[{"year":"2022","citation":{"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>","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>","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>.","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.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022).","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>.","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>."},"date_updated":"2024-02-21T12:41:09Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"research_data","date_published":"2022-04-28T00:00:00Z","day":"28","doi":"10.15479/at:ista:11321","oa":1,"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"}],"file":[{"date_updated":"2022-04-22T09:39:03Z","file_name":"Data_Code.zip","content_type":"application/x-zip-compressed","date_created":"2022-04-22T09:39:03Z","checksum":"96c1b86cdf25481f2a52972fcc45ca7f","file_size":13260571,"file_id":"11326","creator":"larathoo","success":1,"access_level":"open_access","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"11411","relation":"used_in_publication","status":"public"},{"status":"public","id":"9192","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"8254"}]},"ddc":["570"],"status":"public","has_accepted_license":"1","_id":"11321","author":[{"first_name":"Parvathy","last_name":"Surendranadh","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arathoon","first_name":"Louise S","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina"},{"first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2022-04-22T09:42:24Z","article_processing_charge":"No","oa_version":"Published Version","month":"04","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","contributor_type":"project_member","last_name":"Arathoon"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","contributor_type":"project_member","first_name":"Carina","orcid":"0000-0002-7354-8574"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","contributor_type":"project_member","orcid":"0000-0002-4014-8478"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","contributor_type":"project_member","last_name":"Pickup"},{"first_name":"Nicholas H","contributor_type":"project_member","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2022-04-22T09:39:03Z","publisher":"Institute of Science and Technology Austria"},{"type":"journal_article","date_published":"2022-04-08T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["15729613"],"issn":["00224715"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"file_id":"11338","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access","date_updated":"2022-04-29T11:24:23Z","file_name":"2022_JourStatisticalPhysics_Wirth.pdf","content_type":"application/pdf","date_created":"2022-04-29T11:24:23Z","checksum":"f3e0b00884b7dde31347a3756788b473","file_size":362119}],"has_accepted_license":"1","publication":"Journal of Statistical Physics","article_number":"19","month":"04","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"isi":["000780305000001"]},"isi":1,"year":"2022","citation":{"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).","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>.","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>.","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>","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>"},"date_updated":"2023-08-03T06:37:49Z","abstract":[{"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.","lang":"eng"}],"day":"08","doi":"10.1007/s10955-022-02911-9","ddc":["510","530"],"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).","volume":187,"issue":"2","author":[{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","full_name":"Wirth, Melchior","orcid":"0000-0002-0519-4241","last_name":"Wirth","first_name":"Melchior"}],"scopus_import":"1","_id":"11330","intvolume":"       187","title":"A dual formula for the noncommutative transport distance","article_processing_charge":"Yes (via OA deal)","date_created":"2022-04-24T22:01:43Z","department":[{"_id":"JaMa"}],"publication_status":"published","file_date_updated":"2022-04-29T11:24:23Z","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"Springer Nature"},{"external_id":{"isi":["000926506800003"],"arxiv":["2105.11827"]},"isi":1,"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>.","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.","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>","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>","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.","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>.","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."},"year":"2022","date_updated":"2023-08-03T06:38:40Z","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"}],"day":"28","doi":"10.1145/3492321.3519594","arxiv":1,"author":[{"last_name":"Danezis","first_name":"George","full_name":"Danezis, George"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","last_name":"Kokoris Kogias"},{"first_name":"Alberto","last_name":"Sonnino","full_name":"Sonnino, Alberto"},{"full_name":"Spiegelman, Alexander","first_name":"Alexander","last_name":"Spiegelman"}],"scopus_import":"1","_id":"11331","title":"Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus","department":[{"_id":"ElKo"}],"date_created":"2022-04-24T22:01:43Z","article_processing_charge":"No","publication_status":"published","quality_controlled":"1","page":"34-50","publisher":"Association for Computing Machinery","type":"conference","date_published":"2022-03-28T00:00:00Z","oa":1,"publication_identifier":{"isbn":["9781450391627"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2105.11827","open_access":"1"}],"publication":"Proceedings of the 17th European Conference on Computer Systems","month":"03","oa_version":"Preprint","language":[{"iso":"eng"}],"conference":{"name":"EuroSys: European Conference on Computer Systems","start_date":"2022-04-05","end_date":"2022-04-08","location":"Rennes, France"}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"creator":"dernst","file_id":"11726","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2022_CommunMathPhys_Schnelli.pdf","date_updated":"2022-08-05T06:01:13Z","checksum":"bee0278c5efa9a33d9a2dc8d354a6c51","file_size":1141462,"date_created":"2022-08-05T06:01:13Z"}],"date_published":"2022-07-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"language":[{"iso":"eng"}],"publication":"Communications in Mathematical Physics","has_accepted_license":"1","month":"07","oa_version":"Published Version","project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020"}],"ddc":["510"],"volume":393,"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.","isi":1,"external_id":{"isi":["000782737200001"],"arxiv":["2102.04330"]},"date_updated":"2023-08-03T06:34:24Z","citation":{"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>","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>","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.","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>.","short":"K. Schnelli, Y. Xu, Communications in Mathematical Physics 393 (2022) 839–907.","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>.","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."},"year":"2022","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"}],"doi":"10.1007/s00220-022-04377-y","arxiv":1,"day":"01","file_date_updated":"2022-08-05T06:01:13Z","page":"839-907","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"Springer Nature","author":[{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","first_name":"Kevin","last_name":"Schnelli"},{"id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","last_name":"Xu","first_name":"Yuanyuan","full_name":"Xu, Yuanyuan"}],"_id":"11332","scopus_import":"1","title":"Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices","intvolume":"       393","publication_status":"published","department":[{"_id":"LaEr"}],"date_created":"2022-04-24T22:01:44Z","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"publication":"Chemistry - A European Journal","article_number":"e202200807","month":"05","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"url":"https://doi.org/10.1002/chem.202200807","open_access":"1"}],"type":"journal_article","date_published":"2022-05-25T00:00:00Z","oa":1,"publication_identifier":{"issn":["09476539"],"eissn":["15213765"]},"quality_controlled":"1","article_type":"original","publisher":"Wiley","issue":"30","author":[{"last_name":"Thayyil","first_name":"Sampreeth","full_name":"Thayyil, Sampreeth"},{"last_name":"Nishigami","first_name":"Yukinori","full_name":"Nishigami, Yukinori"},{"id":"C94881D2-008F-11EA-8E08-2637E6697425","last_name":"Islam","first_name":"Muhammad J","full_name":"Islam, Muhammad J"},{"first_name":"P. K.","last_name":"Hashim","full_name":"Hashim, P. K."},{"last_name":"Furuta","first_name":"Ken'Ya","full_name":"Furuta, Ken'Ya"},{"first_name":"Kazuhiro","last_name":"Oiwa","full_name":"Oiwa, Kazuhiro"},{"full_name":"Yu, Jian","last_name":"Yu","first_name":"Jian"},{"last_name":"Yao","first_name":"Min","full_name":"Yao, Min"},{"first_name":"Toshiyuki","last_name":"Nakagaki","full_name":"Nakagaki, Toshiyuki"},{"full_name":"Tamaoki, Nobuyuki","last_name":"Tamaoki","first_name":"Nobuyuki"}],"scopus_import":"1","_id":"11333","pmid":1,"intvolume":"        28","title":"Dynamic control of microbial movement by photoswitchable ATP antagonists","article_processing_charge":"No","department":[{"_id":"RySh"}],"date_created":"2022-04-24T22:01:44Z","publication_status":"published","volume":28,"external_id":{"pmid":["35332959"],"isi":["000781658800001"]},"isi":1,"year":"2022","citation":{"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>.","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.","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>","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>","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.","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>.","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)."},"date_updated":"2023-10-03T10:58:31Z","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"}],"day":"25","doi":"10.1002/chem.202200807"},{"language":[{"iso":"eng"}],"month":"05","oa_version":"Published Version","project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"Evolution","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"file_id":"11729","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2022-08-05T06:19:28Z","content_type":"application/pdf","file_name":"2022_Evolution_Freitas.pdf","date_created":"2022-08-05T06:19:28Z","checksum":"c27c025ae9afcf6c804d46a909775ee5","file_size":2855214}],"oa":1,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"date_published":"2022-05-01T00:00:00Z","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_type":"original","publisher":"Wiley","file_date_updated":"2022-08-05T06:19:28Z","page":"899-914","ec_funded":1,"quality_controlled":"1","title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","intvolume":"        76","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"date_created":"2022-04-24T22:01:44Z","article_processing_charge":"No","author":[{"full_name":"Freitas, Susana","last_name":"Freitas","first_name":"Susana"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schwander","first_name":"Tanja","full_name":"Schwander, Tanja"},{"last_name":"Arakelyan","first_name":"Marine","full_name":"Arakelyan, Marine"},{"full_name":"Ilgaz, Çetin","first_name":"Çetin","last_name":"Ilgaz"},{"first_name":"Yusuf","last_name":"Kumlutas","full_name":"Kumlutas, Yusuf"},{"full_name":"Harris, David James","first_name":"David James","last_name":"Harris"},{"last_name":"Carretero","first_name":"Miguel A.","full_name":"Carretero, Miguel A."},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"issue":"5","pmid":1,"_id":"11334","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","ddc":["570"],"volume":76,"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).","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."}],"doi":"10.1111/evo.14462","day":"01","isi":1,"external_id":{"pmid":["35323995"],"isi":["000781632500001"]},"date_updated":"2023-08-03T07:00:28Z","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>.","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>","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.","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>."},"year":"2022"},{"ddc":["570"],"volume":8,"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.","abstract":[{"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.","lang":"eng"}],"day":"01","doi":"10.1126/sciadv.abq1263","citation":{"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>.","short":"N. Amberg, F. Pauler, C. Streicher, S. Hippenmeyer, Science Advances 8 (2022).","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.","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>","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>","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.","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>."},"year":"2022","date_updated":"2023-05-31T12:24:10Z","article_type":"original","publisher":"American Association for the Advancement of Science","file_date_updated":"2023-03-21T14:18:10Z","ec_funded":1,"quality_controlled":"1","intvolume":"         8","title":"Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression","date_created":"2022-04-26T15:04:50Z","department":[{"_id":"SiHi"}],"article_processing_charge":"No","publication_status":"published","issue":"44","author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg"},{"first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"11336","status":"public","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/whole-tissue-shapes-brain-development/"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"success":1,"access_level":"open_access","relation":"main_file","file_id":"12742","creator":"patrickd","date_created":"2023-03-21T14:18:10Z","checksum":"0117023e188542082ca6693cf39e7f03","file_size":2973998,"date_updated":"2023-03-21T14:18:10Z","file_name":"sciadv.abq1263.pdf","content_type":"application/pdf"}],"oa":1,"publication_identifier":{"issn":["2375-2548"]},"type":"journal_article","date_published":"2022-11-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"article_number":"abq1263","month":"11","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"},{"name":"Role of Eed in neural stem cell lineage progression","grant_number":"T0101031","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Science Advances"},{"volume":105,"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.","day":"15","arxiv":1,"doi":"10.1103/PhysRevB.105.165149","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."}],"year":"2022","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.","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>.","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>","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.","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review B 105 (2022).","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>."},"date_updated":"2023-08-03T06:33:33Z","external_id":{"isi":["000806812400004"],"arxiv":["2112.11273"]},"isi":1,"publisher":"American Physical Society","article_type":"original","ec_funded":1,"quality_controlled":"1","date_created":"2022-04-28T08:06:10Z","department":[{"_id":"MaSe"}],"article_processing_charge":"No","publication_status":"published","intvolume":"       105","title":"Entanglement and precession in two-dimensional dynamical quantum phase transitions","_id":"11337","author":[{"first_name":"Stefano","last_name":"De Nicola","orcid":"0000-0002-4842-6671","full_name":"De Nicola, Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Michailidis","first_name":"Alexios","full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2112.11273","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"issn":["2469-9950"],"eisbn":["2469-9969"]},"oa":1,"type":"journal_article","date_published":"2022-04-15T00:00:00Z","language":[{"iso":"eng"}],"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Preprint","article_number":"165149","month":"04","publication":"Physical Review B"},{"quality_controlled":"1","file_date_updated":"2022-05-02T06:26:26Z","publisher":"Springer Nature","article_type":"original","pmid":1,"_id":"11339","scopus_import":"1","author":[{"last_name":"Glover","first_name":"Georgina","full_name":"Glover, Georgina"},{"full_name":"Voliotis, Margaritis","first_name":"Margaritis","last_name":"Voliotis"},{"first_name":"Urszula","last_name":"Łapińska","full_name":"Łapińska, Urszula"},{"last_name":"Invergo","first_name":"Brandon M.","full_name":"Invergo, Brandon M."},{"full_name":"Soanes, Darren","last_name":"Soanes","first_name":"Darren"},{"full_name":"O’Neill, Paul","last_name":"O’Neill","first_name":"Paul"},{"last_name":"Moore","first_name":"Karen","full_name":"Moore, Karen"},{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","last_name":"Nikolic","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela"},{"last_name":"Petrov","first_name":"Peter","full_name":"Petrov, Peter"},{"last_name":"Milner","first_name":"David S.","full_name":"Milner, David S."},{"full_name":"Roy, Sumita","first_name":"Sumita","last_name":"Roy"},{"first_name":"Kate","last_name":"Heesom","full_name":"Heesom, Kate"},{"full_name":"Richards, Thomas A.","last_name":"Richards","first_name":"Thomas A."},{"last_name":"Tsaneva-Atanasova","first_name":"Krasimira","full_name":"Tsaneva-Atanasova, Krasimira"},{"full_name":"Pagliara, Stefano","first_name":"Stefano","last_name":"Pagliara"}],"publication_status":"published","department":[{"_id":"CaGu"}],"date_created":"2022-05-01T22:01:41Z","article_processing_charge":"No","title":"Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells","intvolume":"         5","volume":5,"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).","ddc":["570"],"date_updated":"2023-08-03T06:45:26Z","year":"2022","citation":{"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>.","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.","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>","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>","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.","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>.","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)."},"isi":1,"external_id":{"pmid":["35444215"],"isi":["000784143400001"]},"doi":"10.1038/s42003-022-03336-6","day":"20","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"publication":"Communications Biology","has_accepted_license":"1","oa_version":"Published Version","month":"04","article_number":"385","file":[{"creator":"dernst","file_id":"11342","success":1,"access_level":"open_access","relation":"main_file","file_name":"2022_CommBiology_Glover.pdf","content_type":"application/pdf","date_updated":"2022-05-02T06:26:26Z","file_size":2827723,"checksum":"7c6f76ab17393d650825cc240edc84b3","date_created":"2022-05-02T06:26:26Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-04-20T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["2399-3642"]},"oa":1},{"type":"journal_article","date_published":"2022-04-14T00:00:00Z","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"oa":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2203.10524","open_access":"1"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Journal of Physical Chemistry B","oa_version":"Preprint","month":"04","language":[{"iso":"eng"}],"year":"2022","citation":{"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.","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>.","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>","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>","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.","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>.","short":"I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, E. Trizac, Journal of Physical Chemistry B 126 (2022) 3143–3149."},"date_updated":"2023-08-03T06:42:50Z","external_id":{"arxiv":["2203.10524"],"isi":["000796953700022"]},"isi":1,"day":"14","arxiv":1,"doi":"10.1021/acs.jpcb.2c00028","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"}],"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.","volume":126,"scopus_import":"1","_id":"11340","issue":"16","author":[{"last_name":"Palaia","first_name":"Ivan","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa"},{"full_name":"Goyal, Abhay","last_name":"Goyal","first_name":"Abhay"},{"first_name":"Emanuela","last_name":"Del Gado","full_name":"Del Gado, Emanuela"},{"last_name":"Šamaj","first_name":"Ladislav","full_name":"Šamaj, Ladislav"},{"first_name":"Emmanuel","last_name":"Trizac","full_name":"Trizac, Emmanuel"}],"department":[{"_id":"AnSa"}],"article_processing_charge":"No","date_created":"2022-05-01T22:01:42Z","publication_status":"published","intvolume":"       126","title":"Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring","quality_controlled":"1","page":"3143-3149","publisher":"American Chemical Society","article_type":"original"},{"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-05-05T00:00:00Z","type":"journal_article","file":[{"date_updated":"2022-08-05T06:08:24Z","file_name":"2022_Nature_Lukacisin.pdf","content_type":"application/pdf","date_created":"2022-08-05T06:08:24Z","file_size":25360311,"checksum":"d68cd1596bb9fd819b750fe47c8a138a","file_id":"11727","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"project":[{"grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"}],"month":"05","publication":"Nature","has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1038/s41586-022-04633-0","day":"05","abstract":[{"text":"Intragenic regions that are removed during maturation of the RNA transcript—introns—are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein genes that differ primarily in their introns2,3. Although studies have shed light on the role of ribosomal protein introns under stress and starvation4,5,6, understanding the contribution of introns to ribosome regulation remains challenging. Here, by combining isogrowth profiling7 with single-cell protein measurements8, we show that introns can mediate inducible phenotypic heterogeneity that confers a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, which is mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low levels of Rps22B protein result in prolonged survival under sustained starvation, whereas high levels of Rps22B enable cells to grow faster after transient starvation. Furthermore, yeasts growing at high concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression of Rps22B when approaching the stationary phase. Differential intron-mediated regulation of ribosomal protein genes thus provides a way to diversify the population when starvation threatens in natural environments. Our findings reveal a role for introns in inducing phenotypic heterogeneity in changing environments, and suggest that duplicated ribosomal protein genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness9.","lang":"eng"}],"date_updated":"2023-08-03T06:44:50Z","year":"2022","citation":{"ista":"Lukacisin M, Espinosa-Cantú A, Bollenbach MT. 2022. Intron-mediated induction of phenotypic heterogeneity. Nature. 605, 113–118.","short":"M. Lukacisin, A. Espinosa-Cantú, M.T. Bollenbach, Nature 605 (2022) 113–118.","mla":"Lukacisin, Martin, et al. “Intron-Mediated Induction of Phenotypic Heterogeneity.” <i>Nature</i>, vol. 605, Springer Nature, 2022, pp. 113–18, doi:<a href=\"https://doi.org/10.1038/s41586-022-04633-0\">10.1038/s41586-022-04633-0</a>.","ieee":"M. Lukacisin, A. Espinosa-Cantú, and M. T. Bollenbach, “Intron-mediated induction of phenotypic heterogeneity,” <i>Nature</i>, vol. 605. Springer Nature, pp. 113–118, 2022.","chicago":"Lukacisin, Martin, Adriana Espinosa-Cantú, and Mark Tobias Bollenbach. “Intron-Mediated Induction of Phenotypic Heterogeneity.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-04633-0\">https://doi.org/10.1038/s41586-022-04633-0</a>.","apa":"Lukacisin, M., Espinosa-Cantú, A., &#38; Bollenbach, M. T. (2022). Intron-mediated induction of phenotypic heterogeneity. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-04633-0\">https://doi.org/10.1038/s41586-022-04633-0</a>","ama":"Lukacisin M, Espinosa-Cantú A, Bollenbach MT. Intron-mediated induction of phenotypic heterogeneity. <i>Nature</i>. 2022;605:113-118. doi:<a href=\"https://doi.org/10.1038/s41586-022-04633-0\">10.1038/s41586-022-04633-0</a>"},"isi":1,"external_id":{"isi":["000784934100003"],"pmid":["35444278"]},"volume":605,"acknowledgement":"We thank the IST Austria Life Science Facility, the Miba Machine Shop and M. Lukačišinová for support with the liquid handling robot; the Bioimaging Facility at IST Austria, J. Power and B. Meier at the University of Cologne, and C. Göttlinger at the FACS Analysis Facility at the Institute for Genetics, University of Cologne, for support with flow cytometry experiments; L. Horst for the development of the automated experimental methods in Cologne; J. Parenteau, S. Abou Elela, G. Stormo, M. Springer and M. Schuldiner for providing us with yeast strains; B. Fernando, T. Fink, G. Ansmann and G. Chevreau for technical support; H. Köver, G. Tkačik, N. Barton, A. Angermayr and B. Kavčič for support during laboratory relocation; D. Siekhaus, M. Springer and all the members of the Bollenbach group for support and discussions; and K. Mitosch, M. Lukačišinová, G. Liti and A. de Luna for critical reading of our manuscript. This work was supported in part by an Austrian Science Fund (FWF) standalone grant P 27201-B22 (to T.B.), HFSP program Grant RGP0042/2013 (to T.B.), EU Marie Curie Career Integration Grant No. 303507, and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). A.E.-C. was supported by a Georg Forster fellowship from the Alexander von Humboldt Foundation.","ddc":["570"],"publication_status":"published","date_created":"2022-05-01T22:01:42Z","article_processing_charge":"No","title":"Intron-mediated induction of phenotypic heterogeneity","intvolume":"       605","pmid":1,"_id":"11341","scopus_import":"1","author":[{"id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Lukacisin","orcid":"0000-0001-6549-4177","full_name":"Lukacisin, Martin"},{"full_name":"Espinosa-Cantú, Adriana","last_name":"Espinosa-Cantú","first_name":"Adriana"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"publisher":"Springer Nature","article_type":"original","page":"113-118","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-08-05T06:08:24Z"},{"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","page":"3209-3218","file_date_updated":"2022-08-05T06:13:19Z","article_processing_charge":"Yes (via OA deal)","date_created":"2022-05-02T07:01:59Z","department":[{"_id":"KiMo"}],"publication_status":"published","intvolume":"       108","title":"Vortices nucleation by inherent fluctuations in nematic liquid crystal cells","scopus_import":"1","_id":"11343","author":[{"first_name":"Esteban","last_name":"Aguilera","full_name":"Aguilera, Esteban"},{"first_name":"Marcel G.","last_name":"Clerc","full_name":"Clerc, Marcel G."},{"last_name":"Zambra","first_name":"Valeska","full_name":"Zambra, Valeska","id":"467ed36b-dc96-11ea-b7c8-b043a380b282"}],"acknowledgement":"The authors thank Enrique Calisto,Michal Kowalczyk, and Michel Ferre for fructified discussions. This work was funded by ANID—Millennium Science Initiative Program—ICN17_012. MGC is thankful for financial support from the Fondecyt 1210353 project.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","volume":108,"ddc":["530"],"day":"01","doi":"10.1007/s11071-022-07396-5","abstract":[{"text":"Multistable systems are characterized by exhibiting domain coexistence, where each domain accounts for the different equilibrium states. In case these systems are described by vectorial fields, domains can be connected through topological defects. Vortices are one of the most frequent and studied topological defect points. Optical vortices are equally relevant for their fundamental features as beams with topological features and their applications in image processing, telecommunications, optical tweezers, and quantum information. A natural source of optical vortices is the interaction of light beams with matter vortices in liquid crystal cells. The rhythms that govern the emergence of matter vortices due to fluctuations are not established. Here, we investigate the nucleation mechanisms of the matter vortices in liquid crystal cells and establish statistical laws that govern them. Based on a stochastic amplitude equation, the law for the number of nucleated vortices as a function of anisotropy, voltage, and noise level intensity is set. Experimental observations in a nematic liquid crystal cell with homeotropic anchoring and a negative anisotropic dielectric constant under the influence of a transversal electric field show a qualitative agreement with the theoretical findings.","lang":"eng"}],"year":"2022","citation":{"ista":"Aguilera E, Clerc MG, Zambra V. 2022. Vortices nucleation by inherent fluctuations in nematic liquid crystal cells. Nonlinear Dynamics. 108, 3209–3218.","short":"E. Aguilera, M.G. Clerc, V. Zambra, Nonlinear Dynamics 108 (2022) 3209–3218.","mla":"Aguilera, Esteban, et al. “Vortices Nucleation by Inherent Fluctuations in Nematic Liquid Crystal Cells.” <i>Nonlinear Dynamics</i>, vol. 108, Springer Nature, 2022, pp. 3209–18, doi:<a href=\"https://doi.org/10.1007/s11071-022-07396-5\">10.1007/s11071-022-07396-5</a>.","ieee":"E. Aguilera, M. G. Clerc, and V. Zambra, “Vortices nucleation by inherent fluctuations in nematic liquid crystal cells,” <i>Nonlinear Dynamics</i>, vol. 108. Springer Nature, pp. 3209–3218, 2022.","chicago":"Aguilera, Esteban, Marcel G. Clerc, and Valeska Zambra. “Vortices Nucleation by Inherent Fluctuations in Nematic Liquid Crystal Cells.” <i>Nonlinear Dynamics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11071-022-07396-5\">https://doi.org/10.1007/s11071-022-07396-5</a>.","ama":"Aguilera E, Clerc MG, Zambra V. Vortices nucleation by inherent fluctuations in nematic liquid crystal cells. <i>Nonlinear Dynamics</i>. 2022;108:3209-3218. doi:<a href=\"https://doi.org/10.1007/s11071-022-07396-5\">10.1007/s11071-022-07396-5</a>","apa":"Aguilera, E., Clerc, M. G., &#38; Zambra, V. (2022). Vortices nucleation by inherent fluctuations in nematic liquid crystal cells. <i>Nonlinear Dynamics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11071-022-07396-5\">https://doi.org/10.1007/s11071-022-07396-5</a>"},"date_updated":"2023-08-03T06:46:54Z","external_id":{"isi":["000784871800001"]},"isi":1,"keyword":["Electrical and Electronic Engineering","Applied Mathematics","Mechanical Engineering","Ocean Engineering","Aerospace Engineering","Control and Systems Engineering"],"language":[{"iso":"eng"}],"oa_version":"Published Version","month":"06","has_accepted_license":"1","publication":"Nonlinear Dynamics","file":[{"creator":"dernst","file_id":"11728","success":1,"relation":"main_file","access_level":"open_access","file_name":"2022_NonlinearDyn_Aguilera.pdf","content_type":"application/pdf","date_updated":"2022-08-05T06:13:19Z","file_size":1416049,"checksum":"7d80cdece4e1b1c2106e6772a9622f60","date_created":"2022-08-05T06:13:19Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"issn":["0924-090X"],"eissn":["1573-269X"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-06-01T00:00:00Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"creator":"dernst","file_id":"11349","relation":"main_file","access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2022_ScientificReports_Dranenko.pdf","date_updated":"2022-05-02T09:05:20Z","checksum":"12601b8a5c6b83bb618f92bcb963ecc9","file_size":3564155,"date_created":"2022-05-02T09:05:20Z"}],"date_published":"2022-04-27T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["2045-2322"]},"language":[{"iso":"eng"}],"publication":"Scientific Reports","has_accepted_license":"1","month":"04","article_number":"6868","oa_version":"Published Version","project":[{"grant_number":"I05127","name":"Evolutionary analysis of gene regulation","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"ddc":["570"],"volume":12,"acknowledgement":"The project was initiated with Aygul Minnegalieva and Yulia Yakovleva at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya, and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also thank Peter Vlasov for fruitful discussions.This study was supported by the Russian Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. ","isi":1,"external_id":{"isi":["000788639400032"],"pmid":["35477739"]},"date_updated":"2023-08-03T06:59:49Z","citation":{"short":"N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific Reports 12 (2022).","mla":"Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” <i>Scientific Reports</i>, vol. 12, 6868, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41598-022-10827-3\">10.1038/s41598-022-10827-3</a>.","ista":"Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. 12, 6868.","ama":"Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. <i>Scientific Reports</i>. 2022;12. doi:<a href=\"https://doi.org/10.1038/s41598-022-10827-3\">10.1038/s41598-022-10827-3</a>","apa":"Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., &#38; Bochkareva, O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-022-10827-3\">https://doi.org/10.1038/s41598-022-10827-3</a>","chicago":"Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” <i>Scientific Reports</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41598-022-10827-3\">https://doi.org/10.1038/s41598-022-10827-3</a>.","ieee":"N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” <i>Scientific Reports</i>, vol. 12. Springer Nature, 2022."},"year":"2022","abstract":[{"text":"Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.","lang":"eng"}],"doi":"10.1038/s41598-022-10827-3","day":"27","file_date_updated":"2022-05-02T09:05:20Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"Springer Nature","author":[{"full_name":"Dranenko, NO","first_name":"NO","last_name":"Dranenko"},{"full_name":"Tutukina, MN","last_name":"Tutukina","first_name":"MN"},{"first_name":"MS","last_name":"Gelfand","full_name":"Gelfand, MS"},{"last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"}],"pmid":1,"_id":"11344","scopus_import":"1","title":"Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia","intvolume":"        12","publication_status":"published","department":[{"_id":"FyKo"}],"date_created":"2022-05-02T07:08:42Z","article_processing_charge":"No"},{"file":[{"file_name":"2022_CurrentBiology_Nicolas.pdf","content_type":"application/pdf","date_updated":"2022-08-05T06:29:18Z","file_size":12827717,"checksum":"af3f24d97c016d844df237abef987639","date_created":"2022-08-05T06:29:18Z","creator":"dernst","file_id":"11730","success":1,"access_level":"open_access","relation":"main_file"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-06-06T00:00:00Z","publication_identifier":{"issn":["0960-9822"]},"oa":1,"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Current Biology","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"oa_version":"Published Version","month":"06","volume":32,"acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","ddc":["570"],"year":"2022","citation":{"ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” <i>Current Biology</i>, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022.","chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>.","ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. 2022;32(11):P2375-2389. doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., &#38; Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>","ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>."},"date_updated":"2023-08-03T07:05:36Z","external_id":{"pmid":["35508170"],"isi":["000822399200019"]},"isi":1,"day":"06","doi":"10.1016/j.cub.2022.04.024","abstract":[{"lang":"eng","text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall."}],"quality_controlled":"1","page":"P2375-2389","file_date_updated":"2022-08-05T06:29:18Z","publisher":"Elsevier","article_type":"original","scopus_import":"1","_id":"11351","pmid":1,"issue":"11","author":[{"full_name":"Nicolas, William J.","first_name":"William J.","last_name":"Nicolas"},{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dutka","first_name":"Przemysław","full_name":"Dutka, Przemysław"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"},{"last_name":"Jensen","first_name":"Grant","full_name":"Jensen, Grant"},{"last_name":"Meyerowitz","first_name":"Elliot","full_name":"Meyerowitz, Elliot"}],"department":[{"_id":"FlSc"}],"date_created":"2022-05-04T06:22:06Z","article_processing_charge":"No","publication_status":"published","intvolume":"        32","title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks"},{"day":"13","doi":"10.1103/PRXQuantum.3.020309","abstract":[{"lang":"eng","text":"Micro- and nanoscale optical or microwave cavities are used in a wide range of classical applications and quantum science experiments, ranging from precision measurements, laser technologies to quantum control of mechanical motion. The dissipative photon loss via absorption, present to some extent in any optical cavity, is known to introduce thermo-optical effects and thereby impose fundamental limits on precision measurements. Here, we theoretically and experimentally reveal that such dissipative photon absorption can result in quantum feedback via in-loop field detection of the absorbed optical field, leading to the intracavity field fluctuations to be squashed or antisquashed. A closed-loop dissipative quantum feedback to the cavity field arises. Strikingly, this modifies the optical cavity susceptibility in coherent response measurements (capable of both increasing or decreasing the bare cavity linewidth) and causes excess noise and correlations in incoherent interferometric optomechanical measurements using a cavity, that is parametrically coupled to a mechanical oscillator. We experimentally observe such unanticipated dissipative dynamics in optomechanical spectroscopy of sideband-cooled optomechanical crystal cavitiess at both cryogenic temperature (approximately 8 K) and ambient conditions. The dissipative feedback introduces effective modifications to the optical cavity linewidth and the optomechanical scattering rate and gives rise to excess imprecision noise in the interferometric quantum measurement of mechanical motion. Such dissipative feedback differs fundamentally from a quantum nondemolition feedback, e.g., optical Kerr squeezing. The dissipative feedback itself always results in an antisqueezed out-of-loop optical field, while it can enhance the coexisting Kerr squeezing under certain conditions. Our result applies to cavity spectroscopy in both optical and superconducting microwave cavities, and equally applies to any dissipative feedback mechanism of different bandwidth inside the cavity. It has wide-ranging implications for future dissipation engineering, such as dissipation enhanced sideband cooling and Kerr squeezing, quantum frequency conversion, and nonreciprocity in photonic systems."}],"year":"2022","citation":{"ista":"Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. 2022. Dissipative quantum feedback in measurements using a parametrically coupled microcavity. PRX Quantum. 3(2), 020309.","short":"L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, T.J. Kippenberg, PRX Quantum 3 (2022).","mla":"Qiu, Liu, et al. “Dissipative Quantum Feedback in Measurements Using a Parametrically Coupled Microcavity.” <i>PRX Quantum</i>, vol. 3, no. 2, 020309, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">10.1103/PRXQuantum.3.020309</a>.","ieee":"L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, and T. J. Kippenberg, “Dissipative quantum feedback in measurements using a parametrically coupled microcavity,” <i>PRX Quantum</i>, vol. 3, no. 2. American Physical Society, 2022.","chicago":"Qiu, Liu, Guanhao Huang, Itay Shomroni, Jiahe Pan, Paul Seidler, and Tobias J. Kippenberg. “Dissipative Quantum Feedback in Measurements Using a Parametrically Coupled Microcavity.” <i>PRX Quantum</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">https://doi.org/10.1103/PRXQuantum.3.020309</a>.","ama":"Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. Dissipative quantum feedback in measurements using a parametrically coupled microcavity. <i>PRX Quantum</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">10.1103/PRXQuantum.3.020309</a>","apa":"Qiu, L., Huang, G., Shomroni, I., Pan, J., Seidler, P., &#38; Kippenberg, T. J. (2022). Dissipative quantum feedback in measurements using a parametrically coupled microcavity. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">https://doi.org/10.1103/PRXQuantum.3.020309</a>"},"date_updated":"2023-08-03T07:05:00Z","external_id":{"isi":["000789316700001"]},"isi":1,"acknowledgement":"L.Q. acknowledges fruitful discussions with D. Vitali, R. Schnabel, P.K. Lam, A. Nunnenkamp, and D. Malz. This work is supported by the EUH2020 research and innovation programme under Grant No. 732894 (FET Proactive HOT), and the European Research Council through \r\nGrant No. 835329 (ExCOM-cCEO). This work was further supported by Swiss National Science Foundation under Grant Agreements No. 185870 (Ambizione) and No. 204927. Samples were fabricated at the Center of MicroNanoTechnology (CMi) at EPFL and the Binnig and Rohrer Nanotechnology Center at IBM Research-Zurich.","volume":3,"ddc":["530"],"date_created":"2022-05-08T22:01:43Z","article_processing_charge":"No","department":[{"_id":"JoFi"}],"publication_status":"published","intvolume":"         3","title":"Dissipative quantum feedback in measurements using a parametrically coupled microcavity","scopus_import":"1","_id":"11353","issue":"2","author":[{"id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","first_name":"Liu","full_name":"Qiu, Liu","orcid":"0000-0003-4345-4267"},{"full_name":"Huang, Guanhao","first_name":"Guanhao","last_name":"Huang"},{"last_name":"Shomroni","first_name":"Itay","full_name":"Shomroni, Itay"},{"first_name":"Jiahe","last_name":"Pan","full_name":"Pan, Jiahe"},{"full_name":"Seidler, Paul","first_name":"Paul","last_name":"Seidler"},{"full_name":"Kippenberg, Tobias J.","first_name":"Tobias J.","last_name":"Kippenberg"}],"publisher":"American Physical Society","article_type":"original","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-05-09T07:10:51Z","publication_identifier":{"eissn":["26913399"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-04-13T00:00:00Z","file":[{"access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"11358","file_size":1657177,"checksum":"35ff9ddf1d54f64432e435b660edaeb6","date_created":"2022-05-09T07:10:51Z","file_name":"2022_PRXQuantum_Qiu.pdf","content_type":"application/pdf","date_updated":"2022-05-09T07:10:51Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","project":[{"grant_number":"732894","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","article_number":"020309","month":"04","has_accepted_license":"1","publication":"PRX Quantum","language":[{"iso":"eng"}]},{"page":"591-648","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"Institute of Mathematical Statistics","author":[{"orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo","first_name":"Lorenzo","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E"}],"issue":"2","_id":"11354","scopus_import":"1","title":"The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold","intvolume":"        50","publication_status":"published","date_created":"2022-05-08T22:01:44Z","department":[{"_id":"JaMa"}],"article_processing_charge":"No","volume":50,"acknowledgement":"Research supported by the Sonderforschungsbereich 1060 and the Hausdorff Center for Mathematics. The author gratefully acknowledges funding of his current position at IST Austria by the Austrian Science Fund (FWF) grant F65 and by the European Research Council (ERC, Grant agreement No. 716117, awarded to Prof. Dr. Jan Maas).","isi":1,"external_id":{"isi":["000773518500005"],"arxiv":["1811.11598"]},"date_updated":"2023-10-17T12:50:24Z","citation":{"ista":"Dello Schiavo L. 2022. The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. Annals of Probability. 50(2), 591–648.","mla":"Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space of Probability Measures over a Closed Riemannian Manifold.” <i>Annals of Probability</i>, vol. 50, no. 2, Institute of Mathematical Statistics, 2022, pp. 591–648, doi:<a href=\"https://doi.org/10.1214/21-AOP1541\">10.1214/21-AOP1541</a>.","short":"L. Dello Schiavo, Annals of Probability 50 (2022) 591–648.","ieee":"L. Dello Schiavo, “The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold,” <i>Annals of Probability</i>, vol. 50, no. 2. Institute of Mathematical Statistics, pp. 591–648, 2022.","chicago":"Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space of Probability Measures over a Closed Riemannian Manifold.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AOP1541\">https://doi.org/10.1214/21-AOP1541</a>.","ama":"Dello Schiavo L. The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. <i>Annals of Probability</i>. 2022;50(2):591-648. doi:<a href=\"https://doi.org/10.1214/21-AOP1541\">10.1214/21-AOP1541</a>","apa":"Dello Schiavo, L. (2022). The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AOP1541\">https://doi.org/10.1214/21-AOP1541</a>"},"year":"2022","abstract":[{"text":"We construct a recurrent diffusion process with values in the space of probability measures over an arbitrary closed Riemannian manifold of dimension d≥2. The process is associated with the Dirichlet form defined by integration of the Wasserstein gradient w.r.t. the Dirichlet–Ferguson measure, and is the counterpart on multidimensional base spaces to the modified massive Arratia flow over the unit interval described in V. Konarovskyi and M.-K. von Renesse (Comm. Pure Appl. Math. 72 (2019) 764–800). Together with two different constructions of the process, we discuss its ergodicity, invariant sets, finite-dimensional approximations, and Varadhan short-time asymptotics.","lang":"eng"}],"arxiv":1,"doi":"10.1214/21-AOP1541","day":"01","language":[{"iso":"eng"}],"publication":"Annals of Probability","month":"03","oa_version":"Preprint","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1811.11598"}],"date_published":"2022-03-01T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"issn":["0091-1798"],"eissn":["2168-894X"]}},{"volume":13241,"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 956123 and was funded in part by the FWF project W1255-N23 and by the ERC-2020-AdG 101020093.","ddc":["000"],"doi":"10.1007/978-3-030-99429-7_1","day":"29","abstract":[{"lang":"eng","text":"Contract-based design is a promising methodology for taming the complexity of developing sophisticated systems. A formal contract distinguishes between assumptions, which are constraints that the designer of a component puts on the environments in which the component can be used safely, and guarantees, which are promises that the designer asks from the team that implements the component. A theory of formal contracts can be formalized as an interface theory, which supports the composition and refinement of both assumptions and guarantees.\r\nAlthough there is a rich landscape of contract-based design methods that address functional and extra-functional properties, we present the first interface theory that is designed for ensuring system-wide security properties. Our framework provides a refinement relation and a composition operation that support both incremental design and independent implementability. We develop our theory for both stateless and stateful interfaces. We illustrate the applicability of our framework with an example inspired from the automotive domain."}],"date_updated":"2023-08-03T07:03:40Z","year":"2022","citation":{"short":"E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2022, pp. 3–22.","mla":"Bartocci, Ezio, et al. “Information-Flow Interfaces.” <i>Fundamental Approaches to Software Engineering</i>, vol. 13241, Springer Nature, 2022, pp. 3–22, doi:<a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">10.1007/978-3-030-99429-7_1</a>.","ista":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Information-flow interfaces. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13241, 3–22.","apa":"Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., &#38; Da Costa, A. O. (2022). Information-flow interfaces. In <i>Fundamental Approaches to Software Engineering</i> (Vol. 13241, pp. 3–22). Munich, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">https://doi.org/10.1007/978-3-030-99429-7_1</a>","ama":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Information-flow interfaces. In: <i>Fundamental Approaches to Software Engineering</i>. Vol 13241. Springer Nature; 2022:3-22. doi:<a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">10.1007/978-3-030-99429-7_1</a>","chicago":"Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira Da Costa. “Information-Flow Interfaces.” In <i>Fundamental Approaches to Software Engineering</i>, 13241:3–22. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">https://doi.org/10.1007/978-3-030-99429-7_1</a>.","ieee":"E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa, “Information-flow interfaces,” in <i>Fundamental Approaches to Software Engineering</i>, Munich, Germany, 2022, vol. 13241, pp. 3–22."},"isi":1,"external_id":{"isi":["000782393600001"]},"publisher":"Springer Nature","page":"3-22","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-05-09T06:52:44Z","publication_status":"published","department":[{"_id":"ToHe"}],"date_created":"2022-05-08T22:01:44Z","article_processing_charge":"No","alternative_title":["LNCS"],"title":"Information-flow interfaces","intvolume":"     13241","_id":"11355","scopus_import":"1","author":[{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Da Costa, Ana Oliveira","last_name":"Da Costa","first_name":"Ana Oliveira"}],"file":[{"date_updated":"2022-05-09T06:52:44Z","file_name":"2022_LNCS_Bartocci.pdf","content_type":"application/pdf","date_created":"2022-05-09T06:52:44Z","file_size":479146,"checksum":"7f6f860b20b8de2a249e9c1b4eee15cf","file_id":"11357","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030994280"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-03-29T00:00:00Z","type":"conference","conference":{"location":"Munich, Germany","end_date":"2022-04-07","start_date":"2022-04-02","name":"FASE: Fundamental Approaches to Software Engineering"},"language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"month":"03","publication":"Fundamental Approaches to Software Engineering","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"}],"month":"06","publication":"Science Bulletin","main_file_link":[{"url":"https://doi.org/10.1016/j.scib.2022.04.007","open_access":"1"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2095-9273"],"eissn":["2095-9281"]},"oa":1,"date_published":"2022-06-15T00:00:00Z","type":"journal_article","publisher":"Elsevier","article_type":"letter_note","page":"1105-1107","quality_controlled":"1","publication_status":"published","department":[{"_id":"MaIb"}],"date_created":"2022-05-08T22:01:44Z","article_processing_charge":"No","title":"Distinct electron and hole transports in SnSe crystals","intvolume":"        67","_id":"11356","scopus_import":"1","author":[{"first_name":"Cheng","last_name":"Chang","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"full_name":"Qin, Bingchao","first_name":"Bingchao","last_name":"Qin"},{"full_name":"Su, Lizhong","last_name":"Su","first_name":"Lizhong"},{"last_name":"Zhao","first_name":"Li Dong","full_name":"Zhao, Li Dong"}],"issue":"11","acknowledgement":"This work was supported by the National Science Fund for Distinguished Young Scholars (51925101), National Key Research and Development Program of China (2018YFA0702100), 111 Project (B17002), and Lise Meitner Project (M2889-N).","volume":67,"doi":"10.1016/j.scib.2022.04.007","day":"15","date_updated":"2023-08-03T07:04:10Z","year":"2022","citation":{"ista":"Chang C, Qin B, Su L, Zhao LD. 2022. Distinct electron and hole transports in SnSe crystals. Science Bulletin. 67(11), 1105–1107.","short":"C. Chang, B. Qin, L. Su, L.D. Zhao, Science Bulletin 67 (2022) 1105–1107.","mla":"Chang, Cheng, et al. “Distinct Electron and Hole Transports in SnSe Crystals.” <i>Science Bulletin</i>, vol. 67, no. 11, Elsevier, 2022, pp. 1105–07, doi:<a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">10.1016/j.scib.2022.04.007</a>.","ieee":"C. Chang, B. Qin, L. Su, and L. D. Zhao, “Distinct electron and hole transports in SnSe crystals,” <i>Science Bulletin</i>, vol. 67, no. 11. Elsevier, pp. 1105–1107, 2022.","chicago":"Chang, Cheng, Bingchao Qin, Lizhong Su, and Li Dong Zhao. “Distinct Electron and Hole Transports in SnSe Crystals.” <i>Science Bulletin</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">https://doi.org/10.1016/j.scib.2022.04.007</a>.","apa":"Chang, C., Qin, B., Su, L., &#38; Zhao, L. D. (2022). Distinct electron and hole transports in SnSe crystals. <i>Science Bulletin</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">https://doi.org/10.1016/j.scib.2022.04.007</a>","ama":"Chang C, Qin B, Su L, Zhao LD. Distinct electron and hole transports in SnSe crystals. <i>Science Bulletin</i>. 2022;67(11):1105-1107. doi:<a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">10.1016/j.scib.2022.04.007</a>"},"isi":1,"external_id":{"isi":["000835291100006"]}},{"license":"https://creativecommons.org/licenses/by-nd/4.0/","_id":"11362","author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"}],"article_processing_charge":"No","date_created":"2022-05-12T07:14:01Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Learning verifiable representations","ec_funded":1,"page":"124","file_date_updated":"2022-05-17T15:19:39Z","publisher":"Institute of Science and Technology Austria","citation":{"apa":"Lechner, M. (2022). <i>Learning verifiable representations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11362\">https://doi.org/10.15479/at:ista:11362</a>","ama":"Lechner M. Learning verifiable representations. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11362\">10.15479/at:ista:11362</a>","chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11362\">https://doi.org/10.15479/at:ista:11362</a>.","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022.","short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","mla":"Lechner, Mathias. <i>Learning Verifiable Representations</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11362\">10.15479/at:ista:11362</a>.","ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria."},"year":"2022","date_updated":"2025-07-14T09:10:11Z","day":"12","doi":"10.15479/at:ista:11362","degree_awarded":"PhD","abstract":[{"text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks.","lang":"eng"}],"ddc":["004"],"has_accepted_license":"1","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"oa_version":"Published Version","month":"05","keyword":["neural networks","verification","machine learning"],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"type":"dissertation","date_published":"2022-05-12T00:00:00Z","publication_identifier":{"isbn":["978-3-99078-017-6"]},"oa":1,"supervisor":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"}],"file":[{"access_level":"closed","relation":"source_file","creator":"mlechner","file_id":"11378","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","file_size":13210143,"date_created":"2022-05-13T12:33:26Z","file_name":"src.zip","content_type":"application/zip","date_updated":"2022-05-13T12:49:00Z"},{"access_level":"open_access","relation":"main_file","creator":"mlechner","file_id":"11382","file_size":2732536,"checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","date_created":"2022-05-16T08:02:28Z","file_name":"thesis_main-a2.pdf","content_type":"application/pdf","date_updated":"2022-05-17T15:19:39Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"11366","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7808"},{"relation":"part_of_dissertation","id":"10666","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10665"},{"relation":"part_of_dissertation","id":"10667","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public"},{"author":[{"first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amini, Alexander","last_name":"Amini","first_name":"Alexander"},{"full_name":"Rus, Daniela","first_name":"Daniela","last_name":"Rus"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A"}],"_id":"11366","publication":"arXiv","month":"04","title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","article_number":"2204.07373","publication_status":"submitted","oa_version":"Preprint","date_created":"2022-05-12T13:20:17Z","department":[{"_id":"ToHe"}],"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"language":[{"iso":"eng"}],"ec_funded":1,"date_published":"2022-04-15T00:00:00Z","type":"preprint","external_id":{"arxiv":["2204.07373"]},"date_updated":"2023-08-01T13:36:50Z","citation":{"chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2204.07373\">https://doi.org/10.48550/arXiv.2204.07373</a>.","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” <i>arXiv</i>. .","apa":"Lechner, M., Amini, A., Rus, D., &#38; Henzinger, T. A. (n.d.). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2204.07373\">https://doi.org/10.48550/arXiv.2204.07373</a>","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2204.07373\">10.48550/arXiv.2204.07373</a>","ista":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. arXiv, 2204.07373.","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>ArXiv</i>, 2204.07373, doi:<a href=\"https://doi.org/10.48550/arXiv.2204.07373\">10.48550/arXiv.2204.07373</a>.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, ArXiv (n.d.)."},"year":"2022","abstract":[{"lang":"eng","text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not\r\ncome for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off\r\nbut inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in\r\nconjunction with adversarial robot learning can make adversarial training suitable for real-world robot applications. We evaluate a wide variety of robot learning tasks ranging from autonomous driving in a high-fidelity environment\r\namenable to sim-to-real deployment, to mobile robot gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative side-effects caused by\r\nadversarial training still outweigh the improvements by an order of magnitude. We conclude that more substantial advances in robust learning methods are necessary before they can benefit robot learning tasks in practice."}],"oa":1,"arxiv":1,"doi":"10.48550/arXiv.2204.07373","day":"15","status":"public","related_material":{"record":[{"status":"public","id":"11362","relation":"dissertation_contains"},{"relation":"later_version","id":"12704","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in parts by the ERC-2020-AdG 101020093, National Science Foundation (NSF), and JP\r\nMorgan Graduate Fellowships. We thank Christoph Lampert for inspiring this work.\r\n","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.07373","open_access":"1"}]}]