[{"external_id":{"isi":["000874717200001"],"pmid":["35856919"]},"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"publisher":"Rockefeller University Press","article_number":"e202206127","intvolume":"       221","oa":1,"pmid":1,"oa_version":"Published Version","publication_status":"published","_id":"12272","title":"Plan your trip before you leave: The neutrophils’ search-and-run journey","year":"2022","abstract":[{"lang":"eng","text":"Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant."}],"keyword":["Cell Biology"],"file":[{"success":1,"file_name":"2022_JourCellBiology_Stopp.pdf","relation":"main_file","date_created":"2023-01-30T10:39:34Z","access_level":"open_access","file_size":969969,"content_type":"application/pdf","file_id":"12451","date_updated":"2023-01-30T10:39:34Z","checksum":"6b1620743669679b48b9389bb40f5a11","creator":"dernst"}],"article_processing_charge":"No","isi":1,"scopus_import":"1","doi":"10.1083/jcb.202206127","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"J. A. Stopp and M. K. Sixt, “Plan your trip before you leave: The neutrophils’ search-and-run journey,” <i>Journal of Cell Biology</i>, vol. 221, no. 8. Rockefeller University Press, 2022.","short":"J.A. Stopp, M.K. Sixt, Journal of Cell Biology 221 (2022).","ista":"Stopp JA, Sixt MK. 2022. Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. 221(8), e202206127.","chicago":"Stopp, Julian A, and Michael K Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>.","mla":"Stopp, Julian A., and Michael K. Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>, vol. 221, no. 8, e202206127, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>.","ama":"Stopp JA, Sixt MK. Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. 2022;221(8). doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>","apa":"Stopp, J. A., &#38; Sixt, M. K. (2022). Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>"},"quality_controlled":"1","volume":221,"ddc":["570"],"date_published":"2022-07-20T00:00:00Z","month":"07","publication":"Journal of Cell Biology","status":"public","issue":"8","type":"journal_article","department":[{"_id":"MiSi"}],"has_accepted_license":"1","date_updated":"2026-08-24T22:30:15Z","related_material":{"record":[{"id":"14697","status":"public","relation":"dissertation_contains"}]},"article_type":"original","corr_author":"1","author":[{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"day":"20","date_created":"2023-01-16T10:01:08Z","file_date_updated":"2023-01-30T10:39:34Z"},{"intvolume":"        23","oa":1,"oa_version":"Published Version","publication_status":"published","_id":"11420","title":"Mean-field analysis of piecewise linear solutions for wide ReLU networks","year":"2022","abstract":[{"text":"Understanding the properties of neural networks trained via stochastic gradient descent (SGD) is at the heart of the theory of deep learning. In this work, we take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD for a univariate regularized regression problem. Our main result is that SGD with vanishingly small noise injected in the gradients is biased towards a simple solution: at convergence, the ReLU network implements a piecewise linear map of the inputs, and the number of “knot” points -- i.e., points where the tangent of the ReLU network estimator changes -- between two consecutive training inputs is at most three. In particular, as the number of neurons of the network grows, the SGD dynamics is captured by the solution of a gradient flow and, at convergence, the distribution of the weights approaches the unique minimizer of a related free energy, which has a Gibbs form. Our key technical contribution consists in the analysis of the estimator resulting from this minimizer: we show that its second derivative vanishes everywhere, except at some specific locations which represent the “knot” points. We also provide empirical evidence that knots at locations distinct from the data points might occur, as predicted by our theory.","lang":"eng"}],"arxiv":1,"external_id":{"arxiv":["2111.02278"]},"publication_identifier":{"issn":["1532-4435"],"eissn":["1533-7928"]},"license":"https://creativecommons.org/licenses/by/4.0/","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Journal of Machine Learning Research","ddc":["000"],"month":"04","date_published":"2022-04-01T00:00:00Z","publication":"Journal of Machine Learning Research","status":"public","page":"1-55","type":"journal_article","issue":"130","has_accepted_license":"1","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"date_updated":"2026-08-24T22:30:16Z","related_material":{"record":[{"id":"17465","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"other","url":"https://www.jmlr.org/papers/v23/21-1365.html"}]},"acknowledgement":"We would like to thank Mert Pilanci for several exploratory discussions in the early stage\r\nof the project, Jan Maas for clarifications about Jordan et al. (1998), and Max Zimmer for\r\nsuggestive numerical experiments. A. Shevchenko and M. Mondelli are partially supported\r\nby the 2019 Lopez-Loreta Prize. V. Kungurtsev acknowledges support to the OP VVV\r\nproject CZ.02.1.01/0.0/0.0/16 019/0000765 Research Center for Informatics.\r\n","article_type":"original","corr_author":"1","author":[{"full_name":"Shevchenko, Aleksandr","first_name":"Aleksandr","last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"},{"full_name":"Kungurtsev, Vyacheslav","first_name":"Vyacheslav","last_name":"Kungurtsev"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"}],"language":[{"iso":"eng"}],"day":"01","date_created":"2022-05-29T22:01:54Z","file_date_updated":"2022-05-30T08:22:55Z","file":[{"date_updated":"2022-05-30T08:22:55Z","creator":"cchlebak","checksum":"d4ff5d1affb34848b5c5e4002483fc62","content_type":"application/pdf","file_size":1521701,"file_id":"11422","access_level":"open_access","date_created":"2022-05-30T08:22:55Z","relation":"main_file","file_name":"21-1365.pdf","success":1}],"article_processing_charge":"No","scopus_import":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Shevchenko, Alexander, et al. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130, Journal of Machine Learning Research, 2022, pp. 1–55.","ama":"Shevchenko A, Kungurtsev V, Mondelli M. Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. 2022;23(130):1-55.","apa":"Shevchenko, A., Kungurtsev, V., &#38; Mondelli, M. (2022). Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","chicago":"Shevchenko, Alexander, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2022.","ista":"Shevchenko A, Kungurtsev V, Mondelli M. 2022. Mean-field analysis of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning Research. 23(130), 1–55.","short":"A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research 23 (2022) 1–55.","ieee":"A. Shevchenko, V. Kungurtsev, and M. Mondelli, “Mean-field analysis of piecewise linear solutions for wide ReLU networks,” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130. Journal of Machine Learning Research, pp. 1–55, 2022."},"quality_controlled":"1","volume":23},{"degree_awarded":"PhD","date_updated":"2026-07-06T12:47:25Z","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"has_accepted_license":"1","type":"dissertation","page":"136","status":"public","date_published":"2022-08-19T00:00:00Z","month":"08","ddc":["573"],"file_date_updated":"2023-06-20T22:30:04Z","date_created":"2022-08-19T08:52:30Z","day":"19","language":[{"iso":"eng"}],"author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","first_name":"Michele","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570"}],"corr_author":"1","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","OA_place":"publisher","related_material":{"record":[{"id":"6194","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10077","status":"public"}]},"article_processing_charge":"No","file":[{"date_updated":"2023-06-20T22:30:04Z","embargo_to":"open_access","checksum":"2dbb70c74aaa3b64c1f463e943baf09c","creator":"mnardin","file_size":13515457,"content_type":"application/zip","file_id":"11935","relation":"source_file","date_created":"2022-08-19T16:31:34Z","access_level":"closed","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip"},{"embargo":"2023-06-19","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","date_created":"2022-08-22T09:43:50Z","access_level":"open_access","relation":"main_file","file_id":"11941","file_size":9906458,"content_type":"application/pdf","checksum":"0ec94035ea35a47a9f589ed168e60b48","creator":"mnardin","date_updated":"2023-06-20T22:30:04Z"}],"citation":{"ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>","apa":"Nardin, M. (2022). <i>On the encoding, transfer, and consolidation of spatial memories</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>","mla":"Nardin, Michele. <i>On the Encoding, Transfer, and Consolidation of Spatial Memories</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>.","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>."},"doi":"10.15479/at:ista:11932","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"On the encoding, transfer, and consolidation of spatial memories","_id":"11932","publication_status":"published","oa_version":"Published Version","oa":1,"ec_funded":1,"abstract":[{"text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes.","lang":"eng"}],"year":"2022","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"publisher":"Institute of Science and Technology Austria"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1093/genetics/iyac123","citation":{"ieee":"M. N. Elkrewi <i>et al.</i>, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp,” <i>Genetics</i>, vol. 222, no. 2. Oxford University Press, 2022.","ista":"Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123.","short":"M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon, C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).","chicago":"Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>.","mla":"Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>, vol. 222, no. 2, iyac123, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>.","apa":"Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>","ama":"Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. 2022;222(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>"},"quality_controlled":"1","volume":222,"file":[{"access_level":"open_access","date_created":"2023-01-30T08:59:58Z","relation":"main_file","success":1,"file_name":"2022_Genetics_Elkrewi.pdf","date_updated":"2023-01-30T08:59:58Z","creator":"dernst","checksum":"f79ff5383e882ea3f95f3da47a78029d","file_size":1347136,"content_type":"application/pdf","file_id":"12440"}],"article_processing_charge":"No","isi":1,"scopus_import":"1","related_material":{"record":[{"relation":"research_data","id":"11653","status":"public"},{"status":"public","id":"19386","relation":"dissertation_contains"}]},"corr_author":"1","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the Vicoso group for comments on the manuscript and the ISTA Scientific computing team and the Vienna Biocenter Sequencing facility for technical support.","article_type":"original","author":[{"orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"},{"id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434","last_name":"Khauratovich","first_name":"Uladzislava","full_name":"Khauratovich, Uladzislava"},{"first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"full_name":"Bett, Vincent K","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett"},{"first_name":"Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","full_name":"Mrnjavac, Andrea"},{"full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"last_name":"Sax","id":"701c5602-97d8-11ed-96b5-b52773c70189","first_name":"Luca","full_name":"Sax, Luca"},{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"first_name":"Francisco","last_name":"Hontoria","full_name":"Hontoria, Francisco"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"date_created":"2023-01-16T09:56:10Z","day":"01","language":[{"iso":"eng"}],"file_date_updated":"2023-01-30T08:59:58Z","date_published":"2022-10-01T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["570"],"month":"10","publication":"Genetics","status":"public","issue":"2","type":"journal_article","department":[{"_id":"BeVi"}],"has_accepted_license":"1","date_updated":"2026-08-24T22:30:30Z","publisher":"Oxford University Press","article_number":"iyac123","external_id":{"pmid":["35977389"],"isi":["000850270300001"]},"publication_identifier":{"issn":["1943-2631"]},"project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","call_identifier":"H2020"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","keyword":["Genetics"],"abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"intvolume":"       222","ec_funded":1,"oa":1,"pmid":1,"oa_version":"Published Version","publication_status":"published","_id":"12248","title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp"},{"scopus_import":"1","isi":1,"file":[{"success":1,"file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf","relation":"main_file","date_created":"2022-02-21T08:17:38Z","access_level":"open_access","file_id":"10779","file_size":2366976,"content_type":"application/pdf","creator":"dernst","checksum":"27042a3706ae52a919fed1ac114bf7bb","date_updated":"2022-02-21T08:17:38Z"}],"article_processing_charge":"No","quality_controlled":"1","citation":{"mla":"Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>.","ama":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2022;289(1968):20211985. doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>","apa":"Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., &#38; Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>","chicago":"Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>.","ista":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985.","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.","ieee":"R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022."},"volume":289,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1098/rspb.2021.1985","date_updated":"2026-08-24T22:30:31Z","type":"journal_article","issue":"1968","department":[{"_id":"BeVi"}],"has_accepted_license":"1","status":"public","page":"20211985","month":"02","date_published":"2022-02-09T00:00:00Z","ddc":["570"],"publication":"Proceedings of the Royal Society B: Biological Sciences","day":"09","language":[{"iso":"eng"}],"date_created":"2022-02-20T23:01:31Z","file_date_updated":"2022-02-21T08:17:38Z","author":[{"first_name":"Réka K","last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K"},{"orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Lindholm","first_name":"Anna K.","full_name":"Lindholm, Anna K."},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and from the Swiss National Science Foundation (grant no. 310030_189145).\r\nWe thank Jari Garbely of the Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland, for conducting the PCR verification. Barbara\r\nKonig, Gabi Stichel and A.K.L. collected mouse tissue samples, from the field study led by R.K.K. ","corr_author":"1","article_type":"original","related_material":{"record":[{"id":"19386","status":"public","relation":"dissertation_contains"},{"status":"public","id":"17119","relation":"dissertation_contains"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"call_identifier":"H2020","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"publication_identifier":{"eissn":["1471-2954"]},"external_id":{"pmid":["35135349"],"isi":["000752812800012"]},"publisher":"The Royal Society","publication_status":"published","_id":"10767","title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","oa_version":"Published Version","pmid":1,"intvolume":"       289","oa":1,"ec_funded":1,"year":"2022","abstract":[{"lang":"eng","text":"The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination."}]},{"author":[{"full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","first_name":"Rishabh"},{"last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","full_name":"Hease, William J","orcid":"0000-0001-9868-2166"},{"orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez"},{"full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","first_name":"Georg M"},{"first_name":"Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","orcid":"0000-0003-4345-4267","full_name":"Qiu, Liu"},{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"language":[{"iso":"eng"}],"date_created":"2022-03-27T22:01:45Z","day":"11","file_date_updated":"2022-03-28T08:02:12Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13175"},{"id":"12900","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"18871"}]},"corr_author":"1","acknowledgement":"The authors thank S. Wald and F. Diorico for their help with optical filtering, O. Hosten\r\nand M. Aspelmeyer for equipment, H.G.L. Schwefel for materials and discussions, L.\r\nDrmic and P. Zielinski for software support, and the MIBA workshop at IST Austria for\r\nmachining the microwave cavity. This work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG QUNNECT) and the European\r\nUnion’s Horizon 2020 research and innovation program under grant agreement no.\r\n899354 (FETopen SuperQuLAN). W.H. is the recipient of an ISTplus postdoctoral fellowship\r\nwith funding from the European Union’s Horizon 2020 research and innovation\r\nprogram under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the\r\nrecipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F.\r\nacknowledges support from the Austrian Science Fund (FWF) through BeyondC (F7105)\r\nand the European Union’s Horizon 2020 research and innovation programs under grant\r\nagreement no. 862644 (FETopen QUARTET).","article_type":"original","type":"journal_article","has_accepted_license":"1","department":[{"_id":"JoFi"}],"date_updated":"2026-08-24T22:30:35Z","month":"03","ddc":["530"],"date_published":"2022-03-11T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"}],"publication":"Nature Communications","status":"public","citation":{"ista":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. 2022. Quantum-enabled operation of a microwave-optical interface. Nature Communications. 13, 1276.","short":"R. Sahu, W.J. Hease, A.R. Rueda Sanchez, G.M. Arnold, L. Qiu, J.M. Fink, Nature Communications 13 (2022).","ieee":"R. Sahu, W. J. Hease, A. R. Rueda Sanchez, G. M. Arnold, L. Qiu, and J. M. Fink, “Quantum-enabled operation of a microwave-optical interface,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","mla":"Sahu, Rishabh, et al. “Quantum-Enabled Operation of a Microwave-Optical Interface.” <i>Nature Communications</i>, vol. 13, 1276, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-28924-2\">10.1038/s41467-022-28924-2</a>.","apa":"Sahu, R., Hease, W. J., Rueda Sanchez, A. R., Arnold, G. M., Qiu, L., &#38; Fink, J. M. (2022). Quantum-enabled operation of a microwave-optical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-28924-2\">https://doi.org/10.1038/s41467-022-28924-2</a>","ama":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. Quantum-enabled operation of a microwave-optical interface. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-28924-2\">10.1038/s41467-022-28924-2</a>","chicago":"Sahu, Rishabh, William J Hease, Alfredo R Rueda Sanchez, Georg M Arnold, Liu Qiu, and Johannes M Fink. “Quantum-Enabled Operation of a Microwave-Optical Interface.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-28924-2\">https://doi.org/10.1038/s41467-022-28924-2</a>."},"quality_controlled":"1","volume":13,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41467-022-28924-2","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":1167492,"file_id":"10929","date_updated":"2022-03-28T08:02:12Z","creator":"dernst","checksum":"7c5176db7b8e2ed18a4e0c5aca70a72c","file_name":"2022_NatureCommunications_Sahu.pdf","success":1,"access_level":"open_access","date_created":"2022-03-28T08:02:12Z","relation":"main_file"}],"article_processing_charge":"No","isi":1,"arxiv":1,"year":"2022","abstract":[{"lang":"eng","text":"Solid-state microwave systems offer strong interactions for fast quantum logic and sensing but photons at telecom wavelength are the ideal choice for high-density low-loss quantum interconnects. A general-purpose interface that can make use of single photon effects requires < 1 input noise quanta, which has remained elusive due to either low efficiency or pump induced heating. Here we demonstrate coherent electro-optic modulation on nanosecond-timescales with only 0.16+0.02−0.01 microwave input noise photons with a total bidirectional transduction efficiency of 8.7% (or up to 15% with 0.41+0.02−0.02), as required for near-term heralded quantum network protocols. The use of short and high-power optical pump pulses also enables near-unity cooperativity of the electro-optic interaction leading to an internal pure conversion efficiency of up to 99.5%. Together with the low mode occupancy this provides evidence for electro-optic laser cooling and vacuum amplification as predicted a decade ago."}],"oa_version":"Published Version","publication_status":"published","_id":"10924","title":"Quantum-enabled operation of a microwave-optical interface","intvolume":"        13","ec_funded":1,"oa":1,"pmid":1,"article_number":"1276","publisher":"Springer Nature","project":[{"grant_number":"758053","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"call_identifier":"H2020","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","call_identifier":"H2020"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000767892300013"],"pmid":["35277488"],"arxiv":["2107.08303"]},"publication_identifier":{"eissn":["2041-1723"]}},{"project":[{"call_identifier":"H2020","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip"}],"alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","_id":"10727","publication_status":"published","title":"Pathogen-mediated sexual selection and immunization in ant colonies","oa":1,"ec_funded":1,"year":"2022","abstract":[{"lang":"eng","text":"Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history."}],"file":[{"creator":"smetzler","embargo_to":"open_access","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","date_updated":"2023-02-03T23:30:03Z","file_id":"10728","file_size":6757886,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2022-02-04T15:36:12Z","access_level":"closed","relation":"source_file","file_name":"Thesis_Sina_Metzler.docx"},{"embargo":"2023-02-02","file_name":"Thesis_Sina_Metzler_A2.pdf","date_created":"2022-02-04T15:36:43Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":6314921,"file_id":"10730","date_updated":"2023-02-03T23:30:03Z","creator":"smetzler","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027"},{"relation":"main_file","date_created":"2022-02-07T10:35:02Z","access_level":"open_access","embargo":"2023-02-02","file_name":"Thesis_Sina_Metzler_print.pdf","checksum":"dedd14b7be7a75d63018dbfc68dd8113","creator":"smetzler","date_updated":"2023-02-04T23:30:03Z","file_id":"10742","content_type":"application/pdf","file_size":6882557}],"article_processing_charge":"No","citation":{"ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria.","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>.","mla":"Metzler, Sina. <i>Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>.","ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>","apa":"Metzler, S. (2022). <i>Pathogen-mediated sexual selection and immunization in ant colonies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>"},"doi":"10.15479/AT:ISTA:10727","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"has_accepted_license":"1","date_updated":"2026-04-07T14:30:18Z","degree_awarded":"PhD","month":"02","date_published":"2022-02-07T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"}],"ddc":["570"],"status":"public","author":[{"last_name":"Metzler","id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494"}],"day":"07","date_created":"2022-02-04T15:45:12Z","language":[{"iso":"eng"}],"file_date_updated":"2023-02-04T23:30:03Z","OA_place":"publisher","corr_author":"1"},{"date_updated":"2025-04-15T07:16:55Z","has_accepted_license":"1","department":[{"_id":"HeEd"}],"type":"journal_article","page":"2621–2635","status":"public","publication":"Journal of Ambient Intelligence and Humanized Computing","date_published":"2022-05-01T00:00:00Z","ddc":["000"],"month":"05","file_date_updated":"2022-12-20T23:30:08Z","language":[{"iso":"eng"}],"date_created":"2021-11-02T09:28:55Z","day":"01","author":[{"last_name":"Goudarzi","first_name":"Samira","full_name":"Goudarzi, Samira"},{"full_name":"Sharif, Mohammad","last_name":"Sharif","first_name":"Mohammad"},{"orcid":"0000-0001-6746-4174","full_name":"Karimipour, Farid","first_name":"Farid","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","last_name":"Karimipour"}],"acknowledgement":"The third author acknowledges the funding received from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","article_type":"original","scopus_import":"1","isi":1,"article_processing_charge":"No","file":[{"date_updated":"2022-12-20T23:30:08Z","creator":"fkarimip","checksum":"0a8961416a9bb2be5a1cebda65468bcf","content_type":"application/pdf","file_size":1634958,"file_id":"10279","relation":"main_file","date_created":"2021-11-12T19:38:05Z","access_level":"open_access","embargo":"2022-11-12","file_name":"A Context‑aware Dimension Reduction Framework - Journal of Ambient Intelligence 2021 (Preprint version).pdf"}],"volume":13,"citation":{"ieee":"S. Goudarzi, M. Sharif, and F. Karimipour, “A context-aware dimension reduction framework for trajectory and health signal analyses,” <i>Journal of Ambient Intelligence and Humanized Computing</i>, vol. 13. Springer Nature, pp. 2621–2635, 2022.","short":"S. Goudarzi, M. Sharif, F. Karimipour, Journal of Ambient Intelligence and Humanized Computing 13 (2022) 2621–2635.","ista":"Goudarzi S, Sharif M, Karimipour F. 2022. A context-aware dimension reduction framework for trajectory and health signal analyses. Journal of Ambient Intelligence and Humanized Computing. 13, 2621–2635.","chicago":"Goudarzi, Samira, Mohammad Sharif, and Farid Karimipour. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” <i>Journal of Ambient Intelligence and Humanized Computing</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s12652-021-03569-z\">https://doi.org/10.1007/s12652-021-03569-z</a>.","mla":"Goudarzi, Samira, et al. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” <i>Journal of Ambient Intelligence and Humanized Computing</i>, vol. 13, Springer Nature, 2022, pp. 2621–2635, doi:<a href=\"https://doi.org/10.1007/s12652-021-03569-z\">10.1007/s12652-021-03569-z</a>.","apa":"Goudarzi, S., Sharif, M., &#38; Karimipour, F. (2022). A context-aware dimension reduction framework for trajectory and health signal analyses. <i>Journal of Ambient Intelligence and Humanized Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12652-021-03569-z\">https://doi.org/10.1007/s12652-021-03569-z</a>","ama":"Goudarzi S, Sharif M, Karimipour F. A context-aware dimension reduction framework for trajectory and health signal analyses. <i>Journal of Ambient Intelligence and Humanized Computing</i>. 2022;13:2621–2635. doi:<a href=\"https://doi.org/10.1007/s12652-021-03569-z\">10.1007/s12652-021-03569-z</a>"},"quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1007/s12652-021-03569-z","title":"A context-aware dimension reduction framework for trajectory and health signal analyses","_id":"10208","publication_status":"published","oa_version":"Submitted Version","oa":1,"intvolume":"        13","keyword":["general computer science"],"abstract":[{"lang":"eng","text":"It is practical to collect a huge amount of movement data and environmental context information along with the health signals of individuals because there is the emergence of new generations of positioning and tracking technologies and rapid advancements of health sensors. The study of the relations between these datasets and their sequence similarity analysis is of interest to many applications such as health monitoring and recommender systems. However, entering all movement parameters and health signals can lead to the complexity of the problem and an increase in its computational load. In this situation, dimension reduction techniques can be used to avoid consideration of simultaneous dependent parameters in the process of similarity measurement of the trajectories. The present study provides a framework, named CaDRAW, to use spatial–temporal data and movement parameters along with independent context information in the process of measuring the similarity of trajectories. In this regard, the omission of dependent movement characteristic signals is conducted by using an unsupervised feature selection dimension reduction technique. To evaluate the effectiveness of the proposed framework, it was applied to a real contextualized movement and related health signal datasets of individuals. The results indicated the capability of the proposed framework in measuring the similarity and in decreasing the characteristic signals in such a way that the similarity results -before and after reduction of dependent characteristic signals- have small differences. The mean differences between the obtained results before and after reducing the dimension were 0.029 and 0.023 for the round path, respectively."}],"year":"2022","project":[{"name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342"}],"publication_identifier":{"issn":["1868-5137"],"eissn":["1868-5145"]},"external_id":{"isi":["000712198000001"]},"publisher":"Springer Nature"},{"page":"192-216","status":"public","publication":"Applicable Analysis","month":"01","ddc":["510","515","518"],"date_published":"2022-01-01T00:00:00Z","date_updated":"2024-11-04T13:52:44Z","has_accepted_license":"1","department":[{"_id":"VlKo"}],"issue":"1","type":"journal_article","acknowledgement":"The project of the first author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","article_type":"original","corr_author":"1","file_date_updated":"2021-03-16T23:30:06Z","day":"01","language":[{"iso":"eng"}],"date_created":"2020-03-09T07:06:52Z","author":[{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini"},{"full_name":"Iyiola, Olaniyi S.","first_name":"Olaniyi S.","last_name":"Iyiola"}],"isi":1,"article_processing_charge":"No","file":[{"content_type":"application/pdf","file_size":4282586,"file_id":"8648","date_updated":"2021-03-16T23:30:06Z","creator":"dernst","checksum":"869efe8cb09505dfa6012f67d20db63d","embargo":"2021-03-15","file_name":"2020_ApplicAnalysis_Shehu.pdf","access_level":"open_access","date_created":"2020-10-12T10:42:54Z","relation":"main_file"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1080/00036811.2020.1736287","volume":101,"citation":{"ieee":"Y. Shehu and O. S. Iyiola, “Weak convergence for variational inequalities with inertial-type method,” <i>Applicable Analysis</i>, vol. 101, no. 1. Taylor &#38; Francis, pp. 192–216, 2022.","ista":"Shehu Y, Iyiola OS. 2022. Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. 101(1), 192–216.","short":"Y. Shehu, O.S. Iyiola, Applicable Analysis 101 (2022) 192–216.","chicago":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” <i>Applicable Analysis</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/00036811.2020.1736287\">https://doi.org/10.1080/00036811.2020.1736287</a>.","mla":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” <i>Applicable Analysis</i>, vol. 101, no. 1, Taylor &#38; Francis, 2022, pp. 192–216, doi:<a href=\"https://doi.org/10.1080/00036811.2020.1736287\">10.1080/00036811.2020.1736287</a>.","ama":"Shehu Y, Iyiola OS. Weak convergence for variational inequalities with inertial-type method. <i>Applicable Analysis</i>. 2022;101(1):192-216. doi:<a href=\"https://doi.org/10.1080/00036811.2020.1736287\">10.1080/00036811.2020.1736287</a>","apa":"Shehu, Y., &#38; Iyiola, O. S. (2022). Weak convergence for variational inequalities with inertial-type method. <i>Applicable Analysis</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/00036811.2020.1736287\">https://doi.org/10.1080/00036811.2020.1736287</a>"},"quality_controlled":"1","oa":1,"ec_funded":1,"intvolume":"       101","title":"Weak convergence for variational inequalities with inertial-type method","_id":"7577","publication_status":"published","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Weak convergence of inertial iterative method for solving variational inequalities is the focus of this paper. The cost function is assumed to be non-Lipschitz and monotone. We propose a projection-type method with inertial terms and give weak convergence analysis under appropriate conditions. Some test results are performed and compared with relevant methods in the literature to show the efficiency and advantages given by our proposed methods."}],"year":"2022","arxiv":1,"publication_identifier":{"eissn":["1563-504X"],"issn":["0003-6811"]},"external_id":{"arxiv":["2101.08057"],"isi":["000518364100001"]},"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160"}],"publisher":"Taylor & Francis"},{"day":"09","language":[{"iso":"eng"}],"date_created":"2022-08-23T11:07:59Z","author":[{"last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431"},{"first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","last_name":"Miguel Villalba","orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder"},{"full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M"},{"full_name":"Wei, Donglai","last_name":"Wei","first_name":"Donglai"},{"full_name":"Lin, Zudi","first_name":"Zudi","last_name":"Lin"},{"last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823"},{"full_name":"Troidl, Jakob","first_name":"Jakob","last_name":"Troidl"},{"full_name":"Beyer, Johanna","last_name":"Beyer","first_name":"Johanna"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","first_name":"Yoav","full_name":"Ben Simon, Yoav"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr"},{"full_name":"Cenameri, Alban","first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"full_name":"Broichhagen, Johannes","last_name":"Broichhagen","first_name":"Johannes"},{"full_name":"Grant, Seth G. N.","last_name":"Grant","first_name":"Seth G. N."},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"year":"2022","das_tickbox":"1","corr_author":"1","abstract":[{"lang":"eng","text":"Complex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full <jats:italic>in-silico</jats:italic> reconstruction<jats:sup>1–5</jats:sup>, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches<jats:sup>6–12</jats:sup> facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy<jats:sup>6,13</jats:sup> in extracellularly labelled tissue<jats:sup>14</jats:sup> for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue."}],"OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.16.484431"}],"related_material":{"record":[{"relation":"later_version","id":"13267","status":"public"},{"id":"12470","status":"public","relation":"dissertation_contains"}]},"publication_status":"draft","_id":"11943","date_updated":"2026-08-24T22:31:06Z","title":"Saturated reconstruction of living brain tissue","type":"preprint","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"}],"oa_version":"Preprint","status":"public","month":"05","date_published":"2022-05-09T00:00:00Z","publication":"bioRxiv","oa":1,"citation":{"mla":"Velicky, Philipp, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Wei, D., Lin, Z., Watson, J., … Danzl, J. G. (n.d.). Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Donglai Wei, Zudi Lin, Jake Watson, Jakob Troidl, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, BioRxiv (n.d.).","ista":"Velicky P, Miguel Villalba E, Michalska JM, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. Saturated reconstruction of living brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","ieee":"P. Velicky <i>et al.</i>, “Saturated reconstruction of living brain tissue,” <i>bioRxiv</i>. ."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1101/2022.03.16.484431","article_processing_charge":"No"},{"oa":1,"publication":"bioRxiv","date_published":"2022-08-18T00:00:00Z","month":"08","status":"public","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"}],"oa_version":"Preprint","type":"preprint","title":"Uncovering brain tissue architecture across scales with super-resolution light microscopy","date_updated":"2026-08-24T22:31:06Z","_id":"11950","publication_status":"draft","related_material":{"record":[{"relation":"dissertation_contains","id":"12470","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.08.17.504272"}],"corr_author":"1","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanoscopic synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS leverages fixation-compatible extracellular labeling and advanced optical readout, in particular stimulated-emission depletion and expansion microscopy, to comprehensively delineate cellular structures. It enables 3D-reconstructing single synapses and mapping synaptic connectivity by identification and tailored analysis of putative synaptic cleft regions. Applying CATS to the hippocampal mossy fiber circuitry, we demonstrate its power to reveal the system’s molecularly informed ultrastructure across spatial scales and assess local connectivity by reconstructing and quantifying the synaptic input and output structure of identified neurons.","lang":"eng"}],"das_tickbox":"1","year":"2022","author":[{"first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia","full_name":"Lyudchik, Julia"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","first_name":"Philipp","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431"},{"full_name":"Korinkova, Hana","first_name":"Hana","last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed"},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"full_name":"Cenameri, Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","first_name":"Alessandro","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403"},{"first_name":"Karl","last_name":"Roessler","full_name":"Roessler, Karl"},{"full_name":"Czech, Thomas","first_name":"Thomas","last_name":"Czech"},{"last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"language":[{"iso":"eng"}],"day":"18","date_created":"2022-08-24T08:24:52Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1101/2022.08.17.504272","citation":{"mla":"Michalska, Julia M., et al. “Uncovering Brain Tissue Architecture across Scales with Super-Resolution Light Microscopy.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (n.d.). Uncovering brain tissue architecture across scales with super-resolution light microscopy. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2022.08.17.504272\">https://doi.org/10.1101/2022.08.17.504272</a>","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Uncovering brain tissue architecture across scales with super-resolution light microscopy. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Uncovering Brain Tissue Architecture across Scales with Super-Resolution Light Microscopy.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2022.08.17.504272\">https://doi.org/10.1101/2022.08.17.504272</a>.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, A. Venturino, K. Roessler, T. Czech, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, BioRxiv (n.d.).","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Venturino A, Roessler K, Czech T, Siegert S, Novarino G, Jonas PM, Danzl JG. Uncovering brain tissue architecture across scales with super-resolution light microscopy. bioRxiv, <a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>.","ieee":"J. M. Michalska <i>et al.</i>, “Uncovering brain tissue architecture across scales with super-resolution light microscopy,” <i>bioRxiv</i>. ."}},{"scopus_import":"1","isi":1,"file":[{"content_type":"application/pdf","file_size":4231591,"file_id":"11472","date_updated":"2022-06-30T07:14:48Z","checksum":"a7706b28d24a0e32a55ea04b82a2df43","creator":"dernst","file_name":"2022_PRXQuantum_Sack.pdf","success":1,"access_level":"open_access","date_created":"2022-06-30T07:14:48Z","relation":"main_file"}],"article_processing_charge":"No","quality_controlled":"1","citation":{"ista":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding barren plateaus using classical shadows. PRX Quantum. 3(2), 020365.","short":"S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum 3 (2022).","ieee":"S. Sack, R. A. Medina Ramos, A. Michailidis, R. Kueng, and M. Serbyn, “Avoiding barren plateaus using classical shadows,” <i>PRX Quantum</i>, vol. 3, no. 2. American Physical Society, 2022.","ama":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>","apa":"Sack, S., Medina Ramos, R. A., Michailidis, A., Kueng, R., &#38; Serbyn, M. (2022). Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>","mla":"Sack, Stefan, et al. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>, vol. 3, no. 2, 020365, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>.","chicago":"Sack, Stefan, Raimel A Medina Ramos, Alexios Michailidis, Richard Kueng, and Maksym Serbyn. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>."},"volume":3,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1103/prxquantum.3.020365","date_updated":"2026-08-24T22:31:11Z","issue":"2","type":"journal_article","department":[{"_id":"MaSe"}],"has_accepted_license":"1","status":"public","date_published":"2022-06-29T00:00:00Z","ddc":["530"],"month":"06","publication":"PRX Quantum","language":[{"iso":"eng"}],"date_created":"2022-06-29T20:21:32Z","day":"29","file_date_updated":"2022-06-30T07:14:48Z","author":[{"orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan","first_name":"Stefan","last_name":"Sack","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5"},{"last_name":"Medina Ramos","id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064"},{"first_name":"Richard","last_name":"Kueng","full_name":"Kueng, Richard"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"corr_author":"1","article_type":"original","acknowledgement":"We thank Marco Cerezo, Zoe Holmes, and Nicholas Hunter-Jones for fruitful discussion and valuable feedback. We also acknowledge Adam Smith, Johannes Jakob Meyer, and Victor V. Albert for comments on the paper. The simulations were performed in the Julia programming\r\nlanguage [65] using the Yao module [66]. S.H.S., R.A.M., A.A.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","related_material":{"record":[{"id":"17208","status":"public","relation":"dissertation_contains"},{"status":"public","id":"14622","relation":"dissertation_contains"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899"}],"publication_identifier":{"issn":["2691-3399"]},"external_id":{"arxiv":["2201.08194"],"isi":["000822564300001"]},"article_number":"020365","publisher":"American Physical Society","publication_status":"published","_id":"11471","title":"Avoiding barren plateaus using classical shadows","oa_version":"Published Version","intvolume":"         3","oa":1,"ec_funded":1,"arxiv":1,"year":"2022","abstract":[{"text":"Variational quantum algorithms are promising algorithms for achieving quantum advantage on nearterm devices. The quantum hardware is used to implement a variational wave function and measure observables, whereas the classical computer is used to store and update the variational parameters. The optimization landscape of expressive variational ansätze is however dominated by large regions in parameter space, known as barren plateaus, with vanishing gradients, which prevents efficient optimization. In this work we propose a general algorithm to avoid barren plateaus in the initialization and throughout the optimization. To this end we define a notion of weak barren plateaus (WBPs) based on the entropies of local reduced density matrices. The presence of WBPs can be efficiently quantified using recently introduced shadow tomography of the quantum state with a classical computer. We demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the initialization. In addition, we demonstrate that decreasing the gradient step size, guided by the entropies allows WBPs to be avoided during the optimization process. This paves the way for efficient barren plateau-free optimization on near-term devices. ","lang":"eng"}],"keyword":["General Medicine"]}]