[{"publication_status":"published","keyword":["Concurrent data structure","kD-tree","Nearest neighbor search","Similarity search","Lock-free","Linearizability"],"article_processing_charge":"No","year":"2021","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-09-13T00:00:00Z","page":"27-48","isi":1,"type":"journal_article","oa":1,"publication":"Theoretical Computer Science","status":"public","corr_author":"1","month":"09","date_created":"2021-08-08T22:01:31Z","abstract":[{"lang":"eng","text":"The Nearest neighbour search (NNS) is a fundamental problem in many application domains dealing with multidimensional data. In a concurrent setting, where dynamic modifications are allowed, a linearizable implementation of the NNS is highly desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free concurrent kD-tree, which implements an abstract data type (ADT) that provides the operations Add, Remove, Contains, and NNS. Our implementation is linearizable. The operations in the LFkD-tree use single-word read and compare-and-swap (Image 1 ) atomic primitives, which are readily supported on available multi-core processors. We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world and synthetic datasets. The experiments show that the presented design is scalable and achieves significant speed-up compared to the implementations of an existing sequential kD-tree and a recently proposed multidimensional indexing structure, PH-tree."}],"publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":"       886","author":[{"id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Bapi","first_name":"Bapi","orcid":"0000-0002-2742-4028","last_name":"Chatterjee"},{"first_name":"Ivan","last_name":"Walulya","full_name":"Walulya, Ivan"},{"first_name":"Philippas","last_name":"Tsigas","full_name":"Tsigas, Philippas"}],"title":"Concurrent linearizable nearest neighbour search in LockFree-kD-tree","date_updated":"2024-10-09T21:00:45Z","day":"13","publication_identifier":{"issn":["0304-3975"]},"article_type":"original","external_id":{"isi":["000694718900004"]},"_id":"9827","quality_controlled":"1","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf"}],"department":[{"_id":"DaAl"}],"scopus_import":"1","volume":886,"citation":{"mla":"Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” <i>Theoretical Computer Science</i>, vol. 886, Elsevier, 2021, pp. 27–48, doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">10.1016/j.tcs.2021.06.041</a>.","ieee":"B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest neighbour search in LockFree-kD-tree,” <i>Theoretical Computer Science</i>, vol. 886. Elsevier, pp. 27–48, 2021.","ama":"Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. <i>Theoretical Computer Science</i>. 2021;886:27-48. doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">10.1016/j.tcs.2021.06.041</a>","apa":"Chatterjee, B., Walulya, I., &#38; Tsigas, P. (2021). Concurrent linearizable nearest neighbour search in LockFree-kD-tree. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">https://doi.org/10.1016/j.tcs.2021.06.041</a>","ista":"Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48.","chicago":"Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” <i>Theoretical Computer Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">https://doi.org/10.1016/j.tcs.2021.06.041</a>.","short":"B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021) 27–48."},"doi":"10.1016/j.tcs.2021.06.041"},{"citation":{"mla":"Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” <i>ACS Nano</i>, vol. 15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:<a href=\"https://doi.org/10.1021/acsnano.1c03276\">10.1021/acsnano.1c03276</a>.","ieee":"D. Baranov <i>et al.</i>, “News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience,” <i>ACS Nano</i>, vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021.","ama":"Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. <i>ACS Nano</i>. 2021;15(7):10743–10747. doi:<a href=\"https://doi.org/10.1021/acsnano.1c03276\">10.1021/acsnano.1c03276</a>","apa":"Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E. K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.1c03276\">https://doi.org/10.1021/acsnano.1c03276</a>","ista":"Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747.","chicago":"Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D. Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” <i>ACS Nano</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsnano.1c03276\">https://doi.org/10.1021/acsnano.1c03276</a>.","short":"D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D. Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747."},"doi":"10.1021/acsnano.1c03276","volume":15,"department":[{"_id":"MaIb"}],"scopus_import":"1","quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1021/acsnano.1c03276","open_access":"1"}],"_id":"9829","external_id":{"pmid":["34228432"],"isi":["000679406500002"]},"day":"06","article_type":"original","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"acknowledgement":"K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for their feedback and support of the News in Nanocrystals initiative. The authors thank Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in the organization of the seminar, and Professors Brandi Cossairt (University of Washington) and Gordana Dukovic for their feedback on an earlier version of this manuscript. The authors thank all the seminar speakers and attendees for their interest and continuing participation in the seminar series.","title":"News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience","date_updated":"2026-06-18T19:58:29Z","author":[{"first_name":"Dmitry","last_name":"Baranov","full_name":"Baranov, Dmitry"},{"first_name":"Tara","last_name":"Šverko","full_name":"Šverko, Tara"},{"full_name":"Moot, Taylor","first_name":"Taylor","last_name":"Moot"},{"last_name":"Keller","first_name":"Helena R.","full_name":"Keller, Helena R."},{"last_name":"Klein","first_name":"Megan D.","full_name":"Klein, Megan D."},{"full_name":"Vishnu, E. K.","first_name":"E. K.","last_name":"Vishnu"},{"id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","full_name":"Balazs, Daniel","first_name":"Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs"},{"last_name":"Shulenberger","first_name":"Katherine E.","full_name":"Shulenberger, Katherine E."}],"intvolume":"        15","language":[{"iso":"eng"}],"publisher":"American Chemical Society","date_created":"2021-08-08T22:01:31Z","pmid":1,"abstract":[{"lang":"eng","text":"In 2020, many in-person scientific events were canceled due to the COVID-19 pandemic, creating a vacuum in networking and knowledge exchange between scientists. To fill this void in scientific communication, a group of early career nanocrystal enthusiasts launched the virtual seminar series, News in Nanocrystals, in the summer of 2020. By the end of the year, the series had attracted over 850 participants from 46 countries. In this Nano Focus, we describe the process of organizing the News in Nanocrystals seminar series; discuss its growth, emphasizing what the organizers have learned in terms of diversity and accessibility; and provide an outlook for the next steps and future opportunities. This summary and analysis of experiences and learned lessons are intended to inform the broader scientific community, especially those who are looking for avenues to continue fostering discussion and scientific engagement virtually, both during the pandemic and after."}],"publication":"ACS Nano","ddc":["540"],"month":"07","status":"public","issue":"7","oa":1,"isi":1,"type":"journal_article","page":"10743–10747","date_published":"2021-07-06T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","article_processing_charge":"No","year":"2021"},{"author":[{"last_name":"Rychlewicz","first_name":"Kamil P","id":"85A07246-A8BF-11E9-B4FA-D9E3E5697425","full_name":"Rychlewicz, Kamil P"}],"date_updated":"2024-10-09T20:59:03Z","title":"The positivity of local equivariant Hirzebruch class for toric varieties","article_type":"original","publication_identifier":{"issn":["0024-6093"],"eissn":["1469-2120"]},"day":"01","arxiv":1,"external_id":{"arxiv":["1910.10435"],"isi":["000594805800001"]},"_id":"6965","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.10435"}],"quality_controlled":"1","oa_version":"Preprint","scopus_import":"1","department":[{"_id":"TaHa"}],"volume":53,"doi":"10.1112/blms.12442","citation":{"short":"K.P. Rychlewicz, Bulletin of the London Mathematical Society 53 (2021) 560–574.","chicago":"Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class for Toric Varieties.” <i>Bulletin of the London Mathematical Society</i>. Wiley, 2021. <a href=\"https://doi.org/10.1112/blms.12442\">https://doi.org/10.1112/blms.12442</a>.","apa":"Rychlewicz, K. P. (2021). The positivity of local equivariant Hirzebruch class for toric varieties. <i>Bulletin of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/blms.12442\">https://doi.org/10.1112/blms.12442</a>","ista":"Rychlewicz KP. 2021. The positivity of local equivariant Hirzebruch class for toric varieties. Bulletin of the London Mathematical Society. 53(2), 560–574.","ama":"Rychlewicz KP. The positivity of local equivariant Hirzebruch class for toric varieties. <i>Bulletin of the London Mathematical Society</i>. 2021;53(2):560-574. doi:<a href=\"https://doi.org/10.1112/blms.12442\">10.1112/blms.12442</a>","mla":"Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class for Toric Varieties.” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2, Wiley, 2021, pp. 560–74, doi:<a href=\"https://doi.org/10.1112/blms.12442\">10.1112/blms.12442</a>.","ieee":"K. P. Rychlewicz, “The positivity of local equivariant Hirzebruch class for toric varieties,” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2. Wiley, pp. 560–574, 2021."},"year":"2021","article_processing_charge":"No","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-04-01T00:00:00Z","page":"560-574","type":"journal_article","isi":1,"oa":1,"issue":"2","status":"public","month":"04","publication":"Bulletin of the London Mathematical Society","corr_author":"1","abstract":[{"text":"The central object of investigation of this paper is the Hirzebruch class, a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following the work of Weber, we investigate its equivariant version for (possibly singular) toric varieties. The local decomposition of the Hirzebruch class to the fixed points of the torus action and a formula for the local class in terms of the defining fan are recalled. After this review part, we prove the positivity of local Hirzebruch classes for all toric varieties, thus proving false the alleged counterexample given by Weber.","lang":"eng"}],"date_created":"2019-10-24T08:04:09Z","publisher":"Wiley","language":[{"iso":"eng"}],"intvolume":"        53"},{"year":"2021","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-23T00:00:00Z","page":"32","type":"journal_article","isi":1,"oa":1,"status":"public","publication":"Nature Neuroscience","month":"08","date_created":"2019-11-10T11:23:58Z","pmid":1,"abstract":[{"text":"Human brain organoids represent a powerful tool for the study of human neurological diseases particularly those that impact brain growth and structure. However, many neurological diseases lack obvious anatomical abnormalities, yet significantly impact neural network functions, raising the question of whether organoids possess sufficient neural network architecture and complexity to model these conditions. Here, we explore the network level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex oscillatory network behaviors reminiscent of intact brain preparations. We further demonstrate strikingly abnormal epileptiform network activity in organoids derived from a Rett Syndrome patient despite only modest anatomical differences from isogenically matched controls, and rescue with an unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide an essential foundation for the utilization of human brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery.","lang":"eng"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"OA_type":"green","intvolume":"        24","author":[{"last_name":"Samarasinghe","first_name":"Ranmal A.","full_name":"Samarasinghe, Ranmal A."},{"last_name":"Miranda","orcid":"0000-0001-6618-6889","first_name":"Osvaldo","full_name":"Miranda, Osvaldo","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425"},{"full_name":"Buth, Jessie E.","first_name":"Jessie E.","last_name":"Buth"},{"first_name":"Simon","last_name":"Mitchell","full_name":"Mitchell, Simon"},{"full_name":"Ferando, Isabella","first_name":"Isabella","last_name":"Ferando"},{"last_name":"Watanabe","first_name":"Momoko","full_name":"Watanabe, Momoko"},{"last_name":"Kurdian","first_name":"Arinnae","full_name":"Kurdian, Arinnae"},{"full_name":"Golshani, Peyman","last_name":"Golshani","first_name":"Peyman"},{"full_name":"Plath, Kathrin","first_name":"Kathrin","last_name":"Plath"},{"full_name":"Lowry, William E.","first_name":"William E.","last_name":"Lowry"},{"full_name":"Parent, Jack M.","first_name":"Jack M.","last_name":"Parent"},{"last_name":"Mody","first_name":"Istvan","full_name":"Mody, Istvan"},{"last_name":"Novitch","first_name":"Bennett G.","full_name":"Novitch, Bennett G."}],"date_updated":"2025-07-09T09:00:12Z","title":"Identification of neural oscillations and epileptiform changes in human brain organoids","acknowledgement":"We thank S. Butler, T. Carmichael and members of the laboratory of B.G.N. for helpful discussions and comments on the manuscript; N. Vishlaghi and F. Turcios-Hernandez for technical assistance, and J. Lee, S.-K. Lee, H. Shinagawa and K. Yoshikawa for valuable reagents. We also thank the UCLA Eli and Edythe Broad Stem Cell Research Center (BSCRC) and Intellectual and Developmental Disabilities Research Center microscopy cores for access to imaging facilities. This work was supported by grants from the California Institute for Regenerative Medicine (CIRM) (DISC1-08819 to B.G.N.), the National Institute of Health (R01NS089817, R01DA051897 and P50HD103557 to B.G.N.; K08NS119747 to R.A.S.; K99HD096105 to M.W.; R01MH123922, R01MH121521 and P50HD103557 to M.J.G.; R01GM099134 to K.P.; R01NS103788 to W.E.L.; R01NS088571 to J.M.P.; R01NS030549 and R01AG050474 to I.M.), and research awards from the UCLA Jonsson Comprehensive Cancer Center and BSCRC Ablon Scholars Program (to B.G.N.), the BSCRC Innovation Program (to B.G.N., K.P. and W.E.L.), the UCLA BSCRC Steffy Brain Aging Research Fund (to B.G.N. and W.E.L.) and the UCLA Clinical and Translational Science Institute (to B.G.N.), Paul Allen Family Foundation Frontiers Group (to K.P. and W.E.L.), the March of Dimes Foundation (to W.E.L.) and the Simons Foundation Autism Research Initiative Bridge to Independence Program (to R.A.S. and M.J.G.). R.A.S. was also supported by the UCLA/NINDS Translational Neuroscience Training Grant (R25NS065723), a Research and Training Fellowship from the American Epilepsy Society, a Taking Flight Award from CURE Epilepsy and a Clinician Scientist training award from the UCLA BSCRC. J.E.B. was supported by the UCLA BSCRC Rose Hills Foundation Graduate Scholarship Training Program. M.W. was supported by postdoctoral training awards provided by the UCLA BSCRC and the Uehara Memorial Foundation. O.A.M. and A.K. were supported in part by the UCLA-California State University Northridge CIRM-Bridges training program (EDUC2-08411). We also acknowledge the support of the IDDRC Cells, Circuits and Systems Analysis, Microscopy and Genetics and Genomics Cores of the Semel Institute of Neuroscience at UCLA, which are supported by the NICHD (U54HD087101 and P50HD10355701). We lastly acknowledge support from a Quantitative and Computational Biosciences Collaboratory Postdoctoral Fellowship to S.M. and the Quantitative and Computational Biosciences Collaboratory community, directed by M. Pellegrini.","article_type":"review","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"day":"23","OA_place":"publisher","external_id":{"isi":["000687516300001"],"pmid":["34426698 "]},"_id":"6995","main_file_link":[{"url":"https://doi.org/10.1101/820183","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"volume":24,"citation":{"apa":"Samarasinghe, R. A., Miranda, O., Buth, J. E., Mitchell, S., Ferando, I., Watanabe, M., … Novitch, B. G. (2021). Identification of neural oscillations and epileptiform changes in human brain organoids. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>","ama":"Samarasinghe RA, Miranda O, Buth JE, et al. Identification of neural oscillations and epileptiform changes in human brain organoids. <i>Nature Neuroscience</i>. 2021;24:32. doi:<a href=\"https://doi.org/10.1038/s41593-021-00906-5\">10.1038/s41593-021-00906-5</a>","ista":"Samarasinghe RA, Miranda O, Buth JE, Mitchell S, Ferando I, Watanabe M, Kurdian A, Golshani P, Plath K, Lowry WE, Parent JM, Mody I, Novitch BG. 2021. Identification of neural oscillations and epileptiform changes in human brain organoids. Nature Neuroscience. 24, 32.","mla":"Samarasinghe, Ranmal A., et al. “Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids.” <i>Nature Neuroscience</i>, vol. 24, Springer Nature, 2021, p. 32, doi:<a href=\"https://doi.org/10.1038/s41593-021-00906-5\">10.1038/s41593-021-00906-5</a>.","ieee":"R. A. Samarasinghe <i>et al.</i>, “Identification of neural oscillations and epileptiform changes in human brain organoids,” <i>Nature Neuroscience</i>, vol. 24. Springer Nature, p. 32, 2021.","short":"R.A. Samarasinghe, O. Miranda, J.E. Buth, S. Mitchell, I. Ferando, M. Watanabe, A. Kurdian, P. Golshani, K. Plath, W.E. Lowry, J.M. Parent, I. Mody, B.G. Novitch, Nature Neuroscience 24 (2021) 32.","chicago":"Samarasinghe, Ranmal A., Osvaldo Miranda, Jessie E. Buth, Simon Mitchell, Isabella Ferando, Momoko Watanabe, Arinnae Kurdian, et al. “Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids.” <i>Nature Neuroscience</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>."},"doi":"10.1038/s41593-021-00906-5"},{"author":[{"full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249"},{"full_name":"Shriki, Oren","first_name":"Oren","last_name":"Shriki"},{"last_name":"Herrmann","first_name":"Hans J","full_name":"Herrmann, Hans J"},{"full_name":"de Arcangelis, Lucilla","last_name":"de Arcangelis","first_name":"Lucilla"}],"title":"Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches","date_updated":"2025-04-14T07:44:02Z","day":"13","acknowledgement":"LdA would like to acknowledge the financial support from MIUR-PRIN2017 WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies CAPES and FUNCAP for financial support.","article_type":"original","publication_identifier":{"eissn":["1872-8286"],"issn":["0925-2312"]},"external_id":{"isi":["000704086300015"]},"_id":"7463","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.03.930966"}],"department":[{"_id":"GaTk"}],"scopus_import":"1","volume":461,"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"chicago":"Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>.","short":"F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.","mla":"Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>, vol. 461, Elsevier, 2021, pp. 657–66, doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>.","ieee":"F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches,” <i>Neurocomputing</i>, vol. 461. Elsevier, pp. 657–666, 2021.","ista":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. 461, 657–666.","apa":"Lombardi, F., Shriki, O., Herrmann, H. J., &#38; de Arcangelis, L. (2021). Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>","ama":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. 2021;461:657-666. doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>"},"doi":"10.1016/j.neucom.2020.05.126","publication_status":"published","year":"2021","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-05-13T00:00:00Z","page":"657-666","ec_funded":1,"type":"journal_article","isi":1,"oa":1,"month":"05","status":"public","publication":"Neurocomputing","date_created":"2020-02-06T16:09:14Z","abstract":[{"text":"Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms.","lang":"eng"}],"publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":"       461"},{"external_id":{"pmid":["33065009"],"isi":["000614361000020"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"11","acknowledgement":"We thank Peter Jonas and Peter Somogyi for critically reading the manuscript, Satoshi Kida for helpful discussion, Taijia Makinen for providing the Prox1-creERT2 mouse line, and Hiromu Yawo for the VAMP2-Venus construct. We also thank Vivek Jayaraman, Ph.D.; Rex A. Kerr, Ph.D.; Douglas S. Kim, Ph.D.; Loren L. Looger, Ph.D.; and Karel Svoboda, Ph.D. from the GENIE Project, Janelia Farm Research Campus, Howard Hughes Medical Institute for the viral constructs used for GCaMP6s expression. We also thank Jacqueline Montanaro, Vanessa Zheden, David Kleindienst, and Laura Burnett for technical assistance, as well as Robert Beattie for imaging assistance. This work was supported by a European Research Council Advanced Grant 694539 to R.S.","article_type":"original","related_material":{"link":[{"url":"https://ist.ac.at/en/news/remembering-novelty/","relation":"press_release","description":"News on IST Homepage"}]},"file_date_updated":"2020-10-19T13:31:28Z","title":"Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation","date_updated":"2025-06-12T06:54:22Z","author":[{"id":"384825DA-F248-11E8-B48F-1D18A9856A87","full_name":"Fredes Tolorza, Felipe A","first_name":"Felipe A","last_name":"Fredes Tolorza"},{"first_name":"Maria A","last_name":"Silva Sifuentes","id":"371B3D6E-F248-11E8-B48F-1D18A9856A87","full_name":"Silva Sifuentes, Maria A"},{"first_name":"Peter","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter"},{"last_name":"Kobayashi","first_name":"Kenta","full_name":"Kobayashi, Kenta"},{"orcid":"0000-0002-3937-1330","last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"},{"first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"citation":{"chicago":"Fredes Tolorza, Felipe A, Maria A Silva Sifuentes, Peter Koppensteiner, Kenta Kobayashi, Maximilian A Jösch, and Ryuichi Shigemoto. “Ventro-Dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">https://doi.org/10.1016/j.cub.2020.09.074</a>.","short":"F.A. Fredes Tolorza, M.A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi, M.A. Jösch, R. Shigemoto, Current Biology 31 (2021) P25–38.E5.","mla":"Fredes Tolorza, Felipe A., et al. “Ventro-Dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation.” <i>Current Biology</i>, vol. 31, no. 1, Elsevier, 2021, p. P25–38.E5, doi:<a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">10.1016/j.cub.2020.09.074</a>.","ieee":"F. A. Fredes Tolorza, M. A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi, M. A. Jösch, and R. Shigemoto, “Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation,” <i>Current Biology</i>, vol. 31, no. 1. Elsevier, p. P25–38.E5, 2021.","ista":"Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch MA, Shigemoto R. 2021. Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. Current Biology. 31(1), P25–38.E5.","ama":"Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch MA, Shigemoto R. Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. <i>Current Biology</i>. 2021;31(1):P25-38.E5. doi:<a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">10.1016/j.cub.2020.09.074</a>","apa":"Fredes Tolorza, F. A., Silva Sifuentes, M. A., Koppensteiner, P., Kobayashi, K., Jösch, M. A., &#38; Shigemoto, R. (2021). Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">https://doi.org/10.1016/j.cub.2020.09.074</a>"},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1016/j.cub.2020.09.074","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"volume":31,"scopus_import":"1","department":[{"_id":"MaJö"},{"_id":"RySh"}],"quality_controlled":"1","oa_version":"Published Version","_id":"7551","oa":1,"isi":1,"type":"journal_article","ec_funded":1,"page":"P25-38.E5","date_published":"2021-01-11T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-10-19T13:31:28Z","success":1,"file_id":"8678","file_size":4915964,"access_level":"open_access","content_type":"application/pdf","date_created":"2020-10-19T13:31:28Z","relation":"main_file","file_name":"2021_CurrentBiology_Fredes.pdf","creator":"dernst","checksum":"b7b9c8bc84a08befce365c675229a7d1"}],"publication_status":"published","year":"2021","article_processing_charge":"No","intvolume":"        31","language":[{"iso":"eng"}],"publisher":"Elsevier","date_created":"2020-02-28T10:56:18Z","pmid":1,"abstract":[{"text":"Novelty facilitates formation of memories. The detection of novelty and storage of contextual memories are both mediated by the hippocampus, yet the mechanisms that link these two functions remain to be defined. Dentate granule cells (GCs) of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual memory. However, their key excitatory inputs from the entorhinal cortex are not responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally regulates novelty-induced contextual memory acquisition. Our results show that ventral MCs activity controls memory formation through an intra-hippocampal interaction mechanism gated by novelty.","lang":"eng"}],"has_accepted_license":"1","publication":"Current Biology","month":"01","ddc":["570"],"status":"public","issue":"1"},{"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">https://doi.org/10.1016/j.neuron.2021.01.020</a>.","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","ieee":"W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” <i>Neuron</i>, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.","mla":"Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">10.1016/j.neuron.2021.01.020</a>.","ama":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. <i>Neuron</i>. 2021;109(7):1227-1241.e5. doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">10.1016/j.neuron.2021.01.020</a>","apa":"Mlynarski, W. F., Hledik, M., Sokolowski, T. R., &#38; Tkačik, G. (2021). Statistical analysis and optimality of neural systems. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">https://doi.org/10.1016/j.neuron.2021.01.020</a>","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5."},"doi":"10.1016/j.neuron.2021.01.020","scopus_import":"1","department":[{"_id":"GaTk"}],"volume":109,"_id":"7553","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/848374"}],"external_id":{"isi":["000637809600006"],"pmid":["33592180"]},"day":"07","acknowledgement":"The authors thank Dario Ringach for providing the V1 receptive fields and Olivier Marre for providing the retinal receptive fields. W.M. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers Science grant no. HFSP RGP0032/2018.","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/can-evolution-be-predicted/"}],"record":[{"relation":"dissertation_contains","id":"15020","status":"public"}]},"title":"Statistical analysis and optimality of neural systems","date_updated":"2026-04-07T12:59:24Z","author":[{"last_name":"Mlynarski","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F"},{"first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"first_name":"Thomas R","orcid":"0000-0002-1287-3779","last_name":"Sokolowski","id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"intvolume":"       109","date_created":"2020-02-28T11:00:12Z","pmid":1,"abstract":[{"text":"Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems.","lang":"eng"}],"publisher":"Cell Press","publication":"Neuron","month":"04","corr_author":"1","status":"public","issue":"7","isi":1,"type":"journal_article","ec_funded":1,"oa":1,"page":"1227-1241.e5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-04-07T00:00:00Z","publication_status":"published","year":"2021","article_processing_charge":"No"},{"date_updated":"2023-08-11T10:27:03Z","title":"A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration","author":[{"last_name":"Raso","first_name":"Andrea","full_name":"Raso, Andrea"},{"last_name":"Dirkx","first_name":"Ellen","full_name":"Dirkx, Ellen"},{"last_name":"Sampaio-Pinto","first_name":"Vasco","full_name":"Sampaio-Pinto, Vasco"},{"full_name":"el Azzouzi, Hamid","first_name":"Hamid","last_name":"el Azzouzi"},{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867","last_name":"Cubero","first_name":"Ryan J"},{"full_name":"Sorensen, Daniel W.","last_name":"Sorensen","first_name":"Daniel W."},{"last_name":"Ottaviani","first_name":"Lara","full_name":"Ottaviani, Lara"},{"full_name":"Olieslagers, Servé","last_name":"Olieslagers","first_name":"Servé"},{"full_name":"Huibers, Manon M.","first_name":"Manon M.","last_name":"Huibers"},{"full_name":"de Weger, Roel","first_name":"Roel","last_name":"de Weger"},{"full_name":"Siddiqi, Sailay","first_name":"Sailay","last_name":"Siddiqi"},{"full_name":"Moimas, Silvia","last_name":"Moimas","first_name":"Silvia"},{"full_name":"Torrini, Consuelo","first_name":"Consuelo","last_name":"Torrini"},{"last_name":"Zentillin","first_name":"Lorena","full_name":"Zentillin, Lorena"},{"full_name":"Braga, Luca","first_name":"Luca","last_name":"Braga"},{"full_name":"Nascimento, Diana S.","first_name":"Diana S.","last_name":"Nascimento"},{"full_name":"da Costa Martins, Paula A.","first_name":"Paula A.","last_name":"da Costa Martins"},{"full_name":"van Berlo, Jop H.","first_name":"Jop H.","last_name":"van Berlo"},{"first_name":"Serena","last_name":"Zacchigna","full_name":"Zacchigna, Serena"},{"first_name":"Mauro","last_name":"Giacca","full_name":"Giacca, Mauro"},{"full_name":"De Windt, Leon J.","last_name":"De Windt","first_name":"Leon J."}],"external_id":{"isi":["000683910200042"],"pmid":["34376683"]},"article_type":"original","publication_identifier":{"eissn":["2041-1723"]},"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-32785-0","relation":"erratum"}]},"acknowledgement":"E.D. is supported by a VENI award 916-150-16 from the Netherlands Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship (EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number 627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência, Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).","file_date_updated":"2021-08-10T12:29:59Z","day":"10","_id":"9874","quality_controlled":"1","oa_version":"Published Version","citation":{"short":"A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen, L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas, C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H. van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).","chicago":"Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-25211-4\">https://doi.org/10.1038/s41467-021-25211-4</a>.","ista":"Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 12, 4808.","apa":"Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen, D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-25211-4\">https://doi.org/10.1038/s41467-021-25211-4</a>","ama":"Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-25211-4\">10.1038/s41467-021-25211-4</a>","ieee":"A. Raso <i>et al.</i>, “A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","mla":"Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>, vol. 12, 4808, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-25211-4\">10.1038/s41467-021-25211-4</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-021-25211-4","scopus_import":"1","department":[{"_id":"SaSi"}],"volume":12,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"4808","date_published":"2021-08-10T00:00:00Z","year":"2021","article_processing_charge":"Yes","publication_status":"published","file":[{"file_size":4364333,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-08-10T12:29:59Z","relation":"main_file","checksum":"48d8562e8229e4282f3f354b329722c5","file_name":"2021_NatureCommunications_Raso.pdf","creator":"asandaue","date_updated":"2021-08-10T12:29:59Z","file_id":"9876","success":1}],"isi":1,"type":"journal_article","oa":1,"status":"public","month":"08","ddc":["610","570"],"publication":"Nature Communications","language":[{"iso":"eng"}],"intvolume":"        12","pmid":1,"has_accepted_license":"1","abstract":[{"text":"Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart.","lang":"eng"}],"date_created":"2021-08-10T11:49:20Z","genbank":["GSE178867"],"publisher":"Springer Nature"},{"title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","date_updated":"2025-05-14T10:59:43Z","author":[{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"last_name":"Ruan","first_name":"Deling","full_name":"Ruan, Deling"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"full_name":"Sharma, Manoj K.","first_name":"Manoj K.","last_name":"Sharma"},{"first_name":"Rita","last_name":"Sharma","full_name":"Sharma, Rita"},{"first_name":"XinYi","last_name":"Ye","full_name":"Ye, XinYi"},{"full_name":"Nguyen, Nicholas D.","last_name":"Nguyen","first_name":"Nicholas D."},{"last_name":"Nijjar","first_name":"Sukhranjan","full_name":"Nijjar, Sukhranjan"},{"first_name":"Pamela C.","last_name":"Ronald","full_name":"Ronald, Pamela C."},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"external_id":{"isi":["000685037700012"],"pmid":["34272287"]},"day":"16","acknowledgement":"We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.","file_date_updated":"2021-08-11T09:31:41Z","article_type":"original","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"_id":"9877","quality_controlled":"1","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1073/pnas.2104445118","citation":{"ieee":"J. A. Rodrigues <i>et al.</i>, “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 29. National Academy of Sciences, 2021.","mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>.","ista":"Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences of the United States of America. 118(29), e2104445118.","apa":"Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>","ama":"Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(29). doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>","chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>.","short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences of the United States of America 118 (2021)."},"department":[{"_id":"DaZi"}],"scopus_import":"1","volume":118,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-07-16T00:00:00Z","article_number":"e2104445118","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","year":"2021","file":[{"date_created":"2021-08-11T09:31:41Z","relation":"main_file","checksum":"19e84ad8c03c60222744ee8e16cd6998","creator":"asandaue","file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","file_size":1898360,"access_level":"open_access","content_type":"application/pdf","file_id":"9879","success":1,"date_updated":"2021-08-11T09:31:41Z"}],"isi":1,"type":"journal_article","oa":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","status":"public","month":"07","ddc":["580","570"],"issue":"29","language":[{"iso":"eng"}],"intvolume":"       118","abstract":[{"lang":"eng","text":"Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution."}],"date_created":"2021-08-10T19:30:41Z","pmid":1,"has_accepted_license":"1","publisher":"National Academy of Sciences"},{"date_published":"2021-08-01T00:00:00Z","article_number":"083305","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":4352640,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-10-27T12:57:06Z","relation":"main_file","creator":"cziletti","checksum":"d035be2b894c4d50d90ac5ce252e27cd","file_name":"2021_JMathPhy_Lauritsen.pdf","date_updated":"2021-10-27T12:57:06Z","file_id":"10188","success":1}],"publication_status":"published","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"year":"2021","article_processing_charge":"No","oa":1,"type":"journal_article","isi":1,"month":"08","status":"public","corr_author":"1","ddc":["530"],"publication":"Journal of Mathematical Physics","issue":"8","intvolume":"        62","language":[{"iso":"eng"}],"publisher":"AIP Publishing","has_accepted_license":"1","date_created":"2021-08-12T07:08:36Z","abstract":[{"text":"Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)], we present a modified “floating crystal” trial state for jellium (also known as the classical homogeneous electron gas) with density equal to a characteristic function. This allows us to show that three definitions of the jellium energy coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache [“Equality of the Jellium and uniform electron gas next-order asymptotic terms for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized energy” studied in a series of papers by Serfaty and others, and thus, by the work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate the jellium energy to the order n term in the logarithmic energy of n points on the unit 2-sphere. We improve upon known lower bounds for this renormalized energy. Additionally, we derive formulas for the jellium energy of periodic configurations.","lang":"eng"}],"title":"Floating Wigner crystal and periodic jellium configurations","date_updated":"2024-10-09T21:00:48Z","author":[{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard"}],"external_id":{"isi":["000683960800003"],"arxiv":["2103.07975"]},"arxiv":1,"day":"01","acknowledgement":"The author would like to thank Robert Seiringer for guidance and many helpful comments on this project. The author would also like to thank Mathieu Lewin for his comments on the manuscript and Lorenzo Portinale for providing his lecture notes for the course “Mathematics of quantum many-body systems” in spring 2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these lecture notes.","file_date_updated":"2021-10-27T12:57:06Z","article_type":"original","publication_identifier":{"issn":["0022-2488"],"eissn":["1089-7658"]},"oa_version":"Published Version","quality_controlled":"1","_id":"9891","citation":{"chicago":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0053494\">https://doi.org/10.1063/5.0053494</a>.","short":"A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).","ieee":"A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8. AIP Publishing, 2021.","mla":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8, 083305, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0053494\">10.1063/5.0053494</a>.","apa":"Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0053494\">https://doi.org/10.1063/5.0053494</a>","ama":"Lauritsen AB. Floating Wigner crystal and periodic jellium configurations. <i>Journal of Mathematical Physics</i>. 2021;62(8). doi:<a href=\"https://doi.org/10.1063/5.0053494\">10.1063/5.0053494</a>","ista":"Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 62(8), 083305."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1063/5.0053494","volume":62,"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"RoSe"}]},{"status":"public","month":"08","ddc":["539"],"publication":"Physical Review Letters","issue":"6","intvolume":"       127","language":[{"iso":"eng"}],"publisher":"American Physical Society","date_created":"2021-08-13T09:27:39Z","has_accepted_license":"1","abstract":[{"text":"Eigenstate thermalization in quantum many-body systems implies that eigenstates at high energy are similar to random vectors. Identifying systems where at least some eigenstates are nonthermal is an outstanding question. In this Letter we show that interacting quantum models that have a nullspace—a degenerate subspace of eigenstates at zero energy (zero modes), which corresponds to infinite temperature, provide a route to nonthermal eigenstates. We analytically show the existence of a zero mode which can be represented as a matrix product state for a certain class of local Hamiltonians. In the more general case we use a subspace disentangling algorithm to generate an orthogonal basis of zero modes characterized by increasing entanglement entropy. We show evidence for an area-law entanglement scaling of the least-entangled zero mode in the broad parameter regime, leading to a conjecture that all local Hamiltonians with the nullspace feature zero modes with area-law entanglement scaling and, as such, break the strong thermalization hypothesis. Finally, we find zero modes in constrained models and propose a setup for observing their experimental signatures.","lang":"eng"}],"article_number":"060602","date_published":"2021-08-06T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":5064231,"file_name":"PhysRevLett.127.060602_SOM.pdf","creator":"mserbyn","checksum":"51218f302dcef99d90d1209809fcc874","date_created":"2021-08-13T09:28:08Z","relation":"main_file","date_updated":"2021-08-13T09:28:08Z","success":1,"file_id":"9904"}],"publication_status":"published","year":"2021","article_processing_charge":"Yes (in subscription journal)","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"quality_controlled":"1","oa_version":"Published Version","_id":"9903","doi":"10.1103/physrevlett.127.060602","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).","chicago":"Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.060602\">https://doi.org/10.1103/physrevlett.127.060602</a>.","ista":"Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.","apa":"Karle, V., Serbyn, M., &#38; Michailidis, A. (2021). Area-law entangled eigenstates from nullspaces of local Hamiltonians. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.127.060602\">https://doi.org/10.1103/physrevlett.127.060602</a>","ama":"Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces of local Hamiltonians. <i>Physical Review Letters</i>. 2021;127(6). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.060602\">10.1103/physrevlett.127.060602</a>","ieee":"V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from nullspaces of local Hamiltonians,” <i>Physical Review Letters</i>, vol. 127, no. 6. American Physical Society, 2021.","mla":"Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” <i>Physical Review Letters</i>, vol. 127, no. 6, 060602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.060602\">10.1103/physrevlett.127.060602</a>."},"project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"volume":127,"department":[{"_id":"MaSe"},{"_id":"GradSch"},{"_id":"MiLe"}],"scopus_import":"1","title":"Area-law entangled eigenstates from nullspaces of local Hamiltonians","date_updated":"2026-04-07T11:48:53Z","author":[{"first_name":"Volker","orcid":"0000-0002-6963-0129","last_name":"Karle","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","full_name":"Karle, Volker"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"first_name":"Alexios","last_name":"Michailidis","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2102.13633"],"isi":["000684276000002"]},"arxiv":1,"day":"06","article_type":"letter_note","related_material":{"record":[{"id":"19393","relation":"dissertation_contains","status":"public"}]},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"acknowledgement":"We acknowledge useful discussions with V. Gritsev and A. Garkun and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and M. S. were supported by the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)","file_date_updated":"2021-08-13T09:28:08Z"},{"_id":"9906","quality_controlled":"1","oa_version":"Published Version","scopus_import":"1","department":[{"_id":"SiHi"}],"volume":22,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel, A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences 22 (2021).","chicago":"Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling, Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22168385\">https://doi.org/10.3390/ijms22168385</a>.","ista":"Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 22(16), 8385.","apa":"Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel, L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22168385\">https://doi.org/10.3390/ijms22168385</a>","ama":"Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. <i>International Journal of Molecular Sciences</i>. 2021;22(16). doi:<a href=\"https://doi.org/10.3390/ijms22168385\">10.3390/ijms22168385</a>","mla":"Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 16, 8385, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22168385\">10.3390/ijms22168385</a>.","ieee":"I. Yotova <i>et al.</i>, “LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 16. MDPI, 2021."},"doi":"10.3390/ijms22168385","author":[{"full_name":"Yotova, Iveta","last_name":"Yotova","first_name":"Iveta"},{"full_name":"Hudson, Quanah J.","last_name":"Hudson","first_name":"Quanah J."},{"orcid":"0000-0002-7462-0048","last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"last_name":"Proestling","first_name":"Katharina","full_name":"Proestling, Katharina"},{"last_name":"Haslinger","first_name":"Isabella","full_name":"Haslinger, Isabella"},{"last_name":"Kuessel","first_name":"Lorenz","full_name":"Kuessel, Lorenz"},{"full_name":"Perricos, Alexandra","last_name":"Perricos","first_name":"Alexandra"},{"full_name":"Husslein, Heinrich","first_name":"Heinrich","last_name":"Husslein"},{"full_name":"Wenzl, René","first_name":"René","last_name":"Wenzl"}],"title":"LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line","date_updated":"2025-06-12T06:29:07Z","day":"04","file_date_updated":"2021-08-16T09:29:17Z","acknowledgement":"Open access funding provided by Medical University of Vienna. The authors would like to thank all the participants and health professionals involved in the present study. We want to thank our technical assistants Barbara Widmar and Matthias Witzmann-Stern for their diligent work and constant assistance. We would like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and resources.","publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"article_type":"original","external_id":{"pmid":["34445100"],"isi":["000689147400001"]},"issue":"16","publication":"International Journal of Molecular Sciences","ddc":["570"],"month":"08","status":"public","pmid":1,"date_created":"2021-08-15T22:01:27Z","abstract":[{"lang":"eng","text":"Endometriosis is a common gynecological disorder characterized by ectopic growth of endometrium outside the uterus and is associated with chronic pain and infertility. We investigated the role of the long intergenic noncoding RNA 01133 (LINC01133) in endometriosis, an lncRNA that has been implicated in several types of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions. As expression appeared higher in the epithelial endometrial layer, we performed a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic assays indicated that LINC01133 may promote proliferation and suppress cellular migration, and affect the cytoskeleton and morphology of the cells. Gene ontology analysis of differentially expressed genes indicated that cell proliferation and migration pathways were affected in line with the observed phenotype. We validated upregulation of p21 and downregulation of Cyclin A at the protein level, which together with the quantification of the DNA content using fluorescence-activated cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation may be due to changes in cell cycle. Further, we found testis-specific protein kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation of actin severing protein Cofilin, which could explain changes in the cytoskeleton and cellular migration. These results indicate that endometriosis is associated with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation and migration pathways."}],"has_accepted_license":"1","publisher":"MDPI","language":[{"iso":"eng"}],"intvolume":"        22","publication_status":"published","article_processing_charge":"Yes","year":"2021","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":2646018,"creator":"asandaue","checksum":"be7f0042607ca60549cb27513c19c6af","file_name":"2021_InternationalJournalOfMolecularSciences_Yotova.pdf","date_created":"2021-08-16T09:29:17Z","relation":"main_file","date_updated":"2021-08-16T09:29:17Z","success":1,"file_id":"9922"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"8385","date_published":"2021-08-04T00:00:00Z","type":"journal_article","isi":1,"oa":1},{"external_id":{"pmid":["34361115"],"isi":["000681815400001"]},"day":"01","publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"file_date_updated":"2021-08-16T09:35:56Z","article_type":"original","acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","date_updated":"2025-07-10T12:02:05Z","author":[{"full_name":"Labajová, Naďa","last_name":"Labajová","first_name":"Naďa"},{"full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S.","last_name":"Baranova","orcid":"0000-0002-3086-9124"},{"full_name":"Jurásek, Miroslav","first_name":"Miroslav","last_name":"Jurásek"},{"full_name":"Vácha, Robert","last_name":"Vácha","first_name":"Robert"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin"},{"first_name":"Imrich","last_name":"Barák","full_name":"Barák, Imrich"}],"project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.3390/ijms22158350","citation":{"chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>.","short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021).","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15. MDPI, 2021.","mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15, 8350, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>.","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., &#38; Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>","ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350.","ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. 2021;22(15). doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>"},"department":[{"_id":"MaLo"}],"scopus_import":"1","volume":22,"_id":"9907","oa_version":"Published Version","quality_controlled":"1","ec_funded":1,"isi":1,"type":"journal_article","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"8350","date_published":"2021-08-01T00:00:00Z","publication_status":"published","article_processing_charge":"Yes","year":"2021","file":[{"success":1,"file_id":"9923","date_updated":"2021-08-16T09:35:56Z","creator":"asandaue","file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","checksum":"a4bc06e9a2c803ceff5a91f10b174054","date_created":"2021-08-16T09:35:56Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":6132410}],"language":[{"iso":"eng"}],"intvolume":"        22","has_accepted_license":"1","abstract":[{"lang":"eng","text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. "}],"date_created":"2021-08-15T22:01:27Z","pmid":1,"publisher":"MDPI","status":"public","month":"08","ddc":["570"],"publication":"International Journal of Molecular Sciences","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"issue":"15"},{"file":[{"file_size":2297655,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-08-16T09:49:35Z","file_name":"2021_Genes_Picard.pdf","checksum":"744e60e56d290a96da3c91a9779f886f","creator":"asandaue","date_updated":"2021-08-16T09:49:35Z","success":1,"file_id":"9926"}],"publication_status":"published","year":"2021","article_processing_charge":"Yes","date_published":"2021-08-01T00:00:00Z","article_number":"1136","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","issue":"8","status":"public","ddc":["570"],"month":"08","publication":"Genes","publisher":"MDPI","abstract":[{"lang":"eng","text":"About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems."}],"has_accepted_license":"1","pmid":1,"date_created":"2021-08-15T22:01:27Z","intvolume":"        12","language":[{"iso":"eng"}],"author":[{"last_name":"Picard","orcid":"0000-0002-8101-2518","first_name":"Marion A L","full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bertrand","first_name":"Stéphanie","full_name":"Bertrand, Stéphanie"},{"last_name":"Escriva","first_name":"Hector","full_name":"Escriva, Hector"}],"title":"Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict","date_updated":"2026-04-02T14:05:14Z","day":"01","file_date_updated":"2021-08-16T09:49:35Z","publication_identifier":{"eissn":["2073-4425"]},"article_type":"review","external_id":{"isi":["000690475900001"],"pmid":["34440310"]},"oa_version":"Published Version","quality_controlled":"1","_id":"9908","volume":12,"scopus_import":"1","department":[{"_id":"BeVi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.3390/genes12081136","citation":{"ista":"Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 12(8), 1136.","ama":"Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>","apa":"Picard, M. A. L., Vicoso, B., Bertrand, S., &#38; Escriva, H. (2021). Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>","ieee":"M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","mla":"Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>, vol. 12, no. 8, 1136, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>.","short":"M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).","chicago":"Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>."},"project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}]},{"_id":"9909","oa_version":"Published Version","quality_controlled":"1","citation":{"chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>.","short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","ieee":"Y. Zeng <i>et al.</i>, “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>, vol. 12, no. 8, 1141, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>.","ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.3390/genes12081141","department":[{"_id":"JiFr"}],"scopus_import":"1","volume":12,"date_updated":"2026-04-02T13:57:06Z","title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","author":[{"last_name":"Zeng","first_name":"Yinwei","full_name":"Zeng, Yinwei"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","first_name":"Inge"},{"full_name":"Trinh, Hoang Khai","last_name":"Trinh","first_name":"Hoang Khai"},{"first_name":"Thomas","last_name":"Heugebaert","full_name":"Heugebaert, Thomas"},{"full_name":"Stevens, Christian V.","last_name":"Stevens","first_name":"Christian V."},{"last_name":"Garcia-Maquilon","first_name":"Irene","full_name":"Garcia-Maquilon, Irene"},{"first_name":"Pedro L.","last_name":"Rodriguez","full_name":"Rodriguez, Pedro L."},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Geelen, Danny","last_name":"Geelen","first_name":"Danny"}],"external_id":{"isi":["000690558000001"]},"file_date_updated":"2021-08-16T09:02:40Z","publication_identifier":{"eissn":["2073-4425"]},"acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","article_type":"original","day":"27","status":"public","ddc":["580","570"],"month":"07","publication":"Genes","issue":"8","language":[{"iso":"eng"}],"intvolume":"        12","has_accepted_license":"1","date_created":"2021-08-15T22:01:28Z","abstract":[{"text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.","lang":"eng"}],"publisher":"MDPI","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-07-27T00:00:00Z","article_number":"1141","article_processing_charge":"Yes","year":"2021","publication_status":"published","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":1340305,"checksum":"3d99535618cf9a5b14d264408fa52e97","file_name":"2021_Genes_Zeng.pdf","creator":"asandaue","date_created":"2021-08-16T09:02:40Z","relation":"main_file","date_updated":"2021-08-16T09:02:40Z","file_id":"9919","success":1}],"type":"journal_article","isi":1,"oa":1},{"date_updated":"2025-07-10T12:02:05Z","title":"The limits of normal approximation for adult height","author":[{"full_name":"Slavskii, Sergei A.","first_name":"Sergei A.","last_name":"Slavskii"},{"full_name":"Kuznetsov, Ivan A.","last_name":"Kuznetsov","first_name":"Ivan A."},{"full_name":"Shashkova, Tatiana I.","first_name":"Tatiana I.","last_name":"Shashkova"},{"first_name":"Georgii A.","last_name":"Bazykin","full_name":"Bazykin, Georgii A."},{"last_name":"Axenovich","first_name":"Tatiana I.","full_name":"Axenovich, Tatiana I."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"full_name":"Aulchenko, Yurii S.","first_name":"Yurii S.","last_name":"Aulchenko"}],"external_id":{"isi":["000625853200001"],"pmid":["33664501"]},"acknowledgement":"We are grateful to Marianna Bevova and Pavel Borodin for fruitful discussion and help with conceptualising our findings and to Lennart C. Karssen for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects in control of complex human traits”). The work of SAS, IAK, and TIS were supported by Russian Ministry of Science and Education under the 5–100 Excellence Programme. The work of YSA and TIA was supported by the Ministry of Education and Science of the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4). FAK is supported by the ERC Consolidator Grant (ChrFL: 771209).","file_date_updated":"2021-08-16T09:14:36Z","article_type":"original","publication_identifier":{"eissn":["1476-5438"],"issn":["1018-4813"]},"day":"01","oa_version":"Published Version","quality_controlled":"1","_id":"9910","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.","chicago":"Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>.","apa":"Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., &#38; Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>","ista":"Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091.","ama":"Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. 2021;29(7):1082-1091. doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>","mla":"Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>.","ieee":"S. A. Slavskii <i>et al.</i>, “The limits of normal approximation for adult height,” <i>European Journal of Human Genetics</i>, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021."},"doi":"10.1038/s41431-021-00836-7","project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"volume":29,"scopus_import":"1","department":[{"_id":"FyKo"}],"date_published":"2021-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2021-08-16T09:14:36Z","success":1,"file_id":"9921","file_size":1079395,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-08-16T09:14:36Z","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","creator":"asandaue","checksum":"a676d76f91b0dbe0504c63e469129c2a"}],"year":"2021","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","page":"1082-1091","publication":"European Journal of Human Genetics","status":"public","month":"07","ddc":["576"],"issue":"7","intvolume":"        29","language":[{"iso":"eng"}],"publisher":"Springer Nature","abstract":[{"text":"Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait.","lang":"eng"}],"date_created":"2021-08-15T22:01:28Z","pmid":1,"has_accepted_license":"1"},{"isi":1,"type":"journal_article","oa":1,"page":"56-73","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-11T00:00:00Z","publication_status":"published","year":"2021","article_processing_charge":"Yes","language":[{"iso":"eng"}],"intvolume":"       284","pmid":1,"date_created":"2021-08-15T22:01:29Z","abstract":[{"text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.","lang":"eng"}],"publisher":"Wiley","ddc":["600"],"publication":"Journal of Microscopy","month":"08","status":"public","issue":"1","external_id":{"pmid":["34214188"],"isi":["000683702700001"]},"day":"11","publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"article_type":"original","acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","date_updated":"2026-06-18T19:59:18Z","author":[{"full_name":"Nelson, Glyn","first_name":"Glyn","last_name":"Nelson"},{"last_name":"Boehm","first_name":"Ulrike","full_name":"Boehm, Ulrike"},{"full_name":"Bagley, Steve","last_name":"Bagley","first_name":"Steve"},{"full_name":"Bajcsy, Peter","last_name":"Bajcsy","first_name":"Peter"},{"full_name":"Bischof, Johanna","last_name":"Bischof","first_name":"Johanna"},{"full_name":"Brown, Claire M.","last_name":"Brown","first_name":"Claire M."},{"full_name":"Dauphin, Aurélien","last_name":"Dauphin","first_name":"Aurélien"},{"full_name":"Dobbie, Ian M.","first_name":"Ian M.","last_name":"Dobbie"},{"full_name":"Eriksson, John E.","last_name":"Eriksson","first_name":"John E."},{"first_name":"Orestis","last_name":"Faklaris","full_name":"Faklaris, Orestis"},{"last_name":"Fernandez-Rodriguez","first_name":"Julia","full_name":"Fernandez-Rodriguez, Julia"},{"full_name":"Ferrand, Alexia","first_name":"Alexia","last_name":"Ferrand"},{"last_name":"Gelman","first_name":"Laurent","full_name":"Gelman, Laurent"},{"last_name":"Gheisari","first_name":"Ali","full_name":"Gheisari, Ali"},{"first_name":"Hella","last_name":"Hartmann","full_name":"Hartmann, Hella"},{"first_name":"Christian","last_name":"Kukat","full_name":"Kukat, Christian"},{"full_name":"Laude, Alex","last_name":"Laude","first_name":"Alex"},{"last_name":"Mitkovski","first_name":"Miso","full_name":"Mitkovski, Miso"},{"full_name":"Munck, Sebastian","last_name":"Munck","first_name":"Sebastian"},{"first_name":"Alison J.","last_name":"North","full_name":"North, Alison J."},{"last_name":"Rasse","first_name":"Tobias M.","full_name":"Rasse, Tobias M."},{"last_name":"Resch-Genger","first_name":"Ute","full_name":"Resch-Genger, Ute"},{"last_name":"Schuetz","first_name":"Lucas C.","full_name":"Schuetz, Lucas C."},{"full_name":"Seitz, Arne","first_name":"Arne","last_name":"Seitz"},{"full_name":"Strambio-De-Castillia, Caterina","first_name":"Caterina","last_name":"Strambio-De-Castillia"},{"first_name":"Jason R.","last_name":"Swedlow","full_name":"Swedlow, Jason R."},{"full_name":"Alexopoulos, Ioannis","last_name":"Alexopoulos","first_name":"Ioannis"},{"full_name":"Aumayr, Karin","last_name":"Aumayr","first_name":"Karin"},{"last_name":"Avilov","first_name":"Sergiy","full_name":"Avilov, Sergiy"},{"full_name":"Bakker, Gert Jan","first_name":"Gert Jan","last_name":"Bakker"},{"last_name":"Bammann","first_name":"Rodrigo R.","full_name":"Bammann, Rodrigo R."},{"first_name":"Andrea","last_name":"Bassi","full_name":"Bassi, Andrea"},{"full_name":"Beckert, Hannes","first_name":"Hannes","last_name":"Beckert"},{"last_name":"Beer","first_name":"Sebastian","full_name":"Beer, Sebastian"},{"first_name":"Yury","last_name":"Belyaev","full_name":"Belyaev, Yury"},{"first_name":"Jakob","last_name":"Bierwagen","full_name":"Bierwagen, Jakob"},{"full_name":"Birngruber, Konstantin A.","last_name":"Birngruber","first_name":"Konstantin A."},{"full_name":"Bosch, Manel","first_name":"Manel","last_name":"Bosch"},{"full_name":"Breitlow, Juergen","first_name":"Juergen","last_name":"Breitlow"},{"full_name":"Cameron, Lisa A.","first_name":"Lisa A.","last_name":"Cameron"},{"last_name":"Chalfoun","first_name":"Joe","full_name":"Chalfoun, Joe"},{"first_name":"James J.","last_name":"Chambers","full_name":"Chambers, James J."},{"first_name":"Chieh Li","last_name":"Chen","full_name":"Chen, Chieh Li"},{"last_name":"Conde-Sousa","first_name":"Eduardo","full_name":"Conde-Sousa, Eduardo"},{"full_name":"Corbett, Alexander D.","first_name":"Alexander D.","last_name":"Corbett"},{"full_name":"Cordelieres, Fabrice P.","first_name":"Fabrice P.","last_name":"Cordelieres"},{"last_name":"Nery","first_name":"Elaine Del","full_name":"Nery, Elaine Del"},{"first_name":"Ralf","last_name":"Dietzel","full_name":"Dietzel, Ralf"},{"full_name":"Eismann, Frank","first_name":"Frank","last_name":"Eismann"},{"last_name":"Fazeli","first_name":"Elnaz","full_name":"Fazeli, Elnaz"},{"full_name":"Felscher, Andreas","last_name":"Felscher","first_name":"Andreas"},{"first_name":"Hans","last_name":"Fried","full_name":"Fried, Hans"},{"last_name":"Gaudreault","first_name":"Nathalie","full_name":"Gaudreault, Nathalie"},{"full_name":"Goh, Wah Ing","first_name":"Wah Ing","last_name":"Goh"},{"last_name":"Guilbert","first_name":"Thomas","full_name":"Guilbert, Thomas"},{"full_name":"Hadleigh, Roland","last_name":"Hadleigh","first_name":"Roland"},{"first_name":"Peter","last_name":"Hemmerich","full_name":"Hemmerich, Peter"},{"full_name":"Holst, Gerhard A.","first_name":"Gerhard A.","last_name":"Holst"},{"last_name":"Itano","first_name":"Michelle S.","full_name":"Itano, Michelle S."},{"full_name":"Jaffe, Claudia B.","last_name":"Jaffe","first_name":"Claudia B."},{"first_name":"Helena K.","last_name":"Jambor","full_name":"Jambor, Helena K."},{"last_name":"Jarvis","first_name":"Stuart C.","full_name":"Jarvis, Stuart C."},{"full_name":"Keppler, Antje","first_name":"Antje","last_name":"Keppler"},{"full_name":"Kirchenbuechler, David","first_name":"David","last_name":"Kirchenbuechler"},{"full_name":"Kirchner, Marcel","first_name":"Marcel","last_name":"Kirchner"},{"full_name":"Kobayashi, Norio","first_name":"Norio","last_name":"Kobayashi"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996"},{"full_name":"Kunis, Susanne","last_name":"Kunis","first_name":"Susanne"},{"first_name":"Judith","last_name":"Lacoste","full_name":"Lacoste, Judith"},{"full_name":"Marcello, Marco","first_name":"Marco","last_name":"Marcello"},{"first_name":"Gabriel G.","last_name":"Martins","full_name":"Martins, Gabriel G."},{"last_name":"Metcalf","first_name":"Daniel J.","full_name":"Metcalf, Daniel J."},{"full_name":"Mitchell, Claire A.","first_name":"Claire A.","last_name":"Mitchell"},{"first_name":"Joshua","last_name":"Moore","full_name":"Moore, Joshua"},{"last_name":"Mueller","first_name":"Tobias","full_name":"Mueller, Tobias"},{"full_name":"Nelson, Michael S.","first_name":"Michael S.","last_name":"Nelson"},{"full_name":"Ogg, Stephen","last_name":"Ogg","first_name":"Stephen"},{"full_name":"Onami, Shuichi","first_name":"Shuichi","last_name":"Onami"},{"full_name":"Palmer, Alexandra L.","first_name":"Alexandra L.","last_name":"Palmer"},{"first_name":"Perrine","last_name":"Paul-Gilloteaux","full_name":"Paul-Gilloteaux, Perrine"},{"full_name":"Pimentel, Jaime A.","last_name":"Pimentel","first_name":"Jaime A."},{"last_name":"Plantard","first_name":"Laure","full_name":"Plantard, Laure"},{"first_name":"Santosh","last_name":"Podder","full_name":"Podder, Santosh"},{"full_name":"Rexhepaj, Elton","first_name":"Elton","last_name":"Rexhepaj"},{"last_name":"Royon","first_name":"Arnaud","full_name":"Royon, Arnaud"},{"last_name":"Saari","first_name":"Markku A.","full_name":"Saari, Markku A."},{"first_name":"Damien","last_name":"Schapman","full_name":"Schapman, Damien"},{"last_name":"Schoonderwoert","first_name":"Vincent","full_name":"Schoonderwoert, Vincent"},{"full_name":"Schroth-Diez, Britta","first_name":"Britta","last_name":"Schroth-Diez"},{"last_name":"Schwartz","first_name":"Stanley","full_name":"Schwartz, Stanley"},{"last_name":"Shaw","first_name":"Michael","full_name":"Shaw, Michael"},{"first_name":"Martin","last_name":"Spitaler","full_name":"Spitaler, Martin"},{"full_name":"Stoeckl, Martin T.","last_name":"Stoeckl","first_name":"Martin T."},{"full_name":"Sudar, Damir","last_name":"Sudar","first_name":"Damir"},{"first_name":"Jeremie","last_name":"Teillon","full_name":"Teillon, Jeremie"},{"last_name":"Terjung","first_name":"Stefan","full_name":"Terjung, Stefan"},{"first_name":"Roland","last_name":"Thuenauer","full_name":"Thuenauer, Roland"},{"first_name":"Christian D.","last_name":"Wilms","full_name":"Wilms, Christian D."},{"full_name":"Wright, Graham D.","first_name":"Graham D.","last_name":"Wright"},{"full_name":"Nitschke, Roland","last_name":"Nitschke","first_name":"Roland"}],"citation":{"short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.","chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>.","ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.","apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. Wiley. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. 2021;284(1):56-73. doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>","mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>.","ieee":"G. Nelson <i>et al.</i>, “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” <i>Journal of Microscopy</i>, vol. 284, no. 1. Wiley, pp. 56–73, 2021."},"doi":"10.1111/jmi.13041","scopus_import":"1","department":[{"_id":"Bio"}],"volume":284,"_id":"9911","quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1111/jmi.13041","open_access":"1"}]},{"oa":1,"type":"journal_article","ec_funded":1,"isi":1,"page":"4205–4269","date_published":"2021-12-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2022-05-12T12:50:27Z","file_id":"11365","success":1,"content_type":"application/pdf","access_level":"open_access","file_size":1162454,"creator":"dernst","file_name":"2021_AnnHenriPoincare_Erdoes.pdf","checksum":"8d6bac0e2b0a28539608b0538a8e3b38","relation":"main_file","date_created":"2022-05-12T12:50:27Z"}],"publication_status":"published","year":"2021","article_processing_charge":"Yes (in subscription journal)","intvolume":"        22","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","date_created":"2021-08-15T22:01:29Z","abstract":[{"text":"In the customary random matrix model for transport in quantum dots with M internal degrees of freedom coupled to a chaotic environment via 𝑁≪𝑀 channels, the density 𝜌 of transmission eigenvalues is computed from a specific invariant ensemble for which explicit formula for the joint probability density of all eigenvalues is available. We revisit this problem in the large N regime allowing for (i) arbitrary ratio 𝜙:=𝑁/𝑀≤1; and (ii) general distributions for the matrix elements of the Hamiltonian of the quantum dot. In the limit 𝜙→0, we recover the formula for the density 𝜌 that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special matrix ensemble. We also prove that the inverse square root singularity of the density at zero and full transmission in Beenakker’s formula persists for any 𝜙<1 but in the borderline case 𝜙=1 an anomalous 𝜆−2/3 singularity arises at zero. To access this level of generality, we develop the theory of global and local laws on the spectral density of a large class of noncommutative rational expressions in large random matrices with i.i.d. entries.","lang":"eng"}],"publication":"Annales Henri Poincaré ","ddc":["510"],"month":"12","status":"public","external_id":{"isi":["000681531500001"],"arxiv":["1911.05112"]},"arxiv":1,"day":"01","publication_identifier":{"eissn":["1424-0661"],"issn":["1424-0637"]},"article_type":"original","acknowledgement":"The authors are very grateful to Yan Fyodorov for discussions on the physical background and for providing references, and to the anonymous referee for numerous valuable remarks.","file_date_updated":"2022-05-12T12:50:27Z","title":"Scattering in quantum dots via noncommutative rational functions","date_updated":"2025-04-15T08:04:59Z","author":[{"first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"first_name":"Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H"},{"full_name":"Nemish, Yuriy","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","last_name":"Nemish","orcid":"0000-0002-7327-856X","first_name":"Yuriy"}],"doi":"10.1007/s00023-021-01085-6","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Erdös, L., Krüger, T. H., &#38; Nemish, Y. (2021). Scattering in quantum dots via noncommutative rational functions. <i>Annales Henri Poincaré </i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-021-01085-6\">https://doi.org/10.1007/s00023-021-01085-6</a>","ista":"Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 22, 4205–4269.","ama":"Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative rational functions. <i>Annales Henri Poincaré </i>. 2021;22:4205–4269. doi:<a href=\"https://doi.org/10.1007/s00023-021-01085-6\">10.1007/s00023-021-01085-6</a>","mla":"Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational Functions.” <i>Annales Henri Poincaré </i>, vol. 22, Springer Nature, 2021, pp. 4205–4269, doi:<a href=\"https://doi.org/10.1007/s00023-021-01085-6\">10.1007/s00023-021-01085-6</a>.","ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative rational functions,” <i>Annales Henri Poincaré </i>, vol. 22. Springer Nature, pp. 4205–4269, 2021.","short":"L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré  22 (2021) 4205–4269.","chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum Dots via Noncommutative Rational Functions.” <i>Annales Henri Poincaré </i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00023-021-01085-6\">https://doi.org/10.1007/s00023-021-01085-6</a>."},"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"volume":22,"department":[{"_id":"LaEr"}],"scopus_import":"1","quality_controlled":"1","oa_version":"Published Version","_id":"9912"},{"oa_version":"Published Version","_id":"9920","doi":"10.15479/at:ista:9920","citation":{"ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9920\">10.15479/at:ista:9920</a>","ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","apa":"Peruzzo, M. (2021). <i>Geometric superinductors and their applications in circuit quantum electrodynamics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9920\">https://doi.org/10.15479/at:ista:9920</a>","ieee":"M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021.","mla":"Peruzzo, Matilda. <i>Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9920\">10.15479/at:ista:9920</a>.","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","chicago":"Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9920\">https://doi.org/10.15479/at:ista:9920</a>."},"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"title":"Geometric superinductors and their applications in circuit quantum electrodynamics","date_updated":"2026-04-15T06:43:02Z","author":[{"last_name":"Peruzzo","orcid":"0000-0002-3415-4628","first_name":"Matilda","full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","day":"19","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9928"},{"status":"public","relation":"part_of_dissertation","id":"8755"}]},"file_date_updated":"2021-09-06T08:39:47Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-013-8"]},"status":"public","ddc":["539"],"corr_author":"1","month":"08","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","abstract":[{"text":"This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.","lang":"eng"}],"date_created":"2021-08-16T09:44:09Z","alternative_title":["ISTA Thesis"],"date_published":"2021-08-19T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"relation":"source_file","date_created":"2021-08-16T09:33:21Z","checksum":"3cd1986efde5121d7581f6fcf9090da8","file_name":"GeometricSuperinductorsForCQED.zip","creator":"mperuzzo","file_size":151387283,"content_type":"application/x-zip-compressed","access_level":"closed","file_id":"9924","date_updated":"2021-09-06T08:39:47Z"},{"date_created":"2021-08-18T14:20:06Z","relation":"main_file","checksum":"50928c621cdf0775d7a5906b9dc8602c","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","creator":"mperuzzo","file_size":17596344,"access_level":"open_access","content_type":"application/pdf","file_id":"9939","date_updated":"2021-09-06T08:39:47Z"},{"content_type":"application/pdf","access_level":"closed","file_size":17592425,"creator":"mperuzzo","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","checksum":"37f486aa1b622fe44af00d627ec13f6c","relation":"other","date_created":"2021-08-18T14:20:09Z","date_updated":"2021-09-06T08:39:47Z","description":"Extra copy of the thesis as PDF/A-2b","file_id":"9940"}],"publication_status":"published","keyword":["quantum computing","superinductor","quantum metrology"],"year":"2021","article_processing_charge":"No","oa":1,"type":"dissertation","page":"149"},{"abstract":[{"lang":"eng","text":"There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one, the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wave function. In the other, the junction is added in parallel, which gives rise to an extended phase variable, continuous wave functions, and a rich energy-level structure due to the loop topology. While the corresponding rf superconducting quantum interference device Hamiltonian was introduced as a quadratic quasi-one-dimensional potential approximation to describe the fluxonium qubit implemented with long Josephson-junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits, all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasicharge qubit with strongly enhanced zero-point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high reproducibility of the inductive energy as guaranteed by top-down lithography—a key ingredient for intrinsically protected superconducting qubits."}],"date_created":"2021-08-17T08:14:18Z","has_accepted_license":"1","publisher":"American Physical Society","language":[{"iso":"eng"}],"intvolume":"         2","issue":"4","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"status":"public","publication":"PRX Quantum","ddc":["530"],"month":"11","corr_author":"1","page":"040341","type":"journal_article","isi":1,"ec_funded":1,"oa":1,"year":"2021","keyword":["quantum physics","mesoscale and nanoscale physics"],"article_processing_charge":"No","publication_status":"published","file":[{"file_size":4247422,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-01-18T11:29:33Z","checksum":"36eb41ea43d8ca22b0efab12419e4eb2","file_name":"2021_PRXQuantum_Peruzzo.pdf","creator":"cchlebak","date_updated":"2022-01-18T11:29:33Z","file_id":"10641","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-11-24T00:00:00Z","scopus_import":"1","department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"volume":2,"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2622978C-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, PRX Quantum 2 (2021) 040341.","chicago":"Peruzzo, Matilda, Farid Hassani, Gregory Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” <i>PRX Quantum</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">https://doi.org/10.1103/PRXQuantum.2.040341</a>.","ista":"Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. 2(4), 040341.","apa":"Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., &#38; Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">https://doi.org/10.1103/PRXQuantum.2.040341</a>","ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. <i>PRX Quantum</i>. 2021;2(4):040341. doi:<a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">10.1103/PRXQuantum.2.040341</a>","mla":"Peruzzo, Matilda, et al. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” <i>PRX Quantum</i>, vol. 2, no. 4, American Physical Society, 2021, p. 040341, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">10.1103/PRXQuantum.2.040341</a>.","ieee":"M. Peruzzo <i>et al.</i>, “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction,” <i>PRX Quantum</i>, vol. 2, no. 4. American Physical Society, p. 040341, 2021."},"doi":"10.1103/PRXQuantum.2.040341","_id":"9928","quality_controlled":"1","oa_version":"Published Version","publication_identifier":{"eissn":["2691-3399"]},"file_date_updated":"2022-01-18T11:29:33Z","article_type":"original","related_material":{"record":[{"id":"13057","relation":"research_data","status":"public"},{"relation":"dissertation_contains","id":"9920","status":"public"},{"id":"17133","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"We thank W. Hughes for analytic and numerical modeling during the early stages of this work, J. Koch for discussions and support with the scqubits package, R. Sett, P. Zielinski, and L. Drmic for software development, and G. Katsaros for equipment support, as well as the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility. We thank I. Pop, S. Deleglise, and E. Flurin for discussions. This work was supported by a NOMIS Foundation research grant, the Austrian Science Fund (FWF) through BeyondC (F7105), and IST Austria. M.P. is the recipient of a Pöttinger scholarship at IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","day":"24","arxiv":1,"external_id":{"isi":["000723015100001"],"arxiv":["2106.05882"]},"author":[{"orcid":"0000-0002-3415-4628","last_name":"Peruzzo","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda"},{"full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","orcid":"0000-0001-6937-5773","first_name":"Farid"},{"first_name":"Gregory","last_name":"Szep","full_name":"Szep, Gregory"},{"last_name":"Trioni","first_name":"Andrea","full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko"},{"full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","orcid":"0009-0005-0878-3032","first_name":"Martin"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-15T06:41:46Z","title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction"}]