[{"publication_identifier":{"eissn":["1759-6653"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2024-01-20T00:00:00Z","file":[{"success":1,"relation":"main_file","access_level":"open_access","file_id":"15029","creator":"dernst","date_created":"2024-02-26T09:54:59Z","file_size":5213306,"checksum":"106a40f10443b2e7ba66749844ebbdf1","date_updated":"2024-02-26T09:54:59Z","content_type":"application/pdf","file_name":"2024_GBE_Bett.pdf"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"14705"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Published Version","article_number":"evae006","month":"01","has_accepted_license":"1","publication":"Genome Biology and Evolution","language":[{"iso":"eng"}],"day":"20","doi":"10.1093/gbe/evae006","abstract":[{"lang":"eng","text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species."}],"citation":{"ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006.","mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” <i>Genome Biology and Evolution</i>, vol. 16, no. 1. Oxford University Press, 2024.","chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>.","ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. 2024;16(1). doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>","apa":"Bett, V. K., Macon, A., Vicoso, B., &#38; Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>"},"year":"2024","date_updated":"2025-07-24T11:06:42Z","external_id":{"pmid":["38245839"]},"volume":16,"ddc":["570"],"department":[{"_id":"BeVi"}],"date_created":"2024-02-18T23:01:02Z","article_processing_charge":"Yes","publication_status":"published","intvolume":"        16","title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","_id":"15009","pmid":1,"issue":"1","author":[{"last_name":"Bett","first_name":"Vincent K","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","first_name":"Marwan N"}],"publisher":"Oxford University Press","article_type":"original","quality_controlled":"1","file_date_updated":"2024-02-26T09:54:59Z"},{"main_file_link":[{"url":"https://proceedings.mlr.press/v234/kurtic24a","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"eissn":["2640-3498"]},"oa":1,"type":"conference","date_published":"2024-01-08T00:00:00Z","conference":{"start_date":"2024-01-03","name":"CPAL: Conference on Parsimony and Learning","end_date":"2024-01-06","location":"Hongkong, China"},"language":[{"iso":"eng"}],"oa_version":"Preprint","month":"01","publication":"Proceedings of Machine Learning Research","volume":234,"day":"08","arxiv":1,"abstract":[{"text":"Pruning large language models (LLMs) from the BERT family has emerged as a standard compression benchmark, and several pruning methods have been proposed for this task. The recent “Sparsity May Cry” (SMC) benchmark put into question the validity of all existing methods, exhibiting a more complex setup where many known pruning methods appear to fail. We revisit the question of accurate BERT-pruning during fine-tuning on downstream datasets, and propose a set of general guidelines for successful pruning, even on the challenging SMC benchmark. First, we perform a cost-vs-benefits analysis of pruning model components, such as the embeddings and the classification head; second, we provide a simple-yet-general way of scaling training, sparsification and learning rate schedules relative to the desired target sparsity; finally, we investigate the importance of proper parametrization for Knowledge Distillation in the context of LLMs. Our simple insights lead to state-of-the-art results, both on classic BERT-pruning benchmarks, as well as on the SMC benchmark, showing that even classic gradual magnitude pruning (GMP) can yield competitive results, with the right approach.","lang":"eng"}],"citation":{"ieee":"E. Kurtic, T. Hoefler, and D.-A. Alistarh, “How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark,” in <i>Proceedings of Machine Learning Research</i>, Hongkong, China, 2024, vol. 234, pp. 542–553.","chicago":"Kurtic, Eldar, Torsten Hoefler, and Dan-Adrian Alistarh. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” In <i>Proceedings of Machine Learning Research</i>, 234:542–53. ML Research Press, 2024.","apa":"Kurtic, E., Hoefler, T., &#38; Alistarh, D.-A. (2024). How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In <i>Proceedings of Machine Learning Research</i> (Vol. 234, pp. 542–553). Hongkong, China: ML Research Press.","ama":"Kurtic E, Hoefler T, Alistarh D-A. How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In: <i>Proceedings of Machine Learning Research</i>. Vol 234. ML Research Press; 2024:542-553.","ista":"Kurtic E, Hoefler T, Alistarh D-A. 2024. How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark. Proceedings of Machine Learning Research. CPAL: Conference on Parsimony and Learning, PMLR, vol. 234, 542–553.","mla":"Kurtic, Eldar, et al. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” <i>Proceedings of Machine Learning Research</i>, vol. 234, ML Research Press, 2024, pp. 542–53.","short":"E. Kurtic, T. Hoefler, D.-A. Alistarh, in:, Proceedings of Machine Learning Research, ML Research Press, 2024, pp. 542–553."},"year":"2024","date_updated":"2024-02-26T10:30:52Z","external_id":{"arxiv":["2312.13547"]},"publisher":"ML Research Press","quality_controlled":"1","page":"542-553","article_processing_charge":"No","date_created":"2024-02-18T23:01:03Z","department":[{"_id":"DaAl"}],"publication_status":"published","intvolume":"       234","title":"How to prune your language model: Recovering accuracy on the \"Sparsity May Cry\" benchmark","alternative_title":["PMLR"],"scopus_import":"1","_id":"15011","author":[{"id":"47beb3a5-07b5-11eb-9b87-b108ec578218","last_name":"Kurtic","first_name":"Eldar","full_name":"Kurtic, Eldar"},{"full_name":"Hoefler, Torsten","last_name":"Hoefler","first_name":"Torsten"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}]},{"date_published":"2024-01-01T00:00:00Z","type":"conference","publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783031492716"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.13201"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"31st International Symposium on Graph Drawing and Network Visualization","oa_version":"Preprint","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342","name":"The Wittgenstein Prize"}],"month":"01","language":[{"iso":"eng"}],"conference":{"end_date":"2023-09-22","location":"Isola delle Femmine, Palermo, Italy","name":"GD: Graph Drawing and Network Visualization","start_date":"2023-09-20"},"date_updated":"2024-02-20T09:13:07Z","year":"2024","citation":{"ama":"Pach J, Saghafian M, Schnider P. Decomposition of geometric graphs into star-forests. In: <i>31st International Symposium on Graph Drawing and Network Visualization</i>. Vol 14465. Springer Nature; 2024:339-346. doi:<a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">10.1007/978-3-031-49272-3_23</a>","apa":"Pach, J., Saghafian, M., &#38; Schnider, P. (2024). Decomposition of geometric graphs into star-forests. In <i>31st International Symposium on Graph Drawing and Network Visualization</i> (Vol. 14465, pp. 339–346). Isola delle Femmine, Palermo, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">https://doi.org/10.1007/978-3-031-49272-3_23</a>","chicago":"Pach, János, Morteza Saghafian, and Patrick Schnider. “Decomposition of Geometric Graphs into Star-Forests.” In <i>31st International Symposium on Graph Drawing and Network Visualization</i>, 14465:339–46. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">https://doi.org/10.1007/978-3-031-49272-3_23</a>.","ieee":"J. Pach, M. Saghafian, and P. Schnider, “Decomposition of geometric graphs into star-forests,” in <i>31st International Symposium on Graph Drawing and Network Visualization</i>, Isola delle Femmine, Palermo, Italy, 2024, vol. 14465, pp. 339–346.","mla":"Pach, János, et al. “Decomposition of Geometric Graphs into Star-Forests.” <i>31st International Symposium on Graph Drawing and Network Visualization</i>, vol. 14465, Springer Nature, 2024, pp. 339–46, doi:<a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">10.1007/978-3-031-49272-3_23</a>.","short":"J. Pach, M. Saghafian, P. Schnider, in:, 31st International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 339–346.","ista":"Pach J, Saghafian M, Schnider P. 2024. Decomposition of geometric graphs into star-forests. 31st International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 14465, 339–346."},"external_id":{"arxiv":["2306.13201"]},"arxiv":1,"doi":"10.1007/978-3-031-49272-3_23","day":"01","abstract":[{"text":"We solve a problem of Dujmović and Wood (2007) by showing that a complete convex geometric graph on n vertices cannot be decomposed into fewer than n-1 star-forests, each consisting of noncrossing edges. This bound is clearly tight. We also discuss similar questions for abstract graphs.","lang":"eng"}],"volume":14465,"acknowledgement":"János Pach’s Research partially supported by European Research Council (ERC), grant “GeoScape” No. 882971 and by the Hungarian Science Foundation (NKFIH), grant K-131529. Work by Morteza Saghafian is partially supported by the European Research Council (ERC), grant No. 788183, and by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31.","_id":"15012","scopus_import":"1","author":[{"id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János","last_name":"Pach","full_name":"Pach, János"},{"id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza","last_name":"Saghafian","full_name":"Saghafian, Morteza"},{"first_name":"Patrick","last_name":"Schnider","full_name":"Schnider, Patrick"}],"publication_status":"published","department":[{"_id":"HeEd"}],"date_created":"2024-02-18T23:01:03Z","article_processing_charge":"No","alternative_title":["LNCS"],"title":"Decomposition of geometric graphs into star-forests","intvolume":"     14465","page":"339-346","quality_controlled":"1","ec_funded":1,"publisher":"Springer Nature"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","acknowledgement":"We would like to extend our thanks to members of the Sweeney, Tosches, Shein-Idelson,\r\nYamaguchi, Kelley, and Cline Labs for their contributions to this project, discussion and support.\r\nWe additionally thank the Beckman Institute Clover Center and Viviana Gradinaru (Caltech),\r\nKimberly Ritola (UNC NeuroTools), Flavia Gama Gomez Leite (ISTA Viral Core), and Hüseyin\r\nCihan Önal (Shigemoto Group, ISTA) for their consultation and assistance regarding AAVs, as\r\nwell as Andras Simon and Alberto Joven for feedback and discussions on AAVs in Pleurodeles.\r\nTo do these experiments, we have also benefited from the tremendous support of our animal care and imaging facilities at our respective institutions, as well as the amphibian stock centers\r\n(National Xenopus Resource Center, European Xenopus Resource Center, Xenopus Express)\r\nand our funding sources: U.S. National Science Foundation (NSF) Grant Number IOS 2110086\r\n(D.B.K., L.B.S., M.A.T., A.Y., and H.T.C.); United States-Israel Binational Science Foundation\r\n(BSF) Grant Number 2020702 (M.S.-I.); NSF Award Number 1645105 (G.J.G., M.E.H.); FTI\r\nStrategy Lower Austria Dissertation Grant Number FTI21-D-046 (D.V.); Horizon Europe ERC\r\nStarting Grant Number 101041551 (L.B.S.); NIH grant number R35GM146973 (M.A.T.); Rita Allen\r\nFoundation award number GA_032522_FE (M.A.T.); European Molecular Biology Organization\r\nLong-Term Fellowship ALTF 874-2021 (A.D.); National Science Foundation Graduate Research\r\nFellowship DGE 2036197 (E.C.J.B.); NIH grant number P40OD010997 (M.E.H).","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.02.15.580289"}],"date_published":"2024-02-16T00:00:00Z","type":"preprint","date_updated":"2024-02-20T09:34:25Z","citation":{"short":"E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian, J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma, G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M. Shein-Idelson, M.A. Tosches, L.B. Sweeney, BioRxiv (n.d.).","mla":"Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.02.15.580289\">10.1101/2024.02.15.580289</a>.","ista":"Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ, Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA, Sweeney LB. Adeno-associated viral tools to trace neural development and connectivity across amphibians. bioRxiv, <a href=\"https://doi.org/10.1101/2024.02.15.580289\">10.1101/2024.02.15.580289</a>.","apa":"Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian, G., … Sweeney, L. B. (n.d.). Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.02.15.580289\">https://doi.org/10.1101/2024.02.15.580289</a>","ama":"Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.02.15.580289\">10.1101/2024.02.15.580289</a>","ieee":"E. C. B. Jaeger <i>et al.</i>, “Adeno-associated viral tools to trace neural development and connectivity across amphibians,” <i>bioRxiv</i>. .","chicago":"Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.02.15.580289\">https://doi.org/10.1101/2024.02.15.580289</a>."},"year":"2024","abstract":[{"lang":"eng","text":"The development, evolution, and function of the vertebrate central nervous system (CNS) can be best studied using diverse model organisms. Amphibians, with their unique phylogenetic position at the transition between aquatic and terrestrial lifestyles, are valuable for understanding the origin and evolution of the tetrapod brain and spinal cord. Their metamorphic developmental transitions and unique regenerative abilities also facilitate the discovery of mechanisms for neural circuit remodeling and replacement. The genetic toolkit for amphibians, however, remains limited, with only a few species having sequenced genomes and a small number of transgenic lines available. In mammals, recombinant adeno-associated viral vectors (AAVs) have become a powerful alternative to genome modification for visualizing and perturbing the nervous system. AAVs are DNA viruses that enable neuronal transduction in both developing and adult animals with low toxicity and spatial, temporal, and cell-type specificity. However, AAVs have never been shown to transduce amphibian cells efficiently. To bridge this gap, we established a simple, scalable, and robust strategy to screen AAV serotypes in three distantly-related amphibian species: the frogs Xenopus laevis and Pelophylax bedriagae, and the salamander Pleurodeles waltl, in both developing larval tadpoles and post-metamorphic animals. For each species, we successfully identified at least two AAV serotypes capable of infecting the CNS; however, no pan-amphibian serotype was identified, indicating rapid evolution of AAV tropism. In addition, we developed an AAV-based strategy that targets isochronic cohorts of developing neurons – a critical tool for parsing neural circuit assembly. Finally, to enable visualization and manipulation of neural circuits, we identified AAV variants for retrograde tracing of neuronal projections in adult animals. Our findings expand the toolkit for amphibians to include AAVs, establish a generalizable workflow for AAV screening in non-canonical research organisms, generate testable hypotheses for the evolution of AAV tropism, and lay the foundation for modern cross-species comparisons of vertebrate CNS development, function, and evolution. "}],"oa":1,"doi":"10.1101/2024.02.15.580289","day":"16","language":[{"iso":"eng"}],"author":[{"full_name":"Jaeger, Eliza C.B.","last_name":"Jaeger","first_name":"Eliza C.B."},{"id":"cf391e77-ec3c-11ea-a124-d69323410b58","first_name":"David","last_name":"Vijatovic","full_name":"Vijatovic, David"},{"full_name":"Deryckere, Astrid","first_name":"Astrid","last_name":"Deryckere"},{"full_name":"Zorin, Nikol","first_name":"Nikol","last_name":"Zorin"},{"full_name":"Nguyen, Akemi L.","last_name":"Nguyen","first_name":"Akemi L."},{"id":"eaf2b366-cfd1-11ee-bbdf-c8790f800a05","full_name":"Ivanian, Georgiy","first_name":"Georgiy","last_name":"Ivanian"},{"full_name":"Woych, Jamie","last_name":"Woych","first_name":"Jamie"},{"first_name":"Rebecca C","last_name":"Arnold","full_name":"Arnold, Rebecca C","id":"d6cce458-14c9-11ed-a755-c1c8fc6fde6f"},{"first_name":"Alonso","last_name":"Ortega Gurrola","full_name":"Ortega Gurrola, Alonso"},{"full_name":"Shvartsman, Arik","last_name":"Shvartsman","first_name":"Arik"},{"id":"a9492887-8972-11ed-ae7b-bfae10998254","full_name":"Barbieri, Francesca","first_name":"Francesca","last_name":"Barbieri"},{"id":"85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5","last_name":"Toma","first_name":"Florina-Alexandra","full_name":"Toma, Florina-Alexandra"},{"last_name":"Gorbsky","first_name":"Gary J.","full_name":"Gorbsky, Gary J."},{"full_name":"Horb, Marko E.","last_name":"Horb","first_name":"Marko E."},{"last_name":"Cline","first_name":"Hollis T.","full_name":"Cline, Hollis T."},{"first_name":"Timothy F.","last_name":"Shay","full_name":"Shay, Timothy F."},{"first_name":"Darcy B.","last_name":"Kelley","full_name":"Kelley, Darcy B."},{"first_name":"Ayako","last_name":"Yamaguchi","full_name":"Yamaguchi, Ayako"},{"first_name":"Mark","last_name":"Shein-Idelson","full_name":"Shein-Idelson, Mark"},{"full_name":"Tosches, Maria Antonietta","last_name":"Tosches","first_name":"Maria Antonietta"},{"id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger","first_name":"Lora Beatrice Jaeger","last_name":"Sweeney"}],"_id":"15016","publication":"bioRxiv","month":"02","title":"Adeno-associated viral tools to trace neural development and connectivity across amphibians","publication_status":"submitted","oa_version":"Preprint","project":[{"_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","grant_number":"FTI21-D-046","name":"Entwicklung und Funktion der V1 Interneuronen vom Schwimmen zum Laufen während der Metamorphose von Xenopus"},{"grant_number":"101041551","name":"Development and Evolution of Tetrapod Motor Circuits","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae"}],"article_processing_charge":"No","department":[{"_id":"LoSw"},{"_id":"MaDe"},{"_id":"GaNo"}],"date_created":"2024-02-20T09:20:32Z"},{"oa":1,"publication_identifier":{"issn":["1369-8001"]},"type":"journal_article","date_published":"2024-02-20T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"url":"https://doi.org/10.1016/j.mssp.2024.108231","open_access":"1"}],"article_number":"108231","month":"02","project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated GermaNIum quanTum tEchnology","grant_number":"101069515"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Materials Science in Semiconductor Processing","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"language":[{"iso":"eng"}],"abstract":[{"text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality.","lang":"eng"}],"day":"20","doi":"10.1016/j.mssp.2024.108231","citation":{"short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” <i>Materials Science in Semiconductor Processing</i>, vol. 174, no. 5, 108231, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">10.1016/j.mssp.2024.108231</a>.","ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. <i>Materials Science in Semiconductor Processing</i>. 2024;174(5). doi:<a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">10.1016/j.mssp.2024.108231</a>","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. <i>Materials Science in Semiconductor Processing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">https://doi.org/10.1016/j.mssp.2024.108231</a>","ieee":"Y. Shimura <i>et al.</i>, “Compressively strained epitaxial Ge layers for quantum computing applications,” <i>Materials Science in Semiconductor Processing</i>, vol. 174, no. 5. Elsevier, 2024.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” <i>Materials Science in Semiconductor Processing</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">https://doi.org/10.1016/j.mssp.2024.108231</a>."},"year":"2024","date_updated":"2024-02-26T10:36:35Z","ddc":["530"],"acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","volume":174,"intvolume":"       174","title":"Compressively strained epitaxial Ge layers for quantum computing applications","date_created":"2024-02-22T14:10:40Z","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"article_processing_charge":"No","publication_status":"epub_ahead","issue":"5","author":[{"first_name":"Yosuke","last_name":"Shimura","full_name":"Shimura, Yosuke"},{"last_name":"Godfrin","first_name":"Clement","full_name":"Godfrin, Clement"},{"full_name":"Hikavyy, Andriy","first_name":"Andriy","last_name":"Hikavyy"},{"last_name":"Li","first_name":"Roy","full_name":"Li, Roy"},{"full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios"},{"first_name":"Paola","last_name":"Favia","full_name":"Favia, Paola"},{"last_name":"Han","first_name":"Han","full_name":"Han, Han"},{"full_name":"Wan, Danny","first_name":"Danny","last_name":"Wan"},{"full_name":"de Greve, Kristiaan","last_name":"de Greve","first_name":"Kristiaan"},{"first_name":"Roger","last_name":"Loo","full_name":"Loo, Roger"}],"_id":"15018","article_type":"original","publisher":"Elsevier","quality_controlled":"1"},{"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-02-23T14:20:16Z","ec_funded":1,"page":"158","title":"Genetic information and biological optimization","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"date_created":"2024-02-23T14:02:04Z","article_processing_charge":"No","publication_status":"published","author":[{"full_name":"Hledik, Michal","first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87"}],"_id":"15020","ddc":["576","519"],"abstract":[{"lang":"eng","text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal."}],"day":"23","doi":"10.15479/at:ista:15020","citation":{"apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria."},"year":"2024","date_updated":"2025-06-30T13:21:09Z","keyword":["Theoretical biology","Optimality","Evolution","Information"],"language":[{"iso":"eng"}],"month":"02","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"name":"Understanding the evolution of continuous genomes","grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","has_accepted_license":"1","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"7553","status":"public"},{"status":"public","id":"7606","relation":"part_of_dissertation"},{"status":"public","id":"12081","relation":"part_of_dissertation"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"hledik thesis pdfa 2b.pdf","content_type":"application/pdf","date_updated":"2024-02-23T13:50:53Z","file_size":7102089,"checksum":"b2d3da47c98d481577a4baf68944fe41","date_created":"2024-02-23T13:50:53Z","creator":"mhledik","file_id":"15021","relation":"main_file","access_level":"open_access","success":1},{"checksum":"eda9b9430da2610fee7ce1c1419a479a","file_size":14014790,"date_created":"2024-02-23T13:50:54Z","file_name":"hledik thesis source.zip","content_type":"application/zip","date_updated":"2024-02-23T14:20:16Z","relation":"source_file","access_level":"closed","creator":"mhledik","file_id":"15022"}],"oa":1,"supervisor":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663 - 337X"]},"type":"dissertation","date_published":"2024-02-23T00:00:00Z"},{"publication":"Journal of Chemical Physics","has_accepted_license":"1","month":"02","article_number":"064503","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"language":[{"iso":"eng"}],"date_published":"2024-02-14T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"15034","checksum":"0a5e0ae70849bce674466fc054390ec0","file_size":5452738,"date_created":"2024-02-27T08:12:52Z","content_type":"application/pdf","file_name":"2024_JourChemicalPhysics_Robin.pdf","date_updated":"2024-02-27T08:12:52Z"}],"author":[{"full_name":"Robin, Paul","orcid":"0000-0002-5728-9189","last_name":"Robin","first_name":"Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d"}],"issue":"6","_id":"15024","pmid":1,"scopus_import":"1","title":"Correlation-induced viscous dissipation in concentrated electrolytes","intvolume":"       160","publication_status":"published","department":[{"_id":"EdHa"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2024-02-25T23:00:55Z","file_date_updated":"2024-02-27T08:12:52Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"AIP Publishing","external_id":{"pmid":["38349632"],"arxiv":["2311.11784"]},"date_updated":"2024-02-27T08:16:06Z","citation":{"apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0188215\">https://doi.org/10.1063/5.0188215</a>","ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. <i>Journal of Chemical Physics</i>. 2024;160(6). doi:<a href=\"https://doi.org/10.1063/5.0188215\">10.1063/5.0188215</a>","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” <i>Journal of Chemical Physics</i>, vol. 160, no. 6. AIP Publishing, 2024.","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0188215\">https://doi.org/10.1063/5.0188215</a>.","short":"P. Robin, Journal of Chemical Physics 160 (2024).","mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” <i>Journal of Chemical Physics</i>, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0188215\">10.1063/5.0188215</a>.","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503."},"year":"2024","abstract":[{"lang":"eng","text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions."}],"arxiv":1,"doi":"10.1063/5.0188215","day":"14","ddc":["540"],"volume":160,"acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413."},{"oa":1,"publication_identifier":{"issn":["1050-5164"]},"type":"journal_article","date_published":"2024-02-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2208.12206","open_access":"1"}],"month":"02","project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"oa_version":"Preprint","publication":"Annals of Applied Probability","language":[{"iso":"eng"}],"abstract":[{"text":"We consider quadratic forms of deterministic matrices A evaluated at the random eigenvectors of a large N×N GOE or GUE matrix, or equivalently evaluated at the columns of a Haar-orthogonal or Haar-unitary random matrix. We prove that, as long as the deterministic matrix has rank much smaller than √N, the distributions of the extrema of these quadratic forms are asymptotically the same as if the eigenvectors were independent Gaussians. This reduces the problem to Gaussian computations, which we carry out in several cases to illustrate our result, finding Gumbel or Weibull limiting distributions depending on the signature of A. Our result also naturally applies to the eigenvectors of any invariant ensemble.","lang":"eng"}],"day":"01","arxiv":1,"doi":"10.1214/23-AAP2000","external_id":{"arxiv":["2208.12206"]},"year":"2024","citation":{"chicago":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2024. <a href=\"https://doi.org/10.1214/23-AAP2000\">https://doi.org/10.1214/23-AAP2000</a>.","ieee":"L. Erdös and B. McKenna, “Extremal statistics of quadratic forms of GOE/GUE eigenvectors,” <i>Annals of Applied Probability</i>, vol. 34, no. 1B. Institute of Mathematical Statistics, pp. 1623–1662, 2024.","apa":"Erdös, L., &#38; McKenna, B. (2024). Extremal statistics of quadratic forms of GOE/GUE eigenvectors. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-AAP2000\">https://doi.org/10.1214/23-AAP2000</a>","ama":"Erdös L, McKenna B. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. <i>Annals of Applied Probability</i>. 2024;34(1B):1623-1662. doi:<a href=\"https://doi.org/10.1214/23-AAP2000\">10.1214/23-AAP2000</a>","ista":"Erdös L, McKenna B. 2024. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 34(1B), 1623–1662.","short":"L. Erdös, B. McKenna, Annals of Applied Probability 34 (2024) 1623–1662.","mla":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” <i>Annals of Applied Probability</i>, vol. 34, no. 1B, Institute of Mathematical Statistics, 2024, pp. 1623–62, doi:<a href=\"https://doi.org/10.1214/23-AAP2000\">10.1214/23-AAP2000</a>."},"date_updated":"2024-02-27T08:29:05Z","volume":34,"acknowledgement":"The first author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by Fulbright Austria and the Austrian Marshall Plan Foundation.","intvolume":"        34","title":"Extremal statistics of quadratic forms of GOE/GUE eigenvectors","department":[{"_id":"LaEr"}],"date_created":"2024-02-25T23:00:56Z","article_processing_charge":"No","publication_status":"published","issue":"1B","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","last_name":"Erdös"},{"orcid":"0000-0003-2625-495X","full_name":"McKenna, Benjamin","first_name":"Benjamin","last_name":"McKenna","id":"b0cc634c-d549-11ee-96c8-87338c7ad808"}],"scopus_import":"1","_id":"15025","article_type":"original","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","ec_funded":1,"page":"1623-1662"},{"author":[{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257"},{"id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana","last_name":"Matijevic","first_name":"Ivana"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"_id":"15033","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","intvolume":"        13","publication_status":"epub_ahead","department":[{"_id":"JiFr"}],"date_created":"2024-02-27T07:10:11Z","article_processing_charge":"Yes","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"eLife Sciences Publications","date_updated":"2024-02-28T12:29:43Z","year":"2024","citation":{"ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>.","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>.","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>"},"abstract":[{"lang":"eng","text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in <jats:italic>gn</jats:italic> knockouts. The functional GN mutant variant GN<jats:sup>fewerroots</jats:sup>, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM."}],"doi":"10.7554/elife.68993","day":"21","ddc":["580"],"acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","volume":13,"publication":"eLife","has_accepted_license":"1","month":"02","oa_version":"Published Version","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"language":[{"iso":"eng"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"date_published":"2024-02-21T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["2050-084X"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.68993"}]},{"oa_version":"Published Version","article_number":"12","month":"02","has_accepted_license":"1","publication":"Few-Body Systems","keyword":["Atomic and Molecular Physics","and Optics"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1432-5411"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2024-02-17T00:00:00Z","file":[{"relation":"main_file","success":1,"access_level":"open_access","file_id":"15049","creator":"dernst","date_created":"2024-03-04T07:07:10Z","checksum":"c4e08cc7bc756da69b1b36fda7bb92fb","file_size":436712,"date_updated":"2024-03-04T07:07:10Z","file_name":"2024_FewBodySys_Varshney.pdf","content_type":"application/pdf"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-03-01T11:39:33Z","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"MiLe"}],"publication_status":"published","intvolume":"        65","title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","scopus_import":"1","_id":"15045","author":[{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","last_name":"Varshney","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","file_date_updated":"2024-03-04T07:07:10Z","day":"17","doi":"10.1007/s00601-024-01880-x","arxiv":1,"abstract":[{"lang":"eng","text":"Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport."}],"year":"2024","citation":{"chicago":"Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” <i>Few-Body Systems</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00601-024-01880-x\">https://doi.org/10.1007/s00601-024-01880-x</a>.","ieee":"A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with two degrees of freedom and dissipation,” <i>Few-Body Systems</i>, vol. 65. Springer Nature, 2024.","apa":"Varshney, A., Ghazaryan, A., &#38; Volosniev, A. (2024). Classical ‘spin’ filtering with two degrees of freedom and dissipation. <i>Few-Body Systems</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00601-024-01880-x\">https://doi.org/10.1007/s00601-024-01880-x</a>","ama":"Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees of freedom and dissipation. <i>Few-Body Systems</i>. 2024;65. doi:<a href=\"https://doi.org/10.1007/s00601-024-01880-x\">10.1007/s00601-024-01880-x</a>","ista":"Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 65, 12.","mla":"Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” <i>Few-Body Systems</i>, vol. 65, 12, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00601-024-01880-x\">10.1007/s00601-024-01880-x</a>.","short":"A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024)."},"date_updated":"2024-03-04T07:08:16Z","external_id":{"arxiv":["2401.08454"]},"acknowledgement":"We thank Mikhail Lemeshko and members of his group for many inspiring discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","volume":65,"ddc":["530"]},{"volume":10,"acknowledgement":"This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041).","ddc":["550"],"doi":"10.1126/sciadv.adj6801","day":"23","abstract":[{"lang":"eng","text":"Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling."}],"date_updated":"2024-03-05T09:26:47Z","citation":{"chicago":"Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adj6801\">https://doi.org/10.1126/sciadv.adj6801</a>.","ieee":"J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” <i>Science Advances</i>, vol. 10, no. 8. American Association for the Advancement of Science, 2024.","ama":"Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. <i>Science Advances</i>. 2024;10(8). doi:<a href=\"https://doi.org/10.1126/sciadv.adj6801\">10.1126/sciadv.adj6801</a>","apa":"Bao, J., Stevens, B., Kluft, L., &#38; Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adj6801\">https://doi.org/10.1126/sciadv.adj6801</a>","ista":"Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801.","mla":"Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” <i>Science Advances</i>, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adj6801\">10.1126/sciadv.adj6801</a>.","short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024)."},"year":"2024","external_id":{"pmid":["38394192"]},"publisher":"American Association for the Advancement of Science","article_type":"original","quality_controlled":"1","ec_funded":1,"file_date_updated":"2024-03-04T07:34:00Z","publication_status":"published","date_created":"2024-03-03T23:00:50Z","department":[{"_id":"CaMu"}],"article_processing_charge":"Yes","title":"Intensification of daily tropical precipitation extremes from more organized convection","intvolume":"        10","pmid":1,"_id":"15047","scopus_import":"1","author":[{"id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","full_name":"Bao, Jiawei","last_name":"Bao","first_name":"Jiawei"},{"last_name":"Stevens","first_name":"Bjorn","full_name":"Stevens, Bjorn"},{"full_name":"Kluft, Lukas","first_name":"Lukas","last_name":"Kluft"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","first_name":"Caroline J","last_name":"Muller"}],"issue":"8","file":[{"content_type":"application/pdf","file_name":"2024_ScienceAdv_Bao.pdf","date_updated":"2024-03-04T07:34:00Z","checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","file_size":800926,"date_created":"2024-03-04T07:34:00Z","creator":"dernst","file_id":"15051","success":1,"access_level":"open_access","relation":"main_file"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/","description":"News on ISTA Website","relation":"press_release"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2375-2548"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2024-02-23T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"name":"organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"month":"02","article_number":"eadj6801","publication":"Science Advances","has_accepted_license":"1"},{"page":"1-18","ec_funded":1,"quality_controlled":"1","file_date_updated":"2024-03-04T07:24:43Z","publisher":"The Company of Biologists","article_type":"original","_id":"15048","scopus_import":"1","author":[{"full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pranjic-Ferscha","first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"issue":"4","publication_status":"published","date_created":"2024-03-03T23:00:50Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"article_processing_charge":"Yes (via OA deal)","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","intvolume":"       151","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","volume":151,"ddc":["570"],"date_updated":"2024-03-04T07:28:25Z","citation":{"ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>.","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” <i>Development</i>, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., &#38; Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. 2024;151(4):1-18. doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>"},"year":"2024","doi":"10.1242/dev.202316","day":"01","abstract":[{"lang":"eng","text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm."}],"language":[{"iso":"eng"}],"publication":"Development","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239"}],"month":"02","file":[{"access_level":"open_access","relation":"main_file","success":1,"creator":"dernst","file_id":"15050","file_size":14839986,"checksum":"6961ea10012bf0d266681f9628bb8f13","date_created":"2024-03-04T07:24:43Z","content_type":"application/pdf","file_name":"2024_Development_Schauer.pdf","date_updated":"2024-03-04T07:24:43Z"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"14926","relation":"research_data","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2024-02-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"oa":1},{"language":[{"iso":"eng"}],"oa_version":"None","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"month":"02","article_number":"054305","publication":"Physical Review B","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"date_published":"2024-02-14T00:00:00Z","type":"journal_article","publisher":"American Physical Society","article_type":"original","quality_controlled":"1","ec_funded":1,"publication_status":"published","article_processing_charge":"No","date_created":"2024-03-04T07:41:23Z","department":[{"_id":"BiCh"}],"title":"Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites","intvolume":"       109","_id":"15052","scopus_import":"1","author":[{"first_name":"Ruihuan","last_name":"Cheng","full_name":"Cheng, Ruihuan"},{"id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","last_name":"Zeng","full_name":"Zeng, Zezhu"},{"last_name":"Wang","first_name":"Chen","full_name":"Wang, Chen"},{"full_name":"Ouyang, Niuchang","last_name":"Ouyang","first_name":"Niuchang"},{"last_name":"Chen","first_name":"Yue","full_name":"Chen, Yue"}],"issue":"5","acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (C7002-22Y and 17318122). The authors are grateful for the research computing facilities offered by\r\nITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","volume":109,"doi":"10.1103/physrevb.109.054305","day":"14","abstract":[{"text":"Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity (\r\nκL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower \r\nκL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications.","lang":"eng"}],"date_updated":"2024-03-04T07:48:55Z","year":"2024","citation":{"mla":"Cheng, Ruihuan, et al. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” <i>Physical Review B</i>, vol. 109, no. 5, 054305, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevb.109.054305\">10.1103/physrevb.109.054305</a>.","short":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024).","ista":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. 2024. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 109(5), 054305.","ama":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. <i>Physical Review B</i>. 2024;109(5). doi:<a href=\"https://doi.org/10.1103/physrevb.109.054305\">10.1103/physrevb.109.054305</a>","apa":"Cheng, R., Zeng, Z., Wang, C., Ouyang, N., &#38; Chen, Y. (2024). Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.109.054305\">https://doi.org/10.1103/physrevb.109.054305</a>","chicago":"Cheng, Ruihuan, Zezhu Zeng, Chen Wang, Niuchang Ouyang, and Yue Chen. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” <i>Physical Review B</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevb.109.054305\">https://doi.org/10.1103/physrevb.109.054305</a>.","ieee":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, and Y. Chen, “Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites,” <i>Physical Review B</i>, vol. 109, no. 5. American Physical Society, 2024."}},{"publication_status":"published","department":[{"_id":"MiLe"}],"date_created":"2024-03-04T07:42:52Z","article_processing_charge":"Yes","title":"Multipurpose platform for analog quantum simulation","intvolume":"         6","_id":"15053","scopus_import":"1","author":[{"full_name":"Jin, Shuwei","first_name":"Shuwei","last_name":"Jin"},{"full_name":"Dai, Kunlun","last_name":"Dai","first_name":"Kunlun"},{"full_name":"Verstraten, Joris","first_name":"Joris","last_name":"Verstraten"},{"first_name":"Maxime","last_name":"Dixmerias","full_name":"Dixmerias, Maxime"},{"full_name":"Al Hyder, Ragheed","last_name":"Al Hyder","first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e"},{"full_name":"Salomon, Christophe","first_name":"Christophe","last_name":"Salomon"},{"full_name":"Peaudecerf, Bruno","first_name":"Bruno","last_name":"Peaudecerf"},{"full_name":"de Jongh, Tim","last_name":"de Jongh","first_name":"Tim"},{"last_name":"Yefsah","first_name":"Tarik","full_name":"Yefsah, Tarik"}],"issue":"1","publisher":"American Physical Society","article_type":"original","quality_controlled":"1","file_date_updated":"2024-03-04T07:53:08Z","doi":"10.1103/physrevresearch.6.013158","arxiv":1,"day":"13","abstract":[{"text":"Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator.","lang":"eng"}],"date_updated":"2024-03-04T07:55:29Z","year":"2024","citation":{"ista":"Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation. Physical Review Research. 6(1), 013158.","short":"S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B. Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024).","mla":"Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.” <i>Physical Review Research</i>, vol. 6, no. 1, 013158, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.013158\">10.1103/physrevresearch.6.013158</a>.","ieee":"S. Jin <i>et al.</i>, “Multipurpose platform for analog quantum simulation,” <i>Physical Review Research</i>, vol. 6, no. 1. American Physical Society, 2024.","chicago":"Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose Platform for Analog Quantum Simulation.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevresearch.6.013158\">https://doi.org/10.1103/physrevresearch.6.013158</a>.","ama":"Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum simulation. <i>Physical Review Research</i>. 2024;6(1). doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.013158\">10.1103/physrevresearch.6.013158</a>","apa":"Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C., … Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.6.013158\">https://doi.org/10.1103/physrevresearch.6.013158</a>"},"external_id":{"arxiv":["2304.08433"]},"acknowledgement":"We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel, Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance in the early stages of this project, and Sebastian Will for a critical reading of the manuscript. This work has been supported by Agence Nationale de la Recherche (Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159), CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ (Super2D and SISCo) and DIM QuanTiP.","volume":6,"ddc":["530"],"oa_version":"Published Version","month":"02","article_number":"013158","publication":"Physical Review Research","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy"],"publication_identifier":{"issn":["2643-1564"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2024-02-13T00:00:00Z","type":"journal_article","file":[{"date_updated":"2024-03-04T07:53:08Z","file_name":"2024_PhysicalReviewResearch_Jin.pdf","content_type":"application/pdf","date_created":"2024-03-04T07:53:08Z","file_size":4025988,"checksum":"ba2ae3e3a011f8897d3803c9366a67e2","file_id":"15054","creator":"dernst","relation":"main_file","success":1,"access_level":"open_access"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"01","title":"Divided attention: Unsupervised multi-object discovery with contextually separated slots","oa_version":"Published Version","publication_status":"published","department":[{"_id":"FrLo"}],"article_processing_charge":"No","date_created":"2023-08-22T14:19:59Z","author":[{"last_name":"Lao","first_name":"Dong","full_name":"Lao, Dong"},{"full_name":"Hu, Zhengyang","last_name":"Hu","first_name":"Zhengyang"},{"first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Yang, Yanchao","first_name":"Yanchao","last_name":"Yang"},{"first_name":"Stefano","last_name":"Soatto","full_name":"Soatto, Stefano"}],"publication":"1st Conference on Parsimony and Learning","_id":"14213","has_accepted_license":"1","conference":{"start_date":"2024-01-03","name":"CPAL: Conference on Parsimony and Learning","location":"Hong Kong, China","end_date":"2024-01-03"},"language":[{"iso":"eng"}],"file_date_updated":"2024-02-12T08:40:36Z","quality_controlled":"1","abstract":[{"lang":"eng","text":"We introduce a method to segment the visual field into independently moving regions, trained with no ground truth or supervision. It consists of an adversarial conditional encoder-decoder architecture based on Slot Attention, modified to use the image as context to decode optical flow without attempting to reconstruct the image itself. In the resulting multi-modal representation, one modality (flow) feeds the encoder to produce separate latent codes (slots), whereas the other modality (image) conditions the decoder to generate the first (flow) from the slots. This design frees the representation from having to encode complex nuisance variability in the image due to, for instance, illumination and reflectance properties of the scene. Since customary autoencoding based on minimizing the reconstruction error does not preclude the entire flow from being encoded into a single slot, we modify the loss to an adversarial criterion based on Contextual Information Separation. The resulting min-max optimization fosters the separation of objects and their assignment to different attention slots, leading to Divided Attention, or DivA. DivA outperforms recent unsupervised multi-object motion segmentation methods while tripling run-time speed up to 104FPS and reducing the performance gap from supervised methods to 12% or less. DivA can handle different numbers of objects and different image sizes at training and test time, is invariant to permutation of object labels, and does not require explicit regularization."}],"oa":1,"arxiv":1,"publication_identifier":{"issnl":["1234-4321"]},"day":"03","date_published":"2024-01-03T00:00:00Z","type":"conference","external_id":{"arxiv":["2304.01430"]},"date_updated":"2025-02-13T08:10:28Z","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["000"],"file":[{"date_updated":"2024-02-12T08:40:36Z","content_type":"application/pdf","file_name":"2024_CPAL_Lao.pdf","date_created":"2024-02-12T08:40:36Z","checksum":"8fad894c34f1b3d5a14fb8ffb12f7277","file_size":8038511,"file_id":"14978","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file"}]},{"_id":"14251","pmid":1,"scopus_import":"1","author":[{"last_name":"Tang","first_name":"Han","full_name":"Tang, Han","orcid":"0000-0001-6152-6637","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E"},{"first_name":"KJ","last_name":"Lu","full_name":"Lu, KJ"},{"first_name":"Y","last_name":"Zhang","full_name":"Zhang, Y"},{"last_name":"Cheng","first_name":"YL","full_name":"Cheng, YL"},{"full_name":"Tu, SL","first_name":"SL","last_name":"Tu"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"issue":"1","publication_status":"published","article_processing_charge":"Yes","department":[{"_id":"JiFr"}],"date_created":"2023-09-01T11:32:02Z","title":"Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution","intvolume":"         5","ec_funded":1,"quality_controlled":"1","file_date_updated":"2024-01-30T12:59:57Z","publisher":"Elsevier","article_type":"original","date_updated":"2025-07-02T12:51:02Z","year":"2024","citation":{"apa":"Tang, H., Lu, K., Zhang, Y., Cheng, Y., Tu, S., &#38; Friml, J. (2024). Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">https://doi.org/10.1016/j.xplc.2023.100669</a>","ama":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. <i>Plant Communications</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">10.1016/j.xplc.2023.100669</a>","ieee":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, and J. Friml, “Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution,” <i>Plant Communications</i>, vol. 5, no. 1. Elsevier, 2024.","chicago":"Tang, Han, KJ Lu, Y Zhang, YL Cheng, SL Tu, and Jiří Friml. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” <i>Plant Communications</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">https://doi.org/10.1016/j.xplc.2023.100669</a>.","short":"H. Tang, K. Lu, Y. Zhang, Y. Cheng, S. Tu, J. Friml, Plant Communications 5 (2024).","mla":"Tang, Han, et al. “Divergence of Trafficking and Polarization Mechanisms for PIN Auxin Transporters during Land Plant Evolution.” <i>Plant Communications</i>, vol. 5, no. 1, 100669, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100669\">10.1016/j.xplc.2023.100669</a>.","ista":"Tang H, Lu K, Zhang Y, Cheng Y, Tu S, Friml J. 2024. Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution. Plant Communications. 5(1), 100669."},"external_id":{"pmid":["37528584"]},"doi":"10.1016/j.xplc.2023.100669","day":"08","abstract":[{"text":"The phytohormone auxin and its directional transport through tissues play a fundamental role in development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and exogenous PINs in two bryophytes, Physcomitrium patens and Marchantia polymorpha, and in the flowering plant Arabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while exogenous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In Arabidopsis root epidermis, bryophytic PINs show no defined polarity. Pharmacological interference revealed a strong cytoskeleton dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues of individual species. These results collectively reveal a divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and a co-evolution of PIN sequence-based and cell-based polarity mechanisms.","lang":"eng"}],"volume":5,"acknowledgement":"This work was supported by the ERC grant (PR1023ERC02) to H. T. and J. F., and by the ministry of science and technology (grant number 110-2636-B-005-001) to K. J. L.","ddc":["580"],"publication":"Plant Communications","has_accepted_license":"1","oa_version":"Published Version","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"month":"01","article_number":"100669","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2024-01-08T00:00:00Z","type":"journal_article","publication_identifier":{"issnl":["1234-4567"],"issn":["2590-3462"]},"oa":1,"file":[{"date_created":"2024-01-30T12:59:57Z","checksum":"edbc44c6d4a394d2bf70f92fdbb08f0a","file_size":2825565,"date_updated":"2024-01-30T12:59:57Z","content_type":"application/pdf","file_name":"2023_PlantCommunications_Tang.pdf","success":1,"access_level":"open_access","relation":"main_file","file_id":"14911","creator":"dernst"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"26","doi":"10.1007/s00029-023-00908-0","arxiv":1,"abstract":[{"text":"Let $\\ell$ be a prime number. We classify the subgroups $G$ of $\\operatorname{Sp}_4(\\mathbb{F}_\\ell)$ and $\\operatorname{GSp}_4(\\mathbb{F}_\\ell)$ that act irreducibly on $\\mathbb{F}_\\ell^4$, but such that every element of $G$ fixes an $\\mathbb{F}_\\ell$-vector subspace of dimension 1. We use this classification to prove that the local-global principle for isogenies of degree $\\ell$ between abelian surfaces over number fields holds in many cases -- in particular, whenever the abelian surface has non-trivial endomorphisms and $\\ell$ is large enough with respect to the field of definition. Finally, we prove that there exist arbitrarily large primes $\\ell$ for which some abelian surface\r\n$A/\\mathbb{Q}$ fails the local-global principle for isogenies of degree $\\ell$.","lang":"eng"}],"year":"2024","date_updated":"2025-02-13T11:47:12Z","external_id":{"arxiv":["2206.15240"]},"OA_type":"green","volume":30,"acknowledgement":"It is a pleasure to thank Samuele Anni for his interest in this project and for several discussions on the topic of this paper, which led in particular to Remark 6.30 and to a better understanding of the difficulties with [6]. We also thank John Cullinan for correspondence about [6] and Barinder Banwait for his many insightful comments on the first version of this paper. Finally, we thank the referee for their thorough reading of the manuscript.\r\nOpen access funding provided by Università di Pisa within the CRUI-CARE Agreement. The authors have been partially supported by MIUR (Italy) through PRIN 2017 “Geometric, algebraic and analytic methods in arithmetic\" and PRIN 2022 “Semiabelian varieties, Galois representations and related Diophantine problems\", and by the University of Pisa through PRA 2018-19 and 2022 “Spazi di moduli, rappresentazioni e strutture combinatorie\". The first author is a member of the INdAM group GNSAGA.","article_processing_charge":"Yes (via OA deal)","date_created":"2023-01-16T11:45:53Z","department":[{"_id":"TiBr"}],"publication_status":"epub_ahead","intvolume":"        30","OA_place":"repository","title":"On the local-global principle for isogenies of abelian surfaces","scopus_import":"1","_id":"12312","issue":"2","author":[{"first_name":"Davide","last_name":"Lombardo","full_name":"Lombardo, Davide"},{"last_name":"Verzobio","first_name":"Matteo","full_name":"Verzobio, Matteo","orcid":"0000-0002-0854-0306","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb"}],"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","publication_identifier":{"eissn":["1420-9020"],"issn":["4321-1234"],"issnl":["1022-1824"]},"oa":1,"type":"journal_article","date_published":"2024-01-26T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2206.15240"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Preprint","article_number":"18","month":"01","publication":"Selecta Mathematica","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"oa_version":"Published Version","project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805"}],"month":"01","publication":"Neuron","has_accepted_license":"1","file":[{"date_updated":"2024-02-06T13:56:15Z","content_type":"application/pdf","file_name":"2024_Neuron_Cheung.pdf","date_created":"2024-02-06T13:56:15Z","checksum":"32b3788f7085cf44a84108d8faaff3ce","file_size":5942467,"file_id":"14944","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file"}],"related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0896-6273"],"eisbn":["1234995621"],"issnl":["1234-5678"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2024-01-17T00:00:00Z","type":"journal_article","publisher":"Elsevier","article_type":"comment","page":"230-246.e11","quality_controlled":"1","file_date_updated":"2024-02-06T13:56:15Z","publication_status":"published","date_created":"2023-04-27T09:41:48Z","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"SiHi"},{"_id":"RySh"}],"title":"Multipotent progenitors instruct ontogeny of the superior colliculus","intvolume":"       112","_id":"12875","pmid":1,"scopus_import":"1","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","first_name":"Giselle T","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","first_name":"Florian"},{"orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","last_name":"Krausgruber","full_name":"Krausgruber, Thomas"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen"},{"id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","full_name":"Schrammel, Martin","last_name":"Schrammel","first_name":"Martin"},{"last_name":"Özgen","first_name":"Natalie Y","full_name":"Özgen, Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090"},{"id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","first_name":"Alexis","last_name":"Ivec","full_name":"Ivec, Alexis"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer"}],"issue":"2","acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","volume":112,"ddc":["570"],"doi":"10.1016/j.neuron.2023.11.009","day":"17","abstract":[{"text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.","lang":"eng"}],"date_updated":"2025-05-14T09:39:37Z","year":"2024","external_id":{"pmid":["38096816"]}},{"APC_amount":"12345","external_id":{"pmid":["38167818"],"oaworkID":["w4390499170"]},"year":"2024","citation":{"ieee":"M. Valentini <i>et al.</i>, “Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>.","apa":"Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra, S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>","ama":"Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>","ista":"Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. 15, 169.","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R. Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","mla":"Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>, vol. 15, 169, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>."},"date_updated":"2026-02-26T11:39:00Z","abstract":[{"lang":"eng","text":"Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with ≈ 100% efficiency. The reported results open up the path towards integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on  the same silicon technology compatible platform."}],"day":"02","doi":"10.1038/s41467-023-44114-0","ddc":["530"],"volume":15,"acknowledgement":"We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger, and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the support in the TEM analysis. This research and related results were made possible with the support of the NOMIS\r\nFoundation. It was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research andinnovation programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project, the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290.","researchdata_availability":"yes","author":[{"last_name":"Valentini","first_name":"Marco","full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","first_name":"Oliver","last_name":"Sagi"},{"full_name":"Baghumyan, Levon","first_name":"Levon","last_name":"Baghumyan","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7"},{"last_name":"de Gijsel","first_name":"Thijs","full_name":"de Gijsel, Thijs","id":"a0ece13c-b527-11ee-929d-bad130106eee"},{"last_name":"Jung","first_name":"Jason","full_name":"Jung, Jason","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Calcaterra, Stefano","first_name":"Stefano","last_name":"Calcaterra"},{"last_name":"Ballabio","first_name":"Andrea","full_name":"Ballabio, Andrea"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L","first_name":"Juan L","last_name":"Aguilera Servin"},{"orcid":"0000-0001-9985-9293","full_name":"Aggarwal, Kushagra","first_name":"Kushagra","last_name":"Aggarwal","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb"},{"id":"396A1950-F248-11E8-B48F-1D18A9856A87","full_name":"Janik, Marian","first_name":"Marian","last_name":"Janik"},{"id":"38756BB2-F248-11E8-B48F-1D18A9856A87","full_name":"Adletzberger, Thomas","first_name":"Thomas","last_name":"Adletzberger"},{"full_name":"Seoane Souto, Rubén","last_name":"Seoane Souto","first_name":"Rubén"},{"last_name":"Leijnse","first_name":"Martin","full_name":"Leijnse, Martin"},{"first_name":"Jeroen","last_name":"Danon","full_name":"Danon, Jeroen"},{"full_name":"Schrade, Constantin","first_name":"Constantin","last_name":"Schrade"},{"full_name":"Bakkers, Erik","first_name":"Erik","last_name":"Bakkers"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"dataavailabilitystatement":"All experimental data included in this work are available at https://zenodo.org/records/10119346.","scopus_import":"1","_id":"14793","pmid":1,"intvolume":"        15","title":"Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium","department":[{"_id":"GeKa"}],"article_processing_charge":"Yes","date_created":"2024-01-14T23:00:56Z","publication_status":"published","file_date_updated":"2024-01-17T11:03:00Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"Springer Nature","type":"journal_article","date_published":"2024-01-02T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"oaworkID":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supplementarymaterial":"yes","file":[{"file_name":"2024_NatureComm_Valentini.pdf","content_type":"application/pdf","date_updated":"2024-01-17T11:03:00Z","file_size":2336595,"checksum":"ef79173b45eeaf984ffa61ef2f8a52ab","date_created":"2024-01-17T11:03:00Z","creator":"dernst","file_id":"14825","access_level":"open_access","success":1,"relation":"main_file"}],"has_accepted_license":"1","publication":"Nature Communications","article_number":"169","month":"01","project":[{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"101069515","name":"Integrated GermaNIum quanTum tEchnology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"grant_number":"101115315","name":"Quantum bits with Kitaev Transmons","_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811"},{"grant_number":"P32235","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"grant_number":"F8606","name":"Conventional and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Published Version","language":[{"iso":"eng"}]},{"quality_controlled":"1","page":"902-909.e6","article_type":"original","publisher":"Elsevier","issue":"4","author":[{"full_name":"Csata, Eniko","last_name":"Csata","first_name":"Eniko"},{"last_name":"Perez-Escudero","first_name":"Alfonso","full_name":"Perez-Escudero, Alfonso"},{"last_name":"Laury","first_name":"Emmanuel","full_name":"Laury, Emmanuel"},{"last_name":"Leitner","first_name":"Hanna","full_name":"Leitner, Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7"},{"full_name":"Latil, Gerard","first_name":"Gerard","last_name":"Latil"},{"first_name":"Juerge","last_name":"Heinze","full_name":"Heinze, Juerge"},{"last_name":"Simpson","first_name":"Stephen","full_name":"Simpson, Stephen"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"first_name":"Audrey","last_name":"Dussutour","full_name":"Dussutour, Audrey"}],"dataavailabilitystatement":"no DAS","scopus_import":"1","pmid":1,"_id":"14479","intvolume":"        34","title":"Fungal infection alters collective nutritional intake of ant colonies","date_created":"2023-10-31T13:30:20Z","article_processing_charge":"No","department":[{"_id":"SyCr"}],"publication_status":"published","volume":34,"acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","researchdata_availability":"unclear","external_id":{"pmid":["38307022"]},"citation":{"apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">https://doi.org/10.1016/j.cub.2024.01.017</a>","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. <i>Current Biology</i>. 2024;34(4):902-909.e6. doi:<a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">10.1016/j.cub.2024.01.017</a>","chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” <i>Current Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">https://doi.org/10.1016/j.cub.2024.01.017</a>.","ieee":"E. Csata <i>et al.</i>, “Fungal infection alters collective nutritional intake of ant colonies,” <i>Current Biology</i>, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024.","short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” <i>Current Biology</i>, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:<a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">10.1016/j.cub.2024.01.017</a>.","ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6."},"year":"2024","date_updated":"2026-03-18T11:15:21Z","abstract":[{"text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication.","lang":"eng"}],"day":"26","doi":"10.1016/j.cub.2024.01.017","language":[{"iso":"eng"}],"publication":"Current Biology","month":"02","oa_version":"Preprint","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supplementarymaterial":"yes","main_file_link":[{"url":"https://doi.org/10.1101/2023.10.26.564092","open_access":"1"}],"type":"journal_article","date_published":"2024-02-26T00:00:00Z","oa":1,"publication_identifier":{"issnl":["1234-5678"],"eissn":["1879-0445"],"issn":["0960-9822"]}}]