name":"2023_SciPostPhysics_Brighi.pdf","date_updated":"2023-09-20T10:46:10Z","checksum":"4cef6a8021f6b6c47ab2f2f2b1387ac2","creator":"dernst","content_type":"application/pdf"}],"ddc":["530"],"month":"09","date_updated":"2025-04-14T07:52:05Z","arxiv":1,"day":"13","article_processing_charge":"No","publication_status":"published","ec_funded":1,"_id":"14334","year":"2023","publication_identifier":{"issn":["2542-4653"]},"publication":"SciPost Physics","title":"Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models","author":[{"last_name":"Brighi","full_name":"Brighi, Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro","orcid":"0000-0002-7969-2729"},{"orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko","full_name":"Ljubotina, Marko","last_name":"Ljubotina"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"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."}],"article_type":"original","issue":"3","oa":1,"article_number":"093","file_date_updated":"2023-09-20T10:46:10Z","citation":{"short":"P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (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>.","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.","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.","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>.","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>","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>"},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"fulldoi":"https://doi.org/10.21468/scipostphys.15.3.093","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).","date_created":"2023-09-14T13:08:23Z","publisher":"SciPost Foundation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"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>.","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>","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.","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>.","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."},"file_date_updated":"2023-09-20T10:51:31Z","oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publisher":"Springer Nature","date_created":"2023-09-15T09:56:01Z","fulldoi":"https://doi.org/10.1038/s41477-023-01478-x","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.).","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","day":"01","article_processing_charge":"Yes (in subscription journal)","date_updated":"2024-10-21T06:01:33Z","abstract":[{"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.","lang":"eng"}],"page":"1500-1513","publication":"Nature Plants","author":[{"first_name":"S","last_name":"Roychoudhry","full_name":"Roychoudhry, S"},{"first_name":"K","full_name":"Sageman-Furnas, K","last_name":"Sageman-Furnas"},{"full_name":"Wolverton, C","last_name":"Wolverton","first_name":"C"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"orcid":"0000-0002-0471-8285","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","last_name":"Tan"},{"full_name":"Molnar, Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely"},{"last_name":"De Angelis","full_name":"De Angelis, M","first_name":"M"},{"first_name":"HL","last_name":"Goodman","full_name":"Goodman, HL"},{"first_name":"N","full_name":"Capstaff, N","last_name":"Capstaff"},{"first_name":"Lloyd","full_name":"JPB, Lloyd","last_name":"JPB"},{"first_name":"J","last_name":"Mullen","full_name":"Mullen, J"},{"last_name":"Hangarter","full_name":"Hangarter, R","first_name":"R"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Kepinski","full_name":"Kepinski, S","first_name":"S"}],"title":"Antigravitropic PIN polarization maintains non-vertical growth in lateral roots","publication_identifier":{"issn":["2055-0278"]},"year":"2023","_id":"14339","oa_version":"Published Version","intvolume":"         9","date_published":"2023-09-01T00:00:00Z","type":"journal_article","volume":9,"external_id":{"isi":["001069238800014"],"pmid":["37666965"]},"language":[{"iso":"eng"}],"month":"09","ddc":["580"],"file":[{"date_created":"2023-09-20T10:51:31Z","success":1,"file_id":"14351","access_level":"open_access","relation":"main_file","file_size":9647103,"checksum":"3d6d5d5abb937c14a5f6f0afba3b8624","creator":"dernst","content_type":"application/pdf","file_name":"2023_NaturePlants_Roychoudhry.pdf","date_updated":"2023-09-20T10:51:31Z"}],"quality_controlled":"1","scopus_import":"1","pmid":1,"doi":"10.1038/s41477-023-01478-x","has_accepted_license":"1","status":"public","department":[{"_id":"JiFr"}]},{"department":[{"_id":"BjHo"}],"project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"FWF","name":"Instabilities in pulsating pipe flow in complex fluids","grant_number":"I04188","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E"}],"status":"public","has_accepted_license":"1","corr_author":"1","pmid":1,"scopus_import":"1","related_material":{"link":[{"url":"https://www.ista.ac.at/en/news/pumping-like-the-heart/","relation":"press_release","description":"News on ISTA website"}]},"doi":"10.1038/s41586-023-06399-5","month":"09","quality_controlled":"1","file":[{"content_type":"application/pdf","checksum":"9c9f172ba0a9a301d76fff4229812464","creator":"dernst","date_updated":"2024-06-04T09:24:34Z","file_name":"2023_submittedversion.pdf","success":1,"file_id":"17118","access_level":"open_access","date_created":"2024-06-04T09:24:34Z","file_size":3247252,"relation":"main_file"}],"ddc":["530"],"date_published":"2023-09-07T00:00:00Z","type":"journal_article","intvolume":"       621","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"external_id":{"pmid":["37673988"],"isi":["001168947700009"]},"volume":621,"title":"Turbulence suppression by cardiac-cycle-inspired driving of pipe flow","publication":"Nature","author":[{"last_name":"Scarselli","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M"},{"last_name":"Varshney","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"page":"71-74","abstract":[{"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.","lang":"eng"}],"_id":"14341","year":"2023","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"article_processing_charge":"No","day":"07","publication_status":"published","date_updated":"2025-09-09T12:59:04Z","date_created":"2023-09-17T22:01:09Z","isi":1,"publisher":"Springer Nature","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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.","fulldoi":"https://doi.org/10.1038/s41586-023-06399-5","oa":1,"file_date_updated":"2024-06-04T09:24:34Z","citation":{"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>.","short":"D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.","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.","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>.","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>","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>","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."},"article_type":"original","issue":"7977"},{"doi":"10.1063/5.0161713","scopus_import":"1","corr_author":"1","department":[{"_id":"ZhAl"}],"has_accepted_license":"1","status":"public","volume":123,"external_id":{"arxiv":["2306.09043"],"isi":["001145465400004"]},"language":[{"iso":"eng"}],"intvolume":"       123","date_published":"2023-08-28T00:00:00Z","type":"journal_article","oa_version":"Published Version","quality_controlled":"1","ddc":["530"],"file":[{"file_id":"14353","success":1,"access_level":"open_access","date_created":"2023-09-20T11:36:16Z","file_size":1486715,"relation":"main_file","content_type":"application/pdf","checksum":"89a1b604d58b209fec66c6b6f919ac98","creator":"dernst","date_updated":"2023-09-20T11:36:16Z","file_name":"2023_ApplPhysLetter_Lorenc.pdf"}],"month":"08","date_updated":"2025-09-09T12:58:23Z","arxiv":1,"publication_status":"published","day":"28","article_processing_charge":"Yes (in subscription journal)","_id":"14342","year":"2023","publication_identifier":{"issn":["0003-6951"]},"title":"Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam","publication":"Applied Physics Letters","author":[{"first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","last_name":"Lorenc","full_name":"Lorenc, Dusan"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev"}],"abstract":[{"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.","lang":"eng"}],"issue":"9","article_type":"original","article_number":"091104","oa":1,"citation":{"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>.","short":"D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).","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>","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>","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>.","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.","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."},"file_date_updated":"2023-09-20T11:36:16Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"fulldoi":"https://doi.org/10.1063/5.0161713","acknowledgement":"The work was supported by IST Austria. The authors would like to gratefully acknowledge the help and assistance of Professor John M. Dudley.","publisher":"AIP Publishing","isi":1,"date_created":"2023-09-17T22:01:09Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"month":"01","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2111.14759","open_access":"1"}],"date_published":"2023-01-01T00:00:00Z","type":"conference","intvolume":"      2023","oa_version":"Preprint","language":[{"iso":"eng"}],"external_id":{"arxiv":["2111.14759"]},"volume":2023,"department":[{"_id":"MaKw"}],"status":"public","corr_author":"1","scopus_import":"1","doi":"10.1137/1.9781611977554.ch88","date_created":"2023-09-17T22:01:10Z","publisher":"Society for Industrial and Applied Mathematics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1137/1.9781611977554.ch88","oa":1,"citation":{"short":"M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323.","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.","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.","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>.","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>","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>"},"title":"Fast algorithms for solving the Hamilton cycle problem with high probability","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","full_name":"Anastos, Michael","last_name":"Anastos"}],"publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","page":"2286-2323","abstract":[{"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.","lang":"eng"}],"year":"2023","_id":"14344","conference":{"start_date":"2023-01-22","end_date":"2023-01-25","name":"SODA: Symposium on Discrete Algorithms","location":"Florence, Italy"},"publication_identifier":{"isbn":["9781611977554"]},"day":"01","article_processing_charge":"No","publication_status":"published","arxiv":1,"date_updated":"2024-10-09T21:07:01Z"},{"date_updated":"2025-04-14T13:10:03Z","ec_funded":1,"day":"13","article_processing_charge":"Yes","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"year":"2023","_id":"14361","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"}],"title":"Synchronization in collectively moving inanimate and living active matter","author":[{"first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","last_name":"Riedl","full_name":"Riedl, Michael"},{"id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","first_name":"Isabelle D","full_name":"Mayer, Isabelle D","last_name":"Mayer"},{"full_name":"Merrin, Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn"}],"publication":"Nature Communications","article_type":"original","file_date_updated":"2023-09-25T08:32:37Z","citation":{"short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (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>.","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>.","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>","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>","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."},"oa":1,"article_number":"5633","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.","fulldoi":"https://doi.org/10.1038/s41467-023-41432-1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-24T22:01:10Z","isi":1,"publisher":"Springer Nature","doi":"10.1038/s41467-023-41432-1","scopus_import":"1","pmid":1,"corr_author":"1","status":"public","has_accepted_license":"1","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["37704595"],"isi":["001087583700030"]},"volume":14,"oa_version":"Published Version","date_published":"2023-09-13T00:00:00Z","type":"journal_article","intvolume":"        14","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"file":[{"access_level":"open_access","success":1,"file_id":"14366","date_created":"2023-09-25T08:32:37Z","file_size":2317272,"relation":"main_file","content_type":"application/pdf","creator":"dernst","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","date_updated":"2023-09-25T08:32:37Z","file_name":"2023_NatureComm_Riedl.pdf"}],"ddc":["530","570"],"quality_controlled":"1","month":"09"},{"scopus_import":"1","doi":"10.1016/j.tcs.2023.114129","department":[{"_id":"HeEd"}],"status":"public","corr_author":"1","date_published":"2023-10-25T00:00:00Z","type":"journal_article","intvolume":"       977","oa_version":"Preprint","language":[{"iso":"eng"}],"external_id":{"isi":["001076934000001"],"arxiv":["2212.08424"]},"volume":977,"month":"10","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.08424 "}],"article_processing_charge":"No","day":"25","publication_status":"published","arxiv":1,"date_updated":"2024-10-09T21:07:00Z","publication":"Theoretical Computer Science","title":"Weakly weighted generalised quasi-metric spaces and semilattices","author":[{"first_name":"Ilaria","last_name":"Castellano","full_name":"Castellano, Ilaria"},{"first_name":"Anna","last_name":"Giordano Bruno","full_name":"Giordano Bruno, Anna"},{"id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","first_name":"Nicolò","orcid":"0000-0001-8686-1888","last_name":"Zava","full_name":"Zava, Nicolò"}],"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."}],"_id":"14362","year":"2023","publication_identifier":{"issn":["0304-3975"]},"oa":1,"article_number":"114129","citation":{"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>.","short":"I. Castellano, A. Giordano Bruno, N. Zava, Theoretical Computer Science 977 (2023).","ista":"Castellano I, Giordano Bruno A, Zava N. 2023. Weakly weighted generalised quasi-metric spaces and semilattices. Theoretical Computer Science. 977, 114129.","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>.","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>","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>","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."},"article_type":"original","date_created":"2023-09-24T22:01:11Z","publisher":"Elsevier","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1016/j.tcs.2023.114129"},{"publication_status":"published","day":"20","article_processing_charge":"Yes","date_updated":"2024-10-09T21:07:01Z","abstract":[{"text":"Mitochondrial networks remodel their connectivity, content, and subcellular localization to support optimized energy production in conditions of increased environmental or cellular stress. Microglia rely on mitochondria to respond to these stressors, however our knowledge about mitochondrial networks and their adaptations in microglia in vivo is limited. Here, we generate a mouse model that selectively labels mitochondria in microglia. We identify that mitochondrial networks are more fragmented with increased content and perinuclear localization in vitro vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the injury site after optic nerve crush. Preventing microglial UCP2 increase after injury by selective knockout induces cellular stress. This results in mitochondrial hyperfusion in male microglia, a phenotype absent in females due to circulating estrogens. Our results establish the foundation for mitochondrial network analysis of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects of microglia in other pathologies.","lang":"eng"}],"author":[{"full_name":"Maes, Margaret E","last_name":"Maes","orcid":"0000-0001-9642-1085","first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria","full_name":"Colombo, Gloria","last_name":"Colombo"},{"full_name":"Schoot Uiterkamp, Florianne E","last_name":"Schoot Uiterkamp","first_name":"Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Felix","last_name":"Sternberg","full_name":"Sternberg, Felix"},{"full_name":"Venturino, Alessandro","last_name":"Venturino","orcid":"0000-0003-2356-9403","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elena E.","full_name":"Pohl, Elena E.","last_name":"Pohl"},{"last_name":"Siegert","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"}],"publication":"iScience","title":"Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout","publication_identifier":{"eissn":["2589-0042"]},"year":"2023","_id":"14363","citation":{"ama":"Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. <i>iScience</i>. 2023;26(10). doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107780\">10.1016/j.isci.2023.107780</a>","mla":"Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” <i>IScience</i>, vol. 26, no. 10, 107780, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107780\">10.1016/j.isci.2023.107780</a>.","apa":"Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino, A., Pohl, E. E., &#38; Siegert, S. (2023). Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2023.107780\">https://doi.org/10.1016/j.isci.2023.107780</a>","ista":"Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE, Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 26(10), 107780.","ieee":"M. E. Maes <i>et al.</i>, “Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout,” <i>iScience</i>, vol. 26, no. 10. Elsevier, 2023.","short":"M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino, E.E. Pohl, S. Siegert, IScience 26 (2023).","chicago":"Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg, Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” <i>IScience</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.isci.2023.107780\">https://doi.org/10.1016/j.isci.2023.107780</a>."},"file_date_updated":"2023-11-07T08:53:21Z","article_number":"107780","oa":1,"issue":"10","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publisher":"Elsevier","date_created":"2023-09-24T22:01:11Z","acknowledgement":"We thank the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael Schunn for excellent mouse colony management and support. This research was supported by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback on the project and article.","fulldoi":"https://doi.org/10.1016/j.isci.2023.107780","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","pmid":1,"doi":"10.1016/j.isci.2023.107780","status":"public","has_accepted_license":"1","department":[{"_id":"SaSi"}],"corr_author":"1","oa_version":"Published Version","intvolume":"        26","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"type":"journal_article","date_published":"2023-10-20T00:00:00Z","volume":26,"external_id":{"pmid":["37731609"],"isi":["001080403500001"]},"language":[{"iso":"eng"}],"month":"10","ddc":["570"],"file":[{"file_size":8197935,"relation":"main_file","file_id":"14497","success":1,"access_level":"open_access","date_created":"2023-11-07T08:53:21Z","date_updated":"2023-11-07T08:53:21Z","file_name":"2023_iScience_Maes.pdf","content_type":"application/pdf","checksum":"be1a560efdd96d20712311f4fc54aac2","creator":"dernst"}],"quality_controlled":"1"},{"date_updated":"2025-05-14T11:26:06Z","arxiv":1,"publication_status":"published","article_processing_charge":"No","day":"25","ec_funded":1,"_id":"14364","year":"2023","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"author":[{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"first_name":"James","last_name":"Aspnes","full_name":"Aspnes, James"},{"first_name":"Faith","full_name":"Ellen, Faith","last_name":"Ellen"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"last_name":"Zhu","full_name":"Zhu, Leqi","first_name":"Leqi","id":"a2117c59-cee4-11ed-b9d0-874ecf0f8ac5"}],"title":"Why extension-based proofs fail","publication":"SIAM Journal on Computing","abstract":[{"text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve -set agreement among  processes or approximate agreement on a cycle of length 4 among  processes in a wait-free manner in asynchronous models where processes communicate using objects that can be constructed from shared registers. However, it was unknown whether proofs based on simpler techniques were possible. We show that these impossibility results cannot be obtained by extension-based proofs in the iterated snapshot model and, hence, extension-based proofs are limited in power.","lang":"eng"}],"page":"913-944","issue":"4","article_type":"original","oa":1,"citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/20M1375851\">https://doi.org/10.1137/20M1375851</a>.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, SIAM Journal on Computing 52 (2023) 913–944.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., &#38; Zhu, L. (2023). Why extension-based proofs fail. <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1375851\">https://doi.org/10.1137/20M1375851</a>","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. <i>SIAM Journal on Computing</i>. 2023;52(4):913-944. doi:<a href=\"https://doi.org/10.1137/20M1375851\">10.1137/20M1375851</a>","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” <i>SIAM Journal on Computing</i>, vol. 52, no. 4, Society for Industrial and Applied Mathematics, 2023, pp. 913–44, doi:<a href=\"https://doi.org/10.1137/20M1375851\">10.1137/20M1375851</a>.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2023. Why extension-based proofs fail. SIAM Journal on Computing. 52(4), 913–944.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” <i>SIAM Journal on Computing</i>, vol. 52, no. 4. Society for Industrial and Applied Mathematics, pp. 913–944, 2023."},"acknowledgement":"We would like to thank Valerie King, Toniann Pitassi, and Michael Saks for helpful discussions and Shi Hao Liu for his useful feedback.\r\nThis research was supported by the Natural Science and Engineering Research Council of Canada under grants RGPIN-2015-05080 and RGPIN-2020-04178, a postgraduate scholarship, and a postdoctoral fellowship; a University of Toronto postdoctoral fellowship; the National Science Foundation under grants CCF-1217921, CCF-1301926, CCF-1637385, CCF-1650596, and IIS-1447786; the U.S. Department of Energy under grant ER26116/DE-SC0008923; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement 805223 ScaleML; and the Oracle and Intel corporations. Some of the work on this paper was done while Faith Ellen was visiting IST Austria.","fulldoi":"https://doi.org/10.1137/20M1375851","publisher":"Society for Industrial and Applied Mathematics","isi":1,"date_created":"2023-09-24T22:01:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1137/20M1375851","related_material":{"record":[{"status":"public","id":"6676","relation":"earlier_version"}]},"scopus_import":"1","project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"DaAl"}],"status":"public","volume":52,"external_id":{"arxiv":["1811.01421"],"isi":["001082972300004"]},"language":[{"iso":"eng"}],"intvolume":"        52","type":"journal_article","date_published":"2023-07-25T00:00:00Z","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01421"}],"month":"07"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","date_created":"2023-09-25T08:44:29Z","fulldoi":"https://doi.org/10.1016/j.gim.2023.100938","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"A. Accogli <i>et al.</i>, “Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder,” <i>Genetics in Medicine</i>, vol. 25, no. 11. Elsevier, 2023.","ama":"Accogli A, Lin S-J, Severino M, et al. Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. <i>Genetics in Medicine</i>. 2023;25(11). doi:<a href=\"https://doi.org/10.1016/j.gim.2023.100938\">10.1016/j.gim.2023.100938</a>","apa":"Accogli, A., Lin, S.-J., Severino, M., Kim, S.-H., Huang, K., Rocca, C., … Maroofian, R. (2023). Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. <i>Genetics in Medicine</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gim.2023.100938\">https://doi.org/10.1016/j.gim.2023.100938</a>","mla":"Accogli, Andrea, et al. “Clinical, Neuroradiological, and Molecular Characterization of Mitochondrial Threonyl-TRNA-Synthetase (TARS2)-Related Disorder.” <i>Genetics in Medicine</i>, vol. 25, no. 11, 100938, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.gim.2023.100938\">10.1016/j.gim.2023.100938</a>.","ista":"Accogli A, Lin S-J, Severino M, Kim S-H, Huang K, Rocca C, Landsverk M, Zaki MS, Al-Maawali A, Srinivasan VM, Al-Thihli K, Schaefer GB, Davis M, Tonduti D, Doneda C, Marten LM, Mühlhausen C, Gomez M, Lamantea E, Mena R, Nizon M, Procaccio V, Begtrup A, Telegrafi A, Cui H, Schulz HL, Mohr J, Biskup S, Loos MA, Aráoz HV, Salpietro V, Keppen LD, Chitre M, Petree C, Raymond L, Vogt J, Sawyer LB, Basinger AA, Pedersen SV, Pearson TS, Grange DK, Lingappa L, McDunnah P, Horvath R, Cognè B, Isidor B, Hahn A, Gripp KW, Jafarnejad SM, Østergaard E, Prada CE, Ghezzi D, Gowda VK, Taylor RW, Sonenberg N, Houlden H, Sissler M, Varshney GK, Maroofian R. 2023. Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genetics in Medicine. 25(11), 100938.","short":"A. Accogli, S.-J. Lin, M. Severino, S.-H. Kim, K. Huang, C. Rocca, M. Landsverk, M.S. Zaki, A. Al-Maawali, V.M. Srinivasan, K. Al-Thihli, G.B. Schaefer, M. Davis, D. Tonduti, C. Doneda, L.M. Marten, C. Mühlhausen, M. Gomez, E. Lamantea, R. Mena, M. Nizon, V. Procaccio, A. Begtrup, A. Telegrafi, H. Cui, H.L. Schulz, J. Mohr, S. Biskup, M.A. Loos, H.V. Aráoz, V. Salpietro, L.D. Keppen, M. Chitre, C. Petree, L. Raymond, J. Vogt, L.B. Sawyer, A.A. Basinger, S.V. Pedersen, T.S. Pearson, D.K. Grange, L. Lingappa, P. McDunnah, R. Horvath, B. Cognè, B. Isidor, A. Hahn, K.W. Gripp, S.M. Jafarnejad, E. Østergaard, C.E. Prada, D. Ghezzi, V.K. Gowda, R.W. Taylor, N. Sonenberg, H. Houlden, M. Sissler, G.K. Varshney, R. Maroofian, Genetics in Medicine 25 (2023).","chicago":"Accogli, Andrea, Sheng-Jia Lin, Mariasavina Severino, Sung-Hoon Kim, Kevin Huang, Clarissa Rocca, Megan Landsverk, et al. “Clinical, Neuroradiological, and Molecular Characterization of Mitochondrial Threonyl-TRNA-Synthetase (TARS2)-Related Disorder.” <i>Genetics in Medicine</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.gim.2023.100938\">https://doi.org/10.1016/j.gim.2023.100938</a>."},"file_date_updated":"2023-09-25T08:48:54Z","article_number":"100938","oa":1,"issue":"11","article_type":"original","abstract":[{"lang":"eng","text":"Purpose: \r\nBiallelic variants in TARS2, encoding the mitochondrial threonyl-tRNA-synthetase, have been reported in a small group of individuals displaying a neurodevelopmental phenotype but with limited neuroradiological data and insufficient evidence for causality of the variants.\r\nMethods:\r\nExome or genome sequencing was carried out in 15 families. Clinical and neuroradiological evaluation was performed for all affected individuals, including review of 10 previously reported individuals. The pathogenicity of TARS2 variants was evaluated using in vitro assays and a zebrafish model.\r\nResults:\r\nWe report 18 new individuals harboring biallelic TARS2 variants. Phenotypically, these individuals show developmental delay/intellectual disability, regression, cerebellar and cerebral atrophy, basal ganglia signal alterations, hypotonia, cerebellar signs, and increased blood lactate. In vitro studies showed that variants within the TARS2301-381 region had decreased binding to Rag GTPases, likely impairing mTORC1 activity. The zebrafish model recapitulated key features of the human phenotype and unraveled dysregulation of downstream targets of mTORC1 signaling. Functional testing of the variants confirmed the pathogenicity in a zebrafish model.\r\nConclusion:\r\nWe define the clinico-radiological spectrum of TARS2-related mitochondrial disease, unveil the likely involvement of the mTORC1 signaling pathway as a distinct molecular mechanism, and establish a TARS2 zebrafish model as an important tool to study variant pathogenicity."}],"publication":"Genetics in Medicine","title":"Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder","author":[{"full_name":"Accogli, Andrea","last_name":"Accogli","first_name":"Andrea"},{"full_name":"Lin, Sheng-Jia","last_name":"Lin","first_name":"Sheng-Jia"},{"full_name":"Severino, Mariasavina","last_name":"Severino","first_name":"Mariasavina"},{"first_name":"Sung-Hoon","full_name":"Kim, Sung-Hoon","last_name":"Kim"},{"full_name":"Huang, Kevin","last_name":"Huang","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","first_name":"Kevin","orcid":"0000-0002-2512-7812"},{"full_name":"Rocca, Clarissa","last_name":"Rocca","first_name":"Clarissa"},{"first_name":"Megan","full_name":"Landsverk, Megan","last_name":"Landsverk"},{"full_name":"Zaki, Maha S.","last_name":"Zaki","first_name":"Maha S."},{"first_name":"Almundher","last_name":"Al-Maawali","full_name":"Al-Maawali, Almundher"},{"first_name":"Varunvenkat M.","last_name":"Srinivasan","full_name":"Srinivasan, Varunvenkat M."},{"last_name":"Al-Thihli","full_name":"Al-Thihli, Khalid","first_name":"Khalid"},{"last_name":"Schaefer","full_name":"Schaefer, G. Bradly","first_name":"G. Bradly"},{"full_name":"Davis, Monica","last_name":"Davis","first_name":"Monica"},{"full_name":"Tonduti, Davide","last_name":"Tonduti","first_name":"Davide"},{"full_name":"Doneda, Chiara","last_name":"Doneda","first_name":"Chiara"},{"first_name":"Lara M.","last_name":"Marten","full_name":"Marten, Lara M."},{"last_name":"Mühlhausen","full_name":"Mühlhausen, Chris","first_name":"Chris"},{"full_name":"Gomez, Maria","last_name":"Gomez","first_name":"Maria"},{"first_name":"Eleonora","full_name":"Lamantea, Eleonora","last_name":"Lamantea"},{"full_name":"Mena, Rafael","last_name":"Mena","first_name":"Rafael"},{"last_name":"Nizon","full_name":"Nizon, Mathilde","first_name":"Mathilde"},{"first_name":"Vincent","full_name":"Procaccio, Vincent","last_name":"Procaccio"},{"first_name":"Amber","full_name":"Begtrup, Amber","last_name":"Begtrup"},{"last_name":"Telegrafi","full_name":"Telegrafi, Aida","first_name":"Aida"},{"full_name":"Cui, Hong","last_name":"Cui","first_name":"Hong"},{"first_name":"Heidi L.","full_name":"Schulz, Heidi L.","last_name":"Schulz"},{"full_name":"Mohr, Julia","last_name":"Mohr","first_name":"Julia"},{"full_name":"Biskup, Saskia","last_name":"Biskup","first_name":"Saskia"},{"first_name":"Mariana Amina","last_name":"Loos","full_name":"Loos, Mariana Amina"},{"last_name":"Aráoz","full_name":"Aráoz, Hilda Verónica","first_name":"Hilda Verónica"},{"first_name":"Vincenzo","last_name":"Salpietro","full_name":"Salpietro, Vincenzo"},{"last_name":"Keppen","full_name":"Keppen, Laura Davis","first_name":"Laura Davis"},{"first_name":"Manali","last_name":"Chitre","full_name":"Chitre, Manali"},{"first_name":"Cassidy","last_name":"Petree","full_name":"Petree, Cassidy"},{"first_name":"Lucy","full_name":"Raymond, Lucy","last_name":"Raymond"},{"first_name":"Julie","full_name":"Vogt, Julie","last_name":"Vogt"},{"last_name":"Sawyer","full_name":"Sawyer, Lindsey B.","first_name":"Lindsey B."},{"first_name":"Alice A.","full_name":"Basinger, Alice A.","last_name":"Basinger"},{"first_name":"Signe Vandal","full_name":"Pedersen, Signe Vandal","last_name":"Pedersen"},{"full_name":"Pearson, Toni S.","last_name":"Pearson","first_name":"Toni S."},{"first_name":"Dorothy K.","last_name":"Grange","full_name":"Grange, Dorothy K."},{"full_name":"Lingappa, Lokesh","last_name":"Lingappa","first_name":"Lokesh"},{"full_name":"McDunnah, Paige","last_name":"McDunnah","first_name":"Paige"},{"last_name":"Horvath","full_name":"Horvath, Rita","first_name":"Rita"},{"first_name":"Benjamin","last_name":"Cognè","full_name":"Cognè, Benjamin"},{"first_name":"Bertrand","last_name":"Isidor","full_name":"Isidor, Bertrand"},{"full_name":"Hahn, Andreas","last_name":"Hahn","first_name":"Andreas"},{"full_name":"Gripp, Karen W.","last_name":"Gripp","first_name":"Karen W."},{"first_name":"Seyed Mehdi","last_name":"Jafarnejad","full_name":"Jafarnejad, Seyed Mehdi"},{"full_name":"Østergaard, Elsebet","last_name":"Østergaard","first_name":"Elsebet"},{"first_name":"Carlos E.","full_name":"Prada, Carlos E.","last_name":"Prada"},{"first_name":"Daniele","last_name":"Ghezzi","full_name":"Ghezzi, Daniele"},{"first_name":"Vykuntaraju K.","last_name":"Gowda","full_name":"Gowda, Vykuntaraju K."},{"last_name":"Taylor","full_name":"Taylor, Robert W.","first_name":"Robert W."},{"last_name":"Sonenberg","full_name":"Sonenberg, Nahum","first_name":"Nahum"},{"first_name":"Henry","full_name":"Houlden, Henry","last_name":"Houlden"},{"first_name":"Marie","last_name":"Sissler","full_name":"Sissler, Marie"},{"full_name":"Varshney, Gaurav K.","last_name":"Varshney","first_name":"Gaurav K."},{"first_name":"Reza","full_name":"Maroofian, Reza","last_name":"Maroofian"}],"publication_identifier":{"issn":["1098-3600"]},"_id":"14368","year":"2023","extern":"1","publication_status":"published","day":"01","article_processing_charge":"No","date_updated":"2023-09-25T08:50:10Z","month":"11","ddc":["570"],"file":[{"file_name":"2023_GeneticsMedicine_Accogli.pdf","date_updated":"2023-09-25T08:48:54Z","checksum":"440f0cd8a2ffcbe03c015c1746728387","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":4105513,"date_created":"2023-09-25T08:48:54Z","success":1,"file_id":"14369","access_level":"open_access"}],"quality_controlled":"1","oa_version":"Published Version","intvolume":"        25","date_published":"2023-11-01T00:00:00Z","type":"journal_article","volume":25,"keyword":["Genetics (clinical)"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","scopus_import":"1","doi":"10.1016/j.gim.2023.100938"},{"corr_author":"1","has_accepted_license":"1","status":"public","OA_place":"publisher","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"doi":"10.15479/at:ista:14374","related_material":{"record":[{"id":"10850","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"13207"}]},"ddc":["515","539"],"file":[{"file_id":"14398","access_level":"open_access","date_created":"2023-10-06T11:35:56Z","file_size":2365702,"relation":"main_file","content_type":"application/pdf","checksum":"ef039ffc3de2cb8dee5b14110938e9b6","creator":"broos","date_updated":"2023-10-06T11:35:56Z","file_name":"phd-thesis-draft_pdfa_acrobat.pdf"},{"creator":"broos","checksum":"81dcac33daeefaf0111db52f41bb1fd0","content_type":"application/x-zip-compressed","file_name":"Version5.zip","date_updated":"2023-10-06T11:38:01Z","date_created":"2023-10-06T11:38:01Z","access_level":"closed","file_id":"14399","relation":"source_file","file_size":4691734}],"month":"09","language":[{"iso":"eng"}],"oa_version":"Published Version","degree_awarded":"PhD","type":"dissertation","date_published":"2023-09-30T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"year":"2023","_id":"14374","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap  in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.\r\n\r\nIn the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space."}],"page":"206","author":[{"first_name":"Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","orcid":"0000-0002-9071-5880","last_name":"Roos","full_name":"Roos, Barbara"}],"title":"Boundary superconductivity in BCS theory","date_updated":"2026-04-07T13:27:39Z","supervisor":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"ec_funded":1,"publication_status":"published","day":"30","article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/at:ista:14374","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","date_created":"2023-09-28T14:23:04Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","citation":{"short":"B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023.","chicago":"Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14374\">https://doi.org/10.15479/at:ista:14374</a>.","ista":"Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria.","apa":"Roos, B. (2023). <i>Boundary superconductivity in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14374\">https://doi.org/10.15479/at:ista:14374</a>","mla":"Roos, Barbara. <i>Boundary Superconductivity in BCS Theory</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14374\">10.15479/at:ista:14374</a>.","ama":"Roos B. Boundary superconductivity in BCS theory. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14374\">10.15479/at:ista:14374</a>","ieee":"B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023."},"file_date_updated":"2023-10-06T11:38:01Z","oa":1},{"status":"public","doi":"10.1103/physrevfluids.8.063101","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2209.10916","open_access":"1"}],"quality_controlled":"1","month":"06","external_id":{"arxiv":["2209.10916"]},"volume":8,"language":[{"iso":"eng"}],"keyword":["Fluid Flow and Transfer Processes","Modeling and Simulation","Computational Mechanics"],"intvolume":"         8","type":"journal_article","date_published":"2023-06-14T00:00:00Z","oa_version":"Preprint","year":"2023","_id":"14377","publication_identifier":{"issn":["2469-990X"]},"publication":"Physical Review Fluids","title":"Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter","author":[{"first_name":"Benjamin H.","full_name":"Andersen, Benjamin H.","last_name":"Andersen"},{"first_name":"Julian B","id":"7af6767d-14eb-11ed-b536-a32449ae867c","full_name":"Renaud, Julian B","last_name":"Renaud"},{"first_name":"Jonas","last_name":"Rønning","full_name":"Rønning, Jonas"},{"last_name":"Angheluta","full_name":"Angheluta, Luiza","first_name":"Luiza"},{"first_name":"Amin","last_name":"Doostmohammadi","full_name":"Doostmohammadi, Amin"}],"abstract":[{"text":"Coherent flows of self-propelled particles are characterized by vortices and jets that sustain chaotic flows, referred to as active turbulence. Here, we reveal a crossover between defect-free active turbulence and active turbulence laden with topological defects. Interestingly, we show that concurrent to the crossover from defect-free to defect-laden active turbulence is the restoration of the previously broken SO(2) symmetry signaled by the fast decay of the two-point correlations. By stability analyses of the topological charge density field, we provide theoretical insights on the criterion for the crossover to the defect-laden active turbulent state. Despite the distinct symmetry features between these two active turbulence regimes, the flow fluctuations exhibit universal statistical scaling behaviors at large scales, while the spectrum of polarity fluctuations decays exponentially at small length scales compared to the active energy injection length. These findings reveal a dynamical crossover between distinct spatiotemporal organization patterns in polar active matter.","lang":"eng"}],"date_updated":"2023-10-03T07:25:39Z","arxiv":1,"publication_status":"published","article_processing_charge":"No","day":"14","extern":"1","fulldoi":"https://doi.org/10.1103/physrevfluids.8.063101","publisher":"American Physical Society","date_created":"2023-09-29T08:46:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","article_type":"original","article_number":"063101","oa":1,"citation":{"ieee":"B. H. Andersen, J. B. Renaud, J. Rønning, L. Angheluta, and A. Doostmohammadi, “Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter,” <i>Physical Review Fluids</i>, vol. 8, no. 6. American Physical Society, 2023.","apa":"Andersen, B. H., Renaud, J. B., Rønning, J., Angheluta, L., &#38; Doostmohammadi, A. (2023). Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevfluids.8.063101\">https://doi.org/10.1103/physrevfluids.8.063101</a>","ama":"Andersen BH, Renaud JB, Rønning J, Angheluta L, Doostmohammadi A. Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter. <i>Physical Review Fluids</i>. 2023;8(6). doi:<a href=\"https://doi.org/10.1103/physrevfluids.8.063101\">10.1103/physrevfluids.8.063101</a>","mla":"Andersen, Benjamin H., et al. “Symmetry-Restoring Crossover from Defect-Free to Defect-Laden Turbulence in Polar Active Matter.” <i>Physical Review Fluids</i>, vol. 8, no. 6, 063101, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevfluids.8.063101\">10.1103/physrevfluids.8.063101</a>.","ista":"Andersen BH, Renaud JB, Rønning J, Angheluta L, Doostmohammadi A. 2023. Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter. Physical Review Fluids. 8(6), 063101.","short":"B.H. Andersen, J.B. Renaud, J. Rønning, L. Angheluta, A. Doostmohammadi, Physical Review Fluids 8 (2023).","chicago":"Andersen, Benjamin H., Julian B Renaud, Jonas Rønning, Luiza Angheluta, and Amin Doostmohammadi. “Symmetry-Restoring Crossover from Defect-Free to Defect-Laden Turbulence in Polar Active Matter.” <i>Physical Review Fluids</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevfluids.8.063101\">https://doi.org/10.1103/physrevfluids.8.063101</a>."}},{"title":"Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks","author":[{"last_name":"Ucar","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","orcid":"0000-0003-0506-4217"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Tiilikainen","full_name":"Tiilikainen, Emmi","first_name":"Emmi"},{"last_name":"Liaqat","full_name":"Liaqat, Inam","first_name":"Inam"},{"full_name":"Jakobsson, Emma","last_name":"Jakobsson","first_name":"Emma"},{"first_name":"Harri","full_name":"Nurmi, Harri","last_name":"Nurmi"},{"last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87"}],"publication":"Nature Communications","abstract":[{"lang":"eng","text":"Branching morphogenesis is a ubiquitous process that gives rise to high exchange surfaces in the vasculature and epithelial organs. Lymphatic capillaries form branched networks, which play a key role in the circulation of tissue fluid and immune cells. Although mouse models and correlative patient data indicate that the lymphatic capillary density directly correlates with functional output, i.e., tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms ensuring efficient tissue coverage remain poorly understood. Here, we use the mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing, genetic perturbations, whole-organ reconstructions and theoretical modeling to show that the dermal lymphatic capillaries tile space in an optimal, space-filling manner. This coverage is achieved by two complementary mechanisms: initial tissue invasion provides a non-optimal global scaffold via self-organized branching morphogenesis, while VEGF-C dependent side-branching from existing capillaries rapidly optimizes local coverage by directionally targeting low-density regions. With these two ingredients, we show that a minimal biophysical model can reproduce quantitatively whole-network reconstructions, across development and perturbations. Our results show that lymphatic capillary networks can exploit local self-organizing mechanisms to achieve tissue-scale optimization."}],"year":"2023","_id":"14378","publication_identifier":{"eissn":["2041-1723"]},"article_processing_charge":"Yes","day":"21","publication_status":"published","ec_funded":1,"date_updated":"2025-04-14T07:43:56Z","date_created":"2023-10-01T22:01:13Z","publisher":"Springer Nature","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"fulldoi":"https://doi.org/10.1038/s41467-023-41456-7","acknowledgement":"We thank Dr. Kari Alitalo (University of Helsinki and Wihuri Research Institute) for critical reading of the manuscript, providing Vegfc+/− and Clp24ΔEC mouse strains and for hosting K.V.’s Academy of Finland postdoctoral researcher period (2015–2018). We thank Dr. Sara Wickström (University of Helsinki and Wihuri Research Institute) for providing Sox9:Egfp mouse\r\nstrain and the discussions. We thank Maija Atuegwu and Tapio Tainola for technical assistance. This work received funding from the Academy of Finland (K.V., 315710), Sigrid Juselius Foundation (K.V.), University of Helsinki (K.V.), Wihuri Research Institute (K.V.), the ERC under the European Union’s Horizon 2020 research and innovation program (grant agreement\r\nNo. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.). Part of the work was carried out with the support of HiLIFE Laboratory Animal Centre Core Facility, University of Helsinki, Finland. Imaging was performed at the Biomedicum Imaging Unit, Helsinki University, Helsinki, Finland, with the support of Biocenter Finland. The AAVpreparations were produced at the Helsinki Virus (HelVi) Core.","oa":1,"article_number":"5878","file_date_updated":"2023-10-03T07:46:36Z","citation":{"short":"M.C. Ucar, E.B. Hannezo, E. Tiilikainen, I. Liaqat, E. Jakobsson, H. Nurmi, K. Vaahtomeri, Nature Communications 14 (2023).","chicago":"Ucar, Mehmet C, Edouard B Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma Jakobsson, Harri Nurmi, and Kari Vaahtomeri. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41456-7\">https://doi.org/10.1038/s41467-023-41456-7</a>.","ieee":"M. C. Ucar <i>et al.</i>, “Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Ucar MC, Hannezo EB, Tiilikainen E, Liaqat I, Jakobsson E, Nurmi H, Vaahtomeri K. 2023. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 14, 5878.","ama":"Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41456-7\">10.1038/s41467-023-41456-7</a>","apa":"Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi, H., &#38; Vaahtomeri, K. (2023). Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41456-7\">https://doi.org/10.1038/s41467-023-41456-7</a>","mla":"Ucar, Mehmet C., et al. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” <i>Nature Communications</i>, vol. 14, 5878, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41456-7\">10.1038/s41467-023-41456-7</a>."},"article_type":"original","department":[{"_id":"EdHa"}],"project":[{"call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"status":"public","has_accepted_license":"1","corr_author":"1","pmid":1,"scopus_import":"1","doi":"10.1038/s41467-023-41456-7","month":"09","quality_controlled":"1","file":[{"creator":"dernst","checksum":"4fe5423403f2531753bcd9e0fea48e05","content_type":"application/pdf","file_name":"2023_NatureComm_Ucar.pdf","date_updated":"2023-10-03T07:46:36Z","date_created":"2023-10-03T07:46:36Z","access_level":"open_access","success":1,"file_id":"14384","relation":"main_file","file_size":8143264}],"ddc":["570"],"date_published":"2023-09-21T00:00:00Z","type":"journal_article","intvolume":"        14","oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"pmid":["37735168"],"isi":["001075884500007"]},"volume":14},{"month":"11","quality_controlled":"1","intvolume":"       299","type":"journal_article","date_published":"2023-11-01T00:00:00Z","oa_version":"None","volume":299,"external_id":{"isi":["001083568900001"]},"language":[{"iso":"eng"}],"department":[{"_id":"MaIb"}],"status":"public","scopus_import":"1","doi":"10.1016/j.synthmet.2023.117463","publisher":"Elsevier","isi":1,"date_created":"2023-10-01T22:01:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by 2023 Yeungnam University Research Grant.","fulldoi":"https://doi.org/10.1016/j.synthmet.2023.117463","article_number":"117463","citation":{"chicago":"Mahato, Neelima, Saurabh Singh, Mohammad Faisal, T. V.M. Sreekanth, Sutripto Majumder, Kisoo Yoo, and Jonghoon Kim. “Polycrystalline Phases Grown In-Situ Engendering Unique Mechanism of Charge Storage in Polyaniline-Graphite Composite.” <i>Synthetic Metals</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">https://doi.org/10.1016/j.synthmet.2023.117463</a>.","short":"N. Mahato, S. Singh, M. Faisal, T.V.M. Sreekanth, S. Majumder, K. Yoo, J. Kim, Synthetic Metals 299 (2023).","ieee":"N. Mahato <i>et al.</i>, “Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite,” <i>Synthetic Metals</i>, vol. 299. Elsevier, 2023.","ista":"Mahato N, Singh S, Faisal M, Sreekanth TVM, Majumder S, Yoo K, Kim J. 2023. Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite. Synthetic Metals. 299, 117463.","ama":"Mahato N, Singh S, Faisal M, et al. Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite. <i>Synthetic Metals</i>. 2023;299. doi:<a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">10.1016/j.synthmet.2023.117463</a>","apa":"Mahato, N., Singh, S., Faisal, M., Sreekanth, T. V. M., Majumder, S., Yoo, K., &#38; Kim, J. (2023). Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite. <i>Synthetic Metals</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">https://doi.org/10.1016/j.synthmet.2023.117463</a>","mla":"Mahato, Neelima, et al. “Polycrystalline Phases Grown In-Situ Engendering Unique Mechanism of Charge Storage in Polyaniline-Graphite Composite.” <i>Synthetic Metals</i>, vol. 299, 117463, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">10.1016/j.synthmet.2023.117463</a>."},"article_type":"original","author":[{"full_name":"Mahato, Neelima","last_name":"Mahato","first_name":"Neelima"},{"full_name":"Singh, Saurabh","last_name":"Singh","first_name":"Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269"},{"full_name":"Faisal, Mohammad","last_name":"Faisal","first_name":"Mohammad"},{"full_name":"Sreekanth, T. V.M.","last_name":"Sreekanth","first_name":"T. V.M."},{"last_name":"Majumder","full_name":"Majumder, Sutripto","first_name":"Sutripto"},{"first_name":"Kisoo","full_name":"Yoo, Kisoo","last_name":"Yoo"},{"last_name":"Kim","full_name":"Kim, Jonghoon","first_name":"Jonghoon"}],"publication":"Synthetic Metals","title":"Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite","abstract":[{"lang":"eng","text":"We report on a simple surfactant/template free chemical route for the synthesis of semi-polycrystalline polyaniline-graphite (SPani-graphite) composite and its application as an electroactive material in electrochemical charge storage. The synthesized material exhibits well-defined poly-crystallographic lattices in high resolution transmission electron micrographs and sharp peaks in x-ray diffraction spectra suggesting crystalline nature of the material. The specific capacitance computed from the galvanostatic charge-discharge (GCD) data obtained from 3-electrode cell configuration using 1 M aq. Na2SO4 as an electrolyte was 111.4 F g−1 at a current density of 0.1 A g−1 which rises to 269 F g−1 at an elevated current density of 1.0 A g−1. A similar pattern of increase in the specific capacitance values with an increase in the current density was observed in the results obtained from 2-electrode symmetric device configuration using polymer gel electrolyte (xanthan gum in 1 M aq. Na2SO4). The specific capacitance computed from the GCD data obtained from the device configuration was 20 F g−1 at the current density of 1.0 A g−1. The device delivers an energy density of 1.7 Wh kg−1 and a power density of 2.48 kWh kg−1 at an applied current density of 0.5 A g−1 suggesting an excellent rate capability and power management. In addition, the device exhibits ⁓92 % specific capacitance retention up to 8000 continuous GCD cycles and ⁓80 % coulombic efficiency up to 10,000 continuous GCD cycles indicating excellent cycling stability. The unique feature of increasing specific capacitance with respect to applied current density is attributed to the presence of semi-polycrystalline phases in the SPani-graphite matrix. The material behaves as a surface redox supercapacitor and its unique mechanism of charge storage is discussed in detail in the article."}],"_id":"14379","year":"2023","publication_identifier":{"issn":["0379-6779"]},"publication_status":"published","article_processing_charge":"No","day":"01","date_updated":"2024-01-30T13:55:50Z"},{"month":"09","file":[{"file_name":"2023_MolecularNeurodegeneration_Maes.pdf","date_updated":"2024-01-30T14:33:31Z","checksum":"3aa218ddea4a082d8fd5e196ae55ca06","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":11568350,"date_created":"2024-01-30T14:33:31Z","file_id":"14917","success":1,"access_level":"open_access"}],"ddc":["570"],"quality_controlled":"1","oa_version":"Published Version","type":"journal_article","date_published":"2023-09-26T00:00:00Z","intvolume":"        18","language":[{"iso":"eng"}],"external_id":{"pmid":["37752598"],"isi":["001071403800001"]},"volume":18,"has_accepted_license":"1","status":"public","department":[{"_id":"SaSi"}],"scopus_import":"1","pmid":1,"doi":"10.1186/s13024-023-00659-8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-10-08T22:01:15Z","publisher":"Springer Nature","isi":1,"fulldoi":"https://doi.org/10.1186/s13024-023-00659-8","acknowledgement":"The authors would like to thank Mr. Joel Dietz for management of the mouse colony and helpful advice for conducting quantitative PCR studies and Mr. Santoshi Kinoshita at the Translational Research Initiative in Pathology laboratory at the University of Wisconsin-Madison for cutting sections analyzed in this study.\r\nThis work was supported by National Eye Institute grants R01 EY030123 (RWN), R01 EY018606 (RTL), P30 EY016665 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), T32 EY027721 (RJD) and F31 EY030739 (OJM). Additional funding was provided by the BrightFocus Foundation (RWN) and unrestricted grants from Research to Prevent Blindness, Inc to the Department of Ophthalmology and Visual Sciences (University of Wisconsin-Madison) and to the Department of Ophthalmology (University of Rochester).","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2024-01-30T14:33:31Z","citation":{"ista":"Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. 2023. BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. Molecular Neurodegeneration. 18, 67.","apa":"Maes, M. E., Donahue, R. J., Schlamp, C. L., Marola, O. J., Libby, R. T., &#38; Nickells, R. W. (2023). BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. <i>Molecular Neurodegeneration</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13024-023-00659-8\">https://doi.org/10.1186/s13024-023-00659-8</a>","ama":"Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. <i>Molecular Neurodegeneration</i>. 2023;18. doi:<a href=\"https://doi.org/10.1186/s13024-023-00659-8\">10.1186/s13024-023-00659-8</a>","mla":"Maes, Margaret E., et al. “BAX Activation in Mouse Retinal Ganglion Cells Occurs in Two Temporally and Mechanistically Distinct Steps.” <i>Molecular Neurodegeneration</i>, vol. 18, 67, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13024-023-00659-8\">10.1186/s13024-023-00659-8</a>.","ieee":"M. E. Maes, R. J. Donahue, C. L. Schlamp, O. J. Marola, R. T. Libby, and R. W. Nickells, “BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps,” <i>Molecular Neurodegeneration</i>, vol. 18. Springer Nature, 2023.","chicago":"Maes, Margaret E, Ryan J. Donahue, Cassandra L. Schlamp, Olivia J. Marola, Richard T. Libby, and Robert W. Nickells. “BAX Activation in Mouse Retinal Ganglion Cells Occurs in Two Temporally and Mechanistically Distinct Steps.” <i>Molecular Neurodegeneration</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13024-023-00659-8\">https://doi.org/10.1186/s13024-023-00659-8</a>.","short":"M.E. Maes, R.J. Donahue, C.L. Schlamp, O.J. Marola, R.T. Libby, R.W. Nickells, Molecular Neurodegeneration 18 (2023)."},"oa":1,"article_number":"67","article_type":"original","abstract":[{"text":"Background: \r\nPro-apoptotic BAX is a central mediator of retinal ganglion cell (RGC) death after optic nerve damage. BAX activation occurs in two stages including translocation of latent BAX to the mitochondrial outer membrane (MOM) and then permeabilization of the MOM to facilitate the release of apoptotic signaling molecules. As a critical component of RGC death, BAX is an attractive target for neuroprotective therapies and an understanding of the kinetics of BAX activation and the mechanisms controlling the two stages of this process in RGCs is potentially valuable in informing the development of a neuroprotective strategy.\r\nMethods:\r\nThe kinetics of BAX translocation were assessed by both static and live-cell imaging of a GFP-BAX fusion protein introduced into RGCs using AAV2-mediated gene transfer in mice. Activation of BAX was achieved using an acute optic nerve crush (ONC) protocol. Live-cell imaging of GFP-BAX was achieved using explants of mouse retina harvested 7 days after ONC. Kinetics of translocation in RGCs were compared to GFP-BAX translocation in 661W tissue culture cells. Permeabilization of GFP-BAX was assessed by staining with the 6A7 monoclonal antibody, which recognizes a conformational change in this protein after MOM insertion. Assessment of individual kinases associated with both stages of activation was made using small molecule inhibitors injected into the vitreous either independently or in concert with ONC surgery. The contribution of the Dual Leucine Zipper-JUN-N-Terminal Kinase cascade was evaluated using mice with a double conditional knock-out of both Mkk4 and Mkk7.\r\nResults:\r\nONC induces the translocation of GFP-BAX in RGCs at a slower rate and with less intracellular synchronicity than 661W cells, but exhibits less variability among mitochondrial foci within a single cell. GFP-BAX was also found to translocate in all compartments of an RGC including the dendritic arbor and axon. Approximately 6% of translocating RGCs exhibited retrotranslocation of BAX immediately following translocation. Unlike tissue culture cells, which exhibit simultaneous translocation and permeabilization, RGCs exhibited a significant delay between these two stages, similar to detached cells undergoing anoikis. Translocation, with minimal permeabilization could be induced in a subset of RGCs using an inhibitor of Focal Adhesion Kinase (PF573228). Permeabilization after ONC, in a majority of RGCs, could be inhibited with a broad spectrum kinase inhibitor (sunitinib) or a selective inhibitor for p38/MAPK14 (SB203580). Intervention of DLK-JNK axis signaling abrogated GFP-BAX translocation after ONC.\r\nConclusions:\r\nA comparison between BAX activation kinetics in tissue culture cells and in cells of a complex tissue environment shows distinct differences indicating that caution should be used when translating findings from one condition to the other. RGCs exhibit both a delay between translocation and permeabilization and the ability for translocated BAX to be retrotranslocated, suggesting several stages at which intervention of the activation process could be exploited in the design of a therapeutic strategy.","lang":"eng"}],"publication":"Molecular Neurodegeneration","title":"BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps","author":[{"full_name":"Maes, Margaret E","last_name":"Maes","first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085"},{"first_name":"Ryan J.","last_name":"Donahue","full_name":"Donahue, Ryan J."},{"first_name":"Cassandra L.","last_name":"Schlamp","full_name":"Schlamp, Cassandra L."},{"full_name":"Marola, Olivia J.","last_name":"Marola","first_name":"Olivia J."},{"first_name":"Richard T.","full_name":"Libby, Richard T.","last_name":"Libby"},{"last_name":"Nickells","full_name":"Nickells, Robert W.","first_name":"Robert W."}],"publication_identifier":{"eissn":["1750-1326"]},"_id":"14401","year":"2023","day":"26","article_processing_charge":"Yes","publication_status":"published","date_updated":"2025-04-23T13:09:05Z"}]