[{"external_id":{"arxiv":["2105.04874"],"isi":["000795160200009"]},"isi":1,"year":"2022","citation":{"ista":"Roos B, Seiringer R. 2022. Two-particle bound states at interfaces and corners. Journal of Functional Analysis. 282(12), 109455.","short":"B. Roos, R. Seiringer, Journal of Functional Analysis 282 (2022).","mla":"Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces and Corners.” <i>Journal of Functional Analysis</i>, vol. 282, no. 12, 109455, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">10.1016/j.jfa.2022.109455</a>.","ieee":"B. Roos and R. Seiringer, “Two-particle bound states at interfaces and corners,” <i>Journal of Functional Analysis</i>, vol. 282, no. 12. Elsevier, 2022.","chicago":"Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces and Corners.” <i>Journal of Functional Analysis</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">https://doi.org/10.1016/j.jfa.2022.109455</a>.","ama":"Roos B, Seiringer R. Two-particle bound states at interfaces and corners. <i>Journal of Functional Analysis</i>. 2022;282(12). doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">10.1016/j.jfa.2022.109455</a>","apa":"Roos, B., &#38; Seiringer, R. (2022). Two-particle bound states at interfaces and corners. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">https://doi.org/10.1016/j.jfa.2022.109455</a>"},"date_updated":"2023-10-27T10:37:29Z","abstract":[{"lang":"eng","text":"We study two interacting quantum particles forming a bound state in d-dimensional free\r\nspace, and constrain the particles in k directions to (0, ∞)k ×Rd−k, with Neumann boundary\r\nconditions. First, we prove that the ground state energy strictly decreases upon going from k\r\nto k+1. This shows that the particles stick to the corner where all boundary planes intersect.\r\nSecond, we show that for all k the resulting Hamiltonian, after removing the free part of the\r\nkinetic energy, has only finitely many eigenvalues below the essential spectrum. This paper\r\ngeneralizes the work of Egger, Kerner and Pankrashkin (J. Spectr. Theory 10(4):1413–1444,\r\n2020) to dimensions d > 1."}],"day":"15","arxiv":1,"doi":"10.1016/j.jfa.2022.109455","ddc":["510"],"acknowledgement":"We thank Rupert Frank for contributing Appendix B. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 is gratefully acknowledged.","volume":282,"issue":"12","author":[{"first_name":"Barbara","last_name":"Roos","orcid":"0000-0002-9071-5880","full_name":"Roos, Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425"},{"first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"10850","intvolume":"       282","title":"Two-particle bound states at interfaces and corners","date_created":"2022-03-16T08:41:53Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"article_processing_charge":"Yes (via OA deal)","publication_status":"published","file_date_updated":"2022-08-02T10:37:55Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"Elsevier","type":"journal_article","date_published":"2022-06-15T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["0022-1236"]},"status":"public","related_material":{"record":[{"status":"public","id":"14374","relation":"dissertation_contains"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"11720","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2022-08-02T10:37:55Z","content_type":"application/pdf","file_name":"2022_JourFunctionalAnalysis_Roos.pdf","date_created":"2022-08-02T10:37:55Z","file_size":631391,"checksum":"63efcefaa1f2717244ef5407bd564426"}],"has_accepted_license":"1","publication":"Journal of Functional Analysis","article_number":"109455","month":"06","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"oa_version":"Published Version","keyword":["Analysis"],"language":[{"iso":"eng"}]},{"publication":"Physical Review Letters","article_number":"107701","month":"03","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Preprint","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"keyword":["General Physics and Astronomy"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2022-03-11T00:00:00Z","oa":1,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"related_material":{"record":[{"id":"10029","relation":"earlier_version","status":"public"},{"relation":"dissertation_contains","id":"14547","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/characterizing-super-semi-sandwiches-for-quantum-computing/","relation":"press_release","description":"News on ISTA Website"}]},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2107.03695"}],"issue":"10","author":[{"full_name":"Phan, Duc T","last_name":"Phan","first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Senior","first_name":"Jorden L","full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295","id":"5479D234-2D30-11EA-89CC-40953DDC885E"},{"orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hatefipour, M.","first_name":"M.","last_name":"Hatefipour"},{"first_name":"W. M.","last_name":"Strickland","full_name":"Strickland, W. M."},{"first_name":"J.","last_name":"Shabani","full_name":"Shabani, J."},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym"},{"first_name":"Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","pmid":1,"_id":"10851","intvolume":"       128","title":"Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit","date_created":"2022-03-17T11:37:47Z","department":[{"_id":"MaSe"},{"_id":"AnHi"}],"article_processing_charge":"No","publication_status":"published","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"American Physical Society","external_id":{"arxiv":["2107.03695"],"pmid":[" 35333085"],"isi":["000771391100002"]},"isi":1,"citation":{"short":"D.T. Phan, J.L. Senior, A. Ghazaryan, M. Hatefipour, W.M. Strickland, J. Shabani, M. Serbyn, A.P. Higginbotham, Physical Review Letters 128 (2022).","mla":"Phan, Duc T., et al. “Detecting Induced P±ip Pairing at the Al-InAs Interface with a Quantum Microwave Circuit.” <i>Physical Review Letters</i>, vol. 128, no. 10, 107701, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevlett.128.107701\">10.1103/physrevlett.128.107701</a>.","ista":"Phan DT, Senior JL, Ghazaryan A, Hatefipour M, Strickland WM, Shabani J, Serbyn M, Higginbotham AP. 2022. Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. Physical Review Letters. 128(10), 107701.","apa":"Phan, D. T., Senior, J. L., Ghazaryan, A., Hatefipour, M., Strickland, W. M., Shabani, J., … Higginbotham, A. P. (2022). Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.128.107701\">https://doi.org/10.1103/physrevlett.128.107701</a>","ama":"Phan DT, Senior JL, Ghazaryan A, et al. Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. <i>Physical Review Letters</i>. 2022;128(10). doi:<a href=\"https://doi.org/10.1103/physrevlett.128.107701\">10.1103/physrevlett.128.107701</a>","ieee":"D. T. Phan <i>et al.</i>, “Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit,” <i>Physical Review Letters</i>, vol. 128, no. 10. American Physical Society, 2022.","chicago":"Phan, Duc T, Jorden L Senior, Areg Ghazaryan, M. Hatefipour, W. M. Strickland, J. Shabani, Maksym Serbyn, and Andrew P Higginbotham. “Detecting Induced P±ip Pairing at the Al-InAs Interface with a Quantum Microwave Circuit.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevlett.128.107701\">https://doi.org/10.1103/physrevlett.128.107701</a>."},"year":"2022","date_updated":"2023-11-30T10:56:03Z","abstract":[{"lang":"eng","text":"Superconductor-semiconductor hybrid devices are at the heart of several proposed approaches to quantum information processing, but their basic properties remain to be understood. We embed a twodimensional Al-InAs hybrid system in a resonant microwave circuit, probing the breakdown of superconductivity due to an applied magnetic field. We find a fingerprint from the two-component nature of the hybrid system, and quantitatively compare with a theory that includes the contribution of intraband p±ip pairing in the InAs, as well as the emergence of Bogoliubov-Fermi surfaces due to magnetic field. Separately resolving the Al and InAs contributions allows us to determine the carrier density and mobility in the InAs."}],"day":"11","doi":"10.1103/physrevlett.128.107701","arxiv":1,"volume":128,"acknowledgement":"M. S. acknowledges useful discussions with A. Levchenko and P. A. Lee, and E. Berg. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. J. S. and A. G. acknowledge funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411.W. M. Hatefipour, W. M. Strickland and J. Shabani acknowledge funding from Office of Naval Research Award No. N00014-21-1-2450."},{"scopus_import":"1","_id":"10863","author":[{"full_name":"Davydova, Margarita","first_name":"Margarita","last_name":"Davydova"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn"},{"last_name":"Ishizuka","first_name":"Hiroaki","full_name":"Ishizuka, Hiroaki"}],"department":[{"_id":"MaSe"}],"article_processing_charge":"No","date_created":"2022-03-18T10:20:46Z","publication_status":"published","intvolume":"       105","title":"Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials","quality_controlled":"1","publisher":"American Physical Society","article_type":"letter_note","citation":{"mla":"Davydova, Margarita, et al. “Symmetry-Allowed Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric Materials.” <i>Physical Review B</i>, vol. 105, L121407, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">10.1103/PhysRevB.105.L121407</a>.","short":"M. Davydova, M. Serbyn, H. Ishizuka, Physical Review B 105 (2022).","ista":"Davydova M, Serbyn M, Ishizuka H. 2022. Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. Physical Review B. 105, L121407.","apa":"Davydova, M., Serbyn, M., &#38; Ishizuka, H. (2022). Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">https://doi.org/10.1103/PhysRevB.105.L121407</a>","ama":"Davydova M, Serbyn M, Ishizuka H. Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. <i>Physical Review B</i>. 2022;105. doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">10.1103/PhysRevB.105.L121407</a>","ieee":"M. Davydova, M. Serbyn, and H. Ishizuka, “Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials,” <i>Physical Review B</i>, vol. 105. American Physical Society, 2022.","chicago":"Davydova, Margarita, Maksym Serbyn, and Hiroaki Ishizuka. “Symmetry-Allowed Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric Materials.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">https://doi.org/10.1103/PhysRevB.105.L121407</a>."},"year":"2022","date_updated":"2023-08-03T06:09:56Z","external_id":{"isi":["000800752500001"],"arxiv":["2101.08277"]},"isi":1,"day":"17","arxiv":1,"doi":"10.1103/PhysRevB.105.L121407","abstract":[{"text":"Nonlinear optical responses are commonly used as a probe for studying the electronic properties of materials. For topological materials, studies thus far focused on photogalvanic electric currents, which are forbidden in centrosymmetric materials because they require broken inversion symmetry. In this Letter, we propose a class of symmetry-allowed responses for inversion-symmetric topological insulators with two doubly degenerate bands. We consider a specific example of such a response, the orbital current, and show that the sign of the response reflects the Z2 topological index, i.e., the orbital current changes sign at the transition between trivial and topological insulator phases. This is illustrated in two models of topological insulators: the Bernevig-Hughes-Zhang model and the 1T′ phase of transition metal dichalcogenides.","lang":"eng"}],"volume":105,"acknowledgement":"We are grateful to Takahiro Morimoto and Zhanybek Alpichshev for fruitful discussions. MD was supported by Austrian Agency for International Cooperation in Education and Research (OeAD-GmbH) and by the John Seo Fellowship at MIT. HI was supported by JSPS KAKENHI Grant Numbers JP19K14649 and JP18H03676, and by UTokyo Global Activity Support Program for\r\nYoung Researchers.","publication":"Physical Review B","oa_version":"Preprint","article_number":"L121407","month":"03","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2022-03-17T00:00:00Z","publication_identifier":{"issn":["2469-9969"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2101.08277","open_access":"1"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa":1,"publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"date_published":"2022-06-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"11721","file_size":734482,"checksum":"1cf185e264e04c87cb1ce67a00db88ab","date_created":"2022-08-02T10:40:48Z","content_type":"application/pdf","file_name":"2022_JourFunctionalAnalysis_Ivanov.pdf","date_updated":"2022-08-02T10:40:48Z"}],"month":"06","article_number":"109441","oa_version":"Published Version","publication":"Journal of Functional Analysis","has_accepted_license":"1","language":[{"iso":"eng"}],"abstract":[{"text":"We introduce a new way of representing logarithmically concave functions on Rd. It allows us to extend the notion of the largest volume ellipsoid contained in a convex body to the setting of logarithmically concave functions as follows. For every s>0, we define a class of non-negative functions on Rd derived from ellipsoids in Rd+1. For any log-concave function f on Rd , and any fixed s>0, we consider functions belonging to this class, and find the one with the largest integral under the condition that it is pointwise less than or equal to f, and we call it the John s-function of f. After establishing existence and uniqueness, we give a characterization of this function similar to the one given by John in his fundamental theorem. We find that John s-functions converge to characteristic functions of ellipsoids as s tends to zero and to Gaussian densities as s tends to infinity.\r\nAs an application, we prove a quantitative Helly type result: the integral of the pointwise minimum of any family of log-concave functions is at least a constant cd multiple of the integral of the pointwise minimum of a properly chosen subfamily of size 3d+2, where cd depends only on d.","lang":"eng"}],"doi":"10.1016/j.jfa.2022.109441","arxiv":1,"day":"01","isi":1,"external_id":{"arxiv":["2006.09934"],"isi":["000781371300008"]},"date_updated":"2023-08-02T14:51:11Z","year":"2022","citation":{"ieee":"G. Ivanov and M. Naszódi, “Functional John ellipsoids,” <i>Journal of Functional Analysis</i>, vol. 282, no. 11. Elsevier, 2022.","chicago":"Ivanov, Grigory, and Márton Naszódi. “Functional John Ellipsoids.” <i>Journal of Functional Analysis</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">https://doi.org/10.1016/j.jfa.2022.109441</a>.","ama":"Ivanov G, Naszódi M. Functional John ellipsoids. <i>Journal of Functional Analysis</i>. 2022;282(11). doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">10.1016/j.jfa.2022.109441</a>","apa":"Ivanov, G., &#38; Naszódi, M. (2022). Functional John ellipsoids. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">https://doi.org/10.1016/j.jfa.2022.109441</a>","ista":"Ivanov G, Naszódi M. 2022. Functional John ellipsoids. Journal of Functional Analysis. 282(11), 109441.","short":"G. Ivanov, M. Naszódi, Journal of Functional Analysis 282 (2022).","mla":"Ivanov, Grigory, and Márton Naszódi. “Functional John Ellipsoids.” <i>Journal of Functional Analysis</i>, vol. 282, no. 11, 109441, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">10.1016/j.jfa.2022.109441</a>."},"ddc":["510"],"acknowledgement":"G.I. was supported by the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported by the National Research, Development and Innovation Fund (NRDI) grants K119670 and KKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06 program provided by the NRDI. ","volume":282,"title":"Functional John ellipsoids","intvolume":"       282","publication_status":"published","department":[{"_id":"UlWa"}],"date_created":"2022-03-20T23:01:38Z","article_processing_charge":"Yes (via OA deal)","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory","last_name":"Ivanov","first_name":"Grigory"},{"last_name":"Naszódi","first_name":"Márton","full_name":"Naszódi, Márton"}],"issue":"11","_id":"10887","scopus_import":"1","article_type":"original","publisher":"Elsevier","file_date_updated":"2022-08-02T10:40:48Z","quality_controlled":"1"},{"date_updated":"2023-08-03T06:06:27Z","year":"2022","citation":{"ista":"Lu Q, Zhang Y, Hellner J, Giannini C, Xu X, Pauwels J, Ma Q, Dejonghe W, Han H, Van De Cotte B, Impens F, Gevaert K, De Smet I, Friml J, Molina DM, Russinova E. 2022. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 119(11), e2118220119.","short":"Q. Lu, Y. Zhang, J. Hellner, C. Giannini, X. Xu, J. Pauwels, Q. Ma, W. Dejonghe, H. Han, B. Van De Cotte, F. Impens, K. Gevaert, I. De Smet, J. Friml, D.M. Molina, E. Russinova, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11, e2118220119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>.","chicago":"Lu, Qing, Yonghong Zhang, Joakim Hellner, Caterina Giannini, Xiangyu Xu, Jarne Pauwels, Qian Ma, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>.","ieee":"Q. Lu <i>et al.</i>, “Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11. Proceedings of the National Academy of Sciences, 2022.","apa":"Lu, Q., Zhang, Y., Hellner, J., Giannini, C., Xu, X., Pauwels, J., … Russinova, E. (2022). Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>","ama":"Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(11). doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>"},"isi":1,"external_id":{"pmid":["35254915"],"isi":["000771756300008"]},"doi":"10.1073/pnas.2118220119","day":"07","abstract":[{"text":"Despite the growing interest in using chemical genetics in plant research, small molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or posttranslational modifications, allows the discovery of drug targets or the study of protein–metabolite and protein–protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf, thus revealing cross-talk between brassinosteroid and auxin signaling.","lang":"eng"}],"acknowledgement":"We thank Yanhai Yin for providing the anti-BES1 antibody, Johan Winne and Brenda Callebaut for synthesizing bikinin, Yuki Kondo and Hiroo Fukuda for published materials, Tomasz Nodzy\u0003nski for useful advice, and Martine De Cock for help in preparing the manuscript. This\r\nwork was supported by the China Scholarship Council for predoctoral (Q.L. and X.X.) and postdoctoral (Y.Z.) fellowships; the Agency for Innovation by Science and Technology for a predoctoral fellowship (W.D.); the Research Foundation-Flanders, Projects G009018N and G002121N (E.R.); and the VIB TechWatch Fund (E.R.).","volume":119,"ddc":["580"],"pmid":1,"_id":"10888","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"full_name":"Lu, Qing","last_name":"Lu","first_name":"Qing"},{"first_name":"Yonghong","last_name":"Zhang","full_name":"Zhang, Yonghong"},{"last_name":"Hellner","first_name":"Joakim","full_name":"Hellner, Joakim"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina"},{"full_name":"Xu, Xiangyu","first_name":"Xiangyu","last_name":"Xu"},{"first_name":"Jarne","last_name":"Pauwels","full_name":"Pauwels, Jarne"},{"last_name":"Ma","first_name":"Qian","full_name":"Ma, Qian"},{"full_name":"Dejonghe, Wim","first_name":"Wim","last_name":"Dejonghe"},{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van De Cotte, Brigitte","first_name":"Brigitte","last_name":"Van De Cotte"},{"full_name":"Impens, Francis","first_name":"Francis","last_name":"Impens"},{"full_name":"Gevaert, Kris","first_name":"Kris","last_name":"Gevaert"},{"full_name":"De Smet, Ive","last_name":"De Smet","first_name":"Ive"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Molina","first_name":"Daniel Martinez","full_name":"Molina, Daniel Martinez"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"}],"issue":"11","publication_status":"published","article_processing_charge":"No","department":[{"_id":"JiFr"}],"date_created":"2022-03-20T23:01:39Z","title":"Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling","intvolume":"       119","quality_controlled":"1","file_date_updated":"2022-03-21T09:19:47Z","publisher":"Proceedings of the National Academy of Sciences","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"date_published":"2022-03-07T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1091-6490"]},"oa":1,"file":[{"file_id":"10910","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2022-03-21T09:19:47Z","content_type":"application/pdf","file_name":"2022_PNAS_Lu.pdf","date_created":"2022-03-21T09:19:47Z","checksum":"83e0fea7919570d0b519b41193342571","file_size":2169534}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","oa_version":"Published Version","month":"03","article_number":"e2118220119","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"publication":"Microscopy","month":"03","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/jmicro/dfab048"}],"type":"journal_article","date_published":"2022-03-01T00:00:00Z","oa":1,"publication_identifier":{"issn":["2050-5698"],"eissn":["2050-5701"]},"ec_funded":1,"quality_controlled":"1","page":"i72-i80","article_type":"original","publisher":"Oxford Academic","issue":"Supplement_1","author":[{"first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"10889","pmid":1,"intvolume":"        71","title":"Electron microscopic visualization of single molecules by tag-mediated metal particle labeling","date_created":"2022-03-20T23:01:39Z","article_processing_charge":"No","department":[{"_id":"RySh"}],"publication_status":"published","acknowledgement":"European Research Council Advanced Grant (694539 to R.S.).","volume":71,"external_id":{"isi":["000768384100011"],"pmid":["35275179"]},"isi":1,"citation":{"chicago":"Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules by Tag-Mediated Metal Particle Labeling.” <i>Microscopy</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfab048\">https://doi.org/10.1093/jmicro/dfab048</a>.","ieee":"R. Shigemoto, “Electron microscopic visualization of single molecules by tag-mediated metal particle labeling,” <i>Microscopy</i>, vol. 71, no. Supplement_1. Oxford Academic, pp. i72–i80, 2022.","ama":"Shigemoto R. Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. <i>Microscopy</i>. 2022;71(Supplement_1):i72-i80. doi:<a href=\"https://doi.org/10.1093/jmicro/dfab048\">10.1093/jmicro/dfab048</a>","apa":"Shigemoto, R. (2022). Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. <i>Microscopy</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/jmicro/dfab048\">https://doi.org/10.1093/jmicro/dfab048</a>","ista":"Shigemoto R. 2022. Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. Microscopy. 71(Supplement_1), i72–i80.","mla":"Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules by Tag-Mediated Metal Particle Labeling.” <i>Microscopy</i>, vol. 71, no. Supplement_1, Oxford Academic, 2022, pp. i72–80, doi:<a href=\"https://doi.org/10.1093/jmicro/dfab048\">10.1093/jmicro/dfab048</a>.","short":"R. Shigemoto, Microscopy 71 (2022) i72–i80."},"year":"2022","date_updated":"2023-08-03T06:08:01Z","abstract":[{"text":"Genetically encoded tags have introduced extensive lines of application from purification of tagged proteins to their visualization at the single molecular, cellular, histological and whole-body levels. Combined with other rapidly developing technologies such as clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, proteomics, super-resolution microscopy and proximity labeling, a large variety of genetically encoded tags have been developed in the last two decades. In this review, I focus on the current status of tag development for electron microscopic (EM) visualization of proteins with metal particle labeling. Compared with conventional immunoelectron microscopy using gold particles, tag-mediated metal particle labeling has several advantages that could potentially improve the sensitivity, spatial and temporal resolution, and applicability to a wide range of proteins of interest (POIs). It may enable researchers to detect single molecules in situ, allowing the quantitative measurement of absolute numbers and exact localization patterns of POI in the ultrastructural context. Thus, genetically encoded tags for EM could revolutionize the field as green fluorescence protein did for light microscopy, although we still have many challenges to overcome before reaching this goal.","lang":"eng"}],"day":"01","doi":"10.1093/jmicro/dfab048"},{"language":[{"iso":"eng"}],"month":"02","article_number":"846615","oa_version":"Published Version","project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"_id":"05970B30-7A3F-11EA-A408-12923DDC885E","name":"LGI1 antibody-induced pathophysiology in synapses","grant_number":"I04638"}],"publication":"Frontiers in Neuroanatomy","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"file_name":"2022_FrontiersNeuroanatomy_Eguchi.pdf","content_type":"application/pdf","date_updated":"2022-03-21T09:41:19Z","checksum":"51ec9b90e7da919e22c01a15489eaacd","file_size":2416395,"date_created":"2022-03-21T09:41:19Z","creator":"dernst","file_id":"10911","access_level":"open_access","success":1,"relation":"main_file"}],"oa":1,"publication_identifier":{"eissn":["16625129"]},"date_published":"2022-02-24T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","publisher":"Frontiers","file_date_updated":"2022-03-21T09:41:19Z","ec_funded":1,"quality_controlled":"1","title":"The number and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals","intvolume":"        16","publication_status":"published","date_created":"2022-03-20T23:01:39Z","article_processing_charge":"No","department":[{"_id":"RySh"}],"author":[{"last_name":"Eguchi","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87"},{"id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","last_name":"Le Monnier","first_name":"Elodie","full_name":"Le Monnier, Elodie"},{"last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"_id":"10890","scopus_import":"1","ddc":["570"],"acknowledgement":"This work was supported by the European Research Council advanced grant No. 694539 and the joint German-Austrian DFG and FWF project SYNABS (FWF: I-4638-B) to RS.\r\nThe authors thank Walter Kaufmann for his critical comments on the manuscript.","volume":16,"abstract":[{"lang":"eng","text":"Upon the arrival of action potentials at nerve terminals, neurotransmitters are released from synaptic vesicles (SVs) by exocytosis. CaV2.1, 2.2, and 2.3 are the major subunits of the voltage-gated calcium channel (VGCC) responsible for increasing intraterminal calcium levels and triggering SV exocytosis in the central nervous system (CNS) synapses. The two-dimensional analysis of CaV2 distributions using sodium dodecyl sulfate (SDS)-digested freeze-fracture replica labeling (SDS-FRL) has revealed their numbers, densities, and nanoscale clustering patterns in individual presynaptic active zones. The variation in these properties affects the coupling of VGCCs with calcium sensors on SVs, synaptic efficacy, and temporal precision of transmission. In this study, we summarize how the morphological parameters of CaV2 distribution obtained using SDS-FRL differ depending on the different types of synapses and could correspond to functional properties in synaptic transmission."}],"doi":"10.3389/fnana.2022.846615","day":"24","isi":1,"external_id":{"isi":["000766662700001"],"pmid":["35280978"]},"date_updated":"2024-10-29T07:57:26Z","year":"2022","citation":{"apa":"Eguchi, K., Montanaro-Punzengruber, J.-C., Le Monnier, E., &#38; Shigemoto, R. (2022). The number and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals. <i>Frontiers in Neuroanatomy</i>. Frontiers. <a href=\"https://doi.org/10.3389/fnana.2022.846615\">https://doi.org/10.3389/fnana.2022.846615</a>","ama":"Eguchi K, Montanaro-Punzengruber J-C, Le Monnier E, Shigemoto R. The number and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals. <i>Frontiers in Neuroanatomy</i>. 2022;16. doi:<a href=\"https://doi.org/10.3389/fnana.2022.846615\">10.3389/fnana.2022.846615</a>","chicago":"Eguchi, Kohgaku, Jacqueline-Claire Montanaro-Punzengruber, Elodie Le Monnier, and Ryuichi Shigemoto. “The Number and Distinct Clustering Patterns of Voltage-Gated Calcium Channels in Nerve Terminals.” <i>Frontiers in Neuroanatomy</i>. Frontiers, 2022. <a href=\"https://doi.org/10.3389/fnana.2022.846615\">https://doi.org/10.3389/fnana.2022.846615</a>.","ieee":"K. Eguchi, J.-C. Montanaro-Punzengruber, E. Le Monnier, and R. Shigemoto, “The number and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals,” <i>Frontiers in Neuroanatomy</i>, vol. 16. Frontiers, 2022.","short":"K. Eguchi, J.-C. Montanaro-Punzengruber, E. Le Monnier, R. Shigemoto, Frontiers in Neuroanatomy 16 (2022).","mla":"Eguchi, Kohgaku, et al. “The Number and Distinct Clustering Patterns of Voltage-Gated Calcium Channels in Nerve Terminals.” <i>Frontiers in Neuroanatomy</i>, vol. 16, 846615, Frontiers, 2022, doi:<a href=\"https://doi.org/10.3389/fnana.2022.846615\">10.3389/fnana.2022.846615</a>.","ista":"Eguchi K, Montanaro-Punzengruber J-C, Le Monnier E, Shigemoto R. 2022. The number and distinct clustering patterns of voltage-gated Calcium channels in nerve terminals. Frontiers in Neuroanatomy. 16, 846615."}},{"conference":{"name":"NSV: Numerical Software Verification","start_date":"2021-10-18","location":"New Haven, CT, United States","end_date":"2021-10-19"},"language":[{"iso":"eng"}],"month":"02","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa_version":"None","publication":"Software Verification","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"isbn":["9783030955601"],"issn":["0302-9743"],"eissn":["1611-3349"]},"type":"conference","date_published":"2022-02-22T00:00:00Z","publisher":"Springer Nature","series_title":"LNCS","quality_controlled":"1","page":"3-6","intvolume":"     13124","title":"Quantitative monitoring of software","department":[{"_id":"ToHe"}],"date_created":"2022-03-20T23:01:40Z","article_processing_charge":"No","publication_status":"published","author":[{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"10891","acknowledgement":"The formal framework for quantitative monitoring which is presented in this invited talk was defined jointly with N. Ege Saraç at LICS 2021. This work was supported in part by the Wittgenstein Award Z211-N23 of the Austrian Science Fund.","volume":13124,"abstract":[{"lang":"eng","text":"We present a formal framework for the online black-box monitoring of software using monitors with quantitative verdict functions. Quantitative verdict functions have several advantages. First, quantitative monitors can be approximate, i.e., the value of the verdict function does not need to correspond exactly to the value of the property under observation. Second, quantitative monitors can be quantified universally, i.e., for every possible observed behavior, the monitor tries to make the best effort to estimate the value of the property under observation. Third, quantitative monitors can watch boolean as well as quantitative properties, such as average response time. Fourth, quantitative monitors can use non-finite-state resources, such as counters. As a consequence, quantitative monitors can be compared according to how many resources they use (e.g., the number of counters) and how precisely they approximate the property under observation. This allows for a rich spectrum of cost-precision trade-offs in monitoring software."}],"day":"22","doi":"10.1007/978-3-030-95561-8_1","external_id":{"isi":["000771713200001"]},"isi":1,"year":"2022","citation":{"ieee":"T. A. Henzinger, “Quantitative monitoring of software,” in <i>Software Verification</i>, New Haven, CT, United States, 2022, vol. 13124, pp. 3–6.","chicago":"Henzinger, Thomas A. “Quantitative Monitoring of Software.” In <i>Software Verification</i>, 13124:3–6. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">https://doi.org/10.1007/978-3-030-95561-8_1</a>.","ama":"Henzinger TA. Quantitative monitoring of software. In: <i>Software Verification</i>. Vol 13124. LNCS. Springer Nature; 2022:3-6. doi:<a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">10.1007/978-3-030-95561-8_1</a>","apa":"Henzinger, T. A. (2022). Quantitative monitoring of software. In <i>Software Verification</i> (Vol. 13124, pp. 3–6). New Haven, CT, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">https://doi.org/10.1007/978-3-030-95561-8_1</a>","ista":"Henzinger TA. 2022. Quantitative monitoring of software. Software Verification. NSV: Numerical Software VerificationLNCS vol. 13124, 3–6.","short":"T.A. Henzinger, in:, Software Verification, Springer Nature, 2022, pp. 3–6.","mla":"Henzinger, Thomas A. “Quantitative Monitoring of Software.” <i>Software Verification</i>, vol. 13124, Springer Nature, 2022, pp. 3–6, doi:<a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">10.1007/978-3-030-95561-8_1</a>."},"date_updated":"2023-08-03T06:11:55Z"},{"oa":1,"publication_identifier":{"eissn":["1460-2075"]},"type":"journal_article","date_published":"2022-03-23T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"date_updated":"2022-03-24T13:22:41Z","file_name":"Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosopila.pdf","content_type":"application/pdf","date_created":"2022-03-24T13:22:41Z","file_size":4344585,"checksum":"dba48580fe0fefaa4c63078d1d2a35df","file_id":"10919","creator":"siekhaus","relation":"main_file","access_level":"open_access"}],"article_number":"e109049","month":"03","project":[{"call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077"},{"call_identifier":"FWF","_id":"264CBBAC-B435-11E9-9278-68D0E5697425","name":"Modeling epithelial tissue mechanics during cell invasion","grant_number":"M02379"},{"call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","name":"Drosophila TNFa´s Funktion in Immunzellen","grant_number":"P29638"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"The Embo Journal","language":[{"iso":"eng"}],"abstract":[{"text":"Cellular metabolism must adapt to changing demands to enable homeostasis. During immune responses or cancer metastasis, cells leading migration into challenging environments require an energy boost, but what controls this capacity is unclear. Here, we study a previously uncharacterized nuclear protein, Atossa (encoded by CG9005), which supports macrophage invasion into the germband of Drosophila by controlling cellular metabolism. First, nuclear Atossa increases mRNA levels of Porthos, a DEAD-box protein, and of two metabolic enzymes, lysine-α-ketoglutarate reductase (LKR/SDH) and NADPH glyoxylate reductase (GR/HPR), thus enhancing mitochondrial bioenergetics. Then Porthos supports ribosome assembly and thereby raises the translational efficiency of a subset of mRNAs, including those affecting mitochondrial functions, the electron transport chain, and metabolism. Mitochondrial respiration measurements, metabolomics, and live imaging indicate that Atossa and Porthos power up OxPhos and energy production to promote the forging of a path into tissues by leading macrophages. Since many crucial physiological responses require increases in mitochondrial energy output, this previously undescribed genetic program may modulate a wide range of cellular behaviors.","lang":"eng"}],"day":"23","doi":"10.15252/embj.2021109049","external_id":{"isi":["000771957000001"]},"isi":1,"year":"2022","citation":{"ama":"Emtenani S, Martin ET, György A, et al. Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. <i>The Embo Journal</i>. 2022;41. doi:<a href=\"https://doi.org/10.15252/embj.2021109049\">10.15252/embj.2021109049</a>","apa":"Emtenani, S., Martin, E. T., György, A., Bicher, J., Genger, J.-W., Köcher, T., … Siekhaus, D. E. (2022). Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. <i>The Embo Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2021109049\">https://doi.org/10.15252/embj.2021109049</a>","chicago":"Emtenani, Shamsi, Elliot T Martin, Attila György, Julia Bicher, Jakob-Wendelin Genger, Thomas Köcher, Maria Akhmanova, et al. “Macrophage Mitochondrial Bioenergetics and Tissue Invasion Are Boosted by an Atossa-Porthos Axis in Drosophila.” <i>The Embo Journal</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/embj.2021109049\">https://doi.org/10.15252/embj.2021109049</a>.","ieee":"S. Emtenani <i>et al.</i>, “Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila,” <i>The Embo Journal</i>, vol. 41. Embo Press, 2022.","short":"S. Emtenani, E.T. Martin, A. György, J. Bicher, J.-W. Genger, T. Köcher, M. Akhmanova, M. Pereira Guarda, M. Roblek, A. Bergthaler, T.R. Hurd, P. Rangan, D.E. Siekhaus, The Embo Journal 41 (2022).","mla":"Emtenani, Shamsi, et al. “Macrophage Mitochondrial Bioenergetics and Tissue Invasion Are Boosted by an Atossa-Porthos Axis in Drosophila.” <i>The Embo Journal</i>, vol. 41, e109049, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/embj.2021109049\">10.15252/embj.2021109049</a>.","ista":"Emtenani S, Martin ET, György A, Bicher J, Genger J-W, Köcher T, Akhmanova M, Pereira Guarda M, Roblek M, Bergthaler A, Hurd TR, Rangan P, Siekhaus DE. 2022. Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. The Embo Journal. 41, e109049."},"date_updated":"2023-08-03T06:13:14Z","ddc":["570"],"volume":41,"acknowledgement":"We thank the DGRC (NIH grant 2P40OD010949-10A1) for plasmids, the BDSC (NIH grant P40OD018537) and the VDRC for fly stocks, FlyBase for essential genomic information, the BDGP in situ database for data (Tomancak et al, 2007), the IST Austria Bioimaging facility for support, the VBC Core Facilities for RNA sequencing and analysis, and C. Guet, C. Navarro, C. Desplan, T. Lecuit, I. Miguel-Aliaga, and Siekhaus group members for comments on the manuscript. The VBCF Metabolomics Facility is funded by the City of Vienna through the Vienna Business Agency. This work was supported by the Marie Curie CIG 334077/IRTIM (DES), Austrian Science Fund (FWF) Lise Meitner Fellowship M2379-B28 (MA and DES), Austrian Science Fund (FWF) grant ASI_FWF01_P29638S (DES), NIH/NIGMS (R01GM111779-06 (PR), RO1GM135628-01 (PR), European Research Council (ERC) grant no. 677006 “CMIL” (AB), and Natural Sciences and Engineering Research Council of Canada\r\n(RGPIN-2019-06766) (TRH). ","intvolume":"        41","title":"Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila","department":[{"_id":"DaSi"},{"_id":"LoSw"}],"date_created":"2022-03-24T13:23:09Z","article_processing_charge":"Yes (via OA deal)","publication_status":"published","author":[{"last_name":"Emtenani","first_name":"Shamsi","full_name":"Emtenani, Shamsi","orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Martin, Elliot T","last_name":"Martin","first_name":"Elliot T"},{"full_name":"György, Attila","orcid":"0000-0002-1819-198X","last_name":"György","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","last_name":"Bicher","first_name":"Julia","full_name":"Bicher, Julia"},{"last_name":"Genger","first_name":"Jakob-Wendelin","full_name":"Genger, Jakob-Wendelin"},{"first_name":"Thomas","last_name":"Köcher","full_name":"Köcher, Thomas"},{"id":"3425EC26-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Akhmanova","orcid":"0000-0003-1522-3162","full_name":"Akhmanova, Maria"},{"id":"6de81d9d-e2f2-11eb-945a-af8bc2a60b26","full_name":"Pereira Guarda, Mariana","first_name":"Mariana","last_name":"Pereira Guarda"},{"last_name":"Roblek","first_name":"Marko","full_name":"Roblek, Marko","orcid":"0000-0001-9588-1389","id":"3047D808-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bergthaler","first_name":"Andreas","full_name":"Bergthaler, Andreas"},{"first_name":"Thomas R","last_name":"Hurd","full_name":"Hurd, Thomas R"},{"last_name":"Rangan","first_name":"Prashanth","full_name":"Rangan, Prashanth"},{"last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"10918","article_type":"original","publisher":"Embo Press","file_date_updated":"2022-03-24T13:22:41Z","quality_controlled":"1","ec_funded":1},{"project":[{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"},{"_id":"c08c05c4-5a5b-11eb-8a69-dc6ce49d7973","grant_number":"M03032","name":"Long-range spin exchange for 2D qubits architectures"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Published Version","article_number":"126803","month":"03","has_accepted_license":"1","publication":"Physical Review Letters","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1079-7114"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-03-24T00:00:00Z","file":[{"date_created":"2022-03-28T06:53:39Z","file_size":1266515,"checksum":"6e66ad548d18db9c131f304acbd5a1f4","date_updated":"2022-03-28T06:53:39Z","content_type":"application/pdf","file_name":"2022_PhysRevLetters_Jirovec.pdf","access_level":"open_access","success":1,"relation":"main_file","file_id":"10928","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","article_processing_charge":"No","date_created":"2022-03-24T15:51:11Z","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publication_status":"published","intvolume":"       128","title":"Dynamics of hole singlet-triplet qubits with large g-factor differences","_id":"10920","issue":"12","author":[{"first_name":"Daniel","last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mutter, Philipp M.","first_name":"Philipp M.","last_name":"Mutter"},{"full_name":"Hofmann, Andrea C","first_name":"Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Crippa, Alessandro","orcid":"0000-0002-2968-611X","last_name":"Crippa","first_name":"Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425"},{"full_name":"Rychetsky, Marek","last_name":"Rychetsky","first_name":"Marek"},{"first_name":"David L.","last_name":"Craig","full_name":"Craig, David L."},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","last_name":"Kukucka","first_name":"Josip"},{"first_name":"Frederico","last_name":"Martins","orcid":"0000-0003-2668-2401","full_name":"Martins, Frederico","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E"},{"full_name":"Ballabio, Andrea","first_name":"Andrea","last_name":"Ballabio"},{"first_name":"Natalia","last_name":"Ares","full_name":"Ares, Natalia"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"full_name":"Burkard, Guido ","first_name":"Guido ","last_name":"Burkard"},{"first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"publisher":"American Physical Society","article_type":"original","ec_funded":1,"quality_controlled":"1","file_date_updated":"2022-03-28T06:53:39Z","day":"24","doi":"10.1103/PhysRevLett.128.126803","arxiv":1,"abstract":[{"text":"The spin-orbit interaction permits to control the state of a spin qubit via electric fields. For holes it is particularly strong, allowing for fast all electrical qubit manipulation, and yet an in-depth understanding of this interaction in hole systems is missing. Here we investigate, experimentally and theoretically, the effect of the cubic Rashba spin-orbit interaction on the mixing of the spin states by studying singlet-triplet oscillations in a planar Ge hole double quantum dot. Landau-Zener sweeps at different magnetic field directions allow us to disentangle the effects of the spin-orbit induced spin-flip term from those caused by strongly site-dependent and anisotropic quantum dot g tensors. Our work, therefore, provides new insights into the hole spin-orbit interaction, necessary for optimizing future qubit experiments.","lang":"eng"}],"year":"2022","citation":{"ieee":"D. Jirovec <i>et al.</i>, “Dynamics of hole singlet-triplet qubits with large g-factor differences,” <i>Physical Review Letters</i>, vol. 128, no. 12. American Physical Society, 2022.","chicago":"Jirovec, Daniel, Philipp M. Mutter, Andrea C Hofmann, Alessandro Crippa, Marek Rychetsky, David L. Craig, Josip Kukucka, et al. “Dynamics of Hole Singlet-Triplet Qubits with Large g-Factor Differences.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.128.126803\">https://doi.org/10.1103/PhysRevLett.128.126803</a>.","apa":"Jirovec, D., Mutter, P. M., Hofmann, A. C., Crippa, A., Rychetsky, M., Craig, D. L., … Katsaros, G. (2022). Dynamics of hole singlet-triplet qubits with large g-factor differences. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.128.126803\">https://doi.org/10.1103/PhysRevLett.128.126803</a>","ama":"Jirovec D, Mutter PM, Hofmann AC, et al. Dynamics of hole singlet-triplet qubits with large g-factor differences. <i>Physical Review Letters</i>. 2022;128(12). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.126803\">10.1103/PhysRevLett.128.126803</a>","ista":"Jirovec D, Mutter PM, Hofmann AC, Crippa A, Rychetsky M, Craig DL, Kukucka J, Martins F, Ballabio A, Ares N, Chrastina D, Isella G, Burkard G, Katsaros G. 2022. Dynamics of hole singlet-triplet qubits with large g-factor differences. Physical Review Letters. 128(12), 126803.","short":"D. Jirovec, P.M. Mutter, A.C. Hofmann, A. Crippa, M. Rychetsky, D.L. Craig, J. Kukucka, F. Martins, A. Ballabio, N. Ares, D. Chrastina, G. Isella, G. Burkard, G. Katsaros, Physical Review Letters 128 (2022).","mla":"Jirovec, Daniel, et al. “Dynamics of Hole Singlet-Triplet Qubits with Large g-Factor Differences.” <i>Physical Review Letters</i>, vol. 128, no. 12, 126803, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.126803\">10.1103/PhysRevLett.128.126803</a>."},"date_updated":"2023-08-03T06:14:58Z","external_id":{"isi":["000786542500004"],"arxiv":["2111.05130"]},"isi":1,"volume":128,"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSkłodowska-Curie Grant Agreement No. 844511, No. 75441, and by the FWF-P 30207, I05060, and M3032-N projects. A. B. acknowledges support from the EU Horizon-2020 FET project microSPIRE, ID: 766955. P.M. M. and G. B. acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG—German Research Foundation) under Project No. 450396347. This work was supported by the Royal Society (URF\\R1\\191150) and the European Research Council (Grant Agreement No. 948932), N. A. acknowledges the use of the University of Oxford Advanced Research Computing (ARC) facility.","ddc":["530"]},{"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"oa":1,"date_published":"2022-05-01T00:00:00Z","type":"journal_article","file":[{"date_created":"2022-03-27T17:34:11Z","file_size":19601689,"checksum":"b62188b07f5c000f1638c782ec92da41","date_updated":"2022-03-27T17:34:11Z","content_type":"application/pdf","file_name":"paper.pdf","relation":"main_file","access_level":"open_access","file_id":"10923","creator":"bbickel"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"M-Shop"}],"project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"month":"05","publication":"Computer Graphics Forum","has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1111/cgf.14490","day":"01","abstract":[{"lang":"eng","text":"We study structural rigidity for assemblies with mechanical joints. Existing methods identify whether an assembly is structurally rigid by assuming parts are perfectly rigid. Yet, an assembly identified as rigid may not be that “rigid” in practice, and existing methods cannot quantify how rigid an assembly is. We address this limitation by developing a new measure, worst-case rigidity, to quantify the rigidity of an assembly as the largest possible deformation that the assembly undergoes for arbitrary external loads of fixed magnitude. Computing worst-case rigidity is non-trivial due to non-rigid parts and different joint types. We thus formulate a new computational approach by encoding parts and their connections into a stiffness matrix, in which parts are modeled as deformable objects and joints as soft constraints. Based on this, we formulate worst-case rigidity analysis as an optimization that seeks the worst-case deformation of an assembly for arbitrary external loads, and solve the optimization problem via an eigenanalysis. Furthermore, we present methods to optimize the geometry and topology of various assemblies to enhance their rigidity, as guided by our rigidity measure. In the end, we validate our method on a variety of assembly structures with physical experiments and demonstrate its effectiveness by designing and fabricating several structurally rigid assemblies."}],"date_updated":"2023-08-03T06:17:13Z","citation":{"mla":"Liu, Zhenyuan, et al. “Worst-Case Rigidity Analysis and Optimization for Assemblies with Mechanical Joints.” <i>Computer Graphics Forum</i>, vol. 41, no. 2, Wiley, 2022, pp. 507–19, doi:<a href=\"https://doi.org/10.1111/cgf.14490\">10.1111/cgf.14490</a>.","short":"Z. Liu, J. Hu, H. Xu, P. Song, R. Zhang, B. Bickel, C.-W. Fu, Computer Graphics Forum 41 (2022) 507–519.","ista":"Liu Z, Hu J, Xu H, Song P, Zhang R, Bickel B, Fu C-W. 2022. Worst-case rigidity analysis and optimization for assemblies with mechanical joints. Computer Graphics Forum. 41(2), 507–519.","ama":"Liu Z, Hu J, Xu H, et al. Worst-case rigidity analysis and optimization for assemblies with mechanical joints. <i>Computer Graphics Forum</i>. 2022;41(2):507-519. doi:<a href=\"https://doi.org/10.1111/cgf.14490\">10.1111/cgf.14490</a>","apa":"Liu, Z., Hu, J., Xu, H., Song, P., Zhang, R., Bickel, B., &#38; Fu, C.-W. (2022). Worst-case rigidity analysis and optimization for assemblies with mechanical joints. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14490\">https://doi.org/10.1111/cgf.14490</a>","ieee":"Z. Liu <i>et al.</i>, “Worst-case rigidity analysis and optimization for assemblies with mechanical joints,” <i>Computer Graphics Forum</i>, vol. 41, no. 2. Wiley, pp. 507–519, 2022.","chicago":"Liu, Zhenyuan, Jingyu Hu, Hao Xu, Peng Song, Ran Zhang, Bernd Bickel, and Chi-Wing Fu. “Worst-Case Rigidity Analysis and Optimization for Assemblies with Mechanical Joints.” <i>Computer Graphics Forum</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/cgf.14490\">https://doi.org/10.1111/cgf.14490</a>."},"year":"2022","isi":1,"external_id":{"isi":["000802723900039"]},"volume":41,"acknowledgement":"This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region, China [Project No.: CUHK 14201921] and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767 – MATERIALIZABLE). We thank the anonymous reviewers for their insightful feedback; Christian Hafner for proofreading and discussions; Ziqi Wang,\r\nHaisen Zhao, and Martin Hafskjold Thoresen for the helpful discussions; and the Miba Machine Shop at IST Austria for 3D printing the BUNNY and BOOMERANG models.","ddc":["000"],"publication_status":"published","date_created":"2022-03-27T17:34:17Z","department":[{"_id":"BeBi"}],"article_processing_charge":"No","title":"Worst-case rigidity analysis and optimization for assemblies with mechanical joints","intvolume":"        41","_id":"10922","scopus_import":"1","author":[{"id":"70f0d7cf-ae65-11ec-a14f-89dfc5505b19","first_name":"Zhenyuan","last_name":"Liu","orcid":"0000-0001-9200-5690","full_name":"Liu, Zhenyuan"},{"last_name":"Hu","first_name":"Jingyu","full_name":"Hu, Jingyu"},{"full_name":"Xu, Hao","last_name":"Xu","first_name":"Hao"},{"full_name":"Song, Peng","last_name":"Song","first_name":"Peng"},{"last_name":"Zhang","first_name":"Ran","full_name":"Zhang, Ran"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"first_name":"Chi-Wing","last_name":"Fu","full_name":"Fu, Chi-Wing"}],"issue":"2","publisher":"Wiley","article_type":"original","page":"507-519","ec_funded":1,"quality_controlled":"1","file_date_updated":"2022-03-27T17:34:11Z"},{"date_created":"2022-03-27T22:01:45Z","department":[{"_id":"JoFi"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        13","title":"Quantum-enabled operation of a microwave-optical interface","scopus_import":"1","_id":"10924","author":[{"id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","last_name":"Sahu","first_name":"Rishabh"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J","orcid":"0000-0001-9868-2166","last_name":"Hease","first_name":"William J"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"},{"last_name":"Arnold","first_name":"Georg M","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Liu","last_name":"Qiu","orcid":"0000-0003-4345-4267","full_name":"Qiu, Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M"}],"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-03-28T08:02:12Z","day":"11","arxiv":1,"doi":"10.1038/s41467-022-28924-2","abstract":[{"text":"Solid-state microwave systems offer strong interactions for fast quantum logic and sensing but photons at telecom wavelength are the ideal choice for high-density low-loss quantum interconnects. A general-purpose interface that can make use of single photon effects requires < 1 input noise quanta, which has remained elusive due to either low efficiency or pump induced heating. Here we demonstrate coherent electro-optic modulation on nanosecond-timescales with only 0.16+0.02−0.01 microwave input noise photons with a total bidirectional transduction efficiency of 8.7% (or up to 15% with 0.41+0.02−0.02), as required for near-term heralded quantum network protocols. The use of short and high-power optical pump pulses also enables near-unity cooperativity of the electro-optic interaction leading to an internal pure conversion efficiency of up to 99.5%. Together with the low mode occupancy this provides evidence for electro-optic laser cooling and vacuum amplification as predicted a decade ago.","lang":"eng"}],"year":"2022","citation":{"short":"R. Sahu, W.J. Hease, A.R. Rueda Sanchez, G.M. Arnold, L. Qiu, J.M. Fink, Nature Communications 13 (2022).","mla":"Sahu, Rishabh, et al. “Quantum-Enabled Operation of a Microwave-Optical Interface.” <i>Nature Communications</i>, vol. 13, 1276, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-28924-2\">10.1038/s41467-022-28924-2</a>.","ista":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. 2022. Quantum-enabled operation of a microwave-optical interface. Nature Communications. 13, 1276.","apa":"Sahu, R., Hease, W. J., Rueda Sanchez, A. R., Arnold, G. M., Qiu, L., &#38; Fink, J. M. (2022). Quantum-enabled operation of a microwave-optical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-28924-2\">https://doi.org/10.1038/s41467-022-28924-2</a>","ama":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. Quantum-enabled operation of a microwave-optical interface. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-28924-2\">10.1038/s41467-022-28924-2</a>","chicago":"Sahu, Rishabh, William J Hease, Alfredo R Rueda Sanchez, Georg M Arnold, Liu Qiu, and Johannes M Fink. “Quantum-Enabled Operation of a Microwave-Optical Interface.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-28924-2\">https://doi.org/10.1038/s41467-022-28924-2</a>.","ieee":"R. Sahu, W. J. Hease, A. R. Rueda Sanchez, G. M. Arnold, L. Qiu, and J. M. Fink, “Quantum-enabled operation of a microwave-optical interface,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022."},"date_updated":"2024-10-29T09:11:06Z","external_id":{"arxiv":["2107.08303"],"isi":["000767892300013"]},"isi":1,"acknowledgement":"The authors thank S. Wald and F. Diorico for their help with optical filtering, O. Hosten\r\nand M. Aspelmeyer for equipment, H.G.L. Schwefel for materials and discussions, L.\r\nDrmic and P. Zielinski for software support, and the MIBA workshop at IST Austria for\r\nmachining the microwave cavity. This work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG QUNNECT) and the European\r\nUnion’s Horizon 2020 research and innovation program under grant agreement no.\r\n899354 (FETopen SuperQuLAN). W.H. is the recipient of an ISTplus postdoctoral fellowship\r\nwith funding from the European Union’s Horizon 2020 research and innovation\r\nprogram under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the\r\nrecipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F.\r\nacknowledges support from the Austrian Science Fund (FWF) through BeyondC (F7105)\r\nand the European Union’s Horizon 2020 research and innovation programs under grant\r\nagreement no. 862644 (FETopen QUARTET).","volume":13,"ddc":["530"],"project":[{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105","name":"Integrating superconducting quantum circuits"},{"call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"oa_version":"Published Version","article_number":"1276","month":"03","has_accepted_license":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-03-11T00:00:00Z","file":[{"date_updated":"2022-03-28T08:02:12Z","file_name":"2022_NatureCommunications_Sahu.pdf","content_type":"application/pdf","date_created":"2022-03-28T08:02:12Z","file_size":1167492,"checksum":"7c5176db7b8e2ed18a4e0c5aca70a72c","file_id":"10929","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file"}],"status":"public","related_material":{"record":[{"id":"12900","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"13175","status":"public"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa":1,"publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"date_published":"2022-04-25T00:00:00Z","type":"journal_article","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/jfm.2022.137"}],"month":"04","article_number":"A39","oa_version":"Published Version","publication":"Journal of Fluid Mechanics","language":[{"iso":"eng"}],"abstract":[{"text":"Direct numerical simulations (DNS) of turbulent channel flows up to  Reτ≈1000  are conducted to investigate the three-dimensional (consisting of streamwise wavenumber, spanwise wavenumber and frequency) spectrum of wall pressure fluctuations. To develop a predictive model of the wavenumber–frequency spectrum from the wavenumber spectrum, the time decorrelation mechanisms of wall pressure fluctuations are investigated. It is discovered that the energy-containing part of the wavenumber–frequency spectrum of wall pressure fluctuations can be well predicted using a similar random sweeping model for streamwise velocity fluctuations. To refine the investigation, we further decompose the spectrum of the total wall pressure fluctuations into the autospectra of rapid and slow pressure fluctuations, and the cross-spectrum between them. We focus on evaluating the assumption applied in many predictive models, that is, the magnitude of the cross-spectrum is negligibly small. The present DNS shows that neglecting the cross-spectrum causes a maximum error up to 4.7 dB in the subconvective region for all Reynolds numbers under test. Our analyses indicate that the approximation of neglecting the cross-spectrum needs to be applied carefully in the investigations of acoustics at low Mach numbers, in which the subconvective components of wall pressure fluctuations make important contributions to the radiated acoustic power.","lang":"eng"}],"doi":"10.1017/jfm.2022.137","arxiv":1,"day":"25","isi":1,"external_id":{"isi":["000763547000001"],"arxiv":["2201.04702"]},"date_updated":"2023-08-03T06:20:26Z","year":"2022","citation":{"chicago":"Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of the Wall Pressure Fluctuations in Turbulent Channel Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2022. <a href=\"https://doi.org/10.1017/jfm.2022.137\">https://doi.org/10.1017/jfm.2022.137</a>.","ieee":"B. Yang and Z. Yang, “On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow,” <i>Journal of Fluid Mechanics</i>, vol. 937. Cambridge University Press, 2022.","apa":"Yang, B., &#38; Yang, Z. (2022). On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2022.137\">https://doi.org/10.1017/jfm.2022.137</a>","ama":"Yang B, Yang Z. On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. <i>Journal of Fluid Mechanics</i>. 2022;937. doi:<a href=\"https://doi.org/10.1017/jfm.2022.137\">10.1017/jfm.2022.137</a>","ista":"Yang B, Yang Z. 2022. On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow. Journal of Fluid Mechanics. 937, A39.","short":"B. Yang, Z. Yang, Journal of Fluid Mechanics 937 (2022).","mla":"Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of the Wall Pressure Fluctuations in Turbulent Channel Flow.” <i>Journal of Fluid Mechanics</i>, vol. 937, A39, Cambridge University Press, 2022, doi:<a href=\"https://doi.org/10.1017/jfm.2022.137\">10.1017/jfm.2022.137</a>."},"volume":937,"acknowledgement":"This research is supported by the NSFC Basic Science Center Program for ‘Multiscale Problems in Nonlinear Mechanics’ (no. 11988102), National Key Project (GJXM92579) and the Strategic Priority Research Program (XDB22040104).","title":"On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow","intvolume":"       937","publication_status":"published","date_created":"2022-03-27T22:01:45Z","department":[{"_id":"GradSch"}],"article_processing_charge":"No","author":[{"id":"71b6ff4b-15b2-11ec-abd3-aef6b028cf7e","first_name":"Bowen","last_name":"Yang","orcid":"0000-0002-4843-6853","full_name":"Yang, Bowen"},{"full_name":"Yang, Zixuan","first_name":"Zixuan","last_name":"Yang"}],"_id":"10925","scopus_import":"1","article_type":"original","publisher":"Cambridge University Press","quality_controlled":"1"},{"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://eprints.whiterose.ac.uk/187332/"}],"type":"journal_article","date_published":"2022-03-01T00:00:00Z","oa":1,"publication_identifier":{"eissn":["1464-3766"],"issn":["0260-1230"]},"language":[{"iso":"eng"}],"publication":"Journal of Molluscan Studies","article_number":"eyab049","month":"03","oa_version":"Submitted Version","volume":88,"external_id":{"isi":["000759081600002"]},"isi":1,"year":"2022","citation":{"ista":"Perini S, Butlin R, Westram AM, Johannesson K. 2022. Very short mountings are enough for sperm transfer in Littorina saxatilis. Journal of Molluscan Studies. 88(1), eyab049.","short":"S. Perini, R. Butlin, A.M. Westram, K. Johannesson, Journal of Molluscan Studies 88 (2022).","mla":"Perini, Samuel, et al. “Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” <i>Journal of Molluscan Studies</i>, vol. 88, no. 1, eyab049, Oxford Academic, 2022, doi:<a href=\"https://doi.org/10.1093/mollus/eyab049\">10.1093/mollus/eyab049</a>.","ieee":"S. Perini, R. Butlin, A. M. Westram, and K. Johannesson, “Very short mountings are enough for sperm transfer in Littorina saxatilis,” <i>Journal of Molluscan Studies</i>, vol. 88, no. 1. Oxford Academic, 2022.","chicago":"Perini, Samuel, Rogerk Butlin, Anja M Westram, and Kerstin Johannesson. “Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” <i>Journal of Molluscan Studies</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/mollus/eyab049\">https://doi.org/10.1093/mollus/eyab049</a>.","ama":"Perini S, Butlin R, Westram AM, Johannesson K. Very short mountings are enough for sperm transfer in Littorina saxatilis. <i>Journal of Molluscan Studies</i>. 2022;88(1). doi:<a href=\"https://doi.org/10.1093/mollus/eyab049\">10.1093/mollus/eyab049</a>","apa":"Perini, S., Butlin, R., Westram, A. M., &#38; Johannesson, K. (2022). Very short mountings are enough for sperm transfer in Littorina saxatilis. <i>Journal of Molluscan Studies</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/mollus/eyab049\">https://doi.org/10.1093/mollus/eyab049</a>"},"date_updated":"2023-08-03T06:23:13Z","abstract":[{"lang":"eng","text":"Conflict over reproduction between females and males exists because of anisogamy and promiscuity. Together they generate differences in fitness optima between the sexes and result in antagonistic coevolution of female and male reproductive traits. Mounting duration is likely to be a compromise between male and female interests whose outcome depends on the intensity of sexual selection. The timing of sperm transfer during mounting is critical. For example, mountings may be interrupted before sperm is transferred as a consequence of female or male choice, or they may be prolonged to function as mate guarding. In the highly promiscuous intertidal snail Littorina saxatilis, mountings vary substantially in duration, from less than a minute to more than an hour, and it has been assumed that mountings of a few minutes do not result in any sperm being transferred. Here, we examined the timing of sperm transfer, a reproductive trait that is likely affected by sexual conflict. We performed time-controlled mounting trials using L. saxatilis males and virgin females, aiming to examine indirectly when the transfer of sperm starts. We observed the relationship between mounting duration and the proportion of developing embryos out of all eggs and embryos in the brood pouch. Developing embryos were observed in similar proportions in all treatments (i.e. 1, 5 and 10 or more minutes at which mountings were artificially interrupted), suggesting that sperm transfer begins rapidly (within 1 min) in L. saxatilis and very short matings do not result in sperm shortage in the females. We discuss how the observed pattern can be influenced by predation risk, population density, and female status and receptivity."}],"day":"01","doi":"10.1093/mollus/eyab049","quality_controlled":"1","article_type":"original","publisher":"Oxford Academic","issue":"1","author":[{"first_name":"Samuel","last_name":"Perini","full_name":"Perini, Samuel"},{"full_name":"Butlin, Rogerk","first_name":"Rogerk","last_name":"Butlin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"}],"scopus_import":"1","_id":"10926","intvolume":"        88","title":"Very short mountings are enough for sperm transfer in Littorina saxatilis","department":[{"_id":"BeVi"}],"date_created":"2022-03-27T22:01:46Z","article_processing_charge":"No","publication_status":"published"},{"status":"public","related_material":{"link":[{"relation":"software","url":"https://github.com/ctlab/parallel-rearrangements"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","access_level":"open_access","success":1,"file_id":"10930","creator":"dernst","date_created":"2022-03-28T08:07:46Z","checksum":"4b5688ff9ac86180ccdf7f82fa33d926","file_size":3425744,"date_updated":"2022-03-28T08:07:46Z","file_name":"2022_Bioinformatics_Zabelkin.pdf","content_type":"application/pdf"}],"date_published":"2022-01-15T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["1367-4803"],"eissn":["1460-2059"]},"language":[{"iso":"eng"}],"publication":"Bioinformatics","has_accepted_license":"1","month":"01","oa_version":"Published Version","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"ddc":["000"],"volume":38,"acknowledgement":"The authors thank the 2020 student class of the Bioinformatics Institute, who\r\nused the first versions of the tool and provided many valuable suggestions to\r\nimprove usability. They also thank Louisa Gonzalez Somermeyer for manuscript proofreading\r\nThis work was supported by the National Center for Cognitive Research of\r\nITMO University and JetBrains Research [to A.Z and N.A.]; and the European\r\nUnion’s Horizon 2020 Research and Innovation Programme under the Marie\r\nSkłodowska-Curie [754411 to O.B.].\r\nPaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements.","isi":1,"external_id":{"isi":["000743380100008"]},"date_updated":"2023-08-03T06:21:46Z","citation":{"mla":"Zabelkin, Alexey, et al. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” <i>Bioinformatics</i>, vol. 38, no. 2, Oxford Academic, 2022, pp. 357–63, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btab691\">10.1093/bioinformatics/btab691</a>.","short":"A. Zabelkin, Y. Yakovleva, O. Bochkareva, N. Alexeev, Bioinformatics 38 (2022) 357–363.","ista":"Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. 2022. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 38(2), 357–363.","ama":"Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements and BReaks identification toolkit. <i>Bioinformatics</i>. 2022;38(2):357-363. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btab691\">10.1093/bioinformatics/btab691</a>","apa":"Zabelkin, A., Yakovleva, Y., Bochkareva, O., &#38; Alexeev, N. (2022). PaReBrick: PArallel REarrangements and BReaks identification toolkit. <i>Bioinformatics</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/bioinformatics/btab691\">https://doi.org/10.1093/bioinformatics/btab691</a>","chicago":"Zabelkin, Alexey, Yulia Yakovleva, Olga Bochkareva, and Nikita Alexeev. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” <i>Bioinformatics</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/bioinformatics/btab691\">https://doi.org/10.1093/bioinformatics/btab691</a>.","ieee":"A. Zabelkin, Y. Yakovleva, O. Bochkareva, and N. Alexeev, “PaReBrick: PArallel REarrangements and BReaks identification toolkit,” <i>Bioinformatics</i>, vol. 38, no. 2. Oxford Academic, pp. 357–363, 2022."},"year":"2022","abstract":[{"lang":"eng","text":"Motivation\r\nHigh plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency.\r\nResults\r\nHere, we define the term ‘parallel rearrangements’ as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes."}],"doi":"10.1093/bioinformatics/btab691","day":"15","file_date_updated":"2022-03-28T08:07:46Z","page":"357-363","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"Oxford Academic","author":[{"full_name":"Zabelkin, Alexey","first_name":"Alexey","last_name":"Zabelkin"},{"full_name":"Yakovleva, Yulia","last_name":"Yakovleva","first_name":"Yulia"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"last_name":"Alexeev","first_name":"Nikita","full_name":"Alexeev, Nikita"}],"issue":"2","_id":"10927","scopus_import":"1","title":"PaReBrick: PArallel REarrangements and BReaks identification toolkit","intvolume":"        38","publication_status":"published","article_processing_charge":"No","department":[{"_id":"FyKo"}],"date_created":"2022-03-27T22:01:46Z"},{"ddc":["572"],"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","abstract":[{"lang":"eng","text":"FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments.  Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. "}],"doi":"10.15479/AT:ISTA:10934","day":"05","date_updated":"2024-02-21T12:35:18Z","year":"2022","citation":{"ama":"Radler P. In vitro reconstitution of Escherichia coli divisome activation. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>","apa":"Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">https://doi.org/10.15479/AT:ISTA:10934</a>","ieee":"P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022.","chicago":"Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">https://doi.org/10.15479/AT:ISTA:10934</a>.","mla":"Radler, Philipp. <i>In Vitro Reconstitution of Escherichia Coli Divisome Activation</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>.","short":"P. Radler, (2022).","ista":"Radler P. 2022. In vitro reconstitution of Escherichia coli divisome activation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>."},"publisher":"Institute of Science and Technology Austria","file_date_updated":"2022-04-22T10:15:19Z","ec_funded":1,"title":"In vitro reconstitution of Escherichia coli divisome activation","date_created":"2022-03-31T11:32:32Z","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"article_processing_charge":"No","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp","orcid":" 0000-0001-9198-2182 ","last_name":"Radler","first_name":"Philipp"}],"_id":"10934","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"record":[{"relation":"used_in_publication","id":"11373","status":"public"},{"status":"public","relation":"used_in_publication","id":"14280"}],"link":[{"relation":"software","description":"A custom written code (FRAPdiff) to quantify the Off binding rate and Diffusion coefficient of membrane bound proteins. Written by Christoph Sommer.","url":"https://doi.org/10.5281/zenodo.6400639"}]},"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Inventory for Data repository.docx","date_updated":"2022-04-22T10:15:19Z","file_size":13469,"checksum":"52d50202e04e9daa618a58e686d8ab58","date_created":"2022-04-22T10:15:19Z","creator":"pradler","file_id":"11328","access_level":"open_access","success":1,"relation":"main_file"},{"file_size":2406478929,"checksum":"3e1518dd9fe9266b9bcc67695cb5015c","date_created":"2022-03-31T12:57:36Z","content_type":"application/x-zip-compressed","file_name":"Raw Data 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(4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"contributor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","contributor_type":"supervisor","last_name":"Loose"},{"contributor_type":"researcher","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Caldas","contributor_type":"researcher","first_name":"Paulo"},{"id":"B9577E20-AA38-11E9-AC9A-0930E6697425","first_name":"David","last_name":"Michalik","contributor_type":"researcher"},{"first_name":"Natalia","last_name":"Baranova","contributor_type":"researcher"}],"keyword":["Bacterial cell division","in vitro reconstitution","FtsZ","FtsN","FtsA"],"month":"04","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Submitted Version","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"}],"has_accepted_license":"1"},{"acknowledgement":"We thank Virgile Andreani for useful discussions about the model and parameter inference. We thank Johan Paulsson and Jeffrey J Tabor for kind gifts of plasmids. R was supported by the ANR grant CyberCircuits (ANR-18-CE91-0002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","volume":18,"ddc":["570","000"],"doi":"10.1371/journal.pcbi.1009950","day":"18","abstract":[{"text":"Understanding and characterising biochemical processes inside single cells requires experimental platforms that allow one to perturb and observe the dynamics of such processes as well as computational methods to build and parameterise models from the collected data. Recent progress with experimental platforms and optogenetics has made it possible to expose each cell in an experiment to an individualised input and automatically record cellular responses over days with fine time resolution. However, methods to infer parameters of stochastic kinetic models from single-cell longitudinal data have generally been developed under the assumption that experimental data is sparse and that responses of cells to at most a few different input perturbations can be observed. Here, we investigate and compare different approaches for calculating parameter likelihoods of single-cell longitudinal data based on approximations of the chemical master equation (CME) with a particular focus on coupling the linear noise approximation (LNA) or moment closure methods to a Kalman filter. We show that, as long as cells are measured sufficiently frequently, coupling the LNA to a Kalman filter allows one to accurately approximate likelihoods and to infer model parameters from data even in cases where the LNA provides poor approximations of the CME. Furthermore, the computational cost of filtering-based iterative likelihood evaluation scales advantageously in the number of measurement times and different input perturbations and is thus ideally suited for data obtained from modern experimental platforms. To demonstrate the practical usefulness of these results, we perform an experiment in which single cells, equipped with an optogenetic gene expression system, are exposed to various different light-input sequences and measured at several hundred time points and use parameter inference based on iterative likelihood evaluation to parameterise a stochastic model of the system.","lang":"eng"}],"date_updated":"2022-04-04T10:21:53Z","year":"2022","citation":{"ista":"Davidović A, Chait RP, Batt G, Ruess J. 2022. Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. PLoS Computational Biology. 18(3), e1009950.","short":"A. Davidović, R.P. Chait, G. Batt, J. Ruess, PLoS Computational Biology 18 (2022).","mla":"Davidović, Anđela, et al. “Parameter Inference for Stochastic Biochemical Models from Perturbation Experiments Parallelised at the Single Cell Level.” <i>PLoS Computational Biology</i>, vol. 18, no. 3, e1009950, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009950\">10.1371/journal.pcbi.1009950</a>.","chicago":"Davidović, Anđela, Remy P Chait, Gregory Batt, and Jakob Ruess. “Parameter Inference for Stochastic Biochemical Models from Perturbation Experiments Parallelised at the Single Cell Level.” <i>PLoS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1009950\">https://doi.org/10.1371/journal.pcbi.1009950</a>.","ieee":"A. Davidović, R. P. Chait, G. Batt, and J. Ruess, “Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level,” <i>PLoS Computational Biology</i>, vol. 18, no. 3. Public Library of Science, 2022.","apa":"Davidović, A., Chait, R. P., Batt, G., &#38; Ruess, J. (2022). Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009950\">https://doi.org/10.1371/journal.pcbi.1009950</a>","ama":"Davidović A, Chait RP, Batt G, Ruess J. Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. <i>PLoS Computational Biology</i>. 2022;18(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009950\">10.1371/journal.pcbi.1009950</a>"},"publisher":"Public Library of Science","article_type":"original","quality_controlled":"1","file_date_updated":"2022-04-04T10:14:39Z","publication_status":"published","department":[{"_id":"CaGu"}],"date_created":"2022-04-03T22:01:42Z","article_processing_charge":"No","title":"Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level","intvolume":"        18","_id":"10939","scopus_import":"1","author":[{"full_name":"Davidović, Anđela","last_name":"Davidović","first_name":"Anđela"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait","first_name":"Remy P"},{"first_name":"Gregory","last_name":"Batt","full_name":"Batt, Gregory"},{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","last_name":"Ruess","first_name":"Jakob"}],"issue":"3","file":[{"content_type":"application/pdf","file_name":"2022_PLoSCompBio_Davidovic.pdf","date_updated":"2022-04-04T10:14:39Z","checksum":"458ef542761fb714ced214f240daf6b2","file_size":2958642,"date_created":"2022-04-04T10:14:39Z","creator":"dernst","file_id":"10947","success":1,"relation":"main_file","access_level":"open_access"}],"status":"public","related_material":{"link":[{"relation":"software","url":"https://gitlab.pasteur.fr/adavidov/inferencelnakf"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-03-18T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","month":"03","article_number":"e1009950","publication":"PLoS Computational Biology","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"oa_version":"Preprint","month":"03","article_number":"034032","publication":"Physical Review Applied","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2111.01115","open_access":"1"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["2331-7019"]},"oa":1,"date_published":"2022-03-11T00:00:00Z","type":"journal_article","publisher":"American Physical Society","article_type":"original","quality_controlled":"1","publication_status":"published","date_created":"2022-04-03T22:01:43Z","department":[{"_id":"JoFi"}],"article_processing_charge":"No","title":"Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T","intvolume":"        17","_id":"10940","scopus_import":"1","author":[{"first_name":"J.","last_name":"Krause","full_name":"Krause, J."},{"first_name":"C.","last_name":"Dickel","full_name":"Dickel, C."},{"full_name":"Vaal, E.","last_name":"Vaal","first_name":"E."},{"full_name":"Vielmetter, M.","first_name":"M.","last_name":"Vielmetter"},{"full_name":"Feng, J.","last_name":"Feng","first_name":"J."},{"full_name":"Bounds, R.","first_name":"R.","last_name":"Bounds"},{"full_name":"Catelani, G.","first_name":"G.","last_name":"Catelani"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yoichi","last_name":"Ando","full_name":"Ando, Yoichi"}],"issue":"3","volume":17,"acknowledgement":"We would like to thank Ida Milow for her internship in the laboratory and contributions to our code base. We thank T. Zent and L. Hamdan for technical assistance, and D. Fan for help with setting up the aluminum evaporator. We thank A. Salari, M. Rößler, S. Barzanjeh, M. Zemlicka, F. Hassani, and M. Peruzzo for contributions in the early stages of the experiments. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 741121) and was also funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under CRC 1238 – 277146847 (Subproject B01), as well as under Germany’s Excellence Strategy – Cluster of Excellence Matter and Light for Quantum Computing (ML4Q), EXC 2004/1\r\n– 390534769.","doi":"10.1103/PhysRevApplied.17.034032","arxiv":1,"day":"11","abstract":[{"lang":"eng","text":"Magnetic-field-resilient superconducting circuits enable sensing applications and hybrid quantum computing architectures involving spin or topological qubits and electromechanical elements, as well as studying flux noise and quasiparticle loss. We investigate the effect of in-plane magnetic fields up to 1 T on the spectrum and coherence times of thin-film three-dimensional aluminum transmons. Using a copper cavity, unaffected by strong magnetic fields, we can probe solely the effect of magnetic fields on the transmons. We present data on a single-junction and a superconducting-quantum-interference-device (SQUID) transmon that are cooled down in the same cavity. As expected, the transmon frequencies decrease with increasing field, due to suppression of the superconducting gap and a geometric Fraunhofer-like contribution. Nevertheless, the thin-film transmons show strong magnetic field resilience: both transmons display microsecond coherence up to at least 0.65 T, and T1 remains above 1μs over the entire measurable range. SQUID spectroscopy is feasible up to 1 T, the limit of our magnet. We conclude that thin-film aluminum Josephson junctions are suitable hardware for superconducting circuits in the high-magnetic-field regime."}],"date_updated":"2023-08-03T06:23:58Z","year":"2022","citation":{"ista":"Krause J, Dickel C, Vaal E, Vielmetter M, Feng J, Bounds R, Catelani G, Fink JM, Ando Y. 2022. Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T. Physical Review Applied. 17(3), 034032.","short":"J. Krause, C. Dickel, E. Vaal, M. Vielmetter, J. Feng, R. Bounds, G. Catelani, J.M. Fink, Y. Ando, Physical Review Applied 17 (2022).","mla":"Krause, J., et al. “Magnetic Field Resilience of Three-Dimensional Transmons with Thin-Film Al/AlOx/Al Josephson Junctions Approaching 1 T.” <i>Physical Review Applied</i>, vol. 17, no. 3, 034032, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.17.034032\">10.1103/PhysRevApplied.17.034032</a>.","ieee":"J. Krause <i>et al.</i>, “Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T,” <i>Physical Review Applied</i>, vol. 17, no. 3. American Physical Society, 2022.","chicago":"Krause, J., C. Dickel, E. Vaal, M. Vielmetter, J. Feng, R. Bounds, G. Catelani, Johannes M Fink, and Yoichi Ando. “Magnetic Field Resilience of Three-Dimensional Transmons with Thin-Film Al/AlOx/Al Josephson Junctions Approaching 1 T.” <i>Physical Review Applied</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevApplied.17.034032\">https://doi.org/10.1103/PhysRevApplied.17.034032</a>.","ama":"Krause J, Dickel C, Vaal E, et al. Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T. <i>Physical Review Applied</i>. 2022;17(3). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.17.034032\">10.1103/PhysRevApplied.17.034032</a>","apa":"Krause, J., Dickel, C., Vaal, E., Vielmetter, M., Feng, J., Bounds, R., … Ando, Y. (2022). Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.17.034032\">https://doi.org/10.1103/PhysRevApplied.17.034032</a>"},"isi":1,"external_id":{"arxiv":["2111.01115"],"isi":["000770371400003"]}},{"day":"01","doi":"10.3390/colorants1020010","abstract":[{"lang":"eng","text":"Mica-titania pearlescent pigments (MTs) were previously coated with organic molecules to obtain combination pigments (CPs) for achieving certain improvements or functionalities. Anthocyanins (ACNs) are molecules that can be extracted from natural resources and exhibit color changes via pH modifications of the enclosing medium. The purpose of the study was to produce a new series of CPs by depositing ACNs on MTs at different pH values, to observe the changes in color, and to associate these changes to thermogravimetrically determined deposition efficiencies in light of spectral differences. The extraction and deposition methods were based on aqueous chemistry and were straightforward. The ACN deposition generally increased with increasing pH and correlated with the consistency between the charges of the MT surfaces and the dominant ACN species at a specific pH value. The fluorescence of the CPs was inversely correlated with the deposition quantities invoking the possibility of a quenching effect."}],"year":"2022","citation":{"short":"M.O. Çoruh, G. Gündüz, Ü. Çolak, B. Maviş, Colorants 1 (2022) 149–164.","mla":"Çoruh, Mehmet Orkun, et al. “PH-Dependent Coloring of Combination Effect Pigments with Anthocyanins from Brassica Oleracea Var. Capitata F. Rubra.” <i>Colorants</i>, vol. 1, no. 2, MDPI, 2022, pp. 149–64, doi:<a href=\"https://doi.org/10.3390/colorants1020010\">10.3390/colorants1020010</a>.","ista":"Çoruh MO, Gündüz G, Çolak Ü, Maviş B. 2022. pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. Colorants. 1(2), 149–164.","ama":"Çoruh MO, Gündüz G, Çolak Ü, Maviş B. pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. <i>Colorants</i>. 2022;1(2):149-164. doi:<a href=\"https://doi.org/10.3390/colorants1020010\">10.3390/colorants1020010</a>","apa":"Çoruh, M. O., Gündüz, G., Çolak, Ü., &#38; Maviş, B. (2022). pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. <i>Colorants</i>. MDPI. <a href=\"https://doi.org/10.3390/colorants1020010\">https://doi.org/10.3390/colorants1020010</a>","ieee":"M. O. Çoruh, G. Gündüz, Ü. Çolak, and B. Maviş, “pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra,” <i>Colorants</i>, vol. 1, no. 2. MDPI, pp. 149–164, 2022.","chicago":"Çoruh, Mehmet Orkun, Güngör Gündüz, Üner Çolak, and Bora Maviş. “PH-Dependent Coloring of Combination Effect Pigments with Anthocyanins from Brassica Oleracea Var. Capitata F. Rubra.” <i>Colorants</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/colorants1020010\">https://doi.org/10.3390/colorants1020010</a>."},"date_updated":"2023-08-09T10:12:22Z","acknowledgement":"This research was partly funded by Hacettepe University (Bilimsel Ara¸stırma Projeleri\r\nKoordinasyon Birimi), grant number FHD-2015-8094.The authors are indebted to Ahmet Önal for his supports in acquiring the fluorescence spectra and the decision of excitation wavelengths. The authors also acknowledge use of the services and facilities of UNAM-National Nanotechnology Research Center at Bilkent University and mica donation from Sabuncular Mining Co.","volume":1,"ddc":["570"],"date_created":"2022-04-04T09:03:54Z","article_processing_charge":"Yes","department":[{"_id":"LeSa"}],"publication_status":"published","intvolume":"         1","title":"pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra","_id":"10945","issue":"2","author":[{"full_name":"Çoruh, Mehmet Orkun","orcid":"0000-0002-3219-2022","last_name":"Çoruh","first_name":"Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef"},{"full_name":"Gündüz, Güngör","first_name":"Güngör","last_name":"Gündüz"},{"first_name":"Üner","last_name":"Çolak","full_name":"Çolak, Üner"},{"full_name":"Maviş, Bora","last_name":"Maviş","first_name":"Bora"}],"publisher":"MDPI","article_type":"original","quality_controlled":"1","page":"149-164","file_date_updated":"2022-04-04T10:39:24Z","publication_identifier":{"issn":["2079-6447"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-04-01T00:00:00Z","file":[{"file_id":"10949","creator":"dernst","access_level":"open_access","relation":"main_file","success":1,"date_updated":"2022-04-04T10:39:24Z","content_type":"application/pdf","file_name":"2022_Colorants_Coruh.pdf","date_created":"2022-04-04T10:39:24Z","checksum":"2c15c8d3041ebc36bc64870247081758","file_size":2437988}],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"04","has_accepted_license":"1","publication":"Colorants","language":[{"iso":"eng"}]},{"scopus_import":"1","pmid":1,"_id":"11051","issue":"3","author":[{"full_name":"Liu, Jinqiang","first_name":"Jinqiang","last_name":"Liu"},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"article_processing_charge":"No","date_created":"2022-04-07T07:43:01Z","publication_status":"published","intvolume":"        32","title":"Nuclear pore complex maintenance and implications for age-related diseases","quality_controlled":"1","page":"P216-227","publisher":"Elsevier","article_type":"review","year":"2022","citation":{"chicago":"Liu, Jinqiang, and Martin Hetzer. “Nuclear Pore Complex Maintenance and Implications for Age-Related Diseases.” <i>Trends in Cell Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.tcb.2021.10.001\">https://doi.org/10.1016/j.tcb.2021.10.001</a>.","ieee":"J. Liu and M. Hetzer, “Nuclear pore complex maintenance and implications for age-related diseases,” <i>Trends in Cell Biology</i>, vol. 32, no. 3. Elsevier, pp. P216-227, 2022.","ama":"Liu J, Hetzer M. Nuclear pore complex maintenance and implications for age-related diseases. <i>Trends in Cell Biology</i>. 2022;32(3):P216-227. doi:<a href=\"https://doi.org/10.1016/j.tcb.2021.10.001\">10.1016/j.tcb.2021.10.001</a>","apa":"Liu, J., &#38; Hetzer, M. (2022). Nuclear pore complex maintenance and implications for age-related diseases. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2021.10.001\">https://doi.org/10.1016/j.tcb.2021.10.001</a>","ista":"Liu J, Hetzer M. 2022. Nuclear pore complex maintenance and implications for age-related diseases. Trends in Cell Biology. 32(3), P216-227.","short":"J. Liu, M. Hetzer, Trends in Cell Biology 32 (2022) P216-227.","mla":"Liu, Jinqiang, and Martin Hetzer. “Nuclear Pore Complex Maintenance and Implications for Age-Related Diseases.” <i>Trends in Cell Biology</i>, vol. 32, no. 3, Elsevier, 2022, pp. P216-227, doi:<a href=\"https://doi.org/10.1016/j.tcb.2021.10.001\">10.1016/j.tcb.2021.10.001</a>."},"date_updated":"2022-07-18T08:58:33Z","external_id":{"pmid":["34782239"]},"day":"01","doi":"10.1016/j.tcb.2021.10.001","abstract":[{"lang":"eng","text":"Nuclear pore complexes (NPCs) bridge the nucleus and the cytoplasm and are indispensable for crucial cellular activities, such as bidirectional molecular trafficking and gene transcription regulation. The discovery of long-lived proteins (LLPs) in NPCs from postmitotic cells raises the exciting possibility that the maintenance of NPC integrity might play an inherent role in lifelong cell function. Age-dependent deterioration of NPCs and loss of nuclear integrity have been linked to age-related decline in postmitotic cell function and degenerative diseases. In this review, we discuss our current understanding of NPC maintenance in proliferating and postmitotic cells, and how malfunction of nucleoporins (Nups) might contribute to the pathogenesis of various neurodegenerative and cardiovascular diseases."}],"volume":32,"extern":"1","publication":"Trends in Cell Biology","oa_version":"None","month":"03","keyword":["Cell Biology"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2022-03-01T00:00:00Z","publication_identifier":{"issn":["0962-8924"]},"status":"public","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd"}]