[{"related_material":{"record":[{"status":"public","relation":"research_data","id":"14616"},{"status":"public","id":"14617","relation":"research_data"}],"link":[{"url":"https://git.ista.ac.at/bvicoso/veryoldx","relation":"software"}]},"has_accepted_license":"1","scopus_import":"1","day":"02","citation":{"ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of class Insecta,” <i>Evolution</i>, vol. 77, no. 11. Oxford University Press, pp. 2504–2511, 2023.","mla":"Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>, vol. 77, no. 11, Oxford University Press, 2023, pp. 2504–11, doi:<a href=\"https://doi.org/10.1093/evolut/qpad169\">10.1093/evolut/qpad169</a>.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511.","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>.","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. 2023;77(11):2504-2511. doi:<a href=\"https://doi.org/10.1093/evolut/qpad169\">10.1093/evolut/qpad169</a>","short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511."},"license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"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 the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}],"title":"The X chromosome of insects likely predates the origin of class Insecta","pmid":1,"article_processing_charge":"Yes (in subscription journal)","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-11-28T08:25:28Z","publisher":"Oxford University Press","volume":77,"acknowledgement":"All computational analyses were performed on the server at Institute of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for analytical advice, and Tanja Schwander and Vincent Merel for useful discussions. We also thank Matthew Hahn for comments on an earlier version of the manuscript.","date_created":"2023-11-26T23:00:54Z","year":"2023","page":"2504-2511","article_type":"original","status":"public","doi":"10.1093/evolut/qpad169","date_published":"2023-11-02T00:00:00Z","_id":"14604","month":"11","external_id":{"pmid":["37738212"]},"quality_controlled":"1","publication_status":"published","publication":"Evolution","oa":1,"intvolume":"        77","publication_identifier":{"eissn":["1558-5646"]},"file_date_updated":"2023-11-28T08:12:15Z","language":[{"iso":"eng"}],"type":"journal_article","issue":"11","file":[{"access_level":"open_access","checksum":"b66dc10edae92d38918d534e64dda77c","content_type":"application/pdf","success":1,"date_updated":"2023-11-28T08:12:15Z","file_name":"2023_Evolution_Toups.pdf","relation":"main_file","file_id":"14618","date_created":"2023-11-28T08:12:15Z","file_size":1399102,"creator":"dernst"}],"department":[{"_id":"BeVi"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"author":[{"orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"oa_version":"Published Version"},{"abstract":[{"lang":"eng","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."}],"day":"01","citation":{"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>.","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.","short":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (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>","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.","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>","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>."},"scopus_import":"1","article_type":"original","status":"public","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"volume":108,"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.","date_created":"2023-11-26T23:00:54Z","year":"2023","date_updated":"2023-11-28T07:48:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","article_number":"174302","title":"Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)","article_processing_charge":"No","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"type":"journal_article","issue":"17","quality_controlled":"1","publication_status":"published","publication":"Physical Review B","intvolume":"       108","doi":"10.1103/PhysRevB.108.174302","date_published":"2023-11-01T00:00:00Z","_id":"14605","month":"11","oa_version":"None","author":[{"full_name":"Ouyang, Niuchang","last_name":"Ouyang","first_name":"Niuchang"},{"full_name":"Zeng, Zezhu","last_name":"Zeng","first_name":"Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7"},{"full_name":"Wang, Chen","last_name":"Wang","first_name":"Chen"},{"first_name":"Qi","last_name":"Wang","full_name":"Wang, Qi"},{"last_name":"Chen","full_name":"Chen, Yue","first_name":"Yue"}],"department":[{"_id":"BiCh"}],"ec_funded":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"}],"citation":{"short":"S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium, Usenix, 2023, 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.","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.","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.","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.","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.","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."},"day":"15","scopus_import":"1","has_accepted_license":"1","status":"public","project":[{"_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","grant_number":"F8512","name":"Secure Network and Hardware for Efficient Blockchains"}],"main_file_link":[{"url":"https://eprint.iacr.org/2022/1389","open_access":"1"}],"page":"5359-5376","year":"2023","date_created":"2023-11-26T23:00:55Z","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.","volume":8,"publisher":"Usenix","date_updated":"2023-11-28T09:17:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"article_processing_charge":"No","title":"Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling","type":"conference","file_date_updated":"2023-11-28T09:14:34Z","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781713879497"]},"intvolume":"         8","publication":"32nd USENIX Security Symposium","oa":1,"publication_status":"published","quality_controlled":"1","conference":{"end_date":"2023-08-11","location":"Anaheim, CA, United States","name":"USENIX Security Symposium","start_date":"2023-08-09"},"month":"08","_id":"14609","date_published":"2023-08-15T00:00:00Z","author":[{"full_name":"Das, Sourav","last_name":"Das","first_name":"Sourav"},{"first_name":"Zhuolun","full_name":"Xiang, Zhuolun","last_name":"Xiang"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Ren, Ling","last_name":"Ren","first_name":"Ling"}],"oa_version":"Published Version","department":[{"_id":"ElKo"}],"file":[{"creator":"dernst","file_size":704331,"file_id":"14621","relation":"main_file","date_created":"2023-11-28T09:14:34Z","date_updated":"2023-11-28T09:14:34Z","file_name":"2023_USENIX_Das.pdf","checksum":"1a730765930138e23c6efd2575872641","content_type":"application/pdf","access_level":"open_access","success":1}]},{"article_processing_charge":"Yes (via OA deal)","pmid":1,"title":"Stress granules plug and stabilize damaged endolysosomal membranes","date_updated":"2023-11-27T09:05:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","year":"2023","date_created":"2023-11-27T07:56:37Z","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.","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41586-023-06726-w"}],"article_type":"original","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-023-06882-z","relation":"erratum"}],"record":[{"status":"public","relation":"research_data","id":"14472"}]},"citation":{"ieee":"C. Bussi <i>et al.</i>, “Stress granules plug and stabilize damaged endolysosomal membranes,” <i>Nature</i>. Springer Nature, 2023.","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>.","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.","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>","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>","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)."},"day":"15","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"}],"department":[{"_id":"AnSa"}],"oa_version":"Published Version","author":[{"first_name":"Claudio","last_name":"Bussi","full_name":"Bussi, Claudio"},{"first_name":"Agustín","full_name":"Mangiarotti, Agustín","last_name":"Mangiarotti"},{"full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos","first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"first_name":"Beren","full_name":"Aylan, Beren","last_name":"Aylan"},{"last_name":"Pellegrino","full_name":"Pellegrino, Enrica","first_name":"Enrica"},{"full_name":"Athanasiadi, Natalia","last_name":"Athanasiadi","first_name":"Natalia"},{"last_name":"Fearns","full_name":"Fearns, Antony","first_name":"Antony"},{"first_name":"Angela","full_name":"Rodgers, Angela","last_name":"Rodgers"},{"first_name":"Titus M.","full_name":"Franzmann, Titus M.","last_name":"Franzmann"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"Rumiana","last_name":"Dimova","full_name":"Dimova, Rumiana"},{"full_name":"Gutierrez, Maximiliano G.","last_name":"Gutierrez","first_name":"Maximiliano G."}],"external_id":{"pmid":["37968398"]},"month":"11","_id":"14610","date_published":"2023-11-15T00:00:00Z","doi":"10.1038/s41586-023-06726-w","oa":1,"publication":"Nature","publication_status":"epub_ahead","quality_controlled":"1","type":"journal_article","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"language":[{"iso":"eng"}],"keyword":["Multidisciplinary"]},{"related_material":{"link":[{"url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage","relation":"press_release"}],"record":[{"relation":"research_data","id":"14614","status":"public"}]},"has_accepted_license":"1","scopus_import":"1","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 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."}],"day":"01","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>.","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>","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>","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.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","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.","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>."},"ddc":["570"],"date_updated":"2024-02-21T12:18:35Z","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"msad245","pmid":1,"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","article_processing_charge":"Yes (via OA deal)","article_type":"original","status":"public","project":[{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"},{"name":"Mechanisms and Evolution of Reproductive Plasticity","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","grant_number":"ESP39 49461"}],"volume":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).","date_created":"2023-11-27T16:14:37Z","year":"2023","quality_controlled":"1","publication_status":"published","oa":1,"publication":"Molecular Biology and Evolution","intvolume":"        40","date_published":"2023-12-01T00:00:00Z","doi":"10.1093/molbev/msad245","_id":"14613","month":"12","external_id":{"pmid":["37988296"]},"keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"file_date_updated":"2024-01-02T11:39:38Z","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"language":[{"iso":"eng"}],"type":"journal_article","issue":"12","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"file_size":8623505,"creator":"dernst","file_id":"14727","relation":"main_file","date_created":"2024-01-02T11:39:38Z","date_updated":"2024-01-02T11:39:38Z","file_name":"2023_MolecularBioEvo_Lasne.pdf","success":1,"checksum":"47c1c72fb499f26ea52d216b242208c8","content_type":"application/pdf","access_level":"open_access"}],"department":[{"_id":"BeVi"}],"oa_version":"Published Version","author":[{"first_name":"Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","orcid":"0000-0002-1197-8616","full_name":"Lasne, Clementine","last_name":"Lasne"},{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"},{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups"},{"first_name":"Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","orcid":"0000-0002-1253-6297","full_name":"Layana Franco, Lorena Alexandra","last_name":"Layana Franco"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","last_name":"Macon"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}]},{"oa":1,"month":"12","has_accepted_license":"1","_id":"14614","date_published":"2023-12-01T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"14613","status":"public"}]},"doi":"10.15479/AT:ISTA:14614","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."}],"type":"research_data","file_date_updated":"2023-11-30T14:16:59Z","keyword":["Panorpa","scorpionfly","genome","transcriptome"],"citation":{"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.","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>.","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>.","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>","short":"C. Lasne, M.N. Elkrewi, (2023)."},"day":"01","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:18:35Z","ddc":["576"],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"article_processing_charge":"No","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","department":[{"_id":"BeVi"}],"file":[{"file_name":"panorpaX.zip","date_updated":"2023-11-28T13:15:26Z","content_type":"application/zip","access_level":"open_access","checksum":"cd0f13322b5156819ecaebd2bc8e7d12","success":1,"file_id":"14625","date_created":"2023-11-28T13:15:26Z","relation":"main_file","creator":"clasne","file_size":404968272},{"file_name":"panorpa_readme.txt","date_updated":"2023-11-30T14:16:59Z","checksum":"9ff600416577687a737cb3c96dfcb26c","access_level":"open_access","content_type":"text/plain","success":1,"date_created":"2023-11-30T14:16:59Z","file_id":"14634","relation":"main_file","file_size":2625,"creator":"clasne"}],"status":"public","author":[{"first_name":"Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616","last_name":"Lasne"},{"orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"oa_version":"Published Version","contributor":[{"orcid":"0000-0002-5328-7231","last_name":"Elkrewi","contributor_type":"researcher","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"year":"2023","date_created":"2023-11-27T16:39:19Z"},{"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Dryad","date_updated":"2023-11-28T08:17:31Z","title":"The X chromosome of insects likely predates the origin of Class Insecta","department":[{"_id":"BeVi"}],"article_processing_charge":"No","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.hx3ffbgkt"}],"author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"status":"public","date_created":"2023-11-28T08:01:53Z","year":"2023","oa":1,"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14604"}]},"doi":"10.5061/DRYAD.HX3FFBGKT","date_published":"2023-09-15T00:00:00Z","_id":"14616","has_accepted_license":"1","month":"09","license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference","abstract":[{"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.","lang":"eng"}],"day":"15","citation":{"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>","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>.","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>.","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>","short":"M.A. Toups, B. Vicoso, (2023).","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","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>."}},{"department":[{"_id":"BeVi"}],"title":"The X chromosome of insects likely predates the origin of Class Insecta","article_processing_charge":"No","ddc":["570"],"date_updated":"2023-11-28T08:25:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","date_created":"2023-11-28T08:04:03Z","year":"2023","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8138705"}],"author":[{"last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"status":"public","doi":"10.5281/ZENODO.8138705","date_published":"2023-09-15T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"14604","status":"public"}]},"_id":"14617","has_accepted_license":"1","month":"09","oa":1,"day":"15","citation":{"ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023.","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>.","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>","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>.","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)."},"type":"research_data_reference","abstract":[{"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.","lang":"eng"}],"other_data_license":"MIT License"},{"department":[{"_id":"BiCh"}],"title":"BingqingCheng/solubility: V1.0","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","date_updated":"2023-11-28T08:39:22Z","ddc":["530"],"date_created":"2023-11-28T08:32:18Z","year":"2023","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8398094"}],"status":"public","month":"10","date_published":"2023-10-02T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"14603","status":"public"}]},"doi":"10.5281/ZENODO.8398094","has_accepted_license":"1","_id":"14619","oa":1,"citation":{"ista":"Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>.","ama":"Cheng B. BingqingCheng/solubility: V1.0. 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>.","short":"B. Cheng, (2023).","ieee":"B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.","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>."},"day":"02","type":"research_data_reference","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"}]},{"month":"11","date_published":"2023-11-30T00:00:00Z","doi":"10.15479/at:ista:14622","_id":"14622","publication_status":"published","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"file_date_updated":"2023-12-01T11:10:46Z","publication_identifier":{"issn":["2663 - 337X"]},"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"ec_funded":1,"file":[{"embargo":"2024-11-30","content_type":"application/pdf","access_level":"closed","checksum":"068fd3570506ec42b2faa390de784bc4","file_name":"PhD_Thesis.pdf","date_updated":"2023-12-01T11:10:46Z","creator":"ssack","file_size":11947523,"relation":"main_file","file_id":"14635","date_created":"2023-11-30T15:53:10Z","embargo_to":"open_access"},{"content_type":"application/zip","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","access_level":"closed","date_updated":"2023-12-01T11:10:46Z","file_name":"PhD Thesis (1).zip","file_id":"14636","date_created":"2023-11-30T15:54:11Z","relation":"source_file","creator":"ssack","file_size":18422964}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"oa_version":"Published Version","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","last_name":"Sack","orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11471"},{"id":"13125","relation":"part_of_dissertation","status":"public"},{"id":"9760","relation":"part_of_dissertation","status":"public"}]},"has_accepted_license":"1","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>.","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","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>","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>.","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>"},"day":"30","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","article_processing_charge":"No","supervisor":[{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-12-13T14:47:25Z","publisher":"Institute of Science and Technology Austria","ddc":["530"],"date_created":"2023-11-28T10:58:13Z","year":"2023","status":"public","project":[{"name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"},{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"page":"142"},{"day":"01","citation":{"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.","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>.","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.","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>","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>.","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>","short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023)."},"abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","volume":42,"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_created":"2023-11-29T15:02:03Z","year":"2023","article_type":"original","project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"status":"public","article_number":"168","title":"Procedural metamaterials: A unified procedural graph for metamaterial design","article_processing_charge":"Yes (in subscription journal)","ddc":["531","006"],"publisher":"Association for Computing Machinery","date_updated":"2023-12-04T08:09:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Computer Graphics and Computer-Aided Design"],"file_date_updated":"2023-12-04T08:04:14Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0730-0301","1557-7368"]},"type":"journal_article","issue":"5","doi":"10.1145/3605389","date_published":"2023-10-01T00:00:00Z","_id":"14628","month":"10","quality_controlled":"1","publication_status":"published","publication":"ACM Transactions on Graphics","intvolume":"        42","oa":1,"oa_version":"Published Version","author":[{"first_name":"Liane","full_name":"Makatura, Liane","last_name":"Makatura"},{"full_name":"Wang, Bohan","last_name":"Wang","first_name":"Bohan"},{"last_name":"Chen","full_name":"Chen, Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","first_name":"Yi-Lu"},{"first_name":"Bolei","last_name":"Deng","full_name":"Deng, Bolei"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"}],"file":[{"access_level":"open_access","content_type":"application/zip","checksum":"0192f597d7a2ceaf89baddfd6190d4c8","success":1,"file_name":"tog-22-0089-File004.zip","date_updated":"2023-11-29T15:16:01Z","relation":"main_file","date_created":"2023-11-29T15:16:01Z","file_id":"14630","creator":"yichen","file_size":95467870},{"content_type":"application/zip","access_level":"open_access","checksum":"7fb024963be81933494f38de191e4710","success":1,"file_name":"tog-22-0089-File005.zip","date_updated":"2023-11-29T15:16:01Z","creator":"yichen","file_size":103731880,"relation":"main_file","date_created":"2023-11-29T15:16:01Z","file_id":"14631"},{"file_size":57067476,"creator":"dernst","date_created":"2023-12-04T08:04:14Z","file_id":"14638","relation":"main_file","success":1,"content_type":"application/pdf","access_level":"open_access","checksum":"b7d6829ce396e21cac9fae0ec7130a6b","file_name":"2023_ACMToG_Makatura.pdf","date_updated":"2023-12-04T08:04:14Z"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}]},{"ddc":["570"],"publisher":"Springer Nature","date_updated":"2023-12-04T08:17:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"102","article_processing_charge":"Yes","title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","status":"public","article_type":"original","volume":15,"year":"2023","date_created":"2023-12-04T08:10:55Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.\r\nResults: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.\r\nConclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”."}],"day":"23","citation":{"mla":"Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” <i>Genome Medicine</i>, vol. 15, 102, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13073-023-01258-4\">10.1186/s13073-023-01258-4</a>.","ieee":"S.-J. Lin <i>et al.</i>, “Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity,” <i>Genome Medicine</i>, vol. 15. Springer Nature, 2023.","short":"S.-J. Lin, B. Vona, T. Lau, K. Huang, M.S. Zaki, H.S. Aldeen, E.G. Karimiani, C. Rocca, M.M. Noureldeen, A.K. Saad, C. Petree, T. Bartolomaeus, R. Abou Jamra, G. Zifarelli, A. Gotkhindikar, I.M. Wentzensen, M. Liao, E.E. Cork, P. Varshney, N. Hashemi, M.H. Mohammadi, A. Rad, J. Neira, M.B. Toosi, C. Knopp, I. Kurth, T.D. Challman, R. Smith, A. Abdalla, T. Haaf, M. Suri, M. Joshi, W.K. Chung, A. Moreno-De-Luca, H. Houlden, R. Maroofian, G.K. Varshney, Genome Medicine 15 (2023).","ista":"Lin S-J, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. 2023. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 15, 102.","apa":"Lin, S.-J., Vona, B., Lau, T., Huang, K., Zaki, M. S., Aldeen, H. S., … Varshney, G. K. (2023). Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. <i>Genome Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13073-023-01258-4\">https://doi.org/10.1186/s13073-023-01258-4</a>","ama":"Lin S-J, Vona B, Lau T, et al. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. <i>Genome Medicine</i>. 2023;15. doi:<a href=\"https://doi.org/10.1186/s13073-023-01258-4\">10.1186/s13073-023-01258-4</a>","chicago":"Lin, Sheng-Jia, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda Shujaa Aldeen, Ehsan Ghayoor Karimiani, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” <i>Genome Medicine</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13073-023-01258-4\">https://doi.org/10.1186/s13073-023-01258-4</a>."},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_updated":"2023-12-04T08:15:43Z","file_name":"2023_GenomeMed_Lin.pdf","checksum":"279efd212005549aba817a487d56d363","content_type":"application/pdf","access_level":"open_access","success":1,"date_created":"2023-12-04T08:15:43Z","relation":"main_file","file_id":"14640","file_size":14791081,"creator":"dernst"}],"author":[{"first_name":"Sheng-Jia","full_name":"Lin, Sheng-Jia","last_name":"Lin"},{"first_name":"Barbara","full_name":"Vona, Barbara","last_name":"Vona"},{"last_name":"Lau","full_name":"Lau, Tracy","first_name":"Tracy"},{"orcid":"0000-0002-2512-7812","full_name":"Huang, Kevin","last_name":"Huang","first_name":"Kevin","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3"},{"full_name":"Zaki, Maha S.","last_name":"Zaki","first_name":"Maha S."},{"last_name":"Aldeen","full_name":"Aldeen, Huda Shujaa","first_name":"Huda Shujaa"},{"first_name":"Ehsan Ghayoor","last_name":"Karimiani","full_name":"Karimiani, Ehsan Ghayoor"},{"first_name":"Clarissa","full_name":"Rocca, Clarissa","last_name":"Rocca"},{"first_name":"Mahmoud M.","full_name":"Noureldeen, Mahmoud M.","last_name":"Noureldeen"},{"last_name":"Saad","full_name":"Saad, Ahmed K.","first_name":"Ahmed K."},{"first_name":"Cassidy","full_name":"Petree, Cassidy","last_name":"Petree"},{"last_name":"Bartolomaeus","full_name":"Bartolomaeus, Tobias","first_name":"Tobias"},{"first_name":"Rami","full_name":"Abou Jamra, Rami","last_name":"Abou Jamra"},{"full_name":"Zifarelli, Giovanni","last_name":"Zifarelli","first_name":"Giovanni"},{"last_name":"Gotkhindikar","full_name":"Gotkhindikar, Aditi","first_name":"Aditi"},{"last_name":"Wentzensen","full_name":"Wentzensen, Ingrid M.","first_name":"Ingrid M."},{"last_name":"Liao","full_name":"Liao, Mingjuan","first_name":"Mingjuan"},{"first_name":"Emalyn Elise","full_name":"Cork, Emalyn Elise","last_name":"Cork"},{"last_name":"Varshney","full_name":"Varshney, Pratishtha","first_name":"Pratishtha"},{"first_name":"Narges","full_name":"Hashemi, Narges","last_name":"Hashemi"},{"first_name":"Mohammad Hasan","full_name":"Mohammadi, Mohammad Hasan","last_name":"Mohammadi"},{"full_name":"Rad, Aboulfazl","last_name":"Rad","first_name":"Aboulfazl"},{"full_name":"Neira, Juanita","last_name":"Neira","first_name":"Juanita"},{"first_name":"Mehran Beiraghi","last_name":"Toosi","full_name":"Toosi, Mehran Beiraghi"},{"last_name":"Knopp","full_name":"Knopp, Cordula","first_name":"Cordula"},{"first_name":"Ingo","full_name":"Kurth, Ingo","last_name":"Kurth"},{"last_name":"Challman","full_name":"Challman, Thomas D.","first_name":"Thomas D."},{"last_name":"Smith","full_name":"Smith, Rebecca","first_name":"Rebecca"},{"last_name":"Abdalla","full_name":"Abdalla, Asmahan","first_name":"Asmahan"},{"first_name":"Thomas","last_name":"Haaf","full_name":"Haaf, Thomas"},{"last_name":"Suri","full_name":"Suri, Mohnish","first_name":"Mohnish"},{"first_name":"Manali","last_name":"Joshi","full_name":"Joshi, Manali"},{"last_name":"Chung","full_name":"Chung, Wendy K.","first_name":"Wendy K."},{"last_name":"Moreno-De-Luca","full_name":"Moreno-De-Luca, Andres","first_name":"Andres"},{"first_name":"Henry","full_name":"Houlden, Henry","last_name":"Houlden"},{"first_name":"Reza","full_name":"Maroofian, Reza","last_name":"Maroofian"},{"last_name":"Varshney","full_name":"Varshney, Gaurav K.","first_name":"Gaurav K."}],"oa_version":"Published Version","publication_status":"published","quality_controlled":"1","oa":1,"intvolume":"        15","publication":"Genome Medicine","_id":"14639","date_published":"2023-11-23T00:00:00Z","extern":"1","doi":"10.1186/s13073-023-01258-4","month":"11","file_date_updated":"2023-12-04T08:15:43Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1756-994X"]},"keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"type":"journal_article"},{"ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"file":[{"file_name":"mike_thesis_v06-12-2023.odt","date_updated":"2023-12-06T13:13:26Z","access_level":"closed","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","content_type":"application/vnd.oasis.opendocument.text","file_size":46405919,"creator":"mhenness","file_id":"14648","date_created":"2023-12-06T13:13:26Z","relation":"source_file"},{"date_created":"2023-12-06T13:14:15Z","relation":"main_file","file_id":"14649","file_size":21282155,"creator":"mhenness","embargo_to":"open_access","embargo":"2024-11-30","checksum":"f5203a61eddaf35235bbc51904d73982","content_type":"application/pdf","access_level":"closed","file_name":"mike_thesis_v06-12-2023.pdf","date_updated":"2023-12-06T13:14:15Z"}],"oa_version":"Published Version","author":[{"first_name":"Mike","id":"3F338C72-F248-11E8-B48F-1D18A9856A87","full_name":"Hennessey-Wesen, Mike","last_name":"Hennessey-Wesen"}],"month":"11","_id":"14641","doi":"10.15479/at:ista:14641","date_published":"2023-11-30T00:00:00Z","publication_status":"published","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","type":"dissertation","language":[{"iso":"eng"}],"file_date_updated":"2023-12-06T13:14:15Z","publication_identifier":{"issn":["2663 - 337X"]},"keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"article_processing_charge":"No","title":"Adaptive mutation in E. coli modulated by luxS","publisher":"Institute of Science and Technology Austria","date_updated":"2023-12-07T14:12:25Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"year":"2023","date_created":"2023-12-04T13:17:37Z","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"status":"public","page":"104","has_accepted_license":"1","citation":{"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>.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","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>","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>","ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria.","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>."},"day":"30"},{"project":[{"_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30","grant_number":"P34185","name":"Regulation of mammalian transcription by noncoding RNA"}],"status":"public","year":"2023","date_created":"2023-12-04T14:51:00Z","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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","date_updated":"2023-12-05T10:37:28Z","ddc":["572"],"article_processing_charge":"No","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","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"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","citation":{"ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","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>","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>.","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>.","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.)."},"day":"05","has_accepted_license":"1","oa_version":"Submitted Version","author":[{"first_name":"Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","full_name":"Tluckova, Katarina","last_name":"Tluckova"},{"full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo","first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bernecky","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A"}],"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"department":[{"_id":"CaBe"}],"file":[{"date_updated":"2023-12-05T10:37:02Z","file_name":"2023_Tluckova_etal_REx.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","checksum":"c45608cb97ee36d7b50ba518db8e07b0","file_size":4892920,"creator":"dernst","file_id":"14646","date_created":"2023-12-05T10:37:02Z","relation":"main_file"}],"type":"preprint","file_date_updated":"2023-12-05T10:37:02Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"oa":1,"publication_status":"submitted","month":"12","_id":"14644","date_published":"2023-12-05T00:00:00Z","doi":"10.15479/AT:ISTA:14644"},{"date_created":"2023-12-06T13:07:01Z","year":"2023","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).","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1101/2023.11.30.569337","open_access":"1"}],"author":[{"last_name":"Bose","full_name":"Bose, Mahima","first_name":"Mahima"},{"last_name":"Suresh","full_name":"Suresh, Varun","first_name":"Varun"},{"last_name":"Mishra","full_name":"Mishra, Urvi","first_name":"Urvi"},{"first_name":"Ishita","full_name":"Talwar, Ishita","last_name":"Talwar"},{"full_name":"Yadav, Anuradha","last_name":"Yadav","first_name":"Anuradha"},{"full_name":"Biswas, Shiona","last_name":"Biswas","first_name":"Shiona"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"last_name":"Tole","full_name":"Tole, Shubha","first_name":"Shubha"}],"status":"public","title":"Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway","department":[{"_id":"SiHi"}],"article_processing_charge":"No","date_updated":"2023-12-11T07:37:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cold Spring Harbor Laboratory","citation":{"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>.","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.","short":"M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer, S. Tole, BioRxiv (n.d.).","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>.","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>","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>","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>."},"day":"01","type":"preprint","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"month":"12","doi":"10.1101/2023.11.30.569337","date_published":"2023-12-01T00:00:00Z","_id":"14647","publication":"bioRxiv","oa":1,"publication_status":"submitted"},{"date_updated":"2024-08-07T07:16:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"SciPost Foundation","ddc":["530"],"article_processing_charge":"No","title":"Non-equilibrium dynamics of dipolar polarons","article_number":"232","status":"public","project":[{"name":"A path-integral approach to composite impurities","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_type":"original","year":"2023","date_created":"2023-12-10T13:03:07Z","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.","volume":15,"has_accepted_license":"1","abstract":[{"lang":"eng","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."}],"citation":{"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>","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>.","ista":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. 2023. Non-equilibrium dynamics of dipolar polarons. SciPost Physics. 15(6), 232.","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.","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>."},"day":"07","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"department":[{"_id":"MiLe"}],"file":[{"date_updated":"2023-12-11T07:42:04Z","file_name":"2023_SciPostPhysics_Volosniev.pdf","access_level":"open_access","checksum":"e664372a1fe9d628a9bb1d135ebab7d8","content_type":"application/pdf","success":1,"relation":"main_file","file_id":"14669","date_created":"2023-12-11T07:42:04Z","file_size":3543541,"creator":"dernst"}],"oa_version":"Published Version","author":[{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777"},{"first_name":"Luis","last_name":"Santos","full_name":"Santos, Luis"},{"first_name":"Luisllu A.","last_name":"Peña Ardila","full_name":"Peña Ardila, Luisllu A."}],"publication":"SciPost Physics","intvolume":"        15","oa":1,"publication_status":"published","quality_controlled":"1","arxiv":1,"external_id":{"arxiv":["2305.17969"]},"month":"12","_id":"14650","date_published":"2023-12-07T00:00:00Z","doi":"10.21468/scipostphys.15.6.232","issue":"6","type":"journal_article","file_date_updated":"2023-12-11T07:42:04Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2542-4653"]},"keyword":["General Physics and Astronomy"]},{"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"ec_funded":1,"file":[{"file_id":"14684","relation":"main_file","date_created":"2023-12-13T15:37:55Z","file_size":34101468,"creator":"larathoo","success":1,"access_level":"open_access","checksum":"520bdb61e95e66070e02824947d2c5fa","content_type":"application/pdf","file_name":"Phd_Thesis_LA.pdf","date_updated":"2023-12-13T15:37:55Z"},{"checksum":"d8e59afd0817c98fba2564a264508e5c","access_level":"closed","content_type":"application/zip","file_name":"Phd_Thesis_LA.zip","date_updated":"2023-12-14T08:58:18Z","file_size":31052872,"creator":"larathoo","date_created":"2023-12-13T15:42:23Z","relation":"source_file","file_id":"14685"},{"file_size":10713896,"creator":"larathoo","file_id":"14681","date_created":"2023-12-11T19:24:59Z","relation":"supplementary_material","date_updated":"2023-12-14T08:58:18Z","file_name":"Supplementary_Materials.zip","access_level":"closed","content_type":"application/zip","checksum":"9a778c949932286f4519e1f1fca2820d"}],"oa_version":"Published Version","author":[{"first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S","last_name":"Arathoon"}],"oa":1,"publication_status":"published","month":"12","date_published":"2023-12-12T00:00:00Z","doi":"10.15479/at:ista:14651","_id":"14651","type":"dissertation","file_date_updated":"2023-12-14T08:58:18Z","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-12-22T11:04:45Z","ddc":["570"],"title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","article_processing_charge":"No","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"status":"public","page":"96","date_created":"2023-12-11T19:30:37Z","year":"2023","related_material":{"record":[{"relation":"part_of_dissertation","id":"11411","status":"public"}]},"has_accepted_license":"1","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"}],"citation":{"ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","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>.","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>","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","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>.","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023."},"day":"12"},{"volume":674,"date_created":"2023-12-10T23:00:56Z","year":"2023","author":[{"first_name":"Shyam Lal","full_name":"Gupta, Shyam Lal","last_name":"Gupta"},{"orcid":"0000-0003-2209-5269","full_name":"Singh, Saurabh","last_name":"Singh","first_name":"Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a"},{"first_name":"Sumit","last_name":"Kumar","full_name":"Kumar, Sumit"},{"full_name":"Anupam, Unknown","last_name":"Anupam","first_name":"Unknown"},{"first_name":"Samjeet Singh","last_name":"Thakur","full_name":"Thakur, Samjeet Singh"},{"last_name":"Kumar","full_name":"Kumar, Ashish","first_name":"Ashish"},{"first_name":"Sanjay","last_name":"Panwar","full_name":"Panwar, Sanjay"},{"full_name":"Diwaker, D.","last_name":"Diwaker","first_name":"D."}],"article_type":"original","oa_version":"None","status":"public","article_number":"415539","department":[{"_id":"MaIb"}],"title":"Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys","article_processing_charge":"No","date_updated":"2023-12-12T08:22:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","day":"28","citation":{"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>","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>.","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>","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.","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>.","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."},"publication_identifier":{"issn":["0921-4526"]},"language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"doi":"10.1016/j.physb.2023.415539","date_published":"2023-11-28T00:00:00Z","_id":"14652","month":"11","scopus_import":"1","quality_controlled":"1","publication_status":"epub_ahead","intvolume":"       674","publication":"Physica B: Condensed Matter"},{"day":"23","citation":{"ieee":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced motion tracking for interactive mass spectrometry imaging (IMSI),” <i>International Journal of Mass Spectrometry</i>, vol. 495. Elsevier, 2023.","mla":"Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” <i>International Journal of Mass Spectrometry</i>, vol. 495, 117168, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">10.1016/j.ijms.2023.117168</a>.","chicago":"Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat, and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” <i>International Journal of Mass Spectrometry</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">https://doi.org/10.1016/j.ijms.2023.117168</a>.","ista":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2023. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 495, 117168.","ama":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). <i>International Journal of Mass Spectrometry</i>. 2023;495. doi:<a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">10.1016/j.ijms.2023.117168</a>","apa":"Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., &#38; Müller, T. (2023). Advanced motion tracking for interactive mass spectrometry imaging (IMSI). <i>International Journal of Mass Spectrometry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">https://doi.org/10.1016/j.ijms.2023.117168</a>","short":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International Journal of Mass Spectrometry 495 (2023)."},"abstract":[{"text":"Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen's motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data.","lang":"eng"}],"scopus_import":"1","volume":495,"acknowledgement":"We would like to thank Marco Sealey Cardona, PhD for help with the mouse brain samples and acknowledge the financial support by 1669 Förderkreis of the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and Tyrolean Science Fund (TWF).","date_created":"2023-12-10T23:00:57Z","year":"2023","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ijms.2023.117168"}],"status":"public","supplementarymaterial":"yes","article_number":"117168","title":"Advanced motion tracking for interactive mass spectrometry imaging (IMSI)","article_processing_charge":"Yes (in subscription journal)","date_updated":"2026-03-02T09:38:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","publication_identifier":{"issn":["1387-3806"]},"language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1016/j.ijms.2023.117168","date_published":"2023-11-23T00:00:00Z","_id":"14653","month":"11","quality_controlled":"1","publication_status":"epub_ahead","publication":"International Journal of Mass Spectrometry","oa":1,"intvolume":"       495","dataavailabilitystatement":"Data will be made available on request.","oa_version":"Published Version","author":[{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian","last_name":"Kluibenschedl","full_name":"Kluibenschedl, Florian"},{"first_name":"Anna","full_name":"Ploner, Anna","last_name":"Ploner"},{"first_name":"Christina","last_name":"Meisenbichler","full_name":"Meisenbichler, Christina"},{"last_name":"Konrat","full_name":"Konrat, Robert","first_name":"Robert"},{"last_name":"Müller","full_name":"Müller, Thomas","first_name":"Thomas"}],"department":[{"_id":"GradSch"}],"researchdata_availability":"upon request"},{"file":[{"file_name":"2023_JAMES_Hwong.pdf","date_updated":"2023-12-11T08:08:44Z","success":1,"checksum":"4d060b293da3d203de8769e398edf711","access_level":"open_access","content_type":"application/pdf","file_id":"14670","relation":"main_file","date_created":"2023-12-11T08:08:44Z","file_size":2783677,"creator":"dernst"}],"ec_funded":1,"department":[{"_id":"CaMu"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","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"},"author":[{"full_name":"Hwong, Yi-Ling","orcid":"0000-0001-9281-3479","last_name":"Hwong","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22"},{"first_name":"M.","full_name":"Colin, M.","last_name":"Colin"},{"id":"02eace56-97fc-11ee-b81a-f0939ca85a77","first_name":"Philipp","last_name":"Aglas","full_name":"Aglas, Philipp"},{"first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller"},{"first_name":"S. C.","full_name":"Sherwood, S. C.","last_name":"Sherwood"}],"oa_version":"Published Version","_id":"14654","doi":"10.1029/2023MS003726","date_published":"2023-12-01T00:00:00Z","month":"12","publication_status":"published","quality_controlled":"1","publication":"Journal of Advances in Modeling Earth Systems","intvolume":"        15","oa":1,"file_date_updated":"2023-12-11T08:08:44Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1942-2466"]},"issue":"12","type":"journal_article","article_number":"e2023MS003726","article_processing_charge":"Yes","title":"Assessing memory in convection schemes using idealized tests","ddc":["550"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","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.","volume":15,"year":"2023","date_created":"2023-12-10T23:00:57Z","project":[{"call_identifier":"H2020","name":"organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"status":"public","article_type":"original","has_accepted_license":"1","related_material":{"record":[{"relation":"research_data","id":"14991","status":"public"}]},"scopus_import":"1","day":"01","citation":{"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>.","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>","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>.","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>"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"lang":"eng","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."}]}]