[{"file_date_updated":"2022-03-21T09:19:47Z","oa":1,"abstract":[{"lang":"eng","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."}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ddc":["580"],"has_accepted_license":"1","article_processing_charge":"No","article_number":"e2118220119","day":"07","scopus_import":"1","date_created":"2022-03-20T23:01:39Z","citation":{"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>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>.","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, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>.","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>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>","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.","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>","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. National Academy of Sciences, 2022.","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)."},"quality_controlled":"1","doi":"10.1073/pnas.2118220119","intvolume":"       119","issue":"11","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","year":"2022","status":"public","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.).","external_id":{"pmid":["35254915"],"isi":["000771756300008"]},"author":[{"first_name":"Qing","last_name":"Lu","full_name":"Lu, Qing"},{"first_name":"Yonghong","full_name":"Zhang, Yonghong","last_name":"Zhang"},{"first_name":"Joakim","last_name":"Hellner","full_name":"Hellner, Joakim"},{"first_name":"Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina"},{"first_name":"Xiangyu","last_name":"Xu","full_name":"Xu, Xiangyu"},{"first_name":"Jarne","last_name":"Pauwels","full_name":"Pauwels, Jarne"},{"full_name":"Ma, Qian","last_name":"Ma","first_name":"Qian"},{"first_name":"Wim","last_name":"Dejonghe","full_name":"Dejonghe, Wim"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin"},{"first_name":"Brigitte","last_name":"Van De Cotte","full_name":"Van De Cotte, Brigitte"},{"last_name":"Impens","full_name":"Impens, Francis","first_name":"Francis"},{"first_name":"Kris","full_name":"Gevaert, Kris","last_name":"Gevaert"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Daniel Martinez","last_name":"Molina","full_name":"Molina, Daniel Martinez"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"}],"volume":119,"file":[{"date_updated":"2022-03-21T09:19:47Z","relation":"main_file","creator":"dernst","file_id":"10910","file_size":2169534,"success":1,"file_name":"2022_PNAS_Lu.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2022-03-21T09:19:47Z","checksum":"83e0fea7919570d0b519b41193342571"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-03-07T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"department":[{"_id":"JiFr"}],"title":"Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling","date_updated":"2025-05-14T11:01:45Z","publication_identifier":{"eissn":["1091-6490"]},"isi":1,"pmid":1,"_id":"10888","oa_version":"Published Version","type":"journal_article","publisher":"National Academy of Sciences","publication_status":"published","article_type":"original","month":"03"},{"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.","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-02-22T00:00:00Z","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","first_name":"Thomas A"}],"external_id":{"isi":["000771713200001"]},"volume":13124,"page":"3-6","language":[{"iso":"eng"}],"publication":"Software Verification","year":"2022","scopus_import":"1","quality_controlled":"1","date_created":"2022-03-20T23:01:40Z","citation":{"short":"T.A. Henzinger, in:, Software Verification, Springer Nature, 2022, pp. 3–6.","ieee":"T. A. Henzinger, “Quantitative monitoring of software,” in <i>Software Verification</i>, New Haven, CT, United States, 2022, vol. 13124, pp. 3–6.","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>","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>.","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>.","ista":"Henzinger TA. 2022. Quantitative monitoring of software. Software Verification. NSV: Numerical Software VerificationLNCS vol. 13124, 3–6."},"day":"22","corr_author":"1","intvolume":"     13124","doi":"10.1007/978-3-030-95561-8_1","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","conference":{"end_date":"2021-10-19","location":"New Haven, CT, United States","name":"NSV: Numerical Software Verification","start_date":"2021-10-18"},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF"}],"month":"02","publication_status":"published","type":"conference","publisher":"Springer Nature","series_title":"LNCS","oa_version":"None","isi":1,"publication_identifier":{"isbn":["9783030955601"],"eissn":["1611-3349"],"issn":["0302-9743"]},"_id":"10891","title":"Quantitative monitoring of software","department":[{"_id":"ToHe"}],"date_updated":"2025-04-15T06:25:58Z"},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila","department":[{"_id":"DaSi"},{"_id":"LoSw"}],"date_updated":"2025-06-12T06:20:16Z","isi":1,"acknowledged_ssus":[{"_id":"Bio"}],"publication_identifier":{"eissn":["1460-2075"]},"_id":"10918","ec_funded":1,"pmid":1,"publication_status":"published","publisher":"Embo Press","type":"journal_article","oa_version":"Published Version","month":"03","project":[{"_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","grant_number":"334077"},{"_id":"264CBBAC-B435-11E9-9278-68D0E5697425","grant_number":"M02379","call_identifier":"FWF","name":"Modeling epithelial tissue mechanics during cell invasion"},{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","name":"The role of Drosophila TNF alpha in immune cell invasion","grant_number":"P29638","call_identifier":"FWF"}],"article_type":"original","license":"https://creativecommons.org/licenses/by/4.0/","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"}],"ddc":["570"],"oa":1,"file_date_updated":"2022-03-24T13:22:41Z","article_number":"e109049","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","date_created":"2022-03-24T13:23:09Z","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>","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).","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.","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>.","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>","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."},"quality_controlled":"1","scopus_import":"1","day":"23","corr_author":"1","intvolume":"        41","doi":"10.15252/embj.2021109049","publication":"The Embo Journal","language":[{"iso":"eng"}],"year":"2022","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). ","status":"public","file":[{"date_updated":"2022-03-24T13:22:41Z","relation":"main_file","creator":"siekhaus","file_id":"10919","file_size":4344585,"file_name":"Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosopila.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2022-03-24T13:22:41Z","checksum":"dba48580fe0fefaa4c63078d1d2a35df"}],"date_published":"2022-03-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":41,"external_id":{"isi":["000771957000001"],"pmid":["35319107"]},"author":[{"first_name":"Shamsi","orcid":"0000-0001-6981-6938","full_name":"Emtenani, Shamsi","last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martin","full_name":"Martin, Elliot T","first_name":"Elliot T"},{"full_name":"György, Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","first_name":"Attila"},{"last_name":"Bicher","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","full_name":"Bicher, Julia","first_name":"Julia"},{"first_name":"Jakob-Wendelin","full_name":"Genger, Jakob-Wendelin","last_name":"Genger"},{"last_name":"Köcher","full_name":"Köcher, Thomas","first_name":"Thomas"},{"first_name":"Maria","full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","last_name":"Akhmanova"},{"first_name":"Mariana","id":"6de81d9d-e2f2-11eb-945a-af8bc2a60b26","last_name":"Pereira Guarda","full_name":"Pereira Guarda, Mariana","orcid":"0000-0001-8238-480X"},{"id":"3047D808-F248-11E8-B48F-1D18A9856A87","last_name":"Roblek","full_name":"Roblek, Marko","orcid":"0000-0001-9588-1389","first_name":"Marko"},{"full_name":"Bergthaler, Andreas","last_name":"Bergthaler","first_name":"Andreas"},{"full_name":"Hurd, Thomas R","last_name":"Hurd","first_name":"Thomas R"},{"full_name":"Rangan, Prashanth","last_name":"Rangan","first_name":"Prashanth"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","first_name":"Daria E"}]},{"arxiv":1,"publisher":"American Physical Society","publication_status":"published","type":"journal_article","oa_version":"Published Version","month":"03","project":[{"call_identifier":"H2020","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"P30207","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"},{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"name":"Long-range spin exchange for 2D qubits architectures","grant_number":"M03032","_id":"c08c05c4-5a5b-11eb-8a69-dc6ce49d7973"}],"article_type":"original","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Dynamics of hole singlet-triplet qubits with large g-factor differences","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"date_updated":"2025-04-14T07:44:07Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"isi":1,"publication_identifier":{"eissn":["1079-7114"]},"_id":"10920","ec_funded":1,"pmid":1,"publication":"Physical Review Letters","language":[{"iso":"eng"}],"issue":"12","year":"2022","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.","status":"public","date_published":"2022-03-24T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"10928","creator":"dernst","date_updated":"2022-03-28T06:53:39Z","date_created":"2022-03-28T06:53:39Z","content_type":"application/pdf","access_level":"open_access","checksum":"6e66ad548d18db9c131f304acbd5a1f4","file_size":1266515,"success":1,"file_name":"2022_PhysRevLetters_Jirovec.pdf"}],"volume":128,"external_id":{"pmid":["35394319"],"arxiv":["2111.05130"],"isi":["000786542500004"]},"author":[{"full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","first_name":"Daniel"},{"first_name":"Philipp M.","full_name":"Mutter, Philipp M.","last_name":"Mutter"},{"last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C","first_name":"Andrea C"},{"first_name":"Alessandro","full_name":"Crippa, Alessandro","orcid":"0000-0002-2968-611X","last_name":"Crippa","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425"},{"last_name":"Rychetsky","full_name":"Rychetsky, Marek","first_name":"Marek"},{"full_name":"Craig, David L.","last_name":"Craig","first_name":"David L."},{"first_name":"Josip","full_name":"Kukucka, Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2668-2401","full_name":"Martins, Frederico","last_name":"Martins","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","first_name":"Frederico"},{"full_name":"Ballabio, Andrea","last_name":"Ballabio","first_name":"Andrea"},{"last_name":"Ares","full_name":"Ares, Natalia","first_name":"Natalia"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"last_name":"Isella","full_name":"Isella, Giovanni","first_name":"Giovanni"},{"first_name":"Guido ","full_name":"Burkard, Guido ","last_name":"Burkard"},{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"}],"ddc":["530"],"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"}],"oa":1,"file_date_updated":"2022-03-28T06:53:39Z","article_number":"126803","article_processing_charge":"No","has_accepted_license":"1","date_created":"2022-03-24T15:51:11Z","citation":{"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>.","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>","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>.","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.","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.","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).","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>"},"quality_controlled":"1","scopus_import":"1","day":"24","corr_author":"1","related_material":{"record":[{"id":"18291","status":"public","relation":"popular_science"}]},"intvolume":"       128","doi":"10.1103/PhysRevLett.128.126803"},{"ec_funded":1,"_id":"10922","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"isi":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"date_updated":"2025-04-14T07:28:57Z","title":"Worst-case rigidity analysis and optimization for assemblies with mechanical joints","department":[{"_id":"BeBi"}],"article_type":"original","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"month":"05","oa_version":"Submitted Version","publication_status":"published","publisher":"Wiley","type":"journal_article","doi":"10.1111/cgf.14490","intvolume":"        41","day":"01","scopus_import":"1","quality_controlled":"1","date_created":"2022-03-27T17:34:17Z","citation":{"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.","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>.","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>","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>.","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>","short":"Z. Liu, J. Hu, H. Xu, P. Song, R. Zhang, B. Bickel, C.-W. Fu, Computer Graphics Forum 41 (2022) 507–519.","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."},"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2022-03-27T17:34:11Z","oa":1,"abstract":[{"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.","lang":"eng"}],"ddc":["000"],"external_id":{"isi":["000802723900039"]},"author":[{"first_name":"Zhenyuan","id":"70f0d7cf-ae65-11ec-a14f-89dfc5505b19","last_name":"Liu","full_name":"Liu, Zhenyuan","orcid":"0000-0001-9200-5690"},{"last_name":"Hu","full_name":"Hu, Jingyu","first_name":"Jingyu"},{"full_name":"Xu, Hao","last_name":"Xu","first_name":"Hao"},{"first_name":"Peng","last_name":"Song","full_name":"Song, Peng"},{"first_name":"Ran","full_name":"Zhang, Ran","last_name":"Zhang"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"full_name":"Fu, Chi-Wing","last_name":"Fu","first_name":"Chi-Wing"}],"volume":41,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2022-03-27T17:34:11Z","relation":"main_file","file_id":"10923","creator":"bbickel","file_size":19601689,"file_name":"paper.pdf","date_created":"2022-03-27T17:34:11Z","access_level":"open_access","content_type":"application/pdf","checksum":"b62188b07f5c000f1638c782ec92da41"}],"date_published":"2022-05-01T00:00:00Z","status":"public","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.","year":"2022","issue":"2","publication":"Computer Graphics Forum","language":[{"iso":"eng"}],"page":"507-519"},{"department":[{"_id":"BeVi"}],"title":"Very short mountings are enough for sperm transfer in Littorina saxatilis","date_updated":"2025-05-14T11:05:28Z","isi":1,"publication_identifier":{"eissn":["1464-3766"],"issn":["0260-1230"]},"_id":"10926","publication_status":"published","type":"journal_article","publisher":"Oxford University Press","oa_version":"Submitted Version","main_file_link":[{"url":"https://eprints.whiterose.ac.uk/187332/","open_access":"1"}],"month":"03","article_type":"original","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."}],"oa":1,"article_processing_charge":"No","article_number":"eyab049","scopus_import":"1","date_created":"2022-03-27T22:01:46Z","quality_controlled":"1","citation":{"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 University Press. <a href=\"https://doi.org/10.1093/mollus/eyab049\">https://doi.org/10.1093/mollus/eyab049</a>","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 University Press, 2022. <a href=\"https://doi.org/10.1093/mollus/eyab049\">https://doi.org/10.1093/mollus/eyab049</a>.","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 University Press, 2022, doi:<a href=\"https://doi.org/10.1093/mollus/eyab049\">10.1093/mollus/eyab049</a>.","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.","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>","short":"S. Perini, R. Butlin, A.M. Westram, K. Johannesson, Journal of Molluscan Studies 88 (2022).","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 University Press, 2022."},"day":"01","intvolume":"        88","doi":"10.1093/mollus/eyab049","publication":"Journal of Molluscan Studies","language":[{"iso":"eng"}],"issue":"1","year":"2022","status":"public","date_published":"2022-03-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000759081600002"]},"author":[{"last_name":"Perini","full_name":"Perini, Samuel","first_name":"Samuel"},{"full_name":"Butlin, Rogerk","last_name":"Butlin","first_name":"Rogerk"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"}],"volume":88},{"scopus_import":"1","citation":{"apa":"Zabelkin, A., Yakovleva, Y., Bochkareva, O., &#38; Alexeev, N. (2022). PaReBrick: PArallel REarrangements and BReaks identification toolkit. <i>Bioinformatics</i>. Oxford University Press. <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 University Press, 2022. <a href=\"https://doi.org/10.1093/bioinformatics/btab691\">https://doi.org/10.1093/bioinformatics/btab691</a>.","mla":"Zabelkin, Alexey, et al. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” <i>Bioinformatics</i>, vol. 38, no. 2, Oxford University Press, 2022, pp. 357–63, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btab691\">10.1093/bioinformatics/btab691</a>.","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>","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 University Press, pp. 357–363, 2022.","short":"A. Zabelkin, Y. Yakovleva, O. Bochkareva, N. Alexeev, Bioinformatics 38 (2022) 357–363."},"quality_controlled":"1","date_created":"2022-03-27T22:01:46Z","day":"15","corr_author":"1","intvolume":"        38","related_material":{"link":[{"url":"https://github.com/ctlab/parallel-rearrangements","relation":"software"}]},"doi":"10.1093/bioinformatics/btab691","abstract":[{"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.","lang":"eng"}],"ddc":["000"],"file_date_updated":"2022-03-28T08:07:46Z","oa":1,"article_processing_charge":"No","has_accepted_license":"1","status":"public","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.","date_published":"2022-01-15T00:00:00Z","file":[{"file_id":"10930","creator":"dernst","relation":"main_file","date_updated":"2022-03-28T08:07:46Z","checksum":"4b5688ff9ac86180ccdf7f82fa33d926","date_created":"2022-03-28T08:07:46Z","access_level":"open_access","content_type":"application/pdf","file_name":"2022_Bioinformatics_Zabelkin.pdf","success":1,"file_size":3425744}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000743380100008"]},"author":[{"first_name":"Alexey","full_name":"Zabelkin, Alexey","last_name":"Zabelkin"},{"last_name":"Yakovleva","full_name":"Yakovleva, Yulia","first_name":"Yulia"},{"first_name":"Olga","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva"},{"last_name":"Alexeev","full_name":"Alexeev, Nikita","first_name":"Nikita"}],"volume":38,"publication":"Bioinformatics","language":[{"iso":"eng"}],"page":"357-363","issue":"2","year":"2022","isi":1,"publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"ec_funded":1,"_id":"10927","title":"PaReBrick: PArallel REarrangements and BReaks identification toolkit","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"FyKo"}],"date_updated":"2025-05-14T11:05:09Z","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"month":"01","article_type":"original","publication_status":"published","type":"journal_article","publisher":"Oxford University Press","oa_version":"Published Version"},{"_id":"10939","pmid":1,"isi":1,"publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"date_updated":"2025-09-09T14:29:53Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level","department":[{"_id":"CaGu"}],"month":"03","article_type":"original","publisher":"Public Library of Science","type":"journal_article","publication_status":"published","oa_version":"Published Version","intvolume":"        18","related_material":{"link":[{"url":"https://gitlab.pasteur.fr/adavidov/inferencelnakf","relation":"software"}]},"doi":"10.1371/journal.pcbi.1009950","scopus_import":"1","date_created":"2022-04-03T22:01:42Z","quality_controlled":"1","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.","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>.","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>.","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>","short":"A. Davidović, R.P. Chait, G. Batt, J. Ruess, PLoS Computational Biology 18 (2022).","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.","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>"},"day":"18","article_processing_charge":"No","article_number":"e1009950","has_accepted_license":"1","abstract":[{"lang":"eng","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."}],"ddc":["570","000"],"file_date_updated":"2022-04-04T10:14:39Z","oa":1,"date_published":"2022-03-18T00:00:00Z","file":[{"date_updated":"2022-04-04T10:14:39Z","creator":"dernst","file_id":"10947","relation":"main_file","success":1,"file_name":"2022_PLoSCompBio_Davidovic.pdf","file_size":2958642,"checksum":"458ef542761fb714ced214f240daf6b2","access_level":"open_access","content_type":"application/pdf","date_created":"2022-04-04T10:14:39Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001044208400004"],"pmid":["35303737"]},"author":[{"first_name":"Anđela","last_name":"Davidović","full_name":"Davidović, Anđela"},{"full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P"},{"first_name":"Gregory","full_name":"Batt, Gregory","last_name":"Batt"},{"first_name":"Jakob","orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess"}],"volume":18,"status":"public","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.","year":"2022","language":[{"iso":"eng"}],"publication":"PLoS Computational Biology","issue":"3"},{"status":"public","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.","date_published":"2022-03-11T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":17,"author":[{"last_name":"Krause","full_name":"Krause, J.","first_name":"J."},{"full_name":"Dickel, C.","last_name":"Dickel","first_name":"C."},{"first_name":"E.","full_name":"Vaal, E.","last_name":"Vaal"},{"last_name":"Vielmetter","full_name":"Vielmetter, M.","first_name":"M."},{"last_name":"Feng","full_name":"Feng, J.","first_name":"J."},{"first_name":"R.","last_name":"Bounds","full_name":"Bounds, R."},{"first_name":"G.","last_name":"Catelani","full_name":"Catelani, G."},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"},{"first_name":"Yoichi","full_name":"Ando, Yoichi","last_name":"Ando"}],"external_id":{"isi":["000770371400003"],"arxiv":["2111.01115"]},"publication":"Physical Review Applied","language":[{"iso":"eng"}],"issue":"3","year":"2022","quality_controlled":"1","date_created":"2022-04-03T22:01:43Z","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.","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>.","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>","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>.","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).","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.","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>"},"scopus_import":"1","day":"11","intvolume":"        17","doi":"10.1103/PhysRevApplied.17.034032","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."}],"oa":1,"article_number":"034032","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2111.01115","open_access":"1"}],"month":"03","article_type":"original","arxiv":1,"type":"journal_article","publication_status":"published","publisher":"American Physical Society","oa_version":"Preprint","isi":1,"publication_identifier":{"eissn":["2331-7019"]},"_id":"10940","title":"Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T","department":[{"_id":"JoFi"}],"date_updated":"2023-08-03T06:23:58Z"},{"department":[{"_id":"LeSa"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra","date_updated":"2024-10-14T13:52:09Z","OA_place":"publisher","publication_identifier":{"issn":["2079-6447"]},"_id":"10945","publisher":"MDPI","publication_status":"published","type":"journal_article","oa_version":"Published Version","OA_type":"gold","month":"04","article_type":"original","abstract":[{"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.","lang":"eng"}],"ddc":["570"],"file_date_updated":"2022-04-04T10:39:24Z","oa":1,"article_processing_charge":"Yes","has_accepted_license":"1","DOAJ_listed":"1","quality_controlled":"1","date_created":"2022-04-04T09:03:54Z","citation":{"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>","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>.","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>.","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>","short":"M.O. Çoruh, G. Gündüz, Ü. Çolak, B. Maviş, Colorants 1 (2022) 149–164.","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."},"day":"01","intvolume":"         1","doi":"10.3390/colorants1020010","page":"149-164","language":[{"iso":"eng"}],"publication":"Colorants","issue":"2","year":"2022","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.","status":"public","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","file":[{"date_updated":"2022-04-04T10:39:24Z","creator":"dernst","file_id":"10949","relation":"main_file","file_name":"2022_Colorants_Coruh.pdf","success":1,"file_size":2437988,"checksum":"2c15c8d3041ebc36bc64870247081758","access_level":"open_access","content_type":"application/pdf","date_created":"2022-04-04T10:39:24Z"}],"date_published":"2022-04-01T00:00:00Z","author":[{"first_name":"Mehmet Orkun","last_name":"Çoruh","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","full_name":"Çoruh, Mehmet Orkun","orcid":"0000-0002-3219-2022"},{"last_name":"Gündüz","full_name":"Gündüz, Güngör","first_name":"Güngör"},{"last_name":"Çolak","full_name":"Çolak, Üner","first_name":"Üner"},{"last_name":"Maviş","full_name":"Maviş, Bora","first_name":"Bora"}],"volume":1},{"oa_version":"None","publication_status":"published","publisher":"Elsevier","type":"journal_article","article_type":"review","month":"03","keyword":["Cell Biology"],"date_updated":"2024-10-14T11:14:57Z","title":"Nuclear pore complex maintenance and implications for age-related diseases","pmid":1,"_id":"11051","publication_identifier":{"issn":["0962-8924"]},"year":"2022","issue":"3","page":"P216-227","language":[{"iso":"eng"}],"publication":"Trends in Cell Biology","extern":"1","volume":32,"author":[{"first_name":"Jinqiang","last_name":"Liu","full_name":"Liu, Jinqiang"},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"external_id":{"pmid":["34782239"]},"date_published":"2022-03-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_processing_charge":"No","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."}],"doi":"10.1016/j.tcb.2021.10.001","intvolume":"        32","day":"01","citation":{"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>","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>.","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>.","ista":"Liu J, Hetzer M. 2022. Nuclear pore complex maintenance and implications for age-related diseases. Trends in Cell Biology. 32(3), P216-227.","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>","short":"J. Liu, M. Hetzer, Trends in Cell Biology 32 (2022) P216-227.","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."},"quality_controlled":"1","date_created":"2022-04-07T07:43:01Z","scopus_import":"1"},{"status":"public","acknowledgement":"This work was supported by National Natural Science Foundation of China (52002042), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), 111 Project (B17002) and Lise Meitner Project M 2889-N. This work was also supported by the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the high-performance computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM and TEM measurements.","external_id":{"isi":["000798679100010"]},"author":[{"full_name":"Hong, Tao","last_name":"Hong","first_name":"Tao"},{"full_name":"Guo, Changrong","last_name":"Guo","first_name":"Changrong"},{"last_name":"Wang","full_name":"Wang, Dongyang","first_name":"Dongyang"},{"first_name":"Bingchao","full_name":"Qin, Bingchao","last_name":"Qin"},{"first_name":"Cheng","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"first_name":"Xiang","last_name":"Gao","full_name":"Gao, Xiang"},{"first_name":"Li Dong","full_name":"Zhao, Li Dong","last_name":"Zhao"}],"volume":25,"date_published":"2022-04-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"publication":"Materials Today Energy","year":"2022","day":"01","corr_author":"1","scopus_import":"1","quality_controlled":"1","date_created":"2022-04-10T22:01:39Z","citation":{"ieee":"T. Hong <i>et al.</i>, “Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3,” <i>Materials Today Energy</i>, vol. 25. Elsevier, 2022.","short":"T. Hong, C. Guo, D. Wang, B. Qin, C. Chang, X. Gao, L.D. Zhao, Materials Today Energy 25 (2022).","ama":"Hong T, Guo C, Wang D, et al. Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. <i>Materials Today Energy</i>. 2022;25. doi:<a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">10.1016/j.mtener.2022.100985</a>","chicago":"Hong, Tao, Changrong Guo, Dongyang Wang, Bingchao Qin, Cheng Chang, Xiang Gao, and Li Dong Zhao. “Enhanced Thermoelectric Performance in SnTe Due to the Energy Filtering Effect Introduced by Bi2O3.” <i>Materials Today Energy</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">https://doi.org/10.1016/j.mtener.2022.100985</a>.","mla":"Hong, Tao, et al. “Enhanced Thermoelectric Performance in SnTe Due to the Energy Filtering Effect Introduced by Bi2O3.” <i>Materials Today Energy</i>, vol. 25, 100985, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">10.1016/j.mtener.2022.100985</a>.","apa":"Hong, T., Guo, C., Wang, D., Qin, B., Chang, C., Gao, X., &#38; Zhao, L. D. (2022). Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. <i>Materials Today Energy</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mtener.2022.100985\">https://doi.org/10.1016/j.mtener.2022.100985</a>","ista":"Hong T, Guo C, Wang D, Qin B, Chang C, Gao X, Zhao LD. 2022. Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3. Materials Today Energy. 25, 100985."},"doi":"10.1016/j.mtener.2022.100985","intvolume":"        25","abstract":[{"lang":"eng","text":"SnTe is a promising Pb-free thermoelectric (TE) material with high electrical conductivity. We discovered the synergistic effect of Bi2O3 on enhancing the average power factor (PF) and overall ZT value of the SnTe-based thermoelectric material. The introduction of Bi2O3 forms plenty of SnO2, Bi2O3, and Bi-rich nanoprecipitates. These interfaces between the SnTe matrix and the nanoprecipitates can enhance the average PF through the energy filtering effect. On the other hand, abundant and diverse nanoprecipitates can significantly diminish the lattice thermal conductivity (κlat) through enhanced phonon scattering. The synergistic effect of Bi2O3 resulted in a maximum ZT (ZTmax) value of 0.9 at SnTe-2% Bi2O3 and an average ZT (ZTave) value of 0.4 for SnTe-4% Bi2O3 from 300 K to 823 K. The work provides an excellent reference to develop non-toxic high-performance TE materials."}],"article_processing_charge":"No","article_number":"100985","article_type":"original","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"}],"month":"04","oa_version":"None","publication_status":"published","type":"journal_article","publisher":"Elsevier","publication_identifier":{"eissn":["2468-6069"]},"isi":1,"_id":"11142","title":"Enhanced thermoelectric performance in SnTe due to the energy filtering effect introduced by Bi2O3","department":[{"_id":"MaIb"}],"date_updated":"2025-04-14T09:29:32Z"},{"file_date_updated":"2022-04-15T11:00:58Z","oa":1,"abstract":[{"lang":"eng","text":"Dravet syndrome is a neurodevelopmental disorder characterized by epilepsy, intellectual disability, and sudden death due to pathogenic variants in SCN1A with loss of function of the sodium channel subunit Nav1.1. Nav1.1-expressing parvalbumin GABAergic interneurons (PV-INs) from young Scn1a+/− mice show impaired action potential generation. An approach assessing PV-IN function in the same mice at two time points shows impaired spike generation in all Scn1a+/− mice at postnatal days (P) 16–21, whether deceased prior or surviving to P35, with normalization by P35 in surviving mice. However, PV-IN synaptic transmission is dysfunctional in young Scn1a+/− mice that did not survive and in Scn1a+/− mice ≥ P35. Modeling confirms that PV-IN axonal propagation is more sensitive to decreased sodium conductance than spike generation. These results demonstrate dynamic dysfunction in Dravet syndrome: combined abnormalities of PV-IN spike generation and propagation drives early disease severity, while ongoing dysfunction of synaptic transmission contributes to chronic pathology."}],"ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","article_number":"110580","day":"29","scopus_import":"1","date_created":"2022-04-10T22:01:39Z","quality_controlled":"1","citation":{"ista":"Kaneko K, Currin C, Goff KM, Wengert ER, Somarowthu A, Vogels TP, Goldberg EM. 2022. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Reports. 38(13), 110580.","apa":"Kaneko, K., Currin, C., Goff, K. M., Wengert, E. R., Somarowthu, A., Vogels, T. P., &#38; Goldberg, E. M. (2022). Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">https://doi.org/10.1016/j.celrep.2022.110580</a>","chicago":"Kaneko, Keisuke, Christopher Currin, Kevin M. Goff, Eric R. Wengert, Ala Somarowthu, Tim P Vogels, and Ethan M. Goldberg. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">https://doi.org/10.1016/j.celrep.2022.110580</a>.","mla":"Kaneko, Keisuke, et al. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” <i>Cell Reports</i>, vol. 38, no. 13, 110580, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">10.1016/j.celrep.2022.110580</a>.","ama":"Kaneko K, Currin C, Goff KM, et al. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. <i>Cell Reports</i>. 2022;38(13). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">10.1016/j.celrep.2022.110580</a>","ieee":"K. Kaneko <i>et al.</i>, “Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome,” <i>Cell Reports</i>, vol. 38, no. 13. Elsevier, 2022.","short":"K. Kaneko, C. Currin, K.M. Goff, E.R. Wengert, A. Somarowthu, T.P. Vogels, E.M. Goldberg, Cell Reports 38 (2022)."},"doi":"10.1016/j.celrep.2022.110580","intvolume":"        38","issue":"13","publication":"Cell Reports","language":[{"iso":"eng"}],"year":"2022","status":"public","acknowledgement":"We would like to thank Bernardo Rudy, Joanna Mattis, and Laura Mcgarry for comments on a previous version of the manuscript; Xiaohong Zhang for expert technical support and mouse colony maintenance; Melody Cheng for assistance with generation of the graphical abstract; and Jennifer Kearney for the gift of Scn1a+/− mice. This work was supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under F31NS111803 (to K.M.G.) and K08NS097633 and R01NS110869 (to E.M.G.), the Dravet Syndrome Foundation (to A.S.), an ERC Consolidator Grant (SYNAPSEEK) (to T.P.V.), and the NOMIS Foundation through the NOMIS Fellowships program at IST Austria (to C.C.). The graphical abstract was prepared using BioRender software (BioRender.com).","author":[{"full_name":"Kaneko, Keisuke","last_name":"Kaneko","first_name":"Keisuke"},{"orcid":"0000-0002-4809-5059","full_name":"Currin, Christopher","last_name":"Currin","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","first_name":"Christopher"},{"last_name":"Goff","full_name":"Goff, Kevin M.","first_name":"Kevin M."},{"first_name":"Eric R.","full_name":"Wengert, Eric R.","last_name":"Wengert"},{"last_name":"Somarowthu","full_name":"Somarowthu, Ala","first_name":"Ala"},{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P"},{"first_name":"Ethan M.","last_name":"Goldberg","full_name":"Goldberg, Ethan M."}],"external_id":{"isi":["000779794000001"],"pmid":["35354025"]},"volume":38,"file":[{"file_size":4774216,"file_name":"2022_CellReports_Kaneko.pdf","success":1,"date_created":"2022-04-15T11:00:58Z","access_level":"open_access","content_type":"application/pdf","checksum":"49105c6c27c9af0f37f50a8bbb4d380d","date_updated":"2022-04-15T11:00:58Z","relation":"main_file","file_id":"11172","creator":"dernst"}],"date_published":"2022-03-29T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"TiVo"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"title":"Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome","date_updated":"2025-06-11T14:00:11Z","publication_identifier":{"eissn":["2211-1247"]},"isi":1,"pmid":1,"ec_funded":1,"_id":"11143","oa_version":"Published Version","publication_status":"published","publisher":"Elsevier","type":"journal_article","article_type":"original","month":"03","project":[{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."},{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-03-25T00:00:00Z","volume":375,"author":[{"first_name":"Lizhong","full_name":"Su, Lizhong","last_name":"Su"},{"first_name":"Dongyang","last_name":"Wang","full_name":"Wang, Dongyang"},{"full_name":"Wang, Sining","last_name":"Wang","first_name":"Sining"},{"first_name":"Bingchao","last_name":"Qin","full_name":"Qin, Bingchao"},{"last_name":"Wang","full_name":"Wang, Yuping","first_name":"Yuping"},{"first_name":"Yongxin","full_name":"Qin, Yongxin","last_name":"Qin"},{"first_name":"Yang","last_name":"Jin","full_name":"Jin, Yang"},{"first_name":"Cheng","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"}],"external_id":{"isi":["000778894800038"],"pmid":["35324303"]},"status":"public","acknowledgement":"This work was supported by the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Key Research and Development Program of China (2018YFA0702100), the National Science Fund for Distinguished Young Scholars (51925101), the 111 Project (B17002), the Lise Meitner Project (M2889-N), and the National Key Research and Development Program of China (2018YFB0703600). This work is also supported by the National Postdoctoral Program for Innovative Talents (BX20200028). L.-D.Z. is thankful for the high-performance computing resources at Beihang University.","year":"2022","language":[{"iso":"eng"}],"publication":"Science","page":"1385-1389","issue":"6587","intvolume":"       375","doi":"10.1126/science.abn8997","quality_controlled":"1","citation":{"mla":"Su, Lizhong, et al. “High Thermoelectric Performance Realized through Manipulating Layered Phonon-Electron Decoupling.” <i>Science</i>, vol. 375, no. 6587, American Association for the Advancement of Science, 2022, pp. 1385–89, doi:<a href=\"https://doi.org/10.1126/science.abn8997\">10.1126/science.abn8997</a>.","apa":"Su, L., Wang, D., Wang, S., Qin, B., Wang, Y., Qin, Y., … Zhao, L. D. (2022). High thermoelectric performance realized through manipulating layered phonon-electron decoupling. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abn8997\">https://doi.org/10.1126/science.abn8997</a>","chicago":"Su, Lizhong, Dongyang Wang, Sining Wang, Bingchao Qin, Yuping Wang, Yongxin Qin, Yang Jin, Cheng Chang, and Li Dong Zhao. “High Thermoelectric Performance Realized through Manipulating Layered Phonon-Electron Decoupling.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.abn8997\">https://doi.org/10.1126/science.abn8997</a>.","ista":"Su L, Wang D, Wang S, Qin B, Wang Y, Qin Y, Jin Y, Chang C, Zhao LD. 2022. High thermoelectric performance realized through manipulating layered phonon-electron decoupling. Science. 375(6587), 1385–1389.","ieee":"L. Su <i>et al.</i>, “High thermoelectric performance realized through manipulating layered phonon-electron decoupling,” <i>Science</i>, vol. 375, no. 6587. American Association for the Advancement of Science, pp. 1385–1389, 2022.","short":"L. Su, D. Wang, S. Wang, B. Qin, Y. Wang, Y. Qin, Y. Jin, C. Chang, L.D. Zhao, Science 375 (2022) 1385–1389.","ama":"Su L, Wang D, Wang S, et al. High thermoelectric performance realized through manipulating layered phonon-electron decoupling. <i>Science</i>. 2022;375(6587):1385-1389. doi:<a href=\"https://doi.org/10.1126/science.abn8997\">10.1126/science.abn8997</a>"},"date_created":"2022-04-10T22:01:40Z","scopus_import":"1","corr_author":"1","day":"25","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Thermoelectric materials allow for direct conversion between heat and electricity, offering the potential for power generation. The average dimensionless figure of merit ZTave determines device efficiency. N-type tin selenide crystals exhibit outstanding three-dimensional charge and two-dimensional phonon transport along the out-of-plane direction, contributing to a high maximum figure of merit Zmax of ~3.6 × 10−3 per kelvin but a moderate ZTave of ~1.1. We found an attractive high Zmax of ~4.1 × 10−3 per kelvin at 748 kelvin and a ZTave of ~1.7 at 300 to 773 kelvin in chlorine-doped and lead-alloyed tin selenide crystals by phonon-electron decoupling. The chlorine-induced low deformation potential improved the carrier mobility. The lead-induced mass and strain fluctuations reduced the lattice thermal conductivity. Phonon-electron decoupling plays a critical role to achieve high-performance thermoelectrics."}],"month":"03","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"}],"article_type":"original","publisher":"American Association for the Advancement of Science","type":"journal_article","publication_status":"published","oa_version":"None","_id":"11144","pmid":1,"isi":1,"publication_identifier":{"eissn":["1095-9203"]},"date_updated":"2025-04-14T09:29:32Z","department":[{"_id":"MaIb"}],"title":"High thermoelectric performance realized through manipulating layered phonon-electron decoupling"},{"date_updated":"2025-07-10T11:50:08Z","department":[{"_id":"MaKw"}],"title":"List-decodability with large radius for Reed-Solomon codes","_id":"11145","isi":1,"publication_identifier":{"isbn":["9781665420556"],"issn":["0272-5428"]},"type":"conference","publication_status":"published","publisher":"IEEE","oa_version":"Preprint","arxiv":1,"month":"02","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2012.10584","open_access":"1"}],"article_processing_charge":"No","conference":{"end_date":"2022-02-10","name":"FOCS: Foundations of Computer Science","location":"Denver, CO, United States","start_date":"2022-02-07"},"abstract":[{"lang":"eng","text":"List-decodability of Reed-Solomon codes has re-ceived a lot of attention, but the best-possible dependence between the parameters is still not well-understood. In this work, we focus on the case where the list-decoding radius is of the form r=1−ε for ε tending to zero. Our main result states that there exist Reed-Solomon codes with rate Ω(ε) which are (1−ε,O(1/ε) -list-decodable, meaning that any Hamming ball of radius 1−ε contains at most O(1/ε) codewords. This trade-off between rate and list-decoding radius is best-possible for any code with list size less than exponential in the block length. By achieving this trade-off between rate and list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo, and Wootters, and resolve the main motivating question of their work. Moreover, while their result requires the field to be exponentially large in the block length, we only need the field size to be polynomially large (and in fact, almost-linear suffices). We deduce our main result from a more general theorem, in which we prove good list-decodability properties of random puncturings of any given code with very large distance."}],"oa":1,"intvolume":"      2022","related_material":{"record":[{"status":"public","relation":"later_version","id":"10775"}]},"doi":"10.1109/FOCS52979.2021.00075","scopus_import":"1","citation":{"chicago":"Ferber, Asaf, Matthew Alan Kwan, and Lisa Sauermann. “List-Decodability with Large Radius for Reed-Solomon Codes.” In <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>, 2022:720–26. IEEE, 2022. <a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">https://doi.org/10.1109/FOCS52979.2021.00075</a>.","apa":"Ferber, A., Kwan, M. A., &#38; Sauermann, L. (2022). List-decodability with large radius for Reed-Solomon codes. In <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i> (Vol. 2022, pp. 720–726). Denver, CO, United States: IEEE. <a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">https://doi.org/10.1109/FOCS52979.2021.00075</a>","mla":"Ferber, Asaf, et al. “List-Decodability with Large Radius for Reed-Solomon Codes.” <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>, vol. 2022, IEEE, 2022, pp. 720–26, doi:<a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">10.1109/FOCS52979.2021.00075</a>.","ista":"Ferber A, Kwan MA, Sauermann L. 2022. List-decodability with large radius for Reed-Solomon codes. 62nd Annual IEEE Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science vol. 2022, 720–726.","ama":"Ferber A, Kwan MA, Sauermann L. List-decodability with large radius for Reed-Solomon codes. In: <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>. Vol 2022. IEEE; 2022:720-726. doi:<a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">10.1109/FOCS52979.2021.00075</a>","ieee":"A. Ferber, M. A. Kwan, and L. Sauermann, “List-decodability with large radius for Reed-Solomon codes,” in <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>, Denver, CO, United States, 2022, vol. 2022, pp. 720–726.","short":"A. Ferber, M.A. Kwan, L. Sauermann, in:, 62nd Annual IEEE Symposium on Foundations of Computer Science, IEEE, 2022, pp. 720–726."},"quality_controlled":"1","date_created":"2022-04-10T22:01:40Z","day":"01","year":"2022","publication":"62nd Annual IEEE Symposium on Foundations of Computer Science","language":[{"iso":"eng"}],"page":"720-726","date_published":"2022-02-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2012.10584"],"isi":["000802209600065"]},"author":[{"first_name":"Asaf","full_name":"Ferber, Asaf","last_name":"Ferber"},{"last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan"},{"first_name":"Lisa","last_name":"Sauermann","full_name":"Sauermann, Lisa"}],"volume":2022,"status":"public"},{"type":"journal_article","publisher":"Elsevier","publication_status":"published","oa_version":"Published Version","keyword":["Structural Biology"],"project":[{"name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"month":"06","article_type":"original","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"FlSc"}],"title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","date_updated":"2025-04-15T08:24:50Z","isi":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["1047-8477"]},"_id":"11155","pmid":1,"publication":"Journal of Structural Biology","language":[{"iso":"eng"}],"issue":"2","year":"2022","status":"public","acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","file":[{"checksum":"0b1eb53447aae8e95ae4c12d193b0b00","date_created":"2022-08-02T11:07:58Z","access_level":"open_access","content_type":"application/pdf","file_name":"2022_JourStructuralBiology_Obr.pdf","success":1,"file_size":7080863,"file_id":"11722","creator":"dernst","relation":"main_file","date_updated":"2022-08-02T11:07:58Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-06-01T00:00:00Z","volume":214,"author":[{"orcid":"0000-0003-1756-6564","full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin"},{"first_name":"Wim J.H.","full_name":"Hagen, Wim J.H.","last_name":"Hagen"},{"full_name":"Dick, Robert A.","last_name":"Dick","first_name":"Robert A."},{"last_name":"Yu","full_name":"Yu, Lingbo","first_name":"Lingbo"},{"first_name":"Abhay","last_name":"Kotecha","full_name":"Kotecha, Abhay"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"external_id":{"isi":["000790733600001"],"pmid":["35351542"]},"abstract":[{"text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.","lang":"eng"}],"ddc":["570"],"oa":1,"file_date_updated":"2022-08-02T11:07:58Z","article_number":"107852","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","date_created":"2022-04-15T07:10:26Z","citation":{"short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022).","ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” <i>Journal of Structural Biology</i>, vol. 214, no. 2. Elsevier, 2022.","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. 2022;214(2). doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>","ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>, vol. 214, no. 2, 107852, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>.","apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., &#38; Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>","chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>."},"quality_controlled":"1","scopus_import":"1","day":"01","corr_author":"1","intvolume":"       214","doi":"10.1016/j.jsb.2022.107852"},{"has_accepted_license":"1","article_number":"102350","article_processing_charge":"Yes (via OA deal)","oa":1,"file_date_updated":"2022-08-05T05:56:03Z","abstract":[{"lang":"eng","text":"Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I."}],"ddc":["570"],"doi":"10.1016/j.sbi.2022.102350","intvolume":"        74","day":"01","corr_author":"1","citation":{"ista":"Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.","apa":"Kampjut, D., &#38; Sazanov, L. A. (2022). Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>.","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>, vol. 74, 102350, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>.","ama":"Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. 2022;74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>","ieee":"D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging blueprint for the mechanism,” <i>Current Opinion in Structural Biology</i>, vol. 74. Elsevier, 2022.","short":"D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022)."},"quality_controlled":"1","date_created":"2022-04-15T09:32:35Z","scopus_import":"1","year":"2022","publication":"Current Opinion in Structural Biology","language":[{"iso":"eng"}],"volume":74,"author":[{"last_name":"Kampjut","id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen","first_name":"Domen"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"external_id":{"pmid":["35316665"],"isi":["000829029500020"]},"file":[{"file_size":815607,"file_name":"2022_CurrentOpStructBiology_Kampjut.pdf","success":1,"date_created":"2022-08-05T05:56:03Z","content_type":"application/pdf","access_level":"open_access","checksum":"72bdde48853643a32d42b75f54965c44","date_updated":"2022-08-05T05:56:03Z","relation":"main_file","file_id":"11725","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-06-01T00:00:00Z","status":"public","date_updated":"2024-10-09T21:02:00Z","department":[{"_id":"LeSa"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Structure of respiratory complex I – An emerging blueprint for the mechanism","pmid":1,"_id":"11167","publication_identifier":{"issn":["0959-440X"]},"isi":1,"oa_version":"Published Version","type":"journal_article","publication_status":"published","publisher":"Elsevier","article_type":"original","month":"06","keyword":["Molecular Biology","Structural Biology"]},{"author":[{"last_name":"Gauto","full_name":"Gauto, Diego F.","first_name":"Diego F."},{"last_name":"Macek","full_name":"Macek, Pavel","first_name":"Pavel"},{"first_name":"Duccio","last_name":"Malinverni","full_name":"Malinverni, Duccio"},{"last_name":"Fraga","full_name":"Fraga, Hugo","first_name":"Hugo"},{"first_name":"Matteo","last_name":"Paloni","full_name":"Paloni, Matteo"},{"full_name":"Sučec, Iva","last_name":"Sučec","first_name":"Iva"},{"first_name":"Audrey","last_name":"Hessel","full_name":"Hessel, Audrey"},{"last_name":"Bustamante","full_name":"Bustamante, Juan Pablo","first_name":"Juan Pablo"},{"first_name":"Alessandro","full_name":"Barducci, Alessandro","last_name":"Barducci"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul"}],"external_id":{"isi":["000781498700009"],"pmid":["35395851"]},"volume":13,"date_published":"2022-04-08T00:00:00Z","file":[{"date_updated":"2022-05-02T08:48:00Z","relation":"main_file","file_id":"11348","creator":"dernst","file_size":2637590,"success":1,"file_name":"2022_NatureCommunications_Gauto.pdf","date_created":"2022-05-02T08:48:00Z","access_level":"open_access","content_type":"application/pdf","checksum":"db61d5534e988743d6266d3675d77b08"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We are grateful to Bernhard Brutscher, Alicia Vallet, and Adrien Favier for excellent NMR\r\nplatform operation and management. The plasmid coding for TET2 was kindly provided\r\nby Bruno Franzetti and Jerome Boisbouvier (IBS Grenoble). We thank Anne-Marie Villard\r\nand the RoBioMol platform for preparing the loop deletion construct. The RoBioMol\r\nplatform is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEAUGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL (ANR-10-LABX-49-01), financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBHEUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P. S.) and the French Agence Nationale de la Recherche (ANR), under grant ANR-14-ACHN-0016 (M.P. and A.B.).","status":"public","year":"2022","publication":"Nature Communications","language":[{"iso":"eng"}],"doi":"10.1038/s41467-022-29423-0","intvolume":"        13","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31243-1","relation":"erratum"}]},"day":"08","corr_author":"1","scopus_import":"1","date_created":"2022-04-17T22:01:45Z","citation":{"ama":"Gauto DF, Macek P, Malinverni D, et al. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-29423-0\">10.1038/s41467-022-29423-0</a>","short":"D.F. Gauto, P. Macek, D. Malinverni, H. Fraga, M. Paloni, I. Sučec, A. Hessel, J.P. Bustamante, A. Barducci, P. Schanda, Nature Communications 13 (2022).","ieee":"D. F. Gauto <i>et al.</i>, “Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ista":"Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. 2022. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications. 13, 1927.","chicago":"Gauto, Diego F., Pavel Macek, Duccio Malinverni, Hugo Fraga, Matteo Paloni, Iva Sučec, Audrey Hessel, Juan Pablo Bustamante, Alessandro Barducci, and Paul Schanda. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-29423-0\">https://doi.org/10.1038/s41467-022-29423-0</a>.","mla":"Gauto, Diego F., et al. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” <i>Nature Communications</i>, vol. 13, 1927, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-29423-0\">10.1038/s41467-022-29423-0</a>.","apa":"Gauto, D. F., Macek, P., Malinverni, D., Fraga, H., Paloni, M., Sučec, I., … Schanda, P. (2022). Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-29423-0\">https://doi.org/10.1038/s41467-022-29423-0</a>"},"quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"No","article_number":"1927","file_date_updated":"2022-05-02T08:48:00Z","oa":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution."}],"article_type":"original","month":"04","oa_version":"Published Version","publication_status":"published","publisher":"Springer Nature","type":"journal_article","pmid":1,"_id":"11179","publication_identifier":{"eissn":["2041-1723"]},"isi":1,"date_updated":"2025-06-11T13:31:55Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR","department":[{"_id":"PaSc"}]},{"scopus_import":"1","citation":{"ista":"Postnikova A, Koval N, Nadiradze G, Alistarh D-A. 2022. Multi-queues can be state-of-the-art priority schedulers. Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 353–367.","apa":"Postnikova, A., Koval, N., Nadiradze, G., &#38; Alistarh, D.-A. (2022). Multi-queues can be state-of-the-art priority schedulers. In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 353–367). Seoul, Republic of Korea: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3503221.3508432\">https://doi.org/10.1145/3503221.3508432</a>","mla":"Postnikova, Anastasiia, et al. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2022, pp. 353–67, doi:<a href=\"https://doi.org/10.1145/3503221.3508432\">10.1145/3503221.3508432</a>.","chicago":"Postnikova, Anastasiia, Nikita Koval, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 353–67. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3503221.3508432\">https://doi.org/10.1145/3503221.3508432</a>.","ama":"Postnikova A, Koval N, Nadiradze G, Alistarh D-A. Multi-queues can be state-of-the-art priority schedulers. In: <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2022:353-367. doi:<a href=\"https://doi.org/10.1145/3503221.3508432\">10.1145/3503221.3508432</a>","short":"A. Postnikova, N. Koval, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2022, pp. 353–367.","ieee":"A. Postnikova, N. Koval, G. Nadiradze, and D.-A. Alistarh, “Multi-queues can be state-of-the-art priority schedulers,” in <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Seoul, Republic of Korea, 2022, pp. 353–367."},"date_created":"2022-04-17T22:01:46Z","quality_controlled":"1","day":"02","corr_author":"1","related_material":{"record":[{"relation":"research_data","status":"public","id":"13076"}]},"doi":"10.1145/3503221.3508432","abstract":[{"text":"Designing and implementing efficient parallel priority schedulers is an active research area. An intriguing proposed design is the Multi-Queue: given n threads and m ≥ n distinct priority queues, task insertions are performed uniformly at random, while, to delete, a thread picks two queues uniformly at random, and removes the observed task of higher priority. This approach scales well, and has probabilistic rank guarantees: roughly, the rank of each task removed, relative to remaining tasks in all other queues, is O (m) in expectation. Yet, the performance of this pattern is below that of well-engineered schedulers, which eschew theoretical guarantees for practical efficiency.\r\n\r\nWe investigate whether it is possible to design and implement a Multi-Queue-based task scheduler that is both highly-efficient and has analytical guarantees. We propose a new variant called the Stealing Multi-Queue (SMQ), a cache-efficient variant of the Multi-Queue, which leverages both queue affinity---each thread has a local queue, from which tasks are usually removed; but, with some probability, threads also attempt to steal higher-priority tasks from the other queues---and task batching, that is, the processing of several tasks in a single insert / remove step. These ideas are well-known for task scheduling without priorities; our theoretical contribution is showing that, despite relaxations, this design can still provide rank guarantees, which in turn implies bounds on total work performed. We provide a general SMQ implementation which can surpass state-of-the-art schedulers such as OBIM and PMOD in terms of performance on popular graph-processing benchmarks. Notably, the performance improvement comes mainly from the superior rank guarantees provided by our scheduler, confirming that analytically-reasoned approaches can still provide performance improvements for priority task scheduling.","lang":"eng"}],"oa":1,"article_processing_charge":"No","conference":{"end_date":"2022-04-06","location":"Seoul, Republic of Korea","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","start_date":"2022-04-02"},"status":"public","acknowledgement":"We would like to thank the anonymous reviewers for their useful comments. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-04-02T00:00:00Z","author":[{"last_name":"Postnikova","full_name":"Postnikova, Anastasiia","first_name":"Anastasiia"},{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","full_name":"Koval, Nikita","first_name":"Nikita"},{"first_name":"Giorgi","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"external_id":{"isi":["000883318200025"],"arxiv":["2109.00657"]},"language":[{"iso":"eng"}],"page":"353-367","publication":"Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","year":"2022","isi":1,"publication_identifier":{"isbn":["9781450392044"]},"ec_funded":1,"_id":"11180","title":"Multi-queues can be state-of-the-art priority schedulers","department":[{"_id":"DaAl"}],"date_updated":"2025-04-14T07:49:13Z","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.00657"}],"month":"04","project":[{"call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"type":"conference","publication_status":"published","publisher":"Association for Computing Machinery","oa_version":"Preprint"},{"publication_identifier":{"isbn":["9781450392044"]},"isi":1,"_id":"11181","title":"PathCAS: An efficient middle ground for concurrent search data structures","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"DaAl"}],"date_updated":"2024-10-09T21:02:23Z","month":"04","oa_version":"Published Version","publisher":"Association for Computing Machinery","publication_status":"published","type":"conference","corr_author":"1","day":"02","citation":{"ama":"Brown TA, Sigouin W, Alistarh D-A. PathCAS: An efficient middle ground for concurrent search data structures. In: <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2022:385-399. doi:<a href=\"https://doi.org/10.1145/3503221.3508410\">10.1145/3503221.3508410</a>","ieee":"T. A. Brown, W. Sigouin, and D.-A. Alistarh, “PathCAS: An efficient middle ground for concurrent search data structures,” in <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Seoul, Republic of Korea, 2022, pp. 385–399.","short":"T.A. Brown, W. Sigouin, D.-A. Alistarh, in:, Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2022, pp. 385–399.","ista":"Brown TA, Sigouin W, Alistarh D-A. 2022. PathCAS: An efficient middle ground for concurrent search data structures. Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 385–399.","apa":"Brown, T. A., Sigouin, W., &#38; Alistarh, D.-A. (2022). PathCAS: An efficient middle ground for concurrent search data structures. In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 385–399). Seoul, Republic of Korea: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3503221.3508410\">https://doi.org/10.1145/3503221.3508410</a>","chicago":"Brown, Trevor A, William Sigouin, and Dan-Adrian Alistarh. “PathCAS: An Efficient Middle Ground for Concurrent Search Data Structures.” In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 385–99. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3503221.3508410\">https://doi.org/10.1145/3503221.3508410</a>.","mla":"Brown, Trevor A., et al. “PathCAS: An Efficient Middle Ground for Concurrent Search Data Structures.” <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2022, pp. 385–99, doi:<a href=\"https://doi.org/10.1145/3503221.3508410\">10.1145/3503221.3508410</a>."},"date_created":"2022-04-17T22:01:46Z","quality_controlled":"1","scopus_import":"1","doi":"10.1145/3503221.3508410","oa":1,"file_date_updated":"2022-08-05T09:19:29Z","ddc":["000"],"abstract":[{"lang":"eng","text":"To maximize the performance of concurrent data structures, researchers have often turned to highly complex fine-grained techniques, resulting in efficient and elegant algorithms, which can however be often difficult to understand and prove correct. While simpler techniques exist, such as transactional memory, they can have limited performance or portability relative to their fine-grained counterparts. Approaches at both ends of this complexity-performance spectrum have been extensively explored, but relatively less is known about the middle ground: approaches that are willing to sacrifice some performance for simplicity, while remaining competitive with state-of-the-art handcrafted designs. In this paper, we explore this middle ground, and present PathCAS, a primitive that combines ideas from multi-word CAS (KCAS) and transactional memory approaches, while carefully avoiding overhead. We show how PathCAS can be used to implement efficient search data structures relatively simply, using an internal binary search tree as an example, then extending this to an AVL tree. Our best implementations outperform many handcrafted search trees: in search-heavy workloads, it rivals the BCCO tree [5], the fastest known concurrent binary tree in terms of search performance [3]. Our results suggest that PathCAS can yield concurrent data structures that are relatively easy to build and prove correct, while offering surprisingly high performance."}],"has_accepted_license":"1","conference":{"end_date":"2022-04-06","location":"Seoul, Republic of Korea","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","start_date":"2022-04-02"},"article_processing_charge":"No","acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Collaborative Research and Development grant: CRDPJ 539431-19, the\r\nCanada Foundation for Innovation John R. Evans Leaders Fund with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512, Waterloo Huawei Joint Innovation Lab project “Scalable Infrastructure for Next Generation Data Management Systems”, NSERC Discovery Launch Supplement: DGECR-2019-00048, NSERC Discovery\r\nProgram under the grants: RGPIN-2019-04227 and RGPIN04512-2018, and the University of Waterloo. We would also like to thank the reviewers for their insightful comments.","status":"public","author":[{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Trevor A","first_name":"Trevor A"},{"last_name":"Sigouin","full_name":"Sigouin, William","first_name":"William"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"external_id":{"isi":["000883318200027"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-04-02T00:00:00Z","file":[{"date_updated":"2022-08-05T09:19:29Z","relation":"main_file","creator":"dernst","file_id":"11731","file_size":1128343,"success":1,"file_name":"2022_PPoPP_Brown.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2022-08-05T09:19:29Z","checksum":"8ceea411fa133795cd4903529498eb6b"}],"publication":"Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","language":[{"iso":"eng"}],"page":"385-399","year":"2022"}]