[{"citation":{"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.","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>","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.","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).","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>.","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>."},"day":"08","file_date_updated":"2022-05-02T08:48:00Z","ddc":["570"],"month":"04","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","file_size":2637590,"creator":"dernst","file_name":"2022_NatureCommunications_Gauto.pdf","content_type":"application/pdf","checksum":"db61d5534e988743d6266d3675d77b08","access_level":"open_access","date_updated":"2022-05-02T08:48:00Z","success":1,"date_created":"2022-05-02T08:48:00Z","file_id":"11348"}],"has_accepted_license":"1","article_processing_charge":"No","volume":13,"title":"Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR","author":[{"last_name":"Gauto","full_name":"Gauto, Diego F.","first_name":"Diego F."},{"first_name":"Pavel","last_name":"Macek","full_name":"Macek, Pavel"},{"first_name":"Duccio","full_name":"Malinverni, Duccio","last_name":"Malinverni"},{"last_name":"Fraga","full_name":"Fraga, Hugo","first_name":"Hugo"},{"last_name":"Paloni","full_name":"Paloni, Matteo","first_name":"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"},{"full_name":"Barducci, Alessandro","last_name":"Barducci","first_name":"Alessandro"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"}],"_id":"11179","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."}],"doi":"10.1038/s41467-022-29423-0","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","status":"public","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.).","department":[{"_id":"PaSc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000781498700009"]},"date_published":"2022-04-08T00:00:00Z","date_created":"2022-04-17T22:01:45Z","scopus_import":"1","publisher":"Springer Nature","intvolume":"        13","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"oa":1,"year":"2022","publication":"Nature Communications","date_updated":"2023-08-03T06:54:56Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31243-1","relation":"erratum"}]},"article_number":"1927","article_type":"original"},{"status":"public","publication_status":"published","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).","ec_funded":1,"publication_identifier":{"isbn":["9781450392044"]},"project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","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."}],"doi":"10.1145/3503221.3508432","author":[{"first_name":"Anastasiia","full_name":"Postnikova, Anastasiia","last_name":"Postnikova"},{"first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","full_name":"Koval, Nikita"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"title":"Multi-queues can be state-of-the-art priority schedulers","_id":"11180","article_processing_charge":"No","arxiv":1,"conference":{"end_date":"2022-04-06","start_date":"2022-04-02","location":"Seoul, Republic of Korea","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"oa_version":"Preprint","day":"02","citation":{"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.","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>","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.","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>."},"month":"04","related_material":{"record":[{"id":"13076","status":"public","relation":"research_data"}]},"page":"353-367","publication":"Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","date_updated":"2023-08-03T06:48:35Z","year":"2022","oa":1,"isi":1,"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.00657"}],"publisher":"Association for Computing Machinery","date_published":"2022-04-02T00:00:00Z","external_id":{"isi":["000883318200025"],"arxiv":["2109.00657"]},"scopus_import":"1","date_created":"2022-04-17T22:01:46Z","department":[{"_id":"DaAl"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"_id":"11181","author":[{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","full_name":"Brown, Trevor A","last_name":"Brown"},{"full_name":"Sigouin, William","last_name":"Sigouin","first_name":"William"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"title":"PathCAS: An efficient middle ground for concurrent search data structures","doi":"10.1145/3503221.3508410","abstract":[{"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.","lang":"eng"}],"publication_identifier":{"isbn":["9781450392044"]},"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","publication_status":"published","month":"04","ddc":["000"],"file_date_updated":"2022-08-05T09:19:29Z","day":"02","citation":{"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>.","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>","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.","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.","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>"},"conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","end_date":"2022-04-06","start_date":"2022-04-02","location":"Seoul, Republic of Korea"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"11731","date_created":"2022-08-05T09:19:29Z","file_name":"2022_PPoPP_Brown.pdf","relation":"main_file","file_size":1128343,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"8ceea411fa133795cd4903529498eb6b","success":1,"date_updated":"2022-08-05T09:19:29Z"}],"article_processing_charge":"No","has_accepted_license":"1","oa":1,"year":"2022","date_updated":"2023-08-03T06:49:20Z","publication":"Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","page":"385-399","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"DaAl"}],"scopus_import":"1","date_created":"2022-04-17T22:01:46Z","date_published":"2022-04-02T00:00:00Z","external_id":{"isi":["000883318200027"]},"publisher":"Association for Computing Machinery","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1},{"article_processing_charge":"No","volume":217,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2022_LIPICs_Nikabadi.pdf","relation":"main_file","creator":"dernst","file_size":790396,"access_level":"open_access","content_type":"application/pdf","checksum":"626551c14de5d4091573200ed0535752","success":1,"date_updated":"2022-05-02T07:53:00Z","file_id":"11345","date_created":"2022-05-02T07:53:00Z"}],"conference":{"location":"Strasbourg, France","start_date":"2021-12-13","end_date":"2021-12-15","name":"OPODIS"},"oa_version":"Published Version","file_date_updated":"2022-05-02T07:53:00Z","month":"02","ddc":["510"],"day":"01","citation":{"short":"A. Nikabadi, J. Korhonen, in:, Q. Bramas, V. Gramoli, A. Milani (Eds.), 25th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","ama":"Nikabadi A, Korhonen J. Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. In: Bramas Q, Gramoli V, Milani A, eds. <i>25th International Conference on Principles of Distributed Systems</i>. Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">10.4230/LIPIcs.OPODIS.2021.15</a>","ista":"Nikabadi A, Korhonen J. 2022. Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. 25th International Conference on Principles of Distributed Systems. OPODIS, LIPIcs, vol. 217, 15.","apa":"Nikabadi, A., &#38; Korhonen, J. (2022). Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. In Q. Bramas, V. Gramoli, &#38; A. Milani (Eds.), <i>25th International Conference on Principles of Distributed Systems</i> (Vol. 217). Strasbourg, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.15</a>","ieee":"A. Nikabadi and J. Korhonen, “Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters,” in <i>25th International Conference on Principles of Distributed Systems</i>, Strasbourg, France, 2022, vol. 217.","chicago":"Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection: Induced Subgraphs, Multicolored Problems and Graph Parameters.” In <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas, Vincent Gramoli, and Alessia Milani, Vol. 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.15</a>.","mla":"Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection: Induced Subgraphs, Multicolored Problems and Graph Parameters.” <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas et al., vol. 217, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">10.4230/LIPIcs.OPODIS.2021.15</a>."},"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"Amir Nikabadi: Supported by the LABEX MILYON (ANR-10-LABX-0070) of Université de Lyon, within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR). Janne H. Korhonen: Supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).\r\nWe thank François Le Gall and Masayuki Miyamoto for sharing their work on lower bounds for induced subgraph detection [36].","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"publication_identifier":{"isbn":["9783959772198"],"issn":["1868-8969"]},"doi":"10.4230/LIPIcs.OPODIS.2021.15","abstract":[{"lang":"eng","text":"Subgraph detection has recently been one of the most studied problems in the CONGEST model of distributed computing. In this work, we study the distributed complexity of problems closely related to subgraph detection, mainly focusing on induced subgraph detection. The main line of this work presents lower bounds and parameterized algorithms w.r.t structural parameters of the input graph:\r\n- On general graphs, we give unconditional lower bounds for induced detection of cycles and patterns of treewidth 2 in CONGEST. Moreover, by adapting reductions from centralized parameterized complexity, we prove lower bounds in CONGEST for detecting patterns with a 4-clique, and for induced path detection conditional on the hardness of triangle detection in the congested clique.\r\n- On graphs of bounded degeneracy, we show that induced paths can be detected fast in CONGEST using techniques from parameterized algorithms, while detecting cycles and patterns of treewidth 2 is hard.\r\n- On graphs of bounded vertex cover number, we show that induced subgraph detection is easy in CONGEST for any pattern graph. More specifically, we adapt a centralized parameterized algorithm for a more general maximum common induced subgraph detection problem to the distributed setting. In addition to these induced subgraph detection results, we study various related problems in the CONGEST and congested clique models, including for multicolored versions of subgraph-detection-like problems."}],"editor":[{"last_name":"Bramas","full_name":"Bramas, Quentin","first_name":"Quentin"},{"last_name":"Gramoli","full_name":"Gramoli, Vincent","first_name":"Vincent"},{"last_name":"Milani","full_name":"Milani, Alessia","first_name":"Alessia"}],"_id":"11183","author":[{"first_name":"Amir","full_name":"Nikabadi, Amir","last_name":"Nikabadi"},{"first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","last_name":"Korhonen","full_name":"Korhonen, Janne"}],"title":"Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"intvolume":"       217","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","scopus_import":"1","date_created":"2022-04-17T22:01:47Z","date_published":"2022-02-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaAl"}],"article_number":"15","date_updated":"2022-05-02T07:56:35Z","publication":"25th International Conference on Principles of Distributed Systems","alternative_title":["LIPIcs"],"year":"2022","oa":1},{"has_accepted_license":"1","article_processing_charge":"No","volume":217,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"creator":"dernst","relation":"main_file","file_size":959406,"file_name":"2022_LIPICs_Alistarh.pdf","checksum":"2c7c982174c6f98c4ca6e92539d15086","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-05-02T08:06:33Z","success":1,"date_created":"2022-05-02T08:06:33Z","file_id":"11346"}],"conference":{"end_date":"2021-12-15","location":"Strasbourg, France","start_date":"2021-12-13","name":"OPODIS"},"oa_version":"Published Version","day":"01","citation":{"ista":"Alistarh D-A, Gelashvili R, Rybicki J. 2022. Fast graphical population protocols. 25th International Conference on Principles of Distributed Systems. OPODIS, LIPIcs, vol. 217, 14.","ama":"Alistarh D-A, Gelashvili R, Rybicki J. Fast graphical population protocols. In: Bramas Q, Gramoli V, Milani A, eds. <i>25th International Conference on Principles of Distributed Systems</i>. Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">10.4230/LIPIcs.OPODIS.2021.14</a>","short":"D.-A. Alistarh, R. Gelashvili, J. Rybicki, in:, Q. Bramas, V. Gramoli, A. Milani (Eds.), 25th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","ieee":"D.-A. Alistarh, R. Gelashvili, and J. Rybicki, “Fast graphical population protocols,” in <i>25th International Conference on Principles of Distributed Systems</i>, Strasbourg, France, 2022, vol. 217.","apa":"Alistarh, D.-A., Gelashvili, R., &#38; Rybicki, J. (2022). Fast graphical population protocols. In Q. Bramas, V. Gramoli, &#38; A. Milani (Eds.), <i>25th International Conference on Principles of Distributed Systems</i> (Vol. 217). Strasbourg, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.14</a>","mla":"Alistarh, Dan-Adrian, et al. “Fast Graphical Population Protocols.” <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas et al., vol. 217, 14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">10.4230/LIPIcs.OPODIS.2021.14</a>.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Joel Rybicki. “Fast Graphical Population Protocols.” In <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas, Vincent Gramoli, and Alessia Milani, Vol. 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.14</a>."},"month":"02","file_date_updated":"2022-05-02T08:06:33Z","ddc":["510"],"status":"public","acknowledgement":"Dan Alistarh: This project has received funding from the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (grant agreement No.805223 ScaleML).\r\nJoel Rybicki: This project has received from the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie grant agreement No. 840605.\r\nAcknowledgements We grateful to Giorgi Nadiradze for pointing out a generalisation of the phase clock construction to non-regular graphs. We also thank anonymous reviewers for their useful comments on earlier versions of this manuscript.","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772198"]},"project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"},{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605","name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"Let G be a graph on n nodes. In the stochastic population protocol model, a collection of n indistinguishable, resource-limited nodes collectively solve tasks via pairwise interactions. In each interaction, two randomly chosen neighbors first read each other’s states, and then update their local states. A rich line of research has established tight upper and lower bounds on the complexity of fundamental tasks, such as majority and leader election, in this model, when G is a clique. Specifically, in the clique, these tasks can be solved fast, i.e., in n polylog n pairwise interactions, with high probability, using at most polylog n states per node.\r\nIn this work, we consider the more general setting where G is an arbitrary regular graph, and present a technique for simulating protocols designed for fully-connected networks in any connected regular graph. Our main result is a simulation that is efficient on many interesting graph families: roughly, the simulation overhead is polylogarithmic in the number of nodes, and quadratic in the conductance of the graph. As a sample application, we show that, in any regular graph with conductance φ, both leader election and exact majority can be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability, using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast and space-efficient population protocols for leader election and exact majority on graphs with good expansion properties. We believe our results will prove generally useful, as they allow efficient technology transfer between the well-mixed (clique) case, and the under-explored spatial setting."}],"doi":"10.4230/LIPIcs.OPODIS.2021.14","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"},{"full_name":"Rybicki, Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","orcid":"0000-0002-6432-6646"}],"title":"Fast graphical population protocols","_id":"11184","editor":[{"first_name":"Quentin","full_name":"Bramas, Quentin","last_name":"Bramas"},{"full_name":"Gramoli, Vincent","last_name":"Gramoli","first_name":"Vincent"},{"first_name":"Alessia","last_name":"Milani","full_name":"Milani, Alessia"}],"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       217","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","external_id":{"arxiv":["2102.08808"]},"date_published":"2022-02-01T00:00:00Z","scopus_import":"1","date_created":"2022-04-17T22:01:47Z","department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"14","publication":"25th International Conference on Principles of Distributed Systems","date_updated":"2022-05-02T08:09:39Z","alternative_title":["LIPIcs"],"year":"2022","oa":1},{"author":[{"orcid":"0000-0003-2401-8670","first_name":"Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M"},{"last_name":"Felsner","full_name":"Felsner, Stefan","first_name":"Stefan"}],"title":"Approximating the bundled crossing number","_id":"11185","abstract":[{"lang":"eng","text":"Bundling crossings is a strategy which can enhance the readability of graph drawings. In this paper we consider bundlings for families of pseudosegments, i.e., simple curves such that any two have share at most one point at which they cross. Our main result is that there is a polynomial-time algorithm to compute an 8-approximation of the bundled crossing number of such instances (up to adding a term depending on the facial structure). This 8-approximation also holds for bundlings of good drawings of graphs. In the special case of circular drawings the approximation factor is 8 (no extra term), this improves upon the 10-approximation of Fink et al. [6]. We also show how to compute a 92-approximation when the intersection graph of the pseudosegments is bipartite."}],"doi":"10.1007/978-3-030-96731-4_31","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030967307"],"eissn":["1611-3349"]},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"status":"public","acknowledgement":"This work was initiated during the Workshop on Geometric Graphs in November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during the workshop. The first author has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie grant agreement No 754411. The second author has been supported by the German Research Foundation DFG Project FE 340/12-1.","publication_status":"published","ec_funded":1,"day":"16","citation":{"ieee":"A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,” in <i>WALCOM 2022: Algorithms and Computation</i>, Jember, Indonesia, 2022, vol. 13174, pp. 383–395.","apa":"Arroyo Guevara, A. M., &#38; Felsner, S. (2022). Approximating the bundled crossing number. In <i>WALCOM 2022: Algorithms and Computation</i> (Vol. 13174, pp. 383–395). Jember, Indonesia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">https://doi.org/10.1007/978-3-030-96731-4_31</a>","short":"A.M. Arroyo Guevara, S. Felsner, in:, WALCOM 2022: Algorithms and Computation, Springer Nature, 2022, pp. 383–395.","ista":"Arroyo Guevara AM, Felsner S. 2022. Approximating the bundled crossing number. WALCOM 2022: Algorithms and Computation. WALCOM: Algorithms and ComputationLNCS vol. 13174, 383–395.","ama":"Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. In: <i>WALCOM 2022: Algorithms and Computation</i>. Vol 13174. LNCS. Springer Nature; 2022:383-395. doi:<a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">10.1007/978-3-030-96731-4_31</a>","mla":"Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing Number.” <i>WALCOM 2022: Algorithms and Computation</i>, vol. 13174, Springer Nature, 2022, pp. 383–95, doi:<a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">10.1007/978-3-030-96731-4_31</a>.","chicago":"Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled Crossing Number.” In <i>WALCOM 2022: Algorithms and Computation</i>, 13174:383–95. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">https://doi.org/10.1007/978-3-030-96731-4_31</a>."},"month":"03","conference":{"name":"WALCOM: Algorithms and Computation","end_date":"2022-03-26","location":"Jember, Indonesia","start_date":"2022-03-24"},"oa_version":"Preprint","arxiv":1,"volume":13174,"article_processing_charge":"No","oa":1,"year":"2022","publication":"WALCOM 2022: Algorithms and Computation","date_updated":"2023-09-25T10:56:10Z","related_material":{"record":[{"id":"13969","relation":"later_version","status":"public"}]},"page":"383-395","department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2109.14892"]},"date_published":"2022-03-16T00:00:00Z","scopus_import":"1","date_created":"2022-04-17T22:01:47Z","series_title":"LNCS","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.14892"}],"intvolume":"     13174","publisher":"Springer Nature","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}]},{"scopus_import":"1","date_created":"2022-04-17T22:01:48Z","external_id":{"arxiv":["2106.11932"],"isi":["000779920900001"]},"date_published":"2022-08-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaKw"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"intvolume":"        54","publisher":"Wiley","year":"2022","oa":1,"article_type":"original","page":"1420-1438","date_updated":"2023-08-03T06:47:29Z","publication":"Bulletin of the London Mathematical Society","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2023-02-03T09:43:38Z","month":"08","ddc":["510"],"day":"01","citation":{"ama":"Kwan MA, Sah A, Sawhney M. Large deviations in random latin squares. <i>Bulletin of the London Mathematical Society</i>. 2022;54(4):1420-1438. doi:<a href=\"https://doi.org/10.1112/blms.12638\">10.1112/blms.12638</a>","short":"M.A. Kwan, A. Sah, M. Sawhney, Bulletin of the London Mathematical Society 54 (2022) 1420–1438.","ista":"Kwan MA, Sah A, Sawhney M. 2022. Large deviations in random latin squares. Bulletin of the London Mathematical Society. 54(4), 1420–1438.","ieee":"M. A. Kwan, A. Sah, and M. Sawhney, “Large deviations in random latin squares,” <i>Bulletin of the London Mathematical Society</i>, vol. 54, no. 4. Wiley, pp. 1420–1438, 2022.","apa":"Kwan, M. A., Sah, A., &#38; Sawhney, M. (2022). Large deviations in random latin squares. <i>Bulletin of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/blms.12638\">https://doi.org/10.1112/blms.12638</a>","mla":"Kwan, Matthew Alan, et al. “Large Deviations in Random Latin Squares.” <i>Bulletin of the London Mathematical Society</i>, vol. 54, no. 4, Wiley, 2022, pp. 1420–38, doi:<a href=\"https://doi.org/10.1112/blms.12638\">10.1112/blms.12638</a>.","chicago":"Kwan, Matthew Alan, Ashwin Sah, and Mehtaab Sawhney. “Large Deviations in Random Latin Squares.” <i>Bulletin of the London Mathematical Society</i>. Wiley, 2022. <a href=\"https://doi.org/10.1112/blms.12638\">https://doi.org/10.1112/blms.12638</a>."},"article_processing_charge":"No","volume":54,"has_accepted_license":"1","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"date_updated":"2023-02-03T09:43:38Z","success":1,"checksum":"02d74e7ae955ba3c808e2a8aebe6ef98","content_type":"application/pdf","access_level":"open_access","file_size":233758,"relation":"main_file","creator":"dernst","file_name":"2022_BulletinMathSociety_Kwan.pdf","date_created":"2023-02-03T09:43:38Z","file_id":"12499"}],"arxiv":1,"doi":"10.1112/blms.12638","issue":"4","abstract":[{"text":"In this note, we study large deviations of the number  𝐍  of intercalates ( 2×2  combinatorial subsquares which are themselves Latin squares) in a random  𝑛×𝑛  Latin square. In particular, for constant  𝛿>0  we prove that  exp(−𝑂(𝑛2log𝑛))⩽Pr(𝐍⩽(1−𝛿)𝑛2/4)⩽exp(−Ω(𝑛2))  and  exp(−𝑂(𝑛4/3(log𝑛)))⩽Pr(𝐍⩾(1+𝛿)𝑛2/4)⩽exp(−Ω(𝑛4/3(log𝑛)2/3)) . As a consequence, we deduce that a typical order- 𝑛  Latin square has  (1+𝑜(1))𝑛2/4  intercalates, matching a lower bound due to Kwan and Sudakov and resolving an old conjecture of McKay and Wanless.","lang":"eng"}],"_id":"11186","author":[{"orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","full_name":"Kwan, Matthew Alan"},{"first_name":"Ashwin","full_name":"Sah, Ashwin","last_name":"Sah"},{"full_name":"Sawhney, Mehtaab","last_name":"Sawhney","first_name":"Mehtaab"}],"title":"Large deviations in random latin squares","publication_status":"published","acknowledgement":"We thank Zach Hunter for pointing out some important typographical errors. We also thank the referee for several remarks which helped improve the paper substantially.\r\nKwan was supported by NSF grant DMS-1953990. Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-1745302.","status":"public","publication_identifier":{"eissn":["1469-2120"],"issn":["0024-6093"]}},{"scopus_import":"1","date_created":"2022-04-17T22:01:48Z","date_published":"2022-04-08T00:00:00Z","external_id":{"pmid":["35396471"],"isi":["000781199600011"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"FyKo"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"intvolume":"        19","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-022-01444-z"}],"publisher":"Springer Nature","year":"2022","oa":1,"article_type":"letter_note","page":"374-380","date_updated":"2023-08-03T06:46:09Z","publication":"Nature Methods","oa_version":"Published Version","pmid":1,"month":"04","day":"08","citation":{"mla":"Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” <i>Nature Methods</i>, vol. 19, no. 4, Springer Nature, 2022, pp. 374–80, doi:<a href=\"https://doi.org/10.1038/s41592-022-01444-z\">10.1038/s41592-022-01444-z</a>.","chicago":"Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” <i>Nature Methods</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41592-022-01444-z\">https://doi.org/10.1038/s41592-022-01444-z</a>.","ieee":"S. Knyazev <i>et al.</i>, “Unlocking capacities of genomics for the COVID-19 response and future pandemics,” <i>Nature Methods</i>, vol. 19, no. 4. Springer Nature, pp. 374–380, 2022.","apa":"Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-022-01444-z\">https://doi.org/10.1038/s41592-022-01444-z</a>","ista":"Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19(4), 374–380.","ama":"Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for the COVID-19 response and future pandemics. <i>Nature Methods</i>. 2022;19(4):374-380. doi:<a href=\"https://doi.org/10.1038/s41592-022-01444-z\">10.1038/s41592-022-01444-z</a>","short":"S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan, D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O. Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak, S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E. Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky, R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380."},"volume":19,"article_processing_charge":"No","doi":"10.1038/s41592-022-01444-z","issue":"4","abstract":[{"lang":"eng","text":"During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing."}],"_id":"11187","author":[{"full_name":"Knyazev, Sergey","last_name":"Knyazev","first_name":"Sergey"},{"first_name":"Karishma","full_name":"Chhugani, Karishma","last_name":"Chhugani"},{"first_name":"Varuni","full_name":"Sarwal, Varuni","last_name":"Sarwal"},{"first_name":"Ram","full_name":"Ayyala, Ram","last_name":"Ayyala"},{"full_name":"Singh, Harman","last_name":"Singh","first_name":"Harman"},{"full_name":"Karthikeyan, Smruthi","last_name":"Karthikeyan","first_name":"Smruthi"},{"last_name":"Deshpande","full_name":"Deshpande, Dhrithi","first_name":"Dhrithi"},{"first_name":"Pelin Icer","last_name":"Baykal","full_name":"Baykal, Pelin Icer"},{"full_name":"Comarova, Zoia","last_name":"Comarova","first_name":"Zoia"},{"full_name":"Lu, Angela","last_name":"Lu","first_name":"Angela"},{"full_name":"Porozov, Yuri","last_name":"Porozov","first_name":"Yuri"},{"first_name":"Tetyana I.","last_name":"Vasylyeva","full_name":"Vasylyeva, Tetyana I."},{"full_name":"Wertheim, Joel O.","last_name":"Wertheim","first_name":"Joel O."},{"full_name":"Tierney, Braden T.","last_name":"Tierney","first_name":"Braden T."},{"full_name":"Chiu, Charles Y.","last_name":"Chiu","first_name":"Charles Y."},{"first_name":"Ren","full_name":"Sun, Ren","last_name":"Sun"},{"first_name":"Aiping","full_name":"Wu, Aiping","last_name":"Wu"},{"last_name":"Abedalthagafi","full_name":"Abedalthagafi, Malak S.","first_name":"Malak S."},{"first_name":"Victoria M.","full_name":"Pak, Victoria M.","last_name":"Pak"},{"first_name":"Shivashankar H.","full_name":"Nagaraj, Shivashankar H.","last_name":"Nagaraj"},{"first_name":"Adam L.","full_name":"Smith, Adam L.","last_name":"Smith"},{"first_name":"Pavel","last_name":"Skums","full_name":"Skums, Pavel"},{"first_name":"Bogdan","last_name":"Pasaniuc","full_name":"Pasaniuc, Bogdan"},{"last_name":"Komissarov","full_name":"Komissarov, Andrey","first_name":"Andrey"},{"first_name":"Christopher E.","last_name":"Mason","full_name":"Mason, Christopher E."},{"first_name":"Eric","last_name":"Bortz","full_name":"Bortz, Eric"},{"full_name":"Lemey, Philippe","last_name":"Lemey","first_name":"Philippe"},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694"},{"last_name":"Beerenwinkel","full_name":"Beerenwinkel, Niko","first_name":"Niko"},{"first_name":"Tommy Tsan Yuk","last_name":"Lam","full_name":"Lam, Tommy Tsan Yuk"},{"last_name":"Wu","full_name":"Wu, Nicholas C.","first_name":"Nicholas C."},{"last_name":"Zelikovsky","full_name":"Zelikovsky, Alex","first_name":"Alex"},{"last_name":"Knight","full_name":"Knight, Rob","first_name":"Rob"},{"first_name":"Keith A.","last_name":"Crandall","full_name":"Crandall, Keith A."},{"last_name":"Mangul","full_name":"Mangul, Serghei","first_name":"Serghei"}],"title":"Unlocking capacities of genomics for the COVID-19 response and future pandemics","ec_funded":1,"acknowledgement":"Our paper is dedicated to all freedom-loving people around the world, and to the people of Ukraine who fight for our freedom. We thank William M. Switzer and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions. We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially supported by National Science Foundation grants 2041984. T.L. is supported by the NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund (R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828. M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W. was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S. acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly supported by Molecular Basis of Disease at Georgia State University and NIH awards R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread. J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases (NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V. is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers “Digital biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395) and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the California Department of Public Health, the Innovative Genomics Institute (IGI) at the University of California, Berkeley, and University of California, San Francisco, NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project 206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C. acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported by an ERC Consolidator grant to F.K. (771209–CharFL).","publication_status":"published","status":"public","project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales"}],"publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]}},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"date_created":"2022-04-20T08:59:07Z","acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2022-04-20T00:00:00Z","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","oa":1,"year":"2022","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-19T10:15:54Z","page":"170","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10614"},{"relation":"part_of_dissertation","status":"public","id":"544"}]},"ddc":["570"],"month":"04","file_date_updated":"2023-04-21T22:30:03Z","citation":{"mla":"Wachner, Stephanie. <i>Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>.","chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>.","ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022.","apa":"Wachner, S. (2022). <i>Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>","ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022.","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria."},"day":"20","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"999ab16884c4522486136ebc5ae8dbff","date_updated":"2023-04-21T22:30:03Z","file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","creator":"cchlebak","file_size":8820951,"relation":"main_file","embargo":"2023-04-20","file_id":"11195","date_created":"2022-04-20T09:03:57Z"},{"date_updated":"2023-04-21T22:30:03Z","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"fd92b1e38d53bdf8b458213882d41383","file_name":"Thesis_Stephanie_Wachner_20200414.zip","relation":"source_file","file_size":65864612,"creator":"cchlebak","file_id":"11329","date_created":"2022-04-22T12:41:00Z","embargo_to":"open_access"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","_id":"11193","supervisor":[{"orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"}],"title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","author":[{"first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner","full_name":"Wachner, Stephanie"}],"doi":"10.15479/at:ista:11193","abstract":[{"text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis.","lang":"eng"}],"project":[{"_id":"26199CA4-B435-11E9-9278-68D0E5697425","grant_number":"24800","name":"Tissue barrier penetration is crucial for immunity and metastasis"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","status":"public"},{"ec_funded":1,"publication_status":"published","status":"public","project":[{"call_identifier":"H2020","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","grant_number":"708497","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425"},{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"grant_number":"W01205","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:11196","abstract":[{"text":"One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n","lang":"eng"}],"_id":"11196","author":[{"full_name":"Kim, Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena"}],"title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","supervisor":[{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas"}],"article_processing_charge":"No","has_accepted_license":"1","file":[{"file_id":"11220","date_created":"2022-04-20T14:21:56Z","access_level":"open_access","checksum":"1616a8bf6f13a57c892dac873dcd0936","content_type":"application/pdf","date_updated":"2023-04-20T22:30:03Z","file_name":"Olena_KIM_thesis_final.pdf","file_size":21273537,"creator":"okim","relation":"main_file","embargo":"2023-04-19"},{"file_id":"11221","date_created":"2022-04-20T14:22:56Z","embargo_to":"open_access","file_name":"KIM_thesis_final.zip","creator":"okim","relation":"source_file","file_size":59248569,"date_updated":"2023-04-20T22:30:03Z","access_level":"closed","checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","content_type":"application/x-zip-compressed"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"degree_awarded":"PhD","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ddc":["570"],"file_date_updated":"2023-04-20T22:30:03Z","month":"04","day":"20","citation":{"mla":"Kim, Olena. <i>Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11196\">10.15479/at:ista:11196</a>.","chicago":"Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11196\">https://doi.org/10.15479/at:ista:11196</a>.","ista":"Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria.","short":"O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022.","ama":"Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11196\">10.15479/at:ista:11196</a>","apa":"Kim, O. (2022). <i>Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11196\">https://doi.org/10.15479/at:ista:11196</a>","ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022."},"page":"132","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11222"},{"id":"7473","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-08-18T06:31:52Z","alternative_title":["ISTA Thesis"],"year":"2022","oa":1,"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"date_created":"2022-04-20T09:47:12Z","date_published":"2022-04-20T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"PeJo"},{"_id":"GradSch"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2022-04-22T09:39:03Z","file_id":"11326","creator":"larathoo","file_size":13260571,"relation":"main_file","file_name":"Data_Code.zip","date_updated":"2022-04-22T09:39:03Z","success":1,"content_type":"application/x-zip-compressed","checksum":"96c1b86cdf25481f2a52972fcc45ca7f","access_level":"open_access"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","contributor":[{"first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","contributor_type":"project_member"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","orcid":"0000-0002-7354-8574","contributor_type":"project_member"},{"last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","contributor_type":"project_member"},{"contributor_type":"project_member","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","contributor_type":"project_member"}],"type":"research_data","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"day":"28","citation":{"apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11321\">https://doi.org/10.15479/at:ista:11321</a>","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022).","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11321\">https://doi.org/10.15479/at:ista:11321</a>.","mla":"Surendranadh, Parvathy, et al. <i>Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>."},"month":"04","file_date_updated":"2022-04-22T09:39:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_published":"2022-04-28T00:00:00Z","oa_version":"Published Version","date_created":"2022-04-22T09:42:24Z","date_updated":"2024-02-21T12:41:09Z","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11411"},{"status":"public","relation":"earlier_version","id":"9192"},{"status":"public","relation":"earlier_version","id":"8254"}]},"author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh"},{"orcid":"0000-0003-1771-714X","last_name":"Arathoon","full_name":"Arathoon, Louise S","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7354-8574","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","full_name":"Baskett, Carina"},{"full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}],"oa":1,"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","_id":"11321","year":"2022","abstract":[{"text":"Here are the research data underlying the publication \"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus\" Further information are summed up in the README document. ","lang":"eng"}],"doi":"10.15479/at:ista:11321"},{"oa_version":"Published Version","month":"04","file_date_updated":"2022-04-29T11:24:23Z","ddc":["510","530"],"day":"08","citation":{"chicago":"Wirth, Melchior. “A Dual Formula for the Noncommutative Transport Distance.” <i>Journal of Statistical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10955-022-02911-9\">https://doi.org/10.1007/s10955-022-02911-9</a>.","mla":"Wirth, Melchior. “A Dual Formula for the Noncommutative Transport Distance.” <i>Journal of Statistical Physics</i>, vol. 187, no. 2, 19, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10955-022-02911-9\">10.1007/s10955-022-02911-9</a>.","ama":"Wirth M. A dual formula for the noncommutative transport distance. <i>Journal of Statistical Physics</i>. 2022;187(2). doi:<a href=\"https://doi.org/10.1007/s10955-022-02911-9\">10.1007/s10955-022-02911-9</a>","ista":"Wirth M. 2022. A dual formula for the noncommutative transport distance. Journal of Statistical Physics. 187(2), 19.","short":"M. Wirth, Journal of Statistical Physics 187 (2022).","ieee":"M. Wirth, “A dual formula for the noncommutative transport distance,” <i>Journal of Statistical Physics</i>, vol. 187, no. 2. Springer Nature, 2022.","apa":"Wirth, M. (2022). A dual formula for the noncommutative transport distance. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-022-02911-9\">https://doi.org/10.1007/s10955-022-02911-9</a>"},"volume":187,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"11338","date_created":"2022-04-29T11:24:23Z","access_level":"open_access","checksum":"f3e0b00884b7dde31347a3756788b473","content_type":"application/pdf","success":1,"date_updated":"2022-04-29T11:24:23Z","file_name":"2022_JourStatisticalPhysics_Wirth.pdf","relation":"main_file","creator":"dernst","file_size":362119}],"doi":"10.1007/s10955-022-02911-9","issue":"2","abstract":[{"lang":"eng","text":"In this article we study the noncommutative transport distance introduced by Carlen and Maas and its entropic regularization defined by Becker and Li. We prove a duality formula that can be understood as a quantum version of the dual Benamou–Brenier formulation of the Wasserstein distance in terms of subsolutions of a Hamilton–Jacobi–Bellmann equation."}],"_id":"11330","author":[{"full_name":"Wirth, Melchior","last_name":"Wirth","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","first_name":"Melchior","orcid":"0000-0002-0519-4241"}],"title":"A dual formula for the noncommutative transport distance","ec_funded":1,"publication_status":"published","acknowledgement":"The author wants to thank Jan Maas for helpful comments. He also acknowledges financial support from the Austrian Science Fund (FWF) through Grant Number F65 and from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 716117).\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","status":"public","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["15729613"],"issn":["00224715"]},"scopus_import":"1","date_created":"2022-04-24T22:01:43Z","external_id":{"isi":["000780305000001"]},"date_published":"2022-04-08T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JaMa"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"intvolume":"       187","publisher":"Springer Nature","year":"2022","oa":1,"article_type":"original","article_number":"19","date_updated":"2023-08-03T06:37:49Z","publication":"Journal of Statistical Physics"},{"publication_identifier":{"isbn":["9781450391627"]},"publication_status":"published","status":"public","author":[{"last_name":"Danezis","full_name":"Danezis, George","first_name":"George"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Sonnino, Alberto","last_name":"Sonnino","first_name":"Alberto"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"}],"title":"Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus","_id":"11331","abstract":[{"text":"We propose separating the task of reliable transaction dissemination from transaction ordering, to enable high-performance Byzantine fault-tolerant quorum-based consensus. We design and evaluate a mempool protocol, Narwhal, specializing in high-throughput reliable dissemination and storage of causal histories of transactions. Narwhal tolerates an asynchronous network and maintains high performance despite failures. Narwhal is designed to easily scale-out using multiple workers at each validator, and we demonstrate that there is no foreseeable limit to the throughput we can achieve.\r\nComposing Narwhal with a partially synchronous consensus protocol (Narwhal-HotStuff) yields significantly better throughput even in the presence of faults or intermittent loss of liveness due to asynchrony. However, loss of liveness can result in higher latency. To achieve overall good performance when faults occur we design Tusk, a zero-message overhead asynchronous consensus protocol, to work with Narwhal. We demonstrate its high performance under a variety of configurations and faults.\r\nAs a summary of results, on a WAN, Narwhal-Hotstuff achieves over 130,000 tx/sec at less than 2-sec latency compared with 1,800 tx/sec at 1-sec latency for Hotstuff. Additional workers increase throughput linearly to 600,000 tx/sec without any latency increase. Tusk achieves 160,000 tx/sec with about 3 seconds latency. Under faults, both protocols maintain high throughput, but Narwhal-HotStuff suffers from increased latency.","lang":"eng"}],"doi":"10.1145/3492321.3519594","arxiv":1,"article_processing_charge":"No","day":"28","citation":{"chicago":"Danezis, George, Eleftherios Kokoris Kogias, Alberto Sonnino, and Alexander Spiegelman. “Narwhal and Tusk: A DAG-Based Mempool and Efficient BFT Consensus.” In <i>Proceedings of the 17th European Conference on Computer Systems</i>, 34–50. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3492321.3519594\">https://doi.org/10.1145/3492321.3519594</a>.","mla":"Danezis, George, et al. “Narwhal and Tusk: A DAG-Based Mempool and Efficient BFT Consensus.” <i>Proceedings of the 17th European Conference on Computer Systems</i>, Association for Computing Machinery, 2022, pp. 34–50, doi:<a href=\"https://doi.org/10.1145/3492321.3519594\">10.1145/3492321.3519594</a>.","ama":"Danezis G, Kokoris Kogias E, Sonnino A, Spiegelman A. Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus. In: <i>Proceedings of the 17th European Conference on Computer Systems</i>. Association for Computing Machinery; 2022:34-50. doi:<a href=\"https://doi.org/10.1145/3492321.3519594\">10.1145/3492321.3519594</a>","ista":"Danezis G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2022. Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus. Proceedings of the 17th European Conference on Computer Systems. EuroSys: European Conference on Computer Systems, 34–50.","short":"G. Danezis, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, Proceedings of the 17th European Conference on Computer Systems, Association for Computing Machinery, 2022, pp. 34–50.","apa":"Danezis, G., Kokoris Kogias, E., Sonnino, A., &#38; Spiegelman, A. (2022). Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus. In <i>Proceedings of the 17th European Conference on Computer Systems</i> (pp. 34–50). Rennes, France: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3492321.3519594\">https://doi.org/10.1145/3492321.3519594</a>","ieee":"G. Danezis, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus,” in <i>Proceedings of the 17th European Conference on Computer Systems</i>, Rennes, France, 2022, pp. 34–50."},"month":"03","conference":{"end_date":"2022-04-08","start_date":"2022-04-05","location":"Rennes, France","name":"EuroSys: European Conference on Computer Systems"},"oa_version":"Preprint","publication":"Proceedings of the 17th European Conference on Computer Systems","date_updated":"2023-08-03T06:38:40Z","page":"34-50","oa":1,"year":"2022","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2105.11827","open_access":"1"}],"publisher":"Association for Computing Machinery","isi":1,"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","department":[{"_id":"ElKo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2105.11827"],"isi":["000926506800003"]},"date_published":"2022-03-28T00:00:00Z","scopus_import":"1","date_created":"2022-04-24T22:01:43Z"},{"page":"839-907","article_type":"original","date_updated":"2023-08-03T06:34:24Z","publication":"Communications in Mathematical Physics","year":"2022","oa":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"publisher":"Springer Nature","intvolume":"       393","date_created":"2022-04-24T22:01:44Z","scopus_import":"1","date_published":"2022-07-01T00:00:00Z","external_id":{"isi":["000782737200001"],"arxiv":["2102.04330"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"LaEr"}],"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"Kevin Schnelli is supported in parts by the Swedish Research Council Grant VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Yuanyuan Xu is supported by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced Grant “RMTBeyond” No. 101020331.","project":[{"call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"doi":"10.1007/s00220-022-04377-y","abstract":[{"text":"We show that the fluctuations of the largest eigenvalue of a real symmetric or complex Hermitian Wigner matrix of size N converge to the Tracy–Widom laws at a rate O(N^{-1/3+\\omega }), as N tends to infinity. For Wigner matrices this improves the previous rate O(N^{-2/9+\\omega }) obtained by Bourgade (J Eur Math Soc, 2021) for generalized Wigner matrices. Our result follows from a Green function comparison theorem, originally introduced by Erdős et al. (Adv Math 229(3):1435–1515, 2012) to prove edge universality, on a finer spectral parameter scale with improved error estimates. The proof relies on the continuous Green function flow induced by a matrix-valued Ornstein–Uhlenbeck process. Precise estimates on leading contributions from the third and fourth order moments of the matrix entries are obtained using iterative cumulant expansions and recursive comparisons for correlation functions, along with uniform convergence estimates for correlation kernels of the Gaussian invariant ensembles.","lang":"eng"}],"_id":"11332","title":"Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices","author":[{"orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin"},{"full_name":"Xu, Yuanyuan","last_name":"Xu","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","first_name":"Yuanyuan"}],"volume":393,"article_processing_charge":"No","has_accepted_license":"1","file":[{"date_created":"2022-08-05T06:01:13Z","file_id":"11726","checksum":"bee0278c5efa9a33d9a2dc8d354a6c51","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-08-05T06:01:13Z","success":1,"relation":"main_file","file_size":1141462,"creator":"dernst","file_name":"2022_CommunMathPhys_Schnelli.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"oa_version":"Published Version","ddc":["510"],"file_date_updated":"2022-08-05T06:01:13Z","month":"07","citation":{"ama":"Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices. <i>Communications in Mathematical Physics</i>. 2022;393:839-907. doi:<a href=\"https://doi.org/10.1007/s00220-022-04377-y\">10.1007/s00220-022-04377-y</a>","ista":"Schnelli K, Xu Y. 2022. Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices. Communications in Mathematical Physics. 393, 839–907.","short":"K. Schnelli, Y. Xu, Communications in Mathematical Physics 393 (2022) 839–907.","ieee":"K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices,” <i>Communications in Mathematical Physics</i>, vol. 393. Springer Nature, pp. 839–907, 2022.","apa":"Schnelli, K., &#38; Xu, Y. (2022). Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-022-04377-y\">https://doi.org/10.1007/s00220-022-04377-y</a>","mla":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Wigner Matrices.” <i>Communications in Mathematical Physics</i>, vol. 393, Springer Nature, 2022, pp. 839–907, doi:<a href=\"https://doi.org/10.1007/s00220-022-04377-y\">10.1007/s00220-022-04377-y</a>.","chicago":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Wigner Matrices.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00220-022-04377-y\">https://doi.org/10.1007/s00220-022-04377-y</a>."},"day":"01"},{"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Wiley","intvolume":"        28","main_file_link":[{"url":"https://doi.org/10.1002/chem.202200807","open_access":"1"}],"date_published":"2022-05-25T00:00:00Z","external_id":{"isi":["000781658800001"],"pmid":["35332959"]},"date_created":"2022-04-24T22:01:44Z","scopus_import":"1","department":[{"_id":"RySh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e202200807","article_type":"original","publication":"Chemistry - A European Journal","date_updated":"2023-10-03T10:58:31Z","year":"2022","oa":1,"volume":28,"article_processing_charge":"No","oa_version":"Published Version","citation":{"mla":"Thayyil, Sampreeth, et al. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.” <i>Chemistry - A European Journal</i>, vol. 28, no. 30, e202200807, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/chem.202200807\">10.1002/chem.202200807</a>.","chicago":"Thayyil, Sampreeth, Yukinori Nishigami, Muhammad J Islam, P. K. Hashim, Ken’Ya Furuta, Kazuhiro Oiwa, Jian Yu, Min Yao, Toshiyuki Nakagaki, and Nobuyuki Tamaoki. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.” <i>Chemistry - A European Journal</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/chem.202200807\">https://doi.org/10.1002/chem.202200807</a>.","apa":"Thayyil, S., Nishigami, Y., Islam, M. J., Hashim, P. K., Furuta, K., Oiwa, K., … Tamaoki, N. (2022). Dynamic control of microbial movement by photoswitchable ATP antagonists. <i>Chemistry - A European Journal</i>. Wiley. <a href=\"https://doi.org/10.1002/chem.202200807\">https://doi.org/10.1002/chem.202200807</a>","ieee":"S. Thayyil <i>et al.</i>, “Dynamic control of microbial movement by photoswitchable ATP antagonists,” <i>Chemistry - A European Journal</i>, vol. 28, no. 30. Wiley, 2022.","ista":"Thayyil S, Nishigami Y, Islam MJ, Hashim PK, Furuta K, Oiwa K, Yu J, Yao M, Nakagaki T, Tamaoki N. 2022. Dynamic control of microbial movement by photoswitchable ATP antagonists. Chemistry - A European Journal. 28(30), e202200807.","ama":"Thayyil S, Nishigami Y, Islam MJ, et al. Dynamic control of microbial movement by photoswitchable ATP antagonists. <i>Chemistry - A European Journal</i>. 2022;28(30). doi:<a href=\"https://doi.org/10.1002/chem.202200807\">10.1002/chem.202200807</a>","short":"S. Thayyil, Y. Nishigami, M.J. Islam, P.K. Hashim, K. Furuta, K. Oiwa, J. Yu, M. Yao, T. Nakagaki, N. Tamaoki, Chemistry - A European Journal 28 (2022)."},"day":"25","month":"05","pmid":1,"publication_status":"published","status":"public","publication_identifier":{"issn":["09476539"],"eissn":["15213765"]},"abstract":[{"text":"Adenosine triphosphate (ATP) is the energy source for various biochemical processes and biomolecular motors in living things. Development of ATP antagonists and their stimuli-controlled actions offer a novel approach to regulate biological processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins. The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated the axonemal dynein motor activity for the force generation in a demembranated model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of ATP antagonists significantly differ in their affinity to the ATP binding site.","lang":"eng"}],"issue":"30","doi":"10.1002/chem.202200807","title":"Dynamic control of microbial movement by photoswitchable ATP antagonists","author":[{"full_name":"Thayyil, Sampreeth","last_name":"Thayyil","first_name":"Sampreeth"},{"first_name":"Yukinori","full_name":"Nishigami, Yukinori","last_name":"Nishigami"},{"id":"C94881D2-008F-11EA-8E08-2637E6697425","first_name":"Muhammad J","full_name":"Islam, Muhammad J","last_name":"Islam"},{"last_name":"Hashim","full_name":"Hashim, P. K.","first_name":"P. K."},{"first_name":"Ken'Ya","full_name":"Furuta, Ken'Ya","last_name":"Furuta"},{"first_name":"Kazuhiro","full_name":"Oiwa, Kazuhiro","last_name":"Oiwa"},{"last_name":"Yu","full_name":"Yu, Jian","first_name":"Jian"},{"first_name":"Min","last_name":"Yao","full_name":"Yao, Min"},{"full_name":"Nakagaki, Toshiyuki","last_name":"Nakagaki","first_name":"Toshiyuki"},{"last_name":"Tamaoki","full_name":"Tamaoki, Nobuyuki","first_name":"Nobuyuki"}],"_id":"11333"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"date_created":"2022-04-24T22:01:44Z","scopus_import":"1","date_published":"2022-05-01T00:00:00Z","external_id":{"pmid":["35323995"],"isi":["000781632500001"]},"publisher":"Wiley","intvolume":"        76","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"oa":1,"year":"2022","date_updated":"2023-08-03T07:00:28Z","publication":"Evolution","page":"899-914","article_type":"original","file_date_updated":"2022-08-05T06:19:28Z","ddc":["570"],"pmid":1,"month":"05","citation":{"chicago":"Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>.","mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>.","ama":"Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. <i>Evolution</i>. 2022;76(5):899-914. doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>","ista":"Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 76(5), 899–914.","short":"S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas, D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.","ieee":"S. Freitas <i>et al.</i>, “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” <i>Evolution</i>, vol. 76, no. 5. Wiley, pp. 899–914, 2022.","apa":"Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas, Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>"},"day":"01","oa_version":"Published Version","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"creator":"dernst","relation":"main_file","file_size":2855214,"file_name":"2022_Evolution_Freitas.pdf","date_updated":"2022-08-05T06:19:28Z","success":1,"content_type":"application/pdf","checksum":"c27c025ae9afcf6c804d46a909775ee5","access_level":"open_access","date_created":"2022-08-05T06:19:28Z","file_id":"11729"}],"article_processing_charge":"No","volume":76,"has_accepted_license":"1","_id":"11334","title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","author":[{"first_name":"Susana","full_name":"Freitas, Susana","last_name":"Freitas"},{"last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"last_name":"Schwander","full_name":"Schwander, Tanja","first_name":"Tanja"},{"last_name":"Arakelyan","full_name":"Arakelyan, Marine","first_name":"Marine"},{"first_name":"Çetin","last_name":"Ilgaz","full_name":"Ilgaz, Çetin"},{"first_name":"Yusuf","last_name":"Kumlutas","full_name":"Kumlutas, Yusuf"},{"first_name":"David James","full_name":"Harris, David James","last_name":"Harris"},{"full_name":"Carretero, Miguel A.","last_name":"Carretero","first_name":"Miguel A."},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"doi":"10.1111/evo.14462","abstract":[{"lang":"eng","text":"Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction."}],"issue":"5","project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"ec_funded":1,"acknowledgement":"The authors thank A. van der Meijden and F. Ahmadzadeh for providing specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski for support during field work. The authors also thank S. Qiu for assistance with python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for his comments on\r\na previous version of the manuscript. SF was funded by FCT grant SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation (grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian program for training in modern conservation biology” of Gulbenkian Foundation (Portugal) and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal).","publication_status":"published","status":"public"},{"article_processing_charge":"No","volume":8,"has_accepted_license":"1","file":[{"date_created":"2023-03-21T14:18:10Z","file_id":"12742","creator":"patrickd","file_size":2973998,"relation":"main_file","file_name":"sciadv.abq1263.pdf","date_updated":"2023-03-21T14:18:10Z","success":1,"content_type":"application/pdf","checksum":"0117023e188542082ca6693cf39e7f03","access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","ddc":["570"],"file_date_updated":"2023-03-21T14:18:10Z","month":"11","citation":{"ieee":"N. Amberg, F. Pauler, C. Streicher, and S. Hippenmeyer, “Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression,” <i>Science Advances</i>, vol. 8, no. 44. American Association for the Advancement of Science, 2022.","apa":"Amberg, N., Pauler, F., Streicher, C., &#38; Hippenmeyer, S. (2022). Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abq1263\">https://doi.org/10.1126/sciadv.abq1263</a>","ama":"Amberg N, Pauler F, Streicher C, Hippenmeyer S. Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression. <i>Science Advances</i>. 2022;8(44). doi:<a href=\"https://doi.org/10.1126/sciadv.abq1263\">10.1126/sciadv.abq1263</a>","ista":"Amberg N, Pauler F, Streicher C, Hippenmeyer S. 2022. Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression. Science Advances. 8(44), abq1263.","short":"N. Amberg, F. Pauler, C. Streicher, S. Hippenmeyer, Science Advances 8 (2022).","mla":"Amberg, Nicole, et al. “Tissue-Wide Genetic and Cellular Landscape Shapes the Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression.” <i>Science Advances</i>, vol. 8, no. 44, abq1263, American Association for the Advancement of Science, 2022, doi:<a href=\"https://doi.org/10.1126/sciadv.abq1263\">10.1126/sciadv.abq1263</a>.","chicago":"Amberg, Nicole, Florian Pauler, Carmen Streicher, and Simon Hippenmeyer. “Tissue-Wide Genetic and Cellular Landscape Shapes the Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression.” <i>Science Advances</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/sciadv.abq1263\">https://doi.org/10.1126/sciadv.abq1263</a>."},"day":"01","ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS  Unit)  and  S.  Gharagozlou  for  technical  support.  This  research  was  supported  by  the  Scientific  Service  Units  (SSU)  of  IST  Austria  through  resources  provided  by  the  Imaging  &  Optics Facility (IOF), Lab Support Facility (LSF), and Preclinical Facility (PCF). N.A. received funding   from   the   FWF   Firnberg-Programm   (T   1031).   The   work   was   supported   by   IST   institutional  funds  and  by  the  European  Research  Council  (ERC)  under  the  European  Union’s  Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031"}],"publication_identifier":{"issn":["2375-2548"]},"doi":"10.1126/sciadv.abq1263","abstract":[{"lang":"eng","text":"The generation of a correctly-sized cerebral cortex with all-embracing neuronal and glial cell-type diversity critically depends on faithful radial glial progenitor (RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene expression instructs RGP lineage progression is unknown. Here we utilize Mosaic Analysis with Double Markers (MADM)-based single cell technology and demonstrate that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts at the global tissue-wide level. Conversely, cortical astrocyte production and maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation. We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression that are dependent on complex interplays between intrinsic and tissue-wide properties. In a broader context our results imply a critical role for the genetic and cellular niche environment in neural stem cell behavior."}],"issue":"44","_id":"11336","title":"Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression","author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","full_name":"Amberg, Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207"},{"full_name":"Pauler, Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","full_name":"Streicher, Carmen"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"American Association for the Advancement of Science","intvolume":"         8","date_created":"2022-04-26T15:04:50Z","scopus_import":"1","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"}],"date_published":"2022-11-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"article_number":"abq1263","article_type":"original","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/whole-tissue-shapes-brain-development/"}]},"date_updated":"2023-05-31T12:24:10Z","publication":"Science Advances","year":"2022","oa":1},{"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2112.11273","open_access":"1"}],"intvolume":"       105","publisher":"American Physical Society","external_id":{"isi":["000806812400004"],"arxiv":["2112.11273"]},"date_published":"2022-04-15T00:00:00Z","date_created":"2022-04-28T08:06:10Z","department":[{"_id":"MaSe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","article_number":"165149","publication":"Physical Review B","date_updated":"2023-08-03T06:33:33Z","year":"2022","oa":1,"article_processing_charge":"No","volume":105,"arxiv":1,"oa_version":"Preprint","day":"15","citation":{"ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement and precession in two-dimensional dynamical quantum phase transitions,” <i>Physical Review B</i>, vol. 105. American Physical Society, 2022.","apa":"De Nicola, S., Michailidis, A., &#38; Serbyn, M. (2022). Entanglement and precession in two-dimensional dynamical quantum phase transitions. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.105.165149\">https://doi.org/10.1103/PhysRevB.105.165149</a>","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review B 105 (2022).","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement and precession in two-dimensional dynamical quantum phase transitions. <i>Physical Review B</i>. 2022;105. doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.165149\">10.1103/PhysRevB.105.165149</a>","ista":"De Nicola S, Michailidis A, Serbyn M. 2022. Entanglement and precession in two-dimensional dynamical quantum phase transitions. Physical Review B. 105, 165149.","mla":"De Nicola, Stefano, et al. “Entanglement and Precession in Two-Dimensional Dynamical Quantum Phase Transitions.” <i>Physical Review B</i>, vol. 105, 165149, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.165149\">10.1103/PhysRevB.105.165149</a>.","chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement and Precession in Two-Dimensional Dynamical Quantum Phase Transitions.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevB.105.165149\">https://doi.org/10.1103/PhysRevB.105.165149</a>."},"month":"04","acknowledgement":"We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 850899).\r\nS.D.N. also acknowledges funding from the Institute of Science and Technology (IST) Austria, and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["2469-9950"],"eisbn":["2469-9969"]},"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"Nonanalytic points in the return probability of a quantum state as a function of time, known as dynamical quantum phase transitions (DQPTs), have received great attention in recent years, but the understanding of their mechanism is still incomplete. In our recent work [Phys. Rev. Lett. 126, 040602 (2021)], we demonstrated that one-dimensional DQPTs can be produced by two distinct mechanisms, namely semiclassical precession and entanglement generation, leading to the definition of precession (pDQPTs) and entanglement (eDQPTs) dynamical quantum phase transitions. In this manuscript, we extend and investigate the notion of p- and eDQPTs in two-dimensional systems by considering semi-infinite ladders of varying width. For square lattices, we find that pDQPTs and eDQPTs persist and are characterized by similar phenomenology as in 1D: pDQPTs are associated with a magnetization sign change and a wide entanglement gap, while eDQPTs correspond to suppressed local observables and avoided crossings in the entanglement spectrum. However, DQPTs show higher sensitivity to the ladder width and other details, challenging the extrapolation to the thermodynamic limit especially for eDQPTs. Moving to honeycomb lattices, we also demonstrate that lattices with an odd number of nearest neighbors give rise to phenomenologies beyond the one-dimensional classification."}],"doi":"10.1103/PhysRevB.105.165149","author":[{"id":"42832B76-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","full_name":"De Nicola, Stefano","last_name":"De Nicola","orcid":"0000-0002-4842-6671"},{"first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","full_name":"Michailidis, Alexios"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn"}],"title":"Entanglement and precession in two-dimensional dynamical quantum phase transitions","_id":"11337"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2022-05-02T06:26:26Z","file_id":"11342","relation":"main_file","file_size":2827723,"creator":"dernst","file_name":"2022_CommBiology_Glover.pdf","content_type":"application/pdf","checksum":"7c6f76ab17393d650825cc240edc84b3","access_level":"open_access","date_updated":"2022-05-02T06:26:26Z","success":1}],"has_accepted_license":"1","volume":5,"article_processing_charge":"No","day":"20","citation":{"mla":"Glover, Georgina, et al. “Nutrient and Salt Depletion Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.” <i>Communications Biology</i>, vol. 5, 385, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03336-6\">10.1038/s42003-022-03336-6</a>.","chicago":"Glover, Georgina, Margaritis Voliotis, Urszula Łapińska, Brandon M. Invergo, Darren Soanes, Paul O’Neill, Karen Moore, et al. “Nutrient and Salt Depletion Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03336-6\">https://doi.org/10.1038/s42003-022-03336-6</a>.","ista":"Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O’Neill P, Moore K, Nikolic N, Petrov P, Milner DS, Roy S, Heesom K, Richards TA, Tsaneva-Atanasova K, Pagliara S. 2022. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Communications Biology. 5, 385.","short":"G. Glover, M. Voliotis, U. Łapińska, B.M. Invergo, D. Soanes, P. O’Neill, K. Moore, N. Nikolic, P. Petrov, D.S. Milner, S. Roy, K. Heesom, T.A. Richards, K. Tsaneva-Atanasova, S. Pagliara, Communications Biology 5 (2022).","ama":"Glover G, Voliotis M, Łapińska U, et al. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. <i>Communications Biology</i>. 2022;5. doi:<a href=\"https://doi.org/10.1038/s42003-022-03336-6\">10.1038/s42003-022-03336-6</a>","ieee":"G. Glover <i>et al.</i>, “Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells,” <i>Communications Biology</i>, vol. 5. Springer Nature, 2022.","apa":"Glover, G., Voliotis, M., Łapińska, U., Invergo, B. M., Soanes, D., O’Neill, P., … Pagliara, S. (2022). Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03336-6\">https://doi.org/10.1038/s42003-022-03336-6</a>"},"month":"04","pmid":1,"file_date_updated":"2022-05-02T06:26:26Z","ddc":["570"],"oa_version":"Published Version","publication_identifier":{"eissn":["2399-3642"]},"acknowledgement":"G.G. was supported by an EPSRC DTP PhD studentship (EP/M506527/1). M.V. and K.T.A. gratefully acknowledge financial support from the EPSRC (EP/N014391/1). U.L. was supported through a BBSRC grant (BB/V008021/1) and an MRC Proximity to Discovery EXCITEME2 grant (MCPC17189). This work was further supported by a Royal Society Research Grant (RG180007) awarded to S.P. and a QUEX Initiator grant awarded to S.P. and K.T.A.. D.S.M., T.A.R. and S.P.’s work in this area is also supported by a Marie Skłodowska-Curie project SINGEK (H2020-MSCA-ITN-2015-675752) and the Gordon and Betty Moore Foundation Marine Microbiology Initiative (GBMF5514). B.M.I. acknowledges support from a Wellcome Trust Institutional Strategic Support Award to the University of Exeter (204909/Z/16/Z). This project utilised equipment funded by the Wellcome Trust Institutional Strategic Support Fund (WT097835MF), Wellcome Trust Multi User Equipment Award (WT101650MA) and BBSRC LOLA award (BB/K003240/1).","status":"public","publication_status":"published","author":[{"last_name":"Glover","full_name":"Glover, Georgina","first_name":"Georgina"},{"first_name":"Margaritis","last_name":"Voliotis","full_name":"Voliotis, Margaritis"},{"last_name":"Łapińska","full_name":"Łapińska, Urszula","first_name":"Urszula"},{"last_name":"Invergo","full_name":"Invergo, Brandon M.","first_name":"Brandon M."},{"full_name":"Soanes, Darren","last_name":"Soanes","first_name":"Darren"},{"last_name":"O’Neill","full_name":"O’Neill, Paul","first_name":"Paul"},{"first_name":"Karen","full_name":"Moore, Karen","last_name":"Moore"},{"orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"},{"last_name":"Petrov","full_name":"Petrov, Peter","first_name":"Peter"},{"last_name":"Milner","full_name":"Milner, David S.","first_name":"David S."},{"first_name":"Sumita","full_name":"Roy, Sumita","last_name":"Roy"},{"first_name":"Kate","full_name":"Heesom, Kate","last_name":"Heesom"},{"first_name":"Thomas A.","last_name":"Richards","full_name":"Richards, Thomas A."},{"last_name":"Tsaneva-Atanasova","full_name":"Tsaneva-Atanasova, Krasimira","first_name":"Krasimira"},{"first_name":"Stefano","last_name":"Pagliara","full_name":"Pagliara, Stefano"}],"title":"Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells","_id":"11339","abstract":[{"text":"The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.","lang":"eng"}],"doi":"10.1038/s42003-022-03336-6","intvolume":"         5","publisher":"Springer Nature","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000784143400001"],"pmid":["35444215"]},"date_published":"2022-04-20T00:00:00Z","scopus_import":"1","date_created":"2022-05-01T22:01:41Z","publication":"Communications Biology","date_updated":"2023-08-03T06:45:26Z","article_type":"original","article_number":"385","oa":1,"year":"2022"},{"article_type":"original","page":"3143-3149","publication":"Journal of Physical Chemistry B","date_updated":"2023-08-03T06:42:50Z","year":"2022","oa":1,"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2203.10524"}],"intvolume":"       126","publisher":"American Chemical Society","date_published":"2022-04-14T00:00:00Z","external_id":{"arxiv":["2203.10524"],"isi":["000796953700022"]},"scopus_import":"1","date_created":"2022-05-01T22:01:42Z","department":[{"_id":"AnSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","status":"public","acknowledgement":"We thank Martin Trulsson for useful discussions and for providing us with simulation data. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement 674979-NANOTRANS. The support received from VEGA Grant No. 2/0092/21 is acknowledged.","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"issue":"16","abstract":[{"text":"Like-charge attraction, driven by ionic correlations, challenges our understanding of electrostatics both in soft and hard matter. For two charged planar surfaces confining counterions and water, we prove that, even at relatively low correlation strength, the relevant physics is the ground-state one, oblivious of fluctuations. Based on this, we derive a simple and accurate interaction pressure that fulfills known exact requirements and can be used as an effective potential. We test this equation against implicit-solvent Monte Carlo simulations and against explicit-solvent simulations of cement and several types of clays. We argue that water destructuring under nanometric confinement drastically reduces dielectric screening, enhancing ionic correlations. Our equation of state at reduced permittivity therefore explains the exotic attractive regime reported for these materials, even in the absence of multivalent counterions.","lang":"eng"}],"doi":"10.1021/acs.jpcb.2c00028","author":[{"full_name":"Palaia, Ivan","last_name":"Palaia","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","first_name":"Ivan","orcid":" 0000-0002-8843-9485 "},{"last_name":"Goyal","full_name":"Goyal, Abhay","first_name":"Abhay"},{"first_name":"Emanuela","last_name":"Del Gado","full_name":"Del Gado, Emanuela"},{"first_name":"Ladislav","full_name":"Šamaj, Ladislav","last_name":"Šamaj"},{"full_name":"Trizac, Emmanuel","last_name":"Trizac","first_name":"Emmanuel"}],"title":"Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring","_id":"11340","article_processing_charge":"No","volume":126,"arxiv":1,"oa_version":"Preprint","day":"14","citation":{"apa":"Palaia, I., Goyal, A., Del Gado, E., Šamaj, L., &#38; Trizac, E. (2022). Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring. <i>Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.2c00028\">https://doi.org/10.1021/acs.jpcb.2c00028</a>","ieee":"I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, and E. Trizac, “Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring,” <i>Journal of Physical Chemistry B</i>, vol. 126, no. 16. American Chemical Society, pp. 3143–3149, 2022.","ama":"Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring. <i>Journal of Physical Chemistry B</i>. 2022;126(16):3143-3149. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.2c00028\">10.1021/acs.jpcb.2c00028</a>","short":"I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, E. Trizac, Journal of Physical Chemistry B 126 (2022) 3143–3149.","ista":"Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. 2022. Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring. Journal of Physical Chemistry B. 126(16), 3143–3149.","chicago":"Palaia, Ivan, Abhay Goyal, Emanuela Del Gado, Ladislav Šamaj, and Emmanuel Trizac. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and Water Destructuring.” <i>Journal of Physical Chemistry B</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acs.jpcb.2c00028\">https://doi.org/10.1021/acs.jpcb.2c00028</a>.","mla":"Palaia, Ivan, et al. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and Water Destructuring.” <i>Journal of Physical Chemistry B</i>, vol. 126, no. 16, American Chemical Society, 2022, pp. 3143–49, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.2c00028\">10.1021/acs.jpcb.2c00028</a>."},"month":"04"}]