[{"_id":"14605","quality_controlled":"1","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"citation":{"apa":"Ouyang, N., Zeng, Z., Wang, C., Wang, Q., &#38; Chen, Y. (2023). Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">https://doi.org/10.1103/PhysRevB.108.174302</a>","mla":"Ouyang, Niuchang, et al. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” <i>Physical Review B</i>, vol. 108, no. 17, 174302, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">10.1103/PhysRevB.108.174302</a>.","ista":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. 2023. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical Review B. 108(17), 174302.","short":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (2023).","ieee":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, and Y. Chen, “Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I),” <i>Physical Review B</i>, vol. 108, no. 17. American Physical Society, 2023.","ama":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). <i>Physical Review B</i>. 2023;108(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">10.1103/PhysRevB.108.174302</a>","chicago":"Ouyang, Niuchang, Zezhu Zeng, Chen Wang, Qi Wang, and Yue Chen. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">https://doi.org/10.1103/PhysRevB.108.174302</a>."},"type":"journal_article","scopus_import":"1","abstract":[{"text":"The phonon transport mechanisms and ultralow lattice thermal conductivities (κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein, we study the lattice dynamics and thermal property of AgX under the framework of perturbation theory and the two-channel Wigner thermal transport model based on accurate machine learning potentials. We find that an accurate extraction of the third-order atomic force constants from largely displaced configurations is significant for the calculation of the κL of AgX, and the coherence thermal transport is also non-negligible. In AgI, however, the calculated κL still considerably overestimates the experimental values even including four-phonon scatterings. Molecular dynamics (MD) simulations using machine learning potential suggest an important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency phonon linewidths of AgI at room temperature, which can be related to the simultaneous restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated using MD phonon lifetimes including full-order lattice anharmonicity shows a better agreement with experiments.","lang":"eng"}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)","author":[{"full_name":"Ouyang, Niuchang","last_name":"Ouyang","first_name":"Niuchang"},{"last_name":"Zeng","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","full_name":"Zeng, Zezhu"},{"full_name":"Wang, Chen","last_name":"Wang","first_name":"Chen"},{"last_name":"Wang","first_name":"Qi","full_name":"Wang, Qi"},{"first_name":"Yue","last_name":"Chen","full_name":"Chen, Yue"}],"publisher":"American Physical Society","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"BiCh"}],"date_created":"2023-11-26T23:00:54Z","status":"public","day":"01","volume":108,"ec_funded":1,"oa_version":"None","doi":"10.1103/PhysRevB.108.174302","publication":"Physical Review B","date_updated":"2023-11-28T07:48:55Z","issue":"17","month":"11","intvolume":"       108","date_published":"2023-11-01T00:00:00Z","article_number":"174302","acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (Grants No. 17318122 and No. 17306721). The authors are grateful for the research computing facilities offered by ITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","year":"2023"},{"ddc":["000"],"date_created":"2023-11-26T23:00:55Z","status":"public","day":"15","volume":8,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/1389"}],"publication":"32nd USENIX Security Symposium","date_updated":"2023-11-28T09:17:38Z","oa":1,"intvolume":"         8","month":"08","date_published":"2023-08-15T00:00:00Z","acknowledgement":"The authors would like to thank Amit Agarwal, Andrew Miller, and Tom Yurek for the helpful discussions related to the paper. This work is funded in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship, the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N.","year":"2023","page":"5359-5376","conference":{"name":"USENIX Security Symposium","end_date":"2023-08-11","start_date":"2023-08-09","location":"Anaheim, CA, United States"},"_id":"14609","quality_controlled":"1","citation":{"ama":"Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In: <i>32nd USENIX Security Symposium</i>. Vol 8. Usenix; 2023:5359-5376.","short":"S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium, Usenix, 2023, pp. 5359–5376.","ieee":"S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling,” in <i>32nd USENIX Security Symposium</i>, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376.","ista":"Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. 32nd USENIX Security Symposium. USENIX Security Symposium vol. 8, 5359–5376.","chicago":"Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” In <i>32nd USENIX Security Symposium</i>, 8:5359–76. Usenix, 2023.","apa":"Das, S., Xiang, Z., Kokoris Kogias, E., &#38; Ren, L. (2023). Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In <i>32nd USENIX Security Symposium</i> (Vol. 8, pp. 5359–5376). Anaheim, CA, United States: Usenix.","mla":"Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” <i>32nd USENIX Security Symposium</i>, vol. 8, Usenix, 2023, pp. 5359–76."},"publication_identifier":{"isbn":["9781713879497"]},"file_date_updated":"2023-11-28T09:14:34Z","type":"conference","scopus_import":"1","abstract":[{"text":"Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art.","lang":"eng"}],"project":[{"grant_number":"F8512","name":"Secure Network and Hardware for Efficient Blockchains","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f"}],"publication_status":"published","file":[{"date_created":"2023-11-28T09:14:34Z","date_updated":"2023-11-28T09:14:34Z","file_name":"2023_USENIX_Das.pdf","success":1,"access_level":"open_access","relation":"main_file","checksum":"1a730765930138e23c6efd2575872641","file_size":704331,"creator":"dernst","content_type":"application/pdf","file_id":"14621"}],"title":"Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Das","first_name":"Sourav","full_name":"Das, Sourav"},{"full_name":"Xiang, Zhuolun","last_name":"Xiang","first_name":"Zhuolun"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"full_name":"Ren, Ling","first_name":"Ling","last_name":"Ren"}],"has_accepted_license":"1","publisher":"Usenix","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"ElKo"}]},{"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"citation":{"mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>.","apa":"Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino, E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>","chicago":"Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos, Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>.","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. 2023. doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>","short":"C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature (2023).","ieee":"C. Bussi <i>et al.</i>, “Stress granules plug and stabilize damaged endolysosomal membranes,” <i>Nature</i>. Springer Nature, 2023.","ista":"Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress granules plug and stabilize damaged endolysosomal membranes. Nature."},"type":"journal_article","abstract":[{"text":"<jats:title>Abstract</jats:title><jats:p>Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells<jats:sup>1,2</jats:sup>. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis<jats:sup>3–7</jats:sup>. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for <jats:italic>Mycobacterium tuberculosis</jats:italic>, a human pathogen that exploits endomembrane damage to survive within the host.</jats:p>","lang":"eng"}],"_id":"14610","quality_controlled":"1","publication_status":"epub_ahead","publisher":"Springer Nature","author":[{"full_name":"Bussi, Claudio","last_name":"Bussi","first_name":"Claudio"},{"last_name":"Mangiarotti","first_name":"Agustín","full_name":"Mangiarotti, Agustín"},{"last_name":"Vanhille-Campos","first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo"},{"first_name":"Beren","last_name":"Aylan","full_name":"Aylan, Beren"},{"full_name":"Pellegrino, Enrica","last_name":"Pellegrino","first_name":"Enrica"},{"last_name":"Athanasiadi","first_name":"Natalia","full_name":"Athanasiadi, Natalia"},{"full_name":"Fearns, Antony","first_name":"Antony","last_name":"Fearns"},{"full_name":"Rodgers, Angela","first_name":"Angela","last_name":"Rodgers"},{"full_name":"Franzmann, Titus M.","first_name":"Titus M.","last_name":"Franzmann"},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"Rumiana","last_name":"Dimova","full_name":"Dimova, Rumiana"},{"full_name":"Gutierrez, Maximiliano G.","first_name":"Maximiliano G.","last_name":"Gutierrez"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Stress granules plug and stabilize damaged endolysosomal membranes","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"article_type":"original","pmid":1,"date_created":"2023-11-27T07:56:37Z","day":"15","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41586-023-06726-w"}],"doi":"10.1038/s41586-023-06726-w","publication":"Nature","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-023-06882-z"}],"record":[{"id":"14472","status":"public","relation":"research_data"}]},"oa_version":"Published Version","month":"11","date_published":"2023-11-15T00:00:00Z","acknowledgement":"We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy and High-throughput Screening facilities at the Crick for their support in various aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO U2OS cells. The authors thank N. Chen for providing the purified glycinin protein; Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for helpful discussions and valuable input regarding analysis methods. This work was supported by the Francis Crick Institute (to M.G.G.), which receives its core funding from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and the Wellcome Trust (FC001092). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from the European Respiratory Society and the European Union’s H2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding by the Royal Society and the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations were carried out on the high-performance computing cluster at the Institute of Science and Technology Austria. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.\r\nOpen Access funding provided by The Francis Crick Institute.","date_updated":"2023-11-27T09:05:08Z","keyword":["Multidisciplinary"],"oa":1,"external_id":{"pmid":["37968398"]},"year":"2023"},{"has_accepted_license":"1","publisher":"Oxford University Press","author":[{"orcid":"0000-0002-1197-8616","last_name":"Lasne","first_name":"Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","full_name":"Lasne, Clementine"},{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"},{"orcid":"0000-0002-9752-7380","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Toups, Melissa A"},{"full_name":"Layana Franco, Lorena Alexandra","first_name":"Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","last_name":"Layana Franco","orcid":"0000-0002-1253-6297"},{"full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"14727","content_type":"application/pdf","file_size":8623505,"creator":"dernst","checksum":"47c1c72fb499f26ea52d216b242208c8","access_level":"open_access","relation":"main_file","success":1,"file_name":"2023_MolecularBioEvo_Lasne.pdf","date_updated":"2024-01-02T11:39:38Z","date_created":"2024-01-02T11:39:38Z"}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"article_type":"original","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"citation":{"chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>.","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12. Oxford University Press, 2023.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>.","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>"},"abstract":[{"text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.","lang":"eng"}],"scopus_import":"1","type":"journal_article","file_date_updated":"2024-01-02T11:39:38Z","_id":"14613","quality_controlled":"1","project":[{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"},{"grant_number":"ESP39 49461","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","name":"Mechanisms and Evolution of Reproductive Plasticity"}],"publication_status":"published","date_published":"2023-12-01T00:00:00Z","month":"12","intvolume":"        40","acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","article_number":"msad245","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"date_updated":"2024-02-21T12:18:35Z","acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"issue":"12","external_id":{"pmid":["37988296"]},"license":"https://creativecommons.org/licenses/by/4.0/","year":"2023","volume":40,"pmid":1,"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-11-27T16:14:37Z","day":"01","status":"public","publication":"Molecular Biology and Evolution","doi":"10.1093/molbev/msad245","related_material":{"record":[{"id":"14614","relation":"research_data","status":"public"}],"link":[{"description":"News on ISTA webpage","url":"https://ista.ac.at/en/news/on-the-hunt/","relation":"press_release"}]},"oa_version":"Published Version"},{"year":"2023","article_processing_charge":"No","department":[{"_id":"BeVi"}],"date_updated":"2024-02-21T12:18:35Z","keyword":["Panorpa","scorpionfly","genome","transcriptome"],"file":[{"content_type":"application/zip","file_id":"14625","file_size":404968272,"creator":"clasne","access_level":"open_access","checksum":"cd0f13322b5156819ecaebd2bc8e7d12","relation":"main_file","success":1,"file_name":"panorpaX.zip","date_created":"2023-11-28T13:15:26Z","date_updated":"2023-11-28T13:15:26Z"},{"content_type":"text/plain","file_id":"14634","creator":"clasne","file_size":2625,"checksum":"9ff600416577687a737cb3c96dfcb26c","access_level":"open_access","relation":"main_file","success":1,"file_name":"panorpa_readme.txt","date_updated":"2023-11-30T14:16:59Z","date_created":"2023-11-30T14:16:59Z"}],"oa":1,"author":[{"first_name":"Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","orcid":"0000-0002-1197-8616","last_name":"Lasne","full_name":"Lasne, Clementine"},{"full_name":"Elkrewi, Marwan N","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","last_name":"Elkrewi"}],"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","month":"12","date_published":"2023-12-01T00:00:00Z","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14613"}]},"contributor":[{"last_name":"Elkrewi","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","contributor_type":"researcher"}],"oa_version":"Published Version","doi":"10.15479/AT:ISTA:14614","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-11-27T16:39:19Z","_id":"14614","ddc":["576"],"day":"01","status":"public","citation":{"ista":"Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>.","short":"C. Lasne, M.N. Elkrewi, (2023).","ieee":"C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.” Institute of Science and Technology Austria, 2023.","ama":"Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>","chicago":"Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>.","apa":"Lasne, C., &#38; Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>","mla":"Lasne, Clementine, and Marwan N. Elkrewi. <i>The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>."},"file_date_updated":"2023-11-30T14:16:59Z","type":"research_data","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}]},{"title":"The X chromosome of insects likely predates the origin of Class Insecta","oa":1,"author":[{"full_name":"Toups, Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-11-28T08:17:31Z","publisher":"Dryad","has_accepted_license":"1","month":"09","date_published":"2023-09-15T00:00:00Z","year":"2023","license":"https://creativecommons.org/publicdomain/zero/1.0/","department":[{"_id":"BeVi"}],"article_processing_charge":"No","day":"15","status":"public","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"date_created":"2023-11-28T08:01:53Z","_id":"14616","ddc":["570"],"type":"research_data_reference","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"citation":{"ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","short":"M.A. Toups, B. Vicoso, (2023).","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Dryad, 2023. <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">https://doi.org/10.5061/DRYAD.HX3FFBGKT</a>.","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">https://doi.org/10.5061/DRYAD.HX3FFBGKT</a>","mla":"Toups, Melissa A., and Beatriz Vicoso. <i>The X Chromosome of Insects Likely Predates the Origin of Class Insecta</i>. Dryad, 2023, doi:<a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>."},"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14604"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.hx3ffbgkt"}],"doi":"10.5061/DRYAD.HX3FFBGKT"},{"title":"The X chromosome of insects likely predates the origin of Class Insecta","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"full_name":"Toups, Melissa A","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"other_data_license":"MIT License","date_updated":"2023-11-28T08:25:28Z","publisher":"Zenodo","date_published":"2023-09-15T00:00:00Z","month":"09","has_accepted_license":"1","year":"2023","department":[{"_id":"BeVi"}],"article_processing_charge":"No","status":"public","day":"15","_id":"14617","date_created":"2023-11-28T08:04:03Z","ddc":["570"],"abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"type":"research_data_reference","citation":{"mla":"Toups, Melissa A., and Beatriz Vicoso. <i>The X Chromosome of Insects Likely Predates the Origin of Class Insecta</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>.","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8138705\">https://doi.org/10.5281/ZENODO.8138705</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8138705\">https://doi.org/10.5281/ZENODO.8138705</a>.","short":"M.A. Toups, B. Vicoso, (2023).","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023.","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>"},"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14604"}]},"doi":"10.5281/ZENODO.8138705","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8138705"}]},{"citation":{"mla":"Cheng, Bingqing. <i>BingqingCheng/Solubility: V1.0</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>.","apa":"Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8398094\">https://doi.org/10.5281/ZENODO.8398094</a>","chicago":"Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8398094\">https://doi.org/10.5281/ZENODO.8398094</a>.","ieee":"B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.","ista":"Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>.","short":"B. Cheng, (2023).","ama":"Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>"},"abstract":[{"text":"Data underlying the publication \"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals\" (DOI https://doi.org/10.1063/5.0173341).","lang":"eng"}],"type":"research_data_reference","date_created":"2023-11-28T08:32:18Z","_id":"14619","ddc":["530"],"day":"02","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8398094"}],"doi":"10.5281/ZENODO.8398094","related_material":{"record":[{"id":"14603","relation":"used_in_publication","status":"public"}]},"oa_version":"Published Version","date_published":"2023-10-02T00:00:00Z","has_accepted_license":"1","month":"10","publisher":"Zenodo","date_updated":"2023-11-28T08:39:22Z","oa":1,"author":[{"last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing"}],"title":"BingqingCheng/solubility: V1.0","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"BiCh"}],"year":"2023"},{"date_published":"2023-11-30T00:00:00Z","alternative_title":["ISTA Thesis"],"month":"11","date_updated":"2023-12-13T14:47:25Z","page":"142","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","year":"2023","date_created":"2023-11-28T10:58:13Z","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"ddc":["530"],"status":"public","day":"30","supervisor":[{"full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:14622","related_material":{"record":[{"id":"11471","status":"public","relation":"part_of_dissertation"},{"id":"13125","status":"public","relation":"part_of_dissertation"},{"id":"9760","relation":"part_of_dissertation","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","author":[{"full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","last_name":"Sack","first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5"}],"file":[{"access_level":"closed","embargo":"2024-11-30","checksum":"068fd3570506ec42b2faa390de784bc4","relation":"main_file","content_type":"application/pdf","file_id":"14635","creator":"ssack","file_size":11947523,"embargo_to":"open_access","date_created":"2023-11-30T15:53:10Z","date_updated":"2023-12-01T11:10:46Z","file_name":"PhD_Thesis.pdf"},{"file_id":"14636","content_type":"application/zip","creator":"ssack","file_size":18422964,"access_level":"closed","relation":"source_file","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","file_name":"PhD Thesis (1).zip","date_updated":"2023-12-01T11:10:46Z","date_created":"2023-11-30T15:54:11Z"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"citation":{"mla":"Sack, Stefan. <i>Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>.","apa":"Sack, S. (2023). <i>Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>.","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023."},"file_date_updated":"2023-12-01T11:10:46Z","type":"dissertation","_id":"14622","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices"},{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899"}],"publication_status":"published"},{"status":"public","day":"01","ddc":["531","006"],"date_created":"2023-11-29T15:02:03Z","volume":42,"oa_version":"Published Version","publication":"ACM Transactions on Graphics","doi":"10.1145/3605389","oa":1,"issue":"5","keyword":["Computer Graphics and Computer-Aided Design"],"date_updated":"2023-12-04T08:09:05Z","article_number":"168","acknowledgement":"The authors thank Mina Konaković Luković and Michael Foshey for their early contributions to this project, David Palmer and Paul Zhang for their insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also thank our user study participants and anonymous reviewers.\r\nThis material is based upon work supported by the National Science Foundation\r\n(NSF) Graduate Research Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship; the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075; the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the NewSat project, which is co-funded by the Operational Program for Competitiveness and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under the MIT Portugal program.","date_published":"2023-10-01T00:00:00Z","intvolume":"        42","month":"10","year":"2023","quality_controlled":"1","_id":"14628","abstract":[{"text":"We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration.","lang":"eng"}],"type":"journal_article","file_date_updated":"2023-12-04T08:04:14Z","publication_identifier":{"issn":["0730-0301","1557-7368"]},"citation":{"chicago":"Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3605389\">https://doi.org/10.1145/3605389</a>.","ista":"Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 42(5), 168.","ieee":"L. Makatura <i>et al.</i>, “Procedural metamaterials: A unified procedural graph for metamaterial design,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5. Association for Computing Machinery, 2023.","short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023).","ama":"Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. <i>ACM Transactions on Graphics</i>. 2023;42(5). doi:<a href=\"https://doi.org/10.1145/3605389\">10.1145/3605389</a>","mla":"Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3605389\">10.1145/3605389</a>.","apa":"Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., &#38; Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3605389\">https://doi.org/10.1145/3605389</a>"},"publication_status":"published","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083"}],"title":"Procedural metamaterials: A unified procedural graph for metamaterial design","author":[{"full_name":"Makatura, Liane","first_name":"Liane","last_name":"Makatura"},{"full_name":"Wang, Bohan","last_name":"Wang","first_name":"Bohan"},{"full_name":"Chen, Yi-Lu","first_name":"Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","last_name":"Chen"},{"full_name":"Deng, Bolei","first_name":"Bolei","last_name":"Deng"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"last_name":"Matusik","first_name":"Wojciech","full_name":"Matusik, Wojciech"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-11-29T15:16:01Z","date_created":"2023-11-29T15:16:01Z","file_name":"tog-22-0089-File004.zip","success":1,"relation":"main_file","access_level":"open_access","checksum":"0192f597d7a2ceaf89baddfd6190d4c8","creator":"yichen","file_size":95467870,"content_type":"application/zip","file_id":"14630"},{"file_size":103731880,"creator":"yichen","content_type":"application/zip","file_id":"14631","checksum":"7fb024963be81933494f38de191e4710","access_level":"open_access","relation":"main_file","file_name":"tog-22-0089-File005.zip","success":1,"date_created":"2023-11-29T15:16:01Z","date_updated":"2023-11-29T15:16:01Z"},{"date_created":"2023-12-04T08:04:14Z","date_updated":"2023-12-04T08:04:14Z","file_name":"2023_ACMToG_Makatura.pdf","success":1,"relation":"main_file","access_level":"open_access","checksum":"b7d6829ce396e21cac9fae0ec7130a6b","creator":"dernst","file_size":57067476,"content_type":"application/pdf","file_id":"14638"}],"publisher":"Association for Computing Machinery","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}],"article_processing_charge":"Yes (in subscription journal)"},{"alternative_title":["ISTA Thesis"],"date_published":"2023-11-30T00:00:00Z","month":"11","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"date_updated":"2023-12-07T14:12:25Z","page":"104","year":"2023","day":"30","status":"public","supervisor":[{"full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"date_created":"2023-12-04T13:17:37Z","ddc":["570"],"doi":"10.15479/at:ista:14641","degree_awarded":"PhD","ec_funded":1,"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","author":[{"id":"3F338C72-F248-11E8-B48F-1D18A9856A87","first_name":"Mike","last_name":"Hennessey-Wesen","full_name":"Hennessey-Wesen, Mike"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Adaptive mutation in E. coli modulated by luxS","file":[{"access_level":"closed","relation":"source_file","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","file_size":46405919,"creator":"mhenness","file_id":"14648","content_type":"application/vnd.oasis.opendocument.text","date_updated":"2023-12-06T13:13:26Z","date_created":"2023-12-06T13:13:26Z","file_name":"mike_thesis_v06-12-2023.odt"},{"file_id":"14649","content_type":"application/pdf","embargo_to":"open_access","file_size":21282155,"creator":"mhenness","checksum":"f5203a61eddaf35235bbc51904d73982","embargo":"2024-11-30","relation":"main_file","access_level":"closed","file_name":"mike_thesis_v06-12-2023.pdf","date_updated":"2023-12-06T13:14:15Z","date_created":"2023-12-06T13:14:15Z"}],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"type":"dissertation","file_date_updated":"2023-12-06T13:14:15Z","publication_identifier":{"issn":["2663 - 337X"]},"citation":{"ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria.","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>","chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>.","apa":"Hennessey-Wesen, M. (2023). <i>Adaptive mutation in E. coli modulated by luxS</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>","mla":"Hennessey-Wesen, Mike. <i>Adaptive Mutation in E. Coli Modulated by LuxS</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>."},"_id":"14641","publication_status":"published","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}]},{"month":"12","date_published":"2023-12-05T00:00:00Z","acknowledgement":"We thank B. Kaczmarek and other members of the Bernecky lab for helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid. We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant P34185. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","date_updated":"2023-12-05T10:37:28Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"oa":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","year":"2023","ddc":["572"],"date_created":"2023-12-04T14:51:00Z","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"status":"public","day":"05","doi":"10.15479/AT:ISTA:14644","oa_version":"Submitted Version","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"file_name":"2023_Tluckova_etal_REx.pdf","success":1,"date_created":"2023-12-05T10:37:02Z","date_updated":"2023-12-05T10:37:02Z","file_size":4892920,"creator":"dernst","file_id":"14646","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"c45608cb97ee36d7b50ba518db8e07b0"}],"author":[{"id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Tluckova","full_name":"Tluckova, Katarina"},{"full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","full_name":"Bernecky, Carrie A"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","article_processing_charge":"No","department":[{"_id":"CaBe"}],"language":[{"iso":"eng"}],"citation":{"chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">https://doi.org/10.15479/AT:ISTA:14644</a>.","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>.","mla":"Tluckova, Katarina, et al. <i>Mechanism of Mammalian Transcriptional Repression by Noncoding RNA</i>. Institute of Science and Technology Austria, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>.","apa":"Tluckova, K., Testa Salmazo, A. P., &#38; Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">https://doi.org/10.15479/AT:ISTA:14644</a>"},"file_date_updated":"2023-12-05T10:37:02Z","type":"preprint","abstract":[{"text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression.","lang":"eng"}],"_id":"14644","project":[{"name":"Regulation of mammalian transcription by noncoding RNA","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30","grant_number":"P34185"}],"publication_status":"submitted"},{"abstract":[{"text":"In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and in postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic ligand FGF18 in new born neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons increases Fgf18 expression and enhances gliogenesis in the progenitors. These results fit well with the model that new born neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex.","lang":"eng"}],"type":"preprint","citation":{"ama":"Bose M, Suresh V, Mishra U, et al. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.11.30.569337\">10.1101/2023.11.30.569337</a>","ista":"Bose M, Suresh V, Mishra U, Talwar I, Yadav A, Biswas S, Hippenmeyer S, Tole S. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. bioRxiv, <a href=\"https://doi.org/10.1101/2023.11.30.569337\">10.1101/2023.11.30.569337</a>.","short":"M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer, S. Tole, BioRxiv (n.d.).","ieee":"M. Bose <i>et al.</i>, “Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","chicago":"Bose, Mahima, Varun Suresh, Urvi Mishra, Ishita Talwar, Anuradha Yadav, Shiona Biswas, Simon Hippenmeyer, and Shubha Tole. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2023.11.30.569337\">https://doi.org/10.1101/2023.11.30.569337</a>.","apa":"Bose, M., Suresh, V., Mishra, U., Talwar, I., Yadav, A., Biswas, S., … Tole, S. (n.d.). Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2023.11.30.569337\">https://doi.org/10.1101/2023.11.30.569337</a>","mla":"Bose, Mahima, et al. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2023.11.30.569337\">10.1101/2023.11.30.569337</a>."},"status":"public","day":"01","date_created":"2023-12-06T13:07:01Z","_id":"14647","publication":"bioRxiv","publication_status":"submitted","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.11.30.569337"}],"doi":"10.1101/2023.11.30.569337","oa_version":"Preprint","acknowledgement":"We thank Dr. Shital Suryavanshi and the animal house staff of the Tata Institute of\r\nFundamental Research (TIFR) for their excellent support; Gord Fishell and Goichi Miyoshi for\r\nthe Foxg1 floxed mouse line; Hiroshi Kawasaki for the plasmids pCAG-FGF8 and pCAGsFGFR3c. We thank Prof. S.K. Lee for the Foxg1lox/lox genotyping primers and protocol. We thank Dr. Deepak Modi and Dr. Vainav Patel for allowing us to use the NIRRCH FACS Facility and the staff of the NIRRCH and TIFR FACS facilities for their assistance.\r\nWe thank Denis Jabaudon for his critical comments on the manuscript and members of the\r\nJabaudon lab for helpful discussions. This work was funded by the Department of Atomic\r\nEnergy (DAE), Govt. of India (Project Identification no. RTI4003, DAE OM no.\r\n1303/2/2019/R&D-II/DAE/2079).","publisher":"Cold Spring Harbor Laboratory","date_published":"2023-12-01T00:00:00Z","month":"12","oa":1,"title":"Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bose, Mahima","last_name":"Bose","first_name":"Mahima"},{"last_name":"Suresh","first_name":"Varun","full_name":"Suresh, Varun"},{"first_name":"Urvi","last_name":"Mishra","full_name":"Mishra, Urvi"},{"full_name":"Talwar, Ishita","last_name":"Talwar","first_name":"Ishita"},{"last_name":"Yadav","first_name":"Anuradha","full_name":"Yadav, Anuradha"},{"full_name":"Biswas, Shiona","last_name":"Biswas","first_name":"Shiona"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"},{"full_name":"Tole, Shubha","first_name":"Shubha","last_name":"Tole"}],"date_updated":"2023-12-11T07:37:17Z","department":[{"_id":"SiHi"}],"article_processing_charge":"No","year":"2023","language":[{"iso":"eng"}]},{"external_id":{"arxiv":["2305.17969"]},"year":"2023","date_published":"2023-12-07T00:00:00Z","month":"12","intvolume":"        15","acknowledgement":"We thank Lauriane Chomaz for useful discussions and comments on the manuscript. We also\r\nthank Ragheed Al Hyder for comments on the manuscript.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF),\r\nunder Project No. M2641-N27. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-\r\n390900948 (the Heidelberg STRUCTURES Excellence Cluster). A. G. V. acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the\r\nMarie Skłodowska-Curie Grant Agreement No. 754411. L.A.P.A acknowledges by the PNRR\r\nMUR project PE0000023 - NQSTI and the Deutsche Forschungsgemeinschaft (DFG, German\r\nResearch Foundation) under Germany’s Excellence Strategy - EXC - 2123 Quantum Frontiers390837967 and FOR2247.","article_number":"232","keyword":["General Physics and Astronomy"],"date_updated":"2024-08-07T07:16:53Z","oa":1,"issue":"6","publication":"SciPost Physics","doi":"10.21468/scipostphys.15.6.232","oa_version":"Published Version","ec_funded":1,"volume":15,"ddc":["530"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-12-10T13:03:07Z","status":"public","day":"07","article_processing_charge":"No","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"SciPost Foundation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem"},{"full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","last_name":"Bighin","orcid":"0000-0001-8823-9777"},{"full_name":"Santos, Luis","last_name":"Santos","first_name":"Luis"},{"first_name":"Luisllu A.","last_name":"Peña Ardila","full_name":"Peña Ardila, Luisllu A."}],"title":"Non-equilibrium dynamics of dipolar polarons","file":[{"creator":"dernst","file_size":3543541,"file_id":"14669","content_type":"application/pdf","access_level":"open_access","checksum":"e664372a1fe9d628a9bb1d135ebab7d8","relation":"main_file","file_name":"2023_SciPostPhysics_Volosniev.pdf","success":1,"date_updated":"2023-12-11T07:42:04Z","date_created":"2023-12-11T07:42:04Z"}],"project":[{"grant_number":"M02641","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","name":"A path-integral approach to composite impurities"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"publication_status":"published","publication_identifier":{"issn":["2542-4653"]},"citation":{"short":"A. Volosniev, G. Bighin, L. Santos, L.A. Peña Ardila, SciPost Physics 15 (2023).","ieee":"A. Volosniev, G. Bighin, L. Santos, and L. A. Peña Ardila, “Non-equilibrium dynamics of dipolar polarons,” <i>SciPost Physics</i>, vol. 15, no. 6. SciPost Foundation, 2023.","ista":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. 2023. Non-equilibrium dynamics of dipolar polarons. SciPost Physics. 15(6), 232.","ama":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. Non-equilibrium dynamics of dipolar polarons. <i>SciPost Physics</i>. 2023;15(6). doi:<a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">10.21468/scipostphys.15.6.232</a>","chicago":"Volosniev, Artem, Giacomo Bighin, Luis Santos, and Luisllu A. Peña Ardila. “Non-Equilibrium Dynamics of Dipolar Polarons.” <i>SciPost Physics</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">https://doi.org/10.21468/scipostphys.15.6.232</a>.","apa":"Volosniev, A., Bighin, G., Santos, L., &#38; Peña Ardila, L. A. (2023). Non-equilibrium dynamics of dipolar polarons. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">https://doi.org/10.21468/scipostphys.15.6.232</a>","mla":"Volosniev, Artem, et al. “Non-Equilibrium Dynamics of Dipolar Polarons.” <i>SciPost Physics</i>, vol. 15, no. 6, 232, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">10.21468/scipostphys.15.6.232</a>."},"abstract":[{"text":"We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures.","lang":"eng"}],"arxiv":1,"file_date_updated":"2023-12-11T07:42:04Z","type":"journal_article","_id":"14650","quality_controlled":"1"},{"file":[{"file_name":"Phd_Thesis_LA.pdf","success":1,"date_created":"2023-12-13T15:37:55Z","date_updated":"2023-12-13T15:37:55Z","creator":"larathoo","file_size":34101468,"content_type":"application/pdf","file_id":"14684","checksum":"520bdb61e95e66070e02824947d2c5fa","access_level":"open_access","relation":"main_file"},{"date_created":"2023-12-13T15:42:23Z","date_updated":"2023-12-14T08:58:18Z","file_name":"Phd_Thesis_LA.zip","access_level":"closed","relation":"source_file","checksum":"d8e59afd0817c98fba2564a264508e5c","content_type":"application/zip","file_id":"14685","file_size":31052872,"creator":"larathoo"},{"file_id":"14681","content_type":"application/zip","file_size":10713896,"creator":"larathoo","checksum":"9a778c949932286f4519e1f1fca2820d","relation":"supplementary_material","access_level":"closed","file_name":"Supplementary_Materials.zip","date_created":"2023-12-11T19:24:59Z","date_updated":"2023-12-14T08:58:18Z"}],"title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","author":[{"full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"_id":"14651","publication_identifier":{"issn":["2663 - 337X"]},"citation":{"mla":"Arathoon, Louise S. <i>Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>.","apa":"Arathoon, L. S. (2023). <i>Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria."},"file_date_updated":"2023-12-14T08:58:18Z","type":"dissertation","abstract":[{"text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.","lang":"eng"}],"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"publication_status":"published","date_updated":"2023-12-22T11:04:45Z","acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"month":"12","date_published":"2023-12-12T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2023","page":"96","date_created":"2023-12-11T19:30:37Z","ddc":["570"],"supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"day":"12","status":"public","related_material":{"record":[{"id":"11411","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","ec_funded":1,"degree_awarded":"PhD","doi":"10.15479/at:ista:14651"},{"article_number":"415539","publisher":"Elsevier","date_published":"2023-11-28T00:00:00Z","month":"11","intvolume":"       674","author":[{"full_name":"Gupta, Shyam Lal","first_name":"Shyam Lal","last_name":"Gupta"},{"full_name":"Singh, Saurabh","orcid":"0000-0003-2209-5269","last_name":"Singh","first_name":"Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a"},{"first_name":"Sumit","last_name":"Kumar","full_name":"Kumar, Sumit"},{"first_name":"Unknown","last_name":"Anupam","full_name":"Anupam, Unknown"},{"first_name":"Samjeet Singh","last_name":"Thakur","full_name":"Thakur, Samjeet Singh"},{"first_name":"Ashish","last_name":"Kumar","full_name":"Kumar, Ashish"},{"first_name":"Sanjay","last_name":"Panwar","full_name":"Panwar, Sanjay"},{"last_name":"Diwaker","first_name":"D.","full_name":"Diwaker, D."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys","date_updated":"2023-12-12T08:22:23Z","department":[{"_id":"MaIb"}],"article_processing_charge":"No","article_type":"original","year":"2023","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"text":"In order to demonstrate the stability of newly proposed iridium-based Ir2Cr(In,Sn) and IrRhCr(In,Sn) heusler alloys, we present ab-initio analysis of these alloys by examining various properties to prove their stability. The stability of these alloys can be inferred from different cohesive and formation energies as well as positive phonon frequencies. Their electronic structure results indicate that they are semi-metals in nature. The magnetic moments are computed using the Slater-Pauling formula and exhibit a high value, with the Cr atom contributing the most in all alloys. Mulliken’s charge analysis results show that our alloys contain a range of linkages, mainly ionic and covalent ones. The ductility and mechanical stability of these alloys are confirmed by elastic constants viz. Poisson’s ratio, Pugh’s ratio, and many different types of elastic moduli.","lang":"eng"}],"type":"journal_article","volume":674,"citation":{"chicago":"Gupta, Shyam Lal, Saurabh Singh, Sumit Kumar, Unknown Anupam, Samjeet Singh Thakur, Ashish Kumar, Sanjay Panwar, and D. Diwaker. “Ab-Initio Stability of Iridium Based Newly Proposed Full and Quaternary Heusler Alloys.” <i>Physica B: Condensed Matter</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.physb.2023.415539\">https://doi.org/10.1016/j.physb.2023.415539</a>.","ista":"Gupta SL, Singh S, Kumar S, Anupam U, Thakur SS, Kumar A, Panwar S, Diwaker D. 2023. Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. Physica B: Condensed Matter. 674, 415539.","ieee":"S. L. Gupta <i>et al.</i>, “Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys,” <i>Physica B: Condensed Matter</i>, vol. 674. Elsevier, 2023.","short":"S.L. Gupta, S. Singh, S. Kumar, U. Anupam, S.S. Thakur, A. Kumar, S. Panwar, D. Diwaker, Physica B: Condensed Matter 674 (2023).","ama":"Gupta SL, Singh S, Kumar S, et al. Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. <i>Physica B: Condensed Matter</i>. 2023;674. doi:<a href=\"https://doi.org/10.1016/j.physb.2023.415539\">10.1016/j.physb.2023.415539</a>","mla":"Gupta, Shyam Lal, et al. “Ab-Initio Stability of Iridium Based Newly Proposed Full and Quaternary Heusler Alloys.” <i>Physica B: Condensed Matter</i>, vol. 674, 415539, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.physb.2023.415539\">10.1016/j.physb.2023.415539</a>.","apa":"Gupta, S. L., Singh, S., Kumar, S., Anupam, U., Thakur, S. S., Kumar, A., … Diwaker, D. (2023). Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. <i>Physica B: Condensed Matter</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physb.2023.415539\">https://doi.org/10.1016/j.physb.2023.415539</a>"},"publication_identifier":{"issn":["0921-4526"]},"status":"public","day":"28","quality_controlled":"1","_id":"14652","date_created":"2023-12-10T23:00:56Z","publication":"Physica B: Condensed Matter","publication_status":"epub_ahead","doi":"10.1016/j.physb.2023.415539","oa_version":"None"},{"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"CaMu"}],"article_processing_charge":"Yes","file":[{"checksum":"4d060b293da3d203de8769e398edf711","access_level":"open_access","relation":"main_file","file_id":"14670","content_type":"application/pdf","creator":"dernst","file_size":2783677,"date_updated":"2023-12-11T08:08:44Z","date_created":"2023-12-11T08:08:44Z","success":1,"file_name":"2023_JAMES_Hwong.pdf"}],"author":[{"full_name":"Hwong, Yi-Ling","last_name":"Hwong","orcid":"0000-0001-9281-3479","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","first_name":"Yi-Ling"},{"full_name":"Colin, M.","first_name":"M.","last_name":"Colin"},{"id":"02eace56-97fc-11ee-b81a-f0939ca85a77","first_name":"Philipp","last_name":"Aglas","full_name":"Aglas, Philipp"},{"orcid":"0000-0001-5836-5350","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","full_name":"Muller, Caroline J"},{"last_name":"Sherwood","first_name":"S. C.","full_name":"Sherwood, S. C."}],"title":"Assessing memory in convection schemes using idealized tests","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","has_accepted_license":"1","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576","name":"organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate"}],"quality_controlled":"1","_id":"14654","type":"journal_article","file_date_updated":"2023-12-11T08:08:44Z","abstract":[{"text":"Two assumptions commonly applied in convection schemes—the diagnostic and quasi-equilibrium assumptions—imply that convective activity (e.g., convective precipitation) is controlled only by the large-scale (macrostate) environment at the time. In contrast, numerical experiments indicate a “memory” or dependence of convection also on its own previous activity whereby subgrid-scale (microstate) structures boost but are also boosted by convection. In this study we investigated this memory by comparing single-column model behavior in two idealized tests previously executed by a cloud-resolving model (CRM). Conventional convection schemes that employ the diagnostic assumption fail to reproduce the CRM behavior. The memory-capable org and Laboratoire de Météorologie Dynamique Zoom cold pool schemes partially capture the behavior, but fail to fully exhibit the strong reinforcing feedbacks implied by the CRM. Analysis of this failure suggests that it is because the CRM supports a linear (or superlinear) dependence of the subgrid structure growth rate on the precipitation rate, while the org scheme assumes a sublinear dependence. Among varying versions of the org scheme, the growth rate of the org variable representing subgrid structure is strongly associated with memory strength. These results demonstrate the importance of parameterizing convective memory, and the ability of idealized tests to reveal shortcomings of convection schemes and constrain model structural assumptions.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["1942-2466"]},"citation":{"chicago":"Hwong, Yi-Ling, M. Colin, Philipp Aglas, Caroline J Muller, and S. C. Sherwood. “Assessing Memory in Convection Schemes Using Idealized Tests.” <i>Journal of Advances in Modeling Earth Systems</i>. Wiley, 2023. <a href=\"https://doi.org/10.1029/2023MS003726\">https://doi.org/10.1029/2023MS003726</a>.","ieee":"Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. C. Sherwood, “Assessing memory in convection schemes using idealized tests,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 12. Wiley, 2023.","short":"Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S.C. Sherwood, Journal of Advances in Modeling Earth Systems 15 (2023).","ista":"Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. 2023. Assessing memory in convection schemes using idealized tests. Journal of Advances in Modeling Earth Systems. 15(12), e2023MS003726.","ama":"Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. Assessing memory in convection schemes using idealized tests. <i>Journal of Advances in Modeling Earth Systems</i>. 2023;15(12). doi:<a href=\"https://doi.org/10.1029/2023MS003726\">10.1029/2023MS003726</a>","mla":"Hwong, Yi-Ling, et al. “Assessing Memory in Convection Schemes Using Idealized Tests.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 12, e2023MS003726, Wiley, 2023, doi:<a href=\"https://doi.org/10.1029/2023MS003726\">10.1029/2023MS003726</a>.","apa":"Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., &#38; Sherwood, S. C. (2023). Assessing memory in convection schemes using idealized tests. <i>Journal of Advances in Modeling Earth Systems</i>. Wiley. <a href=\"https://doi.org/10.1029/2023MS003726\">https://doi.org/10.1029/2023MS003726</a>"},"year":"2023","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"12","oa":1,"date_updated":"2024-02-27T07:26:30Z","acknowledgement":"YLH is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. CJM gratefully acknowledges funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). YLH and SCS were supported by the Australian Research Council (FL150100035). The authors thank Brian Mapes, David Fuchs and Siwon Song for stimulating and helpful discussions. MC warmly thanks the LMD team in Paris for their assistance with the LMDZ model. We thank the two anonymous reviewers for their constructive comments that greatly improved this manuscript.","article_number":"e2023MS003726","intvolume":"        15","month":"12","date_published":"2023-12-01T00:00:00Z","ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"id":"14991","relation":"research_data","status":"public"}]},"doi":"10.1029/2023MS003726","publication":"Journal of Advances in Modeling Earth Systems","day":"01","status":"public","date_created":"2023-12-10T23:00:57Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["550"],"volume":15},{"author":[{"full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","first_name":"Valerio","orcid":"0000-0002-9645-6576","last_name":"Sorichetti"},{"full_name":"Lenz, Martin","first_name":"Martin","last_name":"Lenz"}],"title":"Transverse fluctuations control the assembly of semiflexible filaments","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"AnSa"}],"_id":"14655","quality_controlled":"1","citation":{"mla":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” <i>Physical Review Letters</i>, vol. 131, no. 22, 228401, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">10.1103/PhysRevLett.131.228401</a>.","apa":"Sorichetti, V., &#38; Lenz, M. (2023). Transverse fluctuations control the assembly of semiflexible filaments. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">https://doi.org/10.1103/PhysRevLett.131.228401</a>","chicago":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">https://doi.org/10.1103/PhysRevLett.131.228401</a>.","short":"V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).","ista":"Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 131(22), 228401.","ieee":"V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of semiflexible filaments,” <i>Physical Review Letters</i>, vol. 131, no. 22. American Physical Society, 2023.","ama":"Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible filaments. <i>Physical Review Letters</i>. 2023;131(22). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">10.1103/PhysRevLett.131.228401</a>"},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"abstract":[{"lang":"eng","text":"The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division."}],"arxiv":1,"scopus_import":"1","type":"journal_article","publication_status":"published","date_updated":"2023-12-11T07:59:25Z","oa":1,"issue":"22","date_published":"2023-12-01T00:00:00Z","month":"12","intvolume":"       131","article_number":"228401","acknowledgement":"The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable help with understanding the experimental behavior of intermediate filaments, and Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou, and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L. was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03, No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and No. 2021-A0110712066).","year":"2023","external_id":{"arxiv":["2303.03088"]},"date_created":"2023-12-10T23:00:57Z","status":"public","day":"01","volume":131,"oa_version":"Preprint","publication":"Physical Review Letters","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.03088"}],"doi":"10.1103/PhysRevLett.131.228401"},{"has_accepted_license":"1","publisher":"Society of Neuroscience","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Nardin","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","full_name":"Nardin, Michele"},{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455"},{"full_name":"Savin, Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","file":[{"access_level":"closed","embargo":"2024-06-01","relation":"main_file","checksum":"e2503c8f84be1050e28f64320f1d5bd2","creator":"dernst","file_size":2280632,"embargo_to":"open_access","content_type":"application/pdf","file_id":"14674","date_created":"2023-12-11T11:30:37Z","date_updated":"2023-12-11T11:30:37Z","file_name":"2023_JourNeuroscience_Nardin.pdf"}],"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. Society of Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>. Society of Neuroscience, 2023. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>The Journal of Neuroscience</i>, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. 2023;43(48):8140-8156. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>"},"publication_identifier":{"eissn":["1529-2401"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain."}],"file_date_updated":"2023-12-11T11:30:37Z","type":"journal_article","_id":"14656","quality_controlled":"1","project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281511"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"publication_status":"published","date_published":"2023-11-29T00:00:00Z","month":"11","intvolume":"        43","acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","date_updated":"2023-12-11T11:37:20Z","oa":1,"issue":"48","page":"8140-8156","external_id":{"pmid":["37758476"]},"year":"2023","volume":43,"pmid":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-12-10T23:00:58Z","ddc":["570"],"day":"29","status":"public","publication":"The Journal of Neuroscience","doi":"10.1523/JNEUROSCI.0194-23.2023","main_file_link":[{"url":"https://doi.org/10.1523/JNEUROSCI.0194-23.2023","open_access":"1"}],"oa_version":"Published Version","ec_funded":1},{"volume":20,"pmid":1,"status":"public","day":"29","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000","570"],"date_created":"2023-12-10T23:00:58Z","publication":"Journal of the Royal Society, Interface","doi":"10.1098/rsif.2023.0355","ec_funded":1,"oa_version":"Published Version","article_number":"20230355","acknowledgement":"K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T. is supported by Center for Foundations ofModern Computer Science (Charles Univ. project UNCE/SCI/004).","date_published":"2023-11-29T00:00:00Z","intvolume":"        20","month":"11","oa":1,"issue":"208","date_updated":"2025-07-14T09:10:00Z","external_id":{"pmid":["38016637"]},"year":"2023","scopus_import":"1","abstract":[{"text":"Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.","lang":"eng"}],"file_date_updated":"2023-12-11T11:10:32Z","type":"journal_article","citation":{"mla":"Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population Structure.” <i>Journal of the Royal Society, Interface</i>, vol. 20, no. 208, 20230355, The Royal Society, 2023, doi:<a href=\"https://doi.org/10.1098/rsif.2023.0355\">10.1098/rsif.2023.0355</a>.","apa":"Tkadlec, J., Kaveh, K., Chatterjee, K., &#38; Nowak, M. A. (2023). Evolutionary dynamics of mutants that modify population structure. <i>Journal of the Royal Society, Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2023.0355\">https://doi.org/10.1098/rsif.2023.0355</a>","chicago":"Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak. “Evolutionary Dynamics of Mutants That Modify Population Structure.” <i>Journal of the Royal Society, Interface</i>. The Royal Society, 2023. <a href=\"https://doi.org/10.1098/rsif.2023.0355\">https://doi.org/10.1098/rsif.2023.0355</a>.","ama":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants that modify population structure. <i>Journal of the Royal Society, Interface</i>. 2023;20(208). doi:<a href=\"https://doi.org/10.1098/rsif.2023.0355\">10.1098/rsif.2023.0355</a>","ista":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. 20(208), 20230355.","short":"J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society, Interface 20 (2023).","ieee":"J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics of mutants that modify population structure,” <i>Journal of the Royal Society, Interface</i>, vol. 20, no. 208. The Royal Society, 2023."},"publication_identifier":{"eissn":["1742-5662"]},"quality_controlled":"1","_id":"14657","publication_status":"published","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"}],"publisher":"The Royal Society","has_accepted_license":"1","title":"Evolutionary dynamics of mutants that modify population structure","author":[{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"first_name":"Kamran","last_name":"Kaveh","full_name":"Kaveh, Kamran"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2023-12-11T11:10:32Z","date_updated":"2023-12-11T11:10:32Z","file_name":"2023_RoyalInterface_Tkadlec.pdf","success":1,"access_level":"open_access","checksum":"2eefab13127c7786dbd33303c482a004","relation":"main_file","creator":"dernst","file_size":1720243,"file_id":"14673","content_type":"application/pdf"}],"department":[{"_id":"KrCh"}],"article_processing_charge":"Yes (in subscription journal)","article_type":"original","language":[{"iso":"eng"}]}]